Name | Last Name | Location | Summary | 2nd Research Area | Research Area | Lab Affiliation | Job Title |
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Abhishek Agarwal, Ph.D.Postdoctoral Associate |
Agarwal Abhishek Agarwal, Ph.D. | Bar Harbor, ME |
I am PostDoc working with Prof Li at JAX, Farmington. I have a background in computer science, and shifted my interests towards Machine Learning recently. I work on the CUBE project to integrate data across different assays and develop links. But, more recently, I have been working with image processing on COVID-19 detection.
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I have a background in computer science, and shifted my interests towards Machine Learning recently. I work on the CUBE project to integrate data across different assays and develop links. But, more recently, I have been working with image processing on COVID-19 detection. |
Bioinformatics|Computational Biology | Bioinformatics|Computational Biology | The Li Lab | Postdoctoral Associate |
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Alizadeh Elaheh Alizadeh, Ph.D. | Farmington, CT |
I use image processing and shape quantification methods to extract information from imaging data and link them to phenotypes by machine learning approaches.
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My project focuses on combining spatial transcriptomics and imaging data to predict phenotypes in cancer and other diseases. In my previous research I developed TISMorph software (in Matlab) to add new cell shape features which common software were not able to capture. Then I used these features to distinguished between cancer and normal cells with single cell resolution and predicted the function of novel kinases. I also mathematically modeled nuclear Beta-catenin's switch like response to WNT stimulation. During my last four years I have worked closely with biologists, developed a pipeline for them in R, and mentored them to analyze, automatically label plate-based assays and visualize their data. |
Bioinformatics|Cancer|Computational Biology | Bioinformatics|Cancer|Computational Biology | Computational Scientist | |
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Amin Samir B Amin, MBBS, Ph.D. | Farmington, CT |
Working in the comparative genomics field to study spontaneous development of canine and human glioma with emphasis on characterizing evolutionarily constrained (epi)genetic elements and the tissue context during oncogenesis.
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Dr. Amin received his Ph.D. in cancer computational biology from Baylor College of Medicine, Houston, TX in 01/2017. His thesis work was carried out at the UT MD Anderson Cancer Center, and was focused on understanding long non-coding RNA interactions in the context of chromatin organization using integrated analyses of publicly available expression, epigenomic and chromatin interaction data. Before completing Ph.D., Dr. Amin received research training (2008-2011) in computational biology at the Dana-Farber Cancer Institute, Boston, MA where he worked on the assessment of gene expression profiling as predictive biomarker in multiple myeloma. Previously, Dr. Amin received his first professional degree in medicine, MBBS from the Medical College of Maharaja Sayajirao University of Baroda, Vadodara, India in 2005. About | CV | NIH Biosketch |
Bioinformatics|Computational Biology|Genetics and Genomics|Cancer | Bioinformatics|Computational Biology|Genetics and Genomics|Cancer | The Verhaak Lab | Postdoctoral Associate |
Sam ArderyPostdoctoral Associate |
Ardery Sam Ardery | Bar Harbor, ME |
My research interest combines genetic diversity with human disease presentation, prevention, and treatment.
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My long-term research goals include obtaining the necessary skills to begin an independent research group studying the effects of diverse genetics on disease phenotype and treatment, as well as participate in the dissemination of scientific knowledge to the next generation of biological researchers and to the general public. As pre-doctoral staff in the Munger lab, I am able to practice the computational skills necessary to understand the impact of diverse genetics on RNA-sequencing to determine the effectiveness of the various parameters in an experiment. My undergraduate work with Dr. Steve Henle at Carthage College allowed me to gain experience with fluorescent microscopy and CRISPR in order to localize different forms of the Yes-associated protein throughout development of the zebrafish. Outside of research, I enjoy reading and sewing. |
Computational Biology|Genetics and Genomics | Computational Biology|Genetics and Genomics | The Munger Lab | Postdoctoral Associate |
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Audano Peter Audano, III, Ph. D. | Farmington, CT |
Developing tools for genome variant discovery with a focus on complex rearrangements and long-read sequencing.
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Pete has been in the computing industry since 2000 where he worked and earned his BS in Computer Science from Southern Polytechnic State University (now Kennesaw University). In 2012, he left the computing industry to pursue an MS and a PhD from the Georgia Institute of Technology where he developed variant discovery techniques in bacteria and was involved in several small cancer studies with Dr. Fredrik Vannberg. In 2016, he joined the University of Washington under Dr. Evan Eichler where he developed methods to apply long-reads to structural variant discovery. In 2021, he joined the Jackson Laboratory under Dr. Christine Beck to study mechanisms of structural variation. |
Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | The Beck Lab | Lab Staff |
Selcan Aydin, Ph.D.Postdoctoral Associate |
Aydin Selcan Aydin, Ph.D. | Bar Harbor, ME |
My research interest lie at the intersection of genetic diversity and environmental variability, with the goal of elucidating how GxE interactions alter cell fate decisions.
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My long-term goal is to obtain the necessary skills to develop an independent research program focused on studying the effects of genetic and environmental variation on cell-fate decisions using a multi-disciplinary approach that combines wet-lab experiments with mathematical modeling. Towards this goal, I have sought interdisciplinary training in molecular biology, computational and systems biology, and quantitative genetics. As a postdoc in Munger lab, I aim to complement and enhance these skills by training in mouse genetics and developmental biology. As a graduate student working with Drs. Nick Buchler and Paul Magwene, I characterized the effects of natural genetic variation in budding yeast on growth dynamics in response to hyper-osmotic stress. I showed that this phenotype was highly variable in our genetically diverse collection of yeast strains, and then applied bulk segregant analysis to identify genetic variants that mediated this variable response. In my postdoctoral research, I have started exploring GxE interactions in a higher model organism (mouse) within embryonic stem cells. In addition to research, I am actively involved in teaching, mentoring and scientific outreach efforts at JAX. Outside of lab I enjoy the outdoors by hiking, snowshoeing and gardening! |
Complex Traits|Computational Biology|Genetics and Genomics | Complex Traits|Computational Biology|Genetics and Genomics | The Munger Lab | Postdoctoral Associate |
Parithi Balachandran, MSApplication Computational Scientist |
Balachandran Parithi Balachandran, MS | Farmington, CT |
Designs pipelines and develops tools to discover structural variations facilitated by Transposable Elements to better understand the potential mechanisms of their formation.
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Designs pipelines and develops tools to discover structural variations facilitated by Transposable Elements to better understand the potential mechanisms of their formation. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Beck Lab | Lab Staff |
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Barakat Yehya Barakat | Bar Harbor, ME |
I am interested in improving drug discovery for neuropsychiatric disorders using genetics and bioinformatics.
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I worked as a pharmacist following my undergraduate education. Shortly in my clinical work, I was frustrated with the progress of pharmaceuticals in the field of neuropsychiatric disorders. I was especially moved by my friend's struggles with limerence, a disorder that is still undiagnosable and with very little literature surrounding it. I was motivated to go into a research-based program in Boston; there I received my Master's degree in pharmacology and drug development. I got immersed in the field of neurogenetics by my previous mentor Dr. Leon Reijmers and I have decided that's the type of training I want to focus on. I got accepted to the Tufts-JAX collaborative Ph.D. program in neuroscience and I have never made a better choice than to join this program. Under the mentorship of Dr. Vivek Kumar, I feel I will get the training I need to ask and answer critical questions that can lead to better drug targets for neuropsychiatric disorders with unmet needs. My project is involved in understanding the causal mechanisms involved in age dependent hyperactivity disorder and its relationship to cortical cell death. |
Behavioral Disorders|Bioinformatics|Complex Traits|Genetics and Genomics | Behavioral Disorders|Bioinformatics|Complex Traits|Genetics and Genomics | The Kumar Lab | Predoc |
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Beck Christine Beck, Ph.D. | Farmington, CT |
Investigating the mechanisms and consequences of genomic rearrangements with a focus on repetitive elements.
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The mechanisms governing non-recurrent human structural variation (SV) are diverse and often poorly understood. I am investigating how human DNA maintains fidelity in the context of a repetitive genome. For example, human Alu elements number over one million copies per human genome, and recent studies have found that these repeat sequences often mediate SVs in some loci. Through computational, molecular biological and genomic techniques, we will identify regions susceptible to this form of SV and investigate the enzymes that limit or promote Alu-mediated rearrangements. These lines of inquiry could find regions prone to instability in human cancers and lead to targets for therapy. |
Cancer|Computational Biology|Genetics and Genomics | Cancer|Computational Biology|Genetics and Genomics | The Beck Lab | Assistant Professor |
Bello Susan Bello, Ph.D. | Bar Harbor, ME |
Developing phenotype and disease ontologies to capture data from research and support cross-species analyses
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I work as a Senior Scientific Curator on the Mouse Genome Informatics MGI database and on the Alliance of Genome Resources. I also help to develop the Mammalian Phenotype Ontology, the Unified Phenotype Ontology and the Human Disease Ontology. |
Bioinformatics|Genetics and Genomics|Resource Development and Dissemination | Bioinformatics|Genetics and Genomics|Resource Development and Dissemination | Scientific Curator | ||
Daniel BerenzyResearch Assistant I |
Berenzy Daniel Berenzy | Bar Harbor, ME |
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Daniel graduated from Florida Gulf Coast University (FGCU) with a degree in Biotechnology, while working with Dr. Takashi Ueda in the school’s Biotechnology lab. Upon graduating from FGCU, Daniel immediately joined the Tewhey Lab as a Research Assistant and concurrently enrolled in the Professional Science Masters (PSM) program in Bioinformatics at the University of Maine. As a Research Assistant in the Tewhey Lab, Daniel contributes to several different projects in both the “wet” and “dry” lab but his expertise is in Biotechnology methods. In his free time, Daniel studies for a Master’s degree but is also an avid Cyclist, Climber, Kayaker and all-around outdoorsy type. |
Bioinformatics|Computational Biology | Bioinformatics|Computational Biology | The Tewhey Lab | Lab Staff |
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Berger Alexander Berger, B.S. | Bar Harbor, ME |
I use software engineering to solve complex problems in scientific software and scientific software systems.
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I have a B.S. in Applied Mathematics from NYC College of Technology. I started my time at Jax in 2014 as a Software Quality Assurance Intern, joined Computational Sciences as an Associate Scientific Software Engineer in 2016 and became a Scientific Software Engineer in 2018. I'm a "full-stack" engineer who works on a variety of problems including genomics algorithm optimization in C/C++, RESTful API design and implementation using Flask, software reliability engineering, cloud computing, and project and systems design. I'm currently pursuing an M.S. in Computer Science as a member of the inaugural class at The Roux Institute at Northeastern. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | Software Engineer | |
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Blake Judith Blake, Ph.D. | Bar Harbor, ME |
Researches functional and comparative genome informatics, developing systems to integrate and analyze genetic, genomic and phenotypic data.
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My research focuses on functional and comparative genome informatics. I work on the development of systems to integrate and analyze genetic, genomic and phenotypic information. I am one of the principal investigators of the Gene Ontology (GO) Consortium, an international effort to provide controlled structured vocabularies for molecular biology that serve as terminologies, classifications and ontologies to further data integration, analysis and reasoning. My interest in bio-ontologies stems as well from the work I do as a principal investigator with the Mouse Genome Informatics (MGI) project at The Jackson Laboratory. The MGI system is a model-organism community database resource that provides integrated information about the genetics, genomics and phenotypes of the laboratory mouse. My current research projects combine bio-ontologies and database knowledge systems to analyze disease processes with the objective of discovering new molecular elements and pathways that contribute to particular pathologies such as respiratory diseases. |
Genetics and Genomics|Computational Biology|Bioinformatics|Resource Development and Dissemination | Genetics and Genomics|Computational Biology|Bioinformatics|Resource Development and Dissemination | The Blake Lab | Lab Staff|Professor |
Laura Blanco-Berdugo, MSResearch Data Analyst I |
Blanco-Berdugo Laura Blanco-Berdugo, MS | Bar Harbor, ME |
Interested in genetic diversity and evolution of wild and wild-derived mice
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Research focuses on the investigation of genetic diversity and genomic evolution of multiple laboratory strains and wild mice. |
Computational Biology|Genetics and Genomics | Computational Biology|Genetics and Genomics | The Dumont Lab | Lab Staff |
Hannah Blau, Ph.D.Research Software Engineer |
Blau Hannah Blau, Ph.D. | Farmington, CT |
Applies machine learning and text mining techniques to the analysis and curation of the Human Phenotype Ontology and other ontologies under development in the Robinson Lab.
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Hannah Blau completed her Ph.D. in Computer Science at the University of Massachusetts Amherst. She earned the B.A. in French from Yale University and the M.S.E. in Computer and Information Science from the University of Pennsylvania. Prior to JAX, Hannah worked primarily in the areas of data science, machine learning, and natural language processing. She gained international experience at the Artificial Intelligence Center of the Bull Corporation (Louveciennes, France), and in the Machine Learning Group of the Daimler-Benz Research Centre (Ulm, Germany). She worked as a Research Scientist in the Automated Reasoning Group of the Honeywell Technology Center (Minneapolis, Minnesota). While in grad school she served as data scientist in the lab of Professor M. Darby Dyar, Chair of Astronomy at Mount Holyoke College and member of the science team for the Mars Science Laboratory (Curiosity rover). Hannah joined the Robinson Lab in May 2017. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Robinson Lab | Lab Staff |
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Bogue Molly Bogue, Ph.D. | Bar Harbor, ME |
Works on the Mouse Phenome Project, collecting phenotype (measurement) data and disseminating them from the Mouse Phenome Database (MPD).
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A mouse's genetics are reflected in its phenotype, its measurable characteristics including appearance, behavior and physiology. We work on the Mouse Phenome Project, an international collaborative effort seeking to comprehensively characterize a large set of commonly used and genetically diverse strains of mice and other reference populations. All the data are collected and disseminated from the Mouse Phenome Database (MPD) and include data relevant to addiction, atherosclerosis, blood disorders, cancer susceptibility, neurological and behavioral disorders, sensory function defects, hypertension, osteoporosis, obesity and other research areas. MPD also contains extensive genotypic data, which allows for genotype-phenotype association predictions and facilitates efforts to identify and determine the function of genes participating in normal and disease pathways. |
Aging|Bioinformatics|Complex Traits|Computational Biology | Aging|Bioinformatics|Complex Traits|Computational Biology | The Chesler Lab | Research Scientist |
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Boumil Rebecca Boumil, Ph.D. | Bar Harbor, ME |
Investigating the genetics underlying epileptic seizures using mouse models of the disease.
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Our lab studies the “fitful” mouse as a model of generalized idiopathic epilepsy. Fitful mice carry a spontaneous mutation in the Dnm1 gene, which we described in 2010. Disruption of dynamin function in mice impairs SV endocytosis, with a more dramatic effect during high levels of neuronal activity. Heterozygous mice develop spontaneous and handling-induced seizures at 2 to 3 months of age, but otherwise appear normal. Homozygous mice have a more severe phenotype, including seizures that often lead to death before weaning age, ataxia and neurosensory defects, highlighting the importance of synaptic vesicle recycling in the brain. Recently, human patients have been identified with mutations in DNM1. These patients all have very severe early epileptic encephalopathies and present early in life with seizures, developmental delay and intellectual decline among other comorbid issues. Currently, we are employing the Dnm1ftfl and conditional Dnm1null alleles to create inducible genetic models that do not exhibit these polymorphic comorbid effects. Preliminary observations of Dnm1ftfl/flox mice in combination with various neuronal subpopulation-specific Cre strains have demonstrated unique seizure phenotypes. These results suggest the possibility that the behavioral comorbidities may be separate from the seizures and that the gene defect may be pleiotropic in different neuron types. |
Developmental Disorders|Neurodegenerative and Neuromuscular Diseases|Genetics and Genomics|Behavioral Disorders | Developmental Disorders|Neurodegenerative and Neuromuscular Diseases|Genetics and Genomics|Behavioral Disorders | Lab Staff | |
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Bubier Jason Bubier, Ph.D. | Bar Harbor, ME |
Integrating behavioral data across species and making it computable and accessible to the research community.
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I have used my formal training in molecular genetics in a variety of research areas: plant biology, immunology, dermatology and currently mouse behavior. I have been able to dissect the regulation of genes, identify genes underlying traits, map Quantitative Trait Loci (QTL), and identify modifier genes within different inbred populations. Currently I am using integrative functional genomics in the online software www.GeneWeaver.org, developed by Chesler et al., to bring together different types of data across numerous species and to utilize this convergent evidence to elucidate and validate the roles of genes in disease. I am also curating the addiction and alcoholism literature for the database, identifying relevant large-scale genomic studies and making these often incomputable data, computable. |
Complex Traits|Genetics and Genomics|Bioinformatics|Behavioral Disorders | Complex Traits|Genetics and Genomics|Bioinformatics|Behavioral Disorders | The Chesler Lab | Research Scientist |
Carol Bult, Ph.D.Professor, Knowlton Family Chair |
Bult Carol Bult, Ph.D. | Bar Harbor, ME |
Bridges the digital biology divide, by integrating computation and informatics with biomedical research.
