Program Directors
Katherine Nathanson, MD
Pearl Basser Professor for BRCA-Related Research at the Abramson Cancer Center of the University of Pennsylvania
Dr. Katherine Nathanson is a Professor of Medicine in the Division of Translational Medicine and Human Genetics. She also serves as the Associate Director of Population Science, Co-Leader of the Cancer Control Program and Chief Oncogenomics Physician in the Abramson Cancer Center. She was dually trained in Internal Medicine and Clinical Genetics, and so has been practicing Genomic Medicine for her entire career. She has a well-funded NIH-funded research program in the inherited and somatic genetics/genomics of cancer. She has been elected to the American Society of Clinical Investigation and American Association of Physicians. Dr. Nathanson has trained over 25 undergraduates, graduate students, medical residents, and post-doctoral fellows. She co-led the Cancer Biology (Cellular and Molecular Biology) introductory course for three years, and has served on multiple preliminary and thesis committees. She directed the Medical Genetics rotation in Adult Genetics, and the Internal Medicine resident rotation in Medical Genetics for over 10 years. She serves on the Residency Committee for Medical Genetics, on the admissions committee for the MD-PhD program and as co-PI for the Medical Genetics Research Training Grant.
Marylyn D. Ritchie, PhD
Director of the Institute for Biomedical Informatics
Marylyn D. Ritchie, PhD is a Professor in the Department of Genetics, Director of the Center for Translational Bioinformatics, Associate Director for Bioinformatics in the Institute for Biomedical Informatics at the University of Pennsylvania School of Medicine. Dr. Ritchie is also Associate Director for the Penn Center for Precision Medicine. Dr. Ritchie is a translational bioinformatics scientist, biomedical informatician, and computational human geneticist with a focus on developing novel approaches for understanding the relationship between our genome and human phenotypes. She has expertise in developing novel bioinformatics tools for complex analysis of big data in genetics, genomics, and clinical databases, in particular in the area of Pharmacogenomics. Some of her methods include Multifactor Dimensionality Reduction (MDR), the Analysis Tool for Heritable and Environmental Network Associations (ATHENA), and the Biosoftware suite for annotating/ filtering variants and genomic regions as well as building models of biological relevance for gene-gene interactions and rare-variant burden/dispersion tests. Dr. Ritchie has over 15 years of experience in the analysis of complex data and has authored over 300 publications. Dr. Ritchie has received several awards and honors including selection as a Genome Technology Rising Young Investigator in 2006, an Alfred P. Sloan Research Fellow in 2010, a KAVLI Frontiers of Science fellow by the National Academy of Science from 2011-2014, and she was named one of the most highly cited researchers in her field by Thomas Reuters in 2014. Dr. Ritchie has extensive experience in all aspects of genetic epidemiology and translational bioinformatics as it relates to human genomics. She also has extensive expertise in dealing with big data and complex analysis including GWAS, next-generation sequencing, data integration of meta-dimensional omics data, Phenome-wide Association Studies (PheWAS), and development of data visualization approaches.
Current Trainees
Kole Buckley, PhD
Postdoctoral Fellow at University of Pennsylvania
Rachel Hurley, MD, PhD
Clinic Fellow, Pediatric Hematology/Oncology, Children's Hospital of Philadelphia
Dana Layo-Carris, PhD
Postdoctoral Fellow at Children’s Hospital of Philadelphia
Dana Mitchell, PhD
Postdoctoral Fellow at Children's Hospital of Philadelphia
Pankhuri Singhal, PhD
Postdoctoral Fellow at University of Pennsylvania
Trainers
Dr. Almasy’s research focuses on development and application of statistical genetic methods for localization and characterization of genetic variants influencing risk of common complex disorders and related quantitative risk factors. Dr. Almasy currently works with undergraduates through the Penn Undergraduate Research Mentoring Program and the CHOP Research Institute Summer Scholars Program, graduate students in the Genomics and Computational Biology Program, and post-docs and junior faculty and serves as a mentor for several NIH-funded K awards.
Dr. Barash’s research is focused on developing machine learning and statistical methods to understand RNA biogenesis, its regulation, and its role in human disease. His lab develops machine learning algorithms that integrate genomic and genetic data, followed by wet lab experimental verifications.
Dr. Bradbury’s research is focused on the clinical implementation of genomic medicine to promote the health of individuals, families, and communities. Her research evaluates novel delivery models to facilitate dissemination and implementation of cancer genetics and multiplex genetic research results, examining the psychosocial and behavioral outcomes, and impact of genetic and familial risk on children, adolescents, and families. These studies have incorporated diverse approaches to delivery of genetic services, such as internet and videoconferencing.
