UCLA Bioinformatics research operates at the interface of computer science, biology, and mathematics to address the fundamental challenges of contemporary genomic-scale research. UCLA offers an Interdepartmental Bioinformatics PhD.

Jason Ernst, PhD, Professor,    Biological Chemistry, Computer Science, and Computational Medicine. His research focuses on developing and applying machine learning methods for the analysis of high-throughput experimental data to address problems in epigenomics and gene regulation. His research is often conducted in close collaboration with experimental groups.

Eleazar Eskin, PhD, Professor, Computer Science, Human Genetics, and Chair, Computational Medicine. His research seeks to discover the relationships between genetic variation and disease in humans using the tools of bioinformatics. His laboratory takes advantage of recently available human variation reference sets such as the HapMap to improve computational approaches for gene mapping. Other projects in Dr. Eskin's work includes developing methods for discovering the genetic basis of complex traits in model organisms, understanding the genetics of gene expression patterns, and predicting the molecular function of variation to better understand the role of variation in disease.

Sriram Sankararaman, PhD, Associate Professor, Computer Science, and Computational Medicine. His interests lie at the interface of computer science, statistics, and biology. He develops novel statistical models and efficient inference algorithms to analyze large-scale genomic data with the aim of understanding evolutionary processes as well as the genetic basis of complex phenotypes.

Ethical and Community Issues

UCLA has taken a leading role in studying the ethical and social issues that must be an integral part of the current revolution in genetics. UCLA is home to the Institute for Society and Genetics, which provides direction for the co-evolution of science and humanities by promoting innovative and socially relevant research and education.

Patrick Allard, PhD, Associate Professor, Institute for Society and Genetics. The research in the Allard lab focuses on combining genomics, genetic, and toxicological approaches to understand the impact of environmental exposures on the germline and how these impacts may have lasting health effects for several generations. To this aim, he is taking advantage of various innovative models and genetic tools detect chemical disruption of the germline chromatin and in particular of evolutionary conserved epigenetic marks such as histone modifications.

Nanibaa' Garrison, PhD, (Diné, Navajo), Associate Professor, Institute for Society and Genetics, Institute for Precision Health, and the Division of General Internal Medicine & Health Services Research. Dr. Garrison is a bioethicist and geneticist engaged in research to explore perspectives of tribal leaders, physicians, scientists, and policy makers on genetic research with tribes. Her research focuses on the ethical, social, and cultural implications of genetic and genomic research in Indigenous communities. Using community-based research approaches, she engages with tribal communities to develop policies and guidance for tribes. She is a core faculty member of the Summer internship for Indigenous Peoples in Genomics (SING).

Christina Palmer, PhD, Professor Psychiatry & Biobehavioral Sciences and Human Genetics. Her research centers on understanding the personal and social impact of genetic information. She has done seminal work on the role of Connexin 26 genetic testing as an adjunct to newborn deafness, and assessing the impact of genetic testing on Deaf adults and the Deaf community, in collaboration with Deaf scientists at Gallaudet University and other institutions. She is founder and Program Director of UCLA’s new Graduate Program in Genetic Counseling.

Genomic Technologies

Laboratories at UCLA are at the forefront of developing many of the technologies crucial to the future of genomics. Students trained in genomic technologies are expected to gain insight into potential applications and to develop novel technologies themselves.

Chongyuan Luo, PhD, Assistant Professor, Human Genetics. Dr. Luo’s laboratory studies how gene regulatory mechanisms contribute to human diseases including neurodevelopmental disorders. They are developing and applying new genomic and genetic technologies to address long-standing questions in human diseases including the causal cell type(s) of diseases and the functions of non-coding genetic variants. They have developed high-throughput single-cell epigenomic and multi-omic technologies, and use these methods to study the gene regulatory diversity in the brain.

Stanley Nelson, MD, Professor, Human Genetics, Pathology & Laboratory Medicine, and Psychiatry. His laboratory uses genomic approaches towards the study of complex human diseases, Mendelian genetic diseases, and Duchenne muscular dystrophy. He directs the Undiagnosed Diseases Network at UCLA which performs discovery of new rare diseases. He also directs the UCLA Clinical Genomics Center performing Clinical Exome Sequencing, and the California Center for Rare Diseases.

