Academic Year 2010-2011

NIH funds summer research program for community college students The National Institutes of Health has awarded a five-year, $400,000 grant to UCI's Institute for Genomics & Bioinformatics to support a summer research program for first-generation community college students from Orange and Los Angeles counties. The biomedical informatics outreach effort encourages students from low-income, historically underserved ethnic and racial backgrounds to explore research training and career opportunities that combine computational and life sciences. In June, UCI welcomed to the program seven scholars from Rio Hondo, Santa Ana and Santiago Canyon colleges. Each participant works with a graduate student and faculty adviser for 10 weeks and will present findings at a research symposium. For more information, contact Debra Mauzy-Melitz, IGB director of outreach development, at 949-824-2796.

Industry Giants British Petroleum and Royal DSM Back IGB Startup Verdezyne Inc., a UCI startup synthetic biology company that genetically engineers yeasts to eat plant sugars or oils and excrete biofuels and industrial chemicals, has just landed large equity investments from British oil giant British Petroleum and Dutch biochemicals company Royal DSM that will take them through the pilot plant phase to commercialization of their first product, adipic acid. Adipic acid, currently obtained from petroleum, is a starting chemical required for the manufacture of nylon and plastics such as polystyrene. (more)

Professors Lathrop and Kaiser's NIH grant entitled "A Functional Census of p53 Cancer and Suppressor Mutants" is renewed for another four years with $1.6 million in funding from the National Cancer Institute of the NIH. The objective of the grant is to use biological experiments to support computational approaches to identify second site mutations in p53 that can restore activity of p53 mutants found in human cancer.

Assistant Project Scientist Arlo Randall Receives NIH Pathway to Independence Award (K99/R00) Arlo Randall, Assistant Project Scientist and former Biomedical Informatics Training (BIT) Program trainee, has received an NIH Pathway to Independence Award from the National Library of Medicine for the project entitled "Predicting and Engineering Molecular Structures for Biomedical Applications." The Primary purpose of the Pathway to Independence Award program is to increase and maintain a strong cohort of new and talented NIH-supported independent investigators. The program is designed to facilitate a timely transition from a mentored postdoctoral research position to a stable independent research position with independent NIH or other independent research support at an earlier stage than is currently the norm.

IGB Awarded Grant from NIH to Develop Efficient Data Structures and Algorithms for Genomic Sequence Data The long-term objective of this project is to develop and deploy efficient data structures and algorithms for the storage, transmission, querying, privacy protection, and management of large-scale High-Throughput Sequencing (HTS) and genomic information. The project is led by Professor Baldi in collaboration with the laboratories of Professors Goodrich, Jarecki, and Xie.

IGB Receives Biomedical Informatics Training (BIT) Supplement Grant The supplement received from the NIH National Library of Medicine will be used to create two new courses: (1) a BIT graduate course in High-Throughput Sequencing Technologies and Applicaitons to address the revolution in the life-sciences created by these technologies and their use on the UCI campus and the BIT Program through the new UCI Genomics High-Throughput Facility; and (2) a BIT graduate course in Medical Informatics to take advantage of the momentum and synergies associated with the opening of a new state-of-the-art hospital at the UCI Medical Center, the development of the UCI ICTS (Institute for Clinical and Translational Science), and its recent award of a large NIH CTSA (Clinical and Translations Science Award) grant. All course material will be shared with all other NLM informatics training programs over the (2D) Web. In addition, by leveraging unique expertise at UCI in human computer interfaces and virtual realities, the supplement will be used to create the first 3D Web infrastructure for fostering collaborations in education and research, within the BIT Program, the UCI campus, all NLM informatics training programs, and beyond, through the use of virtual worlds and communities.

Academic Year 2009-2010

Wiley Partners with Reaction Explorer to Offer Interactive Organic Chemistry Learning System with Textbooks An evaluation version of Reaction Explorer is available at www.ReactionExplorer.com. Schools interested in adopting Reaction Explorer should contact Petra Recter at Wiley ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). Anyone interested in learning more about Reaction Explorer can contact Reaction Explorer at This e-mail address is being protected from spambots. You need JavaScript enabled to view it . April 2010.

IGB faculty members among the first annual Dean’s Triumvirate Grant recipients at UC Irvine Professors Lathrop, Kaiser, and Chamberlin received $15K for their grant entitled “Reactivation of p53 in Human Cancer by Small Drug-like Molecules”. The triumvirate grant was set up through the UC Irvine School of Medicine to help foster collaborative efforts among the various schools at UC Irvine. January 2010.

