Members

Dr. Hall's research career spans the fields of genetics, genomics, bioinformatics and data science. He received a B.A. in Integrative Biology from the University of California at Berkeley (1998), and worked as a technician for 2 years in Sarah Hake's plant genetics group at the USDA/ARS Plant Gene Expression Center. He received his Ph.D. in genetics from Cold Spring Harbor Laboratory (2003), where his work in Shiv Grewal's laboratory established the first direct link between RNA interference and chromatin-based epigenetic inheritance. As a postdoc with Michael Wigler (2004) and independent Cold Spring Harbor Laboratory Fellow (2004-2007), Dr. Hall used microarray technologies and mouse strain genealogies to conduct the first systematic study of DNA copy number variation hotspots. As a faculty member at the University of Virginia (2007-2014), Washington University (2014-2020) and Yale (2020-present), his work has sought to understand the causes and consequences of genome variation in mammals, with an increasing focus on computational methods development and human genetics. His group has developed bioinformatics tools for variant detection, variant interpretation, sequence alignment, data processing, and data integration. He has led genome-wide studies of human genome variation, heritable gene expression variation, human genetic disorders, tumor evolution, mouse strain variation, genome stability in reprogrammed stem cells, and single-neuron somatic mosaicism in the human brain. Dr. Hall's work has been featured in Science Magazine's Breakthrough of the Year (2003 & 2007), the NIMH Director's "Ten Best of 2013" and The Scientist (2013), and he has received several prestigious awards including the AAAS Newcomb Cleveland Prize (2003), the Burroughs Wellcome Fund Career Award (2006), the NIH Director's New Innovator Award (2009), and the March of Dimes Basil O'Connor Research Award (2010). He has also served as an Associate Editor at Genome Research (2009-2014) and Genes, Genomes and Genetics (2011-2018).Most recently, Dr. Hall has played a leadership role in several large collaborative projects funded by NIH/NHGRI including the Centers for Common Disease Genomics, the AnVIL cloud-based data repository and analysis platform, and the Human Pangenome Project. His current work is focused on two broad goals: (1) mapping variants and genes that confer risk to human disease, with ongoing projects focused on coronary artery disease and cardiometabolic traits in unique and underrepresented populations, and (2) developing methods for the detection and interpretation of human genome variation, with an emphasis on structural variation and other difficult-to-detect forms, and on comprehensive trait association in human disease studies.

Allen Bale, MD, is a clinical geneticist who has spent nearly three decades investigating cancer predisposition syndromes, which occur when a person inherits one or more genes that predispose him or her to cancer. For example, one of the better-known genes that can be inherited with a mutation is the BRCA1 gene. A mutation in this gene increases the risk that a person will develop breast cancer. Dr. Bale also oversees clinical genome sequencing at the Yale Center for Genome Analysis. His research replies on the latest “DNA sequencing technology for the discovery of new human disease genes,” Dr. Bale says. He has collaborated on many research projects, including with the Hospital General de Mexico on hereditary breast and ovarian cancer. Dr. Bale is a professor of genetics at Yale School of Medicine.

Dr. Besse received her bachelors degree in Biomedical Engineering from Brown University in 2003, pre-doctoral training in genetics at the Joslin Diabetes Center at the Harvard Medical School, her M.D. from the University of Connecticut School of Medicine in 2009, and clinical training in Internal Medicine/Nephrology at Yale. Dr. Besse joined Yale School of Medicine faculty in the Department of Internal Medicine, Section of Nephrology in 2019. Her research training in Nephrology has been under the mentorship of Dr. Stefan Somlo, C.N.H Long Professor of Medicine (Nephrology) and Professor of Genetics. Dr. Besse's field of research interest is genetic kidney diseases, with initial focus on polycystic kidney disease. She uses genetic approaches to identify novel disease genes for dominantly inherited polycystic kidney and liver diseases: a phenotypic spectrum from autosomal dominant polycystic kidney disease (ADPKD) to isolated polycystic liver disease (PCLD), and both in vitro and animal models to further disease gene mechanism investigation. Her identification and investigation of multiple genes has contributed understanding to how the central PKD protein, Polycystin-1, matures through the endoplasmic reticulum. She has contributed approaches for gene validation to the field. Dr. Besse has an active research program recruiting patients with genetically unresolved polycystic kidney and/or liver disease or other inherited kidney diseases for projects involving gene/pathway discovery and variant analysis in genetic kidney diseases. The goal of her lab is to have the identification of novel disease genes serve as an entry point for molecular biology investigation that contributes to a better understanding of disease mechanism and the identification of successful targets for treatments.

