Mentors – UConn/JAX-GM Training Grant

Program Directors

Brenton Graveley, Ph.D., is the Chair of the Department of Genetics and Genome Sciences, and Associate Director of the Institute for Systems Genomics. His laboratory uses genomic approaches to study all aspects of RNA biology. His lab has played a key role in the modENCODE and ENCODE projects to functionally annotate the Drosophila and human genomes, with an emphasis on characterizing the transcribed RNAs, how they are processed, and the proteins that bind to them. They also study unusual RNA processing in Drosophila, including trans-splicing, recursive splicing, and alternative splicing.

Charles Lee, Ph.D., FACMG, is the Scientific Director of JAX-GM whose research uses state-of-the-art technologies to study structural genomic variation in human biology, evolution, and disease. Ongoing studies in his group include: 1) accurate identification and annotation of structural variation in human and other vertebrate genomes; 2) the development of new diagnostic assays and platforms for genome medicine; 3) understanding genome evolution in vertebrate species and its impact on genome stability. Dr. Lee has an affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Mentor Faculty and Research

Mark Adams, Ph.D. is Professor and Director of Microbial Services at JAX-GM. Dr. Adams has a rich history in genomics in both industry and academia. As a founding scientist of The Institute for Genomic Research (TIGR) and Celera Genomics he significantly contributed to the sequencing of the first free-living organism, Haemophilus influenzae, directed the Drosophila, human, and mouse genome sequencing projects, and a large-scale re- sequencing program to identify novel SNPs in humans. His research program at JAX-GM focuses on the development and application of approaches for human and mouse microbiome analysis and genomic analysis of the evolution of Gram-negative pathogens. Dr. Adams has an affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Olga Anczuków-Camarda, Ph.D. is Assistant Professor at JAX-GM whose research group studies RNA splicing misregulation and its relationship to cancer, particularly breast and ovarian cancers. Her group uses 3D tissue culture models and patient derived xenografts to mechanistically interrogate computationally-defined RNA alternative splicing characteristics in tumors to determine how these genomic changes contribute to treatment resistance. Dr. Anczuków-Camarda is currently training two M.D./Ph.D. students, one of whom is jointly mentored by Dr. Graveley (co-PD). Dr. Anczuków-Camarda has an affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Christine Beck, Ph.D. is a new joint faculty member and Assistant Professor of Genetics and Genome Sciences at UConn Health and JAX-GM. Dr. Beck’s laboratory studies the mechanisms and consequences of repetitive element-mediated genomic rearrangement, and how the genome maintains fidelity in the face of a higher repetitive genome. Through computational, molecular, and genomic techniques, her group identifies genomic regions susceptible to Alu-mediated structural variation 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. Dr. Beck is currently training a Ph.D. student and serves as thesis committee member for several UConn graduate students.

Gordon Carmichael, Ph.D. is a Professor of Genetics and Genome Sciences at UConn Health whose long research career has largely focused on the expression and function of RNA molecules. Current research includes the study of noncoding RNA, particularly ones that play important roles in development, cellular physiology and disease. Work in Dr. Carmichael’s lab resulted in the discovery of a new class of long noncoding RNAs that may underlie human Prader-Willi Syndrome. His group recently developed a new deep sequencing methodology to identify and study RNA 2’-O methylation, which is important in ribosome maturation and function, and which may also have roles in mRNA translation and fate. They also have current projects concerning dsRNA and its function and fate in cells, including in human embryonic stem cells. Dr. Carmichael has mentored nearly 30 Ph.D. students and 2 postdoctoral fellows over the course of his career. His mentorship strategy encourages independent and innovative thinking with the goal of training young scientists who are self-motivated and well prepared for the challenges they will face.

