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Academic Year 2017-2018

Southern California Biomedical Imaging and Machine Learning Symposium
Co-Organized by IGB and Calit2
Program Schedule and Registration Info
Friday, June 1, 2018

4th Annual UCI RNA Symposium 2018
Program Schedule and Registration Info
Friday, April 6, 2018

Southern California Microbiome Symposium – Connections to the Environment and Health
Co-Organized by IGB, Calit2, and the UCI Data Science Initiative
Program Schedule and Registration Info
Friday, September 22, 2017

Academic Year 2016-2017

Ensembl Workshop
Program Schedule and Registration Info
Thursday, May 4, 2017

2017 RNA Symposium
Program Schedule and Registration Info
Friday, April 14, 2017

PhD Research Fellowships in Artificial Intelligence and Machine Learning at UC Irvine annoucement
The Computer Science department at UC Irvine (UCI) is seeking applicants for PhD research fellowships in artificial intelligence, machine learning, and their related applications, including topics such as deep learning, statistical learning, graphical models, information extraction, computer vision, high-dimensional data analysis, and more.
See Announcement.
Friday, November 18, 2016

Assistant Specialist Position annoucement
The Institute for Genomics and Bioinformatics has a full-time Assistant Specialist position available in the area of statistical machine learning, in particular deep learning, to investigate both theoretical questions as well as applications in the natural sciences, in particular in physics, chemistry, and biology. Necessary qualifications include a PhD in computer science with additional expertise in mathematics as well as at least one, and preferably two, of the fields of application.
See Announcement.
Monday, August 29, 2016

Southern California Microbiome Symposium – Connections to the Environment and Health
Co-Organized by IGB, Calit2, and the UCI Data Science Initiative
Program Schedule and Registration Info
Friday, September 23, 2016

Academic Year 2015-2016

Southern California Machine Learning Symposium
Co-Organized by IGB, Calit2, and the Data Science Initiative
Program Schedule and Registration Info
May 20, 2016

Assistant Specialist Position annoucement
The laboratory of Prof. P. Baldi in the Institute for Genomics and Bioinformatics is looking for a candidate to study machine learning methods, in particular deep learning methods, and their applications to problems in the natural sciences, in particular in all areas of bioinformatics and computational biology. (see more)
November 18, 2015

NIH Genomics Data workshop
11:00 am to 1pm, 105 Sprague Hall
September 29, 2015

Microbiome Connections to Environment and Health Symposium
Co-Organized by IGB, Calit2, and the Data Science Initiative
Program Schedule and Registration Info
September 29, 2015

Academic Year 2014-2015

Code Watch: The best programming book of the decade
“Exercises in Programming Style” by Cristina Videira Lopes is the best programming book to come along in many years. Casting back over many decades, the only book I can compare it to in terms of actionable value is Steve McConnell’s “Code Complete,” and in terms of approachability and sheer fun, it reminds me of Ted Nelson’s classic “Computer Lib/Dream Machines.”

The book is based on a simple idea: program the same task in the manner of 33 different programming styles, ranging from the “good ol’ times” form of a memory-constrained, identifier-free machine, to modern forms such as Map/Reduce and MVC. The task (determining the frequency of words in a text) is simple enough to generally only require a page of code in the style at hand, but is (surprisingly) sufficient to show each style’s signature characteristics. Chapters are typically shorter than eight pages—including source code—and are easily digestible even in our distraction-heavy world.

Read the full story on the SD Times website.
July 29, 2015

UCI to host CSULA students as part of $1.25 million NASA grant
With support from a $1.25 million NASA grant, UC Irvine’s Data Science Initiative, led by Professor Padhraic Smyth, along with Jet Propulsion Laboratory will host Cal State Los Angeles (CSULA) students for short courses on topics such as Introduction to R Programming, Introduction to High Performance Computing, and Introduction to Predictive Modeling. The program is slated to begin this September.
Read more here
July 10, 2015

Q&A with Professors Hancock and Smyth about New Bachelor of Science in Data Science at UC Irvine
Read more here
July 1, 2015

Professor Baldi awarded $150K from NSF
Professor Baldi was awarded $150,000 from NST for his project entitled “A Theory of Local Learning.”
July 1, 2015

IGB Faculty receives the Excellence in Teaching Award
IGB faculty Edward Monuki, Manuela Raffatella, Robert Steele, and Marian Waterman received 2015 SOM Excellence in Teaching Award
June 18, 2015

Stern to help lead national effort to improve criminal evidence analysis, cut wrongful convictions
IGB member Hal Stern, dean of the Donald Bren School of Information & Computer Sciences and professor of statistics, will help lead a new national Forensic Science Center of Excellence. Aimed at improving criminal evidence analysis and reducing wrongful convictions, it will be funded by a five-year, $20 million grant from the National Institute of Standards & Technology. The campus will receive about $4 million, to be used by ICS and social ecology faculty and students. “UC Irvine is honored to be a part of this. There is a critical need to advance the scientific underpinnings for the analysis of forensic evidence – including fingerprints, firearms, marks left by tools, and documents – and to ensure that participants in the law enforcement process have a strong understanding of proper analyses and interpretation,” said Stern, who is principal investigator for UCI. The center, headquartered at Iowa State University, also will partner with Carnegie Mellon University and the University of Virginia. It will incorporate both a research agenda – developing new probabilistic methods and statistical tools – and education to ensure that judges, lawyers and investigators can effectively utilize the results of forensic analyses. For more information, see here.
May 25, 2015

RNA Symposium
RNA Symposium Info.
April 24, 2015

Ihler gives short course on approximate inference at MLSS
Professor Alexander Ihler gave a half-day course on approximate inference in graphical models as part of the 2015 Machine Learning Summer School in Sydney Australia. MLSS is a long-running series of summer schools around the world for graduate students and researchers who want to apply machine learning methods to their research problems. His lecture is available online here.
February 28, 2015

Circadian rhythms prevent metabolism-generated oxygen radical damage
UC Irvine scientists studying the role of circadian rhythms in skin stem cells found that this clock plays a key role in coordinating daily metabolic cycles and cell division.

Their research, which appears Jan. 6 in Cell Reports, shows for the first time how the body’s intrinsic day-night cycles protect and nurture stem cell differentiation.

Furthermore, this work offers novel insights into a mechanism whereby an out of synch circadian clock can contribute to accelerated skin aging and cancers.