Dr. Brodeur has focused on identification of the genes, proteins, and pathways responsible for malignant transformation of neuroblastoma. His preclinical work led to clinical trials of three novel TRK inhibitors. His current interests include the development of more effective, less toxic therapy, such as long-circulating nanomedicines. He is Director of the Cancer Predisposition Program at CHOP, providing clinical evaluation, diagnosis, and medical management of children at increased cancer risk. He also pursues new gene discovery and novel surveillance approaches.
The goal of Dr. Bucan’s research is to understand the genetic basis of neuropsychiatric disorders, using a combination of experimental and computational approaches. She participates in large-scale genomic studies of autism spectrum and bipolar disorders, which have underscored the importance of using family-based approaches to observe the phenotypic consequences of a full spectrum of alleles at interacting disease susceptibility loci. Currently, her lab is using data from whole genome sequencing in multigeneration families.
Dr. Cappola’s research aims to uncover heart failure mechanisms in human subjects and use these insights to improve treatment, using approaches such as applied genomics, population science, laboratory studies, and clinical trials. He leads a multicenter cohort study of advanced heart failure; co-leads a multicenter consortium for human myocardial transcriptomics and systems genetics; and serves as a PI of the NHLBI Heart Failure Clinical Research Network. Within the Cardiovascular Division, he has established programs integrating science and clinical care, platforms for research and training.
Dr. Carroll’s research focuses on translational approaches to understanding the biology of and developing develop improved diagnostic and prognostic tests, as well as new therapies for acute leukemias. Dr. Carroll has trained nearly 30 trainees most of whom are in academic positions and many of whom are leaders in the field of translational research for acute myeloid leukemia. He is currently chair of four thesis committees. Dr. Carroll’s trainees have been highly successful in obtaining funding during training and moving on to academic positions.
Diagnosis of neurodegenerative diseases is largely clinical, with phenotypic disease-defining features. However, it is highly likely that underlying common diagnoses are heterogeneous disease processes. Understanding the biological signatures associated with well-defined subgroups of disease may reveal new targeted therapeutic approaches. Dr. Chen-Plotkin’s group has worked on establishing biological signatures (protein, gene expression profiles) for genetic subgroups of Parkinson disease, frontotemporal dementia, and amyotrophic lateral sclerosis.
Dr. Christie’s research is focused on translational research studies of the risks, pathogenesis, classification, treatment, and outcomes of lung injury in the transplant and non-transplant populations. He has led efforts to define primary graft dysfunction following lung transplantation and elucidated its clinical and molecular epidemiology. His group has applied large scale genotyping methods to identify genetic variation as significant in association with acute respiratory disease syndrome (ARDS) and led the first genome-wide association study of ARDS in trauma subjects.
Dr. Davidson's research is focused on inherited genetic diseases that cause central nervous system dysfunction, with an emphasis on recessive, childhood onset neurodegenerative disease; dominant genetic diseases; and understanding how noncoding RNAs participate in neural development and neurodegenerative diseases process.
Dr. Day’s research program primarily focuses on hypertrophic cardiomyopathy (HCM), and integrates basic, translational, and clinical science. She has trained and mentored many graduate and medical students, residents, and post-doctoral and medical fellows as well as faculty. Her trainees have been highly successful in securing competitive funding and faculty positions.
Dr. De Raedt’s research focuses on both sporadic pediatric and NF1 associated High Grade Glioma, a devastating disease with a median survival of 12 months. The goal of his research is to develop novel successful therapies for children with brain tumors by dissecting the fundamental processes of tumor biology and by developing relevant mouse models. One major area of interest is elucidating the role of cooperating epigenetic tumor suppressors and the development of combination immunotherapies.
Dr. Domchek’s overall research goal is to better understand the clinical applications of genetic susceptibility to breast cancer, to improve risk assessment, screening, prevention and treatment. She has been
extensively involved in research on the management of cancer risk for carriers of pathogenic variants in high and moderate breast cancer susceptibility genes. She has led large multi-institutional studies of outcomes after prophylactic mastectomy and oophorectomy, and clinical trials of therapeutics in BRCA1/2 mutation carriers, including of PARP inhibitors.
Dr. Elenitoba-Johnson’s research has focused on the identification of mechanisms underlying the deregulation of physiologic signaling of hematopoietic and immune cells in the pathogenesis of immunologic and lymphoproliferative disorders. His group has determined the genetics of hematopoietic cancers such as cutaneous T-cell lymphomas, splenic marginal zone lymphoma and transformed follicular lymphoma. Their current studies strive to identify critical mechanisms, genes and pathways that are subverted in diseases of immune hyperactivity, autoimmune diseases and lymphoma.
