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Bioinformatics and Systems Biology Research Areas
- 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
- Structural Bioinformatics and Systems Pharmacology
- Other BISB Research Areas
Biomedical Informatics Research Areas
- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
- Data Models and Knowledge Representation
- Decision Support Systems
- Biomedical Natural Language Processing
- Bioinformatics Applications in Human Disease
- Other BMI Research Areas
Bioinformatics and Systems Biology Research Areas
Quantitative Foundations of Computational Biology
Key to Computational Biology are the approaches and algorithms for processing, analyzing and modeling knowledge, information, and data, that are relevant to research questions from across the life sciences. The development of mathematical and computational methods with probabilistic, statistical, combinatorial, or heuristic foundations continue to drive innovation in Bioinformatics and Systems Biology.
Ludmil Alexandrov
Associate Professor, Cellular and Molecular MedicineAssociate Professor, Bioengineering
BISB Research Area(s):
- 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.
Vineet Bafna
Professor, Computer Science and EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
Research Focus: Bioinformatics Algorithms, Proteomics, Population Genetics
Vikas Bansal
Associate Professor, PediatricsAffiliate Faculty, Computer Science and Engineering
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Computational tools for variant calling, haplotyping and analysis of rare variants in disease association studies
Simone Baumann-Pickering
Associate Professor, Scripps Institution of OceanographyBISB Research Area(s):
- Quantitative Foundations of Computational Biology
Research Focus: The Scripps Acoustic Ecology Laboratory investigates phenological patterns and spatial ecology of cetaceans, interactions of predators and their prey, and adaptations of animals to changes in their environment.
Kit Curtius
Assistant Professor, Biomedical InformaticsBISB Research Area(s):
- 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
Michael Holst
Professor, MathematicsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Proteomics and Metabolomics
Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics
Andrew McCulloch
Professor, BioengineeringProfessor, School of Medicine
BISB Research Area(s):
- 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
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
Research Focus: Human genetic variation, chromatin and gene regulation in immune cells
Jill Mesirov
Professor, School of MedicineAssociate 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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.
Siavash Mirarab
Associate Professor, Electrical and Computer EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
Research Focus: Computational biology, large scale phylogenetics, estimation of species trees from gene trees (phylogenomics), large scale multiple sequence alignment, and metagenomic analysis using phylogenetic placement.
Niema Moshiri
Assistant Teaching Professor, Computer Science and EngineeringBISB Research Area(s):
- 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
Bernhard Palsson
Y.C. Fung Endowed Professor, BioengineeringBISB 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).
Pavel Pevzner
Professor and Ronald R Taylor Chair, Computer Science and EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
Research Focus: Computational Molecular Biology
Debashis Sahoo
Associate Professor, PediatricsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Systems Biology of normal and cancer tissues, Boolean analysis of biological systems, Computational models of stem cell differentiation, Sequencing data analysis
Nicholas Schork
Professor, Scripps Research InstituteBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Developing mathematical, statistical, and computational models and tools to study the genetic basis of complex traits and diseases
Benjamin Smarr
Assistant Professor, BioengineeringAssistant Professor, Halıcıoğlu Data Science Institute
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: What information do biological timeseries hold? What biodynamic interactions generate these signals?
Glenn Tesler
Professor, MathematicsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly
Yatish Turakhia
Assistant Professor, Electrical and Computer EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus:
Algorithms and domain-specific hardware accelerators that enable faster and cheaper progress in biology and medicine.
Computational methods that enable biological discoveries, such as new genotype-phenotype relationships.
Ruth Williams
Professor, MathematicsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Probability Theory, Stochastic Processes
Ronghui (Lily) Xu
Professor, MathematicsProfessor, Herbert Wertheim School of Public Health and Human Longevity Science
Professor, Halıcıoğlu Data Science Institute
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
Research Focus: High dimensional data analysis, Imaging Random effects models, Survival analysis, Clinical trials
Gene Yeo
Professor, Cellular and Molecular MedicineGraduate Program Associate Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Rose Yu
Assistant Professor, Computer Science and EngineeringBISB Research Area(s):
- 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, PediatricsBISB Research Area(s):
- 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.
Comparative and Population Genomics
Sequencing technologies are providing unprecedented opportunities and challenges to Bioinformatics to impact studies of Evolution, Epidemiology, Disease Genes, giving birth to the fields of Personalized Medicine and Pharmacogenomics.
Ludmil Alexandrov
Associate Professor, Cellular and Molecular MedicineAssociate Professor, Bioengineering
BISB Research Area(s):
- 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 OceanographyBISB Research Area(s):
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Ecological, comparative, and functional genomics of marine phytoplankton, Systems biology of microalgae, Genome evolution and evolutionary origins of metabolic function in marine microbes, Transcriptional regulatory networks, Metagenomics, Metatranscriptomics, Microbes, Evolution
Tiffany Amariuta
Assistant Professor, Halıcıoğlu Data Science InstituteAssistant Professor, School of Medicine
BISB Research Area(s):
- 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.
