Participating Faculty

Ruben Abagyan

Research Focus: Structure-based Drug Discovery, Cheminformatics, Drug Repurposing, Computational Pharmacology, Target/pathway Discovery

Ludmil Alexandrov

Research Focus: Using large-scale omics data to study mutational processes causing human cancer, identifying potential cancer prevention strategies with ML and NLP approaches, and developing novel ML tools for better targeting of cancer treatment.

Andrew Allen

Research Focus: Ecological, comparative, and functional genomics of marine phytoplankton, Systems biology of microalgae, Genome evolution and evolutionary origins of metabolic function in marine microbes, Transcriptional regulatory networks, Metagenomics, Metatranscriptomics, Microbes, Evolution

Tiffany Amariuta

Research Focus: We are a statistical genetics lab focusing on developing methods to study complex traits and polygenic diseases in global populations. We are specifically interested in fine-mapping disease genes and their cell types of action, with the goal of finding targets for gene-based therapeutics.

Ferhat Ay

Research Focus: Epigenetics, genomics, chromatin structure, 3D/4D genome/nucleome, statistical methods for analysis of Hi-C and HiChIP data, gene regulation in immune cells, cancer genomics

Vineet Bafna

Research Focus: Bioinformatics Algorithms, Proteomics, Population Genetics

Nuno Bandeira

Research Focus: Bioinformatics and computational mass spectrometry

Vikas Bansal

Research Focus: Computational tools for variant calling, haplotyping and analysis of rare variants in disease association studies

Simone Baumann-Pickering

Research Focus: The Scripps Acoustic Ecology Laboratory investigates phenological patterns and spatial ecology of cetaceans, interactions of predators and their prey, and adaptations of animals to changes in their environment.

Christopher Benner

Research Focus: Transcription, bioinformatics, genomics, innate immunity, chromatin.
We use next-generation sequencing (NGS) and computational analysis to understand the mechanisms responsible for transcription and epigenetic regulation in human development and disease.

Neville Bethel

Research Focus: deep learning, structural biology, de novo design, physics-based simulation

Bogdan Bintu

Research Focus: We develop and apply new imaging tools (including spatial transcriptomics and genomics) to understand how gene regulation information propagates across scales from the molecular events within the nucleus to the organization of cells into tissues and organs, up to the scale of animal behavior.

Steve Briggs

Research Focus: Stem Cell Identity

Wolfgang Busch

Research Focus: Researching and developing plant varieties with enhanced carbon sequestration capabilities for removing CO2 from the atmosphere and thereby counteracting climate change.

Joseph Califano

Research Focus: The Califano laboratory investigates the molecular and immunologic basis of head and neck neoplasia, employing integrative computational techniques in concert with molecular, in vitro, and in vivo techniques to define opportunities for therapeutic intervention in a variety of tumors.

Hannah Carter

Research Focus: Genomics and systems biology for precision cancer medicine, variant interpretation, network analysis, immunogenomics

Alejandro Chavez

Research Focus: High-throughput screens, CRISPR-Cas9, protein language models, functional genomics, technology development, infectious disease and neurodegeneration

Lukas Chavez

Research Focus: Genomic and Epigenomic Alterations in Childhood Cancers

Chi-Hua Chen

Research Focus: Neuroimaging genetics, neuropsychiatric disorders

Christine Cheng

Research Focus: Utilize single cell resolution functional genomic assays and computational methods to study heterogeneous clinical tissue samples and blood immune cell populations in patient samples.

Neil Chi

Research Focus: Bioinformatic, gene regulatory networks, single-cell and imaging analyses/approaches of human disease, stem cell biology and regenerative medicine

Hiutung Chu

Research Focus: host-microbe interactions; gut microbiome; host genetic factors in immunity

Heidi Cook-Andersen

Research Focus: We integrate computational, epigenetic, RNA, and chromatin biology approaches in human, mouse and stem cell models to understand the earliest stages of development -- from the fully differentiated oocyte to the totipotent embryo and successful implantation of the human blastocyst.