Dr. Epstein’s research has focused on the molecular mechanisms of cardiovascular development and implications for understanding and treating human disease. His group has been at the forefront of utilizing animal models of congenital heart disease to determine genetic and molecular pathways required for cardiac morphogenesis, with implications for pediatric and adult cardiovascular disease. Stem cell, angiogenesis and epigenetic studies have had direct implications for the development of new therapeutic agents for heart failure and myocardial infarction.
Dr. Falk’s research goal is to improve clinical care, diagnostic approaches, therapies, and genomic resources for patients with mitochondrial disease, including organizing a global Mitochondrial Disease Sequence Data Resource. Her laboratory group investigates the causes and global metabolic consequences of mitochondrial disease, as well as targeted therapies, in C. elegans, zebrafish, mouse, and human tissue models of genetic-based respiratory chain dysfunction and directs multiple clinical treatment trials in mitochondrial disease patients.
Dr. Goldmuntz’s research group has studied the genetic basis of congenital heart disease and the relationship of genotype to clinical outcomes in this population with the most common, severe type of birth defect. She has mentored many medical students and pediatric cardiology fellows as well as junior faculty to develop their research skills and career paths. Most have pursued an academic career, and many have secured federal funding on mentored grants en route to independent research careers.
Dr. Gonzalez-Alegre’s research crosses basic science, translational, and clinical research with the goal of improving clinical outcomes for patients with dystonia. He studies the neurobiological bases of inherited dystonia, using mouse and cell-based models to better understand disease pathogenesis and to identify new therapeutic targets. His group also is involved in the design and implementation of clinical trials with correlative marker studies, using molecular therapies (such as gene replacement and gene silencing) for inherited brain disorders and Huntington’s disease.
Dr. Hakonarson leads a major commitment from CHOP to genomically characterize over 100,000 children, an initiative that has resulted in the launch of numerous precision medicine programs from novel
discoveries and gained nationwide attention in the Wall Street Journal, New York Times, Time Magazine, Nature and Science. Dr. Hakonarson is a Principal Investigator within the eMERGE, Kids First, and the
TopMed genomics programs. He was the recipient of the inaugural mentoring award by CHOP in 2016 for being a role model mentor of trainees and junior faculty.
Dr. Himes’ research focuses on gaining insights into pathogenesis and treatment of asthma and other pulmonary diseases using biomedical informatics approaches, including via the use Electronic Health Record (EHR) and omics data. She has studied asthma genetics and pharmacogenetics research by participating in genome-wide association studies (GWAS), generating novel omics datasets, and integrating novel and publicly available omics datasets using creative approaches.
Dr. Joffe’s academic work focuses on ethical and policy challenges in biomedical research and on the ethical questions raised by genomic technologies in medicine and science. He has led numerous NIH, PCORI, and foundation-funded studies that have addressed questions such as informed consent and child assent to biomedical research, ethics in clinical trial design, leadership in clinical research, return of individual genomic results to research participants, and the integration of genomic sequencing into cancer care.
Dr. Katona is a physician-scientist who is an expert in gastrointestinal cancer genetics, and his research program focuses on the diagnosis, risk assessment, management, and biology of hereditary gastrointestinal cancer predisposition syndromes. Dr. Katona has been involved in the training of graduate, genetic counseling, and medical students, residents, and post-doctoral and medical fellows, which has led to numerous first-author trainee publications.
Dr. Kim’s primary research focus lies in integrating multi-omics data, biological knowledge, imaging data, and clinical data derived from electronic health records (EHR) to better translate discovery into clinical products. His past projects include developing data integration methods that combine multi-omics data and biological knowledge, predicting clinical outcomes based on those interactions, integrating genomics and imaging data in several phenotypes/diseases, and translational research using EHR-linked biobanks.
Dr. Krantz’s research has focused on projects studying the molecular etiologies of Corneliam de Lange Syndrome, CHOPS syndrome, Pallister-Killian Syndrome, Alagille syndrome, hearing loss, congenital diaphragmatic hernias, and congenital heart defects. His group has identified many new disease genes, novel human disorders, and implicated critical molecular pathways in human developmental disorders.
He has been at the forefront of adapting new genomic technologies clinically and studying how this evolving, complex, and often unclear diagnostic information is understood by clinicians and families.
Dr. Margolis’s research includes the prevention of chronic cutaneous wounds, the treatment of patients with chronic cutaneous wounds, such as diabetic foot ulcers, the treatment of atopic dermatitis, genetic variants of atopic dermatitis, and psoriasis, and the effect of chronic antibiotic exposure in patients with acne. He has mentored 22 trainees in the Master of Science in Clinical Epidemiology (MSCE) program and
has extensive experience mentoring students, fellows, and faculty.