Matteo Pellegrini, PhD, Professor, Molecular, Cell & Developmental Biology. His laboratory develops computational tools to interpret genomic data. These tools permit both high and low-level modeling of transcriptional and epigenetic regulation and signal transduction. His systematic approach integrates data produced by the latest generation of high throughput sequencers, tiling and expression arrays, and mass spectrometers. Dr. Pellegrini helps organize and run the UCLA Bruins-In-Genomics (BIG) Summer Undergraduate Research program, an intensive summer research experience for undergraduates in genomics and bioinformatics and an excellent pipeline into our training program.

Yi Yin, PhD, Assistant Professor, Human Genetics. Her laboratory focuses on developing and applying high-throughput single-cell sequencing technologies to study how the repair of DNA breaks causes error-free and mutational genome rearrangements, and to better understand effects from genomic contexts, genetic mutations and tissue-of-origin.

Medical Genetics

The investigators in this area are at the forefront of disease gene mapping and clinical genetics. Their studies run the gamut from major genes in rare Mendelian traits to modifier genes in common complex disorders, and from large pedigrees in genetic isolates to case/control samples from outbred populations. Students working with these mentors will be extremely well-equipped in human genetics and genetic epidemiology.

Valerie Arboleda, MD, PhD, Assistant Professor, Pathology & Laboratory Medicine, and Human Genetics. Her laboratory studies how genetic variation contributes to both rare neurodevelopment disorders and common diseases using functional genomic approaches (RNA-seq, ChIP-seq, methylation-seq) to (1) understand how rare deleterious mutations in chromatin modifiers affect downstream pathways and human development in a cellular model system, (2) identify modifiers of disease severity and (3) prioritize putative drug targets.

Daniel Geschwind, MD, PhD, Professor, Neurology and Human Genetics. His research addresses human neuropsychiatric diseases such as autism and neurodegenerative diseases and their relationship to the full range of normal human higher cognitive function. He uses tools from network analysis and systems biology to connect molecular pathways to nervous system function in health and disease. He is Director of the UCLA Institute for Precision Health.

Elaine Hsiao, PhD, Associate Professor, Integrative Biology & Physiology. Her laboratory studies interactions between the microbiome, brain, and behavior and how such system interactions may influence the etiopathogenesis and manifestations of gastrointestinal and neurological diseases. In particular, they mine the human microbiota for microbial modulators of host neuroactive molecules, investigating the impact of microbiota-immune system interactions on neurodevelopment and examining the microbiome as an interface between gene-environment interactions in neurological diseases.

Su Yon Jung, PhD, Associate Professor, School of Nursing. She is a molecular genetic cancer epidemiologist. Her long-term research interests are within the field of genome–environmental cancer epidemiology, especially by exploring the role of biochemical–behavioral risk factors and their interactions with genetic and epigenetic markers. She has completed numerous studies of racial disparity in cancer biomarkers, GWA/genomic pathway studies, and epigenetic studies, by focusing on innovative statistical genetics analyses.

Beate Ritz, MD, PhD, Professor, Epidemiology and Environmental Health Sciences. Her research focuses on the health effects of occupational and environmental toxins such as pesticides, ionizing radiation, and air pollution on chronic diseases. For the past decade, she has studied the effects of air pollution on adverse birth outcomes as well as asthma in children in southern California. She collaborates with neuroscientists, human geneticists, and clinicians at UCLA.

Jerome Rotter, MD, Professor, Pediatrics and Human Genetics. He is the Director of the Institute for Translational Genomics and Population Sciences. He conducts large-scale genomic studies of common diseases using outbred American populations and has made major contributions to the understanding of juvenile diabetes, inflammatory bowel disease, and atherosclerosis. These studies have been conducted in collaboration with clinical, physiologic, and epidemiologic investigators, often in multi-site studies such as the IRAS (Insulin Resistance and Atherosclerosis) Family Study, the Mexican-American Hypertension – Insulin Resistance Study (PI), the Mexican-American Coronary Artery Disease (MACAD) Study (PI), the CHS (Cardiovascular Health Study), PARC (Pharmacogenetics of Cardiovascular Risk Factor) Study, ADAGES (African Decent and Glaucoma Evaluation Study) (MPI), and the MESA (Multi-Ethnic Study of Atherosclerosis) Family Study.