Vineet Bafna
Professor, Computer Science and EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
Research Focus: Bioinformatics Algorithms, Proteomics, Population Genetics
Vikas Bansal
Associate Professor, PediatricsAffiliate Faculty, Computer Science and Engineering
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Computational tools for variant calling, haplotyping and analysis of rare variants in disease association studies
Chi-Hua Chen
Associate Adjunct Professor, RadiologyBISB Research Area(s):
- Comparative and Population Genomics
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Neuroimaging genetics, neuropsychiatric disorders
Matteo D'Antonio
Assistant Professor, Biomedical InformaticsBISB Research Area(s):
- 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
Terry Gaasterland
Professor and Director of Scripps Genome Center, Scripps Institution of OceanographyGraduate Program Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
Research Focus: Computational Analysis of Human, Novel, and Microbial Genomes
Joseph Gleeson
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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions
Melissa Gymrek
Associate Professor, School of MedicineAssociate Professor, Computer Science and Engineering
BISB Research Area(s):
- Comparative and Population Genomics
Research Focus: Contribution of complex genetic variation to human phenotypes
Albert Hsiao
Associate Professor in Residence, RadiologyBISB Research Area(s):
- 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 MedicineBISB Research Area(s):
- 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.
Rob Knight
Professor, PediatricsAffiliate Faculty, Computer Science and Engineering
BISB Research Area(s):
- Comparative and Population Genomics
Research Focus: Human microbiome, microbial community ecology, multi-omics analyses
Amit Majithia
Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of MedicineBISB Research Area(s):
- 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
Graham McVicker
Assistant Professor, Salk Institute for Biological StudiesAssistant Adjunct Professor, Cellular and Molecular Medicine
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
Research Focus: Human genetic variation, chromatin and gene regulation in immune cells
Pavel Pevzner
Professor and Ronald R Taylor Chair, Computer Science and EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
Research Focus: Computational Molecular Biology
Nicholas Schork
Professor, Scripps Research InstituteBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Developing mathematical, statistical, and computational models and tools to study the genetic basis of complex traits and diseases
Jonathan Sebat
Director, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Professor of Psychiatry and Cellular & Molecular Medicine, Cellular and Molecular MedicineBISB Research Area(s):
- 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
Glenn Tesler
Professor, MathematicsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus: Combinatorics, Genome Rearrangements, Genome Assembly
Yatish Turakhia
Assistant Professor, Electrical and Computer EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
Research Focus:
Algorithms and domain-specific hardware accelerators that enable faster and cheaper progress in biology and medicine.
Computational methods that enable biological discoveries, such as new genotype-phenotype relationships.
Pandurangan Vijayanand
Professor, La Jolla Institute for ImmunologyAssociate Adjunct Professor, School of Medicine
BISB Research Area(s):
- 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.
Elizabeth Winzeler
Professor, PediatricsBISB Research Area(s):
- Comparative and Population Genomics
- Genetic and Molecular Networks
- Structural Bioinformatics and Systems Pharmacology
Research Focus: We are interested in host pathogen interactions, drug discovery, genetics, genomics and cheminformatics. We use a variety of high throughput, computationally intensive methods to accelerate the drug discovery process. Most of our work is focused on developing new treatments for malaria.
Gene Yeo
Professor, Cellular and Molecular MedicineGraduate Program Associate Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Proteomics and Metabolomics
Mass spectrometry technologies have advanced to provide quantitative information not only of peptides and the proteome, but post-translational modifications, lipids, and metabolic intermediates. Interpreting high dimensional mass spectrometry data poses bioinformatic challenges of high significance to many aspects of research in biofuels, industrial biology, agricultural biology, and biomedicine.
Ruben Abagyan
Professor, School of PharmacyBISB Research Area(s):
- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Structure-based Drug Discovery, Cheminformatics, Drug Repurposing, Computational Pharmacology, Target/pathway Discovery
Andrew Allen
Professor, Scripps Institution of OceanographyBISB Research Area(s):
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Ecological, comparative, and functional genomics of marine phytoplankton, Systems biology of microalgae, Genome evolution and evolutionary origins of metabolic function in marine microbes, Transcriptional regulatory networks, Metagenomics, Metatranscriptomics, Microbes, Evolution
Vineet Bafna
Professor, Computer Science and EngineeringBISB Research Area(s):
- 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
BISB Research Area(s):
- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Bioinformatics and computational mass spectrometry
Steve Briggs
Professor, Biological SciencesBISB Research Area(s):
- Proteomics and Metabolomics
Research Focus: Stem Cell Identity
Pieter Dorrestein
Professor, School of PharmacyBISB Research Area(s):
- Proteomics and Metabolomics
- Genetic and Molecular Networks
Research Focus: Biosynthesis
Michael Holst
Professor, MathematicsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Proteomics and Metabolomics
Research Focus: Numerical Analysis, Scientific Computation, Protein Electrostatics
Vivian Hook
Professor, School of PharmacyBISB Research Area(s):
- Proteomics and Metabolomics
Research Focus: Peptide Neurotransmitters, Protease Mechanisms
Terence Hwa
Distinguished Professor, PhysicsDistinguished Professor, Biological Sciences
BISB Research Area(s):
- Proteomics and Metabolomics
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Use of proteomic and metabolomic approaches to study resource allocation strategies employed during bacterial growth; mechanistic studies of metabolic interactions in bacterial communities
Mohit Jain
Associate Professor, PharmacologyBISB Research Area(s):
- 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
Susan Kaech
Professor, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
BISB Research Area(s):
- 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
Pavel Pevzner
Professor and Ronald R Taylor Chair, Computer Science and EngineeringBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
Research Focus: Computational Molecular Biology
Susan Taylor
Professor, Chemistry and BiochemistryBISB Research Area(s):
- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Relationship of CAPK Structure to Function
Gene Yeo
Professor, Cellular and Molecular MedicineGraduate Program Associate Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Huilin Zhou
Professor, Cellular and Molecular MedicineBISB Research Area(s):
- Proteomics and Metabolomics
- Genetic and Molecular Networks
Research Focus: Proteomics and genome maintenance
Epigenomics and Gene Expression Control
The ability to characterize the chromatin state, its three-dimensional organization, the landscapes of DNA and RNA binding proteins, and the action of regulatory RNAs throughout the genome is broadly impacting biological research such as on differentiation and development, cancer, and immune responses. Bioinformatic analysis tools are critical for such studies, and predictive models of how the genome is expressed are within reach.