"Prix Richelieu" Awarded IGB postdoctoral fellow Alessio Andronico awarded the "Prix Richelieu" for his doctoral thesis defended at the University of Paris VII (Paris Diderot). December 2009.

IGB receives $95K ARRA supplement for the Biomedical Informatics Training (BIT) Program IGB receives $95K ARRA equipment supplement from NIH National Library of Medicine for the Biomedical Informatics Training (BIT) Program. December 2009.

IGB awarded $743,872 from NIH STTR with Verdezyne, Inc. (formerly known as CODA Genomics) IGB’s Computational Biology Research Laboratory (CBRL) under Professor Hatfield was awarded $743,872 from Verdezyne, Inc., as part of NIH STTR grant entitled, “CODA Assebmly of Mutant Genes”. September 2009.

Xiaohui Xie Receives NSF Career Award The National Science Foundation has recently awarded Dr. Xiaohui Xie, IGB faculty from Dept. of Computer Science its prestigious CAREER Award. The CAREER award, one of NSF’s most prestigious and competitive awards for junior researchers, recognizes those who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research. The five-year, $751,980 award will support Dr. Xie' research and educational efforts in bioinformatics and computational biology, an interdisciplinary research area that employs computational and mathematical tools to study biomedical problems. July 2009.

Academic Year 2008-2009

Jarecki awarded Distinguished Assistant Professor Award for Research Stanislaw Jarecki, assistant professor of computer science, has been awarded the annual UC Irvine Distinguished Assistant Professor Award for Research. It is the first time a Bren School professor has received the award. June 2009.

Chloe Azencott awarded IBM Ph.D. Fellowship Chloe Azencott, fourth year Ph.D. student in computer science and IGB BIT trainee has been awarded an IBM Ph.D. Fellowship program for the 2009-2010 academic year. The award which covers tuition and mandatory fees, also comes with a $17,500 stipend. Azencott's, research interest lies in the areas of machine learning applied to the life sciences, more particularly chemistry and chemoinformatics. Under the mentorship of faculty advisor Pierre Baldi, Azencott's research topic is entitled Statistical Machine Learning and Data Mining for Chemoinformatics and Drug Discovery. The IBM Ph.D. Fellowship Awards is an intensely competitive program which honors exceptional Ph.D. students in many academic disciplines and areas of study. IBM pays special attention to an array of focus areas of interest to IBM and fundamental to innovation, including technology that creates new business value, innovative software, new types of computers and interdisciplinary projects. March 2009.

Li receives NSF award to study large-scale data cleaning Chen Li, associate professor of computer science and member of IGB, has received an award for $221,730 from the NSF CluE program to support his research on large-scale data cleaning using cloud computing. March 2009.

Baldi awarded grant in chemical sciences to support development of Reaction Explorer Chancellor's Professor Pierre Baldi has been awarded a grant in the Special Grant Program in Chemical Sciences by the Camille and Henry Dreyfus Foundation. The grant is in support of the development of Reaction Explorer, a new interactive electronic tutorial system for teaching organic reactions, reaction mechanisms, organic synthesis and retrosynthesis at the undergraduate level. Reaction Explorer is an interactive tutorial system for organic chemistry reactions, which enables students to learn about reactions in ways previously unrealized. February 2009

CODA Genomics becomes Verdezyne Carlsbad-based CODA Genomics, formerly located in Laguna Hills and founded by IGB members Rick Lathrop and Wes Hatfield, said Tuesday that it is renaming itself Verdezyne, Inc. Verdezyne is developing technology developed at UC Irvine for engineering proteins, metabolic pathways and microorganisms for the life sciences, chemical, and biofuels markets. The firm, which is venture backed by OVP Venture Partners, Monitor Ventures, the Tech Coast Angels, and the Life Science Angels, said the name change better conveys the company's focus on manufacturing platform chemicals and biofuels. The firm's core technology, licensed from UCI is being applied to the commercial fermentation process, which is used for biofuels and chemicals manufacturing from lignocellulosic materials. November 11, 2008.

IGB awarded $1.09M from NIH IGB Professor Dechter has been awarded $1.09M from NIH for her collaborative research with Prof. Thompson (University of Washington) and Prof. Geiger (Technion University) entitled, “Efficient Software and Algorithms for analyzing Markers Data on General Pedigrees.” September 2008.

IGB Professors awarded $1.25M from NIH IGB Professors Mjolsness and Bardwell has been awarded $1.25M by NIH for their collaborative research on “Stochastic Dynamics for Multiscale Biology.” September 2008.