Mary Sehl, MD, PhD, Associate Clinical Professor, Computational Medicine and Human Genetics. A major focus of her research is in studying DNA methylation patterns associated with aging, and the acceleration of these patterns in disease states, including HIV and cancer. Another focus of her work is in developing mathematical models to study cancer cell population dynamics, and the development of user-friendly stochastic simulation software to accurately and efficiently study in silico models of tumor response to treatment.
Desmond Smith, MD, PhD, Professor, Molecular & Medical Pharmacology. He uses the tools of modern functional genomics to dissect the pathways that connect genotype and phenotype. In particular, he seeks to identify genetic mechanisms underlying complex neurobehavioral traits and their related disorders, such as obesity and addiction. He also develops new tools and technologies for the genetic analysis of mammalian cells. His mission is to study living matter at a genome-wide level and to develop new, highly specific therapeutic strategies for common diseases.

Marc Suchard, MD, PhD, Professor, Human Genetics and Biostatistics. Dr. Suchard is an expert in high-performance statistical computing through massive parallelization, with a focus on inference of stochastic processes in genomics, HIV, evolutionary medicine and the clinical application of statistics. His lab also focusses on the analysis of very large-scale electronic health records (EHRs) for treatment optimization. He has trained 15 MD/PhD and PhD students and four post-docs, five who already hold tenure and four in tenure-track positions.

Model Organisms

Model organisms have been applied very successfully by participating faculty at UCLA in identifying genes contributing to many disorders. Several disease predisposing genes have been cloned, and a unique resource of genome tagged mice is available for mapping new genes and testing their interactions. Because animal models are proving crucial to mapping genes and functional analysis for complex traits, students working with faculty in this area will be well positioned for future careers in either mouse or human genetics.

Paul Barber, PhD, Professor, Ecology & Evolutionary Biology. He integrates genetics, genomics, ecology, and oceanography to understand the evolution of marine biodiversity with the aim of promoting marine conservation. He does his research largely in the context of innovative education programs focused on increasing the participation of underrepresented minorities in science. Barber’s Diversity and Health Disparities Program synthesizes marine and environmental research in the context of health disparities and social justice in an effort to increase the success of underrepresented minority and underserved premedical students.

Esteban Dell'Angelica, PhD, Professor, Human Genetics. The goal of his research is to understand the molecular pathogenesis of monogenic disorders, in particular those affecting intracellular protein trafficking and organelle biogenesis. Using a variety of experimental approaches, including biochemical and cell biological assays in connection with mouse and fly genetics, he is characterizing the biological function of protein complexes. He is committed to excellence in education and mentoring, and is the recipient of a number of teaching awards, most recently the 2020 Kaiser-Permanente Award for Excellence in Teaching.

Leonid Kruglyak, PhD, Professor and Chair of Human Genetics, Professor of Biological Chemistry. His lab conducts experiments in model organisms (currently, the yeast Saccharomyces cerevisiae and the nematode worm Caenorhabditis elegans), as well as computational analyses, aimed at understanding how changes at the level of DNA are shaped by molecular and evolutionary forces, and how these changes lead to all the observable differences among individuals within a species.

Jamie Lloyd-Smith, PhD, Professor, Ecology & Evolutionary Biology and Computational Medicine. His laboratory studies the ecology of infectious diseases in wildlife and human populations. He combines mathematical and computer models with field and laboratory data to understand how infectious diseases spread and evolve, and how to reduce their health impacts.