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The primary theme of my personal research program is “bridging the digital biology divide,” reflecting the critical role that informatics and computational biology play in modern biomedical research. I am a Principal Investigator in the Mouse Genome Informatics (MGI) consortium that develops knowledgebases to advance the laboratory mouse as a model system for research into the genetic and genomic basis of human biology and disease (http://www.informatics.jax.org). Recent research initiatives in my research group include computational prediction of gene function in the mouse and the use of the mouse to understand genetic pathways in normal lung development and disease. My institutional responsibilities at The Jackson Laboratory include serving as the Deputy Director of the Cancer Center and as the Scientific Director of our Patient Derived Xenograft (PDX) and Cancer Avatar program. The PDX program is a resource of deeply characterized and well-annotated "human in mouse" cancer models with a focus on bladder, lung, colon, breast and pediatric cancer. This resource is a powerful platform for research into basic cancer biology (such as tumor heterogeneity and evolution) as well as for translational research into mechanisms of therapy resistance and therapeutic strategies to overcome resistance. |
Complex Traits|Cancer|Genetics and Genomics|Bioinformatics | Complex Traits|Cancer|Genetics and Genomics|Bioinformatics | The Bult Lab | Professor |
John Butts, MSPredoctoral Associate |
Butts John Butts, MS | Bar Harbor, ME |
Comparing mutagenesis techniques to probe the logic underlying cis-regulatory elements.
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John graduated from University of Dayton with a B.S./M.S. in Biology. It was there he first began his interest in gene regulation, particularly cis-regulatory elements, while working with Dr. Thomas Williams studying the evolution of pigmentation patterns in Drosophila. Following graduation John joined Dr. Victoria Meller’s lab at Wayne State University working as Lab Manager and Research Assistant studying the impact of chromatin conformation on dosage compensation in fruit flies. As a PhD student John hopes to continue to probe the logic underlying CREs and how advancements in experimental methods can enhance this study. In his free time John enjoys making music, running, and playing tennis. |
Bioinformatics|Complex Traits|Genetics and Genomics | Bioinformatics|Complex Traits|Genetics and Genomics | The Tewhey Lab | Lab Staff |
Gregory Carter, Ph.D.Professor, The Bernard and Lusia Milch Endowed Chair |
Carter Gregory Carter, Ph.D. | Bar Harbor, ME |
Develops computational strategies using genetic data to understand complex genetic systems involving multiple genes and environmental factors.
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Contemporary technologies such as high-throughput genome sequencing now enable the measurement of biological systems with unprecedented scale, power and precision, creating the opportunity to decipher the genetics that underlie human diseases. The overall goal of our laboratory is to develop novel computational strategies that use these data to understand complex genetic systems in which multiple genes and environmental factors combine to affect biological outcomes. These methods aim to map complex genetic architecture and infer models that predict the outcomes of genetic and environmental variation. We derive network models of interacting genes, integrate disparate phenotypic and molecular data types, critically evaluate models with experimental tests, and seek to understand how biological information is encoded in genetic networks and genomic data. |
Complex Traits|Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | Complex Traits|Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | The Carter Lab | Associate Professor |
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Cary Gregory Cary, Ph.D. | Bar Harbor, ME |
Prioritizing candidate drug targets for diseases with complex etiologies
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My research has focused on the logic of gene expression regulation, particularly in response to stress. In particular, I have utilized and integrated high-dimensional data to address complex questions about regeneration, neurodegeneration, development, and evolution. My role in the Open-AD consortium is to integrate genomic evidence in support of the prioritization and development of new therapeutic targets for the treatment of Alzheimer's disease. |
Aging|Bioinformatics|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | Aging|Bioinformatics|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | The Carter Lab | Lab Staff |
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Castellanos Francisco Castellanos, M.S. | Farmington, CT |
My research interest is in Data Science/Data Engineering within the domain of Bioinformatics and Genome research.
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From the early days of my career, while designing and writing programs, from assembler, to C++, to SQL, to JAVA/J2EE, to NoSQL, to front-end JavaScript framework languages; my passion has been Software Development and Architecture, and the interesting study of surging technologies thereof. My professional background includes experiences in various industries and in diverse capacities which have giving me the opportunity to understand end-to-end intricacies of software development life cycles and software platforms. During my career, I have had the opportunity to plan, architect, develop, and lead software projects and teams with the ultimate goal of providing solutions that meet and exceed stakeholder’s expectations. My 15 years of work experience includes serving in various arenas, such as Supply Chain, E-Commerce Software Platforms, and Insurance industries I recently joined JAX, and I am absolutely thrilled with the opportunity to contribute to the goal of research for tomorrow’s cures and personalized treatments. The world of genome research and bioinformatics is absolutely fascinating, so I am enthusiastic to apply my skills and to broaden my knowledge as a dive deeper into this great domain and inspiring cause. |
Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | Software Engineer | |
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Castro Rodrigo Castro, Ph.D. | Bar Harbor, ME |
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Rodrigo graduated from Georgia State University with a doctoral degree in mathematics, focusing in deep learning research. As a postdoctoral associate in the Tewhey lab, Rodrigo works on generative deep-learning models for cis-regulatory elements and deriving new synthetic elements for desired regulatory functions. In his spare time, Rodrigo enjoys practicing music, biking, and learning about new AI advances. |
Bioinformatics | Bioinformatics | The Tewhey Lab | Lab Staff|Postdoctoral Associate |
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Chandok Harshpreet Chandok, M.S. | Farmington, CT |
Next Generation Sequencing Analysis, Computational Cancer Biology, Pharmacology, Precision Medicine, Translational Research
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I hold a Masters in Bioinformatics minor in Health Informatics. My dissertation revolved around literature based discovery utilized to mine existing drug interaction evidences in the clinical trial Phase I and II studies and predicting novel drug interaction signals with mentions of adverse related events. Few interesting projects during my masters includes mining the highthroughput data to understand changes in gene expression, methylation and variant profiles in cancers such as Glioblastoma Multiforme and lung cancer using the computational methods and systems biology approaches. My research interests are to apply computational and machine learning approaches to understand the molecular mechanisms and biological complexities in tumors leading to better prediction of treatments. |
Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | Bioinformatics/Data Analyst | |
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Chaussabel Damien Chaussabel, Ph.D. | Farmington, CT |
Development of approaches for the analysis, visualization and functional interpretation of large-scale immunological profiling datasets.
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My research has focused on blood transcriptomics and its application in patient-based research, most notably in the field of infectious disease, autoimmune and vaccinology. My primary role at the Jackson Laboratory is to support the development of systems immunology and immunoinformatic research capacity – including through the implementation of training programs and the support of projects and investigators conducting immunology research at Jax. |
Bioinformatics|Computational Biology|Genetics and Genomics|Immune Disorders | Bioinformatics|Computational Biology|Genetics and Genomics|Immune Disorders | Computational Scientist | |
Xiaowen Chen, Ph.D.Research Scientist |
Chen Xiaowen Chen, Ph.D. | Farmington, CT |
I am committed to discovering fundamental principles and biological regulation of cancer cells using computational methods and sequencing datasets.
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I developed the computational algorithms to determine the links between small molecules and microRNAs in human cancers and the pathways associated with adverse drug reactions (ADRs). I developed a strategy to effectively predict the relationship between proteins and ADRs, which markedly improved the screening of ADRs in clinical drug-discovery trials. I used machine learning to identify transcription factors of sub-compartments and perform network topology analysis of sub-compartments to validate the accuracy of Sub-Compartment Identifier algorithm. I used computational and sequencing methodologies to examine the genetic and epigenetic heterogeneity in cancer cells, which is essential for elucidating the initiation and progression of cancer. I also studied lymphomagenesis and identified the epigenetic pattern which contributed to lymphomagenesis. |
Bioinformatics|Computational Biology|Cancer | Bioinformatics|Computational Biology|Cancer | The Li Lab | Research Scientist |
Elissa J. Chesler, Ph.D.Professor, The Ann Watson Symington Chair in Addiction Research |
Chesler Elissa J. Chesler, Ph.D. | Bar Harbor, ME |
Researches the genetics underlying behavior and identifies the biological basis for relationships among behavioral traits.
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My laboratory integrates quantitative genetics, bioinformatics and behavioral science to understand and identify the biological basis for the relationships among behavioral traits. We develop and apply cross-species genomic data integration, advanced computing methods, and novel high-precision, high-diversity mouse populations to find genes associated with a constellation of behavioral disorders and other complex traits. This integrative strategy enables us to relate mouse behavior to specific aspects of human disorders, to test the validity of behavioral classification schemes, and to find genes and genetic variants that influence behavior. |
Genetics and Genomics|Behavioral Disorders|Bioinformatics|Complex Traits | Genetics and Genomics|Behavioral Disorders|Bioinformatics|Complex Traits | The Chesler Lab | Professor |
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Choudhary Anshul Choudhary, Ph.D. | Farmington, CT |
Uncovering temporal dynamics of large collection of cells by applying machine learning and dynamical systems framework to single cell sequencing data.
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I’m a computational scientist working at the intersection of genomics, machine learning and nonlinear dynamics in advancing data-driven scientific discovery. I earned my PhD in physics focusing on the mathematical modeling of dynamical systems (deterministic and stochastic differential equations) on graphs (complex network topologies) to study the emergence of rich spatio-temporal patterns in various complex systems spanning from physics to ecology. After PhD, I did my first postdoc in theoretical ecology group at the Institute for chemistry and biology of marine ecosystems in Germany, where I worked on developing mathematical models of biodiversity in multi-species ecosystems competing for limited resources and developed expertise in applying machine learning methods to learn species-species trait relationships. Subsequently, I took a second postdoc to delve deeper into exploring some fundamental aspects of scientific machine learning from the lens of complex systems gaining insights that would enhance the interpretability and explainability of ML models. At JAX, I'm excited to work on predicting cell fate dynamics by constructing a transcriptome-wide continuous vector field from RNA velocity. |
Bioinformatics|Computational Biology | Bioinformatics|Computational Biology | Lab Staff | |
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Chuang Jeffrey Chuang, Ph.D. | Farmington, CT |
Computational studies of cancer image and sequence data to improve treatment outcomes
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Broad advances in sequencing, imaging, and machine learning are rapidly transforming the nature of biology research, providing rich avenues for discovery at the nexus of experimentation, mechanistic modeling and neural network analysis. My lab uses computational, mathematical, and high-throughput data generation approaches to study how cancer ecosystems function, evolve, and respond to therapeutic treatment. We study problems in cancer sequence and image analysis across a wide spectrum of cancer types, with particular expertise in breast cancer and patient-derived xenografts. Visit the Chuang Personal Lab Site |
Computational Biology|Cancer|Bioinformatics|Genetics and Genomics | Computational Biology|Cancer|Bioinformatics|Genetics and Genomics | The Chuang Lab | Professor |
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Chung Jennifer Chung | Farmington, CT |
Investigating the microbiome and its relationship with the immune system.
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Bioinformatics|Genetics and Genomics | Bioinformatics|Genetics and Genomics | The Weinstock Lab | Predoc |
Gary Churchill, Ph.D.Professor, Karl Gunnar Johansson Chair |
Churchill Gary Churchill, Ph.D. | Bar Harbor, ME |
Employs a systems approach to investigate the genetics of health and disease and complex disease-related traits in the mouse.
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Our lab is actively applying a systems approach to study the genetics of health and disease, incorporating new statistical methods for the investigation of complex disease-related traits in the mouse. We employ a combination of strategies to investigate the genetic basis of these complex traits. We are developing new methods and software that will improve the power of quantitative trait loci mapping and microarray analysis, as well as graphical models that aim to intuitively and precisely characterize the genetic architecture of disease. Within the Center for Genome Dynamics, we are part of a consortium of investigators with a shared interest in a holistic approach to understanding genetics from an evolutionary perspective. With an eye on the future of mouse genetics, we are also establishing two new mouse resources for complex trait analysis: the Collaborative Cross and the Diversity Outbred. |
Complex Traits|Genetics and Genomics|Computational Biology|Aging | Complex Traits|Genetics and Genomics|Computational Biology|Aging | The Churchill Lab | Professor |
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Coleman Ben Coleman | Farmington, CT |
I develop tools to describe the phenotypic features of neurodevelopmental disorders and discover their associated genotypes.
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I am a current MD-PhD student at UConn School of Medicine with a background in physics. I joined the Robinson Lab after two years of medical school to conduct my thesis research. My research focuses on using the Human Phenotype Ontology (HPO) to describe and understand the phenotypic features of neurodevelopmental disorders in a generalizable and computable format. By improving the way we describe patient phenotypes, we will improve our ability to identify the genetic drivers of these phenotypes. To do this, I work with domain experts to expand the HPO's terminology for neurodevelopmental disorders and to develop tools to translate clinical measurements to the HPO. |
Behavioral Disorders|Bioinformatics|Computational Biology|Developmental Disorders | Behavioral Disorders|Bioinformatics|Computational Biology|Developmental Disorders | The Robinson Lab | Lab Staff |
Daniel Danis, Ph.D.Associate Computational Scientist |
Danis Daniel Danis, Ph.D. | Farmington, CT |
I work on development of new algorithms designed to analyze big data to enable precision medicine
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I studied Pharmacy and Normal and Pathological Physiology at Comenius University, Bratislava, Slovakia. During my PhD. study, I developed bioinformatics pipelines for analysis of Whole exome sequencing data with aim to identify DNA mutations leading to metabolic or sensory disorders. At my current position, I work on development of novel algorithms and software tools for integrative analysis of clinical/phenotype data with high-throughput genomics data, such as long read whole genome sequencing. This work includes ingest, curation, and management of large volumes of data which I use for training and validation of statistical models. I am also responsible for assembly of custom bioinformatics pipelines and their deployment on distributed computational systems. Finally, I work on evaluation of models on real patient data with aim to improve diagnostics and enable precision medicine. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Robinson Lab | Computational Scientist |
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Desai Sejal Desai, B.S. | Farmington, CT |
I have been in QA for past 14 years and I have performed testing in various domains like E-Commerce, Servers, Storage and Network Controllers, WITSML, Oil & Gas and Education. I love to test and work with my team to deliver a Quality Software Product to clients.
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Software Engineer | |||
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Dewey Hannah Dewey | Bar Harbor, ME |
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Hannah graduated from the University of Maine with a degree in Mathematics, while working with Dr. Andre Khalil in the CompuMAINE lab. Before joining the Tewhey Lab, Hannah completed postgraduate degrees in Applied Mathematics (2015) and Bioinformatics and Computational Genomics (2019) at Rensselaer Polytechinic Institute and Queens University Belfast respectively, as well as serving as a Peace Corps Volunteer in Namibia. Now, as a data analyst in the Tewhey Lab, Hannah works developing pipelines to be used in the analysis of MPRA count data as well as participating in the analysis itself. In her free time Hannah enjoys baking, sharing said baked goods with other lab members, and knitting. |
Bioinformatics | Bioinformatics | The Tewhey Lab | Lab Staff |
Mary Dolan, Ph.D.Research Scientist |
Dolan Mary Dolan, Ph.D. | Bar Harbor, ME |
Work in biomedical ontology development, comparative genomics, and the development of computational methods and tools for genetic and genomic data integration, statistical analysis, and visualization.
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My early research was in the area of chemical physics performing computational modeling of molecular collisions. My work in biological systems began with post-doctoral work in computational biophysics modeling DNA denaturation. My first work at the Jackson Laboratory, with Carol Bult in collaboration with the University of Maine, was in the development of GenoSIS, a visualization and analysis tool for genome data interpretation using geographic information science concepts and technology. As part of Mouse Genome Informatics I work in Judy Blake's Gene Ontology (GO) group at JAX in the development of computational methods and tools for statistical analysis and visualization. My current research involves the development of OncoCL, an ontology of cancer cell types, to provide a semantic framework for the integration of cancer-associated molecular data and the properties imparted by the corresponding disrupted cellular pathways with conventional pathology data associated with cancer progression. |
Bioinformatics|Cancer|Computational Biology | Bioinformatics|Cancer|Computational Biology | The Bult Lab | Bioinformatics/Data Analyst|Research Scientist |
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Drabkin Harold Drabkin, Ph.D. | Bar Harbor, ME |
As part of the Gene Ontology (GO) project in the Mouse Genome Informatics Database System at The Jackson Laboratory, I participate in functional annotation of gene products ) using the GO, as well as contribute to the overall design and content of the Gene Ontology vocabulary. I am also a curator for the Protein Ontology Project, based at the Protein Information Resource at Georgetown University in D.C., focusing functional annotation of specific protein isoforms and other proteoforms (PTMs).
