BMI Faculty by Research Area | Bioinformatics and Systems Biology

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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

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

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.

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

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

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.

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.

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.

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

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

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.

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

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

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

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.

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

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.

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.

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

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

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

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

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

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.

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.

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.

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 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

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

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.

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

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

Assistant 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

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

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

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.

Other BMI Research Areas

Amy Sitapati

Amy Sitapati

Professor, Biomedical Informatics

BISB Research Area(s):

TBD

BMI Research Area(s):

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