Andrew Allen
Professor, Scripps Institution of OceanographyBISB Research Area(s):
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Ecological, comparative, and functional genomics of marine phytoplankton, Systems biology of microalgae, Genome evolution and evolutionary origins of metabolic function in marine microbes, Transcriptional regulatory networks, Metagenomics, Metatranscriptomics, Microbes, Evolution
Tiffany Amariuta
Assistant Professor, Halıcıoğlu Data Science InstituteAssistant Professor, School of Medicine
BISB Research Area(s):
- 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
BISB Research Area(s):
- 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
Christopher Benner
Assistant Professor, School of MedicineBISB Research Area(s):
- 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
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: We develop and apply new imaging tools (including spatial transcriptomics and genomics) to understand how gene regulation information propagates across scales from the molecular events within the nucleus to the organization of cells into tissues and organs, up to the scale of animal behavior.
Wolfgang Busch
Professor, Salk Institute for Biological StudiesAssociate Adjunct Professor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Researching and developing plant varieties with enhanced carbon sequestration capabilities for removing CO2 from the atmosphere and thereby counteracting climate change.
Joseph Califano
Physician in Chief and Professor, SurgeryMoores 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.
Alejandro Chavez
Associate Professor, PediatricsBISB 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
Lukas Chavez Kuss
Assistant Professor, School of MedicineBISB Research Area(s):
- 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
Christine Cheng
Associate Professor In Residence, PsychiatryBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Utilize single cell resolution functional genomic assays and computational methods to study heterogeneous clinical tissue samples and blood immune cell populations in patient samples.
Neil Chi
Professor, School of MedicineBISB 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
Heidi Cook-Andersen
Assistant Professor, Biological SciencesAssistant Professor, Reproductive Medicine
BISB Research Area(s):
- 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 InformaticsBISB Research Area(s):
- 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 InformaticsBISB Research Area(s):
- 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
Joseph Ecker
Professor and HHMI Investigator, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
Research Focus: Epigenomics of the mammalian brain - human brain cell atlas
Ronald M. Evans
Professor and Director, Gene Expression Lab, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
Research Focus: Role of hormones, both in their normal activities and in disease.
Emma Farley
Assistant Professor, Biological SciencesBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: High-throughput functional assays in developing embryos to decipher how genomes instruct development
Gen-Sheng Feng
Professor, PathologyProfessor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Deciphering the anti-oncogenic effects of pro-oncogenic molecules in liver cancer
Kathleen Fisch
Assistant Professor, Reproductive MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Understanding the molecular mechanisms underlying pregnancy disorders and exposures to improve maternal and child health throughout the lifespan.
Kelly Frazer
Professor, PediatricsDirector, Institute for Genomic Medicine
BISB Research Area(s):
- 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 and Director of Scripps Genome Center, Scripps Institution of OceanographyGraduate Program Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
Research Focus: Computational Analysis of Human, Novel, and Microbial Genomes
Fred (Rusty) Gage
President, Salk Institute for Biological StudiesProfessor, 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
- 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, PediatricsBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Statistical genetics, epigenomics, chromatin, gene regulatory networks, diabetes
Christopher Glass
Professor, Cellular and Molecular MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Enhancer Selection and Functions, Macrophage Subtypes, Genetic Variation, Enhancer Transcription
Alon Goren
Assistant Professor, School of MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Dynamics of epigenomic mechanisms during development and along the cell cycle
Theresa Guo
Assistant Professor, SurgeryBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Splicing alteration in human cancer, with particular focus on HPV mediated head and neck tumors; Interaction between genomic alterations and tumor immunity; post transcriptional and epigenetic regulation of splicing
Olivier Harismendy
Associate Professor, Biomedical InformaticsBISB Research Area(s):
- 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.
Sven Heinz
Assistant Professor, School of MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
Research Focus: Regulation and reprogramming of transcription, cancer epigenetics
Wendy Huang
Assistant Professor, Cellular and Molecular MedicineBISB Research Area(s):
- 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, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
Research Focus: Genomics, Nanostructure Fabrication
Trey Ideker
Professor, Division of Medical GeneticsGraduate 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
Susan Kaech
Professor, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
BISB Research Area(s):
- 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
Louise Laurent
Professor, Reproductive MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Gene Interaction Networks, Biomarker Discovery, Pluripotency, Embryonic Development, Placental Dysfunction, Preeclampsia, Pregnancy complications
Julie Law
Assistant Professor, Salk Institute for Biological StudiesAssistant Adjunct Professor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Chromatin modifications, epigenetics, genomics, gene regulation
Prashant Mali
Professor, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: The Mali laboratory is working in the fields of synthetic biology and regenerative medicine, with a long-term focus on developing tools for enabling gene and cell based human therapeutics.