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As part of the Gene Ontology (GO) project in the Mouse Genome Informatics Database System at The Jackson Laboratory, I participate in functional annotation of gene products ) using the GO, as well as contribute to the overall design and content of the Gene Ontology vocabulary. I am also a curator for the Protein Ontology Project, based at the Protein Information Resource at Georgetown University in D.C., focusing functional annotation of specific protein isoforms and other proteoforms (PTMs). |
Bioinformatics | Bioinformatics | The Bult Lab | Lab Staff|Scientific Curator |
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Dumont Beth Dumont, Ph.D. | Bar Harbor, ME |
Researching the mechanisms that generate genetic diversity through the lens of evolution
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Mutation, recombination, and chromosome assortment account for all genetic diversity in nature, ranging from variants associated with disease to adaptive genetic changes. Despite their fundamental significance to genetic inheritance, the frequencies of mutation and recombination and the strength of chromosome transmission biases vary tremendously among individuals. The broad objective of my research group is to understand the causes of variation in the very mechanisms that generate genetic diversity. Toward this goal, we pursue two complementary research strategies. First, we leverage the recognition that mutation rate, recombination frequency, and biased chromosome transmission are themselves complex genetic traits controlled by multiple genes and their interactions. We combine cytogenetic and genomic approaches for assaying DNA transmission with quantitative genetic analyses in order to identify the genetic and molecular causes of variation in these mechanisms. Second, through targeted investigations of loci with extreme recombination or mutation rates, we aim to illuminate the biological mechanisms that stimulate or suppress these processes. We are currently using this latter approach to investigate recombination rate regulation, patterns of genetic diversity, and the evolutionary history of the mammalian pseudoautosomal region. |
Complex Traits|Computational Biology|Genetics and Genomics|Reproductive Disorders | Complex Traits|Computational Biology|Genetics and Genomics|Reproductive Disorders | The Dumont Lab | Assistant Professor |
Matthew Dunn, B.S.Scientific Software Engineer |
Dunn Matthew Dunn, B.S. | Bar Harbor, ME |
Creating software to help scientists analyze and visualize large data sets. I am also particularly interested in genetics and genomics.
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I worked as a programmer on medical software for 6 years, where I gained a strong background in software development. When a bug could negatively impact the health of a patient, it really impresses upon you the importance of attention to detail, testing, and writing bug-free, supportable, and well-documented code. Since joining JAX in June of 2017, I have been working with the Computational Sciences group on software resources and projects for the Chesler Lab, such as the Mouse Phenome Database website. I have enjoyed picking up and learning new programming languages and frameworks, as well as becoming familiar with various projects and the science behind them. I look forward to picking up more skills, knowledge, and projects in the future. |
Behavioral Disorders|Bioinformatics|Computational Biology|Genetics and Genomics | Behavioral Disorders|Bioinformatics|Computational Biology|Genetics and Genomics | The Chesler Lab | Software Engineer |
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Durkin Daniel Durkin, B.A. | Farmington, CT |
Strong interests in automation, testing, and rapid application development and evolution.
Dedicated to building systems to meet current and future needs.
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A synthetic organic chemist by training, I spent the first few years of my career at the bench. I've been working as a software engineer for more than 15 years, with the last 10 years focused on delivering applications that help enable scientists. Prior to joining JAX, I spent time at the Broad Institute and was exited to be part of a team that worked to deliver the BioAssayResearchDatabase. Since joining the Computational Sciences group here at JAX, I've worked closely with Clinical and was excited to lead the software team that built JAX-Clinical Knowledgebase (CKB) (https://ckb.jax.org/). |
Bioinformatics|Cancer | Bioinformatics|Cancer | Software Engineer | |
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Emerson Jake Emerson, M.S. | Bar Harbor, ME |
As a software engineer I build fast, reliable systems that solve hard problems. I am also interested in causal reasoning, information theory, and logic.
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My professional career started in the US Army Corps of Engineers. While stationed in Alaska, the Marshall Islands, the Republic of Korea and Iraq, I worked as a construction engineer, project manager, explosives and demolitions trainer, and logistics officer. After military service, I have been involved in both the worlds of startups and academia. I have led projects in a variety of fields including: hydrologic warning, field maintenance operations, crisis informatics, oceanographic event analysis, and software development. I have also been an assistant instructor in the Department of Spatial Information Science and Engineering at the University of Maine. I hold a B.S. in mechanical engineering from the U.S. Military Academy at West Point, and a M.S. in environmental engineering from the the Missouri University of Science and Technology. |
Bioinformatics|Complex Traits|Computational Biology | Bioinformatics|Complex Traits|Computational Biology | Computational Scientist|Software Engineer | |
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Englander Ryan Englander | Farmington, CT |
I am investigating splicing-derived neo-antigens in breast and lung cancer using long-read RNA-sequencing in collaboration with the Palucka Lab.
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Leveraging emergent techniques in genetics and immunology to identify and exploit therapeutic vulnerabilities in cancer |
Bioinformatics|Cancer|Genetics and Genomics|Immune Disorders | Bioinformatics|Cancer|Genetics and Genomics|Immune Disorders | The Anczukow Lab|The Palucka Lab | Predoc |
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Fasman Kenneth Fasman, Ph.D. | Farmington, CT |
A leader in scientific collaborative research management, Dr. Fasman directed drug development strategy and performance at Astra Zeneca and served as chief scientific offer at the Adelson Medical Research Foundation prior to joining JAX in 2015.
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Over the last 15 years Fasman has built many connections with JAX, serving on the Laboratory’s scientific advisory board and advising the Genetic Resource Sciences group. He currently serves on the JAX board of scientific counselors. Fasman joins the Laboratory from the Adelson Medical Research Foundation in Needham, Mass., where he has been vice president and chief scientific officer since 2008. From 1998 to 2008, he worked with the international pharmaceutical giant AstraZeneca, rising to director of drug development strategy and performance. From 1992 to 1998, Fasman worked on the human genome project at the Johns Hopkins University School of Medicine and later at the Whitehead Institute/MIT Center for Genome Research. While earning his Ph.D. in biomedical engineering from Hopkins, Fasman co-founded a laboratory software and systems design consulting firm, BME Systems, Inc. |
Data Science at JAX|Computational Biology|Bioinformatics|Cancer | Data Science at JAX|Computational Biology|Bioinformatics|Cancer | Leadership | |
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Ferraj Ardian Ferraj, MS | Farmington, CT |
Investigates the impact of structural variants in diverse genomes with a focus on transposable elements in early development.
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Ardian is a graduate student affiliated with UConn Health and The Jackson Laboratory. Under the supervision of Dr. Christine Beck, he is studying the impact of structural variants on diverse genomes, focusing on the effects of transposable element variants on stem cell transcription. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Beck Lab | Lab Staff|Predoc |
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Flynn Bill Flynn, Ph.D. | Farmington, CT |
My research interests are in machine learning, high performance and distributed computing, data reduction, and data visualization.
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I received my Ph.D.in physics from Rutgers University – New Brunswick in October 2017. During my Ph.D. work, I used machine learning to understand complex epistatic interactions among networks of correlated amino acid substitutions in protein sequence alignments, and I built distributed computational grids to run large parallel molecular dynamics simulations of protein-ligand binding. Here at JAX, I will apply machine learning techniques to new problems at the forefront of genomics and molecular biology. |
Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | Lab Staff | |
Ali Forougi Pour, Ph.D.Postdoctoral Associate |
Forougi Pour Ali Forougi Pour, Ph.D. | Farmington, CT |
Applications of mathematical modeling, statistical models, and machine learning to develop predictive models for integrative data analysis.
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I mostly work on selection and extraction on biological and morphological features that are indicative of outcomes such as response to treatment, risk of relapse, etc. I am also interested on integrating such features across data types for reliable prediction. |
Bioinformatics|Cancer|Computational Biology | Bioinformatics|Cancer|Computational Biology | The Chuang Lab | Postdoctoral Associate |
Mayuko Furuta, Ph.D.Associate Research Scientist |
Furuta Mayuko Furuta, Ph.D. | Farmington, CT |
Investigates the key genomic change in cancers and reproduce and demonstrate the effect in vitro/vivo
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My research interest is focused on investigating key regulatory genes/elements and pathways involved in cancer development from the perspective of genetic alterations. In particular, I am interested in identification of characteristic genetic change which explains phenotype or sensitivity to drugs in a subset of tumors. Moreover, by the integration of next-generation sequencing data with the use of in vivo/vitro patient-derived xenografts and cancer cells, I aim to reproduce and demonstrate their involvement in cancer development. These developed models not only help the better understanding of the mechanism underlie a subset of tumors but also helps the development of novel approaches toward the personalized treatment for patients. |
Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | The Liu Lab | Associate Research Scientist |
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Gargano Michael Gargano, B.S. | Farmington, CT |
Machine Learning, Data-Mining, Full-Stack Web Applications. I aim to bridge the gap between the vast amounts of data and the need for visual, analytical results.
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I am a software engineer, working to make a difference where biology and computer science meet. I specialize in full-stack web applications, scripting, and bioinformatics related technologies such as bioPerl, bioPython, and NGS frameworks. I have additional interest in machine learning and data mining algorithms. I aim to bridge the gap between the vast amounts of data and the need for results or visualizations. |
Behavioral Disorders|Bioinformatics|Cancer|Computational Biology | Behavioral Disorders|Bioinformatics|Cancer|Computational Biology | Software Engineer | |
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Garretson Alexis Garretson, MS | Bar Harbor, ME |
Leveraging genetic diversity and computational techniques to investigate the architecture of complex traits
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Genetically diverse animal models are critical to understanding complex traits. While the use of classical inbred strains has enabled significant genetic research, these strains do not adequately represent the genetic diversity amongst humans. Multiparent populations like the collaborative cross mice and outbred populations like the diversity outbred mice allow us to model human diversity and better understand the genetic architecture of complex traits. Genetic variation itself, however, can also be considered a complex trait that arises from mutation, recombination, and chromosome assortment. Using diverse mouse strains and computational tools, I am investigating how candidate genes can alter mutation rates and resulting population genetic variability. |
Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | The Dumont Lab | Predoc |
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Gastonguay Madeleine Gastonguay | Bar Harbor, ME |
I'm interested in a computational systems genetics approach to mediation analysis of complex traits in mice.
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My research interests lie at the intersection of mathematics and molecular biology. I recently graduated from The University of Connecticut with a degree in Applied Mathematics. During my time there, I worked at UConn Health's Center for Quantitative Medicine, employing a dynamical systems approach to identifying reversion targets for a subtype of Triple Negative Breast Cancer. I also spent a summer working at Metrum Research Group, where I developed a physiologically based pharmacokinetic model to predict maternal and fetal exposure of drugs metabolized by Cytochrome P450 enzymes in pregnant women. As part of the Churchill lab, I am using bayesian statistics to develop a new approach for mediation analysis of complex traits in mice. |
Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | The Churchill Lab | Lab Staff |
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Gega Eva Gega, M.S. | Farmington, CT |
Studying 3D Genome organization and function in human and mouse.
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Studying genome structure and function through the application of high-throughput DNA sequencing and mapping methodologies such as ChIA-PET (chromatin interaction analysis by pair end tag sequencing). Project involvement: |
Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | 3D Genomics Lab|The Wei Lab | Lab Staff |
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Gerdes Gyuricza Isabela Gerdes Gyuricza, BS | Bar Harbor, ME |
I'm interested in using computational biology to understand how genetic variation influences diseases and aging.
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My job is to use bioinformatics tools to understand gene and protein expression in the aging heart. |
Aging|Bioinformatics|Complex Traits|Computational Biology | Aging|Bioinformatics|Complex Traits|Computational Biology | The Churchill Lab | Predoc |
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Gerring Matthew Gerring, MEng | Bar Harbor, ME |
My interests are in making scientific algorithms reproducible and fit to be used by a wide community such that future research can be reliably built upon them.
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Since 1998 I have been developing scientific software, for instance computational fluids dynamics delivered over desktop and the web, data acquisition and analysis at the UK's largest science project (Diamond Light Source) and now with great pleasure at JAX. Scientific software development is where my heart is and what makes be most interested at work (I have solved problems outside this space but they are not as fun!)... |
Aging|Behavioral Disorders|Cancer|Diabetes and Obesity | Aging|Behavioral Disorders|Cancer|Diabetes and Obesity | Lab Staff|Software Engineer | |
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Geuther Brian Geuther, M.S. | Data Science at JAX | Data Science at JAX | The Kumar Lab | Lab Staff|Software Engineer | ||
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Gong Minghao Gong, Ph.D. | Farmington, CT |
Works in the crossroads of microbiology, immunology, and multi-omics analyses (esp. Metabolomics), focused on the metabolomic tools development and the applications of metabolomics in microbe-host interaction and immunological studies.
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I have been working across multiple disciplines including immunology, microbiology, and bioinformatics. My research efforts during my Ph. D has built towards the application of multi-omics approaches to understanding microbe-host interaction. Thrilled by the recent development of metabolomics, I committed my efforts to develop metabolomic tools and analysis pipelines to decipher metabolic phenotypes in immune-related disorders and other diseases. My current research includes developing metabolomic tools to the reconstruction of biochemical networks. The milestone towards this will be developing tools to upgrade genome scale metabolic models by using mass spectrometry data, via a combination of computational, genetic, cellular and isotope tracing techniques. |
Bioinformatics|Computational Biology|Immune Disorders|Infectious Disease Research | Bioinformatics|Computational Biology|Immune Disorders|Infectious Disease Research | The Shuzhao Li Lab | Postdoctoral Associate |
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Grubb Stephen Grubb, M.S. | Bar Harbor, ME |
Primary interests include phenotype data collection as well as dissemination and interpretation of phenotype data; databases for biomedical information; cancer genomics processes and databases.
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I've worked with groups that have developed scientific database-driven web resources and software applications to support biomedical research, clinical trials, and biometry. |
Aging|Behavioral Disorders|Bioinformatics|Complex Traits | Aging|Behavioral Disorders|Bioinformatics|Complex Traits | Software Engineer | |
Annat Haber, Ph.D.Bioinformatics Analyst II |
Haber Annat Haber, Ph.D. | Farmington, CT |
Developing pipelines for curating and analyzing genomic data to study the genetic architecture and population heterogeneity underlying complex diseases
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My background is in evolutionary biology and modeling multidimensional phenotypes. My current work involves analyzing various sources of genomic and epigenomic data to better understand their interactions and role in driving Alzheimer's disease and other complex conditions. I use various computational approaches to model the heterogeneity underlying such conditions, and to align human data with mouse models. |
Aging|Bioinformatics|Complex Traits|Computational Biology | Aging|Bioinformatics|Complex Traits|Computational Biology | The Carter Lab | Lab Staff |
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Hadad Niran Hadad, Ph.D. | Bar Harbor, ME |
My primary research focus is on leveraging genetically diverse mouse populations to uncover genetic and epigenetic mechanisms that govern organismal cognitive aging
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I graduated from The University of Oklahoma with a PhD in neuroscience, and shortly thereafter joined the Kaczorowski lab as a postdoctoral associate. I am intent on leveraging genetically diverse mouse populations to uncover genetic and epigenetic mechanisms that govern organismal aging, and determine to what extent these mechanisms are acting in the brain to confer risk and resilience to Alzheimer's disease. Most of the known risk variants associated with Alzheimer's disease occur in non-coding regions in the genome and are proposed to influence gene targets that are (1) different than those classically been associated with, and (2) act in a cell type specific manner. I use single-cell technologies to characterize the effects of risk variants on their target genes and explore their influence on molecular networks associated with aging and Alzheimer's disease. My goal is test whether identified genetic variants alter the epigenetic landscape, and whether these variants can be targeted to delay or prevent age-related cognitive decline and dementia. |
Aging|Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | Aging|Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | The Kaczorowski Lab | Postdoctoral Associate |
Pille Hallast, Ph.D.Associate Research Scientist |
Hallast Pille Hallast, Ph.D. | Farmington, CT |
Genetic diversity and evolution of complex genomic regions and their association to phenotypes, with a particular focus on the male-specific Y chromosome
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I have always been fascinated by the genetic diversity of the genome, both in terms of its functional consequences, as well as its enormous power as a population genetics tool. My previous studies have focused on population genetics, history and phylogeographic patterns of humans and great apes, and the effects of Y-chromosomal genetic diversity on male in/sub-fertility. Over the years I have become increasingly interested in the diversity and evolution of complex regions and their potential association to phenotypes. Chromosome Y in particular, presents with unique challenges but at the same time offers unique opportunities, with obvious translational implications on male fertility, but also as a tool to investigate male-specific patterns of population structure and migration history. I am currently utilising long-read sequencing technologies and chromatin interaction methods to interrogate previously poorly studied regions, with a longer term research goal of re-evaluating the evolution and structural diversity of known and novel complex genomic regions. |
Computational Biology|Genetics and Genomics | Computational Biology|Genetics and Genomics | The Lee Lab | Associate Research Scientist |
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Hansen Peter Hansen, Ph.D. | Bar Harbor, ME |
Develops software that implements statistical and algorithmic approaches to analyze and integrate immunoprofile and metagenomic data.
