BISB Faculty by Research Area


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.


Email: l2alexandrov@health.ucsd.edu
Phone: (858) 246-2747

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.


Email: vbafna@ucsd.edu
Phone: (858) 822-4978

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


Email: vibansal@ucsd.edu
Phone: (858) 246-1810

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


Email: sbaumann@ucsd.edu
Phone: (858) 534-7280

Simone Baumann-Pickering

Associate Professor, Scripps Institution of Oceanography
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.


Email: kcurtius@health.ucsd.edu

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


Email: tal.einav@lji.org

Tal Einav

Assistant Professor, La Jolla Institute for Immunology
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
  • Bioinformatics Applications in Human Disease

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


Email: mholst@ucsd.edu
Phone: (858) 534-4899

Michael Holst

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

Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics


Email: amcculloch@ucsd.edu
Phone: (858) 534-2547

Andrew McCulloch

Professor, Bioengineering
Professor, School of Medicine
BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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


Email: gmcvicker@salk.edu
Phone: (858) 453-4100

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


Email: jmesirov@ucsd.edu
Phone: (858) 534-5096

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.


Email: smirarabbaygi@ucsd.edu
Phone: (858) 822-6245

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.


Email: niema@ucsd.edu

Niema Moshiri

Associate 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


Email: palsson@ucsd.edu
Phone: (858) 534-5668

Bernhard Palsson

Y.C. Fung Endowed Professor, Bioengineering
BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Genetic and Molecular Networks

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


Email: ppevzner@ucsd.edu
Phone: (858) 822-4365

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


Email: dsahoo@ucsd.edu
Phone: (858) 246-1803

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


Email: nschork@scripps.edu
Phone: (858) 554-5704

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


Email: bsmarr@ucsd.edu

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?


Email: gtesler@ucsd.edu
Phone: (858) 534-5931

Glenn Tesler

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

Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly


Email: yturakhia@ucsd.edu

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.


Email: rjwilliams@ucsd.edu
Phone: (858) 534-6446

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


Email: dwodarz@ucsd.edu
Phone: (949) 422-7155

Dominik Wodarz

Professor, Biological Sciences
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

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


Email: rxu@ucsd.edu
Phone: (858) 534-6380

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


Email: geneyeo@ucsd.edu
Phone: (858) 534-9321

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.


Email: roseyu@ucsd.edu
Phone: (858) 246-4724

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


Email: kzengler@ucsd.edu
Phone: (858) 504-0823

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.


Email: l2alexandrov@health.ucsd.edu
Phone: (858) 246-2747

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.


Email: aallen@ucsd.edu
Phone: (858) 200-1826

Andrew Allen

Professor, Scripps Institution of Oceanography
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


Email: tamariutabartell@ucsd.edu

Tiffany Amariuta

Assistant Professor, Halıcıoğlu Data Science Institute
Assistant Professor, Biomedical Informatics
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.


Email: vbafna@ucsd.edu
Phone: (858) 822-4978

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


Email: vibansal@ucsd.edu
Phone: (858) 246-1810

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


Email: chc101@ucsd.edu
Phone: (858) 822-3865

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


Email: madantonio@health.ucsd.edu
Phone: (858) 822-4368

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


Email: tgaasterland@ucsd.edu
Phone: (858) 822-4600

Terry Gaasterland

Professor, Scripps Institution of Oceanography
Graduate Program Director, Bioinformatics and Systems Biology
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: Computational Analysis of Human, Novel, and Microbial Genomes: Impact of genetic and evolutionary variation on regulation of transcription and on protein domain structure and function. Causal variants leading to dysregulated cellular response to environmental stresses.


Email: jogleeson@ucsd.edu
Phone: (858) 822-3535

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


Email: mgymrek@ucsd.edu
Phone: (858) 822-2496

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


Email: hsiao@ucsd.edu
Phone: (858) 657-6650

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


Email: wendyjmhuang@health.ucsd.edu
Phone: (858) 246-2258

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.


Email: rknight@ucsd.edu

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


Email: amajithia@ucsd.edu
Phone: (858) 822-0727

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


Email: gmcvicker@salk.edu
Phone: (858) 453-4100

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


Email: ppevzner@ucsd.edu
Phone: (858) 822-4365

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


Email: nschork@scripps.edu
Phone: (858) 554-5704

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


Email: jsebat@ucsd.edu
Phone: (858) 534-6526

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


Email: gtesler@ucsd.edu
Phone: (858) 534-5931

Glenn Tesler

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

Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly


Email: yturakhia@ucsd.edu

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.