Academic Year 2007-2008

Smyth receives Google Research Award for Statistical Text Mining Padhraic Smyth, Professor of computer science and IGB’s Medical Informatics Program Leader, has received a gift of $60,000 Google Research Award to support research on statistical text mining of very large document collections using parallel computing. March 2008.

Jarecki receives NSF CAREER Award Stanislaw Jarecki, assistant professor of computer science and member of IGB, has been awarded a $450,000 NSF CAREER research award entitled "Secure Multi-Party Protocols, from Feasibility to Practice". February 2008.

Dechter receives 2007 ACP Research Excellence award Rina Dechter, Professor in Computer science and member of IGB has received the 2007 Association of Constraint Programming Research Excellence award for her program of sustained high quality research in constraint processing, with numerous influential results and great impact on Artificial Intelligence. October 2007.

IGB awarded $1.67 million grant from CODA Genomics and UC Discovery Grant (Press Release) IGB’s Computational Biology Research Laboratory (CBRL) under Professor Hatfield, and the labs of professors Pierre Baldi (Computer Science), Suzanne Sandmeyer (Biological Chemistry) and Nancy Da Silva (Biochemical Engineering) received $1.67 million grant in support of their multidisciplinary project entitled “Optimized Heterologous Pathways for Ethanol Production in Yeast” from CODA Genomics, an Orange County synthetic biology company, and a UC Discovery Grant that provides matching funds for innovative industry-university research partnership. September 4, 2007.

IGB awarded $5.6 million grant from the NIH-National Library of Medicine for the Biomedical Informatics Training (BIT) Program (Press Release) IGB has been awarded $5.6 million over five years from the National Institutes of Health to continue training students to apply advanced computer and information technologies in the biological and medical sciences. The funding will be used to expand the interdisciplinary Biomedical Informatics Training (BIT) program, an initiative led by IGB Director and Chancellor’s Professor Pierre Baldi and Professor G. Wesley Hatfield to train graduate students and postdoctoral fellows in the UCI Donald Bren School of Information and Computer Sciences (ICS), The Henry Samueli School of Engineering, and the schools of physical sciences, biological sciences, and medicine. August 16, 2007.

Graduate students win prestigious data mining competition Chloe Azencott and S. Josh Swamidass, two of IGB BIT graduate students in professor Pierre Baldi’s lab, finished in first and second place respectively in the data mining competition "Agnostic Learning vs. Prior Knowledge" part of the International Joint Conference on Neural Networks (IJCNN) 2007 Conference, the premier conference in the field of neural networks. August 2007.

IGB BIT Graduate student places third in data mining competition IGB BIT graduate student, Christopher Wassman, has placed third at the UC San Diego data mining competition in the graduate/postdoctoral category of the Refinance Prediction task. Wassman is a student of computer science professor and IGB’s Structural Genomics Program Leader, Richard Lathrop. His concentration is in Informatics in Biology and Medicine. August 2007.

Members of IGB receive NSF grant to study modular software design Crista Lopes, associate professor of informatics, and Pierre Baldi, professor of computer science, have received a National Science Foundation grant of over $600,000 in support of their project entitled "Large Scale Empirical Validation of the Aspect-Oriented Design Hypothesis". August 2007.

UCI Awarded $14.5 Million to Support Systems Biology Center (Press Release) UC Irvine has been awarded $14.5 million over five years to support the Center for Complex Biological Systems in which biologists, mathematicians, physicists, engineers and computer scientists collaborate to study why the human body and other organisms work the way they do.

Academic Year 2006-2007

IGB to Sponsor Caltech's Center for Advanced Computing Research (CACR) Workshop created on Interdisciplinary Strategic Issues in e-Science and Cyber-Infrastructure. June 2007.

IGB awarded $41K NIH STTR grant with Planet Biotechnology, Inc. IGB’s Computational Biology Research Laboratory (CBRL) under Professor Hatfield was awarded $41,756 from Planet Biotechnology, Inc., as part of NIH STTR grant entitled, “Optimizing Codon Pair Usage in Genes Encoding Plant-Made Recombinant Proteins.” April 2007.

Goodrich named Chancellor's Professor Michael Goodrich, professor of computer science and member of IGB, was awarded the title of Chancellor's Professor, effective April 1, 2007. The title is conferred for a five-year renewable term and recognizes scholars who have demonstrated unusual academic merit and whose continued promise for scholarly achievement makes them of exceptional value to the university. Goodrich’s research are directed at the design of high-performance algorithms and data structures for solving large-scale problems surrounding the increased demands of computer graphics, information visualization, scientific data analysis, information assurance and security, and the Internet. April 2007.

