All Faculty by Research Area

Bioinformatics and Systems Biology Research Areas


Quantitative Foundations of Computational Biology

Key to Computational Biology are the approaches and algorithms for processing, analyzing and modeling knowledge, information, and data, that are relevant to research questions from across the life sciences. The development of mathematical and computational methods with probabilistic, statistical, combinatorial, or heuristic foundations continue to drive innovation in Bioinformatics and Systems Biology.

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.

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

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

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

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.

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.

Niema Moshiri

Niema Moshiri

Assistant Teaching Professor, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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

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

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

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

Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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

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

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

Comparative and Population Genomics

Sequencing technologies are providing unprecedented opportunities and challenges to Bioinformatics to impact studies of Evolution, Epidemiology, Disease Genes, giving birth to the fields of Personalized Medicine and Pharmacogenomics.

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

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

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

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

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

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

Amit Majithia

Amit Majithia

Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

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

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

Doug Richman

Doug Richman

Professor (Active Emeritus), Pathology

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

Research Focus: HIV disease and pathogenesis

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

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

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

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.

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

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


Proteomics and Metabolomics

Mass spectrometry technologies have advanced to provide quantitative information not only of peptides and the proteome, but post-translational modifications, lipids, and metabolic intermediates. Interpreting high dimensional mass spectrometry data poses bioinformatic challenges of high significance to many aspects of research in biofuels, industrial biology, agricultural biology, and biomedicine.

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

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

Steve Briggs

Steve Briggs

Professor, Biological Sciences

BISB Research Area(s):
  • Proteomics and Metabolomics

Research Focus: Stem Cell Identity

Pieter Dorrestein

Pieter Dorrestein

Assistant Professor, School of Pharmacy

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

Research Focus: Biosynthesis

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

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

Dorothy Sears

Dorothy Sears

Associate Professor, School of Medicine

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

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

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

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.

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

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


Epigenomics and Gene Expression Control

The ability to characterize the chromatin state, its three-dimensional organization, the landscapes of DNA and RNA binding proteins, and the action of regulatory RNAs throughout the genome is broadly impacting biological research such as on differentiation and development, cancer, and immune responses. Bioinformatic analysis tools are critical for such studies, and predictive models of how the genome is expressed are within reach.

Ferhat Ay

Ferhat Ay

Assistant Adjunct 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

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
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

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
BMI Research Area(s):
  • 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

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

Christopher Glass

Christopher Glass

Professor, Cellular and Molecular Medicine

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

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

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

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.

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

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

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

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.

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

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

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

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

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

Dorothy Sears

Dorothy Sears

Associate Professor, School of Medicine

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

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

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.

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

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.

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

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

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


Genetic and Molecular Networks

Biological function is mediated by molecular interactions of genes and proteins. Collecting and interpreting high throughput physical and functional interactomes reveals how cells and organisms function in health and disease, and constitutes a rapidly expanding area of Bioinformatics and Systems Biology.

Ferhat Ay

Ferhat Ay

Assistant Adjunct 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

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

Kelly Frazer

Kelly Frazer

Professor, Pediatrics
Director, Institute for Genomic 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: Using iPSCs for genetic analyses, GWAS, QTL analyses, bioinformatic approaches to understanding human disease, single-cell analyses

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

Christopher Glass

Christopher Glass

Professor, Cellular and Molecular Medicine

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

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

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

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.

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

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 of Medicine and Pediatrics, Division of Endocrinology, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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.

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.

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

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).

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

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

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.

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

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.

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, School of Medicine

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

Research Focus: Molecular epidemiology of HIV and other RNA viruses; Virus phylogenetics and evolution

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.

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

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


Dynamical Systems, Stochastic Processes, and Biological Circuits

Gene regulatory and signal-responsive networks can show complex dynamic and/or stochastic behavior. Combined experimental and theoretical studies reveal emergent properties that determine biological functions, and synthetic biology approaches explore and exploit the design principles of regulatory circuits.

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

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

Jeff Hasty

Jeff Hasty

Associate Professor, Biological Sciences

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

Research Focus: Biodynamics

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

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

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.

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

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

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

Shamim Nemati

Shamim Nemati

Assistant Professor, Biomedical Informatics

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

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).

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

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

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

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

Yingxiao (Peter) Wang

Yingxiao (Peter) Wang

Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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

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

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


Structural Bioinformatics and Systems Pharmacology

Computational studies of protein structure, folding, and molecular interactions are critical for understanding biological function and developing therapeutic compounds. Bioinformatic and physics-based approaches have given rise to fantastic opportunities via in silico docking, screening, structure-based design and chemical genomics to impact personalized medicine.

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

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

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

Michael Gilson

Michael Gilson

Professor, School of Pharmacy

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

Research Focus: Computer-aided drug discovery

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.

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

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

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.

Biomedical Informatics Research Areas


Predictive Modeling and Personalized Medicine

Pattern recognition on clinical data has enabled the development of predictive models for diagnosis and prognosis of human disease. However, the predictive power of these models can be enhanced with genetic data that are increasingly being generated via high throughput technologies, and more recently via whole-genome sequencing. Integrating clinical and molecular data to build, evaluate, and implement accurate prediction models for personalized medicine is a new exciting field of research for biomedical informatics specialists. The impact of personalized medicine on patient outcomes is only beginning to be understood, and this burgeoning area of research and development requires skills in computer science, statistics, and life sciences.