Aldons Lusis, PhD, Professor, Human Genetics, Medicine, and Microbiology, Immunology & Molecular Genetics (MIMG). His laboratory uses the combination of genetics, molecular biology, and informatics to investigate pathways underlying common cardiovascular and metabolic disorders. They exploit natural genetic variation among inbred strains of mice (and among human populations when possible) to identify novel targets and formulate hypotheses, and perform validation using experimental perturbations in mice. A major focus has been the interactions of lipid metabolism and inflammation in cardiovascular disease and metabolic syndrome.

Karen Reue, PhD, Professor, Human Genetics. Her research goal is to identify novel genes and pathways that are required for metabolic homeostasis, which are dysregulated in conditions such as obesity, lipodystrophy, diabetes and atherosclerosis. Recent work is focused on investigating the mechanisms underlying sex differences in obesity and cardiovascular disease using mouse models.

Population Genetics

Nandita Garud, PhD, Assistant Professor, Ecology & Evolutionary Biology, and Human Genetics. Her laboratory focuses on quantifying the mode and tempo of evolution in natural populations, with an emphasis on the microbiome. She synthesizes population genetics, statistics, and analysis of population genomic data, including metagenomic data, to develop and apply new computational methods to make population genetic inferences from publicly available data, and data generated by collaborators.

Kirk Lohmueller, PhD, Professor, Ecology & Evolutionary Biology and Human Genetics. His lab develops and implements statistical methods to study genetic variation in humans and other species. His research is focused on understanding natural selection, particularly the removal of deleterious mutations (i.e., negative selection). He also specializes in applying genetic variation data to the inference of population history and personal identification.

Bogdan Pasaniuc, PhD, Associate Professor, Pathology and Human Genetics. His research focuses on medical population genetics. His lab develops computational and statistical methods for understanding the genetic architecture of common diseases. He is particularly interested in methods that leverage the genetic diversity across and within populations for large-scale studies. More specifically, he develops approaches for analyzing large-scale genomic data sets such as sequencing studies, genome-wide association studies, and fine-mapping studies.

Statistical Genomics

UCLA has one of the largest and most productive groups of statistical geneticists in the world. Trainees are exposed to a rich environment fostering statistical modeling, algorithm development, and genomic data analysis.

Kenneth Lange, PhD, Professor, Human Genetics and Computational Medicine. His research interests include genetic epidemiology, population genetics, membrane physiology, demography, oncology, medical imaging, stochastic processes, and optimization theory. Many of his landmark papers predate by a decade or more the current flood of biological applications of hidden Markov chains, Markov chain Monte Carlo, and high-dimensional optimization. He was the Chair of the Department of Human Genetics and the Department of Biomathematics (now Computational Medicine). He founded the GATP program in 2002, and was the PI for 15 years. He received the American Society of Human Genetics 2020 Motulsky-Childs Award for Excellence in Human Genetics Education, and was recently elected as a member of the National Academy of Sciences.

Jingyi Li, PhD, Associate Professor, Statistics and Human Genetics. Her research is at the junction of statistics and biology. She focuses on developing statistical and computational methods motivated by important questions in biomedical sciences and abundant information in big genomic and health related data. Research topics include association measures, high-dimensional variable selection, classification metrics, next-generation RNA sequencing, and comparative genomics.

Janet Sinsheimer, PhD, Professor, Human Genetics, Biostatistics, and Computational Medicine. Her research program involves the derivation and application of statistical techniques for mapping complex trait and disease genes. Most recently, her group has been working on omics applications that range from understanding the metabolomic and genetic signatures of non-alcoholic liver disease to characterizing the expression, epigenomic and microbiome data. She also collaborates on the statistical analysis for a variety of cancer-related, clinically-oriented projects ranging from the evaluation of the effectiveness of bilingual web-based cancer genetics education materials for the deaf to physician accessible cancer modeling software (BioSimulator). She was the Co-Director of the GATP for eight years.

Hua Zhou, PhD, Professor, Biostatistics. His research interests include numerical optimization problems, particularly those arising from statistical analysis of high-dimensional data such as large-scale genomic data. He has developed penalization methods for association screening of genome-wide association (GWAS) and next generation sequencing (NGS) data, and a nonlinear dimension reduction approach for genotype aggregation and association mapping. Currently he is working on genome-wide QTL association mapping based on family designs, genotype imputation, transcriptomics data analysis based on RNA-seq technology, and statistical methods for analyzing microbiome data.