Jeffery Chuang, Ph.D. is Associate Professor at JAX-GM whose computational research group studies problems at the intersection of cancer, evolution, and functional genomics. Currently the focus of most research projects is the evolutionary understanding genetic aspects of resistance. These projects involve the detailed analysis of dissected tumor samples and xenografts, development of therapy regimens, and optimization of sequencing analysis approaches in order to identify the effect of each on intratumoral population data. Studies for these include the creation of computational pipelines for detection, quantification, and clinical interpretation of mutations and gene expression changes for a variety of cancers. His group also has expertise in large scale data science approaches for cancer and gene regulation. Dr. Chuang has mentored 2 Ph.D. students to completion, with 2 current students in the lab, and more than 10 postdocs. He is head of the graduate education committee at JAX-GM, for which he develops policies for students, contribute to admissions, and provides informal guidance to a number of students across the institute. Dr. Chuang has an affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Justin Cotney, Ph.D. is an Assistant Professor at UConn and highly committed to training the next generation of scientists. As a postdoctoral trainee himself, he mentored several graduate students and performed community outreach by exposing children and teens in the New Haven area to molecular biology and genetics. He also participated in science fairs as a mentor and judge on several occasions. He takes a very hands-on approach to mentoring his current graduate student and postdoc as well as students for which he is a thesis committee member. His group is interested in how gene regulatory elements, namely enhancers, control gene expression during mammalian development. They aim to understand how new gene regulatory functions evolve, to identify mechanisms of enhancer function over large genomic distances, and globally identify variants of enhancer sequences that are associated with human disease.

Arthur Günzl, Ph.D. is a Professor in the Department of Genetics and Genome Sciences at UConn Health. Dr. Günzl’s research is focused on studying gene expression mechanisms in the parasite Trypanosoma brucei using genomic methods to study protein-DNA interactions and RNA processing. Dr. Günzl’s has mentored numerous graduate students, postdoctoral fellows and undergraduate students, which has been a priority in his academic career. His trainees have been awarded an NIAID/F30 grant, the 2015 Henderson Award for most outstanding PhD thesis at UConn Health, an internal grant for excellence in undergraduate summer research, and several prizes for oral and poster presentations at meetings. Dr. Günzl has served as Associate Advisor for more than 20 graduate students.

J. Travis Hinson, M.D. is a joint faculty member as Assistant Professor at UConn and JAX-GM. The goal of Dr. Hinson’s research is to understand how human genetic variation results in cardiovascular disorders especially focused on inherited forms of heart failure. In combination with his clinical training as a board-certified specialist in cardiovascular medicine, he has developed human genetics expertise through positional cloning of monogenic human disorders, computational expertise in large-scale genomic analyses, and development of multi-disciplinary functional models that range from yeast to induced pluripotent stem cells (iPSCs), which allow him to approach cardiovascular disorders from an innovative perspective. Since starting his lab in 2016, his group developed an improved cardiac microtissue platform that they have used to study isogenic models of hypertrophic cardiomyopathy secondary to two actin binding beta myosin heavy chain mutations, which they generated. He currently mentors 2 M.D./Ph.D. students, 1 M.D. student (who was recently awarded an HHMI Medical Fellowship) and 2 postdoctoral fellows. Dr. Hinson has affiliated appointments in both the Department of Medicine and the Department of Genetics and Genome Sciences at UConn Health.

Christopher Heinen, Ph.D., Professor of Medicine, Center for Molecular Oncology has extensive experience in mentoring young trainees in my research laboratory over a seventeen-year career. I have mentored six students who have completed their Ph.D.s, one current Ph.D. candidate, two current M.D./Ph.D. candidates, one postdoc, two Master’s students and six undergraduates. I am committed to providing a safe and supportive training environment that emphasizes experimental rigor and responsibility in everything we do. I attempt to fully support my trainees in all aspects of their career development, as evidenced by their successful transition to multiple next steps including medicine, academic research and industry. I am also the current Director of Postdoctoral Affairs at UConn Health in addition to various roles in Graduate Education. My research laboratory is interested in understanding the molecular genetics of colorectal cancer, particularly the role of defects in the DNA mismatch repair (MMR) pathway.

