Biomedical Informatics Faculty
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Ludmil Alexandrov
Associate Professor, Cellular and Molecular MedicineAssociate Professor, Bioengineering
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Biomedical Natural Language Processing
Research Focus: Using large-scale omics data to study mutational processes causing human cancer, identifying potential cancer prevention strategies with ML and NLP approaches, and developing novel ML tools for better targeting of cancer treatment.
Tiffany Amariuta
Assistant Professor, Halıcıoğlu Data Science InstituteAssistant Professor, Biomedical Informatics
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Bioinformatics Applications in Human Disease
Research Focus: We are a statistical genetics lab focusing on developing methods to study complex traits and polygenic diseases in global populations. We are specifically interested in fine-mapping disease genes and their cell types of action, with the goal of finding targets for gene-based therapeutics.
Ferhat Ay
Associate Professor, La Jolla Institute for ImmunologyAssistant Adjunct Professor, Pediatrics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Epigenetics, genomics, chromatin structure, 3D/4D genome/nucleome, statistical methods for analysis of Hi-C and HiChIP data, gene regulation in immune cells, cancer genomics
Christopher Benner
Assistant Professor, School of Medicine- Epigenomics and Gene Expression Control
- Bioinformatics Applications in Human Disease
Research Focus:
Transcription, bioinformatics, genomics, innate immunity, chromatin.
We use next-generation sequencing (NGS) and computational analysis to understand the mechanisms responsible for transcription and epigenetic regulation in human development and disease.
Hannah Carter
Associate Professor, Division of Medical Genetics- Genetic and Molecular Networks
- Structural Bioinformatics and Systems Pharmacology
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Genomics and systems biology for precision cancer medicine, variant interpretation, network analysis, immunogenomics
Lukas Chavez Kuss
Assistant Professor, School of Medicine- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Chromatin and Gene Regulation in Childhood Cancers
Chi-Hua Chen
Associate Adjunct Professor, Radiology- Comparative and Population Genomics
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Neuroimaging genetics, neuropsychiatric disorders
Heidi Cook-Andersen
Assistant Professor, Biological SciencesAssistant Professor, Reproductive Medicine
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: We integrate computational, epigenetic, RNA, and chromatin biology approaches in human, mouse and stem cell models to understand the earliest stages of development -- from the fully differentiated oocyte to the totipotent embryo and successful implantation of the human blastocyst.
Kit Curtius
Assistant Professor, Biomedical Informatics- Quantitative Foundations of Computational Biology
- Epigenomics and Gene Expression Control
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Mathematical models of cancer evolution, optimization of cancer screening and surveillance, epigenetic aging, translational risk prediction tools
Matteo D'Antonio
Assistant Professor, Biomedical Informatics- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
Research Focus: Associations between genetic variation, molecular phenotypes, complex traits and disease
Tal Einav
Assistant Professor, La Jolla Institute for Immunology- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Antibody-virus interactions, predicting each person's vaccine response, personalized medicine
Robert El-Kareh
Associate Clinical Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Clinical informatics, clinical decision support, diagnostic safety, quality improvement, patient safety
Kelly Frazer
Professor, PediatricsDirector, Institute for Genomic Medicine
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Using iPSCs for genetic analyses, GWAS, QTL analyses, bioinformatic approaches to understanding human disease, single-cell analyses
Terry Gaasterland
Professor, Scripps Institution of OceanographyGraduate Program Director, Bioinformatics and Systems Biology
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Computational Analysis of Human, Novel, and Microbial Genomes: Impact of genetic and evolutionary variation on regulation of transcription and on protein domain structure and function. Causal variants leading to dysregulated cellular response to environmental stresses.
Rodney Gabriel
Assistant Clinical Professor, School of Medicine- Predictive Modeling and Personalized Medicine
Research Focus: Perioperative outcomes, pharmacogenomics, machine learning, predictive modeling, regional anesthesia, acute pain.
Fred (Rusty) Gage
President, Salk Institute for Biological StudiesProfessor, Laboratory of Genetics, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences
- Epigenomics and Gene Expression Control
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu
Joseph Gleeson
Professor, Neurosciences (School of Medicine)Director of Neurogenetics, Rady Children's Institute for Genomic Medicine
- Comparative and Population Genomics
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions
Olivier Harismendy
Associate Professor, Biomedical Informatics- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: My laboratory develops genome-wide assays and analysis for personalized cancer care. Particular focus includes genetics of cancer susceptibility and drug response, secure computing and data sharing.
Michael Hogarth
Clinical Professor, Biomedical Informatics- Data Models and Knowledge Representation
- Biomedical Natural Language Processing
Research Focus: Development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.
Albert Hsiao
Associate Professor in Residence, Radiology- Comparative and Population Genomics
- Bioinformatics Applications in Human Disease
Research Focus: Artificial Intelligence, Cardiovascular, COVID-19, x-ray, CT, MRI, Point-of-care Ultrasound
Wendy Huang
Assistant Professor, Cellular and Molecular Medicine- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: To assess the contributions of RNA-binding proteins and their associated non-coding RNAs to host immune homeostasis and autoimmune pathologies.