Bogi Andersen, professor of biological chemistry and medicine, and Enrico Gratton, professor of biomedical engineering, focused their efforts on the epidermis, the outermost protective layer of the skin that is maintained and healed by long-lived stem cells. Read more here.
February 28, 2015

Anthony James, UC Irvine professor of microbiology and molecular genetics, comments on the mosquito gene trial in the Florida Keys.
Read more here.
February 19, 2015

Qing Nie elected a Fellow of the American Physical Society (APS)
Election to Fellowship in the American Physical Society is limited to no more than one half of one percent of the membership in the American Physical Society. The criterion for election is exceptional contributions to the physics enterprise; e.g., outstanding physics research, important applications of physics, leadership in or service to physics, or significant contributions to physics education. Fellowship is a distinct honor signifying recognition by one's professional peers. Professor Qing Nie was elected for groundbreaking work on the application of mathematical and computational methods to important problems in systems biology.
December 4, 2014

Mjolsness named American Association for the Advancement of Science fellow
Professor of Computer Science Eric Mjolsness has been been made a fellow of the American Association for the Advancement of Science for his distinguished contributions to the fields of computer science and biology, particularly for new computational models of gene regulation (networks of genes that turn each other on, off or partly on) and resulting technologies. For more details, see here.
November 25, 2014

Professor Eric Mjolsness named AAS fellow
Eric Mjolsness, Professor of Computer Sciences, has been named a Fellow of the American Association for the Advancement of Science (AAAS). Election as an AAAS Fellow is an honor bestowed upon AAAS members by their peers. Read more here.
November 24, 2014

Informatics professor Crista Lopes balances academia with an active open-source development career
A banner above a podium invites attendees to “please take a seat” as they trickle into the September 2013 OpenSimulator Community Conference (OSCC).

With its black-tiled floor and green and blue décor, the conference space recalls the modern, tech-inspired campuses of Google or Microsoft. A panel of six industry professionals and academics sit on stage preparing to speak. Some fidget, flicking their hair back and tapping their feet.

After introductory remarks, informatics professor Crista Lopes from UC Irvine’s Donald Bren School of Information and Computer Sciences takes the podium. Today, however, she’s going by the pseudonym Diva Canto. She looks different, too: Her brunette hair has been traded for an elaborate, fiery red-orange updo.

Lopes lectures on OpenSimulator, an open-source platform that allows users to run virtual-world Second Life environments on their own servers. She includes statistics like: OpenSimulator is a project with 124 contributors representing over 400,000 lines of code, and it took an estimated 107 years of individual effort crammed into 6 years of communal work to develop the platform. Read more here.
November 20, 2014

A team led by Yongsheng Shi published a study in the journal Genes & Development that gives new insights into the mechanism for mRNA 3’ processing
Read more here.
November 1, 2014

UCI scientists identify lesion-healing mechanisms is psoriasis
A UC Irvine-led study has revealed the underlying genetic factors that help repair skin lesions caused by psoriasis, which could engender new methods of controlling the lingering condition. Dr. Bogi Andersen, professor of biological chemistry and endocrinology at UCI, and colleagues discovered that a gene called grainyhead – known to be important in epidermal development and wound healing – triggers a repair pathway for psoriasis lesions. Conversely, they found that deletion of this gene increased the severity and longevity of the disfiguring patches. Read more here.
October 27, 2014

ACM BCB: The 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics
Newport Beach Marriott Hotel and Spa, Newport Beach, CA
Conference Site and Registration info.
September 20-23, 2014

Microbiome Connections to Environment, Health and Disease Symposium
Program Schedule.
September 20-23, 2014

Chancellor’s Professor Pierre Baldi receives Google Faculty Research Awards
As part of Google’s mission to “organize the world's information and make it universally accessible and useful,” Faculty Research Awards identify and support faculty pursuing research of mutual interest at internationally renowned universities. The award is an unrestricted gift, and is typically funded at the amount needed to support one graduate student for one year. Baldi received $65,000 for his proposal, “Deep Learning and Dropout.” The proposal studies the properties of dropout — a recently introduced deep learning approach with applications in computer vision, speech recognition and natural language processing — and seeks to develop optimized randomization strategies and algorithms for deep learning, to be applied to challenging problems in the natural sciences and other areas.
September 1, 2014

Academic Year 2013-2014

Smyth gives keynote talk at top artificial intelligence conference
Professor Padhraic Smyth gave an invited keynote talk at the recent AAAI Conference on Artificial Intelligence (AAAI-14). Held July 27-31 in Quebec City, Canada, the conference promotes research in artificial intelligence and scientific exchange among AI researchers, practitioners, scientists and engineers in affiliated disciplines. Read more
August 2, 2014

Strict genomic partitioning by biological clock separates key metabolic functions
Much of the liver’s metabolic functions is governed by circadian rhythms – our own body clock – and UC Irvine researchers have now found two independent mechanisms by which this occurs. The study, published online today in Cell, reveals new information about the body clock’s sway over metabolism and points the way to more focused drug treatments for liver disease and such metabolic disorders as obesity and diabetes. Read more here.
July 31, 2014

Deep learning makes search for exotic particles easier
UCI researchers, Professors Pierre Baldi and Daniel Whiteson, develop computing techniques that could aid hunt for Higgs bosons. Read more here.
July 2, 2014

Stephen White receives top award from The Protein Society
Stephen H. White, emeritus professor of physiology & biophysics, will be honored by The Protein Society, which will bestow its Carl Brändén Award, which is sponsored by Rigaku Corporation. White is receiving this award in recognition of his many contributions to the field of membrane protein folding, his long service to the protein science community and his skills as an educator of graduate students and postdocs in particular. His research has provided much fundamental insight into the thermodynamics of folding in and on the membrane. He also has made major contributions to multiple scientific societies, including The Protein Society, and –among other service activities – maintains the widely-utilized Membrane Proteins of Known 3D Structure website. The Protein Society, the only international society devoted to furthering research aimed at understanding proteins, will confer the awards at the 28th Annual Symposium of The Protein Society, July 27-30, in San Diego.
July 1, 2014

Smyth to head new Data Science Initiative
Professor Padhraic Smyth has been named the director of a new campus-wide initiative with a focus on coordinating and linking the activities of researchers and students across campus involved in various aspects of data science. UCI’s Data Science Initiative was initiative was started on July 1, 2014 and is sponsored by the Provost through the Office of Academic Initiatives. Find out more here.
June 9, 2014

Gillian Hayes first to hold new Kleist informatics chair
Gillian Hayes, associate professor of informatics in the Donald Bren School of Information & Computer Sciences, has been named the first holder of the Robert A. and Barbara L. Kleist Chair in Informatics. The Regents of the University of California established this endowed chair in April through a generous donation from the Kleists, longtime supporters of ICS and UC Irvine. The chair is intended to recognize and support the research, teaching and service activities of an informatics scholar of distinction focused on health and technology. Hayes has published extensive work in areas as diverse as autism, asthma, premature infancy and cancer. Using innovative research methods, she enlists community partners to ensure that her research results translate into real-world outcomes. Read more here.
June 4, 2014