Se-Jin Lee, M.D., Ph.D. is joint faculty as Professor of Genetics and Genome Sciences at UConn Health and JAX-GM and the discoverer of the gene myostatin, a negative regulator of muscle mass. Dr. Lee recently joined our institutions, having spent the past 26 years at Johns Hopkins University School of Medicine. While at Johns Hopkins, Dr. Lee successfully mentored 7 graduate students and was an active member of the graduate program. Dr. Lee studies the role of signaling molecules in regulating embryonic development and adult tissue homeostasis. He focuses on the superfamily of secreted proteins that are structurally related to transforming growth factor-Β (TGF-Β). Dr. Lee and his team are currently working to elucidate the mechanism of action of myostatin as well as the mechanisms by which the activity of myostatin is regulated.

James Li, Ph.D. is a Professor in the Department of Genetics and Genome Sciences at UConn Health. Dr. Li’s research is focused on understanding the developmental biology in the central nervous system, particularly the cerebellum. His laboratory makes extensive use of traditional and single-cell RNA-seq technologies to characterize the gene expression and splicing regulatory programs involved in this process. Dr. Li has graduated three pre-doctoral students who have gone on to continue careers in research.

Edison Liu, M.D. is the President and CEO of JAX. His group studies the functional genomics of cancer, particularly breast cancer, with a current emphasis on systems genomics, cancer maintenance, and determining therapeutic sensitivity and resistance. They also explore how structural changes in the cancer genome determine primary cancer growth and affect therapeutic sensitivity and resistance. To this end, they recently discovered a new chromotype in some triple negative breast cancers that confers sensitivity to platinum-based therapeutics, with clear implications for the value of cancer sequencing to inform patient treatment. Over the course of Dr. Liu’s career, he has mentored 28 postdocs, with an additional 3 currently in his group, and 18 graduate students. Dr. Liu has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Julia Oh, Ph.D. is an Assistant Professor at JAX-GM whose research goal is to better understand the host- microbiome interactions that result in human disease, and to use this information to develop microbe-based therapeutics for prevention and treatment. Her lab uses a combination of computational and molecular techniques to achieve these goals including; high-resolution genomic reconstruction, comparative genomics, genetic manipulation via phage transduction and CRISPR/Cas9, and high-throughput screening of non- traditional model organisms. Since starting her lab in 2015, she has recruited 4 postdoctoral fellows, a M.D.- Ph.D. student, and a D.M.D./Ph.D. student. Each trainee has a detailed mentoring plan designed to capitalize on both computational and experimental training as well as soft skills such as writing, presentation, grant-writing, and networking, all of which are necessary to become a successful independent scientist. Dr. Oh has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Karolina Palucka, M.D., Ph.D. is Professor and Associate Director for Cancer Immunology at JAX-GM, as well as a clinical oncologist and cancer immunologist, specializing in human immunology. Her research is aimed at understanding, controlling, and manipulating the body’s own immune response as the basis for developing new vaccines and immunotherapies against infectious diseases and human cancers. Current projects in her laboratory are designed to develop next generation models of humanized mice and to establish a proof-of- concept that these improved mice enable generation of fully autologous, patient-specific, immunocytes. Over her career, Dr. Palucka has trained 22 postdoctoral fellows, 7 Ph.D. students, and many more Masters, undergraduate and high school students. Dr. Palucka has affiliated appointment in the Department of Immunology at UConn Health.

Stefan Pinter, Ph.D. is a new Assistant Professor of Genetics and Genomic Sciences at UConn Health who studies how chromosome topology, non-coding (nc)RNA, and chromatin modifiers orchestrate gene expression. His lab develops novel and scalable genomic methodology to explore several poorly-understood aspects of gene regulation, particularly at the intersection of genome architecture and transcription. Projects in his group are interdisciplinary, spanning molecular biology and computational techniques, and includes methods that probe chromatin composition (ChIP-) and conformation (4C-), non-coding RNA interactions (Chart-) and expression (RNA-seq). Dr. Pinter has 2 Ph.D. students currently in his group, and serves as mentor to a rotation student, an undergrad intern, and a predoctoral visiting student. He is highly committed to training the next generation of genomic scientists, who will benefit from a systems-level view of biology and the computational know-how to address their research question.

