Bioinformatics and Systems Biology Faculty

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Ruben Abagyan

Ruben Abagyan

Professor, School of Pharmacy

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Structural molecular biophysics

Ludmil Alexandrov

Ludmil Alexandrov

Assistant Professor, Cellular and Molecular Medicine
Assistant Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology

Research Focus: Using large-scale omics data to study mutational processes causing human cancer, identify potential cancer prevention strategies, and develop novel approaches for targeted cancer treatment.

Ferhat Ay

Ferhat Ay

Assistant Professor, Pediatrics

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

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

Vineet Bafna

Professor, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Proteomics and Metabolomics

Research Focus: Bioinformatics Algorithms, Proteomics, Population Genetics

Nuno Bandeira

Nuno Bandeira

Assistant Professor, Computer Science and Engineering

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Bioinformatics and computational mass spectrometry

Vikas Bansal

Vikas Bansal

Assistant Professor, Pediatrics

BISB Research Area(s):
  • 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

Christopher Benner

Christopher Benner

Assistant Professor in Residence, School of Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease
Steve Briggs

Steve Briggs

Professor, Biological Sciences

BISB Research Area(s):
  • Proteomics and Metabolomics

Research Focus: Stem Cell Identity

Hannah Carter

Hannah Carter

Assistant Professor of Medicine, Division of Medical Genetics

BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Structural Bioinformatics, Systems Biology, Machine Learning, Cancer, Personalized Medicine and Genetic Variation

Lukas Chavez

Lukas Chavez

Assistant Professor, School of Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

Research Focus: Chromatin and Gene Regulation in Childhood Cancers

Pieter Dorrestein

Pieter Dorrestein

Assistant Professor, School of Pharmacy

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Genetic and Molecular Networks

Research Focus: Biosynthesis

Joseph Ecker

Joseph Ecker

Professor, Biological Sciences

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

Research Focus: Molecular biology and genetics of plants

Ronald M. Evans

Ronald M. Evans

Professor and Director, Salk Institute for Biological Studies

BISB Research Area(s):
  • Epigenomics and Gene Expression Control

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

Emma Farley

Emma Farley

Assistant Professor, Biological Sciences

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

Kelly Frazer

Kelly Frazer

Professor, Pediatrics
Director, Institute for Genomic Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

Research Focus: Functional Genomics, Omics integration, High-throughput Sequencing, Induced pluripotent stem cells

Terry Gaasterland

Terry Gaasterland

Professor and Director of Scripps Genome Center, Marine Biology Research Division
Graduate Program Associate Director, Bioinformatics and Systems Biology

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control

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

Kyle Gaulton

Kyle Gaulton

Assistant Professor, Pediatrics

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

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

Michael Gilson

Michael Gilson

Professor, School of Pharmacy

BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Computer-aided drug discovery

Christopher Glass

Christopher Glass

Professor, Cellular and Molecular Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Joseph Gleeson

Joseph Gleeson

Professor/HHMI Investigator, Neurosciences (School of Medicine)

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control

Research Focus: Neurosciences, Brain Development, Cell Proliferation, Neurogenetics, Seizures

Lawrence Goldstein

Lawrence Goldstein

Professor, Cellular and Molecular Medicine

BISB Research Area(s):
  • Genetic and Molecular Networks

Research Focus: Intracellular Movement in Neurons

Alon Goren

Alon Goren

Assistant Professor, School of Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

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

Melissa Gymrek

Melissa Gymrek

Assistant Professor, Computer Science and Engineering
Assistant Professor, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics

Research Focus: Contribution of complex genetic variation to human phenotypes

Nan Hao

Nan Hao

Assistant Professor, Biological Sciences

BISB Research Area(s):
  • 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

Olivier Harismendy

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • 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

Jeff Hasty

Associate Professor, Biological Sciences

BISB Research Area(s):
  • Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Biodynamics

Michael Holst

Michael Holst

Professor, Mathematics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Proteomics and Metabolomics

Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics

Vivian Hook

Vivian Hook

Professor, School of Pharmacy

BISB Research Area(s):
  • Proteomics and Metabolomics

Research Focus: Peptide Neurotransmitters, Protease Mechanisms

Xiaohua Huang

Xiaohua Huang

Assistant Professor, Bioengineering

BISB Research Area(s):
  • Epigenomics and Gene Expression Control

Research Focus: Genomics, Nanostructure Fabrication

Terence Hwa

Terence Hwa

Professor, Physics
Professor, Biological Sciences

BISB Research Area(s):
  • 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

Lilia Iakoucheva

Associate Professor, Psychiatry

BISB Research Area(s):
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Trey Ideker

Trey Ideker

Professor, Division of Medical Genetics
Graduate Program Director, Bioinformatics and Systems Biology

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

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

Suckjoon Jun

Suckjoon Jun

Assistant Professor, Physics
Assistant Professor, Biological Sciences

BISB Research Area(s):
  • 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

Amy Kiger

Assistant Professor, Biological Sciences

BISB Research Area(s):
  • Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Rob Knight

Rob Knight

Professor, Pediatrics
Affiliate Faculty, Computer Science and Engineering

BISB Research Area(s):
  • Comparative and Population Genomics

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

Richard Kolodner

Richard Kolodner

Professor, School of Medicine

BISB Research Area(s):
  • Genetic and Molecular Networks

Research Focus: Gene recombination

Louise Laurent

Louise Laurent

Associate Professor, Reproductive Medicine

BISB Research Area(s):
  • 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

Julie Law

Assistant Professor, Salk Institute for Biological Studies

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

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

Nathan E. Lewis

Nathan E. Lewis

Associate Professor, Pediatrics

BISB Research Area(s):
  • 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

Amit Majithia

Assistant Professor, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Genetic and Molecular Networks