Kristen Brennand, PhD is the Elizabeth Mears and House Jameson Professor of Psychiatry and Professor of Genetics at Yale University School of Medicine. She first established her independent laboratory in the Pamela Sklar Division of Psychiatric Genomics at the Icahn School of Medicine at Mount Sinai in 2012, after having completed post-doctoral training at the Salk Institute for Biological Studies and PhD studies at Harvard University. Dr. Brennand’s research combines expertise in genomic engineering, neuroscience, and stem cells, to identify the mechanisms that underlie brain disease. Her focus lies in resolving the convergence of, and complex interplay between, the many risk variants linked to disease, towards the goal of facilitating the clinical translation of genetic findings.  Dr. Brennand’s work is funded by the National Institutes of Health, the New York Stem Cell Foundation, the Brain Research Foundation, and the Brain and Behavior Research Foundation.

Martina Brueckner obtained her BS and MD degrees from the University of Virginia, followed by a Pediatric Residency at the University of Pittsburgh and a Pediatric Cardiology Fellowship at Yale University School of Medicine. Her clinical and research focus is genetics of congenital heart disease (CHD). The goal of the lab's work is to determine the genetic cause and developmental mechanisms underlying CHD with a focus on the function of cilia in heart development. Our work aims to bridge research in the basic developmental biology mechanisms underlying development of the embryonic left-right axis with clinical pediatric cardiology and cardiac genetics. The laboratory has been integral in understanding the cellular and molecular mechanism underlying vertebrate LR asymmetry, identifying genes and mechanism by which motile and immotile cilia establish an early asymmetric calcium signal that is essential to normal LR development of the heart. As part of the Pediatric Cardiac Genomics Consortium (PCGC), we are now combining our understanding of the basic biology underlying left-right development with state-of-the-art genomic approaches to a more comprehensive understanding of human CHD. We are focusing on the ability to identify the genetic causes of CHD, and to directly test putative genetic causes of human CHD identified from genomic analysis of patient DNA in animal model systems including mouse and zebrafish, and finally to  link genetic and developmental mechanisms of CHD to improved care of patients with CHD.Dr. Brueckner's clinical focus is on patients with genetic causes of congenital heart disease. It has become increasingly apparent that a large portion of cardiovascular disease in children and adolescents has as its underlying etiology a genetic defect. Dr. Brueckner co-founded one of the first pediatric cardiac genetics clinics at Yale-New Haven Children's Hospital. The clinic provides comprehensive diagnostic evaluation and follow-up care for patients with genetic-cardiovascular disease. Dr. Brueckner has been a staff cardiologist since completing her fellowship at Yale in 1990.

Haoyu Cheng is a tenure-track Assistant Professor at the Department of Biomedical Informatics and Data Science (BIDS) at Yale University. His research is dedicated to creating highly efficient computational methodologies for genomic applications, such as genome assembly, read alignment, variant calling, and string indexing. He has developed a series of de novo genome assembly algorithms (e.g. hifiasm) that have been extensively utilized across a variety of large-scale sequencing projects, including the Human Pangenome Reference Consortium, the Vertebrate Genomes Project, and the Darwin Tree of Life project. Within these projects, he also works closely with collaborators to explore the applications of genome assemblies. Haoyu was a Postdoctoral Scholar working with Dr. Heng Li at Dana-Farber Cancer Institute and Harvard Medical School. He obtained his Ph.D. degree in Computer Science from the University of Science and Technology of China, under the supervision of Dr. Yun Xu. Selected publications 1. Cheng H, Asri M, Lucas J, Koren S, Li H. “Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.” Nat Methods (2024). 2. Cheng H, Jarvis ED, Fedrigo O, Koepfli KP, Urban L, Gemmell NJ, Li H. “Haplotype-resolved assembly of diploid genomes without parental data.” Nat Biotechnol (2022). 3. Cheng H, Concepcion GT, Feng X, Zhang H, Li H. “Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.” Nat Methods (2021). 4. Cheng H, Wu M, Xu Y. “FMtree: a fast locating algorithm of FM-indexes for genomic data.” Bioinformatics (2018).

Keith Choate M.D., Ph.D., is a physician-scientist who employs tools of human genetics to understand fundamental mechanisms of disease. His laboratory studies rare inherited and mosaic skin disorders to identify novel genes responsible for epidermal differentiation and development.  His laboratory has identified the genetic basis of over 12 disorders and has developed new therapeutic approaches informed by genetic findings.  His laboratory is funded by the National Institute of Arthritis and of Musculoskeletal and Skin Diseases, a division of the National Institutes of Health.Dr. Choate mentors undergraduate, graduate, and medical students in his laboratory, teaches at Yale Medical School, and trains resident physicians and fellows.