Kit Curtius

Research Focus: Mathematical models of cancer evolution, optimization of cancer screening and surveillance, epigenetic aging, translational risk prediction tools

Matteo D'Antonio

Research Focus: Combining genome-wide association studies and polygenic risk scores with environmental variables, lifestyle and social determinants of health to predict disease risk using machine learning and deep learning methods. Using large language models to predict disease

Pieter Dorrestein

Research Focus: Biosynthesis

Joseph Ecker

Research Focus: Epigenomics of the mammalian brain - human brain cell atlas

Tal Einav

Research Focus: Antibody-virus interactions, predicting each person's vaccine response, personalized medicine

Robert El-Kareh

Research Focus: Clinical informatics, clinical decision support, diagnostic safety, quality improvement, patient safety

Ronald M. Evans

Research Focus: Role of hormones, both in their normal activities and in disease.

Emma Farley

Research Focus: High-throughput functional assays in developing embryos to decipher how genomes instruct development

Gen-Sheng Feng

Research Focus: Deciphering the anti-oncogenic effects of pro-oncogenic molecules in liver cancer

Kathleen Fisch

Research Focus: Understanding the molecular mechanisms underlying pregnancy disorders and exposures to improve maternal and child health throughout the lifespan.

Kelly Frazer

Research Focus: Using iPSCs for genetic analyses, GWAS, QTL analyses, bioinformatic approaches to understanding human disease, single-cell analyses

Terry Gaasterland

Research Focus: Computational Analysis of Human, Novel, and Microbial Genomes: Impact of genetic and evolutionary variation on regulation of transcription and on protein domain structure and function. Causal variants leading to dysregulated cellular response to environmental stresses.

Rodney Gabriel

Research Focus: Perioperative outcomes, pharmacogenomics, machine learning, predictive modeling, regional anesthesia, acute pain.

Fred (Rusty) Gage

Research Focus: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu

Kyle Gaulton

Research Focus: Statistical genetics, epigenomics, chromatin, gene regulatory networks, diabetes

Michael Gilson

Research Focus: Computer-aided drug discovery

Christopher Glass

Research Focus: Enhancer Selection and Functions, Macrophage Subtypes, Genetic Variation, Enhancer Transcription

Joseph Gleeson

Research Focus: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions

Alon Goren

Research Focus: Dynamics of epigenomic mechanisms during development and along the cell cycle

Theresa Guo

Research Focus: Splicing alteration in human cancer, with particular focus on HPV mediated head and neck tumors; Interaction between genomic alterations and tumor immunity; post transcriptional and epigenetic regulation of splicing

Melissa Gymrek

Research Focus: Contribution of complex genetic variation to human phenotypes

Nan Hao

Research Focus: Dynamic regulation of signaling and transcriptional networks in single cells

Jeff Hasty

Research Focus: Biodynamics

Sven Heinz

Research Focus: Regulation and reprogramming of transcription, cancer epigenetics

Michael Hogarth

Research Focus: Development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.

Michael Holst

Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics

Vivian Hook

Research Focus: Peptide Neurotransmitters, Protease Mechanisms

Albert Hsiao

Research Focus: Artificial Intelligence, Cardiovascular, COVID-19, x-ray, CT, MRI, Point-of-care Ultrasound

Xiaohua Huang

Research Focus: Genomics, Nanostructure Fabrication

Terence Hwa

Research Focus: Use of proteomic and metabolomic approaches to study resource allocation strategies employed during bacterial growth; mechanistic studies of metabolic interactions in bacterial communities

Lilia Iakoucheva

Research Focus: Autism, genetics, gene expression, protein interactions, systems biology, networks, psychiatric diseases, whole genome sequencing

Trey Ideker

Research Focus: Biological Networks, Cellular Modeling, Cancer Genomics, Epigenetic Aging

Mohit Jain

Research Focus: Human Biology, Metabolic Biochemistry, Integrative Biology, Mass Spectrometry, Metabolomics

Fay Jiang

Adrian Jinich

Susan Kaech

Research Focus: Understanding how Memory T Cells are produced during infection and vaccination

Amy Kiger

Research Focus: Genomics, Cellular Morphogenesis, RNAi, Image Analysis of Microscopy Data

Kevin King

Research Focus: The King Lab studies diseases in which the immune system becomes activated even though there is no infection, such as heart attacks, metabolic disease, autoimmunity, or cancer. He combines conventional biological methods with novel bioengineering techniques to develop therapies that limit organ dysfunction and promote healing, repair and regeneration.

