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Computational Biology and Bioinformatics (CBB) Track

CBB Track Leadership

  • Cynthia Brandt

    Co-Director of Graduate Admissions, CBB Track

    Professor of Emergency Medicine and of Anesthesiology

    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.

  • Mark Gerstein

    Co-Director of Graduate Studies, CBB Track

    Albert L Williams Professor of Biomedical Informatics and Professor of Molecular Biophysics & Biochemistry, of Computer Science, and of Statistics & Data Science

    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. 

  • Corey O'Hern

    Co-Director of Graduate Admissions, CBB Track

    Professor; Assoc Prof Dept of Mechanical Engineering & Materials Science and Physics; Associate Professor

    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.

  • Hongyu Zhao

    Co-Director of Graduate Studies, CBB Track

    Department Chair and Ira V. Hiscock Professor of Biostatistics, Professor of Genetics and Professor of Statistics and Data Science

    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 genetics, molecular biology, 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, and image analysis. He has published over 510 articles in statistics, human genetics, bioinformatics, and proteomics, and edited two books on human genetics analysis and statistical genomics. He has trained over 80 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.

Registrar

Faculty

  • Julien Berro

    Associate Professor of Molecular Biophysics and Biochemistry, and of Cell Biology

    Research Interests
    • Biophysics
    • Cell Biology
    • Cytoskeleton
    • Endocytosis
    • Kinetics
    • Microscopy
    • Microscopy, Fluorescence
    • Models, Theoretical
    • Schizosaccharomyces
    • Nonlinear Dynamics
    • Microscopy, Confocal
    • Mechanics
    • Systems Biology
    • Mathematical Concepts
    • Machine Learning
    • Single Molecule Imaging

    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

    Professor of Dermatology, Pathology, and Immunobiology; Co-Leader, Genetics, Genomics and Epigenetics, Yale Cancer Center; Interim Director, Yale Center for Immuno-Oncology; Director, Yale SPORE in Skin Cancer

    Research Interests
    • Cell Biology
    • Dermatology
    • Melanoma
    • Neoplasm Metastasis
    • Pathology

    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, 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.

  • Cynthia Brandt

    Co-Director of Graduate Admissions, CBB Track

    Professor of Emergency Medicine and of Anesthesiology

    Research Interests
    • Health Services
    • Medical Informatics
    • Medical Informatics Applications
    • Preventive Medicine
    • Public Health
    • Public Health Informatics
    • Informatics

    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

    Professor of Emergency Medicine

    Research Interests
    • Anesthesiology
    • Emergency Medicine
    • Medical Informatics
    • Technology
    • Databases, Genetic

    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.

  • Phillips Professor of Mathematics

    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

    Associate Professor of Neurology; Associate Professor of Genetics

    Research Interests
    • Arthritis, Rheumatoid
    • Autoimmune Diseases
    • Diabetes Mellitus, Type 1
    • Genetics
    • Genetics, Medical
    • Genetics, Population
    • Graves Disease
    • Immune System Diseases
    • Lupus Erythematosus, Systemic
    • Multiple Sclerosis
    • Thyroiditis, Autoimmune
    • Inflammatory Bowel Diseases
    • Human Genome Project
    • Computational Biology
    • Autoimmune Diseases of the Nervous System
    • Demyelinating Autoimmune Diseases, CNS
    • Genomics
    • Genetic Research
    • Systems Biology

    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 W. Crawford

    Associate Professor of Biostatistics, Associate Professor of Ecology and Evolutionary Biology, Associate Professor of Management, and Associate Professor of Statistics and Data Science

    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.

  • Professor of Molecular, Cellular, and Developmental Biology

    Research Interests
    • Plants

    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.

  • Richard Flavell

    Sterling Professor of Immunobiology; Investigator, Howard Hughes Medical Institute

    Research Interests
    • Biology
    • Diabetes Mellitus
    • DNA, Recombinant
    • Immune System
    • Immunity
    • Lyme Disease
    • Autoimmunity
    • Gene Expression
    • Gene Transfer Techniques
    • Mice, Knockout
    • Cell Lineage
    • Lyme Neuroborreliosis

    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 National Academy 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.

  • Joel Gelernter

    Foundations Fund Professor of Psychiatry and Professor of Genetics and of Neuroscience; Director, Division of Human Genetics (Psychiatry)

    Research Interests
    • Affective Disorders, Psychotic
    • Alcoholism
    • Anxiety Disorders
    • China
    • Genetics
    • Genetics, Population
    • Israel
    • Polymorphism, Genetic
    • Psychiatry
    • Stress Disorders, Post-Traumatic
    • Thailand
    • Global Health
    • Substance-Related Disorders
  • Mark Gerstein

    Co-Director of Graduate Studies, CBB Track

    Albert L Williams Professor of Biomedical Informatics and Professor of Molecular Biophysics & Biochemistry, of Computer Science, and of Statistics & Data Science

    Research Interests
    • Biochemistry
    • Biophysics
    • DNA
    • Medical Informatics
    • Computational Biology
    • Genomics
    • Proteomics

    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 Giraldez

    Fergus F. Wallace Professor of Genetics; Chair, Genetics

    Research Interests
    • Developmental Biology
    • Gene Expression Regulation, Developmental
    • Computational Biology
    • Genomics
    • Systems Biology
    • Autism Spectrum Disorder
    • RNA Recognition Motif

    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- ).

