Computational Biology and Bioinformatics (CBB) Track

Dr. Brandt completed a general Preventive Medicine residency at Madigan Army Medical Center in 1989 and a post-doctoral fellowship sponsored by the National Library of Medicine at Yale School of Medicine in 1997. She is board certified in Preventive Medicine and Clinical Informatics. Her research is interdisciplinary and focuses on issues related to the design, development and use of informatics tools in the domain of clinical research, as well as health services research.

After graduating from Harvard with a A.B. in physics in 1989, Prof. Mark Gerstein earned a doctorate in theoretical chemistry and biophysics from Cambridge University in 1993. He did postdoctoral research in bioinformatics at Stanford University from 1993 to 1996. He came to Yale in 1997 as an assistant professor in the Department of Molecular Biophysics and Biochemistry, and since 1999, in the Computer Science Department. He was named an associate professor in 2001, and the following year became co-director of the Yale Computational Biology and Bioinformatics Program. Gerstein has published appreciably in the scientific literature, with >400 publications in total, including a number of them in prominent venues, such as Science, Nature, and Scientific American. His research is focused on bioinformatics, and he is particularly interested in data science & data mining, macromolecular geometry & simulation, human genome annotation & disease genomics, and genomic privacy. 

Prof. O'Hern is a Professor of Mechanical Engineering & Materials Science and Physics, co-founder of the Integrated Graduate Program in Physical and Engineering Biology, and Director of Undergraduate Programs for the Raymond and Beverly Sackler Institute for Biological, Physical, and Engineering Sciences. His research employs theoretical and computational methods (e.g. all-atom and coarse-grained molecular dynamics simulations) to tackle a broad range of fundamental questions in soft matter and biological physics. Current projects include the dynamics of protein folding, unfolding, and
aggregation, the binding and self-assembly of proteins, and the structural
and mechanical properties of cells and tissues in the context of collective cell motion and wound healing.

Dr. Hongyu Zhao is the Ira V. Hiscock Professor of Biostatistics and Professor of Statistics and Data Science and Genetics, Chair of the Biostatistics Department and the Co-Director of Graduate Studies of the Inter-Departmental Program in Computational Biology and Bioinformatics at Yale University. He received his B.S. in Probability and Statistics from Peking University in 1990 and Ph.D. in Statistics from the University of California at Berkeley in 1995. His research interests are the applications of statistical methods in molecular biology, genetics, drug developments, and precision medicine.

Some of his recent projects include large scale genome wide studies to identify genetic variants underlying complex diseases, genetic risk prediction, biological network modeling and analysis, disease biomarker identification, genome annotation, cancer genomics, microbiome analysis, single cell analysis, image analysis, and systems biology study of herbal medicine. He has published over 480 articles in statistics, human genetics, bioinformatics, and proteomics, and edited two books on human genetics analysis and statistical genomics. He has trained over 70 doctoral and post-doctoral students, many of whom are holding tenured or tenure-track positions at major universities in the states and overseas.

Dr. Zhao is a Co-Editor of the Journal of the American Statistical Association Theory and Methods, and serves on the editorial boards of several leading statistical and genetics journals. He was the recipient of the Mortimer Spiegelman Award for a top statistician in health statistics under the age of 40 awarded by the American Public Health Association and the Pao-Lu Hsu Award from the International Chinese Statistical Association. His research has also been recognized by the Evelyn Fix Memorial Medal and Citation by UC Berkeley, a Basil O'Connor Starter Scholar Award by the March of Dimes Foundation, election to the fellowship of the American Association for the Advancement of Science, the American Statistical Association, and the Institute of Mathematical Statistics.

Julien Berro was initially trained in Applied Mathematics, Physics and Computer Sciences at the Institut National Polytechnique of Grenoble, France. He obtained his Ph.D. in Mathematical Modeling in Biology at Université Joseph Fourier, Grenoble, France, where he worked with Jean-Louis Martiel and Laurent Blanchoin on mathematical models for actin filament biochemistry and mechanics. After a brief tenure as an assistant professor in the department of Mathematics at Université Claude Bernard, Lyon, France, he decided to further his training by learning cell biology and quantitative microscopy in the laboratory of Tom Pollard at Yale University. Since he started his own laboratory in 2013, he has combined experimental, computational, and theoretical approaches to uncover the mechanisms of molecular machineries that produce forces in the cell, with a particular focus on the actin cytoskeleton and endocytosis.

Marcus Bosenberg M.D., Ph.D., is a physician scientist who directs a leading melanoma research laboratory, is Co-Leader of the Genomics, Genetics and Epigenetics Program of the Yale Cancer Center, Co-Director of the Yale SPORE in Skin Cancer, and is a practicing dermatopathologist at Yale Dermatopathology through Yale Medicine.

In his research, Dr. Bosenberg studies the genetics and cellular changes that result in melanoma, the leading cause of skin cancer deaths. His laboratory has developed several widely utilized mouse models in order to study how melanoma forms and progresses, to test new melanoma therapies, and how the immune system can be stimulated to fight melanoma. He works to translate basic scientific findings into improvements in melanoma diagnosis and therapy. He has published over 100 peer-reviewed articles, is a member of the Yale Cancer Center Executive Committee, and is a faculty member of the Raymond and Beverly Sackler Institute for Biological, Physical, and Engineering Sciences.

Dr. Bosenberg mentors undergraduate, graduate, medical, and MD-PhD students in his laboratory, teaches at Yale School of Medicine, and trains resident physicians, fellows, and postdoctoral fellows.

Dr. Brandt completed a general Preventive Medicine residency at Madigan Army Medical Center in 1989 and a post-doctoral fellowship sponsored by the National Library of Medicine at Yale School of Medicine in 1997. She is board certified in Preventive Medicine and Clinical Informatics. Her research is interdisciplinary and focuses on issues related to the design, development and use of informatics tools in the domain of clinical research, as well as health services research.