The Maris laboratory focuses on defining the genetic basis of childhood cancers, with a particular focus on neuroblastoma, to define clinically actionable new diagnostics and/or therapeutics. The lab integrates germline genetics, tumor genomics including clonal evolution, and epigenetic regulatory mechanisms in a comprehensive approach to cancers that arise during normal human development. The lab admixes quantitative and qualitative scientists and has a highly translational focus with the integration of genomic biomarker based clinical trials.
Dr. Mathieson studies the genetic and evolutionary basis of human complex traits, focusing on anthropometric, metabolic, and disease-related phenotypes. He is committed to training and mentoring computational researchers, supporting others in using computational tools, and in translating basic genomic science into clinical practice. Dr. Mathieson is a member of the Genomics and Computational Biology and Genetics & Epigenetics graduate groups and teaches an upper undergraduate/intro graduate course in computational biology.
Dr. Maxwell leads a translational human genetics and genomics research laboratory studying mechanisms of tumor formation in inherited cancer syndrome, focusing on the broad range of tumor types affected by DNA repair deficiency, in particular breast and prostate cancers. She uses deep phenotyping including machine learning-based phenotyping algorithms coupled with high-level bioinformatics analysis of existing whole exome sequencing and single nucleotide polymorphism arrays to study genotype-phenotype interactions.
Dr. Minn’s laboratory is focused on understanding how common solid tumors acquire treatment resistance to both conventional therapies and immunotherapies, and how resistance can be overcome utilizing data-driven genomics approaches. Hypothesis generation and testing relies on integrating data obtained from animal models, molecular biology, genome-wide profiling, immune profiling, clinical data mining, and statistical modeling. They have identified multiple regulatory networks and signaling pathways that not only predict but also promote treatment resistance to targeted and immunotherapies.
Dr. Musunuru's research focuses on the genetics of heart disease and seeks to identify genetic factors that protect against disease and use them to develop new therapies. He has trained and mentored
many graduate and medical students, residents, and post-doctoral and medical fellows as well as faculty. His 70 trainees have been highly successful in securing competitive funding and faculty positions.
Dr. Rader’s research employs human genetics for identification of novel pathways involved in metabolic and cardiovascular phenotypes and diseases, and their implications for personalized and translational medicine. His studies focus on genotype-directed deep phenotyping of individuals with Mendelian conditions or rare mutations. He leads a functional genomics laboratory in which his team attempts to discern the biology of pathways identified through human genetics studies with the goal of development of novel therapeutic approaches.
Dr. Ritchie is interested in the relationship between the genome and the phenome. Her research group develops novel computational and statistical methodology and extend state-of-the-art bioinformatics tools to understand the genetic architecture of complex traits. Their primary focus is on the integration of clinical data from electronic health records or clinical trials with genomics data from genome-wide SNP arrays or whole exome/genome sequencing. They also use analytic approaches for building predictive models of disease risk including polygenic risk scores and integrative risk scores.
Dr. Simpkins’s research focus in on identifying novel strategies to overcome drug resistance, such as PARP inhibitor and platinum resistance, in ovarian cancer and translate these findings to the clinic. Her laboratory has developed a preclinical drug development platform (e.g. organoids, patient derived xenografts) characterized by genomics and proteomics. This platform is used to identify biomarkers predicting response to DNA damage response inhibitors and optimize strategies to overcome resistance with the goal of bringing therapeutics with strong preclinical evidence to the clinic in biomarker focused phase I/II clinical trials.
Dr. Susztak’s research is aimed towards the understanding of molecular pathways that govern chronic kidney disease development. She has banked and analyzed (combined genetic, epigenetic, and genomic approaches) a large number of healthy and diseased human kidney tissue samples. Integrative analysis of epigenetic and genetic settings in diseased cells provides a rational basis for modeling the critical biological pathways involved in mediating progressive disease in individual patients. The primary interest of the laboratory is to identify therapeutic targets for chronic kidney disease, with a special emphasis on diabetic kidney disease.
Dr. Tishkoff studies genomic and phenotypic variation in ethnically diverse Africans. Her research combines field work, laboratory research, and computational methods to examine African population history and how genetic variation can affect a wide range of practical issues, such as why humans have differential susceptibility to disease, how they metabolize drugs, and how they adapt through evolution. She has trained and mentored numerous undergraduate and graduate students and post-doctoral fellows that have been highly successful in obtaining faculty positions. She leads the Penn Center for Global Genomics and Health Equity.
The central aim of Dr. Voight’s research is to understand the genetic, biological, and evolutionary basis of metabolic and cardiovascular phenotypes in human populations. He constructs computational and statistical tools grounded in principles of population biology and quantitative genetics, applying them to genetic data collected across thousands of entire human genomes. Dr. Voight is Chair of the Graduate Group in Genomics and Computational Biology.