Rob Knight

Research Focus: Human microbiome, microbial community ecology, multi-omics analyses

Richard Kolodner

Research Focus: Gene recombination

Jejo Koola

Research Focus: Practicing internist in the field of hospital medicine and clinical informatics. Research focus is on using informatics tools (including predictive analytics, natural language processing, and information visualization) to improve the care of multi-morbid hospital patients.

Pallav Kosuri

Research Focus: The Kosuri Lab studies how movement gives rise to biological function across scales, from molecular motors to muscles. We take a cross-disciplinary approach that makes use of molecular design, computational methods, and functional imaging.

Tsung-Ting Kuo

Research Focus: Blockchain Technologies, Machine Learning, Natural Language Processing

Louise Laurent

Research Focus: Gene Interaction Networks, Biomarker Discovery, Pluripotency, Embryonic Development, Placental Dysfunction, Preeclampsia, Pregnancy complications

Julie Law

Research Focus: Chromatin modifications, epigenetics, genomics, gene regulation

Nathan E. Lewis

Research Focus: Systems biology approaches for multi-omics and single cell omics to study diseases involving metabolism, glycobiology, cell-cell communication, and to guide cell engineering for drug development.

Hojun Li

Research Focus: Multi-omic analysis of human patient samples, functional genomics of stem cells and hematopoiesis, blood disorders and leukemia

Amit Majithia

Research Focus: Insulin resistance, functional genomics, pharmacogenetics, cardiometabolic disease, diabetes

Prashant Mali

Research Focus: The Mali laboratory is working in the fields of synthetic biology and regenerative medicine, with a long-term focus on developing tools for enabling gene and cell based human therapeutics.

Andrew McCammon

Research Focus: Enzymes and Ligand Binding

Andrew McCulloch

Research Focus: Multi-scale biology of heart and musculoskeletal system to elucidate the biological principles underlying heart failure, congenital heart disease, arrhythmia and elite human performance

Graham McVicker

Research Focus: The McVicker Laboratory studies how human genetic variation affects chromatin state and gene regulation.

Jill Mesirov

Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.

Christian Metallo

Research Focus: Metabolism, system biology, mass spectrometry, flux analysis, cancer, stem cell biology

Siavash Mirarab

Research Focus: Evolution, phylogenetics, phylogenomics, multiple sequence alignment, Genome skimming, HIV dynamics

Niema Moshiri

Research Focus: Computational viral epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development

Eran Mukamel

Research Focus: Computational neuroscience, brain cell differentiation and development, computational analysis of brain-network dynamics

Samuel Myers

Research Focus: Information processing via biochemical networks in cellular decision making

Shamim Nemati

Research Focus: Signal Processing, Dynamical Systems, Multivariate Time Series, Point Process, Deep Learning, Reinforcement Learning, Video Processing, and Natural Language Processing

Lucila Ohno-Machado

Research Focus: Biomedical Informatics, predictive modeling, biomedical data analytics

Abraham Palmer

Research Focus: Quantitative genetic studies of behavior using fish, mice, rats and humans. Applying statistical genetics and genomics approaches to understanding behavior.

Bernhard Palsson

Research Focus: The development of computational biology methods (flux-balance analysis, and modal analysis), genome-scale models (M models, ME models), data analytic methods (iModulons, pangenomics, alleleome, structural proteomics).

Bjoern Peters

Research Focus: Immunology, Adapative Immunity, Epitopes, Knowledge Representation, Infectious Disease, Cancer, Allergy, Autoimmunity, Machine Learning, Big Data, Systems Biology

Pavel Pevzner

Research Focus: Computational Molecular Biology

Tariq Rana

Research Focus: Gene regulatory networks

Anjana Rao

Research Focus: Understanding how signalling pathways control gene expression, using T cells and other cells of the immune system as models

Miguel Reina-Campos

Research Focus: Harnessing the power of tissue immune networks against infections and cancer

Bing Ren

Research Focus: Gene Regulatory Networks

Scott Rifkin

Research Focus: Evolutionary Biology-Patterns of Gene Expression

Michael Rosenfeld

Research Focus: Mammalian Neurosystem Development

Debashis Sahoo

Research Focus: Systems Biology of normal and cancer tissues, Boolean analysis of biological systems, Computational models of stem cell differentiation, Sequencing data analysis

Sandra Sanchez-Roige

Research Focus: Our research aims to advance precision psychiatry using genetic, genomic, medical bioinformatic, and cross-species translational approaches.