Graham McVicker
Assistant Professor, Salk Institute for Biological StudiesAssistant Adjunct Professor, Cellular and Molecular Medicine
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
Research Focus: Human genetic variation, chromatin and gene regulation in immune cells
Eran Mukamel
Assistant Professor, Cognitive ScienceBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Computational neuroscience, brain cell differentiation and development, computational analysis of brain-network dynamics
Lucila Ohno-Machado
Professor, Biomedical InformaticsBISB Research Area(s):
- 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, PsychiatryBISB 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.
Tariq Rana
Distinguished Professor, PediatricsBISB 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.
Anjana Rao
Professor, La Jolla Institute for ImmunologyAdjunct Professor, Pharmacology
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Understanding how signalling pathways control gene expression, using T cells and other cells of the immune system as models
Bing Ren
Professor, Cellular and Molecular MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Gene Regulatory Networks
Michael Rosenfeld
Professor, School of MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Mammalian Neurosystem Development
Debashis Sahoo
Associate Professor, PediatricsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Systems Biology of normal and cancer tissues, Boolean analysis of biological systems, Computational models of stem cell differentiation, Sequencing data analysis
Jonathan Sebat
Director, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Professor of Psychiatry and Cellular & Molecular Medicine, Cellular and Molecular MedicineBISB Research Area(s):
- 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
Pablo Tamayo
Professor, School of MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Development of analysis methods for the functional characterization of cancer genomes including RNAi and CRISPR genetic dependencies. Computational methods, probability and statistics, data analysis, machine learning, computational biology and cancer research.
Pandurangan Vijayanand
Professor, La Jolla Institute for ImmunologyAssociate Adjunct Professor, School of Medicine
BISB Research Area(s):
- 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, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Live cell imaging, genetic and epigenetic regulations, immunoengineering, therapeutics
Wei Wang
Professor, Chemistry and BiochemistryProfessor, Cellular and Molecular Medicine
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Epigenomics, 3D genome, systems biology, protein engineering
Gene Yeo
Professor, Cellular and Molecular MedicineGraduate Program Associate Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Kun Zhang
Professor, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: We develop technologies related to single-cell analyses of genome, epigenome and transcriptome, as well as single-cell imaging and lineage tracing. These novel technologies are applied to stem cell fate conversion, human brain mapping and human disease studies.
Sheng Zhong
Professor, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Discovery of RNA-RNA, RNA-DNA, protein-protein, and drug-protein interactions by sequencing.
Genetic and Molecular Networks
Biological function is mediated by molecular interactions of genes and proteins. Collecting and interpreting high throughput physical and functional interactomes reveals how cells and organisms function in health and disease, and constitutes a rapidly expanding area of Bioinformatics and Systems Biology.
Ludmil Alexandrov
Associate Professor, Cellular and Molecular MedicineAssociate Professor, Bioengineering
BISB Research Area(s):
- 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 OceanographyBISB Research Area(s):
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Ecological, comparative, and functional genomics of marine phytoplankton, Systems biology of microalgae, Genome evolution and evolutionary origins of metabolic function in marine microbes, Transcriptional regulatory networks, Metagenomics, Metatranscriptomics, Microbes, Evolution
Ferhat Ay
Associate Professor, La Jolla Institute for ImmunologyAssistant Adjunct Professor, Pediatrics
BISB Research Area(s):
- 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
Bogdan Bintu
Assistant Professor, Cellular and Molecular MedicineAssistant Professor, Bioengineering
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: We develop and apply new imaging tools (including spatial transcriptomics and genomics) to understand how gene regulation information propagates across scales from the molecular events within the nucleus to the organization of cells into tissues and organs, up to the scale of animal behavior.
Wolfgang Busch
Professor, Salk Institute for Biological StudiesAssociate Adjunct Professor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Researching and developing plant varieties with enhanced carbon sequestration capabilities for removing CO2 from the atmosphere and thereby counteracting climate change.
Hannah Carter
Associate Professor, Division of Medical GeneticsBISB Research Area(s):
- 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, PediatricsBISB 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
Lukas Chavez Kuss
Assistant Professor, School of MedicineBISB Research Area(s):
- 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
Christine Cheng
Associate Professor In Residence, PsychiatryBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Utilize single cell resolution functional genomic assays and computational methods to study heterogeneous clinical tissue samples and blood immune cell populations in patient samples.
Neil Chi
Professor, School of MedicineBISB 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
Heidi Cook-Andersen
Assistant Professor, Biological SciencesAssistant Professor, Reproductive Medicine
BISB Research Area(s):
- 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.
Matteo D'Antonio
Assistant Professor, Biomedical InformaticsBISB Research Area(s):
- 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 PharmacyBISB Research Area(s):
- Proteomics and Metabolomics
- Genetic and Molecular Networks
Research Focus: Biosynthesis
Gen-Sheng Feng
Professor, PathologyProfessor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Deciphering the anti-oncogenic effects of pro-oncogenic molecules in liver cancer
Kathleen Fisch
Assistant Professor, Reproductive MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Understanding the molecular mechanisms underlying pregnancy disorders and exposures to improve maternal and child health throughout the lifespan.