UC Irvine School of Medicine researchers identify link between colon cancer and metabolism
Read more about Professor Marian Waterman’s research here.
May 14, 2014

Book it
Professor Rina Dechter recently published a new book based upon her extensive work in artificial intelligent with application to machine learning, titled Reasoning with Probabilistic and Deterministic Graphical Models: Exact Algorithms. Read more here.
May 6, 2014

Verdezyne receives $48 million financing at ceremony attended by President Barack Obabma
Verdezyne Inc., a UCI IGB faculty founded synthetic biology company that genetically engineers yeasts to eat renewable plant sugars or oils to replace petrochemicals has received a $48 million equity investment to accelerate the commercial production of adipic acid and other biopolymers required for the production of nylon and other materials such as polystyrenes. (more)
April 28, 2014

UCI, Chapman students craft apps to aid people with autism
Imagine a digital tool uniquely created for people with autism – one that works the way they think, reacts to their needs and inspires them to learn. Students from UC Irvine and Chapman University are competing this week in the second annual Autism App Jam for the right to say, “There’s an app for that.” Read more here.
April 16, 2014

Manuela Raffatellu has been selected as a Kavli Frontiers Fellow of the National Academy of Sciences.
The Academy's Kavli Frontiers of Science symposia bring together outstanding young scientists to discuss exciting advances and opportunities in a broad range of disciplines. Read more here.
April 2014

2014 Opportunity Awards
Congratulations to the IGB members winning this year's CCBS Opportunity Awards competition based on the theme of Big Data!

Title: Prediction of complex developmental phenotypes using multiple data types Participants: Daniel Newkirk, Kyoko Yokomori / Phoebe Valdes, Anne Calof / Yi Li, Xiaohui Xie

Title: Multi-scale reconstruction of the early embryo: imaging and modeling Participants: Huijing Du/William Holmes/Qing Nie/Soledad Mocel/Ken Cho

Title: Large-scale spatiotemporal network analysis of cortical neuronal circuit connections Participants: Tian Hong, Qing Nie/Taruna Ikrar/Xiangmin Xu

Title: High-throughput data acquisition for large data set analysis of the spatiotemporal dynamics of chromatin organization: Interplay between transcription and DNA repair Participants: Paolo Annibale/Enrico Gratton/Xianduo Kong/Kyoko Yokomori
March 2014

Professor Paolo Sassone-Corsi is featured in the Orange County Register Story, “Time Travelers: UCI Scientist is OC’s Circadian Rhythm King”
Read more here.
February 21, 2014

Douglas Tobias named a Fellow of the American Physical Society
January 28, 2014

When conferences go virtual by Crista Lopes
Read more here.
January 6, 2014

Sheryl Tsai partners with UC San Diego to capture Biosynthesis in motion
Chemists have caught molecules in the act of biosynthesis revealing an animated view of how a fundamental piece of cellular machinery operates. The system they observed, a critical metabolic pathway, generates fatty acids, essential components of fats and structures such as cell membranes. Nature published their findings in the early online edition December 22. Read more here.
December 23, 2013

Nutrition influences metabolism through circadian rhythms, UCI study finds
A high-fat diet affects the molecular mechanism controlling the internal body clock that regulates metabolic functions in the liver, UC Irvine scientists have found. Disruption of these circadian rhythms may contribute to metabolic distress ailments, such as diabetes, obesity and high blood pressure. Read more here.
December 19, 2013

Epigenetics Symposium
Beckman Center of the National Academies of Sciences and Engineering, Irvine, CA This is the second of a series of symposia on epigenetics and chromatin research aimed at bringing together the scientific community of Southern California. The focus of this two-day Symposium is on the most recent and exciting findings that have implicated various epigenetic and chromatin remodeling pathways in cellular and physiological responses. This Symposium is organized by the Center for Epigenetics and Metabolism, together with INSERM Unite 904 and the Institute for Genomics and Bioinformatics at UCI.

The Symposium will be followed by a workshop with Pierre Baldi and Matteo Pellegrini on emerging methodologies and the use of biocomputing in genomics and epigenomics.
December 12-13, 2013

Professors Rina Dechter and Padhraic Smyth Elected as 2013 ACM Fellows
The Association for Computing Machinery (ACM), the world’s largest educational and scientific computing society, has announced two faculty members have earned prestigious honors. Computer science professors Rina Dechter and Padhraic Smyth have been named 2013 ACM Fellows. Read more here.
December 10, 2013

Professor Leslie Thompson and Qing Nie named fellows of the American Association for the Advancement of Science, the world’s largest general scientific society.
UC Irvine neurobiologist Leslie Thompson and mathematician Qing Nie have been named fellows of the American Association for the Advancement of Science. Election as an AAAS fellow is an honor bestowed upon association members by their peers. Thompson, a professor of psychiatry & human behavior, was selected for her distinguished contributions to the Huntington’s disease field, particularly relating to mechanisms underlying the cause of the disease, to medical school teaching and to HD-related professional societies. Nie, a professor of mathematics, was chosen for his work in the field of systems biology and for developing pioneering educational programs for students in mathematical and systems biology. This year’s 388 new AAAS fellows will be formally announced in the AAAS News & Notes section of the Nov. 29 issue of the journal Science. Each will be presented with an official certificate and a gold rosette pin Feb. 15 at the AAAS Fellows Forum during the 2014 AAAS annual meeting in Chicago. Nie and Thompson are the 133rd and 134th UC Irvine researchers to be named AAAS fellows.
November 13, 2013

Mortazavi receives NIH Director's New Innovator Award
IGB faculty member, Ali Mortazavi from the Department of Developmental and Cell Biology, has been named a recipient of the prestigious 2013 National Institutes of Health Director's New Innovator Awards. The highly selective award program supports projects by early-career researchers that show potential to transform scientific fields and accelerate the translation of research into new ways to improve human health. His project will explore how DNA codes the precise activities of genes involved with development. His lab will create methods to measure how this gene expression is affected by changes in the organization of DNA in embryonic stem cells as they differentiate into neurons and cardiac muscle cells. Mortazavi believes his research will identify fundamental principles of gene regulation as well as the specific DNA elements critical to stem cell differentiation.
September 30, 2013

Microbiome Connections to Health and Disease Symposium
Program Schedule and Registration Info
September 24, 2013

Academic Year 2012-2013

Professor Pierre Baldi receives $450K from NSF
Professor Pierre Baldi receives NSF grant for his project, “RI: Small: Deep Learning: Theory, Algorithms, and Applications.”
August 19, 2013

Professors Natalia Komarova and Dominik Wodarz’s research article on gun controlfFeatured in U.S. News and World Report
Their article "Dependence of the Firearm-Related Homicide Rate on Gun Availability: A Mathematical Analysis", which was published in PLOS One in July, has been featured in U.S. News and World Report.
August 15, 2013

Professor Pierre Baldi selected as ICSB Fellow
The International Society for Computational Biology has selected Chancellor’s Professor Pierre Baldi as an ISCB Fellow. The ISCB Fellows program honors members who have distinguished themselves through outstanding contributions to the fields of computational biology and bioinformatics. The 2013 fellows were recognized at the Intelligent Systems for Molecular Biology conference, held July 21-23 in Berlin.

