BMI Faculty by Research Area


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.

Lukas Chavez

Lukas Chavez

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

Robert El-Kareh

Robert El-Kareh

Associate 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.

Olivier Harismendy

Olivier Harismendy

Assistant 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
  • Biomedical Natural Language Processing

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

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

Assistant 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


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
  • Biomedical Natural Language Processing

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


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

Assoc Physician Dipl, 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.


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 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

Assistant 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


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.

Michael Hogarth

Michael Hogarth

Assoc Physician Dipl, 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.

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
  • Biomedical Natural Language Processing

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


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.

Ferhat Ay

Ferhat Ay

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 in Residence, School of Medicine

BISB Research Area(s):
  • Epigenomics and Gene Expression Control
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease
Lukas Chavez

Lukas Chavez

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

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

Olivier Harismendy

Olivier Harismendy

Assistant 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

Albert Hsiao

Assistant Professor in Residence, Radiology

BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

Research Focus: Cardiac and vascular imaging

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

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

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 HIV epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development

Yingxiao (Peter) Wang

Yingxiao (Peter) Wang

Professor, Bioengineering

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Dynamical Systems, Stochastic Processes, and Biological Circuits
BMI Research Area(s):
  • Bioinformatics Applications in Human Disease

Research Focus: Live cell imaging, genetic and epigenetic regulations, immunoengineering, therapeutics

Joel Wertheim

Joel Wertheim

Assistant 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 and other RNA viruses; Virus phylogenetics and evolution


Other BMI Research Areas

Hannah Carter

Hannah Carter

Assistant Professor of Medicine, Division of Medical Genetics

BISB Research Area(s):
  • Structural Bioinformatics and Systems Pharmacology
BMI Research Area(s):
  • TBD

Research Focus: Structural Bioinformatics, Systems Biology, Machine Learning, Cancer, Personalized Medicine and Genetic Variation

Nicholas Schork

Nicholas Schork

Professor, Scripps Research Institute

BISB Research Area(s):
  • Quantitative Foundations of Computational Biology
  • Comparative and Population Genomics
BMI Research Area(s):
  • TBD

Research Focus: Developing mathematical, statistical, and computational models and tools to study the genetic basis of complex traits and diseases