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

Associate Professor, Cellular and Molecular Medicine
Associate Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Biomedical Natural Language Processing

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.

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

Associate Professor, Pediatrics
Affiliate Faculty, Computer Science and Engineering

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

Simone Baumann-Pickering

Simone Baumann-Pickering

Associate Professor, Marine Biology Research Division

BISB Research Area(s):
  • 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.

Kit Curtius

Kit Curtius

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • 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

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
Assistant Adjunct Professor, Cellular and Molecular Medicine

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
BMI Research Area(s):
  • 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.

Siavash Mirarab

Siavash Mirarab

Associate 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 viral epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development

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

Associate 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

Benjamin Smarr

Benjamin Smarr

Assistant Professor, Bioengineering
Assistant Professor, Halıcıoğlu Data Science Institute

BISB Research Area(s):
  • 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?

Glenn Tesler

Glenn Tesler

Professor, Mathematics

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

Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly

Yatish Turakhia

Yatish Turakhia

Assistant Professor, Electrical and Computer Engineering

BISB Research Area(s):
  • 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.

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
Professor, Herbert Wertheim School of Public Health and Human Longevity Science
Professor, Halıcıoğlu Data Science Institute

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.

Rose Yu

Rose Yu

Assistant Professor, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Decision Support Systems

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

Karsten Zengler

Karsten Zengler

Adjunct Professor, Pediatrics

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

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.

Ludmil Alexandrov

Ludmil Alexandrov

Associate Professor, Cellular and Molecular Medicine
Associate Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Biomedical Natural Language Processing

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

Andrew Allen

Professor, Integrative Oceanography Division

BISB Research Area(s):
  • 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

Tiffany Amariuta

Tiffany Amariuta

Assistant Professor, Halıcıoğlu Data Science Institute
Assistant Professor, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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

Associate Professor, Pediatrics
Affiliate Faculty, Computer Science and Engineering

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

Chi-Hua Chen

Chi-Hua Chen

Associate Adjunct Professor, Radiology

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

Research Focus: Neuroimaging genetics, neuropsychiatric disorders

Matteo D'Antonio

Matteo D'Antonio

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine

Research Focus: Associations between genetic variation, molecular phenotypes, complex traits and disease

Terry Gaasterland

Terry Gaasterland

Professor and Director of Scripps Genome Center, Marine Biology Research Division
Graduate Program 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, Neurosciences (School of Medicine)
Director of Neurogenetics, Rady Children's Institute for Genomic 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: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions

Melissa Gymrek

Melissa Gymrek

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

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

Research Focus: Contribution of complex genetic variation to human phenotypes

Albert Hsiao

Albert Hsiao

Associate Professor in Residence, Radiology

BISB Research Area(s):
  • Comparative and Population Genomics
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Wendy Huang

Wendy Huang

Assistant Professor, Cellular and Molecular Medicine

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

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
Assistant Adjunct Professor, Cellular and Molecular Medicine

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

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

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

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

Glenn Tesler

Glenn Tesler

Professor, Mathematics

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

Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly

Yatish Turakhia

Yatish Turakhia

Assistant Professor, Electrical and Computer Engineering

BISB Research Area(s):
  • 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

Pandurangan Vijayanand

Professor, La Jolla Institute for Immunology
Associate Adjunct Professor, School of Medicine

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

Elizabeth Winzeler

Elizabeth Winzeler

Professor, Pediatrics

BISB Research Area(s):
  • 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.

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.


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

Andrew Allen

Andrew Allen

Professor, Integrative Oceanography Division

BISB Research Area(s):
  • 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

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

Professor, School of Pharmacy
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

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

Terence Hwa

Terence Hwa

Distinguished Professor, Physics
Distinguished Professor, Biological Sciences

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

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

Mohit Jain

Mohit Jain

Associate Professor, Pharmacology

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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

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

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.

Huilin Zhou

Huilin Zhou

Professor, Cellular and Molecular Medicine

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

Research Focus: Proteomics and genome maintenance


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.

Andrew Allen

Andrew Allen

Professor, Integrative Oceanography Division

BISB Research Area(s):
  • 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

Tiffany Amariuta

Tiffany Amariuta

Assistant Professor, Halıcıoğlu Data Science Institute
Assistant Professor, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Ferhat Ay

Ferhat Ay

Associate Professor, La Jolla Institute for Immunology
Assistant Adjunct Professor, Pediatrics

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

Christopher Benner

Christopher Benner

Assistant Professor, School of Medicine

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

Bogdan Bintu

Bogdan Bintu

Assistant Professor, Cellular and Molecular Medicine
Assistant Professor, Bioengineering

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

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

Wolfgang Busch

Wolfgang Busch

Professor, Salk Institute for Biological Studies
Associate Adjunct Professor, Biological Sciences

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

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

Joseph Califano

Joseph Califano

Physician in Chief and Professor, Surgery
Moores Cancer Director and Head and Neck Cancer Center Director, Surgery

BISB Research Area(s):
  • 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.