Baldi named AAAI Fellow Pierre Baldi, Chancellor's Professor and Director of the Institute for Genomics and Bioinformatics, has been named a fellow of the Association for the Advancement of Artificial Intelligence (AAAI). April 2007.

Alumnus publishes book on cross-layer design Raja Jurdak, a former graduate student of professors Crista Lopes and Pierre Baldi, and now a post-doctoral fellow at the University College, Dublin, has recently published a book entitled "Wireless AdHoc and Sensor Networks -- A Cross-Layer Design Perspective." February 2007.

NSF CAREER: Tools for Analyzing, Modeling, and Comparing Protein-Protein Interaction Networks Natasa Przulj, Assistant Professor in the Department of Computer Science and member of IGB, has been awarded an NSF Career Award on Tools for Analyzing, Modeling, and Comparing Protein-Protein Interaction Networks. January 2007.

Baldi named Chancellor's Professor Pierre Baldi, professor of computer science and biological chemistry and director of the Institute for Genomics and Bioinformatics, has been awarded the title of Chancellor's Professor, effective Wednesday, Nov. 1. The title is conferred for a five-year renewable term and recognizes scholars who have demonstrated unusual academic merit and whose continued promise for scholarly achievement makes them of exceptional value to the university. Baldi's research areas include: bioinformatics, computational biology probabilistic modeling and machine learning. November 2006.

Academic Year 2005-2006

NSF Study will probe the Quintessence of Surprise
Multi-institutional study investigates new digital understanding of how brains perceive novelty and importance. Information theorists, Pierre Baldi of UC Irvine and Laurent Itti of USC are joining with electro physiologist, Douglas Muñoz of Queens University, Canada, on the study.

Two IGB Faculties to be Honored with Innovation Award on UCI's 40th Anniversary
UCI Professors, Richard Lathrop, Department of Computer Science, and G. Wesley Hatfield, Department of Microbiology and Molecular Genetics, will be recognized for their unique entrepreneurial contributions at a November 9th ceremony honoring UCI's most significant innovators. The event is part of celebration activities surrounding UCI's 40th anniversary.

IGB Post-doctoral Cancer Researcher Secures Prestigious Appointments
Irvine, California, October, 2005, Chin-Rang Yang, a recent postdoctoral alumnus of the Biomedical Informatics Training (BIT) Program administered by the UCI Institute for Genomics and Bioinformatics (IGB), has accepted an appointment as an Assistant Professor in the Department of Oncology of the Simmons Comprehensive Cancer Center at the University of Texas Southwestern Medical Center at Dallas. He will also be awarded a joint appointment in the Department of Bioengineering at the University of Texas at Dallas and serve as a systems biology liaison between the medical school and the UT Dallas campus.

IGB awarded $1.8 million NIH grant
Irvine, California, September 26, 2005, The National Cancer Institute of the NIH has awarded a trio of IGB researchers a grant to apply machine learning and experimental analyses to the activities of the tumor-suppressing protein p53. Pierre Baldi, Rainer Brachmann and Richard Lathrop expect to contribute key information for new anti-cancer drugs.

IGB Associate Director and DermTech International Receive UC Discovery Grant
Irvine, California, June 23, 2005, DermTech International, an early-stage biotechnology company developing skin sampling technologies, announced receipt of a one-year UC Discovery Grant in the amount of $138,000 for research with G. Wesley Hatfield, UCI Professor of Microbiology and Molecular Genetics.

IGB Technology Licensed to CODA Genomics, Inc.
Irvine, California, April 27, 2005, Technology developed at the Institute for Genomics and Bioinformatics (IGB) by Richard Lathrop and G. Wesley Hatfield has been licensed under an exclusive agreement between the University of California and CODA Genomics, a start-up company that will commercialize the DNA assembly and protein expression optimization work developed by the two IGB researchers.

Tenure-Track Faculty Positions

Academic Year 2003-2004

IGB Awarded $7 million to Advance Biomedical Research
UC Irvine's Institute for Genomics and Bioinformatics, has been awarded four grants totaling nearly $7 million to further biomedical computing research and improve educational training.

Academic Year 2002-2003

Institute for Genomics and Bioinformatics awarded $4.3 million
Irvine, California, May 30, 2002, IGB has been awarded a $4.3 million multiyear training grant from the National Institutes of Health to consolidate current UCI bioinformatics training programs into a comprehensive, campus-wide initiative.