Participating Faculty
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Ruben Abagyan
Professor, School of Pharmacy- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Structure-based Drug Discovery, Cheminformatics, Drug Repurposing, Computational Pharmacology, Target/pathway Discovery
Ludmil Alexandrov
Associate Professor, Cellular and Molecular MedicineAssociate Professor, Bioengineering
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Biomedical Natural Language Processing
Research Focus: Using large-scale omics data to study mutational processes causing human cancer, identifying potential cancer prevention strategies with ML and NLP approaches, and developing novel ML tools for better targeting of cancer treatment.
Andrew Allen
Professor, Scripps Institution of Oceanography- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Ecological, comparative, and functional genomics of marine phytoplankton, Systems biology of microalgae, Genome evolution and evolutionary origins of metabolic function in marine microbes, Transcriptional regulatory networks, Metagenomics, Metatranscriptomics, Microbes, Evolution
Tiffany Amariuta
Assistant Professor, Halıcıoğlu Data Science InstituteAssistant Professor, Biomedical Informatics
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Bioinformatics Applications in Human Disease
Research Focus: We are a statistical genetics lab focusing on developing methods to study complex traits and polygenic diseases in global populations. We are specifically interested in fine-mapping disease genes and their cell types of action, with the goal of finding targets for gene-based therapeutics.
Ferhat Ay
Associate Professor, La Jolla Institute for ImmunologyAssistant Adjunct Professor, Pediatrics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Epigenetics, genomics, chromatin structure, 3D/4D genome/nucleome, statistical methods for analysis of Hi-C and HiChIP data, gene regulation in immune cells, cancer genomics
Vineet Bafna
Professor, Computer Science and Engineering- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
Research Focus: Bioinformatics Algorithms, Proteomics, Population Genetics
Nuno Bandeira
Professor, School of PharmacyProfessor, Computer Science and Engineering
- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Bioinformatics and computational mass spectrometry
Vikas Bansal
Associate Professor, PediatricsAffiliate Faculty, Computer Science and Engineering
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Computational tools for variant calling, haplotyping and analysis of rare variants in disease association studies
Simone Baumann-Pickering
Associate Professor, Scripps Institution of Oceanography- Quantitative Foundations of Computational Biology
Research Focus: The Scripps Acoustic Ecology Laboratory investigates phenological patterns and spatial ecology of cetaceans, interactions of predators and their prey, and adaptations of animals to changes in their environment.
Christopher Benner
Assistant Professor, School of Medicine- Epigenomics and Gene Expression Control
- Bioinformatics Applications in Human Disease
Research Focus:
Transcription, bioinformatics, genomics, innate immunity, chromatin.
We use next-generation sequencing (NGS) and computational analysis to understand the mechanisms responsible for transcription and epigenetic regulation in human development and disease.
Bogdan Bintu
Assistant Professor, Cellular and Molecular MedicineAssistant Professor, Bioengineering
- 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.
Steve Briggs
Professor, Biological Sciences- Proteomics and Metabolomics
Research Focus: Stem Cell Identity
Wolfgang Busch
Professor, Salk Institute for Biological StudiesAssociate Adjunct Professor, Biological Sciences
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Researching and developing plant varieties with enhanced carbon sequestration capabilities for removing CO2 from the atmosphere and thereby counteracting climate change.
Joseph Califano
Physician in Chief and Professor, SurgeryMoores Cancer Director and Head and Neck Cancer Center Director, Surgery
- Epigenomics and Gene Expression Control
Research Focus: The Califano laboratory investigates the molecular and immunologic basis of head and neck neoplasia, employing integrative computational techniques in concert with molecular, in vitro, and in vivo techniques to define opportunities for therapeutic intervention in a variety of tumors.
Hannah Carter
Associate Professor, Division of Medical Genetics- Genetic and Molecular Networks
- Structural Bioinformatics and Systems Pharmacology
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Genomics and systems biology for precision cancer medicine, variant interpretation, network analysis, immunogenomics
Alejandro Chavez
Associate Professor, Pediatrics- 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
Lukas Chavez Kuss
Assistant Professor, School of Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Chromatin and Gene Regulation in Childhood Cancers
Chi-Hua Chen
Associate Adjunct Professor, Radiology- Comparative and Population Genomics
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Neuroimaging genetics, neuropsychiatric disorders
Christine Cheng
Associate Professor In Residence, Psychiatry- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Utilize single cell resolution functional genomic assays and computational methods to study heterogeneous clinical tissue samples and blood immune cell populations in patient samples.