Kelly Frazer
Professor, PediatricsDirector, Institute for Genomic Medicine
BISB Research Area(s):
- 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
Kyle Gaulton
Assistant Professor, PediatricsBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Statistical genetics, epigenomics, chromatin, gene regulatory networks, diabetes
Christopher Glass
Professor, Cellular and Molecular MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Enhancer Selection and Functions, Macrophage Subtypes, Genetic Variation, Enhancer Transcription
Joseph Gleeson
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
- 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 MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Dynamics of epigenomic mechanisms during development and along the cell cycle
Theresa Guo
Assistant Professor, SurgeryBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Splicing alteration in human cancer, with particular focus on HPV mediated head and neck tumors; Interaction between genomic alterations and tumor immunity; post transcriptional and epigenetic regulation of splicing
Nan Hao
Associate Professor, Biological SciencesBISB Research Area(s):
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Dynamic regulation of signaling and transcriptional networks in single cells
Olivier Harismendy
Associate Professor, Biomedical InformaticsBISB Research Area(s):
- 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.
Wendy Huang
Assistant Professor, Cellular and Molecular MedicineBISB Research Area(s):
- 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.
Terence Hwa
Distinguished Professor, PhysicsDistinguished Professor, Biological Sciences
BISB Research Area(s):
- Proteomics and Metabolomics
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Use of proteomic and metabolomic approaches to study resource allocation strategies employed during bacterial growth; mechanistic studies of metabolic interactions in bacterial communities
Lilia Iakoucheva
Associate Professor, PsychiatryBISB Research Area(s):
- 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
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Biological Networks, Cellular Modeling, Cancer Genomics, Epigenetic Aging
Mohit Jain
Associate Professor, PharmacologyBISB Research Area(s):
- 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
Susan Kaech
Professor, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
BISB Research Area(s):
- 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
Richard Kolodner
Professor, School of MedicineBISB Research Area(s):
- Genetic and Molecular Networks
Research Focus: Gene recombination
Louise Laurent
Professor, Reproductive MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Gene Interaction Networks, Biomarker Discovery, Pluripotency, Embryonic Development, Placental Dysfunction, Preeclampsia, Pregnancy complications
Julie Law
Assistant Professor, Salk Institute for Biological StudiesAssistant Adjunct Professor, Biological Sciences
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Chromatin modifications, epigenetics, genomics, gene regulation
Nathan E. Lewis
Associate Professor, PediatricsBISB Research Area(s):
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Systems biology approaches for integration of disparate data types to study diseases involving metabolism, glycobiology, and to guide cell engineering for drug development.
Amit Majithia
Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of MedicineBISB Research Area(s):
- 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, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: The Mali laboratory is working in the fields of synthetic biology and regenerative medicine, with a long-term focus on developing tools for enabling gene and cell based human therapeutics.
Jill Mesirov
Professor, School of MedicineAssociate 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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.
Abraham Palmer
Professor, PsychiatryBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Quantitative genetic studies of behavior using fish, mice, rats and humans. Applying statistical genetics and genomics approaches to understanding behavior.
Bernhard Palsson
Y.C. Fung Endowed Professor, BioengineeringBISB 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).
Bing Ren
Professor, Cellular and Molecular MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Gene Regulatory Networks
Michael Rosenfeld
Professor, School of MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Mammalian Neurosystem Development
Debashis Sahoo
Associate Professor, PediatricsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Systems Biology of normal and cancer tissues, Boolean analysis of biological systems, Computational models of stem cell differentiation, Sequencing data analysis
Julian Schroeder
Professor, Biological SciencesBISB Research Area(s):
- Genetic and Molecular Networks
Research Focus: Climate change resistance and drought resistance and plant stress signal transduction. Discovery of signaling networks and biological sensors, using systems biological approaches, transcriptomics, proteomics and genome editing.
Shankar Subramaniam
Professor, BioengineeringBISB Research Area(s):
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Functional Genomics
Pablo Tamayo
Professor, School of MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Development of analysis methods for the functional characterization of cancer genomes including RNAi and CRISPR genetic dependencies. Computational methods, probability and statistics, data analysis, machine learning, computational biology and cancer research.
Wei Wang
Professor, Chemistry and BiochemistryProfessor, Cellular and Molecular Medicine
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Epigenomics, 3D genome, systems biology, protein engineering
Joel Wertheim
Associate Professor, School of MedicineBISB Research Area(s):
- 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
Elizabeth Winzeler
Professor, PediatricsBISB Research Area(s):
- Comparative and Population Genomics
- Genetic and Molecular Networks
- Structural Bioinformatics and Systems Pharmacology
Research Focus: We are interested in host pathogen interactions, drug discovery, genetics, genomics and cheminformatics. We use a variety of high throughput, computationally intensive methods to accelerate the drug discovery process. Most of our work is focused on developing new treatments for malaria.
Gene Yeo
Professor, Cellular and Molecular MedicineGraduate Program Associate Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Karsten Zengler
Adjunct Professor, PediatricsBISB Research Area(s):
- 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, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: We develop technologies related to single-cell analyses of genome, epigenome and transcriptome, as well as single-cell imaging and lineage tracing. These novel technologies are applied to stem cell fate conversion, human brain mapping and human disease studies.
Sheng Zhong
Professor, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
Research Focus: Discovery of RNA-RNA, RNA-DNA, protein-protein, and drug-protein interactions by sequencing.
Huilin Zhou
Professor, Cellular and Molecular MedicineBISB 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.
