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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.
Hannah Carter
Assistant 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
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
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 personalized surveillance, epigenetic aging, translational risk prediction tools
Robert El-Kareh
Associate 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.
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
Assistant 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
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
Assistant 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
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
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
Assoc Physician Dipl, 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.
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 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
Assistant 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
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
Assoc Physician Dipl, 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.
Ferhat Ay
Assistant Adjunct Professor, PediatricsBISB 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 in Residence, School of MedicineBISB Research Area(s):
- Epigenomics and Gene Expression Control
- Bioinformatics Applications in Human Disease
Hannah Carter
Assistant 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
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
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 personalized 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
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
Assistant 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):
- Epigenomics and Gene Expression Control
- Genetic and Molecular Networks
- Dynamical Systems, Stochastic Processes, and Biological Circuits
- Bioinformatics Applications in Human Disease
Research Focus: Non-coding RNA, RNA binding proteins, gene expression analysis, immune 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
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
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 HIV epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development
Joel Wertheim
Assistant Professor, School of MedicineBISB Research Area(s):
- Genetic and Molecular Networks
- Bioinformatics Applications in Human Disease
Research Focus: Molecular epidemiology of HIV and other RNA viruses; Virus phylogenetics and evolution
Nicholas Schork
Professor, Scripps Research InstituteBISB Research Area(s):
- Quantitative Foundations of Computational Biology
- Comparative and Population Genomics
- TBD
Research Focus: Developing mathematical, statistical, and computational models and tools to study the genetic basis of complex traits and diseases