Kei-Hoi Cheung, PhD has distinguished himself as a researcher and educator in the field of Biomedical Informatics with a growing national and international reputation. A particular strength is Dr. Cheung’s ability to forge strong, productive collaborations with a range of different bioscience researchers at Yale, in which his contributions include the development of complex databases and informatics tools that are critical for the research projects being performed. In the context of these collaborations, Dr. Cheung is simultaneously able to carry out his own informatics research on issues involved in robust interoperation and integration of databases and tools in the biosciences. In addition to giving talks and presentations at national and international meetings, he has published his own informatics research in peer-reviewed journals and conference proceedings, as well as contributing to publications focused on his collaborators’ research. He has established a broad base of collaborations with faculty in different departments at Yale, including Genetics, Pathology, Computer Science, Biostatistics, Molecular Biophysics and Biochemistry, and Biology. He was Director of Biostatistics and Bioinformatics Core of the NIDA Proteomics Center, focused on collaborative informatics support of neuroproteomics research at Yale. In addition to being a collaborator on numerous grants, Dr. Cheung has been PI on several federal grants (NIH and NSF). Dr. Cheung is also a core faculty member of Yale's Ph.D. Program in Computational Biology and Bioinformatics.

Dr. Cheung’ s research interests include the semantic web using the next generation of web technologies to integrate life science data and tools, and is co-editor of two books for Springer-Verlag titled: “Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences” and “Semantic e-Science”, respectively. Dr. Cheung also led the BioRDF task force (2008-2010) of the Semantic Web for Health Care and Life Sciences Interest Group that is an international community engaging in the creative use of Semantic Web in biomedicine. In addition, Dr. Cheung has recently embarked on natural language processing (NLP) projects in annotating, extracting and retrieving information from clinical text as part of the Veteran Administration (VA) electronic medical records. In summary, Dr. Cheung’s biomedical informatics expertise in database/semantic web research and NLP tool development, his national and international recognition as a researcher/educator, and his research contributions in these areas exemplify the attributes of a prominent researcher in biomedical informatics.

Coifman is a member of the American Academy of Arts and Sciences, the
Connecticut Academy of Science and Engineering, and the National Academy
of Sciences. He is a recipient of the 1996 DARPA Sustained Excellence
Award, the 1996 Connecticut Science Medal, the 1999 Pioneer Award of the
International Society for Industrial and Applied Science, and the 1999
National Medal of Science.

Chris Cotsapas is a geneticist whose primary interest is in understanding the biological processes underlying diseases of the immune system. He has published several highly cited papers on genome-wide association studies of disease, gene expression genetics and evolutionary biology. For more information please see our lab website.

Chris obtained his BSc in Biochemistry from Imperial College London in 2000 and his PhD in Biochemistry and Molecular Genetics from the University of New South Wales, Sydney in 2007.

Forrest Crawford's work focuses on mathematical and statistical problems related to discrete structures and stochastic processes in epidemiology, public health, biomedicine, and evolutionary science.

Prof. Dellaporta studied at the University of Rhode Island (1972-76), Iowa State University (1976-78) and at the Worcester Polytechnic Institute (1978-81). His postdoctoral studies in plant molecular genetics were conducted at the Cold Spring Harbor Laboratory (1981-83). He has held positions of Staff Scientist at Cold Spring Harbor (1983-86), Assistant (1986-89), Associate (1990-96) and Full Professor (1996-present) in the Department of Molecular, Cellular and Developmental Biology at Yale University. His research program has focused on the genomic and computational biology of agronomic traits in crops such as of maize, rice and other cereals, including contributions to the identification and utility of of genetic diversity. He has co-authored numerous publications in scientific journals such as Cell, Nature, Science, Proc. Natl. Acad. Sciences, and Genetics, among others, and has served on the scientific advisory panels at the National Institute of Health, the National Science Foundation and the United States Department of Agriculture. Dr. Dellaporta has served a member of the Board of Control of the Connecticut Agricultural Experiment Station.

Dr. Flavell is Sterling Professor of Immunobiology at Yale University School of Medicine, and an Investigator of the Howard Hughes Medical Institute. He received his B.Sc. (Honors) in 1967 and Ph.D. in 1970 in biochemistry from the University of Hull, England, and performed postdoctoral work in Amsterdam (1970-72) with Piet Borst and in Zurich (1972-73) with Charles Weissmann. Before accepting his current position in 1988, Dr. Flavell was first Assistant Professor (equivalent) at the University of Amsterdam (1974-79); then Head of the Laboratory of Gene Structure and Expression at the National Institute for Medical Research, Mill Hill, London (1979-82); and subsequently President and Chief Scientific Officer of Biogen Research Corporation, Cambridge, Massachusetts (1982-88). Dr. Flavell is a fellow of the Royal Society, a member of the National Academy of Sciences as well as the Institute of Medicine. Richard Flavell uses transgenic and gene-targeted mice to study Innate and Adaptive immunity, T cell tolerance and activation in immunity and autoimmunity,apoptosis, and regulation of T cell differentiation.

After graduating from Harvard with a A.B. in physics in 1989, Prof. Mark Gerstein earned a doctorate in theoretical chemistry and biophysics from Cambridge University in 1993. He did postdoctoral research in bioinformatics at Stanford University from 1993 to 1996. He came to Yale in 1997 as an assistant professor in the Department of Molecular Biophysics and Biochemistry, and since 1999, in the Computer Science Department. He was named an associate professor in 2001, and the following year became co-director of the Yale Computational Biology and Bioinformatics Program. Gerstein has published appreciably in the scientific literature, with >400 publications in total, including a number of them in prominent venues, such as Science, Nature, and Scientific American. His research is focused on bioinformatics, and he is particularly interested in data science & data mining, macromolecular geometry & simulation, human genome annotation & disease genomics, and genomic privacy. 

Antonio studied Chemistry and Molecular Biology at the University of Cadiz and the University Autonoma of Madrid. During undergraduate, he worked with Gines Morata at the CBM in Madrid. Antonio did his PhD with Stephen Cohen at the EMBL (Heidelberg) (1998-2002) and a post-doc with Alex Schier at the Skirball Institute (NYU) and Harvard (2003-2006). Antonio established his laboratory at Yale in 2007 where he investigates the regulatory codes that shape gene expression during embryonic development. He was Director of Graduate Studies (2012-2016) and is currently Chair of the Genetics Department (2017- ).

