CII Distinguished Lecture Series: Reverse-Engineering Biological Systems

Center for Infection and Immunity Distinguished Lecture Series
Monday, November 7, 2011
2:00-3:00PM

Humphrey’s Auditorium
Vanderbilt Clinic - 622 W. 168th Street
14th Floor – Room 240

Reverse-Engineering Biological Systems

Pierre Baldi, PhD
Chancellor's Professor in the School of Information and Computer Sciences and the Department of Biological Chemistry
Director of the Institute for Genomics and Bioinformatics
University of California, Irvine

We introduce Crick, an integrative intelligent expert system for systems molecular biology. At its core, the system uses databases of transcription factor and a Bayesian statistical approach to derive comprehensive, genome-wide, maps of regulatory elements. These maps can be used in turn to infer core regulatory circuits and loops. These inferences are then augmented and refined by integrating them with many other kinds of data, such as: (1) Gene Ontology; (2) Protein-protein interaction; (3) RNA; (4) Gene Expression; (5) Epigenetics; (6) Chromatin and DNA 3D structure; (7) SNPs; (8) Drugs; (9) Metabolic; and (10) Scientific literature. This integrative approach is similar in spirit to IBM's Watson system for the game of Jeopardy. Examples of collaborative projects based on the predictions made by Crick and their experimental validations are also described together with a discussion of future challenges and opportunities.

About Dr. Baldi:

Pierre Baldi is Chancellor's Professor in the School of Information and Computer Sciences and the Department of Biological Chemistry and the Director of the Institute for Genomics and Bioinformatics at the University of California, Irvine. Born and raised in Europe, he received his PhD from the California Institute of Technology in 1986.  From 1986 to 1988 he was a postdoctoral fellow at the University of California, San Diego.  From 1988 to 1995 he held faculty and member of the technical staff positions at the California Institute of Technology and at the Jet Propulsion Laboratory. He was CEO of a startup company from 1995 to 1999 and joined UCI in 1999.  His research work is at the interface of the computational and life sciences, in particular the application of AI and statistical machine learning methods to problems in chemoinformatics, genomics, proteomics, and systems biology.

He is credited with pioneering the use of Hidden Markov Models (HMMs), graphical models, and recursive neural networks in bioinformatics. Dr. Baldi has published over 250 peer-reviewed research articles and four books:Modeling the Internet and the We--Probabilistic Methods and Algorithms, Wiley, (2003); DNA Microarrays and Gene Regulation--From Experiments to Data Analysis and Modeling, Cambridge University Press, (2002); The Shattered Self--The End of Evolution, MIT Press, (2001); Bioinformatics: the Machine Learning Approach, MIT Press, Second Edition (2001).

His group has developed widely used databases, software, and web servers including the ChemDB database and chemoinformatics portal for the prediction of molecular properties and applications in chemical synthesis and drug discovery, the SCRATCH suite of protein feature predictors, the Cyber-T program for the differential analysis of gene expression data using Bayesian statistical methods, and the MotifMap system for charting transcription factor binding sites on a genome-wide scale and for supporting gene regulatory mechanisms inferences in healthy and disease system. He is the recipient of the 1993 Lew Allen Award, the 1999 Laurel Wilkening Faculty Innovation Award, a 2006 Microsoft Research Award, and the 2010 E. R. Caianiello Prize for research in machine learning. He is a Fellow of the Association for the Advancement of Science (AAAS) and the Association for the Advancement of Artificial Intelligence (AAAI).