Biomedical Informatics Track

Biomedical Informatics Graduate Training Program

Genome sequencing projects are rapidly providing the genetic blueprint of organisms across the kingdoms of life. These sequences are catalyzing our abilities to understand biological systems at levels never before possible. However, new genomic technologies are generating overwhelming amounts of data that must be processed and analyzed. These massive amounts of data have created a critical need for theoretical, algorithmic, software, and hardware advances in storing, retrieving, networking, processing, modeling, analyzing, and visualizing biological and medical information. These needs are inspiring new concepts in computer science, such as genetic algorithms, artificial neural networks, computer viruses, synthetic immune systems, DNA computing methods, artificial life, and hybrid DNA gene chips. Because of these developments, computer science applications in the fields of biology and medicine showcase the latest advances in core computer science from hardware to software, from algorithms to databases, and from theory to user interfaces. This cross-fertilization has enriched both fields and will continue to do so in the coming decades. However, interdisciplinary graduate programs in bioinformatics remain scarce and the pool of individuals with training in both computational and biomedical sciences is still exceedingly small. To meet this challenge, UCI has developed an interdisciplinary, Biomedical Informatics Training (BIT) Program that is coordinated with existing graduate degree programs in the Department of Information and Computer Science, the School of Biological Sciences/College of Medicine, and the School of Physical Sciences. The BIT Program provides in-depth graduate training in computational and life sciences with an emphasis in bioinformatics approaches to problems in molecular structure prediction and determination, and comparative and functional genomics, areas of great strength at UCI. MBGB students join the BIT Program through the Bioinformatics training track. At the end of the first year, students choose a thesis advisor in the Bioinformatics track, and upon acceptance into the BIT Program, a thesis co-advisor in computer science. Students in the BIT Program will take courses from a menu designed to ensure that, regardless of their primary expertise, each obtains a set of core skills related to molecular biology, genetics, biochemistry, computer modeling of biological systems, statistics, programming, and database development.

Courses Offered:

Required:

Math 7: Basic Statistics, Basic inferential statistics including confidence intervals and hypothesis testing on means and proportions, t-distribution, Chi Square, regression and correlation, F-distribution and nonparametric statistics.

ICS 21: Introduction to Computer Science, Introduces fundamental concepts related to computer software design and construction. Develops initial design and programming skills using a high-level programming language (primarily C++/Java). Introduces useful computer-based tools for analysis, expression, discovery.

ICS 184: File and Database Management, Database system architecture--data structures, storage structures, and data languages. Alternate approaches to database management systems: relational approach, hierarchical approach, network approach. Database security and integrity. Query processing.

ICS 277A: Representations & Algorithms for Molecular Biology, Introduction to computational methods in molecular biology. Computational approaches to understanding and predicting the structure, function, interactions, and evolution of DNA, RNA, proteins, and related molecules and processes.

ICS 277B: Probabilistic modeling of Biological Data, A unified Bayesian probabilistic framework for modeling and mining biological data. Applications range from sequence (DNA, RNA, proteins) to gene expression data. Graphical models, Markov models, stochastic grammars, structure prediction, gene finding, evolution, DNA arrays, single- and multiple-gene analysis.

ICS 209: Seminar in Informatics in Biology and Medicine, Current research and research trends in bioinformatics and medical informatics. Forum for presentation and criticism by students of recently published research and work in progress.

*Appropriate Electives:

ICS 274: Probabilistic Learning - Theory and Algorithms
ICS 276A: Neural Networks
ICS 276C: Cognitive and Computational Neuroscience
ICS 278: Data Mining
DCB 210: Developmental Genetics
DCB 231B: Cell Biology
DCB 231D: Cellular & Developmental Neurobiology
BC 207: Advanced Molecular Genetics
EE 251: Molecular Evolutionary Methods

*See the UCI General Catalog for additional course offerings in the Schools of Biological and Physical Sciences, the College of Medicine, and the Department of Information and Computer Science.

MBGB Faculty (Primary Thesis Advisors):

