Biomedical Informatics Faculty | Bioinformatics and Systems Biology

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Ludmil Alexandrov

Ludmil Alexandrov

Associate Professor, Cellular and Molecular Medicine
Associate Professor, Bioengineering

BISB Research Area(s):

Quantitative Foundations of Computational Biology
Comparative and Population Genomics
Genetic and Molecular Networks

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Biomedical Natural Language Processing

Research Focus: Using large-scale omics data to study mutational processes causing human cancer, identifying potential cancer prevention strategies with ML and NLP approaches, and developing novel ML tools for better targeting of cancer treatment.

Tiffany Amariuta

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

BISB Research Area(s):

Comparative and Population Genomics
Epigenomics and Gene Expression Control

BMI Research Area(s):

Bioinformatics Applications in Human Disease

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

Ferhat Ay

Ferhat Ay

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

BISB Research Area(s):

Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Bioinformatics Applications in Human Disease

Research Focus: Epigenetics, genomics, chromatin structure, 3D/4D genome/nucleome, statistical methods for analysis of Hi-C and HiChIP data, gene regulation in immune cells, cancer genomics

Christopher Benner

Christopher Benner

Assistant Professor, School of Medicine

BISB Research Area(s):

Epigenomics and Gene Expression Control

BMI Research Area(s):

Bioinformatics Applications in Human Disease

Research Focus: Transcription, bioinformatics, genomics, innate immunity, chromatin.
We use next-generation sequencing (NGS) and computational analysis to understand the mechanisms responsible for transcription and epigenetic regulation in human development and disease.

Hannah Carter

Hannah Carter

Associate Professor, Division of Medical Genetics

BISB Research Area(s):

Genetic and Molecular Networks
Structural Bioinformatics and Systems Pharmacology

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Genomics and systems biology for precision cancer medicine, variant interpretation, network analysis, immunogenomics

Lukas Chavez Kuss

Lukas Chavez Kuss

Assistant Professor, School of Medicine

BISB Research Area(s):

Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Chromatin and Gene Regulation in Childhood Cancers

Chi-Hua Chen

Chi-Hua Chen

Associate Adjunct Professor, Radiology

BISB Research Area(s):

Comparative and Population Genomics

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Neuroimaging genetics, neuropsychiatric disorders

Heidi Cook-Andersen

Heidi Cook-Andersen

Assistant Professor, Biological Sciences
Assistant Professor, Reproductive Medicine

BISB Research Area(s):

Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Bioinformatics Applications in Human Disease

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

Kit Curtius

Kit Curtius

Assistant Professor, Biomedical Informatics

BISB Research Area(s):

Quantitative Foundations of Computational Biology
Epigenomics and Gene Expression Control

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Mathematical models of cancer evolution, optimization of cancer screening and surveillance, epigenetic aging, translational risk prediction tools

Matteo D'Antonio

Matteo D'Antonio

Assistant Professor, Biomedical Informatics

BISB Research Area(s):

Comparative and Population Genomics
Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Predictive Modeling and Personalized Medicine

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

Robert El-Kareh

Robert El-Kareh

Associate Clinical Professor, Biomedical Informatics

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Decision Support Systems

Research Focus: Clinical informatics, clinical decision support, diagnostic safety, quality improvement, patient safety

Kelly Frazer

Kelly Frazer

Professor, Pediatrics
Director, Institute for Genomic Medicine

BISB Research Area(s):

Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Bioinformatics Applications in Human Disease

Research Focus: Using iPSCs for genetic analyses, GWAS, QTL analyses, bioinformatic approaches to understanding human disease, single-cell analyses

Rodney Gabriel

Rodney Gabriel

Assistant Clinical Professor, School of Medicine

BMI Research Area(s):

Predictive Modeling and Personalized Medicine

Research Focus: Perioperative outcomes, pharmacogenomics, machine learning, predictive modeling, regional anesthesia, acute pain.

Fred (Rusty) Gage

Fred (Rusty) Gage

President, Salk Institute for Biological Studies
Professor, Laboratory of Genetics, Salk Institute for Biological Studies
Adjunct Professor, Biological Sciences

BISB Research Area(s):

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

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Adult central nervous system, Neurogenesis, Modeling neurondegenerative & neuropsychiatric disorders, Neuronal mosaicism & diversity, Human evolution; Somatic retrotransposition, LINE-1, & Alu

Joseph Gleeson

Joseph Gleeson

Professor, Neurosciences (School of Medicine)
Director of Neurogenetics, Rady Children's Institute for Genomic Medicine

BISB Research Area(s):

Comparative and Population Genomics
Genetic and Molecular Networks

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions

Olivier Harismendy

Olivier Harismendy

Associate Professor, Biomedical Informatics

BISB Research Area(s):

Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: My laboratory develops genome-wide assays and analysis for personalized cancer care. Particular focus includes genetics of cancer susceptibility and drug response, secure computing and data sharing.

Michael Hogarth

Michael Hogarth

Clinical Professor, School of Medicine

BMI Research Area(s):

Data Models and Knowledge Representation
Biomedical Natural Language Processing

Research Focus: Development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.

Albert Hsiao

Associate Professor in Residence, Radiology

BISB Research Area(s):

Comparative and Population Genomics

BMI Research Area(s):

Bioinformatics Applications in Human Disease

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

Wendy Huang

Wendy Huang

Assistant Professor, Cellular and Molecular Medicine

BISB Research Area(s):

Comparative and Population Genomics
Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Bioinformatics Applications in Human Disease

Research Focus: To assess the contributions of RNA-binding proteins and their associated non-coding RNAs to host immune homeostasis and autoimmune pathologies.