Email: vijay@lji.org

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.


Email: ewinzeler@ucsd.edu
Phone: (858) 822-3339

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.


Email: geneyeo@ucsd.edu
Phone: (858) 534-9321

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.


Email: rabagyan@ucsd.edu

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


Email: aallen@ucsd.edu
Phone: (858) 200-1826

Andrew Allen

Professor, Scripps Institution of Oceanography
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


Email: vbafna@ucsd.edu
Phone: (858) 822-4978

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


Email: nbandeira@ucsd.edu
Phone: (858) 534-8666

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


Email: sbriggs@ucsd.edu
Phone: (858) 534-5372

Steve Briggs

Professor, Biological Sciences
BISB Research Area(s):
  • Proteomics and Metabolomics

Research Focus: Stem Cell Identity


Email: pdorrestein@ucsd.edu
Phone: (858) 534-6607

Pieter Dorrestein

Professor, School of Pharmacy
BISB Research Area(s):
  • Proteomics and Metabolomics
  • Genetic and Molecular Networks

Research Focus: Biosynthesis


Email: mholst@ucsd.edu
Phone: (858) 534-4899

Michael Holst

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

Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics


Email: vhook@ucsd.edu
Phone: (858) 822-6682

Vivian Hook

Professor, School of Pharmacy
BISB Research Area(s):
  • Proteomics and Metabolomics

Research Focus: Peptide Neurotransmitters, Protease Mechanisms


Email: hwa@ucsd.edu
Phone: (858) 534-7263

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


Email: mjain@ucsd.edu
Phone: (858) 822-5854

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


Email: smkaech@ucsd.edu

Susan Kaech

Professor, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences
BISB Research Area(s):
  • Proteomics and Metabolomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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


Email: ppevzner@ucsd.edu
Phone: (858) 822-4365

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


Email: staylor@ucsd.edu
Phone: (858) 534-3677

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


Email: geneyeo@ucsd.edu
Phone: (858) 534-9321

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.


Email: huzhou@ucsd.edu
Phone: (858) 534-0038

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.


Email: aallen@ucsd.edu
Phone: (858) 200-1826

Andrew Allen

Professor, Scripps Institution of Oceanography
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


Email: tamariutabartell@ucsd.edu

Tiffany Amariuta

Assistant Professor, Halıcıoğlu Data Science Institute
Assistant Professor, Biomedical Informatics
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.


Email: ferhatay@lji.org
Phone: (858) 752-6612

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


Email: cbenner@ucsd.edu
Phone: (858) 534-9449

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.


Email: bbintu@ucsd.edu

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.


Email: wobusch@ucsd.edu

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.


Email: jcalifano@health.ucsd.edu
Phone: (858) 822-7766

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.


Email: chavez2@health.ucsd.edu

Alejandro Chavez

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

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


Email: lukaschavez@ucsd.edu

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


Email: csc003@ucsd.edu

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.


Email: nchi@ucsd.edu
Phone: (858) 822-1842

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


Email: hcookandersen@ucsd.edu
Phone: (858) 246-2805

Heidi Cook-Andersen

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


Email: kcurtius@health.ucsd.edu

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


Email: madantonio@health.ucsd.edu
Phone: (858) 822-4368

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


Email: ecker@salk.edu
Phone: (858) 453-4100

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


Email: evans@salk.edu

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.


Email: efarley@ucsd.edu
Phone: (858) 246-2559

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


Email: gfeng@ucsd.edu
Phone: (858) 822-5441

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


Email: kfisch@health.ucsd.edu
Phone: (858) 534-9452

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.


Email: kafrazer@health.ucsd.edu
Phone: (858) 246-0208

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


Email: tgaasterland@ucsd.edu
Phone: (858) 822-4600

Terry Gaasterland

Professor, Scripps Institution of Oceanography
Graduate Program Director, Bioinformatics and Systems Biology
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: Computational Analysis of Human, Novel, and Microbial Genomes: Impact of genetic and evolutionary variation on regulation of transcription and on protein domain structure and function. Causal variants leading to dysregulated cellular response to environmental stresses.