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Peter Hansen studied Bioinformatics at Freie Universität Berlin, Germany. He worked as a research associate at the Institute of Medical Genetics and Human Genetics of the Charité University Hospital in Berlin and received his Ph.D. degree in Mathematics and Computer Science in 2019. He gained practical experience in collaboration with human geneticist at the Charité University Hospital and developmental biologists Max Planck Institute for Molecular Genetics. Furthermore, he developed various software tools for NGS data analysis including the ChIP-seq peak caller Q and a desktop application named GOPHER for the design of capture Hi-C probes. Peter joined the Robinson Lab in April 2019. He will contribute to a project that aims to improve diagnosis and therapy of ME/CFS by developing software that integrates immunoprofile and metagenomics data using machine learning techniques. |
Bioinformatics | Bioinformatics | The Robinson Lab | Lab Staff |
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Harder Jeffrey Harder, Ph.D. | Bar Harbor, ME |
Researching axon degeneration and the roles of immunity in the central nervous system and diet in glaucoma.
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I joined the Simon John lab in the spring of 2013, excited by the opportunity of working with Dr. John and using a multidisciplinary approach in my research. Using DBA/2J mice as a model of glaucoma, my current research focuses on axon degeneration, the role of innate immunity in the central nervous system, and the role of diet in neurodegeneration. This includes studying the role of JNKs in glaucomatous injury and working to identify early signaling events that may initiate injury. For another project, I am collaborating with faculty from Dalhousie University, working on defining human genes responsible for exfoliation syndrome glaucoma. I also work closely with fellow postdoc Pete Williams and help direct two research assistants in the lab. This opportunity to collaborate and manage while working through complex projects is broadening my conceptual thinking abilities both scientifically and managerially, and improving the array of skill sets necessary for running a lab. |
Genetics and Genomics|Complex Traits|Bioinformatics | Genetics and Genomics|Complex Traits|Bioinformatics | Associate Research Scientist | |
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Hariramani Nidhi Hariramani, MSc | Farmington, CT |
Perform laboratory research which include sample processing, biomolecule isolation and molecule analyses like PCR, qPCR, and library preparation for sequencing.
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Prepare amplicon and shot gun libraries to sequence on different illumina platforms to investigate the functional role of microbiome on several diseases. Perform microbiological and molecular biology laboratory techniques such as qPCR, MALDI, making media and buffer solutions, bacterial culture and streaking, DNA extraction and purification, PCR, gel electrophoresis and imaging. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Weinstock Lab | Lab Staff |
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Hession Leinani Hession | Bar Harbor, ME |
Computational and Systems approaches to biology
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Leinani is a research intern who graduated from New College of Florida in 2019. The focus of her undergraduate studies was Biology and Computer Science, and she wrote a senior thesis on the intersection of AI and creativity from an embodied, dynamical systems perspective. Leinani is excited to work on computational/Machine Learning approaches to biology at the Kumar Lab. She is currently working on projects related to aging and nociception. |
Computational Biology | Computational Biology | The Kumar Lab | Lab Staff |
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Heuer Sarah Heuer, B.Sc. | Bar Harbor, ME |
I am interested in understanding how microglia activation states cause neurodegenerative phenotypes in Alzheimer's disease and dementia.
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Alzheimer's disease (AD) is the leading cause of age-related dementia, but the underlying causal mechanisms of AD neurodegenerative phenotypes are relatively unknown. Microglia, the resident immune cells of the central nervous system, are known to participate in pruning of neuronal synapses under homeostatic conditions, and produce diverse activation states in the AD brain with relatively unknown consequence. By combining the Howell lab's expertise in mouse genetics and neurodegeneration, my background in immunology and genetics, and collaborative resources at JAX, we are investigating how states of activated microglia cause susceptibility to neurodegenerative phenotypes at the level of the neuronal synapse. |
Aging|Bioinformatics|Genetics and Genomics|Immune Disorders | Aging|Bioinformatics|Genetics and Genomics|Immune Disorders | The Howell Lab | Predoc |
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Hill David Hill, Ph.D. | Bar Harbor, ME |
Working in ontology and biological data capture and representation.
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Although trained as a developmental biologist, I have been working since 2000 in the area of semantic data integration for biological knowledge. Sequencing of whole genomes and development of large-scale genomic technologies, coupled with traditional experimental biomedical research, has resulted in the generation of vast amounts of information about genes and how they function. My work in the Blake lab focuses on two aspects of making our knowledge about genes manageable and accessible to researchers. First, I am an ontology developer for The Gene Ontology Consortium, working to develop formal networks to describe how genes act and how they achieve their overall biological objective in a species-neutral context using modern ontology-development principles. Second, I manage biological data capture and representation, particular those data derived from studies of the laboratory mouse. My work is integrated into two major bioinformatics resources: Gene Ontology and Mouse Genome Informatics. |
Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Bioinformatics | Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Bioinformatics | The Bult Lab | Research Scientist|Scientific Curator |
Gareth Howell, Ph.D.Associate Professor, Diana Davis Spencer Foundation Chair for Glaucoma Research |
Howell Gareth Howell, Ph.D. | Bar Harbor, ME |
Applies genetics and genomics approaches to study age-related neurodegeneration associated with Alzheimer’s disease, dementia and glaucoma.
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In the Howell lab, we apply genetics and genomics approaches to identify fundamental processes involved in the initiation and early propagation of age-related neurodegenerative diseases, focusing on Alzheimer's disease, non-Alzheimer's dementia and glaucoma. Understanding these processes provides the greatest opportunity of therapeutic intervention. We are particularly interested in the role of non-neuronal cells including astrocytes, monocyte-derived cells (such as microglia), endothelial cells and pericytes. In previous work, I applied novel genomics and bioinformatics strategies to identify new molecular stages of glaucoma that preceded morphological changes. Genetic knockout and/or pharmaceutical approaches showed that targeting the complement cascade and endothelin system significantly lessened glaucomatous neurodegeneration in mice. Our work with glaucoma continues in collaboration with Dr. Simon John, and we are also now applying similar genetics and genomics strategies to understand initiating and early stages of Alzheimer's disease, vascular dementia and other dementias. A major aim is to combine knowledge from human genetic studies with the strengths of mouse genetics to develop new and improved mouse models for dementias and make them readily available to scientific community. Gareth Howell at University of Maine Gareth Howell at Tufts University
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Genetics and Genomics|Bioinformatics|Aging|Neurodegenerative and Neuromuscular Diseases | Genetics and Genomics|Bioinformatics|Aging|Neurodegenerative and Neuromuscular Diseases | The Howell Lab | Associate Professor |
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Iyer Aditya Mahadevan Iyer, Ph.D. | Bar Harbor, ME |
Exploring the roles of epigenetic factors in the context of mammalian spermatogenesis
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Meiotic recombination is required to produce gametes in all sexually reproducing organisms. Additionally, recombination provides the raw material for evolution to act upon and makes the science of genetics possible. Given that meiotic recombination occurs in the context of dynamically changing chromatin, how DNA and proteins are organized at hotspots to establish a permissive environment for successful introduction and resolution of double-strand breaks (DSBs) remains a fundamental question in reproductive biology. My overarching research goal is to understand the mechanisms regulating chromatin organization during meiosis and spermatogenesis. Aditya Mahadevan Iyer on ORCID
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Bioinformatics|Computational Biology|Developmental Disorders|Genetics and Genomics | Bioinformatics|Computational Biology|Developmental Disorders|Genetics and Genomics | The Baker Lab | Postdoctoral Associate |
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Johnson Kevin C. Johnson, Ph.D. | Farmington, CT |
The major focus of my research program is to investigate the epigenetic reprogramming along the continuum of cancer initiation to disease progression.
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I am currently a postdoctoral associate in the laboratory of Dr. Roel Verhaak where my research has focused on brain tumor evolution and heterogeneity. To uncover the evolutionary trajectories that brain tumors take from initial diagnosis to disease recurrence, I co-led an international longitudinal brain tumor sequencing project. Computational analyses of these collected genomics data helped establish the order of somatic events throughout a tumor’s molecular life history and identified the most common evolutionary routes under selective therapeutic pressures. These findings were recently published in Nature, and I continue to be involved with projects that leverage this rich dataset. In a separate study, I have sought to deeply characterize the epigenetic heterogeneity that exists within brain tumors. To this end, I established a single-cell DNA methylation assay that enables genome-wide coverage of the epigenome and applied it to human brain tumor specimens. |
Bioinformatics|Cancer|Genetics and Genomics|Computational Biology | Bioinformatics|Cancer|Genetics and Genomics|Computational Biology | The Verhaak Lab | Research Scientist |
Jethro Johnson, Ph. D.Alumni|Postdoctoral Associate |
Johnson Jethro Johnson, Ph. D. | Farmington, CT |
Studying host-microbiome interactions at a functional genomic level.
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Dr. Johnson has a PhD in nutritional ecology and completed a career development fellowship in computational genomics before joining the Weinstock Lab. His interest is in leveraging next-generation sequencing technologies to study how environmental factors, such as nutrition, influence host-microbiome interactions at a functional genomic level. |
Computational Biology|Genetics and Genomics|Diabetes and Obesity | Computational Biology|Genetics and Genomics|Diabetes and Obesity | The Weinstock Lab | Alumni|Postdoctoral Associate |
Catherine Cook Kaczorowski, Ph.D.Professor, Evnin Family Chair in Alzheimer’s Research |
Kaczorowski Catherine Cook Kaczorowski, Ph.D. | Bar Harbor, ME |
Identify early causative events that underlie cognitive deficits associated with ‘normal’ aging and Alzheimer’s disease
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To get a different answer you need to ask the question differently.Alzheimer’s disease currently affects 5 million Americans and despite decades of research we do not yet have a treatment that can even substantially slow the devastating symptoms let alone cure the inevitable cognitive decline. Work in my laboratory to address this situation was launched not by asking what causes the disease, but by posing the counterintuitive question: “What makes some people resistant to the disease”? In looking for the answer to this disarmingly simple question my laboratory is now leading a unique attack on Alzheimer’s and age-related dementia by focusing on identifying and validating the genetic factors that protect individuals from cognitive decline. Integrated with broad collaborative efforts, my team of interns, research scientists, postdoctoral fellows and graduate students are working on a variety of projects that seek to understand these “genetic mechanisms and biomarkers of resilience” with the ultimate goal of turning these protective factors into novel therapies. |
Neurodegenerative and Neuromuscular Diseases|Aging|Genetics and Genomics|Resource Development and Dissemination | Neurodegenerative and Neuromuscular Diseases|Aging|Genetics and Genomics|Resource Development and Dissemination | The Kaczorowski Lab | Associate Professor |
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Kadin James Kadin, Ph.D. | Bar Harbor, ME |
Providing database development and web delivery for the Mouse Genome Informatics consortium.
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The Mouse Genome Informatics consortium (MGI) integrates data from over 40 external resources with hand-curated data from published literature to provide an integrated data resource/website that facilitates the use of the mouse as a model for human disease and biology. My role in MGI is to co-direct, with Joel Richardson, the technical work behind theresource. This includes overseeing the hardware and software architecture and thesoftware/database development for both the back end, where data is loaded/integrated,and the front end website, where data is made available for public researchers. This worksupports most of the MGI programs, including the Mouse Genome Database (MGD) and the Gene Expression Database (GXD). |
Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Bioinformatics|Resource Development and Dissemination | Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Bioinformatics|Resource Development and Dissemination | The Bult Lab|The Ringwald Lab | Lab Staff|Senior Research Scientist |
Guy Karlebach, Ph.D.Associate Research Scientist |
Karlebach Guy Karlebach, Ph.D. | Farmington, CT |
Modeling of transcription and its variation with extrinsic or intrinsic triggers.
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I model data generated by high-throughout omics technologies in order to explain variation in gene expression and alternative splicing under various conditions such as different cell types, biological sex or viral infection. The resulting models can be used to derive hypotheses about the processes that lead to disease and suggest novel therapeutic targets. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Robinson Lab | Associate Research Scientist |
Stephen KeeganBioinformatics Analyst |
Keegan Stephen Keegan | Bar Harbor, ME |
Provide novel therapeutic targets for Alzheimer's Disease as part of TREAT-AD
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I am interested in modeling complex biological systems. My current focus is to combine multiple data modalities; provide as much insight into Alzheimer's Disease as possible. My previous work was implementing machine learning techniques on high-dimensional transcriptomics data to identify key driver genes in the disease progression of Alzheimer's Disease. |
Aging|Bioinformatics|Complex Traits|Computational Biology | Aging|Bioinformatics|Complex Traits|Computational Biology | The Carter Lab | Lab Staff |
Kwondo Kim, Ph.D.Postdoctoral Associate |
Kim Kwondo Kim, Ph.D. | Farmington, CT |
My studies focus on evolution and function implications of structural variations in human population.
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I introduce myself as a computational biologist studying evolution using genomics approaches. Before joining JAX, I have been studying evolution of mammalian including human and livestock animals using population genomics approach. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Lee Lab | Postdoctoral Associate |
Minji Kim, Ph.D.Postdoctoral Associate |
Kim Minji Kim, Ph.D. | Farmington, CT |
Computational Biology, 3D Genome Organization
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Studying the role of chromatin interactions in gene regulation by leveraging 3D genome mapping technologies. |
Computational Biology|Bioinformatics|Genetics and Genomics | Computational Biology|Bioinformatics|Genetics and Genomics | The Chuang Lab | Lab Staff |
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Kizhatil Krish Kizhatil, Ph.D. | Bar Harbor, ME |
Glaucoma causes blindness in more than 70 million people worldwide. Research is currently being conducted to uncover the underlying mechanisms of this disease.
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Glaucoma causes blindness in more than 70 million people worldwide. A major causal risk factor for glaucoma is the elevation of intraocular pressure (IOP). An increased resistance to the drainage of aqueous humor (the clear fluid filling the front of the eye) from the anterior chamber of the eye causes IOP elevation. However, the molecular mechanisms underlying both IOP elevation and aqueous humor drainage remain unknown. My goal is to fill this gap in knowledge. Using novel genetic tools,modern techniques and a variety of mouse lines, I am presently determining the molecular mechanism of aqueous humor outflow through the Schlemm’s canal (SC), a critical component of the pressure-dependent conventional outflow pathway. We have developed novel techniques and tools to measure outflow and study the SC at a cellular level. Using these tools we have already recently discovered that the SC is a unique vessel that has both lymphatic and blood vessel like characteristics. We are currently exploiting this new finding to obtain information regarding the molecular mechanisms of IOP elevation that can be leveraged to design new therapeutic interventions to prevent glaucoma. |
Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Developmental Disorders|Bioinformatics | Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Developmental Disorders|Bioinformatics | Research Scientist | |
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Kohar Vivek Kohar, Ph.D. | Bar Harbor, ME |
Develops computational methods, pipelines, web apps, and simulation tools to analyze and model data from NGS multi omics and video-based assays.
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Studies the complex biological processes using machine learning and physics-based dynamical (linear/nonlinear) models using data-driven analysis. Develops computational methods, tools, pipelines, and interactive web apps to construct, model, simulate, and visualize the gene regulatory networks in various biological processes using literature-based evidence as well as RNA-Seq (bulk/single-cell), ATAC Seq, and CHiP Seq data. Employs deep learning on video-based assays and genomics data from behavioral studies to connect behavior and genetics. |
Bioinformatics|Genetics and Genomics|Infectious Disease Research|Complex Traits | Bioinformatics|Genetics and Genomics|Infectious Disease Research|Complex Traits | Affiliated Scientist | |
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Kolishovski Georgi Kolishovski, M.S. | Bar Harbor, ME |
I am interested in high performance computing, statistical analysis, and biological systems modeling.
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My primary focus at JAX is on developing data management systems and tools for the exploration and visualization of complex biological data and its interpretation. As part of a multidisciplinary team at JAX, I frequently collaborate with both experimental and computational scientists on data analysis and visualization projects. In my role as a Scientific Software Engineer, I am leading the JAX Synteny Browser, a novel tool for interactive visualization of regions of conserved synteny between two genomes based on their biological properties such as function and phenotypes. Another hallmark initiative that I am closely involved in is JAX’s Patient–Derived Xenografts (PDX) program, a platform for data management, visualizations, analysis, reporting of cancer models studies. I lead the implementation of interactive visualizations for cancer treatment response studies (SOC) and develop automated software to run robust pipelines for the analysis of genomic variations in cancer models. I am also a key member of the Mouse Phenome Database (MPD) project, an integrated platform to explore physiology and behavior through genetics and genomics, for which I create highly interactive data visualization tools using the latest cutting edge and open source technologies. In addition, I also teach several data science and programming courses/workshops at JAX on coding skills in R, Python and SQL. |
Data Science at JAX | Data Science at JAX | Software Engineer | |
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Krupke Debbie Krupke | Bar Harbor, ME |
Senior Scientific Curator on the Mouse Models of Human Cancer Database (MMHCdb)
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I work as a Senior Scientific Curator on the Mouse Models of Human Cancer Database (MMHCdb) (formerly known as the Mouse Tumor Biology (MTB) Database). The MMHCdb is part of the Mouse Genome Informatics (MGI) group here at The Jackson Laboratory. Education
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Cancer|Genetics and Genomics|Bioinformatics | Cancer|Genetics and Genomics|Bioinformatics | Scientific Curator | |
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Kuffler Lauren Kuffler | Bar Harbor, ME |
Studying the genomics of complex diseases.