Dr. Murat Gunel, Professor of Neurosurgery, assumed the position of chief of Neurovascular Surgery Program in January of 2001. Dr. Gunel is a board certified neurosurgeon and is a fellow of the American College of Surgeons. He has special interest in treating brain aneurysms and vascular malformations with special emphasis on arterio-venous malformations and cavernous malformations. He also has expertise in occlusive vascular disorders such as carotid disease and gamma knife surgery (radiosurgery).

His laboratory interests parallel his expertise in clinical neurovascular surgery and focus on gene discovery in disorders of the nervous system and its vasculature. Dr. Gunel's lab completed the two largest genome wide association studies (GWAS) aimed at understanding common variants that underlie intracranial aneurysm genetic risk based on the analysis of over 20,000 subjects. In addition, he is interested in the identification of genes important in human brain development through the study of rare, consanguineous families with recessive forms of malformations of cortical development.

Monika Jadi obtained her Ph.D. in Neuroengineering at the University of Southern California and did her postdoctoral training at the Salk Institute for Biological Studies in the Computational Neurobiology Laboratory. At Yale, she is an Assistant Professor in the Departments of Psychiatry and Neuroscience. 

Dr. Jadi’s research involves discovering computational principles that are critical for flexible information processing in the brain, using cross-disciplinary approaches from applied physics and computer science.  Her doctoral research resulted in the first characterization of computational flexibility mediated by location-specificity of synaptic inhibition in active dendrites of neurons, a ubiquitous anatomical signature in cortical circuits. She has studied models of cortical networks during her postdoctoral work, and proposed a novel mechanism of cortical oscillations that is controlled by the direct and indirect stimulation of inhibitory neurons. Subsequently, she has explored mechanisms of flexible modulation of cortical dynamics that are mediated by different inhibitory neuronal classes in the cortex. Complementing her computational modelling work, she has used novel data analysis methods to explore the temporal dynamics of population coding in the visual cortex. The current focus of her lab is using computational modeling as well as data modeling tools such as machine learning to study computations, information flow, temporal dynamics of population codes and role of neuromodulation in canonical columnar circuits of the cortex. Dr. Jadi is a recipient of the NIH Pathway to Independence award during her postdoctoral and early faculty years.

The Jadi Lab

Dr. Justice is a Clinical Epidemiologist who has developed multiple large national cohorts based on data from the Veterans Affairs Healthcare System Electronic Medical Record enhanced with National Death Index and CMS data, patient completed surveys, DNA and tissue repositories, and stored pathology samples. She has two decades of experience in the processes required to clean, validate, and standardize raw EMR data and in its analysis using standard statistical methods, machine learning techniques, and cross cohort validations. The oldest and best known of her projects is the Veterans Aging Cohort Study (VACS). VACS is an ongoing, longitudinal study of >170,000 United States veterans with and without HIV infection continuously funded by National Institutes of Health (NIH) since 1996. She has developed and validated widely used indices including a prognostic index, the VACS Index, and a patient reported symptom index, the HIV Symptom Index. She is the principal investigator of the National Cancer Institute provocative questions grant HIV and Aging Mechanisms for Hepatocellular Cancer, has published over 400 peer reviewed manuscripts, and has presented work at the United Nations, The International AIDS Society, The Royal Medical College in London, the White House, and Congress. She is a member of the National Cancer Institute Ad hoc Subcommittee on HIV and AIDS Malignancy and the HIV and Aging Working Group, NIH Office of AIDS Research. She has recently joined the International Advisory Boards of Lancet HIV and Journal of the International AIDS Society.  

Dr. Naftali Kaminski is, as of July 1st, 2013, the Boehringer-Ingelheim Endowed Professor of Internal Medicine and Chief of Pulmonary, Critical Care and Sleep Medicine, at Yale School of Medicine. Before that he was a tenured professor of Medicine, Pathology, Computational Biology and Human Genetics, and the Dorothy P. and Richard P. Simmons Endowed Chair for Pulmonary Research at the University of Pittsburgh. Dr. Kaminski was the director of the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease and the Lung, Blood and Vascular Center for Genomic Medicine at the division of Pulmonary, Allergy and Critical Care Medicine in University of Pittsburgh. Dr Kaminski received his medical degree from the Hebrew University - Hadassah Medical School in Jerusalem, Israel, and completed a residency in Internal Medicine at Hadassah Mount-Scopus University Hospital in Jerusalem, and a fellowship in pulmonary medicine at Sheba Medical Center in Tel-Hashomer, Israel. Dr Kaminski received his basic science training in Dean Sheppard's laboratory at the Lung Biology Center at UCSF and in functional genomics and microarray technology at the Functional Genomics laboratory at Roche Bioscience, Palo-Alto. After his fellowship in 2000, Dr. Kaminski was appointed head of Functional Genomics at Sheba Medical Center in Israel, before being recruited to head the Simmons Center at the University of Pittsburgh in 2002.

Dr. Kaminski's main research interests involve applying genomic approaches to elucidate basic mechanisms and improve diagnosis and treatment of Idiopathic Pulmonary Fibrosis (IPF), a chronic mostly lethal and currently untreatable scarring lung disease and other chronic lung diseases such Chronic Obstructive Pulmonary Disease (COPD), severe asthma and sarcoidosis. His group pioneered the application of high throughput genome scale transcript profiling in advanced lung disease. Among his key discoveries are: The discovery that matrix metalloproteases such as MMP7 and MMP19 have significant active roles in determining the lung phenotype in patients with IPF, demonstrating that microRNAs, a family of small non-coding RNAs, are differentially expressed in IPF, and that some of them such are mechanistically involved in lung fibrosis, and the discovery that the outcome of patients with IPF can be predicted based on the expression of peripheral blood proteins and genes, a finding with practical implication because of the need for risk stratification and transplant prioritization. More recently Dr. Kaminski's team identified a potential antifibrotic role for thyroid hormone signaling, a novel discovery with significant therapeutic implications. Dr. Kaminski has a strong interest in integrating high throughput ‘omics’ data, such as genome scale DNA variants, coding and non-coding RNAs, microbiome and metabolome information with clinical information to generate tools for personalized medicine of lung diseases that are significantly more precise, predictive and patient centered than anything that is currently available.