Peter Robinson, M.D., M.S. is Professor of Computational Biology at JAX-GM with an affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health. His 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. 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. While in Germany, Dr. Robinson mentored students at every level (Bachelor, Master, PhD from the Free University) and hosted guest students from Italy, France, Slovakia, and Syria. Dr. Robinson currently mentors a MD/PhD student from UConn Health. Dr. Robinson has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Paul Robson, Ph.D. is an Associate Professor and the Director of the Single Cell Biology Laboratory located JAX-GM, and is a joint Core faculty with UConn. Dr. Robson has mentored 9 Ph.D. students and 8 postdoctoral fellows, the majority of whom have gone onto careers as professors or researchers in industry. He currently co- mentors a UConn graduate student with Dr. George Kuchel. Throughout his career, Dr. Robson has been instrumental in the development and improvement of single cell genomic technologies and their application in human health and disease. His lab currently uses droplet-based single cell transcriptomics technologies to discover heterogeneity in both normal and diseased tissues. He also studies mammalian embryology and uses single cell transcriptomics better understand cell fate in early development. Dr. Robson has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Blanka Rogina, Ph.D. is an Associate Professor in the Department of Genetics and Genome Sciences and Director of the Genetics and Developmental Biology Graduate Program at UConn Health. Dr. Rogina’s research is focused on identifying and characterizing the molecular mechanism of aging and finding key players that contribute to extended healthspan and longevity. Dr. Rogina has identified and determined the role of several genes in Drosophila health and longevity, including Indy, rpd3 and dSir2. Dr. Rogina is currently making extensive use of RNA-seq to identify gene expression and splicing changes that correlate with longevity. Dr. Rogina has graduated 3 PhD, one MD/PhD, and one DDS/PhD graduates. In addition, she has served as the Chair of the Advisory Committee for ~25 PhD, and MD/PhD students.

Michael Stitzel, Ph.D. is an Assistant Professor at JAX-GM with an affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health. His research focuses on the genomics of type 2 diabetes.His group 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, his lab investigates how the islet epigenome is altered under different stimulatory and stress conditions. They are also pursuing targeted modification of cells’ epigenomes to facilitate production of bona fide pancreatic islet cells from pluripotent stem cells or other terminally differentiated cells. Dr. Stitzel currently mentors a UConn Health Ph.D. student. Dr. Stitzel has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Duygu Ucar, Ph.D. is an Assistant Professor at JAX-GM and computational scientist with interdisciplinary training in data science, epigenomics, and the biology of aging. The overarching goal of her lab is to build integrative and innovative computational resources to uncover intricate regulatory programs in human cells and understand how these programs are disrupted by aging and aging-related diseases. To achieve this, she leverages next-generation-sequencing approaches (e.g., high-throughput sequencing, ATAC-seq, HiCHIP) and integrates these disparate datatypes to generate comprehensive genomic landscapes in different cells. Dr. Ucar’s innovative approach is bolstered by several successful collaborations with clinicians and biologists to give context to her groups’ findings in health, disease, and aging. She is highly committed to training the next generation of scientists at the intersection of computational sciences and aging biology; she currently mentors 1 UConn Ph.D. student and 1 postdoctorate researcher. Dr. Ucar has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Derya Unutmaz, M.D. is a Professor at JAX-GM. His current research probes the immunobiology of human T cells, with a focus on decoding their developmental and differentiation states, as well as the mechanisms of their activation and regulation during normal and disease conditions. Many of the research projects ongoing in his group look at the immunity of aging, particularly in the context of HIV, which causes “accelerated aging” of the immune system due to chronic inflammation. Other ongoing projects are directed at understanding 1) how metabolism and the microbiome influence the immune system during aging; 2) the anti-aging properties of metformin on human T cell differentiation and senescence; and 3) the regenerative capacity of T cells. His overall goal is to translate this knowledge into viable strategies for regenerating and reprogramming human T-cell responses to treat pathological conditions such as aging, infectious diseases or autoimmunity. Dr. Unutmaz has a long history of successful mentorship. To date, he has trained 12 Ph.D. or M.D./Ph.D. students and 4 postdocs, and is currently training 3 UConn graduate students. Dr. Unutmaz has affiliated appointment in the Department of Immunology at UConn Health.

