Participating Faculty

Ruben Abagyan

• Proteomics and Metabolomics
• Structural Bioinformatics and Systems Pharmacology

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

Ludmil Alexandrov

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics
• Epigenomics and Gene Expression Control

• Biomedical Natural Language Processing
• Bioinformatics Applications in Human Disease

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

• Comparative and Population Genomics
• Proteomics and Metabolomics
• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Ferhat Ay

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

• Bioinformatics Applications in Human Disease

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

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics
• Proteomics and Metabolomics

Research Focus: Bioinformatics Algorithms, Proteomics, Population Genetics

Nuno Bandeira

• Proteomics and Metabolomics
• Structural Bioinformatics and Systems Pharmacology

Research Focus: Bioinformatics and computational mass spectrometry

Vikas Bansal

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics

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

Simone Baumann-Pickering

• Quantitative Foundations of Computational Biology

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

• Epigenomics and Gene Expression Control

• Bioinformatics Applications in Human Disease

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.

Steve Briggs

• Proteomics and Metabolomics

Research Focus: Stem Cell Identity

Joseph Califano

• Epigenomics and Gene Expression Control

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

• Genetic and Molecular Networks
• Structural Bioinformatics and Systems Pharmacology

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

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

Lukas Chavez

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

Research Focus: Chromatin and Gene Regulation in Childhood Cancers

Chi-Hua Chen

• Comparative and Population Genomics

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

Research Focus: Neuroimaging genetics, neuropsychiatric disorders

Neil Chi

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Kit Curtius

• Quantitative Foundations of Computational Biology
• Epigenomics and Gene Expression Control

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

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

Pieter Dorrestein

• Proteomics and Metabolomics
• Genetic and Molecular Networks

Research Focus: Biosynthesis

Joseph Ecker

• Epigenomics and Gene Expression Control

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

Robert El-Kareh

• Predictive Modeling and Personalized Medicine
• Decision Support Systems

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

Ronald M. Evans

• Epigenomics and Gene Expression Control

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

Emma Farley

• Epigenomics and Gene Expression Control
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Gen-Sheng Feng

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Kelly Frazer

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

• Bioinformatics Applications in Human Disease

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

Terry Gaasterland

• Comparative and Population Genomics
• Epigenomics and Gene Expression Control

Research Focus: Computational Analysis of Human, Novel, and Microbial Genomes

Rodney Gabriel

• Predictive Modeling and Personalized Medicine

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

Fred (Rusty) Gage

• Epigenomics and Gene Expression Control
• Dynamical Systems, Stochastic Processes, and Biological Circuits

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

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

Kyle Gaulton

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Michael Gilson

• Structural Bioinformatics and Systems Pharmacology

Research Focus: Computer-aided drug discovery

Christopher Glass

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Joseph Gleeson

• Comparative and Population Genomics
• Genetic and Molecular Networks

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

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

Alon Goren

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Theresa Guo

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

• Comparative and Population Genomics

Research Focus: Contribution of complex genetic variation to human phenotypes

Nan Hao

• Genetic and Molecular Networks
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Olivier Harismendy

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

Research Focus: My laboratory develops genome-wide assays and analysis for personalized cancer care. Particular focus includes genetics of cancer susceptibility and drug response, secure computing and data sharing.

Jeff Hasty

• Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Biodynamics

Sven Heinz

• Epigenomics and Gene Expression Control

Research Focus: High-throughput sequencing assay development, Bioinformatics, Epigenetics, Hematology, Immunology, Molecular Biology, Mouse Genetics, Server Hardware.

Michael Hogarth

• Data Models and Knowledge Representation
• Biomedical Natural Language Processing

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

• Quantitative Foundations of Computational Biology
• Proteomics and Metabolomics

Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics

Vivian Hook

• Proteomics and Metabolomics

Research Focus: Peptide Neurotransmitters, Protease Mechanisms

Albert Hsiao

• Comparative and Population Genomics

• Bioinformatics Applications in Human Disease

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

Wendy Huang

• Comparative and Population Genomics
• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

• Bioinformatics Applications in Human Disease

Research Focus: To assess the contributions of RNA-binding proteins and their associated non-coding RNAs to host immune homeostasis and autoimmune pathologies.

Xiaohua Huang

• Epigenomics and Gene Expression Control

Research Focus: Genomics, Nanostructure Fabrication

Terence Hwa

• Epigenomics and Gene Expression Control
• Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Genetic and biomolecular circuits, Metabolism and growth physiology, Self-organization and pattern formation in biofilm and development

Lilia Iakoucheva

• Genetic and Molecular Networks

• Bioinformatics Applications in Human Disease

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

Trey Ideker

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Mohit Jain

• Proteomics and Metabolomics
• Genetic and Molecular Networks
• Structural Bioinformatics and Systems Pharmacology

• Bioinformatics Applications in Human Disease

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

Suckjoon Jun

• Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Biophysics. Use physics and engineering to explain why biological systems are the way they are.

Amy Kiger

• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Rob Knight

• Comparative and Population Genomics

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

Richard Kolodner

• Genetic and Molecular Networks

Research Focus: Gene recombination

Jejo Koola

• Predictive Modeling and Personalized Medicine
• Biomedical Natural Language Processing

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.

Tsung-Ting Kuo

• Predictive Modeling and Personalized Medicine
• Privacy Technology, Data Sharing, and Big Data Analytics

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

Louise Laurent

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Julie Law

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Nathan E. Lewis

• Genetic and Molecular Networks
• Dynamical Systems, Stochastic Processes, and Biological Circuits
• Structural Bioinformatics and Systems Pharmacology

Research Focus: Systems biology approaches for integration of disparate data types to study diseases involving metabolism, glycobiology, and to guide cell engineering for drug development.