Email: gage@salk.edu
Phone: (858) 453-4100

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


Email: kgaulton@ucsd.edu
Phone: (858) 822-3640

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


Email: ckg@ucsd.edu
Phone: (858) 534-6011

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


Email: agoren@ucsd.edu
Phone: (858) 246-0943

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


Email: twguo@health.ucsd.edu
Phone: (858) 246-4541

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


Email: oharismendy@ucsd.edu
Phone: (858) 246-0248

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.


Email: sheinz@ucsd.edu
Phone: (858) 534-9492

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


Email: wendyjmhuang@health.ucsd.edu
Phone: (858) 246-2258

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.


Email: x2huang@ucsd.edu
Phone: (858) 822-2155

Xiaohua Huang

Associate Professor, Bioengineering
BISB Research Area(s):
  • Epigenomics and Gene Expression Control

Research Focus: Genomics, Nanostructure Fabrication


Email: tideker@ucsd.edu
Phone: (858) 822-4558

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


Email: smkaech@ucsd.edu

Susan Kaech

Professor, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences
BISB Research Area(s):
  • Proteomics and Metabolomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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


Email: llaurent@ucsd.edu
Phone: (858) 246-1403

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


Email: jlaw@salk.edu
Phone: (858) 453-4100 x1880

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


Email: pmali@ucsd.edu
Phone: (858) 822-5794

Prashant Mali

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.


Email: gmcvicker@salk.edu
Phone: (858) 453-4100

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


Email: emukamel@ucsd.edu

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


Email: machado@ucsd.edu
Phone: (858) 822-4931

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


Email: aap@ucsd.edu
Phone: (858) 534-2093

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.


Email: trana@ucsd.edu
Phone: (858) 246-1100

Tariq Rana

Distinguished Professor, Pediatrics
BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Multidisciplinary approaches to discover fundamental mechanisms of RNA biology that regulate immune response to viral infections and cancer, vaccines, and immunotherapies.


Email: anrao@ucsd.edu

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


Email: biren@ucsd.edu
Phone: (858) 822-5766

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


Email: mrosenfeld@ucsd.edu
Phone: (858) 534-5858

Michael Rosenfeld

Professor, School of Medicine
BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

Research Focus: Mammalian Neurosystem Development


Email: dsahoo@ucsd.edu
Phone: (858) 246-1803

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


Email: jsebat@ucsd.edu
Phone: (858) 534-6526

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


Email: ptamayo@ucsd.edu
Phone: (858) 246-2385

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.


Email: vijay@lji.org

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.


Email: wei-wang@ucsd.edu
Phone: (858) 822-4240

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


Email: yiw015@ucsd.edu
Phone: (217) 898-2810

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


Email: geneyeo@ucsd.edu
Phone: (858) 534-9321

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.


Email: k4zhang@ucsd.edu
Phone: (858) 822-7876

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.


Email: szhong@ucsd.edu
Phone: (858) 246-1118

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.


Email: l2alexandrov@health.ucsd.edu
Phone: (858) 246-2747

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.


Email: aallen@ucsd.edu
Phone: (858) 200-1826

Andrew Allen

Professor, Scripps Institution of Oceanography
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


Email: ferhatay@lji.org
Phone: (858) 752-6612

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


Email: bbintu@ucsd.edu

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.


Email: wobusch@ucsd.edu

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.


Email: hkcarter@health.ucsd.edu
Phone: (858) 822-4706

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


Email: chavez2@health.ucsd.edu

Alejandro Chavez

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

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


Email: lukaschavez@ucsd.edu

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


Email: csc003@ucsd.edu

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.


Email: nchi@ucsd.edu
Phone: (858) 822-1842

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


Email: hcookandersen@ucsd.edu
Phone: (858) 246-2805

Heidi Cook-Andersen

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


Email: madantonio@health.ucsd.edu
Phone: (858) 822-4368

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


Email: pdorrestein@ucsd.edu
Phone: (858) 534-6607

Pieter Dorrestein

Professor, School of Pharmacy
BISB Research Area(s):
  • Proteomics and Metabolomics
  • Genetic and Molecular Networks

Research Focus: Biosynthesis


Email: gfeng@ucsd.edu
Phone: (858) 822-5441

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


Email: kfisch@health.ucsd.edu
Phone: (858) 534-9452

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.