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Bioinformatics|Data Science at JAX|Complex Traits | Bioinformatics|Data Science at JAX|Complex Traits | The Carter Lab | Predoc |
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Kumar Swarup Kumar, MD | Farmington, CT |
My research focuses on interpreting high-throughput genomic and phenotypic analysis of tumor samples specifically that of the breast tumor micro-environment
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I am a clinical fellow with the University of Connecticut in Hematology and Medical oncology. I also hold a physician fellow - visiting scientist position at the Jackson Laboratory for training in cancer genomics for a period of 1.5 years. My research interest lies in studying the interactions of immunity with tumors as well as identifying strategies to effect treatment of cancers. My focus is on computing gene expression profiling of tumor samples as well as experimental design and methodology. I have previously worked as a research trainee at Mayo Clinic Rochester with the department of Gastroenterology and Hepatology. |
Cancer|Bioinformatics|Computational Biology | Cancer|Bioinformatics|Computational Biology | The Palucka Lab | Predoc |
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Kumar Vivek Kumar, Ph.D. | Bar Harbor, ME |
Understand the genetic and neurobiological basis of complex behaviors that are important in psychiatric conditions such as addiction, ADHD, and depression using genomic, neural circuit, and computational tools.
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The Kumar Lab consists of geneticists, neuroscientists, and computer scientists. We are passionate about discovering novel targets and models for mental illness through innovation at the confluence of computational, genetic, and genomic methods. Broadly, we are interested in development of better animal models and animal phenotyping methods for human psychiatric illnesses. We use computer vision approaches to quantitate behavior and functional approaches to understand its underlying neuronal and genetic architecture. We have developed high-throughput computer vision based methods for ethologically relevant animal phenotyping. In functional genomics work, we use QTL and mutagenesis approaches to discover novel pathways that can be targeted for addiction therapeutics. Our approaches are flexible and can be applied towards many psychiatric phenotypes. In sum, we are a leading research group using genetics as its foundation, and a combination of biochemistry, physiology, imaging, and computer vision techniques to dissect complex behavior in mammals. Dr. Kumar carried out undergraduate research at The University of Chicago with Dr. Bob Haselkorn. He received his PhD at UCSD working with Dr. Michael G. Rosenfeld and structurally and biochemically characterized transcriptional co-repressors. During his postdoctoral work, Dr. Kumar trained with Dr. Joseph S. Takahashi at Northwestern and UT Southwestern and worked on functional genomics approaches to dissect the genetics of addiction. |
Behavioral Disorders|Genetics and Genomics|Complex Traits|Bioinformatics | Behavioral Disorders|Genetics and Genomics|Complex Traits|Bioinformatics | The Kumar Lab | Associate Professor |
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Lamoureux Anna Lamoureux, B.S. | Bar Harbor, ME |
Front-end development, data visualization with D3, and UI/UX for web-based applications to be used by the scientific community
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I work on teams to develop and improve internal software-based tools used by researchers within the lab. I am also involved in the JAX Diversity Strain Informatics project which will bring everything regarding CC/DO mice into one space where the scientific community can access data, tools, and educational resources. Most of my work is front-end, utilizing tools like D3, and UI/UX, but I'm always looking to improve and expand my knowledge to work towards becoming a full-stack developer. My primary languages and tools are: Javascript, Python, HTML/CSS, D3, Sketch |
Data Science at JAX | Data Science at JAX | Software Engineer | |
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Larson Peter Larson, BS | Farmington, CT |
Engineering the human skin microbiome to treat diseases and prevent infections.
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I've brought my background in synthetic biology to the Oh Lab with the aspiration to leverage the human microbiome (the bacteria, fungi, viruses, and other microbes that live on us) to promote health, prevent infections, and treat diseases. Here I have been engineering Staphylococcus epidermidis, a ubiquitous skin commensal, to detect and kill pathogens, as well as secrete therapeutics. Additionally, I have been conducting a sizable clinical metagenome study investigating the relationship between aging, health, and the microbiome. This study should help us understand how we can leverage the microbiome to promote healthy aging, combat chronic illnesses, and prevent infections commonly acquired by older adults in healthcare settings. Finally, I have been exploring the use of human skin explants and stem cell derived skin “organoids” to model human skin microbiome interactions. This will allow us and others to test engineered skin microbiome therapeutics, and better identify mechanisms by which the skin microbiome modulates health and disease. |
Aging|Bioinformatics|Computational Biology|Genetics and Genomics | Aging|Bioinformatics|Computational Biology|Genetics and Genomics | The Oh Lab | Predoc |
Raman Akinyanju Lawal, Ph.D.Postdoctoral Associate |
Lawal Raman Akinyanju Lawal, Ph.D. | Bar Harbor, ME |
Unraveling the evolutionary forces that give rise to the observed genetic diversity in the house mouse
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Genetic diversity is critical for the survival of any species. It is also central to the understanding of why one population, under similar environmental challenges, survives over another. I am primarily focused on determining the underlying evolutionary mechanisms shaping the observed genetic diversity found in the wild house mice. The wild house mice are invasive species with a long history of adaptation to new and the most extreme habitat. Unraveling the mystery of such adaptation is important for biomedical discoveries. View Raman Lawal on Research Gate |
Computational Biology|Genetics and Genomics | Computational Biology|Genetics and Genomics | The Dumont Lab | Postdoctoral Associate |
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Lee Byoungkoo Lee, Ph.D. | Farmington, CT |
Research projects:
ENCODE ChIA-PET data processing, NGS data processing pipeline, 3D genomics --
Research interests:
Genome Science, long-read sequencing
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I have worked on 3D genomics, such as ChIA-PET (chromatin interaction analysis by paired-end tag sequencing) and ChIA-Drop (droplet-based and barcode-linked sequencing). I have contributed to develop ChIA-PET data processing pipeline (ChIA-PIPE) and ChIA-Drop data processing pipeline (ChIA-DropBox). Currently, I am working on ENCODE project, ChIA-PET data processing, data quality assessment, and data submission to ENCODE DCC. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | 3D Genomics Lab|The Wei Lab | Lab Staff|Research Scientist |
Charles Lee, Ph.D., FACMGScientific Director and Professor, The Jackson laboratory for Genomic Medicine, Robert Alvine Family Endowed Chair |
Lee Charles Lee, Ph.D., FACMG | Farmington, CT |
The study of structural genomic variation in human biology, evolution and disease
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The research laboratory of Dr. Charles Lee at The Jackson Laboratory for Genomic Medicine develops and applies state-of-the-art technologies to study structural genomic variation and its contribution to human diseases, and vertebrate genome evolution. |
Genetics and Genomics|Bioinformatics|Computational Biology|Aging | Genetics and Genomics|Bioinformatics|Computational Biology|Aging | The Lee Lab | Leadership|Professor |
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Lek Sai Lek | Farmington, CT |
Bioinformatics, Cloud/High Performance Computing, Pipeline Development, Microbiome, Cancer biology, Precision Medicine, Genetics, and Genomics
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I hold a M.S. in Computer Science with a background and hands on experience in High Performance Computing, Analysis Pipeline Development, Genome Assembly & Annotation, Microbiome Data Analysis, Long-Read Sequencing (PacBio & Oxford Nanopore). Previously I worked in The Genome Institute (Washingtion University School of Medicine in St. Louis), The Weinstock Lab and Microbial Genomic Services at JAX. I am now a member of Computational Sciences and working on Pipeline developments & Microbiome related projects. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | Lab Staff | |
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Li Shuzhao Li, Ph.D. | Farmington, CT |
Metabolomics for precision medicine; ImmunoMetabolomics and multi-omics modeling of immune system
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The application of high-resolution mass spectrometry now enables the measurement in human samples the metabolome, lipidome and small molecules of dietary, microbial and environmental origins. This revolutionary information fills a major gap between genome and environment, with broad applications to diseases and precision medicine. We combine experimental approaches with computational algorithms that identify pathway patterns and integrate chemical reactions and biology. Current projects:
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Bioinformatics|Computational Biology|Immune Disorders|Resource Development and Dissemination | Bioinformatics|Computational Biology|Immune Disorders|Resource Development and Dissemination | The Shuzhao Li Lab | Associate Professor |
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Li Sheng Li, Ph.D. | Farmington, CT |
Applies data integration and machine learning to advance the frontiers of cancer epigenomics and evolution.
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My research interest is to understand the inner workings of cancer cells – the genetic and epigenetic heterogeneity that drive cancer initiation and progression. We utilize computational and sequencing methodologies to identify and characterize the essential epigenetic lesions that guide cancer cells to evolve and escape from anti-cancer therapy. The ultimate goal is to develop novel methods to predict and address tumor evolution. |
Cancer|Computational Biology|Bioinformatics|Genetics and Genomics | Cancer|Computational Biology|Bioinformatics|Genetics and Genomics | The Li Lab | Assistant Professor |
Yang Liu, Ph.D.Postdoctoral Associate |
Liu Yang Liu, Ph.D. | Farmington, CT |
I am interested in epigenetic pattern recognition of cancer, biomedical big data mining, third-generation sequencing data pattern mining.
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I was admitted to Xi'an Jiaotong University at the age of 15. And I received my B. S., and Ph.D. degrees from Xi'an Jiaotong University, China in 2004, and 2010, respectively. Before I worked in Blekinge Institute of Technology, Sweden and Zhengzhou University, China. I have published more than 15 journal and conference papers in the areas of machine learning with uncertainty, E-Health system and DNA computing. At JAX, I engaged in multi-omic data analysis and algorithm development, including epigenetic pattern mining and algorithm development of cancer, and DNA methylation pattern mining research. |
Bioinformatics|Computational Biology|Cancer | Bioinformatics|Computational Biology|Cancer | The Li Lab | Postdoctoral Associate |
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Marches Radu Marches, Ph.D. | Farmington, CT |
Investigating changes in innate and adaptive immune cells in the contexts of aging and vaccination.
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My research is focused on the study of epigenetic, transcriptional and splice-variant transcriptome changes in innate and adaptive immune cells in the context of aging and vaccination. The integrated genomic analysis is correlated with specific functional analyses involving the key innate and adaptive immune cell subsets and the magnitude of specific immune response of the vaccinated subjects. The overall goal is to determine the epigenetic factors and transcriptional alterations associated with immunosenescence, which is linked to a decline in the protective immunity including response to vaccination. |
Computational Biology|Genetics and Genomics|Bioinformatics | Computational Biology|Genetics and Genomics|Bioinformatics | The Ucar Lab | Associate Research Scientist |
Francesca Menghi, Ph.D.Associate Research Scientist |
Menghi Francesca Menghi, Ph.D. | Farmington, CT |
Studies critical genomic changes implicated in ovarian and breast cancers.
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At the Jackson Laboratory for Genomic Medicine, I am involved in several projects that explore the genome-wide patterns of genetic and transcriptional alterations characterizing human cancers. In particular,I am interested in the identification of key regulatory genes and/or pathways as well as complex rearrangement profiles, which may explain tumor initiation and progression as well as provide valuable targets for the development of novel therapeutic approaches and prognostic biomarkers. At present, I am investigating critical genomic aberrations implicated in ovarian and breast cancer tumorigenesis. By exploiting next-generation sequencing technologies combined with in vitro cell culture models and in vivo patient-derived xenografts, I aim at a better understanding of the individuality of cancer genomes and at the development of novel approaches toward the personalized management of cancer patients. |
Computational Biology|Genetics and Genomics | Computational Biology|Genetics and Genomics | The Liu Lab | Associate Research Scientist |
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Moskwa Nicholas Moskwa, Ph.D. | Farmington, CT |
Working with transcriptional and genomic data that inform cell differentiation.
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In general I am interested in cell differentiation. To resolve how cells differentiate, I have used a combination of large transcriptional data, computer modeling and cell culture for finding signaling pathways. At a broader level, I am curious how cells from different origins approach heterogeneity for performing specific tasks. |
Bioinformatics|Computational Biology|Developmental Disorders|Genetics and Genomics | Bioinformatics|Computational Biology|Developmental Disorders|Genetics and Genomics | The Lee Lab | Lab Staff |
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Munger Steven Munger, Ph.D. | Bar Harbor, ME |
Conducting research to elucidate and compare the transcriptional network structure and dynamics driving organogenesis.
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It has become clear that genetic background, including both common and rare variants, significantly influences disease susceptibility, severity, prognosis and even treatment effectiveness. Most genetic variants assert subtle effects in isolation, but certain combinations can disrupt normal homeostasis and sensitize an individual to disorder. Thus, many complex diseases have resisted classification by single-gene experimental and/or statistical modeling approaches. A comprehensive characterization of the genetic etiology of complex disorders and disease must account for the effects of all inputs (e.g. genetic variation) on all outputs (e.g. transcription, measures of structure/function) in the context of the affected system. My overarching research goals are to 1) characterize the transcriptional network architecture underlying normal organ development and homeostasis, 2) predict the genes, gene-gene interactions, and coregulated gene cohorts with major roles in this process, and 3) identify and validate genetic mutations with individual small effects that together disrupt the buffering capacity of the transcriptional network and cause a disordered/disease state. To that end, I take a systems genetics approach that integrates advanced computational methods and experimental validation techniques to next-generation genetic mapping populations, including the mouse Collaborative Cross and Diversity Outcross, to elucidate and compare the transcriptional network structure and dynamics driving organogenesis (the embryonic gonad at the critical time point of primary sex determination) and adult tissue homeostasis (liver). |
Complex Traits|Genetics and Genomics|Developmental Disorders|Reproductive Disorders | Complex Traits|Genetics and Genomics|Developmental Disorders|Reproductive Disorders | The Munger Lab | Assistant Professor |
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Naggert Jürgen Naggert, Ph.D. | Bar Harbor, ME |
Researches the complex genetics of metabolic syndrome, involving obesity, cardiovascular disease and type 2 diabetes.
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Obesity and Type 2 diabetes mellitus (T2D) are highly prevalent metabolic diseases that afflict a large proportion of the aging population in the United States. Nearly 40 percent of adults are obese, and about 10 percent of individuals over 65 have T2D. These diseases, together with cardiovascular disease, should be viewed as aspects of a metabolic syndrome that is a result of the interaction of many genes, rather than a collection of separate entities. To illustrate the complexity of the issue, there are approximately 500 to 1,000 genes in mice that may lead to obesity when mutated. Our program aims to identify new obesity and type 2 diabetes mutations and their genetic modifiers and to determine how the underlying mutations cause the disease phenotype. One focus of our investigations are ciliopathies (diseases caused by impaired function of primary cilia), which combine aspects of metabolic syndrome with sensory loss. Our laboratory identified a human gene, ALMS1, that is mutated in patients with Alström syndrome, a rare inherited condition characterized by childhood obesity, retinal and cochlear (inner ear) degeneration, type 2 diabetes, proliferative and dilated cardiomyopathy, hepatosteatitis, and kidney disease. |
Complex Traits|Bioinformatics|Computational Biology|Genetics and Genomics | Complex Traits|Bioinformatics|Computational Biology|Genetics and Genomics | The Naggert Lab | Professor |
Djamel Nehar-Belaid, Ph.D.Associate Research Scientist |
Nehar-Belaid Djamel Nehar-Belaid, Ph.D. | Farmington, CT |
Systems immunologist using single cell approaches to understand the immune system
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I have been developing computational pipelines to analyze human blood cells transcriptomics data at the single cell resolution in different contexts including SLE, aging, and influenza vaccination. My main project focusses on understanding how the single cell RNA-seq data can help resolving the SLE transcriptional signatures described decades ago. This analysis allowed a more accurate classification of lupus patients based on specific cell types. This first direct comparison of childhood and adult SLE confirmed the presence of similar transcriptional patterns across age groups and enabled patient classification according to disease activity. Currently, my research includes understanding how the immune system varies: 1) during aging at the steady state (lifespan project): aimed at analyzing blood transcriptomes from infants, children, young and older adults; and 2) after in vivo stimulation (e.g. influenza vaccination): aimed at analyzing the responsiveness to influenza vaccine in the groups indicated above. |
Aging|Bioinformatics|Computational Biology|Immune Disorders | Aging|Bioinformatics|Computational Biology|Immune Disorders | The Verhaak Lab | Associate Research Scientist |
Alex Nesta, MSPredoctoral Associate |
Nesta Alex Nesta, MS | Farmington, CT |
Combines computational and wet lab techniques to investigate the impact of transposable elements on disease transcriptomes.
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Alex is a graduate student affiliated with UCONN Health and The Jackson Laboratory. Under the supervision of Dr. Christine Beck, he is investigating the mechanisms that regulate splicing of exons derived from transposable elements. |
Bioinformatics|Cancer|Genetics and Genomics | Bioinformatics|Cancer|Genetics and Genomics | The Beck Lab | Lab Staff |
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Neuhauser Steven Neuhauser | Bar Harbor, ME |
Software engineer focused on public facing tools for searching and visualizing data related to mouse models of human cancer.
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Software engineer for Mouse Models of Human Cancer Database (formerly MTB), MouseMine, PDXFinder and PDXNet. |
Bioinformatics|Cancer | Bioinformatics|Cancer | Lab Staff|Software Engineer | |
Hoan Nguyen, Ph.D.Bioinformatics Analyst III |
Nguyen Hoan Nguyen, Ph.D. | Farmington, CT |
My research focuses on developing and applying an innovative translational bioinformatics to interpret genome variation and understand the microbial mechanisms of pathogenicity.