Since completing his clinical training, Dr. Kaminski authored more than 260 research papers, review articles and book chapters and has given numerous invited talks at national and International conferences. Since he finished his fellowship in 2000, Dr. Kaminski has been consistently funded by NIH and is the PI of multiple NIH grants. Dr. Kaminski was a recipient of the Marvin I. Schwarz Award for contributions to patient care and research in pulmonary fibrosis from the Coalition for Pulmonary Fibrosis in 2010 and the University of Pittsburgh Innovator Award in 2012. In 2013, Dr. Kaminski received the American Thoracic Society Recognition of Scientific Achievements award, as well the Helmholtz Institute International Fellow. In 2015 he was elected to the Association of American Physicians. In 2016 he was elected as Fellow of the European Respiratory Society (ERS) , and won the the European Respiratory Society Gold medal for Interstitial Lung Disease. In 2018, Dr. Kaminski received the Andy Tager Excellence in Mentorship Award from the Respiratory Cell and Molecular Biology Assembly of the American Thoracic Society and was elected fellow  of the American Thoracic Society. Dr. Kaminski is active on the ATS and was the editor of “Gene Express”, a column on genomics in the initial days of the ATS Website, a member and chair of the Program Committee of the Assembly on Respiratory Cell and Molecular Biology of the ATS, and member of the ATS Research Advocacy Committee, and Chair of the Assembly on Respiratory, Cell, and Molecular Biology at the American Thoracic Society. He was an associate editor of the American Journal of Respiratory and Critical care Medicine, a member of multiple editorial boards and currently is the Deputy Editor of Thorax, BMJ. Dr. Kaminski is the current President of the Association of Pulmonary, Critical Care and Sleep Division Directors.

Dr. Kaminski is passionate about training physician scientists for the challenges of 21st century medicine, and especially in the vocabulary, skills and technology of the new fields of genomics, bioinformatics, computational and system biology and their application to understanding the basic mechanisms that govern lung health and disease as well as to designed personalized medicine approaches and has mentored multiple MD and PhD scientists, of them many have productive and well funded independent career. He has most recently recognized for his commitment to mentoring with the American Thoracic Society Andy Tager excellence in mentoring award.

Dr. Steven Kleinstein is a computational immunologist with a combination of "big data" analysis and immunology domain expertise. His research interests include both developing new computational methods and applying these methods to study human immune responses. Dr. Kleinstein received a B.A.S. in Computer Science from the University of Pennsylvania and a Ph.D. in Computer Science from Princeton University. He is currently an Associate Professor of Pathology (with a secondary appointment in Immunobiology) at the Yale School of Medicine, and a member of the Interdepartmental Program in Computational Biology and Bioinformatics (CBB), and the Human and Translational Immunology Program. 

Specific areas of research focus include:

• High-throughput B cell receptor (BCR) repertoire profiling (AIRR-seq or Rep-seq)
• Immune signature of human infection and vaccination responses

Smita Krishnaswamy was trained as a computer scientist with a Ph.D. from the University of Michigan's EECS department where her research focused on algorithms for automated synthesis and verification of nanoscale logic circuits that exhibit probabilistic effects. During her Ph.D., she received a best paper award at DATE 2005 (a top conference in the field of design automation), and an outstanding dissertation award. She published numerous first-author papers on probabilistic network models and algorithms for VLSICAD. In addition, her dissertation was published as a book by Springer in 2013. Following her Ph.D., she joined IBM's TJ Watson Research Center as a scientist in the systems division, where she focused on formal methods for automated error detection. Her Deltasyn algorithm was eventually utilized in IBMs p and z series high-performance chips. She then switched her research efforts to biology. Her postdoctoral training was completed at Columbia University in the systems biology department where she focused on learning computational models of cellular signaling from single-cell mass cytometry data.

Although technologies such as mass cytometry, and single-cell RNA sequencing, are able to generate high-dimensional high-throughput single-cell data, the computational, modeling and visualization techniques needed to analyze and make sense of this data are still lacking. Smita's research addresses this challenge by developing scalable computational methods for analyzing and learning predictive network models from massive biological datasets. Her methods for characterizing interactions in cellular signaling networks, published in a recent Science paper, reveal the computation performed by cells as they process signals in terms of stochastic response functions. Smita, along with experimental collaborators, have applied these methods to T cell signaling and have found that signaling response functions are reconfigured through differentiation and disease. For example, Smita and her collaborators found that subtle alterations in receptor-proximal signaling in non-obese diabetic (NOD) mice are amplified through signaling cascades leading to larger defects in downstream signals responsible for damping immune response. Her ongoing work involves creating more sophisticated and accurate models of transformational biological processes by combining both single-cell signaling and genomic data. At Yale, she is creating a forward-looking and interdisciplinary research group that is focused on developing computational techniques to solve today’s challenging biological and medical problems.

Harlan Krumholz is a cardiologist and health care researcher at Yale University and Yale-New Haven Hospital. He received a BS from Yale, an MD from Harvard Medical School, and a Masters in Health Policy and Management from the Harvard University School of Public Health. He is the Harold H. Hines, Jr. Professor of Medicine and Director of the Yale Center for Outcomes Research and Evaluation (CORE), one of the nation’s first and most productive research units dedicated to producing innovations to improve patient outcomes and promote better population health. He is also a Director of the Robert Wood Johnson Foundation Clinical Scholars Program, which prepares talented physicians to become future health care leaders.

Dr. Krumholz has been honored by membership in the Institute of Medicine, the Association of American Physicians, and the American Society for Clinical Investigation. He was named a Distinguished Scientist of the American Heart Association. He was elected to the Board of Trustees of the American College of Cardiology and the Board of Directors of the American Board of Internal Medicine, and was appointed by the U.S. government to the Board of Governors of the Patient-Centered Outcomes Research Institute. He is a 2014 recipient of the Friendship Award from the People’s Republic of China in recognition of his collaborative efforts to develop a national cardiovascular research network.