Neil Chi
Professor, School of Medicine- 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
Heidi Cook-Andersen
Assistant Professor, Biological SciencesAssistant Professor, Reproductive Medicine
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- 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.
Kit Curtius
Assistant Professor, Biomedical Informatics- Quantitative Foundations of Computational Biology
- Epigenomics and Gene Expression Control
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Mathematical models of cancer evolution, optimization of cancer screening and surveillance, epigenetic aging, translational risk prediction tools
Matteo D'Antonio
Assistant Professor, Biomedical Informatics- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
Research Focus: Associations between genetic variation, molecular phenotypes, complex traits and disease
Pieter Dorrestein
Professor, School of Pharmacy- Proteomics and Metabolomics
- Genetic and Molecular Networks
Research Focus: Biosynthesis
Joseph Ecker
Professor and HHMI Investigator, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
- Epigenomics and Gene Expression Control
Research Focus: Epigenomics of the mammalian brain - human brain cell atlas
Tal Einav
Assistant Professor, La Jolla Institute for Immunology- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Antibody-virus interactions, predicting each person's vaccine response, personalized medicine
Robert El-Kareh
Associate Clinical Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Clinical informatics, clinical decision support, diagnostic safety, quality improvement, patient safety
Ronald M. Evans
Professor and Director, Gene Expression Lab, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
- Epigenomics and Gene Expression Control
Research Focus: Role of hormones, both in their normal activities and in disease.
Emma Farley
Assistant Professor, Biological Sciences- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: High-throughput functional assays in developing embryos to decipher how genomes instruct development
Gen-Sheng Feng
Professor, PathologyProfessor, Biological Sciences
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Deciphering the anti-oncogenic effects of pro-oncogenic molecules in liver cancer
Kathleen Fisch
Assistant Professor, Reproductive Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Understanding the molecular mechanisms underlying pregnancy disorders and exposures to improve maternal and child health throughout the lifespan.
Kelly Frazer
Professor, PediatricsDirector, Institute for Genomic Medicine
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Using iPSCs for genetic analyses, GWAS, QTL analyses, bioinformatic approaches to understanding human disease, single-cell analyses
Terry Gaasterland
Professor, Scripps Institution of OceanographyGraduate Program Director, Bioinformatics and Systems Biology
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- 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.
Rodney Gabriel
Assistant Clinical Professor, School of Medicine- Predictive Modeling and Personalized Medicine
Research Focus: Perioperative outcomes, pharmacogenomics, machine learning, predictive modeling, regional anesthesia, acute pain.
Fred (Rusty) Gage
President, Salk Institute for Biological StudiesProfessor, Laboratory of Genetics, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu
Kyle Gaulton
Assistant Professor, Pediatrics- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Statistical genetics, epigenomics, chromatin, gene regulatory networks, diabetes
Michael Gilson
Professor, School of Pharmacy- Structural Bioinformatics and Systems Pharmacology
Research Focus: Computer-aided drug discovery
Christopher Glass
Professor, Cellular and Molecular Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Enhancer Selection and Functions, Macrophage Subtypes, Genetic Variation, Enhancer Transcription
Joseph Gleeson
Professor, Neurosciences (School of Medicine)Director of Neurogenetics, Rady Children's Institute for Genomic Medicine
- Comparative and Population Genomics
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions
Alon Goren
Assistant Professor, School of Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Dynamics of epigenomic mechanisms during development and along the cell cycle
Theresa Guo
Assistant Professor, Surgery- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Splicing alteration in human cancer, with particular focus on HPV mediated head and neck tumors; Interaction between genomic alterations and tumor immunity; post transcriptional and epigenetic regulation of splicing
Melissa Gymrek
Associate Professor, School of MedicineAssociate Professor, Computer Science and Engineering
- Comparative and Population Genomics
Research Focus: Contribution of complex genetic variation to human phenotypes
Nan Hao
Associate Professor, Biological Sciences- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Dynamic regulation of signaling and transcriptional networks in single cells
Olivier Harismendy
Associate Professor, Biomedical Informatics- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: My laboratory develops genome-wide assays and analysis for personalized cancer care. Particular focus includes genetics of cancer susceptibility and drug response, secure computing and data sharing.