Lilia Iakoucheva

Lilia Iakoucheva

Associate Professor, Psychiatry

BISB Research Area(s):

Genetic and Molecular Networks

BMI Research Area(s):

Bioinformatics Applications in Human Disease

Research Focus: Autism, genetics, gene expression, protein interactions, systems biology, networks, psychiatric diseases, whole genome sequencing

Mohit Jain

Mohit Jain

Associate Professor, Pharmacology

BISB Research Area(s):

Proteomics and Metabolomics
Genetic and Molecular Networks
Structural Bioinformatics and Systems Pharmacology

BMI Research Area(s):

Bioinformatics Applications in Human Disease

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

Susan Kaech

Susan Kaech

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

BISB Research Area(s):

Proteomics and Metabolomics
Epigenomics and Gene Expression Control
Genetic and Molecular Networks

BMI Research Area(s):

Bioinformatics Applications in Human Disease

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

Kevin King

Kevin King

Associate Professor, School of Medicine
Associate Professor, Bioengineering

BISB Research Area(s):

TBD

BMI Research Area(s):

TBD

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

Jejo Koola

Jejo Koola

Assistant Clinical Professor, School of Medicine

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Biomedical Natural Language Processing

Research Focus: Practicing internist in the field of hospital medicine and clinical informatics. Research focus is on using informatics tools (including predictive analytics, natural language processing, and information visualization) to improve the care of multi-morbid hospital patients.

Pallav Kosuri

Pallav Kosuri

Assistant Professor, Salk Institute for Biological Studies

BISB Research Area(s):

TBD

BMI Research Area(s):

TBD

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

Tsung-Ting Kuo

Tsung-Ting Kuo

Assistant Professor, Biomedical Informatics

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Privacy Technology, Data Sharing, and Big Data Analytics

Research Focus: Blockchain Technologies, Machine Learning, Natural Language Processing

Amit Majithia

Amit Majithia

Assistant Professor of Medicine and Pediatrics, Division of Endocrinology, School of Medicine

BISB Research Area(s):

Comparative and Population Genomics
Genetic and Molecular Networks

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Insulin resistance, functional genomics, pharmacogenetics, cardiometabolic disease, diabetes

Andrew McCulloch

Andrew McCulloch

Professor, Bioengineering
Professor, School of Medicine

BISB Research Area(s):

Quantitative Foundations of Computational Biology
Dynamical Systems, Stochastic Processes, and Biological Circuits
Structural Bioinformatics and Systems Pharmacology

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

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

Jill Mesirov

Jill Mesirov

Professor, School of Medicine
Associate Vice Chancellor, Computational Health Sciences,
Professor of Medicine, Division of Medical Genetics

BISB Research Area(s):

Quantitative Foundations of Computational Biology
Genetic and Molecular Networks

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

Research Focus: Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.

Niema Moshiri

Niema Moshiri

Associate Teaching Professor, Computer Science and Engineering

BISB Research Area(s):

Quantitative Foundations of Computational Biology

BMI Research Area(s):

Bioinformatics Applications in Human Disease

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

Shamim Nemati

Shamim Nemati

Associate Professor, Biomedical Informatics

BISB Research Area(s):

Dynamical Systems, Stochastic Processes, and Biological Circuits

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Decision Support Systems

Research Focus: Signal Processing, Dynamical Systems, Multivariate Time Series, Point Process, Deep Learning, Reinforcement Learning, Video Processing, and Natural Language Processing

Lucila Ohno-Machado

Lucila Ohno-Machado

Professor, Biomedical Informatics

BISB Research Area(s):

Epigenomics and Gene Expression Control

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Privacy Technology, Data Sharing, and Big Data Analytics

Research Focus: Biomedical Informatics, predictive modeling, biomedical data analytics

Johannes Schoeneberg

Johannes Schoeneberg

Assistant Professor, Pharmacology
Assistant Professor, Chemistry and Biochemistry

BISB Research Area(s):

TBD

BMI Research Area(s):

TBD

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

Jonathan Sebat

Jonathan Sebat

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

BISB Research Area(s):

Comparative and Population Genomics
Epigenomics and Gene Expression Control

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Bioinformatics Applications in Human Disease

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

Amy Sitapati

Amy Sitapati

Clinical Professor, Biomedical Informatics

BMI Research Area(s):

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

Pandurangan Vijayanand

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

BISB Research Area(s):

Comparative and Population Genomics
Epigenomics and Gene Expression Control

BMI Research Area(s):

Bioinformatics Applications in Human Disease

Research Focus: Continually evolving genomic tools and single cell analysis technologies are revolutionizing our understanding of the human immune system in health and disease.

Joel Wertheim

Joel Wertheim

Associate Professor, School of Medicine

BISB Research Area(s):

Genetic and Molecular Networks

BMI Research Area(s):

Bioinformatics Applications in Human Disease

Research Focus: Molecular epidemiology of HIV, SARS-CoV-2, and other RNA viruses; Viral phylogenetics and evolution

Rose Yu

Rose Yu

Assistant Professor, Computer Science and Engineering

BISB Research Area(s):

Quantitative Foundations of Computational Biology
Dynamical Systems, Stochastic Processes, and Biological Circuits

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Decision Support Systems

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

Karsten Zengler

Karsten Zengler

Adjunct Professor, Pediatrics

BISB Research Area(s):

Quantitative Foundations of Computational Biology
Genetic and Molecular Networks
Dynamical Systems, Stochastic Processes, and Biological Circuits

BMI Research Area(s):

Predictive Modeling and Personalized Medicine
Privacy Technology, Data Sharing, and Big Data Analytics
Data Models and Knowledge Representation
Bioinformatics Applications in Human Disease

Research Focus: Our lab studies microbe-microbe and host-microbe interactions. The goal is to predict how complex systems react to perturbations and to design strategies to change the trajectory.