Lukas Chavez Kuss

Lukas Chavez Kuss

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

Christine Cheng

Christine Cheng

Associate Professor In Residence, Psychiatry

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

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

Neil Chi

Neil Chi

Professor, School of Medicine

BISB Research Area(s):
  • 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

Kit Curtius

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • 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

Matteo D'Antonio

Matteo D'Antonio

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine

Research Focus: Associations between genetic variation, molecular phenotypes, complex traits and disease

Joseph Ecker

Joseph Ecker

Professor and HHMI Investigator, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences

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

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

Ronald M. Evans

Ronald M. Evans

Professor and Director, Gene Expression Lab, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences

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

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

Gen-Sheng Feng

Gen-Sheng Feng

Professor, Pathology
Professor, Biological Sciences

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

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

Kathleen Fisch

Kathleen Fisch

Assistant Professor, Reproductive Medicine

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

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

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 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

Fred (Rusty) Gage

Fred (Rusty) Gage

President, Salk Institute for Biological Studies
Professor, Laboratory of Genetics, Salk Institute for Biological Studies
Adjunct 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: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu

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

Theresa Guo

Theresa Guo

Assistant Professor, Surgery

BISB Research Area(s):
  • 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

Olivier Harismendy

Olivier Harismendy

Associate 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.

Sven Heinz

Sven Heinz

Assistant Professor, School of Medicine

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

Research Focus: Regulation and reprogramming of transcription, cancer epigenetics

Xiaohua Huang

Xiaohua Huang

Associate Professor, Bioengineering

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

Research Focus: Genomics, Nanostructure Fabrication

Wendy Huang

Wendy Huang

Assistant Professor, Cellular and Molecular Medicine

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

Trey Ideker

Trey Ideker

Professor, Division of Medical Genetics
Graduate Program Associate 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

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
Assistant Adjunct Professor, Biological Sciences

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

Associate 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
Assistant Adjunct Professor, Cellular and Molecular Medicine

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

Abraham Palmer

Abraham Palmer

Professor, Psychiatry

BISB Research Area(s):
  • 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.

Anjana Rao

Anjana Rao

Professor, La Jolla Institute for Immunology
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

Associate 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

Jonathan Sebat

Jonathan Sebat

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

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

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.

Pandurangan Vijayanand

Pandurangan Vijayanand

Professor, La Jolla Institute for Immunology
Associate Adjunct Professor, School of Medicine

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

Yingxiao (Peter) Wang

Professor, Bioengineering

BISB Research Area(s):
  • 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

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

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

Professor, Bioengineering

BISB Research Area(s):
  • 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.


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.

Ludmil Alexandrov

Ludmil Alexandrov

Associate Professor, Cellular and Molecular Medicine
Associate Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Biomedical Natural Language Processing

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

Andrew Allen

Professor, Integrative Oceanography Division

BISB Research Area(s):
  • 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

Ferhat Ay

Associate Professor, La Jolla Institute for Immunology
Assistant Adjunct Professor, Pediatrics

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

Bogdan Bintu

Bogdan Bintu

Assistant Professor, Cellular and Molecular Medicine
Assistant Professor, Bioengineering

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

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

Wolfgang Busch

Wolfgang Busch

Professor, Salk Institute for Biological Studies
Associate Adjunct Professor, Biological Sciences

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

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

Hannah Carter

Hannah Carter

Associate Professor, Division of Medical Genetics

BISB Research Area(s):
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • 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 Kuss

Lukas Chavez Kuss

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

Christine Cheng

Christine Cheng

Associate Professor In Residence, Psychiatry

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

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

Neil Chi

Neil Chi

Professor, School of Medicine

BISB Research Area(s):
  • 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

Matteo D'Antonio

Matteo D'Antonio

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine

Research Focus: Associations between genetic variation, molecular phenotypes, complex traits and disease

Pieter Dorrestein

Pieter Dorrestein

Professor, School of Pharmacy

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

Research Focus: Biosynthesis

Gen-Sheng Feng

Gen-Sheng Feng

Professor, Pathology
Professor, Biological Sciences

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

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

Kathleen Fisch

Kathleen Fisch

Assistant Professor, Reproductive Medicine

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

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

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

Joseph Gleeson

Joseph Gleeson

Professor, Neurosciences (School of Medicine)
Director of Neurogenetics, Rady Children's Institute for Genomic 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: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions

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

Theresa Guo

Theresa Guo

Assistant Professor, Surgery

BISB Research Area(s):
  • 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

Nan Hao

Nan Hao

Associate 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

Associate 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.