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My research focuses on developing and applying an innovative translational bioinformatics approach to interpret genome variation and understand the microbial mechanisms of pathogenicity. Briefly, my current work contains 4 main axes:
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Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Weinstock Lab | Lab Staff |
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Oh Julia Oh, Ph.D. | Farmington, CT |
Our central goal is to develop microbiome therapeutics to treat human disease. We use diverse tools like genomics and synthetic biology to investigate our microbiome’s role in our health and engineer therapeutics.
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Our central goal is to develop microbiome therapeutics to treat human disease. We use diverse tools like genomics and synthetic biology to investigate our microbiome’s role in our health and engineer therapeutics. |
Infectious Disease Research|Genetics and Genomics|Bioinformatics|Skin Disease | Infectious Disease Research|Genetics and Genomics|Bioinformatics|Skin Disease | The Oh Lab | Assistant Professor |
O'Neill Francis O'Neill, Ph.D. | Farmington, CT |
My primary area of research is the identification of cancer specific proteins and the development of novel anti-cancer immunotherapies for solid tumors, such as osteosarcoma.
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My primary area of research is the identification of cancer specific proteins and the development of novel anti-cancer immunotherapies for solid tumors, such as osteosarcoma. Utilizing high performance computing, we combine RNA sequencing and protein analysis in a proteogenomics workflow. The Jackson Laboratory for Genomic performs both long-read sequencing (Pacific Biosciences platform) and short-read sequencing (Illumina platform) on oncology patient samples. Our hybrid sequencing approach allows for generating a highly accurate cancer transcriptome upon which we can explore multiple biological mechanisms, such as RNA splicing and chromosomal rearrangements, leading to cancer specific mRNA isoforms. Mass spectrometry identification of isoform specific peptides aids in selecting candidates for validation in the laboratory. A central goal of my research is to expand current cancer treatment options and provide novel therapeutic agents with improved tumor specificity. |
Bioinformatics|Cancer|Computational Biology|Diabetes and Obesity | Bioinformatics|Cancer|Computational Biology|Diabetes and Obesity | The Lau Lab | Postdoctoral Associate | |
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Paisie Carolyn Paisie, Ph.D. | Farmington, CT |
My research interests are in bioinformatics, cancer biology, genetics, and genomics.
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I received my PhD in Integrated Biomedical Science, concentration in cancer biology, from Ohio State University and my MS in Biomedical & Health Informatics from University of Washington. During my PhD, I focused on mouse genetics and genomics from the perspective of a bench scientist; my dissertation work involved investigating mutation types and numbers in preneoplastic cells and tissues from Fhit knockout mice. I completed a postdoctoral fellowship and MS degree simultaneously at the University of Washington where I investigated differential gene expression in the parasite Leishmania donovani. |
Computational Biology|Bioinformatics|Cancer|Genetics and Genomics | Computational Biology|Bioinformatics|Cancer|Genetics and Genomics | Bioinformatics/Data Analyst | |
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Pan Ziwei Pan | Farmington, CT |
I am interested in applying machine learning and advanced statistical modelling into biological questions.
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I am a graduate student in Biomedical Sciences in Uconn Health with the supervisor of Dr. Sheng Li. I am interested in applying machine learning and advanced statistical modeling into biological questions. |
Bioinformatics|Computational Biology|Genetics and Genomics|Cancer | Bioinformatics|Computational Biology|Genetics and Genomics|Cancer | The Li Lab | Predoc |
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Pandey Ravi Pandey, Ph.D. | Farmington, CT |
Developing computational pipelines and employing computational strategies using genomic data to understand the genetics of complex diseases.
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Currently, I am involved in carrying out analysis of large-scale data sets to understand the genetics of neurodegenerative diseases. I will be analyzing data from clinical samples and mouse models of Alzheimer's disease to determine how genetic risk factors lead to dementia. Additionally, characterize the effects on the retina of genetic mutations that increase risk for eye disease. This work will substantially broaden our knowledge of the molecular mechanisms behind common neurodegenerative diseases. Previously, I have been working on problems like understanding the evolution of genomes by identification of evolutionary strata in sex chromosomes of mammals, birds and plants using Markov model of segmentation and clustering, which can further help in resolving many epigentics related problems like X chromosome inactivation, Identification of horizontally transferred genes, which can have evolutionary, ecological and potential biotechnological significance in recipient species and more robust taxonomic profiling of metagenomic data. Beside this, I have been also involved in many projects, which were focused on differential gene expression, functional and pathway analysis of NGS/RNA-seq data. |
Bioinformatics|Computational Biology|Neurodegenerative and Neuromuscular Diseases|Complex Traits | Bioinformatics|Computational Biology|Neurodegenerative and Neuromuscular Diseases|Complex Traits | The Carter Lab | Lab Staff |
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Perry Michelle Perry | Bar Harbor, ME |
Developmental biology, genetics, disease models, nomenclature
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As an allele and phenotypes curator, I assign official nomenclature to alleles and strain as well create genotypes with phenotypic descriptions for disease models. |
Bioinformatics | Bioinformatics | Scientific Curator | |
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Peterson Jim Peterson, M.S. | Bar Harbor, ME |
As a software engineer my primary areas of interests include image processing, mathematical algorithms and optimization.
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I recently joined Jackson after many years of diverse commercial software development, including consumer, professional and medical software and firmware. Most recently I worked on a team that developed image processing algorithms for detection of physical features in coronary OCT (optical coherent tomography) scans. Prior to that I developed the image processing chain for a disposable endoscope used for direct visualization of pancreatic ducts. For this product I also designed the control feedback algorithm for automatic illumination control. I also worked on the image processing chain for an optical particle analysis system. While the system had its origin in marine biology research, it's also been used in pharmaceutical and industrial applications. Prior to working with the scientific and medical communities I worked for many years in commercial mapping. In addition to developing consumer and professional mapping applications, I also developed the software for a multi-sensor 360-degree panoramic camera. The purpose of this camera was to collect mapping data from a moving terrestrial platform to complement data collected from the aerial platforms. I look forward to applying these experiences to the diverse problems at Jackson. |
Computational Biology | Computational Biology | Software Engineer | |
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Petkov Petko Petkov, Ph.D. | Bar Harbor, ME |
Investigating genetics/mechanisms of recombination and role of PRDM9.
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My research interests involve two scientific themes: 1) meiotic recombination and genes that affect recombination positioning and activity; and 2) chromatin organization and its role in differentiation and gene expression. Our work in meiotic recombination resulted in the discovery of the major recombination positioning gene in mice and humans, Prdm9. PRDM9 is a histone methyltransferase that binds DNA via its zinc finger domain and creates open chromatin structure, thereby setting the stage for double-strand break (DSB) initiation and subsequent recombination events. We developed Affinity-seq, an in vitro approach for detecting all DNA-binding sites of PRDM9 genome-wide, which we are now applying to other DNA-binding proteins with the goal of developing improved prediction programs for motifs and binding sites. We also found that PRDM9 functions are dependent on its interaction with several other proteins, of which we have identified EWSR1, EHMT2, and CDYL, and that its methyltransferase activity at recombination hotspots is not only dependent on its DNA-binding specificity, but is also affected by local chromatin structure and is subject to trans regulation by distant genes. Recently, I turned my attention to the role of chromatin structure on hepatocyte development and function. We found unusually diverse distributions of chromatin marks in hepatocytes of different strains, and determined that responses of these chromatin-mark distributions to corticosteroid treatment involved the same pathways across strains but not necessarily the same genes. We specifically addressed the influence of trans-acting factors on chromatin-activating marks in hepatocytes of two mouse lines, C57BL/6J and DBA/2J, using their F1 hybrids and derivative recombinant inbred lines as tools for detecting trans-acting regulators. We are now extending these studies to determine the genes regulating the positioning of open and closed chromatin in hepatocytes of Diversity Outbred (DO) mice, an enormously diverse mouse population derived from eight founder strains, and how they affect gene expression. My work on recombination hotspots, PRDM9, initiation of meiotic recombination, and the role of chromatin structure and protein interactors has resulted in over thirty publications to date in journals including Science, PLOS Biology, PLOS Genetics, Genome Biology, Current Biology, Trends in Genetics, Nature Reviews Genetics, Epigenetics and Chromatin, Genetics and Genome Research. |
Cancer|Reproductive Disorders|Genetics and Genomics|Computational Biology | Cancer|Reproductive Disorders|Genetics and Genomics|Computational Biology | Senior Research Scientist | |
Vivek Philip, Ph.D.Director, Computational Sciences |
Philip Vivek Philip, Ph.D. | Bar Harbor, ME |
My interests lie in the application of statistical methodologies to the area of genetics, specifically quantitative trait genetics and genomics for hypothesis generation and validation.
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I hold a PhD in Life Sciences from University of Tennessee/Oak Ridge National Laboratory Genome Science and Technology Program, with a focus in statistical and quantitative trait genetics of behavioral traits in genetic reference populations and integrative functional genomics of behavior across species and experimental platforms. During my Ph.D. program I investigated the increased precision and resolution in QTL mapping using mouse reference populations including the expanded BXD recombinant inbred (RI) strain panel and the Collaborative Cross (CC) reference population The BXD RI study highlighted the increase in statistical power obtained in using the expanded BXD RI strain panel. The CC study highlighted the increased allelic variation and QTL mapping precision achieved. Upon completion of my Ph.D., I joined the Computational Sciences - Statistics and Analysis group at The Jackson Laboratory in 2012 as a biostatistician, with responsibilities including QTL analysis, expression QTL analysis, gene expression analysis, statistical modeling of diverse biological datasets, and statistical consulting. In addition to my contributions towards the field of quantitative trait genetics and statistical genetics, I have undertaken several other data analysis tasks involving differential gene expression analysis using next generation sequencing technologies, leading to the generation of new or validation of existing hypothesis. For a complete list of my published work, please visit my NCBI bibliography. |
Behavioral Disorders|Bioinformatics|Complex Traits|Computational Biology | Behavioral Disorders|Bioinformatics|Complex Traits|Computational Biology | The Kaczorowski Lab | Director |
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Rasicci Daniel Rasicci | Bar Harbor, ME |
I am interested in studying genomics and proteomics to gain a better understanding of complex developmental and pathological pathways.
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While studying for my BS in bioinformatics I helped research the SOX family of transcription factors, looking at functional domain analysis using molecular dynamics simulations and evolutionary analysis of variants. I graduated in 2018. I started working as a research assistant to Dr. Kevin Peterson in 2019, maintaining multiple lines of mice to study the Hedgehog signaling pathway during embryonic development. We are currently working to study the regulatory mechanisms of the Gli transcription factors. |
Bioinformatics|Developmental Disorders|Genetics and Genomics | Bioinformatics|Developmental Disorders|Genetics and Genomics | The Murray Lab | Lab Staff |
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Rastegari Farzaneh Rastegari | Farmington, CT |
Computational Genomics, Bioinformatics, Genetics and Genomics, Microbiome Data Analysis, Cancer, Infectious Disease, Immune disorders.
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Analyzing microbial data with applying innovative computational genomic and bioinformatic methods to find out relationships between microbiome and different factors like diseases. |
Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | The Weinstock Lab | Predoc |
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Reinholdt Laura Reinholdt, Ph.D. | Bar Harbor, ME |
Dr. Reinholdt’s research focuses on comparative and functional mammalian genomics, reproductive development and stem cell biology.
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Dr. Reinholdt’s research interests are in the development and application of genetic approaches for understanding the etiology and functional consequences of genome variation in the germ line and in pluripotent cells. Dr. Reinholdt is also committed to genetic resource development and has made significant contributions to the early development of high throughput sequencing approaches for genomic discovery in the mouse genome, and more recently the development of novel ES and iPSC cell lines from genetically diverse mice that are enabling platforms for cellular systems genetics. |
Complex Traits|Genetics and Genomics|Resource Development and Dissemination|Cancer | Complex Traits|Genetics and Genomics|Resource Development and Dissemination|Cancer | The Reinholdt Lab | Associate Professor |
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Richardson Joel Richardson, Ph.D. | Bar Harbor, ME |
Leads the software and database development teams that support a number of critical data resources.
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The focus of my work is bioinformatics, specifically, the design, implementation,management and evolution of community databases. I have been intimately involved in the Mouse Genome Informatics (MGI) program since 1992. MGI provides online access to high-quality, comprehensive, and up-to-date information about the laboratory mouse, to support its use as a model for understanding human health and disease. Together with Jim Kadin, I lead the software and database development teams that support a number of resources,including the Mouse Genome Database (MGD – HG000330), the Gene eXpression Database for mouse development (GXD – HD062499), the Mouse Tumor Database (MTB –CA089713), and the International Mouse Strain Resource (IMSR - LM009693). I am also PI of the MouseMine project (HG004834), which provides a fast, powerful new data warehouse for accessing MGI data. |
Genetics and Genomics|Bioinformatics|Resource Development and Dissemination|Computational Biology | Genetics and Genomics|Bioinformatics|Resource Development and Dissemination|Computational Biology | The Bult Lab|The Ringwald Lab | Lab Staff|Senior Research Scientist |
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Ringwald Martin Ringwald, Ph.D. | Bar Harbor, ME |
Develops and enhances the Gene Expression Database (GXD), which captures, integrates and displays mouse developmental expression data generated world-wide.
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Our main focus is the Gene Expression Database (GXD), which captures and integrates mouse expression data generated by biomedical researchers worldwide, with particular emphasis on mouse development. Gene expression data can provide researchers with critical insights into the function of genes and the molecular mechanisms of development, differentiation and disease. By combining different types of expression data and adding new data on a daily basis, GXD provides increasingly complete information about expression profiles of transcripts and proteins in wild-type and mutant mice. We work closely with the other Mouse Genome Informatics (MGI) projects to provide the community with integrated access to genotypic, expression and phenotypic, and disease-related data. Thus, one can search for expression data and images in many different ways, using numerous biologically and biomedically relevant parameters. |
Bioinformatics|Developmental Disorders|Genetics and Genomics|Resource Development and Dissemination | Bioinformatics|Developmental Disorders|Genetics and Genomics|Resource Development and Dissemination | The Ringwald Lab | Associate Professor |
Peter Robinson, M.D., MSc.Professor of Computational Biology |
Robinson Peter Robinson, M.D., MSc. | Farmington, CT |
Develops algorithms and software for the analysis of exome and genome sequences.
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Peter Robinson studied Mathematics and Computer Science at Columbia University and Medicine at the University of Pennsylvania. He completed training as a Pediatrician at the Charité University Hospital in Berlin, Germany. His group developed the Human Phenotype Ontology (HPO), which is now an international standard for computation over human disease that is used by the Sanger Institute, several NIH-funded groups including the Undiagnosed Diseases Program, Genome Canada, the rare diseases section of the UK's 100,000 Genomes Project, and many others. The group develops algorithms and software for the analysis of exome and genome sequences and has used whole-exome sequencing and other methods to identify a number of novel disease genes, including CA8, PIGV, PIGO, PGAP3, IL-21R, PIGT, and PGAP2. |
Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Robinson Lab | Professor |
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Roopenian Derry Roopenian, Ph.D. | Bar Harbor, ME |
Conducts research to understand why the immune system causes autoimmune diseases and to devise methods to predict and treat them.
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The overall goals of our laboratory are to understand why the immune system causes autoimmune diseases and to devise methods to predict and treat them. We develop and use mouse strains that provide models for human diseases such as lupus, rheumatoid arthritis and epidermolysis bullosa. We use a combination of genetics, molecular biological and cellular immunological tools to dissect the molecular and cellular processes that cause these diseases. Finally, we study the mechanisms that affect the persistence of antibodies and antibody-based therapeutics. The information gained from all of these approaches is then used to devise possible therapeutic approaches that can be translated to human treatments. |
Complex Traits|Resource Development and Dissemination|Computational Biology|Immune Disorders | Complex Traits|Resource Development and Dissemination|Computational Biology|Immune Disorders | The Roopenian Lab | Professor |
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Rubinstein Jill Rubinstein, MD, PhD | Farmington, CT |
Computational Oncology studies that integrate clinical, genomic, and imaging data to explore the dynamics of tumor heterogeneity and evolution in response to treatment.
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Tumors are continually evolving collections of cells, characterized by a dynamic interplay among heterogeneous sub-clonal populations that expand and contract under innate and imposed selective pressures. My research couples deep learning imaging techniques with high-resolution molecular assays and matched clinical information to analyze tumors through a framework of evolution. We study the impact of treatment on the dynamics of the tumor ecosystem to elucidate resistance mechanisms and identify potential targets for intervention. |
Bioinformatics|Cancer|Complex Traits|Computational Biology | Bioinformatics|Cancer|Complex Traits|Computational Biology | The Chuang Lab | Research Scientist |
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Sabnis Gautam Sabnis, Ph.D. | Bar Harbor, ME |
I am interested in using statistical science for answering research questions related to biological science. This involves developing statistical and computational methods for discovering inherent hidden structures in complex biological data and drawing meaningful inferences through such structures.
