Data Science: Pre & Postdoctoral Training

I joined King Abdullah University of Science and Technology to start my Ph.D. study in 2010. I was a member of the Structural and Functional Bioinformatics group, led by Prof. Xin Gao. My research focus was on determining the 3D structures of proteins using Nuclear Magnetic Resonance (NMR) data. My research during Ph.D. resulted in five journal papers published in Bioinformatics, Plos One, Journal of Biomolecular NMR, Scientific Reports, and IEEE/ACM Transactions on Computational Biology and Bioinformatics.

In 2017, I started my first postdoctoral training. I joined the group of Prof. Jianyang Zeng in Institute for Interdisciplinary Information Sciences, Tsinghua University. Prof. Zeng gave me all the trust and freedom to do proper research. He suggested me a very promising research topic about 3D genome modeling using Hi-C and FISH data. My work in this project resulted in a Nature Communications paper that was published earlier this year (2019). Also, I worked on another related project about 3D genome modeling using single-cell Hi-C data. This second project gave good results, and its manuscript is still under preparation.

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.

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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!

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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.

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

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

I received my Ph.D. in Biochemistry and Molecular Biology from Huazhong Agricultural University where I studied the genetic and biochemical bases of rice metabolome variation by an approach combined genomics, genetics and metabolomics. Previously, I received my B.S. in Biological Science at Huazhong Agricultural University. After getting my Ph.D., I joined Dr. Wei Chia-Lin’s lab at DOE Joint Genome Institute, working on the epigenetic control of drought response in sorghum.

Currently I am a postdoctoral associate in our Genome Technologies group. My researches focus on developing ultra-long read sequencing methods with the third generation single-molecule sequencing technologies and applying them with other cutting edge genome technologies to identify the genomic structural variations in cancer genome.

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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My Ph.D. work was aimed at understanding the function of the TH2BS11ph histone modification and linker histone variant H1t in the context of processes that occur during the meiotic prophase I of rodents. We showed that TH2BS11ph histone mark is associated with two classes of chromatin domains in spermatocytes: DNA repair domains of the XY body and Transcription start sites. This is the first study documenting the role of a post-translational modification of a germ cell-specific histone variant in meiotic prophase I related events (Mahadevan et al, Epigenetics and Chromatin, 2019). We demonstrated the close association of the linker histone variant H1t at repeat-associated chromatin domains in vivo, apart from its localization at the rDNA element. These repeat elements were found to be repressed by DNA methylation and repressive histone modifications like H3K9me3 and H4K20me3 in vivo. We hypothesize that H1t might induce local chromatin relaxation to recruit protein factors necessary to Transposable element repression (Mahadevan et al., Epigenetics and Chromatin, 2020).

Continuing with my interest of study, my projects at the Baker lab would be aimed at decoding the epigenetic phenomena related to various developmental pathways like ES cell pluripotency/differentiation and meiotic recombination in mouse model systems.

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 completed my undergraduate studies in Biotechnology at IIT Roorkee, India. This was followed by a project in the Axon Regeneration Lab at IISc Bangalore, under Dr. Ramanan's supervision. I am currently a Graduate Assistant in the Stitzel and Ucar lab at JAX-GM.

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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Develops computational approaches using phenotype data to identify complex genetic networks and gene interactions relevant to AD.

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.

Developing deep learning algorithms including graph embedding and link prediction techniques in knowledge graphs constructed from networks of genes, drugs and diseases to predict new treatments for diseases.

Implementing machine learning algorithms to analyze immune profiling and clinical data of patients with chronic fatigue syndrome.

Implementing methods for translational bioinformatics with a focus on whole exome and whole genome sequencing.

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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