Alejandro Chavez
Associate Professor, PediatricsBISB 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
Christine Cheng
Associate Professor In Residence, PsychiatryBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Utilize single cell resolution functional genomic assays and computational methods to study heterogeneous clinical tissue samples and blood immune cell populations in patient samples.
Emma Farley
Assistant Professor, Biological SciencesBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: High-throughput functional assays in developing embryos to decipher how genomes instruct development
Fred (Rusty) Gage
President, Salk Institute for Biological StudiesProfessor, 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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu
Nan Hao
Associate Professor, Biological SciencesBISB Research Area(s):
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Dynamic regulation of signaling and transcriptional networks in single cells
Jeff Hasty
Professor, Biological SciencesBISB Research Area(s):
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Biodynamics
Terence Hwa
Distinguished Professor, PhysicsDistinguished Professor, Biological Sciences
BISB Research Area(s):
- Proteomics and Metabolomics
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Use of proteomic and metabolomic approaches to study resource allocation strategies employed during bacterial growth; mechanistic studies of metabolic interactions in bacterial communities
Suckjoon Jun
Professor, PhysicsProfessor, Biological Sciences
BISB Research Area(s):
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Biophysics. Use physics and engineering to explain why biological systems are the way they are.
Amy Kiger
Associate Professor, Biological SciencesBISB Research Area(s):
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Genomics, Cellular Morphogenesis, RNAi, Image Analysis of Microscopy Data
Nathan E. Lewis
Associate Professor, PediatricsBISB Research Area(s):
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Systems biology approaches for integration of disparate data types to study diseases involving metabolism, glycobiology, and to guide cell engineering for drug development.
Andrew McCulloch
Professor, BioengineeringProfessor, School of Medicine
BISB Research Area(s):
- 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
Christian Metallo
Associate Professor, BioengineeringBISB Research Area(s):
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Metabolism, system biology, mass spectrometry, flux analysis, cancer, stem cell biology
Eran Mukamel
Assistant Professor, Cognitive ScienceBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Computational neuroscience, brain cell differentiation and development, computational analysis of brain-network dynamics
Shamim Nemati
Associate Professor, Biomedical InformaticsBISB Research Area(s):
- 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
Anjana Rao
Professor, La Jolla Institute for ImmunologyAdjunct Professor, Pharmacology
BISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Understanding how signalling pathways control gene expression, using T cells and other cells of the immune system as models
Scott Rifkin
Associate Professor, Biological SciencesBISB Research Area(s):
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Evolutionary Biology-Patterns of Gene Expression
Debashis Sahoo
Associate Professor, PediatricsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Systems Biology of normal and cancer tissues, Boolean analysis of biological systems, Computational models of stem cell differentiation, Sequencing data analysis
Benjamin Smarr
Assistant Professor, BioengineeringAssistant 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?
Shankar Subramaniam
Professor, BioengineeringBISB Research Area(s):
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Functional Genomics
Gurol Suel
Professor, Biological SciencesBISB Research Area(s):
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Identifying systems-level design principles of cellular differentiation circuits
Yingxiao (Peter) Wang
Professor, BioengineeringBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Live cell imaging, genetic and epigenetic regulations, immunoengineering, therapeutics
Ruth Williams
Professor, MathematicsBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: Probability Theory, Stochastic Processes
Gene Yeo
Professor, Cellular and Molecular MedicineGraduate Program Associate Director, Bioinformatics and Systems Biology
BISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
Research Focus: We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Rose Yu
Assistant Professor, Computer Science and EngineeringBISB Research Area(s):
- 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, PediatricsBISB Research Area(s):
- 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.
Structural Bioinformatics and Systems Pharmacology
Computational studies of protein structure, folding, and molecular interactions are critical for understanding biological function and developing therapeutic compounds. Bioinformatic and physics-based approaches have given rise to fantastic opportunities via in silico docking, screening, structure-based design and chemical genomics to impact personalized medicine.
Ruben Abagyan
Professor, School of PharmacyBISB Research Area(s):
- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Structure-based Drug Discovery, Cheminformatics, Drug Repurposing, Computational Pharmacology, Target/pathway Discovery
Nuno Bandeira
Professor, School of PharmacyProfessor, Computer Science and Engineering
BISB Research Area(s):
- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Bioinformatics and computational mass spectrometry
Hannah Carter
Associate Professor, Division of Medical GeneticsBISB Research Area(s):
- 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
Michael Gilson
Professor, School of PharmacyBISB Research Area(s):
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Computer-aided drug discovery
Mohit Jain
Associate Professor, PharmacologyBISB Research Area(s):
- 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
Nathan E. Lewis
Associate Professor, PediatricsBISB Research Area(s):
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Systems biology approaches for integration of disparate data types to study diseases involving metabolism, glycobiology, and to guide cell engineering for drug development.
Andrew McCammon
Professor, Chemistry and BiochemistryBISB Research Area(s):
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Enzymes and Ligand Binding
Andrew McCulloch
Professor, BioengineeringProfessor, School of Medicine
BISB Research Area(s):
- 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
Tariq Rana
Distinguished Professor, PediatricsBISB 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.
Palmer Taylor
Professor and Dean, School of PharmacyBISB Research Area(s):
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Neurotransmission Biochemistry
Susan Taylor
Professor, Chemistry and BiochemistryBISB Research Area(s):
- Proteomics and Metabolomics
- Structural Bioinformatics and Systems Pharmacology
Research Focus: Relationship of CAPK Structure to Function
Elizabeth Winzeler
Professor, PediatricsBISB 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.