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As a Biostatistician in the Kumar Lab, I work with the team on research problems related to addiction and behavioral disorders. |
The Kumar Lab | Biostatistician | ||
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Sasner Michael Sasner, Ph.D. | Bar Harbor, ME |
Focuses on creating and characterizing mouse models that accurately model human disease and therefore can be used to understand neurodegenerative disease and be used in the development of new therapies.
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As the Associate Director of Genetic Resource Science Model Development and Bioinformatics, I oversee the group responsible for the selection and importation of new mouse strains into the Repository. We curate strain information and develop tools that enable the public to access the information in our extensive strain database. I also work on creating and characterizing mouse models that accurately model human disease and can be used in understanding neurodegenerative disease and in the development of new therapies. Ongoing projects are listed below. The Jackson Laboratory Alzheimer's Disease CenterAlzheimer's disease is the most common cause of dementia. It is characterized by brain pathology including amyloid plaques composed of Abeta and intracellular tangles made up of hyperphosphorylated tau protein. Abeta is a cleavage product of the amyloid precursor protein (APP), and mutations in APP and its processing enzymes (including the presenilins, Bace) are thought to be one cause of familial AD. The Jackson Laboratory offers a variety of genetic models for AD research, including strains expressing APP and presenilin (PSEN1) mutations, strains expressing mutant APP in either a constitutive or inducible manner, strains expressing mutant tau (Mapt), strains with Presenilin mutations, strains with Apoe mutations, and strains with Bace mutations. These models develop Alzheimer's-related characteristics as they age. Parkinson's Disease Mouse Model ResourceParkinson's disease is characterized by the loss of dopamine-producing cells in the substantia nigra. While the earliest and most obvious symptoms are movement disorders including tremor, rigidity, gait abnormalities and bradykinesia (slowness of movement), there are many other manifestations, including cognitive, emotional and sleep disorders. Accumulation of alpha-synuclein deposits in the brain lead to the formation of Lewy bodies, a diagnostic marker of PD. The Michael J. Fox Foundation for Parkinson’s Research (MJFF) supports our program to develop, characterize, and distribute genetically engineered mice and information useful for their selection and use. Other model development projectsChordomaWith funding from the Chordoma Foundation, we are developing and characterizing novels models of this rare form of skull and spine cancer. Dravet SyndromeWith funding from the Dravet Syndrome Foundation, we have created a novel model of this form of early onset epilepsy. This model is currently being validated. |
Genetics and Genomics|Resource Development and Dissemination|Bioinformatics|Aging | Genetics and Genomics|Resource Development and Dissemination|Bioinformatics|Aging | Research Scientist | |
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Saul Michael Saul, Ph.D. | Bar Harbor, ME |
Using computation, genetics, and genomics, I study neurobiology and behavior.
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My perspective on biology celebrates what diversity can teach us. Within the mouse species, I study genetically diverse populations such as the BXD, Collaborative Cross, and Diversity Outbred. With Elissa Chesler and colleagues in the CSNA, my work has reiterated that who a mouse is – their genetic makeup and its sex – matters greatly to how a mouse behaves and how their brain responds. I am particularly interested in comparative and cross-species techniques, which give us perspective on the conserved systems that underpin similar behaviors spanning the animal kingdom. Though I now work in Computational Science, my training was as a mouse behavioral neuroscientist who studies genetics and genomics. My work convinced me that biologists must do two things to understand complex systems like the brain: 1) collaborate with each other, and 2) use high-throughput techniques like next-generation sequencing and high-performance computing. I am delighted to collaborate with multiple investigators at JAX, where I apply the skills I attained in computational work to find the new biology of disease that will lead us to better treatments. |
Aging|Behavioral Disorders|Bioinformatics|Complex Traits | Aging|Behavioral Disorders|Bioinformatics|Complex Traits | Computational Scientist | |
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Sheehan Susan Sheehan, BA, MS | Bar Harbor, ME |
Researches the genetics that effect declining kidney function with age with a focus on quantifying histological changes with age.
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I joined JAX in 2001 and have been working on the genetics of renal function since 2003. We utilize many of the resources at JAX to explore the decline of renal function with age. I especially enjoy developing new models and tool to assess kidney function in mice. |
Aging|Computational Biology|Genetics and Genomics | Aging|Computational Biology|Genetics and Genomics | The Korstanje Lab | Lab Staff |
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Sheppard Keith Sheppard | Bar Harbor, ME |
Software Development, Machine Learning, Visualization and Image Processing. My goal is to leverage these technical interests to develop software tools that help advance behavioral and genomics research.
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My role within the Kumar Lab is to develop software tools that enable and accelerate research into addiction and other behavioral disorders. This often involves developing deep neural networks or employing other computational methods to extract and analyze behavioral metrics of mice observed under many different experimental conditions. I enjoy being challenged to find or develop computational methods that allow our researchers to extract and analize the data that they need to answer important biological questions. |
The Kumar Lab | Lab Staff | ||
Daniel Skelly, Ph.D.Senior Computational Scientist |
Skelly Daniel Skelly, Ph.D. | Bar Harbor, ME |
Biologist and data scientist harnessing single cell functional genomics and genetically diverse mice to study complex traits
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Variation in observable traits, such as disease susceptibility, is pervasive in the natural world. Recent advances in sequencing and computation are providing us with an unprecedented view of patterns of genetic variation within species. A major outstanding challenge is to identify and characterize the specific genetic variants affecting complex traits, and the mechanisms through which they do so. I am a biologist and data scientist who uses single cell functional genomics to understand the genetic basis of complex traits. I utilize genetically diverse model organism populations together with the methodology of statistical and quantitative genetics to reveal novel mechanistic insights into the biology of complex traits. My background and interests include cancer, cardiovascular disease, diabetes, and obesity/metabolic disorders. |
Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | The Rosenthal Lab | Research Scientist |
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Smith Cynthia Smith, Ph.D. | Bar Harbor, ME |
Comparative phenotype analysis and bioinformatics can be used to analyze congenital defects and pathological processes with the objective of discovering new molecular elements and pathways that contribute to disease states.
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My research focuses on comparative phenotype analysis and bioinformatics. I develop systems to integrate and analyze phenotypic information in the context of the genetics and genomics data of the laboratory mouse within the Mouse Genome Informatics (MGI) project. I am primary developer of the Mammalian Phenotype Ontology (MP), a controlled, structured vocabulary to annotate phenotype data, enabling data integration, analysis and computational reasoning. My current research projects include developing ontological relationships among other human and model organism phenotype ontologies and database knowledge systems to develop comparative analysis tools. These tools will be used to analyze congenital defects and pathological processes with the objective of discovering new molecular elements and pathways that contribute to disease states.
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Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Bioinformatics | Computational Biology|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases|Bioinformatics | The Bult Lab | Research Scientist |
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Somarakis Antonios Somarakis | Farmington, CT |
Analysis and pipeline development of spatial proteomics and trascriptomics data employing machine learning techniques.
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My project focuses on the analysis of spatial single-cell proteomics data (e.g. Imaging Mass Cytometry, CODEX) and spatial transcriptomics data (e.g. Visium Spatial Gene Expression by 10x). Previously, in collaboration with biologists from Leiden University Medical Center I have developed interactive pipelines for the analysis of single-cell high-resolution images (ImaCyTe, SpaCeCo). My research interests also include the analysis of single-cell tissue images with Graph Convolutional Networks. |
Bioinformatics|Cancer | Bioinformatics|Cancer | Computational Scientist | |
Catrina Spruce, MS, BSResearch Lab Associate Manager |
Spruce Catrina Spruce, MS, BS | Bar Harbor, ME |
Studying fluid changes in chromatin state and the resulting gene expression changes.
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My primary interest is understanding how the chromatin environment primes gene expression. To study fluid changes in chromatin state and the resulting gene expression changes, we use mouse ESCs and follow them through early development from pluripotency to germline commitment. To investigate epigenetic differences among individuals, we use diverse mouse strains to represent diversity among human beings, studying two paradigms to through the lens of individual diversity: differences in naïve state that impact early development, and differences in mature brain striatum that impact susceptibility to addiction. |
Computational Biology|Genetics and Genomics | Computational Biology|Genetics and Genomics | The Baker Lab | Lab Staff |
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Stafford Grace Stafford, Ph.D. | Bar Harbor, ME |
Analyzing and structuring data to facilitate research and break down silos.
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I joined The Jackson Laboratory's Computational Sciences Department to become the Deployment Lead in the Lab’s involvement in the NCI Cancer Biomedical Informatics Grid® (caBIG®) initiative and stayed on as a member of the Stats and Analysis group. My background in protein and genomic databases and conceptual representations of life sciences research has enabled me to contribute to the clinical and the PDX programs. I continue to gain experience in analysis of next generation sequencing, calling on my history of bench research in cancer, pharmacology, and transcriptional regulation. I have experienced the roller coaster ride of small start up companies and welcome the opportunity to be part of the JAX community. On any given day, I may spend time wrangling data for PIs or collaborators, launching a DNA-seq analysis, tracking down data for a potential PDX customer and checking out a new analysis tool or online database. |
Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | Bioinformatics|Cancer|Computational Biology|Genetics and Genomics | Bioinformatics/Data Analyst | |
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Stearns Timothy M. Stearns, B.S., M.S. | Bar Harbor, ME |
Leveraging the use of statistics and computational resources to reveal the genetic basis for disease.
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My initial contributions to science were the result of a Master of Science education program (University of Illinois - Champaign-Urbana) endeavor to identify quantitative trait loci affecting swine meat characteristics. Shortly after my leave of the University, I joined The Jackson Laboratory in 2007. The numerous collaborations that took place at the Laboratory have resulted in publications pertaining to a variety of conditions including: alopecia areata, asthma, cancer (of the brain, lung and skin), diabetes, chronic kidney disease, eye disease, and reproductive disorder. The general aim of these studies is to provide mouse model information as a method to improve human health. My role in these studies has been as a biostatistician consultant. For a complete list of my published work, please visit my NCBI bibliography. |
Bioinformatics|Computational Biology | Bioinformatics|Computational Biology | Biostatistician | |
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Stitzel Michael Stitzel, Ph.D. | Farmington, CT |
(De)coding the regulatory landscape of human pancreatic islets and other metabolic cell types health and diabetes
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Type 2 diabetes is a disease of genes and environment. My laboratory studies the epigenome of human pancreatic islets and their developmental precursor cells. One aim is to use the epigenome as a read-out of effects of type 2 diabetes genetic variants on islet gene expression programs and function. Emerging evidence suggests that normal or disease-predisposing conditions can actually alter a cell's epigenome and lead to abnormal cellular functions. To this end, my lab is investigating how the islet epigenome is altered under different stimulatory and stress conditions. Finally, we are pursuing targeted modification of cells’ epigenomes to facilitate production of bona fide pancreatic islet cells from pluripotent stem cells or other terminally differentiated cells. |
Genetics and Genomics|Diabetes and Obesity|Bioinformatics|Complex Traits | Genetics and Genomics|Diabetes and Obesity|Bioinformatics|Complex Traits | The Stitzel Lab | Associate Professor |
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Sundberg Beth Sundberg, M.S. | Bar Harbor, ME |
Design and develop relational databases; software quality assurance testing
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Ms. Sundberg has been involved with computer applications for 40 years. She developed herd health management software in 1976, a database for managing pesticide chemicals for the state of Indiana in the mid 1970s, and worked on various other projects for the Administrative Data Processing Center at Purdue University. During the past thirty years she has worked on a project for managing mouse breeding colonies (JAX Colony Management System, JCMS) and a relational database for medical records management (The Mouse Disease Information System, MoDIS). MoDIS was developed in 1987 to manage histopathological data from The Jackson Laboratory massive mouse production colony as well as research data. Over the years this evolved to integrate the Mouse Anatomy Ontology (MA) and Mouse Pathology Ontology (MPATH), to eventually provide an integrated tool for storage of basic research discoveries, linking gross and photomicrographs to case materials, and getting this information into publicly accessible databases such as Pathbase (http://www.Pathbase.net), and Mouse Genome Informatics (http://www.informatics.jax.org/). Currently she is working with the Computational Sciences PDX (patient-derived xenograft) platform team of software engineers. |
Computational Biology | Computational Biology | Software Engineer | |
Sabriya Syed, Ph.D.Associate Research Scientist |
Syed Sabriya Syed, Ph.D. | Farmington, CT |
Sabriya studies how genomic and epigenomic factors impact chromatin organization.
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Sabriya completed her PhD in 2016 at the Mayo Graduate School in Rochester, MN where she studied the genome-wide epigenetic mechanisms underlying cellular transitions of the Interstitial cells of Cajal in the gastrointestinal tract. During this time Sabriya became interested in understanding how the epigenomic landscape impacts chromatin organization. To pursue this, Sabriya joined the Imbalzano Lab at the University of Massachusetts Medical School where she explored the role of arginine methyl transferase Prmt5 in mediating higher order chromatin structure in preadipocytes prior to and during adipogenesis using methods like ChIP-Seq and Hi-C. For this work, Sabriya was awarded the Ruth L. Kirschstein NRSA Postdoctoral Fellowship from 2019-2021. After this, Sabriya joined the Lee Lab as an Associate Research Scientist where she is currently exploring how structural variants in humans affect genome organization and modulate transcription. |
Bioinformatics|Genetics and Genomics | Bioinformatics|Genetics and Genomics | The Lee Lab | Associate Research Scientist |
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Taylor Aaron Taylor, Ph.D. | Farmington, CT |
Multi-omic profiling of pediatric brain and bone cancer to discover novel prognostic biomarkers and therapeutic targets.
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The purpose of my research at the Ching Lau Lab is to examine genomic and epigenomic data from pediatric cancers in order to discover molecular phenotypes, prognostic biomarkers, and candidate therapeutic targets. My work includes method and pipeline development for integration of multi-omic data in the analysis of pediatric brain and bone tumors to develop a better molecular understanding of these often-lethal cancers. Currently, my research focuses on osteosarcoma, ependymoma, and intracranial germ cell tumors. |
Cancer|Bioinformatics|Computational Biology|Genetics and Genomics | Cancer|Bioinformatics|Computational Biology|Genetics and Genomics | The Lau Lab | Postdoctoral Associate |
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Telpoukhovskaia Maria Telpoukhovskaia, Ph.D. | Bar Harbor, ME |
Discovering and targeting microglial pathways involved in cognitive resilience and decline to improve memory during “normal” aging and dementias.
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Dementia is an outcome of several neurodegenerative diseases, with no treatments currently available. Microglia, the brain’s immune cells, are implicated in resilience and susceptibility to cognitive decline. The goal of my research is to define the interplay between transcriptomic and functional changes that impact behavior in genetically diverse mouse models of cognitive decline and, subsequently, to discover small molecules that intervene in memory loss. |
Aging|Bioinformatics|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | Aging|Bioinformatics|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases | The Kaczorowski Lab | Associate Research Scientist |
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Tewhey Ryan Tewhey, Ph.D. | Bar Harbor, ME |
Identifying the precise genetic mechanisms for complex traits and disease risk
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The past decade has seen a transformational change in our understanding of the human genome and the role it plays in influencing disease risk. Large-scale projects such as Encyclopedia of DNA Elements (ENCODE) have identified which non-coding regions correlate with gene regulatory function. Furthermore, the proliferation of genome wide association studies (GWAS) and scans for recent positive selection have identified thousands of loci that influence human health. Taken together, these efforts show the predominant contributors of heritability for complex phenotypes are common polymorphisms that reside within non-coding regions of the genome. However, despite our progress in mapping cis-regulatory elements (CREs) and genetic signatures correlated with disease, very few examples exist that mechanistically link genotypic variation to disease risk. This gap in our understanding is based on our inability to understand the sequence context of active CREs and their targets, without which it is difficult to identify single nucleotide variants that directly modulate gene expression. Thus, given the correct technological advances each disease association can become an untapped entry point that has the potential to transform our understanding of disease etiology. The mission of our research group is to (1) characterize and learn the grammar of cis-regulatory elements, in both mouse and human models, using novel technological approaches such as high-throughput reporter assays and CRISPR based screens of non-coding regions in the genome. (2) Build upon the knowledge from genome wide association studies and leverage this resource of genetic risk to disease in human populations to construct better animal models that precisely reflect disease phenotypes. |
Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics | The Tewhey Lab | Assistant Professor |
Harianto Tjong, Ph.D.Computational Scientist |
Tjong Harianto Tjong, Ph.D. | Farmington, CT |
My primary research field is three-dimensional genome organization which includes development of computational analysis methods from data generated using genome technologies such as ChIA-PET, ChIA-Drop, and HiC-based sequencing techniques.
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As computational scientist under the Dept. of Genome Technologies, my main role include supporting scientific research in the group and R&D team for GT production.