Dr. Krumholz is the editor of Circulation: Cardiovascular Quality and Outcomes, and editor of CardioExchange, a social media site of the publisher of the New England Journal of Medicine. He has published more than 800 articles and is the author of two books, one on smoking cessation and another on reducing the risk of heart disease. He has a regular blog on Forbes.com and has contributed to the New York Times Wellness blog, the New York Times op-ed page, and National Public Radio Shots blog.

Monkol received an undergraduate degree in Engineering (Computer Engineering) in 2000 at the University of New South Wales (UNSW) and then worked for IBM for 3.5 years. He returned to UNSW and completed undergraduate degrees in Science (Physiology) and Engineering (Bioinformatics) and received the University Medal in 2007. He completed his PhD (Medicine) at the University of Sydney in 2012 with the thesis topic: Functional differences between alpha-actinin-2 and alpha-actinin-3. Monkol did his post-doctoral training in Daniel MacArthur’s lab based at Massachusetts General Hospital, Harvard Medical School and the Broad Institute.  

He was the lead author/analyst for the Exome Aggregation Consortium (ExAC) project that was published in Nature 2016. He went on to lead the NIH funded Broad Center for Mendelian Genomics (CMG) analysis team. As lead analyst, he oversaw the analysis strategy for all major CMG collaborations and organized monthly meetings to foster sharing of new methods and analysis amongst the rare disease community. He also coordinated the data processing and preliminary analysis of NIH Gabriella Miller Kids First (GMKF) cohorts sequenced or reprocessed at the Broad Institute.

Monkol has a strong passion for rare muscle disease research as a patient with Limb Girdle Muscular dystrophy (LGMD2G). During his time in the Broad Institute, he lead the exome/genome analysis of MYOSEQ (European cohort of >1000 LGMD patients) and SeqNMD (an international consortium of undiagnosed rare muscle diseases) which has resulted in novel disease gene discovery.

Bluma (Bibi) Lesch works on the genetics and epigenetics of reproduction and development, with a special interest in the evolution of epigenetic and chromatin states in mammals. Understanding the evolution of gene regulation in gametes requires integrating information across a wide range of biological scales, from the regulation of molecules to the development of individuals to the evolution of species. Dr. Lesch’s work brings together these divergent approaches to thinking about biology.

Dr. Lesch earned her B.S. from Yale University in 2003. She obtained her Ph.D. in 2010 from Rockefeller University and her M.D. in 2011 from Weill Cornell Medical College in New York City.  She was a postdoctoral fellow at the Whitehead Institute in Cambridge, MA, from 2011-2017, where she was awarded an NIH Kirschstein postdoctoral fellowship and also named a Hope Funds for Cancer Research postdoctoral fellow.  She received a Burroughs Wellcome Career Award for Medical Scientists in 2015, and returned to New Haven to join the Yale faculty in 2017.

Morgan Levine is a ladder-rank Assistant Professor in the Department of Pathology at the Yale School of Medicine and a member of both the Yale Combined Program in Computational Biology and Bioinformatics, and the Yale Center for Research on Aging. Her work relies on an interdisciplinary approach, integrating theories and methods from statistical genetics, computational biology, and mathematical demography to develop biomarkers of aging for humans and animal models using high-dimensional omics data. As PI or co-Investigator on multiple NIH-, Foundation-, and University-funded projects, she has extensive experience using systems-level and machine learning approaches to track epigenetic, transcriptomic, and proteomic changes with aging and incorporate this information to develop measures of risk stratification for major chronic diseases, such as cancer and Alzheimer’s disease. Her work also involves development of systems-level outcome measures of aging, aimed at facilitating evaluation for Geroprotective Interventions. A number of the existing biological aging measures she has developed are being applied in both basic and observational research. Finally, her lab is also involved in a number of collaborations to examine shared molecular signatures in normal aging and cancer.

The Eugene Higgins Professor of Cell Biology, Professor of Genetics, of Obstetrics, Gynecology, and Reproductive Sciences, and of Dermatology, Founding Director of Yale Stem Cell Center. Dr. Lin’s work is focused on the self-renewing mechanism of stem cells, using Drosophila germline stem cells, mouse germline stem cells, mouse  embryonic stem cells, Hydra, and planarian stem cells as models.  He also studies germline development and stem cell-related cancers. 

 Dr. Lin received his B.S. degree from Fudan University (1982), and his Ph.D. degree from Cornell University (1990). Following his postdoctoral research at the Carnegie Institution of Washington, he joined the faculty of Duke University Medical School in 1994, where he rose to the rank of Full Professor.  He founded and directed the Duke Stem Cell Research Program (2005-2006), and moved to Yale in 2006 to establish and direct the Yale Stem Cell Center, building it from just two labs in 2006 to currently one of the largest stem cell research organizations in the world with 97 member labs.  In 2014, with Yale's support, he became the Founding Dean (Adjunct) of School of Life Science and Technology at ShanghaiTech University in China, and has rapidly established a world-class faculty and educational programs in the School.

 Dr. Lin has made key contributions to the demonstration of stem cell asymmetric division and the proof of the stem cell niche theory.  He discovered the Argonaute/Piwi gene family and elucidated their essential function in stem cell self-renewal and germline development. He is also a discoverer of a novel class of non-coding small RNAs called PIWI-interacting RNAs (piRNAs), a discovery hailed by the Science Magazine as one of the Ten Scientific Breakthroughs in 2006.  More recently, he proposed and demonstrated the crucial roles of the Piwi-piRNA pathway in epigenetic programming and in post-transcriptional regulation of mRNA and lncRNA.