Baldi, who directs the Institute for Genomics and Bioinformatics at UC Irvine, also is a fellow of the American Association for the Advancement of Science, the Institute of Electrical and Electronics Engineers, the Association for Computing Machinery, and the Association for the Advancement of Artificial Intelligence.

His research focuses on understanding biological and artificial intelligence, through the development of machine learning and data mining approaches to study fundamental problems in chemo- and bio-informatics, systems biology, and computational neuroscience. His group has developed databases and software applications for use in numerous biology and chemistry settings, including comparing genomes, predicting protein properties, understanding gene regulation, and screening and designing new drugs.
August 2, 2013

An interdisciplinary team led by Dr. Ken Cho receives large NIH grant to explore gene regulatory networks controlling cell fate in early vertebrate development
The $3M award from NICHD will support three UCI faculty, Dr. Ken Cho and Dr. Ali Mortazavi in Developmental & Cell Biology and Dr. Eric Mjolsness in Computer Science, along with their colleagues Dr.Aaron Zorn (Cincinnati Children’s Hospital), and Dr. Taira Masanor (U. of Tokyo) in their study of early development.

Their project focuses on a major unanswered question in biology: How is differentiation of the many cell types found in adult vertebrates specified by the organisms genome? Using the frog as a model system, they will combine experimental, genomic, and computational approaches to examine the mechanisms controlling formation of the endoderm. Production of a thorough endodermal gene regulatory network in frog will provide information that will be applicable to reprogramming of stem cells to endodermal lineages in other vertebrates, including humans.
August 2, 2013

Professor Padhraic Smyth serves as Program Chair for UAI 2013 Conference
Computer science professor Padhraic Smyth served as program chair for the 29th Conference on Uncertainty in Artificial Intelligence (UAI 2013), held July 11-15 in Bellevue, Wash. Sponsored by Microsoft Research, Google, Facebook, Amazon, Toyota and IBM, UAI is the leading international conference on the use of probabilistic models and algorithms in artificial intelligence and machine learning. More than 240 papers were submitted to the conference; 73 were accepted for presentation at the meeting, after extensive peer review by a program committee of over 200 researchers in the area
August 1, 2013

Douglas Tobias named a 2013 American Chemical Society Fellow
Douglas Tobias was named 2013 ACS Fellow. ACS Fellows are awarded for their outstanding accomplishment in scientific research, education, and public service.
July 29, 2013

Professor Cristina Lopes receives $140K from American Heart Association
Professor Cristina Lopes receives American Heart Association grant for her project entitled “Spatial augmented reality games for post-stroke rehabilitation.’” This is a joint collaboration with Dr. Steven Cramer.
July 1, 2013

Ihler receives NSF CAREER Award
Alexander Ihler, associate professor of computer science, has been awarded the National Science Foundation’s (NSF) Faculty Early Career Development (CAREER) Award for his project, “Estimation and Decisions in Graphical Models.” Ihler will receive $442,000 over five years for his CAREER project, which seeks to develop a new framework for exact and approximate methods for advanced computational reasoning problems. It extends the abilities of intelligent systems to reasoning and decision-making under uncertainty, and it applies and tests these methods on a variety of application domains, including sensor networks and computer vision.

The CAREER program is the NSF’s most prestigious award for junior faculty members. Awardees are chosen because they exemplify the role of teacher-scholars through outstanding research, excellent education, and the integration of education and research within the context of the mission of their organizations.

Ihler joined the UC Irvine faculty in 2007. His research focuses on artificial intelligence and machine learning, specifically on statistical methods for learning from data and on approximate inference techniques for graphical models. Applications of his work include data mining and information fusion in sensor networks, computer vision and image processing, and computational biology.
July 1, 2013

NIH awards UCI $10 million to study early-life origins of adolescent mental disorders
With $10 million in new federal funding, UC Irvine researchers will study how maternal signals and care before and after birth may increase an infant’s vulnerability to adolescent cognitive and emotional problems, such as risky behaviors, addiction and depression. Read more here
June 11, 2013

Gaut profiled in Scientist Magazine
EEB Professor Brandon Gaut reviews his career in a profile in Scientist Magazine. Read more here
June 6, 2013

Circadian rhythms control body’s response to intestinal infections, UCI-led study finds
Circadian rhythms can boost the body’s ability to fight intestinal bacterial infections, UC Irvine researchers have found. This suggests that targeted treatments may be particularly effective for pathogens such as salmonella that prompt a strong immune system response governed by circadian genes. It also helps explain why disruptions in the regular day-night pattern – as experienced by, say, night-shift workers or frequent fliers – may raise susceptibility to infectious diseases.

UC Irvine’s Paolo Sassone-Corsi, one of the world’s leading researchers on circadian rhythm genetics, and microbiologist Manuela Raffatellu led the study, which appears this week in the early online edition of Proceedings of the National Academy of Sciences. Marina Bellet, a postdoctoral researcher from Italy’s University of Perugia also played a key role in the experiments. Read more here.
May 31, 2013

Amanda Janesick to be presented the Most Promising Future Faculty Member Award
Congratulations to Amanda Janesick, who is a graduate student in the Blumberg lab and BIT Trainees, for her Most Promising Future Faculty Member Award. Recipients were competitively selected by the Academic Senate Council on Student Experience based on nominations made by faculty and students. The award comes with a one quarter dissertation fellowship and will be presented at the 20th Annual Celebration of Teaching ceremony, Friday, April 12, 2013.
April 1, 2013

Xiaohui Xie and Chen Li awarded $662k NIH grant
Computer science faculty Xiaohui Xie and Chen Li have been awarded a three-year grant of nearly $662,000 from the National Institutes of Health (NIH) to develop new computational tools essential for future advances in sequencing human genomes. The primary goal of the NIH-funded research is to develop computational algorithms and open-source software to improve both the efficiency and accuracy of next-generation sequencing analysis tools and expand the accessibility of those tools to previously understudied regions of the genome.
March 3, 2013

