Data Science: Pre & Postdoctoral Training

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.

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

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!

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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.

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Dr. Floris Barthel obtained his Doctor of Medicine (M.D.) degree from the Vrije Universiteit Amsterdam, The Netherlands where he developed an interest in malignant brain tumor (glioma) biology. He joined the laboratory of Dr. Roel Verhaak at the MD Anderson Cancer Center in Houston, Texas for a research fellowship to satisfy his scientific curiosity. There he trained in computational biology and performed the data analysis for several large translational studies investigating the molecular markers of gliomas. Dr. Barthel subsequently relocated to The Jackson Laboratory (JAX) for Genomic Medicine in Farmington, Connecticut where he was awarded the JAX scholar award. The JAX scholar award is a competitive institutional award supporting exceptional postdoctoral fellows become independent investigators.

Shortly after, he was awarded a K99/R00 pathway to independence award to study epigenetic strategies of telomerase reactivation in cancer. He has since been training in molecular biology while continuing translational research on malignant gliomas and telomere maintenance. He has published his research findings in various reputable journals, including Nature, Cell, and Nature Genetics. He was recently named a ForbeckScholar in lieu of his achievements and will attend yearly scholar meetings. He aims to build a basic and translational research program focused on identifying therapeutic vulnerabilities among telomere maintenance pathways in glioma.

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.

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.

Daniel Danis on ORCID

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.

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.

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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.

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My job is to use bioinformatics tools to understand gene and protein expression in the aging heart.

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.

Niran Hadad on ORCID

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.

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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.

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

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.

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Kevin C. Johnson on ORCID

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.

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.

Swarup Kumar on ORCIDID

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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.

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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.

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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.

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Zhiyuan received his Ph.D. degree at College of Life Science, Wuhan University. In Ph.D. training, his work was focused on regulation of Notch signaling and long-noncoding RNA. Currently, Zhiyuan is a Postdoctoral associate in Dr. Shengdong Ke’s Lab at The Jackson Laboratory. He envisions his research to investigate the roles of m6A modification in neurogenesis. How dysregulation of epitranscriptome contributes to brain disorders? What’s the mechanism of m6A signaling modulating the tempo of cortical neurogenesis? How does the cellular machinery target m6A to the correct transcripts? Answering these questions will advance the understanding of brain development and cell fate decision. Meanwhile, Zhiyuan is also interested in deep learning. He is devoted to develop a novel method to predict m6A sites and discover its biological significance.

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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.

Analyzing microbial data with applying innovative computational genomic and bioinformatic methods to find out relationships between microbiome and different factors like diseases.

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.

In 2013, I graduated from the College of the Holy Cross where I had work with Dr. Kenneth Mills on studying protein splicing. After college, I worked as a research assistant in Dr. Rameen Beroukhim's lab at the Dana-Farber Cancer Institute. In the Beroukhim lab, I worked with graduate student, William Gibson, and postdoctoral fellow, Brenton Paolella on validating the splicing factor SF3B1 as a CYCLOPS gene. In 2015, I began the University of Connecticut MD/PhD program, and joined the Anczukow lab in 2017.

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.

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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.

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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.

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Lidya Wooldridge on ORCID

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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