Dr. Lin has provided numerous services to the scientific community and beyond. His past services included the Treasurer and Member of Executive committee of the International Society for Stem Cell Research (ISSCR, 2013-2016), Chair of the ISSCR Finance Committee (2013-2016), of the ISSCR Publications Committee (2009-2012), and of the 2011 Annual Meeting Program Committee (2010-2011).  He also served on other ISSCR committees, the NIH study sections (1998-2005, 2007, 2012, 2014), the NIH Director’s Pioneer Award Selection Committee (2009), the External Advisory Board of the Progenitor Cell Biology Consortium, NHLBI, NIH (2010-2012), the Board of Directors of the Society of Chinese Biological Investigators (2002-2008), the Council of the Society of Chinese Bioscientists in America (2008-2011), the Council of Connecticut Academy of Science and Engineering (2013-2016), the Advisory Council of RIKEN Center for Developmental Biology, Japan (2007-2015), the Scientific Advisory Board of the Jane Coffin Childs Memorial Fund for Medical Research (2011-2015), National Key Stem Cell Research Advisory Committee, Chinese Ministry of Science and Technology (2011-2014), and the Council of Shantou University (2010-2015).  He was a co-founder and Core Member of the Connecticut State Government Life Sciences Advisory Group (2011-2012).

Currently, he serves on the Board of Directors of the ISSCR (2009-), the Medical Advisory Board of New York Stem Cell Foundation (2009-), the NIH CMIR Study section (2019-), and is a Visiting Chair Professor of Tsinghua University (2002-).

Dr. Lin has served on Editorial Boards of Stem Cells (2005-2008), Biology of Reproduction (2009-2010), Journal of Cell Biology (2009-2014), Current Opinion in Cell Biology (2009-2014), Cell Research (2010-), Cell Stem Cells (2007-), StemBook (2007-), Stem Cell Reports (2013-), National Science Review (2013-), and Science China (2013-).  He was a Featured Editor of Nature Reports Stem Cells (2009), and led the establishment of the ISSCR journal Stem Cell Reports (2010-2012).

 Dr. Lin received many awards and honors, including the Jane Coffin Childs Fellowship for Medical Research (1990), American Cancer Society Junior Faculty Research Award (1996), the March of Dimes Basil O'Connor Scholar Research Award (1996), the David and Lucile Packard Fellowship for Science and Engineering (1996), the G. Harold and Leila Y. Mathers Award (2007, 2011, 2015), the American Society of Andrology Lecturer Award (2008), the Laura Hartenbaum Breast Cancer Foundation’s Legacy for Hope Award (2009), the Ellison Medical Foundation Senior Scholar Award (2010), the NIH Director’s Pioneer Award (2010), the NIH MERIT Award (2012), the Ray Wu Award (the highest honor by the Chinese Biological Investigators Society; 2013), and the Society for the Study of Reproduction Research Award (2015). He is a Member of US National Academy of Sciences (2018-), a Member of American academy of Arts and Sciences (2018-), and an Fellow of the American Association for the Advancement of Science (2010-).

Dr. Ma received his Ph.D. degree in statistics at University of Wisconsin in 2004. Prior to arriving at Yale, Dr. Ma was a Senior Fellow in Collaborative Health Studies Coordinating Center (CHSCC) and Department of Biostatistics at University of Washington. He has been involved in developing novel statistical and bioinformatics methodologies for analysis of cancer (NHL, breast cancer, melanoma, lung cancer), mental disorders, and cardiovascular diseases. He has also been involved in health economics research, with special interest in health insurance in developing countries.

Robert A. McDougal, Ph.D. is an Assistant Professor in the Health Informatics Division of the Department of Biostatistics. He is affiliated with the Computational Biology and Bioinformatics graduate program, the Yale Center for Medical Informatics, and the Center for Biomedical Data Science. His research focuses on developing methods for aggregating, computationally representing, analyzing, and modeling experimental data, with emphasis on understanding brain function and dysfunction.

Dr. McDougal is currently a PI on two NIH grants: one which develops techniques to mine, visualize, and disseminate neuroscience information, and one that seeks to build efficient methods for simulating the interaction of intracellular and network dynamics in the brain. Recent collaborations include a project to detect trends in the use of animal models and interventions in the Alzheimer's literature, and a project to use computational modeling to interpret magnetoencephalography (MEG) data. As an elected member of the NeuroML Editorial Board, he helps design future standards for sharing computational neuroscience models.

Dr. McDougal earned his Ph.D. in Mathematics from The Ohio State University in 2011. He did postdoctoral training at Yale in computer science, neurobiology, and medical informatics; during the later, he earned an MS in Computational Biology and Bioinformatics from Yale. From 2016 until joining the Department of Biostatistics in 2019, he was an Associate Research Scientist at Yale University in the Department of Neuroscience.

Dr. Miller-Jensen is working on systems-scale approaches to studying virus infection, latency, and gene expression with a focus on HIV, an important human carcinogen in conjunction with other agents. Cancer is now a leading cause of death in HIV infected individuals. Other areas of interest are attempts to better understand replication and evolution of VSV, a potential oncolytic agent, and development of methods to examine the secretory profile of single cells.

Dr. Noonan received his undergraduate degree in Biology and English Literature (Honors) from Binghamton University in upstate New York. He carried out his graduate work with Dr. Richard Myers in the Department of Genetics, Stanford University, and received his Ph.D. in 2004. He did his postdoctoral work in Dr. Edward Rubin's lab at the Lawrence Berkeley National Laboratory and the U.S. Department of Energy Joint Genome Institute. Dr. Noonan joined the Yale Genetics faculty in September 2007.

Prof. O'Hern is a Professor of Mechanical Engineering & Materials Science and Physics, co-founder of the Integrated Graduate Program in Physical and Engineering Biology, and Director of Undergraduate Programs for the Raymond and Beverly Sackler Institute for Biological, Physical, and Engineering Sciences. His research employs theoretical and computational methods (e.g. all-atom and coarse-grained molecular dynamics simulations) to tackle a broad range of fundamental questions in soft matter and biological physics. Current projects include the dynamics of protein folding, unfolding, and
aggregation, the binding and self-assembly of proteins, and the structural
and mechanical properties of cells and tissues in the context of collective cell motion and wound healing.