CML professor Charless Fowlkes receives NSF Career Award
Charless Fowlkes, assistant professor of computer science, has been awarded the National Science Foundation’s Faculty Early Career Development (CAREER) Award for his project, “Combinatorial Inference and Learning for Fusing Recognition and Perceptual Grouping.” The CAREER program is NSF’s most prestigious award for junior faculty members. Awardees are chosen because they exemplify the role of teacher-scholars through outstanding research, excellent education, and the integration of education and research within the context of the mission of their organizations.
March 2, 2013

Dr. Arthur Lander has been named the Donald Bren Professor of Developmental & Cell Biology
This endowed chair recognizes Dr. Lander as one of the nation’s foremost scholars in the exciting new field of systems biology. Dr. Lander founded the UCI Center for Complex Biological Systems (CCBS) in 2001 and continues to serve as the director. The center facilitates collaborative work of biologists, mathematicians, physicists, engineers, and computer scientists to obtain a more comprehensive understanding of complex biological systems. NIH recently awarded Dr. Lander and the CCBS a 5-year, $11.5 million grant to continue support of center activities. This funds both research but other programs including a nationally acclaimed residential short course in systems biology each year and community engagement projects. For more see here.
February 28, 2013

UCI team finds new target for treating wide spectrum of cancers
IGB’s multidisciplinary team of biologists, chemists and computer scientists have identified an elusive pocket on the surface of the p53 protein that can be targeted by cancer-fighting drugs. The finding heralds a new treatment approach, as mutant forms of this protein are implicated in nearly 40 percent of diagnosed cases of cancer, which kills more than half a million Americans each year. Read more here.
January 30, 2013

Chancellor’s Professor Pierre Baldi named ACM Fellow
Irvine, Calif., December 12, 2012 - Pierre Baldi, professor in the UC Irvine Donald Bren School of Information and Computer Sciences and director of the Institute for Genomics and Bioinformatics, has been named a 2012 ACM Fellow for his contributions to artificial intelligence and statistical machine learning for bioinformatics. Read more here.
December 12, 2012

Steven C. George receives NIH funds for development of tissue chips to help predict drug safety
Professor Steven C. Goerge received one of 10 grants from the NIH aimed at creating 3-D chips with living cells and tissues that accurately model the structure and function of human organs such as the lung, liver and heart. Read more here.
December 12, 2012

IGB faculty Bruce Blumberg, Ken Cho, Hartmut Luecke, and Greg Weiss elected American Association for the Advancement of Science (AAAS) Fellows
AAAS members are being honored this year for their efforts to advance science or its applications.

Bruce Blumberg, professor of developmental & cell biology, pharmaceutical sciences and biomedical engineering, for his contributions to the field of developmental biology, particularly for increasing understanding of the interactions between environmental signals and the developmental origins of disease.

Ken Cho, professor of developmental & cell biology, for his additions to developmental biology, such as identifying the mechanism of Spemann’s organizer and the importance of growth factor signaling during early embryogenesis.

Hartmut Luecke, professor of molecular biology & biochemistry, physiology & biophysics and computer science, for his contributions to the fields of structural biology and membrane protein crystallography.

Gregory Weiss, professor of chemistry and molecular biology & biochemistry, for his contributions to the field of chemical biology, especially for expanding the technique of bacteriophage peptide and protein display into new interdisciplinary areas
November 29, 2012

Dr. Arthur Lander, awarded $11.5 million grant from NIH to support the UCI Center for Complex Biological Systems
Dr. Lander is the founder and director of the Center which is dedicated to systems biology research. The grant provides 5 years of support for the collaborative work of biologists, mathematicians, physicists, engineers, and computer scientists to obtain a more comprehensive understanding of complex biological systems.
October 12, 2012

Gaut elected President of the Society for Molecular Biology Evolution
EEB Professor Brandon Gaut was elected President of the Society for Molecular Biology and Evolution. This is the premier society for evolutionary biology and evolutionary genetics. The society publishes the journals Molecular Biology and Evolution and Genome Biology and Evolution. Brandon takes the position formerly held by EEB Professors Walter Fitch, a cofounder of the journal and the society, John Avise, and Mike Clegg
September 12, 2012

Academic Year 2011-2012

High-Throughput Sequencing and Other Methods: from Technology to Discovery
Program Schedule
June 7, 2012

Shared Instrumentation grant awarded to IGB for $600K.
Professor Suzanne Sandmeyer, IGB Associate Director and the Director of the UCI Genomics High Throughput Facility (GHTF) was awarded $600K in Shared Instrumentation grant from NIH to purchase a PacBio RS Single Molecule, Real Time SMT) DNA Sequencer. Campus also has committed $795K over the next 5 years to help the GHTF with the maintenance of the DNA sequencer.
May 1, 2012

Circadian rhythms have profound influence on metabolic output, UCI study reveals
By analyzing the hundreds of metabolic products present in the liver, researchers with the UC Irvine Center for Epigenetics & Metabolism have discovered that circadian rhythms — our own body clock — greatly control the production of such key building blocks as amino acids, carbohydrates and lipids. Read more here.
March 19, 2012

UCI-CHOC Pediatric Cancer Genomic Project
Professor Baldi has been awarded $270K from the Children Hospital of Orange County for a joint pediatric cancer genomic project.
March 12, 2012

Atet Kao wins Best Poster Award in Technological Innovations
Atet Kao, IGB BIT trainee in Professor Lan Huang’s lab, won the "Best Poster Award in Technological Innovations" at the 2nd Protein Degradation Pathways in Health and Diseases meeting in San Diego.
February, 2012

Anthony James elected a 2011 Fellows of the Entomological Society of America (ESA).
The designation of ESA Fellow recognizes individuals who have made outstanding contributions to entomology. He was honored for the creation of pioneering approaches to the application of research data and products to create new paradigms for arthropod management that are considered highly progressive in the area of their use.
January 2012

UC Irvine News Brief: Pierre Baldi named IEEE fellow
Pierre Baldi, Chancellor’s Professor in the Donald Bren School of Information & Computer Sciences and director of the Institute for Genomics & Bioinformatics, has been named a fellow of the Institute of Electrical & Electronics Engineers for his contributions to machine learning and its applications in the life sciences. Current projects in his laboratory include mining high-throughput genomic data and developing expert systems for chemistry and systems biology to better understand the computations carried by metabolic, signaling and gene regulatory networks and to identify new diagnostic and therapeutic strategies. IEEE is the world’s leading professional association for advancing technology for humanity, publishing 30 percent of the literature in the fields of electrical and electronics engineering and computer science. It boasts 385,000 members in 160 countries and has named 312 fellows this year.
December 6, 2011