Elizabeth B. Claus, MD, PhD is Professor and Director of Medical Research in the Yale University School of Public Health as well as Attending Neurosurgeon and Director of Stereotactic Radiosurgery within the Department of Neurosurgery at Brigham and Women’s Hospital in Boston. She is a member of the board of advisors for the Acoustic Neuroma Association (ANA) as well as the Central Brain Tumor Registry of the United States (CBTRUS). Dr. Claus' work is focused in cancer and genetic epidemiology with an emphasis on the development of risk models for breast and brain tumors. She is the overall PI of the Meningioma Consortium, the Meningioma Genome-Wide Association Study, and the Yale Acoustic Neuroma Study as well as a co-investigator of the GLIOGENE (Genes for Glioma) and International Glioma Case/Control (GICC) projects. In addition to her research activities, Dr. Claus is a Board-certified neurosurgeon who completed her residency in neurosurgery at Yale-New Haven Hospital and her fellowship in neurosurgical oncology at Brigham and Women’s Hospital. Her clinical focus is on the treatment of meningioma, glioma, acoustic neuroma and brain metastases.  Claus launched the International Low-Grade Glioma (LGG) Registry in 2016 to discover why some people develop LGG, a slow growing but malignant brain tumor primarily affecting young adults, while others do not. The goal of the registry is also to learn more about the effect of this diagnosis and the associated treatments on daily life including the ability to work, drive, sleep, exercise, or take care of oneself and/or a family member. Recently Dr. Claus and a team of fellow scientists received funds from the National Cancer Institute to investigate the molecular evolution of LGG. The project, OPTimIzing engageMent in discovery of molecular evolution of low grade glioma” or OPTIMUM, will enroll 500 participants diagnosed with LGG and who have had two or more surgeries for their glioma and genotype these tumors to establish a comprehensive genomic characterization of the glioma tumors across time.

Dr. Erson Omay is an Assistant Professor of Neurosurgery and Biomedical Informatics and Data Science. Following the completion of her Ph.D. in Computer Science at Case Western Reserve University, she transitioned to Yale, where she served as a postdoctoral researcher in GunelLab within the Department of Neurosurgery. There, she conducted bioinformatic analyses for brain tumor genomics projects. Since assuming the role of Assistant Professor in 2020 within the same department, Dr. Erson Omay has expanded her research projects to the application of integrative methods for studying multi-level, multi-omic datasets. Her primary focus lies in understanding tumor heterogeneity, investigating rare subtypes, and elucidating the molecular mechanisms of poorly understood central nervous system (CNS) tumors. Dr. Erson Omay plays a key role in the computational analysis arm of the Precision Medicine initiative in the Department of Neurosurgery. Actively engaged in exploring the application of computational methods, her focus is on advancing personalized approaches for primary brain tumors. With a commitment to collaboration, she actively seeks partnerships both within and beyond the medical school, aspiring to apply her computational expertise to enhance the molecular characterization of diverse disease types.

I am a Neurologist with subspecialty training in Neurocritical Care and Stroke, and an Epidemiologist with expertise in Population Genetics and Big Data. While on clinical duties, I treat critically ill patients that have sustained a significant neurological injury due to ischemic stroke, subarachnoid hemorrhage, intraparenchymal hemorrhage, traumatic brain injury, seizures, recent neurosurgery, decompensated neuromuscular diseases, and several others. My research lies at the interphase of clinical neurology, neuroimaging, population genetics and genomic medicine. I am interested in understanding how common and rare genetic variation influences the occurrence, severity, functional outcome and recurrence of stroke, both hemorrhagic and ischemic. Genetic variants influencing these phenotypes can be used for numerous applications, including: (1) identification of novel biological mechanisms involved in causing stroke and determining its severity and outcome, (2) answering non-genetic epidemiological questions using gene mutations as instruments (in the statistical sense of the word), and (3) risk stratification of patients according to their genetic profile. Through the International Stroke Genetics Consortium, I work in close collaboration with numerous investigators interested in stroke genomics from around the world.

Joel Gelernter, MD, is Foundations Fund Professor of Psychiatry and Professor of Genetics and Neurobiology; and Director, Division of Human Genetics (Psychiatry), at the Yale University School of Medicine. The research focus of his laboratory is genetics of psychiatric illness – phenotypes including cocaine, opioid, nicotine, cannabis, and alcohol dependence, posttraumatic stress disorder (PTSD), depression, and panic and other anxiety disorders. He also studies a range of related phenotypes, including pharmacogenomics; and basic issues in population and complex trait genetics. The overall approach involves study of genetic polymorphism and sequence variation, on a molecular level and from the perspective of population genetics. Dr Gelernter’s laboratory published genomewide association studies (GWAS) for cocaine, cannabis, and opioid dependence, PTSD, alcohol dependence, nicotine dependence, and several related traits. All of these studies have resulted in the identification of novel risk loci.