Amy Sitapati
Professor, Biomedical InformaticsBISB Research Area(s):
- TBD
- TBD
Research Focus: Registries, Population Health Informatics, NIH All of Us Precision Medicine, Equity in Clinical Informatics, Artificial Intelligence and Predictive Analytics, Learning Health System, Public Health Informatics and Vital Records, Quality Analytics and Informatics, Applied Health System Informatics
Biomedical Informatics Research Areas
Predictive Modeling and Personalized Medicine
Pattern recognition on clinical data has enabled the development of predictive models for diagnosis and prognosis of human disease. However, the predictive power of these models can be enhanced with genetic data that are increasingly being generated via high throughput technologies, and more recently via whole-genome sequencing. Integrating clinical and molecular data to build, evaluate, and implement accurate prediction models for personalized medicine is a new exciting field of research for biomedical informatics specialists. The impact of personalized medicine on patient outcomes is only beginning to be understood, and this burgeoning area of research and development requires skills in computer science, statistics, and life sciences.
Ludmil Alexandrov
Associate Professor, Cellular and Molecular MedicineAssociate Professor, Bioengineering
BISB Research Area(s):
- 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.
Hannah Carter
Associate Professor, Division of Medical GeneticsBISB Research Area(s):
- 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
Lukas Chavez Kuss
Assistant Professor, School of MedicineBISB Research Area(s):
- 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, RadiologyBISB Research Area(s):
- Comparative and Population Genomics
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Neuroimaging genetics, neuropsychiatric disorders
Kit Curtius
Assistant Professor, Biomedical InformaticsBISB Research Area(s):
- 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 InformaticsBISB Research Area(s):
- 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
Robert El-Kareh
Associate Clinical Professor, Biomedical InformaticsBMI Research Area(s):
- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Clinical informatics, clinical decision support, diagnostic safety, quality improvement, patient safety
Rodney Gabriel
Assistant Clinical Professor, School of MedicineBMI Research Area(s):
- 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
BISB Research Area(s):
- 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
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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions
Olivier Harismendy
Associate Professor, Biomedical InformaticsBISB Research Area(s):
- 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.
Jejo Koola
Assistant Clinical Professor, School of MedicineBMI Research Area(s):
- Predictive Modeling and Personalized Medicine
- Biomedical Natural Language Processing
Research Focus: Practicing internist in the field of hospital medicine and clinical informatics. Research focus is on using informatics tools (including predictive analytics, natural language processing, and information visualization) to improve the care of multi-morbid hospital patients.
Tsung-Ting Kuo
Assistant Professor, Biomedical InformaticsBMI Research Area(s):
- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
Research Focus: Blockchain Technologies, Machine Learning, Natural Language Processing
Amit Majithia
Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of MedicineBISB Research Area(s):
- 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
Andrew McCulloch
Professor, BioengineeringProfessor, School of Medicine
BISB Research Area(s):
- 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
Jill Mesirov
Professor, School of MedicineAssociate 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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.
Shamim Nemati
Associate Professor, Biomedical InformaticsBISB Research Area(s):
- 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 InformaticsBISB Research Area(s):
- 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
Jonathan Sebat
Director, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Professor of Psychiatry and Cellular & Molecular Medicine, Cellular and Molecular MedicineBISB Research Area(s):
- 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
Rose Yu
Assistant Professor, Computer Science and EngineeringBISB Research Area(s):
- 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, PediatricsBISB Research Area(s):
- 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.
Privacy Technology, Data Sharing, and Big Data Analytics
Whole genome sequences from humans are increasingly being collected for clinical care. Dealing with personal health information requires full compliance with current regulations designed to protect individual privacy. Technologies to preserve privacy in disclosed data allow broader, safer sharing of health information for research and healthcare quality improvement. The rapid collection of data from electronic health records has promoted greater awareness of the need to combine technology and privacy solutions for data sharing. Building accurate predictive models that utilize these data will only be possible if these data can be shared in a privacy-protecting manner, hence the field of privacy technology has been experiencing enormous growth in the past few years, represented by a range of innovations in both theory and applications.
Tsung-Ting Kuo
Assistant Professor, Biomedical InformaticsBMI Research Area(s):
- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
Research Focus: Blockchain Technologies, Machine Learning, Natural Language Processing
Lucila Ohno-Machado
Professor, Biomedical InformaticsBISB Research Area(s):
- 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
Karsten Zengler
Adjunct Professor, PediatricsBISB Research Area(s):
- 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.
Data Models and Knowledge Representation
Because research is multi-institutional and lots of data are required to recognize meaningful patterns, it is important to harmonize data collected at different institutions through the use of appropriate data models. Developing automated ontology mapping tools and structuring data and knowledge in a computable format are important pillars of biomedical computing. Although strategies have been developing for several years, before the advent of big healthcare data the need for and efficacy of innovative approaches were not fully appreciated by the biomedical scientific community. Research on data models and representation frameworks has permitted the combination of data from several sources for analytics that support a variety of applications, including decision support systems.
Michael Hogarth
Clinical Professor, School of MedicineBMI Research Area(s):
- Data Models and Knowledge Representation
- Biomedical Natural Language Processing
Research Focus: Development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.
Karsten Zengler
Adjunct Professor, PediatricsBISB Research Area(s):
- 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.