New York Times: UC Irvine's Anthony James has developed a genetic modification that makes female mosquitoes unable to fly, bite people or mate.
Read more here.
December 6, 2011

Professor Padharic Smyth serves as Program Chair for KDD-2011
Computer science professor Padhraic Smyth is the Program Chair for the 17th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. Considered the premier annual international research conference on data mining, the event this year drew a record-setting 1,000+ attendees. Approximately 725 research papers were submitted (another record), of which 125 were accepted for oral or poster presentation at the meeting. The review process involved more than 350 reviewers and 35 senior program committee members. Keynote presenters include Peter Norvig (Google), Stephen Boyd (Stanford University), David Haussler (UC Santa Cruz) and Judea Pearl (UCLA).
September 3, 2011

Professor Max Welling appointed Associate Editor for IEEE Transactions on Pattern Analysis and Machine Intelligence
Computer science professor Max Welling is now Associate Editor-in-Chief for IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI). Welling has previously served as Associate Editor for TPAMI, which is one of the highest impact journals in the general area of artificial intelligence and machine learning. In addition to participating in the review process, Welling is helping to organize a number of special issues on timely topics in machine learning.
September 2, 2011

Academic Year 2010-2011

Bioinformatics boosters. Summer research program exposes community college students to emerging field.
For aspiring computer engineer Anthony Hizon, spending the summer in a biological chemistry lab at UC Irvine’s School of Medicine was quite an eye-opener.

“Talking to the Ph.D. students in the lab gave me new ideas about my future,” says Hizon, one of seven participants in the newly launched UCI Biomedical Informatics Training Undergraduate Summer Research Program for community college students. “I’ve learned that bioinformatics is a viable career option for me, and I’m now thinking about going to graduate school.” Read more here.
August 22, 2011

UC Irvine News Brief: NIH funds summer research program for community college students
Supported by a five-year, $400,000 grant to UCI's Institute for Genomics & Bioinformatics, the 10-week outreach effort encourages those from low-income, historically underserved ethnic and racial backgrounds to explore career opportunities combining computational and life sciences. Read more here.
July 22, 2011

2011 Biomedical Informatics Training (BIT) Program Symposium
This years topic is about High–throughput sequencing coupled to chromatin immuno–precipitation (ChIP–Seq) is widely used in characterizing genome–wide binding patterns of transcription factors, cofactors, chromatin modifiers, and other DNA binding proteins. A key step in ChIP–Seq data analysis is to map short reads from high–throughput sequencing to a reference genome and identify peak regions enriched with short reads. Although several methods have been proposed for ChIP–Seq analysis, most existing methods only consider reads that can be uniquely placed in the reference genome, and therefore have low power for detecting peaks located within repeat sequences. Here we introduce a probabilistic approach for ChIP–Seq data analysis which utilizes all reads, providing a truly genome–wide view of binding patterns. Reads are modeled using a mixture model corresponding to K enriched regions and a null genomic background. We use maximum likelihood to estimate the locations of the enriched regions, and implement an expectation–maximization (E–M) algorithm, called AREM, to update the alignment probabilities of each read to different genomic locations.

Program Schedule and Abstract
May 19, 2011

Dr. Manuela Raffatellu received the 2011 Chancellor’s Award for Excellence in Fostering Undergraduate Research in recognition of her outstanding work in mentoring undergraduate students.
May 10, 2011

Industry giants British Petroleum and Royal DSM back IGB startup Verdezyne 
(Adapted from an article by Jeff St. John http://gigaom.com/author/jeffstjohn/)

Verdezyne Inc., a synthetic biology company that genetically engineers yeast that eat plant sugars and excrete biofuels and biochemicals, has just landed an undisclosed equity investment from British oil giant BP and Dutch biochemicals company Royal DSM. Mark this news down as another biotech-based startup teaming up with the industry incumbents to facilitate commercialization of their green fuels and bio-chemicals.

The undisclosed round will fund the Carlsbad, Calif.-based startup’s operations through the next few years, as well as help it build two pilot plants to churn out both ethanol and adipic acid, a precursor to nylon and other polymers, Previous VC investors, Monitor Ventures and OVP Venture Partners, also took part in the new round. Read more here.
May 9, 2011

Memorial tribute for Walter Fitch on May 26
EEB and the School of Biological Sciences remembers the remarkable life of our longtime colleague Dr. Walter Fitch, who passed away on March 11. Walter meant a great deal to countless people on our campus and beyond. We will hold a memorial tribute on May 26 at the Arnold and Mabel Beckman Center of the National Academies of Sciences and Engineering. We hope you can attend and join in our reflection of a life well spent.
April 11, 2011

Professor Natalia Komarova recognized by Athletics for her outstanding service to the mission of UC Irvine
Professor Natalia Komarova was recognized by Athletics for her outstanding academic achievement and her contribution to the mission of UC Irvine. Professor Komarova was recognized at the recommendation of the Athletic Director's Faculty Advisory Group. The program of recognizing faculty members began in 2010 and was the instituted by Athletic Director Michael Izzito highlight the incredible faculty we have at UCI.

Professor Komarova has received many honors and awards in the past. In 2002, Natalia, then a member of the Institute for Advanced Study in Princeton, New Jersey, won the first "Prize for Promise" award, a $100,000 award given by Student Achievement and Advocacy Services. The award "recognizes young women of exceptional ability, ambition, boldness, brilliance and dedication within their field of expertise." She then received a Sloan Fellowship in 2005, which is one of the most prestigious awards available to young scholars. In 2006-2007, she was awarded the UCI Academic Senate Distinguished Assistant Professor Award for Research, and in 2009 she received the UCI School of Physical Sciences Award for Excellence in Undergraduate Teaching.
March 30, 2011

HTS to P4 Medicine at UCI
Program Schedule
February 18, 2011

New computer school dean is team player
New computer school dean Hal Stern is a statistician and sports lover. Read more about the new dean here
November 24, 2011

EEB faculty Long, Rose and Thornton published in Nature
EEB faculty Tony Long, Michael Rose and Kevin Thornton have collaborated in a study of sequence variation in Drosophila melanogaster that have been evolved in long-term experimental populations. Read more here
September 17, 2011

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.
September 1, 2011

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.
September 1, 2011

Center Member wins Koenderink Prize at European Conference on Computer vision
Max Welling, professor of computer science, has been awarded European Conference on Computer Vision’s Koenderink Prize in recognition of his computer vision research paper that has “withstood the test of time.” Entitled “Unsupervised Learning of Models for Recognition,” the paper was originally published in 2000. The research paper presents a method to learn object class models from unlabeled and unsegmented cluttered scenes for the purpose of visual object recognition.
September 1, 2011