Wendy Huang

Wendy Huang

Assistant Professor, Cellular and Molecular Medicine

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

Terence Hwa

Terence Hwa

Distinguished Professor, Physics
Distinguished Professor, Biological Sciences

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

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

Lilia Iakoucheva

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 Associate 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

Mohit Jain

Mohit Jain

Associate Professor, Pharmacology

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Richard Kolodner

Richard Kolodner

Professor, School of Medicine

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

Research Focus: Gene recombination

Louise Laurent

Louise Laurent

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
Assistant Adjunct Professor, Biological Sciences

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

Associate 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
BMI Research Area(s):
  • 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.

Abraham Palmer

Abraham Palmer

Professor, Psychiatry

BISB Research Area(s):
  • 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

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

Associate 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.

Edward Stites

Edward Stites

Assistant Professor, Salk Institute for Biological Studies
Assistant Adjunct Professor, Dermatology

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

Research Focus: Using mathematical and computational models to study the behaviors of genetic signaling networks implicated in cancer.

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

Associate 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, SARS-CoV-2, and other RNA viruses; Viral phylogenetics and evolution

Elizabeth Winzeler

Elizabeth Winzeler

Professor, Pediatrics

BISB Research Area(s):
  • 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.

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

Adjunct Professor, Pediatrics

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

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

Professor, Bioengineering

BISB Research Area(s):
  • 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.

Huilin Zhou

Huilin Zhou

Professor, Cellular and Molecular Medicine

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

Research Focus: Proteomics and genome maintenance


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.

Christine Cheng

Christine Cheng

Associate Professor In Residence, Psychiatry

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

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

Emma Farley

Emma Farley

Assistant Professor, Biological Sciences

BISB Research Area(s):
  • 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

Fred (Rusty) Gage

Fred (Rusty) Gage

President, Salk Institute for Biological Studies
Professor, Laboratory of Genetics, Salk Institute for Biological Studies
Adjunct 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: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu

Nan Hao

Nan Hao

Associate 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

Professor, Biological Sciences

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

Research Focus: Biodynamics

Terence Hwa

Terence Hwa

Distinguished Professor, Physics
Distinguished Professor, Biological Sciences

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

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

Suckjoon Jun

Suckjoon Jun

Professor, Physics
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

Associate 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

Associate 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

Professor, La Jolla Institute for Immunology
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

Associate 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

Associate 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

Benjamin Smarr

Benjamin Smarr

Assistant Professor, Bioengineering
Assistant Professor, Halıcıoğlu Data Science Institute

BISB Research Area(s):
  • 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?

Edward Stites

Edward Stites

Assistant Professor, Salk Institute for Biological Studies
Assistant Adjunct Professor, Dermatology

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

Research Focus: Using mathematical and computational models to study the behaviors of genetic signaling networks implicated in cancer.

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

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

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.

Rose Yu

Rose Yu

Assistant Professor, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Decision Support Systems

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

Karsten Zengler

Karsten Zengler

Adjunct Professor, Pediatrics

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


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

Nuno Bandeira

Nuno Bandeira

Professor, School of Pharmacy
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

Associate Professor, Division of Medical Genetics

BISB Research Area(s):
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • 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

Michael Gilson

Michael Gilson

Professor, School of Pharmacy

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

Research Focus: Computer-aided drug discovery

Mohit Jain

Mohit Jain

Associate Professor, Pharmacology

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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
  • 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.


Other BISB Research Areas

Heidi Cook-Andersen

Heidi Cook-Andersen

Assistant Professor, Reproductive Medicine
Assistant Professor, Biological Sciences

BISB Research Area(s):
  • TBD
BMI Research Area(s):
  • TBD

Research Focus: Human embryo development and improving infertility treatments

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Susan Kaech

Professor, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences

BISB Research Area(s):
  • TBD
BMI Research Area(s):
  • TBD

Research Focus: Memory T cells

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.

Ludmil Alexandrov

Ludmil Alexandrov

Associate Professor, Cellular and Molecular Medicine
Associate Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Biomedical Natural Language Processing

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.