Jeff Hasty
Professor, Biological Sciences- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Biodynamics
Sven Heinz
Assistant Professor, School of Medicine- Epigenomics and Gene Expression Control
Research Focus: Regulation and reprogramming of transcription, cancer epigenetics
Michael Hogarth
Clinical Professor, Biomedical Informatics- Data Models and Knowledge Representation
- Biomedical Natural Language Processing
Research Focus: Development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.
Michael Holst
Professor, Mathematics- Quantitative Foundations of Computational Biology
- Proteomics and Metabolomics
Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics
Vivian Hook
Professor, School of Pharmacy- Proteomics and Metabolomics
Research Focus: Peptide Neurotransmitters, Protease Mechanisms
Albert Hsiao
Associate Professor in Residence, Radiology- Comparative and Population Genomics
- Bioinformatics Applications in Human Disease
Research Focus: Artificial Intelligence, Cardiovascular, COVID-19, x-ray, CT, MRI, Point-of-care Ultrasound
Wendy Huang
Assistant Professor, Cellular and Molecular Medicine- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: To assess the contributions of RNA-binding proteins and their associated non-coding RNAs to host immune homeostasis and autoimmune pathologies.
Xiaohua Huang
Associate Professor, Bioengineering- Epigenomics and Gene Expression Control
Research Focus: Genomics, Nanostructure Fabrication
Terence Hwa
Distinguished Professor, PhysicsDistinguished Professor, Biological Sciences
- Proteomics and Metabolomics
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Use of proteomic and metabolomic approaches to study resource allocation strategies employed during bacterial growth; mechanistic studies of metabolic interactions in bacterial communities
Lilia Iakoucheva
Associate Professor, Psychiatry- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Autism, genetics, gene expression, protein interactions, systems biology, networks, psychiatric diseases, whole genome sequencing
Trey Ideker
Professor, Division of Medical GeneticsGraduate Program Associate Director, Bioinformatics and Systems Biology
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Biological Networks, Cellular Modeling, Cancer Genomics, Epigenetic Aging
Mohit Jain
Associate Professor, Pharmacology- Proteomics and Metabolomics
- Genetic and Molecular Networks
- Structural Bioinformatics and Systems Pharmacology
- Bioinformatics Applications in Human Disease
Research Focus:
Human Biology, Metabolic Biochemistry, Integrative Biology, Mass Spectrometry, Metabolomics
Suckjoon Jun
Professor, PhysicsProfessor, Biological Sciences
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Biophysics. Use physics and engineering to explain why biological systems are the way they are.
Susan Kaech
Professor, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Understanding how Memory T Cells are produced during infection and vaccination
Amy Kiger
Associate Professor, Biological Sciences- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Genomics, Cellular Morphogenesis, RNAi, Image Analysis of Microscopy Data
Kevin King
Associate Professor, School of MedicineAssociate Professor, Bioengineering
- TBD
- 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.
Rob Knight
Professor, PediatricsAffiliate Faculty, Computer Science and Engineering
- Comparative and Population Genomics
Research Focus: Human microbiome, microbial community ecology, multi-omics analyses
Richard Kolodner
Professor, School of Medicine- Genetic and Molecular Networks
Research Focus: Gene recombination
Jejo Koola
Assistant Clinical Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Biomedical Natural Language Processing
Research Focus: Practicing internist in the field of hospital medicine and clinical informatics. Research focus is on using informatics tools (including predictive analytics, natural language processing, and information visualization) to improve the care of multi-morbid hospital patients.
Pallav Kosuri
Assistant Professor, Salk Institute for Biological Studies- TBD
- 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.
Tsung-Ting Kuo
Assistant Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
Research Focus: Blockchain Technologies, Machine Learning, Natural Language Processing
Louise Laurent
Professor, Reproductive Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Gene Interaction Networks, Biomarker Discovery, Pluripotency, Embryonic Development, Placental Dysfunction, Preeclampsia, Pregnancy complications
Julie Law
Assistant Professor, Salk Institute for Biological StudiesAssistant Adjunct Professor, Biological Sciences
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Chromatin modifications, epigenetics, genomics, gene regulation
Nathan E. Lewis
Associate Professor, Pediatrics- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Systems biology approaches for integration of disparate data types to study diseases involving metabolism, glycobiology, and to guide cell engineering for drug development.