Decision Support Systems
Clinicians and biomedical researchers are often overwhelmed with information and may have difficulties in translating information into actions that have a direct or indirect effect on biomedical knowledge and human health. The design and implementation of effective decision support systems to assist biomedical researchers and/or clinicians perform their tasks in a well-informed manner have the potential to change the biomedical research is conducted and way medicine is practiced. Deep understanding of computational challenges for specific applications areas is required for the assembly of multi-disciplinary teams that can build effective decision support systems.
Robert El-Kareh
Associate Clinical Professor, Biomedical InformaticsBMI Research Area(s):
- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Clinical informatics, clinical decision support, diagnostic safety, quality improvement, patient safety
Shamim Nemati
Associate Professor, Biomedical InformaticsBISB Research Area(s):
- 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
Rose Yu
Assistant Professor, Computer Science and EngineeringBISB Research Area(s):
- 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
Biomedical Natural Language Processing
The wide adoption of electronic health records (EHR) is important for proper collection data that can be used in further computation. However, most of the EHR information is still presented in narrative form. Systems that can understand the language in these documents and structure the data for computation are critical for data analysis and predictive modeling that serve as bases for decision support systems. Natural language processing techniques derived for non-biomedical texts do not always work in biomedical text. For this reason, specialized biomedical natural language processing is necessary and constitutes an important area of research and development in biomedical informatics.
Ludmil Alexandrov
Associate Professor, Cellular and Molecular MedicineAssociate Professor, Bioengineering
BISB Research Area(s):
- 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.
Michael Hogarth
Clinical Professor, School of MedicineBMI Research Area(s):
- Data Models and Knowledge Representation
- Biomedical Natural Language Processing
Research Focus: Development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.
Jejo Koola
Assistant Clinical Professor, School of MedicineBMI Research Area(s):
- Predictive Modeling and Personalized Medicine
- Biomedical Natural Language Processing
Research Focus: Practicing internist in the field of hospital medicine and clinical informatics. Research focus is on using informatics tools (including predictive analytics, natural language processing, and information visualization) to improve the care of multi-morbid hospital patients.
Bioinformatics Applications in Human Disease
Human disease is a result of genetic and environmental factors. New bioinformatics algorithms can be applied to a combination of genetic, clinical, and environmental factors to help understand disease processes and build predictive models for diagnosis and/or prognosis. Given the heterogeneity of data that are involved, specialized training is necessary to allow innovation in the integration, analysis, and sharing of human subject data related to health and disease.
Tiffany Amariuta
Assistant Professor, Halıcıoğlu Data Science InstituteAssistant Professor, School of Medicine
BISB Research Area(s):
- 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
BISB Research Area(s):
- 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
Christopher Benner
Assistant Professor, School of MedicineBISB Research Area(s):
- 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.
Hannah Carter
Associate Professor, Division of Medical GeneticsBISB Research Area(s):
- 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
Lukas Chavez Kuss
Assistant Professor, School of MedicineBISB Research Area(s):
- 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, RadiologyBISB Research Area(s):
- Comparative and Population Genomics
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Neuroimaging genetics, neuropsychiatric disorders
Heidi Cook-Andersen
Assistant Professor, Biological SciencesAssistant Professor, Reproductive Medicine
BISB Research Area(s):
- 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 InformaticsBISB Research Area(s):
- 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
Kelly Frazer
Professor, PediatricsDirector, Institute for Genomic Medicine
BISB Research Area(s):
- 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
Fred (Rusty) Gage
President, Salk Institute for Biological StudiesProfessor, 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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu
Joseph Gleeson
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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions
Olivier Harismendy
Associate Professor, Biomedical InformaticsBISB Research Area(s):
- 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.
Albert Hsiao
Associate Professor in Residence, RadiologyBISB Research Area(s):
- 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 MedicineBISB Research Area(s):
- 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.
Lilia Iakoucheva
Associate Professor, PsychiatryBISB Research Area(s):
- 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
Mohit Jain
Associate Professor, PharmacologyBISB Research Area(s):
- 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
Susan Kaech
Professor, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
BISB Research Area(s):
- 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
Amit Majithia
Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of MedicineBISB Research Area(s):
- 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
Andrew McCulloch
Professor, BioengineeringProfessor, School of Medicine
BISB Research Area(s):
- 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
Jill Mesirov
Professor, School of MedicineAssociate 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
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.
Niema Moshiri
Assistant Teaching Professor, Computer Science and EngineeringBISB Research Area(s):
- 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
Jonathan Sebat
Director, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Professor of Psychiatry and Cellular & Molecular Medicine, Cellular and Molecular MedicineBISB Research Area(s):
- 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
Pandurangan Vijayanand
Professor, La Jolla Institute for ImmunologyAssociate Adjunct Professor, School of Medicine
BISB Research Area(s):
- 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.
Joel Wertheim
Associate Professor, School of MedicineBISB Research Area(s):
- 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
Karsten Zengler
Adjunct Professor, PediatricsBISB Research Area(s):
- 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.
Amy Sitapati
Professor, Biomedical InformaticsBISB Research Area(s):
- TBD
- TBD
Research Focus: Registries, Population Health Informatics, NIH All of Us Precision Medicine, Equity in Clinical Informatics, Artificial Intelligence and Predictive Analytics, Learning Health System, Public Health Informatics and Vital Records, Quality Analytics and Informatics, Applied Health System Informatics