Track coordinator - Ruslan Aphasizhev, +

Hoda Anton-Culver, + Ph.D., Professor of Epidemiology, Department of Medicine, and Microbiology & Molecular Genetics
    Cancer and genetic epidemiology, statistical and molecular genetics, medical informatics
Lee Bardwell, + Ph.D., Assistant Professor of Developmental and Cell Biology
    Coupling of cell signaling to gene expression
Bruce Blumberg, + Ph.D., Assistant Professor of Developmental and Cell Biology
    Gene regulation by nuclear hormone receptors in vertebrate development and adult physiology
Hung Fan, + Ph.D., Professor of Molecular Biology & Biochemistry
    Molecular Biology of Retroviruses, Immunology, cancer biology, gene therapy
Anand Ganesan, + M.D./Ph.D., Assistant Professor of Dermatology
    Identify the key molecular regulators of melanin production, melanoma cell survival, and melanoma chemoresistance in human cells
Lan Huang, + Ph.D., Assistant Professor of Physiology & Biophysics and Development & Cell Biology
    Proteomics/mass spectrometry, signaling networks, posttranslational modifications, biomarkers in cancer
Steven Lipkin, + M.D./Ph.D., Professor of Medicine and Biological Chemistry
    High density oligonucleotide array design and analysis
Haoping Liu, + Ph.D., Assistant Professor of Biological Chemistry
    Signaling in development, yeast morphogenesis and pathogenesis
Ray Luo, + Ph.D., Assistant Professor of Molecular Biology & Biochemistry
    Computational biology, protein structure prediction and folding mechanisms, protein-protein and protein-ligand interactions
Suzanne Sandmeyer, + Ph.D., Professor and Chair of Biological Chemistry & Director of the UCI DNA Microarray Core Facility
    Molecular genetics of a position-specific yeast retrovirus-like element, functional genomics, gene regulation using DNA arrays and proteomics
Ming Tan, + Ph.D., Assistant Professor of Microbiology and Molecular Genetics
    Global gene regulation in Chlamydia using DNA arrays and proteomics
Leslie M. Thompson, + Ph.D., Assistant Professor of Psychiatry and Biological Chemistry
    Molecular and biochemical mechanisms of disease pathogenesis and therapeutic approaches to human neurodegenerative disease
Sheryl Tsai, + Ph.D., Assistant Professor of Molecular Biology & Biochemistry
    Application of bioinformatics to drug design and large protein complexes
Doug Wallace, + Ph.D., Professor of Biological Chemistry and Ecology & Evolutionary Biology
    Human mitochondrial genetics and molecular medicine
Tau-Mu Yi, + Ph.D., Assistant Professor of Developmental and Cell Biology
    G-protein signal transduction; cell polarization; Systems Biology.

ICS Faculty (Thesis Co-Advisors):

Pierre Baldi, + Ph.D., Professor & Director of Institute for Genomics and Bioinformatics.
    Bioinformatics, computational biology, probabilistic modeling, and machine learning
Dennis Kibler, + Ph.D., Professor of Information and Computer Science
    Machine learning methods based on genome and gene expression data to find regulatory elements, promoters and unexpected structures
Richard Lathrop, + Ph.D., Associate Professor Information and Computer Science
    Bioinformatics, computational biology, machine learning, artificial intelligence, protein structure prediction, drug discovery, genetic regulation
Wanda Pratt, + Ph.D., Assistant Professor of Information and Computer Science
    Artificial intelligence, human-computer interaction, medical informatics
Padhraic Smyth, + Ph.D., Associate Professor of Information and Computer Science
     Probabilistic modeling, computational statistics, pattern recognition

School of Biological Sciences Faculty (Thesis Co-Advisors):

Albert F. Bennett, + Ph.D., Professor and Chair of Ecology & Evolutionary Biology
    Environmental and evolutionary physiology of animals
Robin M. Bush, + Ph.D., Assistant Research Biologist of Ecology & Evolutionary Biology
     Molecular evolution of pathogenic organisms
Walter M. Fitch, + Ph.D., Professor of Ecology & Evolutionary Biology
     Molecular evolutions
Brandon S. Gaut, + Ph.D., Associate Professor of Ecology & Evolutionary Biology
     Evolutionary genetics of plant systems, with emphasis on molecular evolution and population genetics
Anthony D. Long, + Ph.D., Assistant Professor of Ecology & Evolutionary Biology
     Elucidating the molecular genetic basis of polygenic characters using Drosophila melanogaster

School of Physical Sciences Faculty (Thesis Co-Advisors):

Richard A. Chamberlin, + Ph.D., Professor of Chemistry
     Chemical synthesis. excitatory neurotransmitter receptors, potassium channel blockers, phosphatase inhibitors, and proteins containing non-natural amino acid residues
James S. Nowick, + Ph.D., Professor of Chemistry and Director of the Chemical Biology Initiative
     Design of small to medium sized organic molecules that mimic the structures of proteins
A. J. Shaka, + Ph.D., Professor of Chemistry
     Development of nuclear magnetic resonance techniques for the structure determination of molecules in solution
Douglas J. Tobias, + Ph.D., Assistant Professor of Epidemiology
     Using atomic-scale computer simulation techniques to study the structure of biological molecules
David L. Van Vranken, + Ph.D., Associate Professor of Epidemiology
     Using organic synthesis to connect fundamental chemical principles with biological phenomena such as cancer and aging
Gregory A. Weiss, + Ph.D., Assistant Professor of Chemistry and Co-Director of the Chemical Biology Initiative
     Using molecular evolution in a test tube (phage display) to explore the chemistry and biology of cells

Courses Offered:

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