Amit Majithia
Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of Medicine- Comparative and Population Genomics
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Insulin resistance, functional genomics, pharmacogenetics, cardiometabolic disease, diabetes
Prashant Mali
Professor, Bioengineering- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: The Mali laboratory is working in the fields of synthetic biology and regenerative medicine, with a long-term focus on developing tools for enabling gene and cell based human therapeutics.
Andrew McCammon
Professor, Chemistry and Biochemistry- Structural Bioinformatics and Systems Pharmacology
Research Focus: Enzymes and Ligand Binding
Andrew McCulloch
Professor, BioengineeringProfessor, School of Medicine
- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Structural Bioinformatics and Systems Pharmacology
- 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
Graham McVicker
Assistant Professor, Salk Institute for Biological StudiesAssistant Adjunct Professor, Cellular and Molecular Medicine
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
Research Focus: Human genetic variation, chromatin and gene regulation in immune cells
Jill Mesirov
Professor, School of MedicineAssociate Vice Chancellor, Computational Health Sciences,
Professor of Medicine, Division of Medical Genetics
- Quantitative Foundations of Computational Biology
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.
Christian Metallo
Associate Professor, Bioengineering- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Metabolism, system biology, mass spectrometry, flux analysis, cancer, stem cell biology
Siavash Mirarab
Associate Professor, Electrical and Computer Engineering- Quantitative Foundations of Computational Biology
Research Focus: Computational biology, large scale phylogenetics, estimation of species trees from gene trees (phylogenomics), large scale multiple sequence alignment, and metagenomic analysis using phylogenetic placement.
Niema Moshiri
Associate Teaching Professor, Computer Science and Engineering- Quantitative Foundations of Computational Biology
- Bioinformatics Applications in Human Disease
Research Focus: Computational viral epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development
Eran Mukamel
Assistant Professor, Cognitive Science- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Computational neuroscience, brain cell differentiation and development, computational analysis of brain-network dynamics
Shamim Nemati
Associate Professor, Biomedical Informatics- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Signal Processing, Dynamical Systems, Multivariate Time Series, Point Process, Deep Learning, Reinforcement Learning, Video Processing, and Natural Language Processing
Lucila Ohno-Machado
Professor, Biomedical Informatics- Epigenomics and Gene Expression Control
- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
Research Focus: Biomedical Informatics, predictive modeling, biomedical data analytics
Abraham Palmer
Professor, Psychiatry- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Quantitative genetic studies of behavior using fish, mice, rats and humans. Applying statistical genetics and genomics approaches to understanding behavior.
Bernhard Palsson
Y.C. Fung Endowed Professor, Bioengineering- 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).
Pavel Pevzner
Professor and Ronald R Taylor Chair, Computer Science and Engineering- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
Research Focus: Computational Molecular Biology
Tariq Rana
Distinguished Professor, Pediatrics- 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.
Anjana Rao
Professor, La Jolla Institute for ImmunologyAdjunct Professor, Pharmacology
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Understanding how signalling pathways control gene expression, using T cells and other cells of the immune system as models
Bing Ren
Professor, Cellular and Molecular Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Gene Regulatory Networks
Scott Rifkin
Associate Professor, Biological Sciences- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Evolutionary Biology-Patterns of Gene Expression
Michael Rosenfeld
Professor, School of Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Mammalian Neurosystem Development
Debashis Sahoo
Associate Professor, Pediatrics- 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
Johannes Schoeneberg
Assistant Professor, PharmacologyAssistant Professor, Chemistry and Biochemistry
- TBD
- 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.
Nicholas Schork
Professor, Scripps Research Institute- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Developing mathematical, statistical, and computational models and tools to study the genetic basis of complex traits and diseases
Julian Schroeder
Professor, Biological Sciences- Genetic and Molecular Networks
Research Focus: Climate change resistance and drought resistance and plant stress signal transduction. Discovery of signaling networks and biological sensors, using systems biological approaches, transcriptomics, proteomics and genome editing.