  • Jeffrey R Gruen

    Professor of Pediatrics (Neonatology) and of Genetics; Faculty, Investigative Medicine Program, Yale Graduate School of Arts and Sciences

    Research Interests
    • Dyslexia
    • Genetics
    • Language
    • Language Development Disorders
    • Learning Disorders
    • Investigative Techniques
    • Neonatology
    • Pediatrics

    Dr. Gruen received his BS and his MD degrees from Tulane University in New Orleans. He has been at Yale since beginning internship training in pediatrics in 1981, which was followed by subspecialty training in neonatology and research training in molecular genetics with Dr. Sherman Weissman. Dr. Gruen formally joined the faculty at Yale in 1988, splitting his time as a neonatology attending in the Newborn Intensive Care Unit (NICU) at Yale-New Haven Hospital and his lab where he initially mapped the gene for hemochromatosis. By 2000, the focus of his lab turned to mapping and identifying the reading disability (dyslexia) gene locus on chromosome 6 (DYX2). His lab was the first to generate high-resolution genetic markers, genetic association maps, and gene expression maps of DYX2. These studies led to the identification of DCDC2, a dyslexia gene that was cited by the journal Science as the 5th top breakthrough of 2005. The lab performed an NIH funded clinical study of DCDC2 and other genes related to reading and language in the ALSPAC birth cohort of 10,000 children and mothers. These studies identified the transcriptional control element called READ1, and READ1 alleles that are detrimental and protective for reading disability and language impairment. Dr. Gruen is the principal investigator for the Yale Genes, Reading and Dyslexia (GRaD) Study, a ground-breaking case-control study of dyslexia in 1,400 Hispanic American and African American children recruited from seven sites across North America. He was the Yale site PI for the NIH Pediatric Imaging NeuroGenetics (PING) Data Resource Study of 1,575 normal children, ages 3-20 years. Most recently, Dr. Gruen started the New Haven Lexinome Project, a new six-year longitudinal study of the genetics of response-to-intervention spanning the entire 2015 and 2016 New Haven Public Schools first grade classes. The goals of the New Haven Lexinome Project are to determine risk for learning disabilities conferred by specific genetic variants for presymptomatic diagnosis, and to determine how genetic variants inform intervention for precision/personal education. In addition to his research, Dr. Gruen continues to attend 8 weeks each year in the NICU at the Children’s Hospital at Yale-New Haven.

  • Murat Gunel

    Nixdorff-German Professor of Neurosurgery and Professor of Genetics and of Neuroscience; Chair, Department of Neurosurgery; Chief, Neurosurgery, Yale New Haven Health System; Chair, Perioperative Executive Leadership Committee; Director, Residency Program; Member, National Academy of Medicine; Co-Director, Yale Program on Neurogenetics

    Research Interests
    • Aneurysm
    • Brain
    • Genetics
    • Molecular Biology
    • Neurobiology
    • Neurosurgery
    • Hemangioma, Cavernous, Central Nervous System

    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 P. Jadi

    Assistant Professor of Psychiatry and of Neuroscience

    Research Interests
    • Autistic Disorder
    • Cerebral Cortex
    • Dendrites
    • Electrophysiology
    • Interneurons
    • Neurobiology
    • Neurosciences
    • Schizophrenia
    • Models, Statistical
    • Computational Biology

    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

  • Amy Justice

    C.N.H. Long Professor of Medicine (General Medicine) and Professor of Public Health (Health Policy); Co-Leader, Cancer Microbiology

    Research Interests
    • Aging
    • Chronic Disease
    • Health Policy
    • Internal Medicine
    • Medical Oncology
    • Veterans
    • HIV Infections

    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.  

  • Naftali Kaminski

    Boehringer Ingelheim Pharmaceuticals, Inc. Professor of Medicine (Pulmonary); Section Chief, Pulmonary, Critical Care & Sleep Medicine

    Research Interests
    • Emphysema
    • Fibrosis
    • Genetics, Medical
    • Lung Diseases
    • RNA
    • Gene Expression
    • Genomics
    • MicroRNAs
    • Metalloproteases
    • Biomarkers, Pharmacological

    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 scientific achievements are: The discovery of novel molecules  with significant active roles in pulmonary fibrosis, including matrix metalloproteases (MMP7, MMP19) and phosphatases (SHP2, MKP5) , demonstrating that microRNAs, a family of small non-coding RNAs, are differentially expressed in IPF, and that some of them (let-7, mir-29, mir-33) 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, and performed single cell RNA sequencing on >300,000 cells obtained from patients with advanced lung disease and created an online freely available data dissemination tool (www.IPFCellAtlas.com). 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 systems biology models of lung diseases and to develop precision medicine approaches 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 275 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 recently the Deputy Editor of Thorax, BMJ. Dr. Kaminski served as the President of the Association of Pulmonary, Critical Care and Sleep Division Directors in 2019.

    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.

  • Steven Kleinstein

    Professor

    Research Interests
    • Autoimmune Diseases
    • Computing Methodologies
    • Immune System Diseases
    • Influenza Vaccines
    • Information Science
    • Lyme Disease
    • Pattern Recognition, Automated
    • Virus Diseases
    • West Nile virus
    • Computational Biology
    • Autoimmune Diseases of the Nervous System
    • Immune System Phenomena
    • Mathematical Concepts
    • Patient-Specific Modeling

    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 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 signatures of human infection and vaccination responses


  • Yuval Kluger

    Professor of Pathology

    Research Interests
    • Breast Neoplasms
    • Information Science
    • Pattern Recognition, Automated
    • Genetic Variation
    • Nevi and Melanomas
    • Genetic Structures
    • Mathematical Concepts
  • Smita Krishnaswamy

    Assistant Professor of Genetics and of Computer Science

    Research Interests
    • Genetics
    • Computational Biology
    • Single-Cell Analysis

    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.