Email: kafrazer@health.ucsd.edu
Phone: (858) 246-0208

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


Email: tgaasterland@ucsd.edu
Phone: (858) 822-4600

Terry Gaasterland

Professor, Scripps Institution of Oceanography
Graduate Program Director, Bioinformatics and Systems Biology
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: Computational Analysis of Human, Novel, and Microbial Genomes: Impact of genetic and evolutionary variation on regulation of transcription and on protein domain structure and function. Causal variants leading to dysregulated cellular response to environmental stresses.


Email: kgaulton@ucsd.edu
Phone: (858) 822-3640

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


Email: ckg@ucsd.edu
Phone: (858) 534-6011

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


Email: jogleeson@ucsd.edu
Phone: (858) 822-3535

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


Email: agoren@ucsd.edu
Phone: (858) 246-0943

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


Email: twguo@health.ucsd.edu
Phone: (858) 246-4541

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


Email: nhao@ucsd.edu
Phone: (858) 822-1766

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


Email: oharismendy@ucsd.edu
Phone: (858) 246-0248

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.


Email: wendyjmhuang@health.ucsd.edu
Phone: (858) 246-2258

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.


Email: hwa@ucsd.edu
Phone: (858) 534-7263

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


Email: lilyak@ucsd.edu
Phone: (858) 822-1878

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


Email: tideker@ucsd.edu
Phone: (858) 822-4558

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


Email: mjain@ucsd.edu
Phone: (858) 822-5854

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


Email: smkaech@ucsd.edu

Susan Kaech

Professor, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences
BISB Research Area(s):
  • Proteomics and Metabolomics
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

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


Email: rkolodner@ucsd.edu
Phone: (858) 534-7804

Richard Kolodner

Professor, School of Medicine
BISB Research Area(s):
  • Genetic and Molecular Networks

Research Focus: Gene recombination


Email: llaurent@ucsd.edu
Phone: (858) 246-1403

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


Email: jlaw@salk.edu
Phone: (858) 453-4100 x1880

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


Email: n4lewis@ucsd.edu

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.


Email: amajithia@ucsd.edu
Phone: (858) 822-0727

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


Email: pmali@ucsd.edu
Phone: (858) 822-5794

Prashant Mali

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.


Email: jmesirov@ucsd.edu
Phone: (858) 534-5096

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.


Email: aap@ucsd.edu
Phone: (858) 534-2093

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.


Email: palsson@ucsd.edu
Phone: (858) 534-5668

Bernhard Palsson

Y.C. Fung Endowed Professor, Bioengineering
BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Genetic and Molecular Networks

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


Email: biren@ucsd.edu
Phone: (858) 822-5766

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


Email: mrosenfeld@ucsd.edu
Phone: (858) 534-5858

Michael Rosenfeld

Professor, School of Medicine
BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Genetic and Molecular Networks

Research Focus: Mammalian Neurosystem Development


Email: dsahoo@ucsd.edu
Phone: (858) 246-1803

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


Email: jischroeder@ucsd.edu
Phone: (858) 534-7759

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.


Email: shsubramaniam@ucsd.edu
Phone: (858) 822-0986

Shankar Subramaniam

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

Research Focus: Functional Genomics


Email: ptamayo@ucsd.edu
Phone: (858) 246-2385

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.


Email: wei-wang@ucsd.edu
Phone: (858) 822-4240

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


Email: jwertheim@health.ucsd.edu
Phone: (619) 543-5069

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


Email: ewinzeler@ucsd.edu
Phone: (858) 822-3339

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.


Email: geneyeo@ucsd.edu
Phone: (858) 534-9321

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.


Email: kzengler@ucsd.edu
Phone: (858) 504-0823

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.


Email: k4zhang@ucsd.edu
Phone: (858) 822-7876

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.


Email: szhong@ucsd.edu
Phone: (858) 246-1118

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.


Email: huzhou@ucsd.edu
Phone: (858) 534-0038

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.


Email: chavez2@health.ucsd.edu

Alejandro Chavez

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

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


Email: csc003@ucsd.edu

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.