Amit Majithia

• Comparative and Population Genomics
• Genetic and Molecular Networks

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

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

Prashant Mali

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

• Structural Bioinformatics and Systems Pharmacology

Research Focus: Enzymes and Ligand Binding

Andrew McCulloch

• Dynamical Systems, Stochastic Processes, and Biological Circuits
• Structural Bioinformatics and Systems Pharmacology

Research Focus: Mathematical Modeling of Heart Cells and Tissue

Graham McVicker

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics
• Epigenomics and Gene Expression Control

Research Focus: Human genetic variation, chromatin and gene regulation in immune cells

Jill Mesirov

• Quantitative Foundations of Computational Biology
• Genetic and Molecular Networks

• Predictive Modeling and Personalized Medicine
• Bioinformatics Applications in Human Disease

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

• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Siavash Mirarab

• Quantitative Foundations of Computational Biology

Research Focus: Computational biology, large scale phylogenetics, estimation of species trees from gene trees (phylogenomics), large scale multiple sequence alignment, and metagenomic analysis using phylogenetic placement.

Niema Moshiri

• Quantitative Foundations of Computational Biology

• Bioinformatics Applications in Human Disease

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

Eran Mukamel

• Epigenomics and Gene Expression Control
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Saket Navlakha

• Quantitative Foundations of Computational Biology
• Genetic and Molecular Networks

Research Focus: Algorithms in nature, biological networks and systems biology, information processing and computation in biological systems

Shamim Nemati

• Dynamical Systems, Stochastic Processes, and Biological Circuits

• Predictive Modeling and Personalized Medicine
• Decision Support Systems

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

Lucila Ohno-Machado

• Epigenomics and Gene Expression Control

• Predictive Modeling and Personalized Medicine
• Privacy Technology, Data Sharing, and Big Data Analytics

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

Abraham Palmer

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Bernhard Palsson

• Genetic and Molecular Networks
• Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Development of methods to analyze metabolic dynamics (flux-balance analysis and modal analysis) and the formulation of complete models of selected cells (the red blood cell, E. coli, CHO cells, and several human pathogens).

Pavel Pevzner

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics
• Proteomics and Metabolomics

Research Focus: Computational Molecular Biology

Anjana Rao

• Epigenomics and Gene Expression Control
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Bing Ren

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

Research Focus: Gene Regulatory Networks

Scott Rifkin

• Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Evolutionary Biology-Patterns of Gene Expression

Michael Rosenfeld

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

Research Focus: Mammalian Neurosystem Development

Debashis Sahoo

• Quantitative Foundations of Computational Biology
• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Nicholas Schork

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics

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

Julian Schroeder

• Genetic and Molecular Networks

Research Focus: Climate change resistance and drought resistance and plant stress signal transduction. Discovery of signaling networks and biological sensors, using systems biological approaches, transcriptomics, proteomics and genome editing.

Jonathan Sebat

• Comparative and Population Genomics
• Epigenomics and Gene Expression Control

Research Focus: Genome informatics, psychiatric genetics, copy number variation (CNV), de novo mutation

Benjamin Smarr

• Quantitative Foundations of Computational Biology
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Shankar Subramaniam

• Genetic and Molecular Networks
• Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Functional Genomics

Gurol Suel

• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Pablo Tamayo

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

• Structural Bioinformatics and Systems Pharmacology

Research Focus: Neurotransmission Biochemistry

Susan Taylor

• Proteomics and Metabolomics
• Structural Bioinformatics and Systems Pharmacology

Research Focus: Relationship of CAPK Structure to Function

Glenn Tesler

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics

Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly

Yatish Turakhia

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics

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

• Comparative and Population Genomics
• Epigenomics and Gene Expression Control

• Bioinformatics Applications in Human Disease

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

Yingxiao (Peter) Wang

• Epigenomics and Gene Expression Control
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Wei Wang

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

Joel Wertheim

• Genetic and Molecular Networks

• Bioinformatics Applications in Human Disease

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

Ruth Williams

• Quantitative Foundations of Computational Biology
• Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Probability Theory, Stochastic Processes

Elizabeth Winzeler

• Comparative and Population Genomics
• Genetic and Molecular Networks
• Structural Bioinformatics and Systems Pharmacology

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.

Ronghui (Lily) Xu

• Quantitative Foundations of Computational Biology

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

Gene Yeo

• Quantitative Foundations of Computational Biology
• Comparative and Population Genomics
• Proteomics and Metabolomics
• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks
• Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Rose Yu

• Quantitative Foundations of Computational Biology
• Dynamical Systems, Stochastic Processes, and Biological Circuits

• Predictive Modeling and Personalized Medicine
• Decision Support Systems

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

Karsten Zengler

• Quantitative Foundations of Computational Biology
• Genetic and Molecular Networks
• Dynamical Systems, Stochastic Processes, and Biological Circuits

• Predictive Modeling and Personalized Medicine
• Privacy Technology, Data Sharing, and Big Data Analytics
• Data Models and Knowledge Representation
• Bioinformatics Applications in Human Disease

Research Focus: Our lab studies microbe-microbe and host-microbe interactions. The goal is to predict how complex systems react to perturbations and to design strategies to change the trajectory.

Kun Zhang

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

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

• Epigenomics and Gene Expression Control
• Genetic and Molecular Networks

Research Focus: Discovery of RNA-RNA, RNA-DNA, protein-protein, and drug-protein interactions by sequencing.