Lilia Iakoucheva
Associate Professor, Psychiatry- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Autism, genetics, gene expression, protein interactions, systems biology, networks, psychiatric diseases, whole genome sequencing
Mohit Jain
Associate Professor, Pharmacology- Proteomics and Metabolomics
- Genetic and Molecular Networks
- Structural Bioinformatics and Systems Pharmacology
- Bioinformatics Applications in Human Disease
Research Focus:
Human Biology, Metabolic Biochemistry, Integrative Biology, Mass Spectrometry, Metabolomics
Susan Kaech
Professor, Salk Institute for Biological StudiesAdjunct Professor, Biological Sciences
- Proteomics and Metabolomics
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Understanding how Memory T Cells are produced during infection and vaccination
Kevin King
Associate Professor, School of MedicineAssociate Professor, Bioengineering
- TBD
- TBD
Research Focus: The King Lab studies diseases in which the immune system becomes activated even though there is no infection, such as heart attacks, metabolic disease, autoimmunity, or cancer. He combines conventional biological methods with novel bioengineering techniques to develop therapies that limit organ dysfunction and promote healing, repair and regeneration.
Jejo Koola
Assistant Clinical Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Biomedical Natural Language Processing
Research Focus: Practicing internist in the field of hospital medicine and clinical informatics. Research focus is on using informatics tools (including predictive analytics, natural language processing, and information visualization) to improve the care of multi-morbid hospital patients.
Pallav Kosuri
Assistant Professor, Salk Institute for Biological Studies- TBD
- TBD
Research Focus: The Kosuri Lab studies how movement gives rise to biological function across scales, from molecular motors to muscles. We take a cross-disciplinary approach that makes use of molecular design, computational methods, and functional imaging.
Tsung-Ting Kuo
Assistant Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
Research Focus: Blockchain Technologies, Machine Learning, Natural Language Processing
Amit Majithia
Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of Medicine- Comparative and Population Genomics
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Insulin resistance, functional genomics, pharmacogenetics, cardiometabolic disease, diabetes
Andrew McCulloch
Professor, BioengineeringProfessor, School of Medicine
- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Structural Bioinformatics and Systems Pharmacology
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Multi-scale biology of heart and musculoskeletal system to elucidate the biological principles underlying heart failure, congenital heart disease, arrhythmia and elite human performance
Jill Mesirov
Professor, School of MedicineAssociate Vice Chancellor, Computational Health Sciences,
Professor of Medicine, Division of Medical Genetics
- Quantitative Foundations of Computational Biology
- Genetic and Molecular Networks
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.
Niema Moshiri
Associate Teaching Professor, Computer Science and Engineering- Quantitative Foundations of Computational Biology
- Bioinformatics Applications in Human Disease
Research Focus: Computational viral epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development
Shamim Nemati
Associate Professor, Biomedical Informatics- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Signal Processing, Dynamical Systems, Multivariate Time Series, Point Process, Deep Learning, Reinforcement Learning, Video Processing, and Natural Language Processing
Lucila Ohno-Machado
Professor, Biomedical Informatics- Epigenomics and Gene Expression Control
- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
Research Focus: Biomedical Informatics, predictive modeling, biomedical data analytics
Johannes Schoeneberg
Assistant Professor, PharmacologyAssistant Professor, Chemistry and Biochemistry
- TBD
- TBD
Research Focus: Our group uses experimental and computational approaches to study the link between mitochondrial dynamics and neurological diseases that are caused by mitochondrial dysfunction, using 4D adaptive optics lattice light-sheet microscopy, brain organoids, human induced pluripotent stem cells, and machine learning.
Jonathan Sebat
Director, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Professor of Psychiatry and Cellular & Molecular Medicine, Cellular and Molecular Medicine- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Predictive Modeling and Personalized Medicine
- Bioinformatics Applications in Human Disease
Research Focus: Human Genetics, Statistical Genetics, Whole genome sequencing, Long Read Sequencing. Autism, Genetic Therapies for Neurological Disease
Amy Sitapati
Clinical Professor, Biomedical Informatics- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
- Data Models and Knowledge Representation
- Decision Support Systems
Research Focus: Biomedical Informatics, Registries, Population Health, Precision Medicine, Vital Records Informatics, Artificial Intelligence, Quality Informatics, Health Analytics
Pandurangan Vijayanand
Professor, La Jolla Institute for ImmunologyAssociate Adjunct Professor, School of Medicine
- Comparative and Population Genomics
- Epigenomics and Gene Expression Control
- Bioinformatics Applications in Human Disease
Research Focus: Continually evolving genomic tools and single cell analysis technologies are revolutionizing our understanding of the human immune system in health and disease.
Joel Wertheim
Associate Professor, School of Medicine- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Molecular epidemiology of HIV, SARS-CoV-2, and other RNA viruses; Viral phylogenetics and evolution
Dominik Wodarz
Professor, Biological Sciences- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
Research Focus: Mathematical models of infectious diseases, virus-immune system interactions, carcinogenesis, and cancer therapy; Evolutionary theory and evolutionary dynamics.
Rose Yu
Assistant Professor, Computer Science and Engineering- Quantitative Foundations of Computational Biology
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Decision Support Systems
Research Focus: Machine learning, spatiotemporal modeling, deep learning, dynamical systems
Karsten Zengler
Adjunct Professor, Pediatrics- Quantitative Foundations of Computational Biology
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Predictive Modeling and Personalized Medicine
- Privacy Technology, Data Sharing, and Big Data Analytics
- Data Models and Knowledge Representation
- Bioinformatics Applications in Human Disease
Research Focus: Our lab studies microbe-microbe and host-microbe interactions. The goal is to predict how complex systems react to perturbations and to design strategies to change the trajectory.