Johannes Schoeneberg

Research Focus: Our group uses experimental and computational approaches to study the link between mitochondrial dynamics and neurological diseases that are caused by mitochondrial dysfunction, using 4D adaptive optics lattice light-sheet microscopy, brain organoids, human induced pluripotent stem cells, and machine learning.

Nicholas Schork

Research Focus: Developing mathematical, statistical, and computational models and tools to study the genetic basis of complex traits and diseases

Julian Schroeder

Research Focus: Heat and drought resistance mechanisms and network in plants and plant stress signal transduction. Discovery of signaling networks and biological sensors, using systems biological approaches, transcriptomics, proteomics and genome editing.

Jonathan Sebat

Research Focus: Human Genetics, Statistical Genetics, Whole genome sequencing, Long Read Sequencing. Autism, Genetic Therapies for Neurological Disease

Amy Sitapati

Research Focus: Biomedical Informatics, Registries, Population Health, Precision Medicine, Vital Records Informatics, Artificial Intelligence, Quality Informatics, Health Analytics

Benjamin Smarr

Research Focus: What information do biological timeseries hold? What biodynamic interactions generate these signals?

Shankar Subramaniam

Research Focus: Functional Genomics

Gurol Suel

Research Focus: Identifying systems-level design principles of cellular differentiation circuits

Pablo Tamayo

Research Focus: Development of analysis methods for the functional characterization of cancer genomes including RNAi and CRISPR genetic dependencies. Computational methods, probability and statistics, data analysis, machine learning, computational biology and cancer research.

Palmer Taylor

Research Focus: Neurotransmission Biochemistry

Susan Taylor

Research Focus: Relationship of CAPK Structure to Function

Glenn Tesler

Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly

Yatish Turakhia

Research Focus: Algorithms and domain-specific hardware accelerators that enable faster and cheaper progress in biology and medicine.
Computational methods that enable biological discoveries, such as new genotype-phenotype relationships.

Pandurangan Vijayanand

Research Focus: Continually evolving genomic tools and single cell analysis technologies are revolutionizing our understanding of the human immune system in health and disease.

Wei Wang

Research Focus: Epigenomics, 3D genome, systems biology, protein engineering

Yingxiao (Peter) Wang

Research Focus: Live cell imaging, genetic and epigenetic regulations, immunoengineering, therapeutics

Joel Wertheim

Research Focus: Molecular epidemiology of HIV, SARS-CoV-2, and other RNA viruses; Viral phylogenetics and evolution

Ruth Williams

Research Focus: Probability Theory, Stochastic Processes

Elizabeth Winzeler

Research Focus: We are interested in host pathogen interactions, drug discovery, genetics, genomics and cheminformatics. We use a variety of high throughput, computationally intensive methods to accelerate the drug discovery process. Most of our work is focused on developing new treatments for malaria.

Dominik Wodarz

Research Focus: Mathematical models of infectious diseases, virus-immune system interactions, carcinogenesis, and cancer therapy; Evolutionary theory and evolutionary dynamics.

Ronghui (Lily) Xu

Research Focus: High dimensional data analysis, Imaging Random effects models, Survival analysis, Clinical trials

Gene Yeo

Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.

Rose Yu

Research Focus: Machine learning, spatiotemporal modeling, deep learning, dynamical systems

Karsten Zengler

Research Focus: Our lab studies microbe-microbe and host-microbe interactions. The goals are i) to predict how complex systems react to perturbations and ii) to design strategies to change the trajectory.

Kun Zhang

Research Focus: We develop technologies related to single-cell analyses of genome, epigenome and transcriptome, as well as single-cell imaging and lineage tracing. These novel technologies are applied to stem cell fate conversion, human brain mapping and human disease studies.

Sheng Zhong

Research Focus: Omics, Gene Regulation, RNA, Aging, Alzheimer's Disease, AI

Huilin Zhou

Research Focus: Proteomics and genome maintenance