Academic Year 2009-2010

Professors Lathrop and Kaiser's NIH grant entitled "A Functional Census of p53 Cancer and Suppressor Mutants" is renewed
Professors Lathrop and Kaiser’s project 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.
August 10, 2010

Padhraic Smyth Named Fellow of the Association for Advancement of Artificial Intelligence
Padhraic Smyth, professor of computer science and director of the CML, has been named a fellow of the Association for Advancement of Artificial Intelligence (AAAI). Recognized for his significant contributions to the theory and practice of statistical machine learning, Smyth is one of only eight researchers worldwide who has been named AAAI Fellows this year. The AAAI Fellows program recognizes individuals who have made significant, sustained contributions to the field of artificial intelligence — a lifetime honor.
July 22, 2010

IGB Receives $216K 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.
July 1, 2010

Systems Biology of Stem Cells
The Systems Biology of Stem Cells Symposium, to be held in Irvine, California, May 24–25, 2010, is devoted to state–of–the art research at the intersection between systems biology and stem cell biology. Topics will include stem cell genomics and epigenomics; gene regulatory networks underlying pluripotency; feedback regulation of proliferation and lineage progression; and cancer stem cells. A diverse set of experimental, mathematical and computational methodologies will be represented among the featured talks. Meeting activities will include a poster session and a banquet on May 25th.
May 24-25, 2010

2010 Biomedical Informatics Training (BIT) Program Symposium
This symposium brings opportunity for the BIT predoctoral and postdoctoral trainees to present their theses and postdoctoral research projects. The NIH–NLM funded Biomedical Informatics Training (BIT) Program provides in–depth training to students in either computational or life sciences, and trains them to working competence in the cross–discipline with emphases in bioinformatics approaches to problems in molecular structure/function prediction and determination, comparative and functional genomics, chemical informatics, and computational and systems biology.

Program Schedule and Abstract
May 19, 2010

Wiley Partners with Reaction Explorer to Offer Interactive Organic Chemistry Learning System with Textbooks
a global leader in higher education publishing, is partnering with Irvine-based Reaction Explorer to bring new capabilities to the online organic chemistry market.

“As a worldwide leader in higher education, Wiley is always looking for the latest tools to help students succeed,” said Petra Recter, Associate Publisher, Wiley. “Reaction Explorer is a great example of our ability to identify and obtain such leading edge solutions. By accessing Reaction Explorer through WileyPLUS, our robust online teaching and learning solution for organic chemistry, students will be able to achieve a higher level of understanding of the intricacies of organic chemistry reactions, syntheses, and mechanisms.” Read more here.
April 10, 2010

IGB awarded $131K NIH SBIR grant with Planet Biotechnology, Inc.
IGB’s Computational Biology Research Laboratory (CBRL) under Professors Lathrop and Hatfield was awarded $131,374 from Planet Biotechnology, Inc., as part of NIH SBIR grant entitled, “Maximizing Expression of Immunoglobulins in Plants.”
April 1, 2010

Transposable Elements (Mobile DNA Symposium)
The symposium will include discussion of DNAs that mobilize to cause surface antigenic variation in bacteria, retroelements that cause mutations in human germline DNA, cut and paste DNA elements used in genetic engineering and elements in yeast and plants that by accumulating in specific regions may drive chromosomal function itself and even ribozymes that occur in viruses as well as host genomes. The Mobile DNA Symposium will feature two outside speakers, Dr. John Moran, U. Michigan and Dr. Peter Atkinson, U. Riverside. Dr. Moran studies human LINE element mobility in embryonic cells and Dr. Atkinson studies applications of hAT DNA cut and paste elements in genetic engineering. However, a major goal of the Symposium is to bring together for the first time, faculty from UCI who study transposable elements in bacteria, yeast, mosquitoes, plants, and the test tube! We hope to see you there

Program Schedule and Abstract
February 19, 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 10, 2010

IGB awarded $744K NIH STTR Phase II grant with Coda Genomics, Inc
IGB’s Computational Biology Research Laboratory (CBRL) under Professors Hatfield and Lathrop was awarded $744,265 from Coda Genomics, Inc., as part of NIH STTR Phase II grant entitled, “CODA Assembly of Mutant Genes.”
January 1, 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

Lopes speaks at Intel CTO keynote address
Cristina Lopes, Associate Professor of Informatics participated as a guest speaker in the keynote address at SuperComputing '09 in Portland Oregon. The Keynote was delivered by Justin Rattner, CTO of Intel. Lopes was a guest at Rattner's keynote, in her role as one of the main architects of OpenSim.

Justin Rattner's opening keynote address at SuperComputing'09 message addressed how the super-computing industry has stagnated, and the only thing that will save it from collapse is a drastic change on what people think of as "super-computing." Other guests were Aaron Duffy, a biology researcher at Utah State University, and Shenlei Winkler, CEO of the Fashion Design Institute.

Lopes' research is related to languages and communication systems. The ultimate goal of her research is to deepen the knowledge about communication, in particular in systems that involve humans and machines. With this utopic goal in mind, she has done work in a variety of fields such as programming languages, security and applications of audio signal processing.
November 2009

Fowlkes, Ramanan and Desai awarded Marr Prize in Kyoto, Japan
A paper entitled "Discriminative models for multi-class object layout" by PhD student Chaitanya Desai and Assistant Professors Deva Ramanan and Charless Fowlkes received the Marr Prize at the International Conference on Computer Vision (ICCV) held the first week of October in Kyoto, Japan.

The prize is awarded to the best paper at ICCV and is considered one of the top honors in computer vision. The award is named after David Marr, a theoretical neuroscientist who made profound contributions to the theory of both human and machine vision in the 1970's.

The paper describes research on a new approach to modeling contextual relations between objects in an image (e.g. bottles are often seen resting on top of tables but not the other way around). The system automatcially learns these relations from example images and uses this information to outperform existing approaches to object detection.

Fowlkes' research is in computational vision, both in understanding the information processing capabilities of the human visual system and in developing machine vision systems. He is also interested in applying computer vision techniques to automating the analysis of biological data and developing algorithmic tools for understanding morphology and spatial aspects of gene expression.

Ramanan's research interests span computer vision, machine learning, and computer graphics. His past work focused on the analysis of human movement from video, including tracking people and recognizing their actions. Current interests include object recognition, large-scale image/video processing, structured-prediction approaches to learning, and activity recognition.
October 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.

Academic Year 2008-2009

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.

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.