Systems Genetics

Systems genetics analyzes the many networks (gene regulatory, molecular, cellular, and physiological) that transmit genetic information into complex traits, including common diseases. It often examines intermediate molecular structures, such as transcript and protein or metabolite abundance, to understand the bridge from genotype variation to the variety of observed phenotypes.

Eran Halperin, PhD, Professor, Computer Science and Computational Medicine. His research focuses on the development of computational tools for the analysis of genetic data; particularly in the development of tools that enable and facilitate genetic and epigenetic studies of common complex diseases, such as cancer, rheumatoid arthritis, or cardiovascular diseases. These studies shed important light on the biological mechanisms of these diseases, and they will pave the way to improved diagnosis and a personalize treatment based on an individual's genetics.

Alex Hoffman, PhD, Professor, Microbiology, Immunology & Molecular Genetics (MIMG). His research focuses on cell signaling systems and network dynamics that determine biological specificity. He has studied how the epigenome may be altered by inducible signaling systems to alter the cellular steady state. In his lab computational modeling and bioinformatic analysis is iterated with experimental work in animals at single-molecule to genome-wide scales. He is the director of the Institute for Quantitative and Computational Biosciences (QCBio). He is deeply committed to undergraduate and graduate research training. He has been the PI of two T32 Training Grants. Since coming to UCLA, 20 graduate students have earned PhD’s in his laboratory. He is chair of the UCLA Committee for Diversity and Equity (CDE) and the Chancellor’s Council on Diversity. He launched the UCLA Bruins-In-Genomics (BIG) Summer Undergraduate Research program.

Steve Horvath, PhD, Professor, Human Genetics and Biostatistics. He develops statistical and bioinformatics methods for studying cancer genetics and complex disease mapping. His research interests include gene networks, systems biology, allelic association tests for mapping complex disease genes, and data mining methods. His research in data mining focuses on supervised and unsupervised methods for analyzing gene expression data. A major focus of his lab is the development of molecular biomarkers of aging, and his epigenetic clock research has garnered international recognition.

Roel Ophoff, PhD, Professor, Psychiatry & Biobehavioral Sciences, and Human Genetics. His research interest is the genetic architecture of complex human traits, in particular neuropsychiatric disorders and neurobehavioral traits, including bipolar disorder (BP) and schizophrenia. He applies genomic approaches to study the role of genetic variation, gene expression and epigenetic changes in disease susceptibility and disease progression. He is the co-director of an NINDS-funded postdoctoral T32 training program in Neurobehavioral Genetics.

Paivi Pajukanta, MD, PhD, Professor, Human Genetics. Dr. Pajukanta investigates the integrative genomics of complex cardiovascular and metabolic disorders. She is especially interested in combining molecular genetic approaches with new statistical and bioinformatics tools to identify and characterize DNA sequence variants contributing to common cardiovascular disorders, and is carrying out studies in an admixed Mexican population. She is the Director of the UCLA Genetics & Genomics graduate program.

Harold Pimentel, PhD, Assistant Professor, Computational Medicine and Human Genetics. His research goal is to understand gene regulation by building broadly applicable computational tools to analyze high-throughput genomic assays. This approach works by carefully investigating the experimental design and developing data-driven models using computer science and high-dimensional statistics to better understand how genes regulate each other and how disease disrupts gene networks.

Xinshu Xiao, PhD, Professor, Integrative Biology & Physiology. Dr. Xiao is primarily interested in understanding how the unexpectedly small number of genes in our cells leads to the extraordinary spectrum of phenotypic diversity. In particular, she focuses on RNA processing and regulation which have proved pivotal to human health and disease. She uses a combination of approaches in genomics, bioinformatics, molecular biology and systems biology. This work is made possible by the revolutionary high-throughput sequencing technologies that have transformed modern biology into an information-rich science. She also serves as the Director of the Bioinformatics Interdepartmental Program.