Jonathan Sebat
Director, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Professor of Psychiatry and Cellular & Molecular Medicine, Cellular and Molecular Medicine- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- 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
Amy Sitapati
Clinical Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
- Data Models and Knowledge Representation
- Decision Support Systems
Research Focus: Biomedical Informatics, Registries, Population Health, Precision Medicine, Vital Records Informatics, Artificial Intelligence, Quality Informatics, Health Analytics
Benjamin Smarr
Assistant Professor, BioengineeringAssistant Professor, Halıcıoğlu Data Science Institute
- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: What information do biological timeseries hold? What biodynamic interactions generate these signals?
Shankar Subramaniam
Professor, Bioengineering- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Functional Genomics
Gurol Suel
Professor, Biological Sciences- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Identifying systems-level design principles of cellular differentiation circuits
Pablo Tamayo
Professor, School of Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Development of analysis methods for the functional characterization of cancer genomes including RNAi and CRISPR genetic dependencies. Computational methods, probability and statistics, data analysis, machine learning, computational biology and cancer research.
Palmer Taylor
Professor and Dean, School of Pharmacy- Structural Bioinformatics and Systems Pharmacology
Research Focus: Neurotransmission Biochemistry
Susan Taylor
Professor, Chemistry and Biochemistry- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Relationship of CAPK Structure to Function
Glenn Tesler
Professor, Mathematics- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly
Yatish Turakhia
Assistant Professor, Electrical and Computer Engineering- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus:
Algorithms and domain-specific hardware accelerators that enable faster and cheaper progress in biology and medicine.
Computational methods that enable biological discoveries, such as new genotype-phenotype relationships.
Pandurangan Vijayanand
Professor, La Jolla Institute for ImmunologyAssociate Adjunct Professor, School of Medicine
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Bioinformatics Applications in Human Disease
Research Focus: Continually evolving genomic tools and single cell analysis technologies are revolutionizing our understanding of the human immune system in health and disease.
Yingxiao (Peter) Wang
Professor, Bioengineering- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Live cell imaging, genetic and epigenetic regulations, immunoengineering, therapeutics
Wei Wang
Professor, Chemistry and BiochemistryProfessor, Cellular and Molecular Medicine
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Epigenomics, 3D genome, systems biology, protein engineering
Joel Wertheim
Associate Professor, School of Medicine- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Molecular epidemiology of HIV, SARS-CoV-2, and other RNA viruses; Viral phylogenetics and evolution
Ruth Williams
Professor, Mathematics- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Probability Theory, Stochastic Processes
Elizabeth Winzeler
Professor, Pediatrics- 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.
Dominik Wodarz
Professor, Biological Sciences- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- 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.
Ronghui (Lily) Xu
Professor, MathematicsProfessor, Herbert Wertheim School of Public Health and Human Longevity Science
Professor, Halıcıoğlu Data Science Institute
- Quantitative Foundations of Computational Biology
Research Focus: High dimensional data analysis, Imaging Random effects models, Survival analysis, Clinical trials
Gene Yeo
Professor, Cellular and Molecular MedicineGraduate Program Associate Director, Bioinformatics and Systems Biology
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Rose Yu
Assistant Professor, Computer Science and Engineering- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Machine learning, spatiotemporal modeling, deep learning, dynamical systems
Karsten Zengler
Adjunct Professor, Pediatrics- Quantitative Foundations of Computational Biology
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
- Data Models and Knowledge Representation
- Bioinformatics Applications in Human Disease
Research Focus: Our lab studies microbe-microbe and host-microbe interactions. The goal is to predict how complex systems react to perturbations and to design strategies to change the trajectory.
Kun Zhang
Professor, Bioengineering- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: We develop technologies related to single-cell analyses of genome, epigenome and transcriptome, as well as single-cell imaging and lineage tracing. These novel technologies are applied to stem cell fate conversion, human brain mapping and human disease studies.
Sheng Zhong
Professor, Bioengineering- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Discovery of RNA-RNA, RNA-DNA, protein-protein, and drug-protein interactions by sequencing.
Huilin Zhou
Professor, Cellular and Molecular Medicine- Proteomics and Metabolomics
- Genetic and Molecular Networks
Research Focus: Proteomics and genome maintenance