Dr Pusztai is Professor of Medicine at Yale University and Director of Breast Cancer Translational Research and Co-Director of the Cancer Center Genomics, Genetics, and Epigenetics Program. Dr. Pusztai is also Chair of the Breast Cancer Research Committee of the South West Oncology Group (SWOG). He received his medical degree from the Semmelweis University of Medicine in Budapest, and his D.Phil. degree from the University of Oxford in England. His research group has made important contributions to establish that estrogen receptor-positive and-negative breast cancers have fundamentally different molecular, clinical and epidemiological characteristics. He has been a pioneer in evaluating gene expression profiling as a diagnostic technology to predict chemotherapy and endocrine therapy sensitivity and have shown that different biological processes are involved in determining the prognosis and treatment response in different breast cancer subtypes. His group has also developed new bioinformatics tools to integrate information from across different data platforms in order to define the molecular pathways that are disturbed in individual cancers and could provide the bases for individualized treatment strategies. He made important contributions to clarify the clinical value of preoperative (neoadjuvant) chemotherapy in different breast cancer subtypes. Dr Pusztai is also principal investigator of several clinical trials investigating new drugs, including immunotherapies for breast cancer. He has published over 250 scientific manuscripts in high impact medical journals including the NEJM, JAMA, Journal of Clinical Oncology, Nature Biotechnology, PNAS, Lancet Oncology and JNCI. He is among the top 1% most highly cited clinical investigators in medicine over the past 10 years according to a 2015 Thomson Reuters report. He is Associate Editor of the Journal of National Cancer Institute (JNCI), member of the Scientific Advisory Board of the Breast Cancer Research Foundation, former member of the NCI North American Breast Cancer Steering Committee and Co-Chair of the Trans-ALTTO Committee and Chair of the Data Safety Monitoring Committee of the OPTIMA trial in the United Kingdom.

Anna Marie Pyle is the William Edward Gilbert Professor of Molecular, Cellular and Developmental Biology and Professor of Chemistry at Yale University.She has been a Howard Hughes Medical Institute Investigator since 1997.Dr. Pyle obtained her undergraduate degree in Chemistry from Princeton University and received her Ph.D. in Chemistry from Columbia University in 1990, where she worked with Professor Jacqueline K. Barton. Dr. Pyle was a postdoctoral fellow in the laboratory of Thomas Cech at the University of Colorado. Dr. Pyle formed her own research group in 1992 in the Department of Biochemistry and Molecular Biophysics at Columbia University Medical Center.In 2002, she moved to Yale University, where she leads a research group that specializes in structure and function of large RNA molecules and RNA remodeling enzymes.Dr. Pyle teaches the undergraduate Molecular Biology course at Yale and she is Chair of the Building Committee for the new Yale Biology Building.Dr. Pyle is the Chair of the MSFA Study Section at the NIH, and previously served as a permanent member on the MSFE, and MGB Study Sections.At Brookhaven National labs, she serves on the Science and Technology Steering Committee and on Beamline Advisory Teams at the NSLSII light source.Dr. Pyle is the Co-Editor of Methods in Enzymology and serves on the Editorial Board of the Journal of Molecular Biology.Dr. Pyle is the author of over 160 publications and has mentored more than 40 graduate students and postdocs.The Pyle laboratory uses a diverse set of biochemical techniques, including crystallography and enzymology, to understand the structural complexity of large RNA molecules. She pioneered the study of RNA helicase enzymes and other RNA-stimulated ATPases that serve as translocases, RNA remodeling enzymes and signaling enzymes in the cell.Her experimental work is complemented by efforts to develop new computational tools for modeling, analyzing and predicting RNA structure.

Gordon M. Shepherd grew up in Iowa, and received his B.S. at Iowa State College in 1955, M.D. at Harvard in 1959, and D.Phil. at Oxford in 1962. After postdoctoral training at NIH, MIT and the Karolinska Institute he joined the faculty at Yale Medical School, where he is Professor of Neuroscience. He introduced the olfactory system as a model for analyzing the properties of neurons and synapses in the brain and the formation of neural images of olfactory molecules. His research has contributed to properties of neuronal dendrites and spines, olfactory processing, and development of the new fields of computational neuroscience, brain microcircuits, neuroinformatics, and neurogastronomy. He has trained over 70 graduate students, postdoctoral fellows and visiting scientists, and published over 280 articles and reviews, with continuous grant support since 1966. His books include The Synaptic Organization of the Brain (5 ed.), Neurobiology (3 ed.), Handbook of Brain Microcircuits, and Neurogastronomy; in the history of neuroscience are Foundations of the Neuron Doctrine, Creating Modern Neuroscience, and Mosso's Circulation of Blood in the Human Brain. He has been chief editor of the Journal of Neurophysiology and Journal of Neuroscience. Visiting positions have included the University of Pennsylvania, College de France, Simon Fraser University, Santa Fe Institute, Ecole Normale Superieure, Institute Pasteur, and Oxford University. He served as a Deputy Provost of Yale University, received honorary degrees from the Universities of Copenhagen and Pavia, and is a member of the American Academy of Arts and Sciences and past president of the Association for Chemoreception Sciences and the Cajal Club.

Dr. Stern earned a BS in Biology at MIT in 1976. He received a PhD in Biology in 1983 at University of California, San Diego, and the Salk Institute with S.I.T. Kennedy and Bart Sefton for dissertation research that elucidated the coronavirus lytic cycle. Dr. Stern returned to R.A. Weinberg’s lab at the MIT Cancer Center and Whitehead Institute for Biomedical Research in 1983. There, Dr. Stern’s postdoctoral work pioneered analysis of neu/ErbB2/HER2, an important human oncogene. As a Yale Pathology faculty member since 1988, Dr. Stern’s research has focused on the roles of eleven growth factors and four receptors of the EGF family in malignant transformation, especially in breast cancer, and he has also made significant contributions to the understanding of DNA damage response signaling pathways. Dr. Stern’s current work in breast cancer and melanoma includes developing approaches to countering rapid resistance to anti-cancer agents that target cancer signaling pathways. Dr. Stern is active in cancer training at Yale and in the Yale Cancer Center scientific leadership. He is co-leader of the Signal Transduction Research Program and Associate Director of Shared Resources of the Yale Cancer Center.