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

Robert El-Kareh

Robert El-Kareh

Associate Professor, Biomedical Informatics

BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Decision Support Systems

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

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

Rodney Gabriel

Rodney Gabriel

Assistant Clinical Professor, School of Medicine

BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine

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

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.

Jejo Koola

Jejo Koola

Assistant Clinical Professor, School of Medicine

BMI Research Area(s):
  • 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

Tsung-Ting Kuo

Assistant Professor, Biomedical Informatics

BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Privacy Technology, Data Sharing, and Big Data Analytics
  • Biomedical Natural Language Processing

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

Amit Majithia

Amit Majithia

Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

Shamim Nemati

Shamim Nemati

Assistant Professor, Biomedical Informatics

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

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


Privacy Technology, Data Sharing, and Big Data Analytics

Whole genome sequences from humans are increasingly being collected for clinical care. Dealing with personal health information requires full compliance with current regulations designed to protect individual privacy. Technologies to preserve privacy in disclosed data allow broader, safer sharing of health information for research and healthcare quality improvement. The rapid collection of data from electronic health records has promoted greater awareness of the need to combine technology and privacy solutions for data sharing. Building accurate predictive models that utilize these data will only be possible if these data can be shared in a privacy-protecting manner, hence the field of privacy technology has been experiencing enormous growth in the past few years, represented by a range of innovations in both theory and applications.

Tsung-Ting Kuo

Tsung-Ting Kuo

Assistant Professor, Biomedical Informatics

BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Privacy Technology, Data Sharing, and Big Data Analytics
  • Biomedical Natural Language Processing

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

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


Data Models and Knowledge Representation

Because research is multi-institutional and lots of data are required to recognize meaningful patterns, it is important to harmonize data collected at different institutions through the use of appropriate data models. Developing automated ontology mapping tools and structuring data and knowledge in a computable format are important pillars of biomedical computing. Although strategies have been developing for several years, before the advent of big healthcare data the need for and efficacy of innovative approaches were not fully appreciated by the biomedical scientific community. Research on data models and representation frameworks has permitted the combination of data from several sources for analytics that support a variety of applications, including decision support systems.

Michael Hogarth

Michael Hogarth

Assoc Physician Dipl, School of Medicine

BMI Research Area(s):
  • 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.


Decision Support Systems

Clinicians and biomedical researchers are often overwhelmed with information and may have difficulties in translating information into actions that have a direct or indirect effect on biomedical knowledge and human health. The design and implementation of effective decision support systems to assist biomedical researchers and/or clinicians perform their tasks in a well-informed manner have the potential to change the biomedical research is conducted and way medicine is practiced. Deep understanding of computational challenges for specific applications areas is required for the assembly of multi-disciplinary teams that can build effective decision support systems.

Robert El-Kareh

Robert El-Kareh

Associate Professor, Biomedical Informatics

BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Decision Support Systems

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

Shamim Nemati

Shamim Nemati

Assistant Professor, Biomedical Informatics

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


Biomedical Natural Language Processing

The wide adoption of electronic health records (EHR) is important for proper collection data that can be used in further computation. However, most of the EHR information is still presented in narrative form. Systems that can understand the language in these documents and structure the data for computation are critical for data analysis and predictive modeling that serve as bases for decision support systems. Natural language processing techniques derived for non-biomedical texts do not always work in biomedical text. For this reason, specialized biomedical natural language processing is necessary and constitutes an important area of research and development in biomedical informatics.

Michael Hogarth

Michael Hogarth

Assoc Physician Dipl, School of Medicine

BMI Research Area(s):
  • 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.

Jejo Koola

Jejo Koola

Assistant Clinical Professor, School of Medicine

BMI Research Area(s):
  • 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

Tsung-Ting Kuo

Assistant Professor, Biomedical Informatics

BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Privacy Technology, Data Sharing, and Big Data Analytics
  • Biomedical Natural Language Processing

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


Bioinformatics Applications in Human Disease

Human disease is a result of genetic and environmental factors. New bioinformatics algorithms can be applied to a combination of genetic, clinical, and environmental factors to help understand disease processes and build predictive models for diagnosis and/or prognosis. Given the heterogeneity of data that are involved, specialized training is necessary to allow innovation in the integration, analysis, and sharing of human subject data related to health and disease.

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
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

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
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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.

Albert Hsiao

Albert Hsiao

Assistant Professor in Residence, Radiology

BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

Research Focus: Cardiac and vascular imaging

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

Amit Majithia

Amit Majithia

Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

Niema Moshiri

Niema Moshiri

Assistant Teaching Professor, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Yingxiao (Peter) Wang

Yingxiao (Peter) Wang

Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Joel Wertheim

Joel Wertheim

Assistant Professor, School of Medicine

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

Research Focus: Molecular epidemiology of HIV and other RNA viruses; Virus phylogenetics and evolution