Email: tal.einav@lji.org

Tal Einav

Assistant Professor, La Jolla Institute for Immunology
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
  • Bioinformatics Applications in Human Disease

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


Email: efarley@ucsd.edu
Phone: (858) 246-2559

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


Email: gage@salk.edu
Phone: (858) 453-4100

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


Email: nhao@ucsd.edu
Phone: (858) 822-1766

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


Email: jmhasty@ucsd.edu
Phone: (858) 822-3442

Jeff Hasty

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

Research Focus: Biodynamics


Email: hwa@ucsd.edu
Phone: (858) 534-7263

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


Email: jun@ucsd.edu
Phone: (858) 534-2384

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.


Email: akiger@ucsd.edu
Phone: (858) 822-4594

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


Email: n4lewis@ucsd.edu

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.


Email: amcculloch@ucsd.edu
Phone: (858) 534-2547

Andrew McCulloch

Professor, Bioengineering
Professor, School of Medicine
BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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


Email: cmetallo@ucsd.edu

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


Email: emukamel@ucsd.edu

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


Email: snemati@health.ucsd.edu

Shamim Nemati

Associate 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


Email: anrao@ucsd.edu

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


Email: sarifkin@ucsd.edu
Phone: (858) 822-5748

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


Email: dsahoo@ucsd.edu
Phone: (858) 246-1803

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


Email: bsmarr@ucsd.edu

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?


Email: shsubramaniam@ucsd.edu
Phone: (858) 822-0986

Shankar Subramaniam

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

Research Focus: Functional Genomics


Email: gsuel@ucsd.edu
Phone: (858) 534-0036

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


Email: yiw015@ucsd.edu
Phone: (217) 898-2810

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


Email: rjwilliams@ucsd.edu
Phone: (858) 534-6446

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


Email: dwodarz@ucsd.edu
Phone: (949) 422-7155

Dominik Wodarz

Professor, Biological Sciences
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

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


Email: geneyeo@ucsd.edu
Phone: (858) 534-9321

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.


Email: roseyu@ucsd.edu
Phone: (858) 246-4724

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


Email: kzengler@ucsd.edu
Phone: (858) 504-0823

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.


Email: rabagyan@ucsd.edu

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


Email: nbandeira@ucsd.edu
Phone: (858) 534-8666

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


Email: hkcarter@health.ucsd.edu
Phone: (858) 822-4706

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


Email: mgilson@ucsd.edu
Phone: (858) 822-0622

Michael Gilson

Professor, School of Pharmacy
BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Computer-aided drug discovery


Email: mjain@ucsd.edu
Phone: (858) 822-5854

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


Email: n4lewis@ucsd.edu

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.


Email: jmccammon@ucsd.edu
Phone: (858) 534-2905

Andrew McCammon

Professor, Chemistry and Biochemistry
BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Enzymes and Ligand Binding


Email: amcculloch@ucsd.edu
Phone: (858) 534-2547

Andrew McCulloch

Professor, Bioengineering
Professor, School of Medicine
BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • Predictive Modeling and Personalized Medicine
  • Bioinformatics Applications in Human Disease

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


Email: trana@ucsd.edu
Phone: (858) 246-1100

Tariq Rana

Distinguished Professor, Pediatrics
BISB Research Area(s):
  • Epigenomics and Gene Expression Control
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Multidisciplinary approaches to discover fundamental mechanisms of RNA biology that regulate immune response to viral infections and cancer, vaccines, and immunotherapies.


Email: pwtaylor@ucsd.edu
Phone: (858) 534-1366

Palmer Taylor

Professor and Dean, School of Pharmacy
BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology

Research Focus: Neurotransmission Biochemistry


Email: staylor@ucsd.edu
Phone: (858) 534-3677

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


Email: ewinzeler@ucsd.edu
Phone: (858) 822-3339

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


Email: krking@ucsd.edu

Kevin King

Associate Professor, School of Medicine
Associate Professor, Bioengineering
BISB Research Area(s):
  • TBD
BMI Research Area(s):
  • TBD

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


Email: pkosuri@salk.edu

Pallav Kosuri

Assistant Professor, Salk Institute for Biological Studies
BISB Research Area(s):
  • TBD
BMI Research Area(s):
  • TBD

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


Email: jschoeneberg@ucsd.edu

Johannes Schoeneberg

Assistant Professor, Pharmacology
Assistant Professor, Chemistry and Biochemistry
BISB Research Area(s):
  • TBD
BMI Research Area(s):
  • TBD

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