Professor Townsend received his Ph.D. in 2002 in organismic and evolutionary biology from Harvard University, under the advisement of Daniel Hartl. His Ph.D. was entitled "Population genetic variation in genome-wide gene expression: modeling, measurement, and analysis", and constituted the first population genetic analysis of genome-wide gene expression variation. After making use of the model budding yeast S. cerevisiae for his Ph.D. research, Dr. Townsend accepted an appointment as a Miller Fellow at the University of California-Berkeley in the Department of Plant and Microbial Biology, where he worked to develop molecular tools, techniques, and analysis methodologies for functional genomics studies with the filamentous fungal model species Neurospora crassa, co-advised by Berkeley fungal evolutionary biologist John Taylor and molecular mycologist Louise Glass. In 2004, he accepted his first appointment as an Assistant Professor in the Department of Molecular and Cell Biology at the University of Connecticut. In 2006 he was appointed as an Assistant Professor the Department of Ecology and Evolutionary Biology at Yale University. In 2013 he began to work on statistical approaches to fit mathematical models of disease spread and emergence, and to work on the somatic evolution of cancer, and was appointed as an Associate Professor of Biostatistics and Ecology & Evolutionary Biology, in 2017 he was named Elihu Associate Professor of Biostatistics and Ecology & Evolutionary Biology, and in 2018 he was appointed Elihu Professor of Biostatistics and Ecology & Evolutionary Biology.

Günter P. Wagner is an evolutionary geneticist with training in biochemcial engineering, zoology and mathematics from the University of Vienna, Austria. He spent six postdoctoral years at the Max Planck Institutes for Biophysical Chemistry (Goettingen, Germany) and for Developmental Biology (Tübingen, Germany). His academic career started at the University of Vienna and in 1991 he received a call to assume a full professorship at the Biology Department at Yale. From 1996 to 2001 he was Chair of the Department of Ecology and Evolutionary Biology at Yale, and in 2010 his lab moved to the Systems Biology Institute at Yale's West Campus.

Dr. Wagner's research interest is the evolution of gene regulation as it pertains to the origin of evolutionary novelties. In particular the lab is focusing on the evolution of the endometrial stromal cells in the context of the evolutionary origin of pregnancy. Another focus of my lab is the developmental basis of character identity, as for instance in the case of digit identity of birds.

In 1992 Dr. Wagner received the MacArthur Fellowship for my research on the developmental basis of homology and in 1997 he was elected both to become corresponding member of the Austrian Academy of Sciences, and Fellow of the American Association for the Advancement of Science. In 2010 Dr, Wagner was elected to the American Academy of Arts and Sciences.

Dr. Wang is Associate professor of Biostatistics at Yale School of Public Health. Her research focuses on combining genetics, genomics, immunology, and statistical modeling to answer biologically important questions in genetic epidemiological studies and cancer research. Dr. Wang's statistical expertise lies in kernel machine methods, mixed effects models, correlated data, and longitudinal data analysis. She develops statistically innovative methods and computationally efficient tools in large-scale genetic and genomic studies to identify genetic susceptibility variants and advance the understanding of the etiology of complex diseases including alcohol and drug abuse, asthma, obesity, cardiovascular diseases, and cancer. Current studies include using next-generation sequencing data to detect rare genetic variants in longitudinal genetic studies, combining knowledge in genomics and immunology to understand the risk of breast cancer survival, and differential gene expression in single-cell RNA sequencing data.

Dr. Zhang published over 300 research articles and monographs in theory and applications of statistical methods and in several areas of biomedical research including epidemiology, genetics, child and women health, mental health, substance use, and reproductive medicine. He directed a training program in mental health research that was funded by the NIMH. He directs the Collaborative Center for Statistics in Science that coordinates the Reproductive Medicine Network to evaluate treatment effectiveness for infertility. He is a fellow of the American Statistical Association and a fellow of the Institute of Mathematical Statistics. He was named the 2008 Myrto Lefokopoulou distinguished lecturer by Harvard School of Public Health and a Medallion Lecturer by the Institute of Mathematical Statistics. In 2011, he received the Royan International Award on Reproductive Health. Dr. Zhang serves as an Editor of the Journal of the American Statistical Association and the president of the International Chinese Statistical Association.

Dr. Hongyu Zhao is the Ira V. Hiscock Professor of Biostatistics and Professor of Statistics and Data Science and Genetics, Chair of the Biostatistics Department and the Co-Director of Graduate Studies of the Inter-Departmental Program in Computational Biology and Bioinformatics at Yale University. He received his B.S. in Probability and Statistics from Peking University in 1990 and Ph.D. in Statistics from the University of California at Berkeley in 1995. His research interests are the applications of statistical methods in molecular biology, genetics, drug developments, and precision medicine.

Some of his recent projects include large scale genome wide studies to identify genetic variants underlying complex diseases, genetic risk prediction, biological network modeling and analysis, disease biomarker identification, genome annotation, cancer genomics, microbiome analysis, single cell analysis, image analysis, and systems biology study of herbal medicine. He has published over 480 articles in statistics, human genetics, bioinformatics, and proteomics, and edited two books on human genetics analysis and statistical genomics. He has trained over 70 doctoral and post-doctoral students, many of whom are holding tenured or tenure-track positions at major universities in the states and overseas.

Dr. Zhao is a Co-Editor of the Journal of the American Statistical Association Theory and Methods, and serves on the editorial boards of several leading statistical and genetics journals. He was the recipient of the Mortimer Spiegelman Award for a top statistician in health statistics under the age of 40 awarded by the American Public Health Association and the Pao-Lu Hsu Award from the International Chinese Statistical Association. His research has also been recognized by the Evelyn Fix Memorial Medal and Citation by UC Berkeley, a Basil O'Connor Starter Scholar Award by the March of Dimes Foundation, election to the fellowship of the American Association for the Advancement of Science, the American Statistical Association, and the Institute of Mathematical Statistics.