Paola Vera-Licona, Ph.D. is an Assistant Professor of Cell Biology at UConn Health. Dr. Vera-Licona is also the group leader of the Computational Systems Medicine Research Group at the Center for Quantitative Medicine at UConn Health. She is an inter-disciplinary scientist with a background in mathematics and computational systems biology. She specializes in the design, implementation, and application of algorithms for the modeling, analysis, simulation, and control of biological systems. While the mathematical and computational tools her group uses are varied, many of the approaches developed have a flavor of fields such as discrete mathematics (graph theory and combinatorics), algebra, computational algebra as well as machine learning and network science. Dr. Vera-Licona has a deep commitment to education, mentoring, and outreach. She has worked to improve the learning of mathematics in elementary school in Mexico. She has developed workshops to teach to biology and mathematics high school teachers innovative ways to present their course materials in Virginia. She also later adapted this workshop for undergraduate level education. Currently she is co-PI and mentor of a 10-week undergraduate summer research program “Modeling and Simulation in Systems Biology”, sponsored by the NSF Research Experiences for Undergraduates program and an analogous program run by the Department of Health Career Opportunity Programs, a minority-serving program at UConn Health, to encourage undergraduate students to enroll in biomedical sciences graduate programs.

Roel Verhaak, Ph.D. is Professor and Associate Director of Computational Biology at JAX-GM. His group works on computational cancer biology with a research focus on the analysis of cancer genomics data to improve our understanding of cancer biology. They have a specialized research interest in understanding disease progression of brain tumors, particularly glioblastoma and glioma. His lab primarily uses high throughput sequencing and computational analysis to achieve their research goals. Throughout his career, Dr. Verhaak has made every effort to provide the trainees in his laboratory with the highest possible quality in mentoring. Five former postdocs are now independent faculty including CPRIT Scholar Dr. Siyuan Zheng. Five previous and current trainees successfully competed for Fellowship funding, including an American Cancer Society Fellowshipand a K99 transition to independence award from NIH. His group currently includes 5 postdoctoral trainees. Dr. Verhaak has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

George Weinstock, Ph.D. is Professor, Evnin Family Chair, and Director Microbial Genomics at JAX-GM. Dr. Weinstock has studied genomics and microbiology for over 40 years and has led many genome projects of human, microbes, and other organisms. He was a principal in the NIH Human Genome Project and Human Microbiome Project, a Director of the large-scale genome centers at Baylor College of Medicine and Washington University, and a member of numerous advisory boards to genome centers and projects. He has been at the forefront of DNA sequencing technology and management and analysis of ever-increasingly large datasets and has been an innovator in methods for microbial genetics, application of DNA sequencing in genomics, software for genome analysis, and clinical and veterinary applications of genomics. Dr. Weinstock has mentored >75 predoctoral and postdoctoral trainees for careers in science; many of which now hold research-related positions in academia, industry, government or law. Dr. Weinstock has affiliated appointment in the Department of Genetics and Genome Sciences at UConn Health.

Ming Xu, Ph.D., Assistant Professor in Genetics and Genome Sciences, Center on Aging. Cellular senescence is one of the major players contributing to the fundamental aging process. My lab is leveraging novel mouse models and primary human cells as tools to examine the role and underlying mechanism of senescent cells in various conditions in mammals, and we aim to find new drugs to target senescent cells in order to alleviate a range of diseases as a group. I have been officially mentoring 3 postdocs, 1 MD/PhD student, and 1 PhD student. One of my postdocs, Dr. Yueying Zhou, recently joined Central South University as an Assistant Professor. In addition, I have trained 2 summer students and 3 rotation students.