Hannah Carter

Hannah Carter

Associate Professor, Division of Medical Genetics

BISB Research Area(s):
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • 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 Kuss

Lukas Chavez Kuss

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

Chi-Hua Chen

Chi-Hua Chen

Associate Adjunct Professor, Radiology

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

Research Focus: Neuroimaging genetics, neuropsychiatric disorders

Kit Curtius

Kit Curtius

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • 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

Matteo D'Antonio

Matteo D'Antonio

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine

Research Focus: Associations between genetic variation, molecular phenotypes, complex traits and disease

Robert El-Kareh

Robert El-Kareh

Associate Clinical 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

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.

Fred (Rusty) Gage

Fred (Rusty) Gage

President, Salk Institute for Biological Studies
Professor, Laboratory of Genetics, Salk Institute for Biological Studies
Adjunct 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: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu

Joseph Gleeson

Joseph Gleeson

Professor, Neurosciences (School of Medicine)
Director of Neurogenetics, Rady Children's Institute for Genomic 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: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions

Olivier Harismendy

Olivier Harismendy

Associate 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

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

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
BMI Research Area(s):
  • 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.

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

Jonathan Sebat

Jonathan Sebat

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

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

Rose Yu

Rose Yu

Assistant Professor, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Decision Support Systems

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

Karsten Zengler

Karsten Zengler

Adjunct Professor, Pediatrics

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


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

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

Karsten Zengler

Karsten Zengler

Adjunct Professor, Pediatrics

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


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

Clinical Professor, 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.

Karsten Zengler

Karsten Zengler

Adjunct Professor, Pediatrics

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


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 Clinical 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

Rose Yu

Rose Yu

Assistant Professor, Computer Science and Engineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Decision Support Systems

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


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.

Ludmil Alexandrov

Ludmil Alexandrov

Associate Professor, Cellular and Molecular Medicine
Associate Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Biomedical Natural Language Processing

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.

Michael Hogarth

Michael Hogarth

Clinical Professor, 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.


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.

Tiffany Amariuta

Tiffany Amariuta

Assistant Professor, Halıcıoğlu Data Science Institute
Assistant Professor, School of Medicine

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Ferhat Ay

Ferhat Ay

Associate Professor, La Jolla Institute for Immunology
Assistant Adjunct Professor, Pediatrics

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

Christopher Benner

Christopher Benner

Assistant Professor, School of Medicine

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

Hannah Carter

Hannah Carter

Associate Professor, Division of Medical Genetics

BISB Research Area(s):
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • 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 Kuss

Lukas Chavez Kuss

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

Chi-Hua Chen

Chi-Hua Chen

Associate Adjunct Professor, Radiology

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

Research Focus: Neuroimaging genetics, neuropsychiatric disorders

Kit Curtius

Kit Curtius

Assistant Professor, Biomedical Informatics

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • 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

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

Fred (Rusty) Gage

Fred (Rusty) Gage

President, Salk Institute for Biological Studies
Professor, Laboratory of Genetics, Salk Institute for Biological Studies
Adjunct 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: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu

Joseph Gleeson

Joseph Gleeson

Professor, Neurosciences (School of Medicine)
Director of Neurogenetics, Rady Children's Institute for Genomic 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: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions

Olivier Harismendy

Olivier Harismendy

Associate 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

Associate Professor in Residence, Radiology

BISB Research Area(s):
  • Comparative and Population Genomics
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

Wendy Huang

Wendy Huang

Assistant Professor, Cellular and Molecular Medicine

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

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

Mohit Jain

Mohit Jain

Associate Professor, Pharmacology

BISB Research Area(s):
  • Proteomics and Metabolomics
  • Genetic and Molecular Networks
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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

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

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
BMI Research Area(s):
  • 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.

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

Jonathan Sebat

Jonathan Sebat

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

BISB Research Area(s):
  • Comparative and Population Genomics
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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

Pandurangan Vijayanand

Pandurangan Vijayanand

Professor, La Jolla Institute for Immunology
Associate Adjunct Professor, School of Medicine

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

Joel Wertheim

Joel Wertheim

Associate 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, SARS-CoV-2, and other RNA viruses; Viral phylogenetics and evolution

Karsten Zengler

Karsten Zengler

Adjunct Professor, Pediatrics

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


Other BMI Research Areas

Heidi Cook-Andersen

Heidi Cook-Andersen

Assistant Professor, Reproductive Medicine
Assistant Professor, Biological Sciences

BISB Research Area(s):
  • TBD
BMI Research Area(s):
  • TBD

Research Focus: Human embryo development and improving infertility treatments

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Susan Kaech

Professor, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences

BISB Research Area(s):
  • TBD
BMI Research Area(s):
  • TBD

Research Focus: Memory T cells