Dr. Gershkovich joined Pathology Department in 2004 shortly after completing the NLM funded fellowship training at Yale Center for Medical Informatics. Since that time, he led the development of novel, cutting-edge software to mesh emerging technologies with existing commercial Laboratory Information System, robotic laboratory instruments, Digital Pathology equipment, and the Hospital EMR.  Dr. Gershkovich is interested in clinical systems engineering, information visualization, DNA sequencing analysis, NLP, and full-text search of clinical data. He is currently focusing on how to better assemble, compile, and deliver relevant information at the point where a clinical decision needs to be made.The underlying philosophy in his software development is pragmatic reasoning which typically leads to the development of working systems that have meaningful impact on clinical care. The systems developed by his engineering group integrate into the daily workflow of the Pathology Department improving quality and efficiency of patient care and clinical operations.  At the onset of COVID epidemics, his group rapidly created and deployed a suite of software modules to support SARS-CoV-2 testing, further demonstrating that implanting software engineering activities in clinical services and translational research is essential for modern patient care.This work is critical for patient safety, the integration and accuracy of new diagnostic techniques, continuous quality improvement, and impactful workflow reengineering in medicine.

After graduating from Harvard with an 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 and in 2003 became co-director of the Yale Computational Biology and Bioinformatics Program. Gerstein has published appreciably in the scientific literature, with an H index of ~185 and >600 publications in total, including a number of them in prominent venues, such as Science, Nature, Cell, and Scientific American. His research is focused on biomedical data science, and he is particularly interested in machine learning, macromolecular 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 was Chair of the Genetics Department (2017-2023).

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. How genes can change language. Short video showing how our genes could account for a substantial amount of the diversity of languages around the world

Caroline is the Scientific Director and Advisor to the Chair of Genetics at Yale School of Medicine. She is also the Director of the Office for Strategic Research Development, responsible for increasing research innovation and discovery through strategic portfolio planning, advisory and collaboration. Caroline leads cross-functional capacity building activities in high growth areas including rare disease research, population/preventative health screening, and IND-enabling R&D for gene- and cell-based therapies. She plays a key role in enabling highly efficient operational processes/systems across basic and clinical research. Caroline was born in Brisbane, Australia and earned her undergraduate degree in Genetics at the University of Queensland, Australia. She earned her PhD in developmental genetics under Prof Melissa Little at the Institute for Molecular Bioscience and her postdoc in molecular reprogramming under Prof Ihor Lemishka at the Mount Sinai School of Medicine, NY. Following her postdoc, Caroline moved to Cambridge, UK, where she took on a new role as Reviews Editor for the journal Development, covering the stem cells and regeneration fields. Caroline was recruited to Yale in 2018 and is a co-Investigator on several large NIH grants in the clinical-translational space. In addition to her scientific training, she has extensive experience in project management, leadership and research administration. She is currently completing her MBA degree at the Yale School of Management, specializing in the healthcare sector.

Dr. Laura Huckins is an Associate Professor in the Department of Psychiatry. She received her masters in BioEngineering from Imperial College London in 2011, and her PhD in Molecular Biology and Psychiatric Genetics from the University of Cambridge in 2015. Her research focuses primarily on studying psychiatric disorders, with an emphasis on eating disorders and PTSD, as well as development and application of multi-omic methods to interpret the functional consequences of GWAS variants. Her lab focuses particularly on Eating Disorders and PTSD; to this end, she is co-chair of the PGC Eating Disorders working group.Dr. Huckins' work is funded by the Klarman Family Foundation, the National Institute of Mental Health, and the National Institute of Environmental Health Sciences.

I am physician scientist active both in basic research and clinical practice. My research interests are to 1) uncover the genetic and epigenetic bases of neurodevelopmental disorders or rare diseases with neurodevelopmental defects; 2) model genetic diseases using human patients derived cellular models and genetic mutant mice; 3) understand the circuit and molecular mechanisms underlying autism spectrum disorder; 4) develop novel molecular and epigenetic targeted therapies for genetic and epigenetic diseases. My clinical expertise is on clinical and biochemical genetics of rare and undiagnosed diseases in children and adult. I am Director of Yale NORD Center of Excellence and Principal Investigator of Yale Diagnostic Center of Excellence for Undiagnosed Diseases-NIH Undiagnosed Disease Network Phase III

We are interested in the molecular mechanisms that cause critical illness in infants and children. We enroll patients with birth defects or other critical illness that cannot be explained by an acquired illness and perform exome sequencing in order to identify candidate genes that may explain the child's disease. Then we model the candidate gene in order to understand its function. In the context of birth defects, we employ the high-throughput human disease model, Xenopus tropicalis in which we can knockout desired genes and examine phenotypes in just three days.Traditionally gene discovery in these patients was very challenging, but now not only is candidate gene discovery efficient but we can rapidly model the human disease and understand gene function in model organisms or patient cells.