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

Prashant Mali

Prashant Mali

Assistant Professor, Bioengineering

BISB Research Area(s):
  • 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

Andrew McCammon

Professor, Chemistry and Biochemistry

BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Enzymes and Ligand Binding

Andrew McCulloch

Andrew McCulloch

Professor, Bioengineering

BISB Research Area(s):
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Mathematical Modeling of Heart Cells and Tissue

Graham McVicker

Graham McVicker

Assistant Professor, Salk Institute for Biological Studies

BISB Research Area(s):
  • 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

Jill Mesirov

Professor, School of Medicine
Associate Vice Chancellor, Computational Health Sciences,
Professor of Medicine, Division of Medical Genetics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Genetic and Molecular Networks

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

Christian Metallo

Assistant Professor, Bioengineering

BISB Research Area(s):
  • Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Siavash Mirarab

Siavash Mirarab

Assistant Professor, Electrical and Computer Engineering

BISB Research Area(s):
  • 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.

Eran Mukamel

Eran Mukamel

Assistant Professor, Cognitive Science

BISB Research Area(s):
  • 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

Saket Navlakha

Assistant Professor, Salk Institute for Biological Studies

BISB Research Area(s):
  • 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

Lucila Ohno-Machado

Lucila Ohno-Machado

Professor, Biomedical Informatics

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Privacy Technology, Data Sharing, and Big Data Analytics

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

Bernhard Palsson

Bernhard Palsson

Professor, Bioengineering

BISB Research Area(s):
  • 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

Pavel Pevzner

Professor and Ronald R Taylor Chair, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Proteomics and Metabolomics

Research Focus: Computational Molecular Biology

Anjana Rao

Anjana Rao

Adjunct Professor, Pharmacology

BISB Research Area(s):
  • 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

Bing Ren

Professor, Cellular and Molecular Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

Research Focus: Gene Regulatory Networks

Doug Richman

Doug Richman

Professor, Pathology

BISB Research Area(s):
  • Comparative and Population Genomics

Research Focus: HIV disease and pathogenesis

Scott Rifkin

Scott Rifkin

Assistant Professor, Biological Sciences

BISB Research Area(s):
  • Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Evolutionary Biology-Patterns of Gene Expression

Michael Rosenfeld

Michael Rosenfeld

Professor, School of Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

Research Focus: Mammalian Neurosystem Development

Debashis Sahoo

Debashis Sahoo

Assistant Professor, Pediatrics

BISB Research Area(s):
  • 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

Nicholas Schork

Professor, Scripps Research Institute

BISB Research Area(s):
  • 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

Julian Schroeder

Professor, Biological Sciences

BISB Research Area(s):
  • 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.

Dorothy Sears

Dorothy Sears

Associate Professor, School of Medicine

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

Research Focus: Mechanisms and biomarkers of nsulin resistance, type 2 diabetes, obesity, breast cancer, PPARgamma, inflammation

Jonathan Sebat

Jonathan Sebat

Chief, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Associate Professor of Psychiatry and Cellular & Molecular Medicine, Cellular and Molecular Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control

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

Shankar Subramaniam

Shankar Subramaniam

Professor, Bioengineering

BISB Research Area(s):
  • Genetic and Molecular Networks
  • Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Functional Genomics

Gurol Suel

Gurol Suel

Associate Professor, Biological Sciences

BISB Research Area(s):
  • Dynamical Systems, Stochastic Processes, and Biological Circuits

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

Pablo Tamayo

Pablo Tamayo

Professor, School of Medicine

BISB Research Area(s):
  • 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

Palmer Taylor

Professor and Dean, School of Pharmacy

BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Neurotransmission Biochemistry

Susan Taylor

Susan Taylor

Professor, Chemistry and Biochemistry

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Relationship of CAPK Structure to Function

Glenn Tesler

Glenn Tesler

Associate Professor, Mathematics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics

Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly

Yingxiao (Peter) Wang

Yingxiao (Peter) Wang

Associate Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Molecular engineering for cellular imaging and reprogramming, quantitative bio-image with applications in mechano-biology of stem cells and cancer

Wei Wang

Wei Wang

Professor, Chemistry and Biochemistry
Professor, Cellular and Molecular Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

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

Joel Wertheim

Joel Wertheim

Assistant Professor of Medicine, Division of Infectious Diseases, School of Medicine

BISB Research Area(s):
  • Genetic and Molecular Networks

Research Focus: RNA viruses. HIV transmission networks.

Ruth Williams

Ruth Williams

Professor, Mathematics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits

Research Focus: Probability Theory, Stochastic Processes

Elizabeth Winzeler

Elizabeth Winzeler

Professor, Pediatrics

BISB Research Area(s):
  • Comparative and Population Genomics
  • Proteomics and Metabolomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: My laboratory uses big data approaches to solve problems in global health. The lab also offers training in cheminformatics and chemical genomics.

Ronghui (Lily) Xu

Ronghui (Lily) Xu

Professor, Mathematics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology

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

Gene Yeo

Gene Yeo

Professor, Cellular and Molecular Medicine
Graduate Program Associate Director, Bioinformatics and Systems Biology

BISB Research Area(s):
  • 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
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Privacy Technology, Data Sharing, and Big Data Analytics
  • Bioinformatics Applications in Human Disease

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

Karsten Zengler

Karsten Zengler

Professor, Pediatrics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Genetic and Molecular Networks

Research Focus: We study microbial interactions, using multi-omics analysis and community modeling

Kun Zhang

Kun Zhang

Professor, Bioengineering

BISB Research Area(s):
  • 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

Sheng Zhong

Associate Professor, Bioengineering

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

Research Focus: Development of molecular technologies, Stem Cell, Epigenomics, Single-cell Technologies, Statistical Methods, Algorithm, Network Models