HIV/AIDS: Over 60 new drug leads – from yeast
RealHealthNews talks to Suzanne Sandmeyer of the Institute of Genomics and Bioinformatics at the University of California, Irvine.

Mobile genetic elements in single-celled yeast, which are models for the HIV virus, have yielded new secrets of how HIV might replicate in the human body. The result: over 60 new targets for HIV/AIDS drug development. But there is a problem – the targets are human. Just like malaria, just like all pathogens exposed to drug treatments, the HIV virus is slowly developing drug resistance. But the virus is powerless alone: it needs certain human genes to replicate. These genes are a potential source of novel drug targets, but very few appropriate target genes have been identified so far.

Now a new study, conducted by Suzanne Sandmeyer and colleagues at the University of California, reports the discovery of 130 host genes that affect the replication of a model retrovirus – not HIV, but a free-floating cluster of genes with similar properties that lives in the cells of yeast. Read more here.
May 5, 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. Read more here.
September 4, 2007.

Academic Year 2006-2007

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. Read more here.
August 29, 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.

IGB awarded $5.6 million grant from the NIH-National Library of Medicine for the Biomedical Informatics Training (BIT) Program
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. Read more here.
August 16, 2007 .

UCI Awarded $14.4 Million to Support Systems Biology Center
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. Read more here.
August 1, 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
IMichael 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

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.
October 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. Read more here.
December 2005

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. Read more here.
November 2005

UCI received a $1M Howard Hughes Med. Institute (HHMI)grant
UCI received a $1M Howard Hughes Med. Institute (HHMI) grant for the development of a program in Mathematical, Computational and Systems Biology. 10 such grants were made nationally.

Project Director: Arthur Lander Co-PD: Qing Nie (Math), Eric Mjolsness, Steven George, Wesley Hatfield Title: Mathematical, Computational and Systems Biology
November 1, 2005

IGB awarded $123K DARPA Subcontract from UCSD.
Professor Baldi received $123K subcontract from UCSD as part of DARPA project entitled, “Interactive Neurotechnology for Image Analysis.”
October 1, 2005

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. Read more here.
October 1, 2005

IGB awarded $1.8 million NIH grant
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. Read more here.
September 26, 2005

Academic Year 2004-2005

IGB awarded $176K NIH STTR grant with Coda Genomics, Inc.
IGB’s Computational Biology Research Laboratory (CBRL) under Professors Hatfield and Lathrop was awarded $176,261 from Coda Genomics, Inc., as part of NIH STTR grant entitled, “CODA Assembly of Mutant Genes.”
August 1, 2005

IGB awarded $311K NSF grant
Professor Baldi was awarded $311,291 from NSF for his project entitled, “Mining Structured Data with Applications in Chemistry and Biology.”
July 1, 2005

IGB Associate Director and DermTech International Receive UC Discovery Grant
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. Read more here.
June 23, 2005

IGB Technology Licensed to CODA Genomics, Inc.
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. Read more here.
April 27, 2005

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.
December, 2004

Academic Year 2003-2004

IGB Awarded $270K Equipment Grant from NSF
UC Irvine's Institute for Genomics and Bioinformatics has been awarded $269,989 equipment grant from NSF to purchase cluster and server for computational biology efforts in IGB. Campus has committed additional $115,714 towards the equipment purchase.
October 1, 2003

$1.5 million NSF:ITR grant awarded to Professors Lathrop and Hatfield
Richard Lathrop, ICS professor, and Wesley Hatfield, professor of microbiology and molecular genetics in the College of Medicine and associate director of the IGB , received a four-year, $1.5 million grant to advance the use of computational methods for building complex genomic DNA sequences. “Human limitations in building new complex strings that produce desired RNA and protein products can be overcome by using computers to distribute the computational burden,” Lathrop said. “This has important applications in biotechnology, anti-bioterrorism and medicine. For example, we have built genes for biomedical scientists who are studying SARS, small-pox, and cancer.”
September 15, 2003

$4.9 million FIBR grant awarded to associate professor Eric Mjolsness
Associate Professor Eric Mjolsness received a five-year, $4.9 million award from the Frontiers in Integrative Biological Research (FIBR) program — a new National Science Foundation (NSF) program supporting biological research and outreach that crosses academic disciplines . Along with supporting key research at the university, the grants are an indicator of the rising profile of UCI's interdisciplinary studies in biology and computer science.

“The support from the National Science Foundation reflects the growing visibility of UCI's Institute for Genomics and Bioinformatics,” said William H. Parker, vice chancellor for research, who oversees UCI's research institutes. “Receiving support from the new FIBR program is particularly rewarding and appropriate given the university's well-established multi-disciplinary approach to research and education.”

Pierre Baldi, director of the IGB, concurred. “Since its creation, the IGB's mission has been to foster innovative research and educational programs that apply computer science to health science research and applications.” Baldi is a professor in the School of Information and Computer Science (ICS) with a joint appointment in the College of Medicine. “FIBR's support isn't just welcome, given our common mission, it is also appropriate.”

Working with plant developmental biologist Elliot Meyerowitz at the California Institute of Technology, Mjolsness will provide a quantitative and cellular description of plant development based on advances in biological knowledge, microscopy, image processing and applied biomathematics.

“This work will allow us to create scientifically valuable computer simulations that help us understand how large numbers of genes and proteins coordinate their activities in living cells and multicellular tissues,” Mjolsness said.

Good simulations can help biologists prioritize their hypotheses or invent new ones, before testing them in the laboratory, Mjolsness explained. “This can greatly reduce the cost of making scientific discoveries. Eventually such discoveries could lead to new biotechnology for agriculture or medicine.”

The FIBR grant also will support outreach programs designed to introduce K-12 teachers and students to new techniques for understanding biology , culminating in a summer institute at UCI.

“Along with demonstrating how computer science applies to biology and the health sciences, we hope this grant will encourage more students underrepresented in the sciences to further their studies in computing and information technology,” said Debra J. Richardson, interim ICS dean. “We expect the outreach activities to culminate in a summer institute in which 30 high school students will learn about the latest research in plant growth and development.”
September 1, 2003

IGB receives $1.86 million NIH grant
Associate Professor Eric Mjolsness received $1.86 million grant from the National Institutes of Health to develop a computable, predictive scientific understanding of how cells may signal one another and interact.
September 1, 2003

Associate Professor Eric Mjolsness receives $230K subcontract from UCLA
Associate Professor Eric Mjolsness receives $229,695 subcontract from UCLA for their project entitled “Institute for Cell Mimetic Space Explortation (CMISE).
September 1, 2003

Institute for Genomics and Bioinformatics awarded $4.3 million
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. Read more here.
September 1, 2003