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Bioinformatics|Computational Biology|Genetics and Genomics | Bioinformatics|Computational Biology|Genetics and Genomics | The Wei Lab | Lab Staff |
Dong-Binh Tran, Ph.D.Research Data Analyst II |
Tran Dong-Binh Tran, Ph.D. | Farmington, CT |
My works focus on characterizing, identifying, and quantifying the microbial abundance, the community composition and the complex relationships among microbiome, host and environment in different biological conditions.
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Using basic and advanced statistical and data mining methods as well as high dimensional data visualization techniques, I perform downstream analysis including both multivariate parametric and non-parametric methods, test microbiome hypotheses and high resolution visualization for large scale data (network analysis). I also exploit and apply data regression and data dynamic modeling like as random forests, linear mixed models, Markov multi-state modeling as well as probabilistic modeling for microbial metagenomic data. |
Computational Biology | Computational Biology | The Weinstock Lab | Lab Staff |
Fotios Tsetsos, Ph.D.Associate Computational Scientist |
Tsetsos Fotios Tsetsos, Ph.D. | Farmington, CT |
Investigating the impact of structural variation on complex disorders and their evolution. Studying the bilateral translation of human genomic findings to mice.
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I study the genetics of complex diseases in humans, with focus on neuropsychiatric and metabolic disorders. I am particularly interested in investigating the polygenic nature of traits, pleiotropy and the missing heritability. A substantial part of my study focuses on population genetics, historical genetics, archaeogenomics, and the evolutionary history of modern humans, along with their implication for diseases and traits in modern humans. At JAX I am focusing on identifying the contribution of structural variation to the heritability of complex disorders, the evolutionary and population genetics aspects of structural variation, and the bilateral translation of human genetic findings to mice. |
Aging|Bioinformatics|Complex Traits|Developmental Disorders | Aging|Bioinformatics|Complex Traits|Developmental Disorders | The Lee Lab | Computational Scientist |
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Tyler Anna Tyler, Ph.D. | Bar Harbor, ME |
Models gene interactions (epistasis) in model organisms and humans.
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I am interested in understanding how interactions between genes (epistasis) contribute to the genetic architecture of complex traits. My adviser, Greg Carter, previously developed an analytical method, called the Combined Analysis of Pleiotropy and Epistasis (CAPE), that combines information across multiple phenotypes to constrain possible epistatic models and thereby infer the direction of interaction between genetic variants. I have packaged the analytical pipeline into a freely available R package. CAPE has been used to infer directed epistatic networks in yeast, Drosophila, and mice, and I am currently working to adapt the method for use in human populations. This adaptation will include development of a new software package for detection and interpretation of epistatic interactions in medical genetics. |
Complex Traits|Computational Biology|Bioinformatics|Genetics and Genomics | Complex Traits|Computational Biology|Bioinformatics|Genetics and Genomics | The Carter Lab | Associate Research Scientist |
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Ucar Duygu Ucar, Ph.D. | Farmington, CT |
Develops computational models using genome datasets to study gene regulation and identify hypotheses for genomic medicine.
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Next-generation sequencing technologies have revolutionized biological research and provided unique opportunities to study broad and novel questions about the regulation of gene expression. With these technologies, there has been an exponential increase in the types and amount of high-throughput datasets pertaining to the dynamics of gene expression. These data include gene expression data and genome-wide maps of nucleosome occupancy and open chromatin, epigenetic marks and transcription factor binding sites in cells and organisms under various experimental conditions. In my lab, we develop computational models to take advantage of genomics datasets to study the dynamics and mechanisms of transcriptional gene regulation and identify testable hypotheses for genomic medicine. Visit the Ucar Personal Lab Site |
Computational Biology|Aging|Diabetes and Obesity|Genetics and Genomics | Computational Biology|Aging|Diabetes and Obesity|Genetics and Genomics | The Ucar Lab | Associate Professor |
Lacy UlloaAcademic Year Fellow |
Ulloa Lacy Ulloa | Farmington, CT |
Utilizing computational modeling and data analytics to identify causative and actionable biomarkers associated with pediatric acute myeloid leukemia (AML).
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I am excited to be pursuing an independent research project under the mentorship of Dr. Lau and Lau Lab associates. The primary focus of my research involves integrating computer graphics with scientific visualization to analyze gene expression data from novel pediatric AML trials. Through comparing a variety of patient populations, I am endeavoring to identify biomarkers that may serve as future therapeutic targets. In addition to enhancing my knowledge of bioinformatics, I am working to develop the skills exhibited by members of successful research teams. |
Bioinformatics|Cancer|Computational Biology | Bioinformatics|Cancer|Computational Biology | The Lau Lab | Lab Staff |
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Varn Frederick Varn, Ph.D. | Farmington, CT |
Employs genomic and computational approaches to investigate how the immune response shapes brain tumor development.
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Dr. Varn received his Ph.D in Molecular and Systems Biology from Dartmouth College in 2018. While at Dartmouth, his thesis work focused on developing and applying computational methods to investigate the factors influencing the immune response in different cancer types. As a postdoctoral associate at JAX, his research projects integrate his background in computational biology, cancer biology, and immunology to study how the immune response shapes brain tumor evolution. |
Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | Bioinformatics|Computational Biology|Cancer|Genetics and Genomics | The Verhaak Lab | Postdoctoral Associate |
Roel Verhaak, Ph.D.Professor and Associate Director of Computational Biology, The Florine Deschenes Roux Chair for Genomics and Computational Biology |
Verhaak Roel Verhaak, Ph.D. | Farmington, CT |
Brain tumors, sequencing, computational biology.
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We are a computational cancer biology lab with a research focus on the analysis of cancer genomics data to improve our understanding of cancer biology. We have a specialized research interest in understanding disease progression of brain tumors, and to study the role of extrachromosomal DNA amplifications in cancer. Our group combines wet lab approaches for functional modeling with large datasets and computational methods. |
Cancer|Bioinformatics|Computational Biology|Genetics and Genomics | Cancer|Bioinformatics|Computational Biology|Genetics and Genomics | The Verhaak Lab | Professor |
Anita Voigt, Ph.D.Postdoctoral Associate |
Voigt Anita Voigt, Ph.D. | Farmington, CT |
Working on understanding the fundamental roles of the microbiome, particularly the skin and the gut microbiome.
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Anita, a joint postdoctoral fellow with the Oh and Weinstock groups, is most recently from Heidelberg, Germany, where she studied with Dr. Peer Bork and Dr. Magnus von Knebel Doeberitz on numerous microbiome projects related to colorectal cancer and methods development. She is interested in understanding the fundamental roles of the microbiome, particularly the skin and the gut microbiome, in health and disease. |
Computational Biology|Genetics and Genomics|Skin Disease|Cancer | Computational Biology|Genetics and Genomics|Skin Disease|Cancer | The Oh Lab | Postdoctoral Associate |
Taylor WadeLab Staff|Postbaccalaureate |
Wade Taylor Wade | Farmington, CT |
The role of extrachromasomal DNA in brain tumors
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Bioinformatics|Computational Biology | Bioinformatics|Computational Biology | The Verhaak Lab | Lab Staff|Postbaccalaureate |
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Walton Dave Walton, B.A. | Bar Harbor, ME |
Primary focus is developing scientific software tools to further the research of Jackson Laboratory faculty.
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I am a full-stack principal level scientific software developer with a passion for software development that enables scientific research. I have over two decades of experience in a variety of industries, with a focus in biotechnology. My primary development tools include: Python, Java, Groovy, AngularJS, JavaScript, D3, Bootstrap, PostgreSQL, MySQL and Oracle. I have worked on large scale enterprise LIMS for collecting, tracking, processing and reporting patient samples; command-line analysis tools for scientific data; web applications for the presentation of analyzed results; and API’s to allow other programs access to data and tools using RESTful web services and JMS. My role at Jackson Laboratory is one of technical leadership on multi-developer projects, using agile techniques, striving to provide meaningful/usable systems in a timely manner. |
Bioinformatics|Computational Biology | Bioinformatics|Computational Biology | Software Engineer | |
George Weinstock, Ph.D.Professor, Evnin Family Chair and Director of Microbial Genomics |
Weinstock George Weinstock, Ph.D. | Farmington, CT |
Leverages advanced technologies to investigate infectious diseases, human and other mammalian microbiomes, and their clinical impact.
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In the last decade, leaps in DNA sequencing technologies have transformed our ability to collect and analyze genomic information. This revolution has opened up entirely new areas of study from human to microbial and infectious disease research. Currently, understanding the microbiome (the vast collection of microbes in our body with which we coexist), its interactions with its host (us) and its contributions to health and disease is a vital new research area that he is focusing on. The Weinstock Laboratory leverages advanced technologies to investigate infectious diseases and mammalian microbiomes. |
Infectious Disease Research|Cancer|Genetics and Genomics|Immune Disorders | Infectious Disease Research|Cancer|Genetics and Genomics|Immune Disorders | The Weinstock Lab | Professor |
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Wells Julie Wells, Ph.D. | Bar Harbor, ME |
Research into lung development and role of miRNAs to better understand cancer, other lung diseases.
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My research focuses on the regulation of gene expression during lung development and in disease. Recent research projects include measuring gene expression in the lungs of three strains of mice during development from embryonic day E9.5 to maturity at 8 weeks of age and developing a new technique to identify direct messenger RNA (mRNA) targets of microRNAs (miRNAs). I am using a new technique, referred to as RIP-SIR, to study miRNA regulated gene expression during the progression of pulmonary adenocarcinoma in two mouse models. In a related project, serum samples collected from these lung tumor-bearing mice were analyzed to identify expression profiles of circulating miRNAs that may indicate the presence of early stage pulmonary adenocarcinoma. A new project is expanding upon this work and using patient-derived xenograft (PDX) mice to answer basic questions about which miRNAs are secreted from tumors and enter the circulatory system. Finally, as a member of a collaborative group headed by Dr. Patricia Donahoe, I am investigating gene expression in the developing mouse diaphragm and determining how novel mutations identified by this group contribute to congenital diaphragmatic hernia, a condition that is often associated with a fatal respiratory phenotype. |
Cancer|Developmental Disorders|Computational Biology|Genetics and Genomics | Cancer|Developmental Disorders|Computational Biology|Genetics and Genomics | The Bult Lab | Research Scientist |
Chee Hong Wong, MSAssociate Director, Genomic Technology Data Science |
Wong Chee Hong Wong, MS | Farmington, CT |
Transforming biological data into actionable insights.
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As a passionate technologist who has borrowed ideas heavily from biology in my exciting and challenging 13-years IT careers spanning multitude business sectors, I have never regretted venturing into the life science 18 years ago. My research focus has always been using computational approaches to acquire biological insights from the data. This is commonly done with the many great open-source tools from the research communities. I have had to develop instrument control software and new algorithm to fill in the voids. I have worked extensively on genomic, transcriptomic, epigenomic, proteomics, and glycoproteomics data. My current work focus include long-read and single-cell application in cancer genomes and regulome. |
Bioinformatics|Genetics and Genomics | Bioinformatics|Genetics and Genomics | The Wei Lab | Lab Staff |
Wooldridge Lydia Wooldridge, Ph.D. | Bar Harbor, ME |
To study the evolution of genes related to fertility and sexual reproduction, and to use this information to understand infertility in humans.
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The broad goal of my research is to understand causes of infertility. Currently, I am studying meiotic recombination rate. Too few recombination events leads to infertility, therefore proper recombination is essential for gamete production and thus species survival. It is well established that recombination rate varies widely across species, individuals, and even within an individual's gamete pool. However, the exact loci and mechanisms controlling these variations are largely unknown. I am working to identify the loci responsible for recombination rate variation, as well as working to understand the exact relationship between recombination rate and fertility. |
Computational Biology|Genetics and Genomics|Reproductive Disorders | Computational Biology|Genetics and Genomics|Reproductive Disorders | The Dumont Lab | Postdoctoral Associate | |
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Wotton Janine Wotton, Ph.D. | Bar Harbor, ME |
I study the neural mechanisms underlying animal behavior using the tools of computational neuroscience and machine learning.
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I strive to create models with explanatory power and predictive value to enhance our understanding of biological systems. My goal is to apply this knowledge to improve biomedical outcomes. |
Aging|Behavioral Disorders|Data Science at JAX | Aging|Behavioral Disorders|Data Science at JAX | Lab Staff | |
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Yu Miao Yu, Ph.D. | Farmington, CT |
My research interest is high resolution mass spectrometry based data analysis and applications in 'omics' study.
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My research is focused on the mediation roles of molecular between exposures and health outcomes. I developed PMDDA data analysis workflow to perform exhaustive metabolomics annotations. I also proposed the concept of 'reactomics' to retrieving general chemical relationships among molecular in biological samples. Meanwhile, I developed 'gatekeeper' model to screen the molecular sensitive to multiple exposures. With background from both wet lab and dry lab, I am trying to improve regular statistical or machine learning model with biochemistry knowledge. I am also interested in reproducible research and built a R based data analysis image (xcmsrocker) for reproducible metabolomics data analysis. |
Bioinformatics|Computational Biology | Bioinformatics|Computational Biology | Computational Scientist | |
Chun Yu, Ph.D.Associate Research Scientist |
Yu Chun Yu, Ph.D. | Farmington, CT |
The importance of understanding the role of vaccinations and the ways in which they can be improved.
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My research focuses on comparative phenotype analysis and bioinformatics. I develop systems to integrate and analyze phenotypic information in the context of the genetics and genomics data of the laboratory mouse within the Mouse Genome Informatics (MGI) project. I am primary developer of the Mammalian Phenotype Ontology (MP), a controlled, structured vocabulary to annotate phenotype data, enabling data integration, analysis and computational reasoning. My current research projects include developing ontological relationships among other human and model organism phenotype ontologies and database knowledge systems to develop comparative analysis tools. These tools will be used to analyze congenital defects and pathological processes with the objective of discovering new molecular elements and pathways that contribute to disease states. |
Complex Traits|Computational Biology|Genetics and Genomics|Bioinformatics | Complex Traits|Computational Biology|Genetics and Genomics|Bioinformatics | The Palucka Lab | Associate Research Scientist |
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Yurieva Marina Yurieva, Ph.D. | Farmington, CT |
Cloud computing and development of Bioinformatics pipelines for multi-omics data to understand RNA biology (splicing and lncRNAs), Immunology, Asthma and Cancer
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I have a diverse expertise in analysis of Multi-omics datasets, Immunology, Microbiome, Developmental Biology, RNA biology and Cloud Computing. During my Ph.D. I studied the downstream targets of Hox genes in developing hindbrain using mouse, zebrafish and chick models. My postdoc was focused on developing Bioinformatics pipelines for the analysis of microbiome data and various immunological studies. Currently I am developing pipelines for identification of lncRNAs and splicing events in RNA-seq datasets and integrating various omics data. |
Bioinformatics|Cancer|Computational Biology|Immune Disorders | Bioinformatics|Cancer|Computational Biology|Immune Disorders | Lab Staff | |
Zhao Dacheng Zhao | Farmington, CT |
I have joined Verhaak lab to study the role of ecDNA in cancer
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Bioinformatics|Cancer | Bioinformatics|Cancer | The Verhaak Lab | Predoc | |
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Zhao Lihong Zhao, Ph.D. | Bar Harbor, ME |
Conducts research on neurological diseases and genetic modifiers.
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My first research program focuses on the regulation of the de novo ceramide biosynthesis pathway that determines cellular profiles of sphingolipid metabolites, i.e. sphingoid long-chain bases (LCBs) and ceramide (acylated LCB) species, which have been implicated in many neurological diseases. Using mouse models generated in The Jackson Laboratory or contributed to the mouse depository at The Jackson Laboratory, I have been working toward elucidating the potentially specific neural functions and pathological roles of different LCBs and ceramides, respectively, in two related projects.My second research program focuses on the transcription network controlling photoreceptor differentiation and how deregulation of this network causes photoreceptor degeneration. We adopted a genetic approach to identify novel regulators of this network by searching for genetic modifiers of rd7, a mutation of the transcription factor NR2E3 causing a retinopathy called Enhanced S-Cone Syndrome. We have found several modifiers that suppress rd7. Currently, we are trying to identify the underlying genes and assess their interactions with other genes’ encoding factors involved in photoreceptor differentiation. |
Genetics and Genomics|Computational Biology|Developmental Disorders|Neurodegenerative and Neuromuscular Diseases | Genetics and Genomics|Computational Biology|Developmental Disorders|Neurodegenerative and Neuromuscular Diseases | Associate Research Scientist | |
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Zhou Wei Zhou, Ph.D. | Farmington, CT |
Wei has a strong background in host-microbe interaction and evolution of microbial pathogens. He is interested in developing computational tools to more efficiently characterize the microbiome using metagenomic data.
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Wei is broadly interested in evolution and ecology of microbes in complex communities using genomic methods. Before joining the Oh Lab, he worked with Dr. Dustin Brisson in the University of Pennsylvania to study host-microbe interaction and evolution of microbial pathogens. Presently he is developing computational tools that characterize microbes and microbial interactions more effectively and with less necessary domain expertise.
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Computational Biology|Genetics and Genomics|Bioinformatics|Infectious Disease Research | Computational Biology|Genetics and Genomics|Bioinformatics|Infectious Disease Research | The Oh Lab | Computational Scientist |