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  • Biomedical Informatics & Computational Biology

    Research BulletinSpring/Summer 2008

    In collaboration with:


    Seed Grant Yields Bountiful HarvestU of M-Mayo-IBM collaboration providesproof-of-principle for larger grant

    Darrin York, Ph.D., develops computational methods forsimulating the catalysis of chemical reactions mediatedby RNA. Yuan-Ping Pang, Ph.D., explores the subcellularmechanisms behind complex physiological processes.Carlos Sosa, Ph.D., is advancing applications for ultra-fast computers that hold huge promise for unlocking themysteries of molecular interactions.

    After BICB gave the three researchers an opportunity totalk at a networking event just over a year ago, theydecided to combine forces. They applied for and receiveda $100,000 BICB seed grant to apply IBM computationalchemist Sosas emerging high-speed computingcapabilities, and the multi-scale quantum modelingapproaches developed by York, an associate professor ofchemistry at the University of Minnesota, to solvequestions Pang, a professor of pharmacology at the MayoClinic, is asking related to rational drug design ofreactivators and irreversible inhibitors.

    The expertise incomputational methodsdevelopment forquantum simulationshere at the U of M wasa perfect marriage withhigh-performancecomputing architecturesof IBM to go after highimpact problems inrational drug designspearheaded at theMayo Clinic, Yorksays. These problemsrequire accuratemodeling of molecularrecognition and chemical bond formation and cleavageevents in complex biological environments.

    The outcome is the epitome of what cross-disciplinary,cross-institutional research is all about. Results ofresearch funded by the seed grant allowed York to addsome key just in time findings to a proposal he hadpreviously submitted to the National Institutes of Health(NIH). The proposal subsequently yielded a four-year,$1.1 million NIH grant, and York is convinced theproof-of-principle results from the BICB seed grant gavehim the competitive edge he needed. The first series ofpapers highlighting the new simulation methods waspublished this past spring in Journal of the AmericanChemical Society and Chemistry & Biology.

    York also credits BICB for catalyzing the collaborationwith Sosa and Pang. Though the three knew of and wereinterested in each others work, he says, In this financialclimate, its a real challenge to take already overcommittedexternally funded research groups and get them togetherto nucleate around a new idea, and then actually follow

    continued on page 3

    The York group has pioneered multi-scalequantum simulation methods to study themolecular mechanisms of RNA enzymes,such as the the hammerhead and hairpinribozymes, and elucidate the origin of theircatalytic capability.


    Trainee ProfileAndrew NorganHow can we keep deadly virusesfrom replicating? Mayo ClinicM.D.-Ph.D. student AndrewNorgan is pursuing the answerwith the help of a two-yearBICB traineeship.

    Norgan is one of 10 graduatestudents awarded financialsupport during BICBs firstgranting round last year. Hisresearch focuses on applyingcomputational methodology toscreen for chemicals that caninhibit budding, part of viralreplication. What he discoversmay prove useful in developingdrugs that inhibit HIV and otherviruses from replicating. Norganis working with Carlos Sosa,Ph.D., of IBM; DavidKatzmann, Ph.D., andJean-Pierre Kocher, Ph.D.,of Mayo Clinic; and ClaudiaNeuhauser, Ph.D., of theUniversity of Minnesota.

    The BICB program has beenreally helpful, Norgan says. Itestablishes a framework forscientific collaboration, and thatin turn has allowed me to goplaces with my research that Iwouldnt otherwise be able to go.

    WelcomeWelcome to the first issue of the BICB Research Bulletin. We are enthusiasticabout the many things we have going on, and happy to have the opportunityto share the excitement and momentum with you. This bulletin providesan overview of some of the accomplishments that arose from the first yearof BICBs existence, as well as a preview of whats ahead.

    The Biomedical Informatics and Computational Biology (BICB) programis sponsored by the University of Minnesota Rochester. The U of M, incollaboration with the Hormel Institute, Mayo Clinic, and IBM,established the BICB programas a way to harness the Rochester regionsstrong resources in education, medicine, and technology to create world-class graduate and research programs in two of biosciences fastest-growingfields: biomedical informatics and computational biology.

    Our first round of seed grants and traineeships has yielded results evenbeyond our optimistic projections. More than 40 investigators have investedthe resources we have provided to initiate exciting new interdisciplinary andmulti-institutional research projects. Their collaborations have opened thedoor to new lines of research, new interactions, and even to new resources inthe form of federal competitive grant funding.

    Rich opportunities for interaction were provided by three symposia wesponsored for 200708. These symposia brought scientists and scholarstogether from business, industry, and academia, sparking new ideas forpartnerships to advance discovery.

    The University of Minnesota is moving to set in place a graduate programthat will train the leaders of tomorrow in biomedical informatics andcomputational biology. The proposal to create M.S. and Ph.D. programs inthis vibrant and fast-paced field will go to the Board of Regents forapproval in July, and we anticipate a favorable outcome.

    We are now gearing up to select and fund the 2008-09 seed grants andtraineeships, as well launch a postdoctoral research fellowship program (seeannouncement on page 6), and moving into our next round ofinterdisciplinary collaborative symposia. Please join us as we look forwardto a bright future for BICB, Rochester, and the quest for better healththrough biomedical informatics and computational biology.

    The University of Minnesota BICB Planning Team (lefto right): Michael Olesen; Vipin Kumar,Ph.D.; Jim Clausen; Claudia Neuhauser, Ph.D.; and Dick Westerlund.


    Seed Grant Yields Bountiful Harvestcontinued from page 1

    up by devoting the requiredresources so that they mightdemonstrate sufficient feasibilityand promise to secure large-scalesustained funding and make realbreakthroughs. By providingresearchers with an open forumto explore how their effortsmight interface, and theopportunity to compete for seedproject support, the BICBprogram lowered the activationbarrier for launching a promisinginterdisciplinary collaboration.


    For More InformationContact:

    Michael OlesenProgram Director forBioscience, UMR

    UMTC Telephone:612-625-6414

    UMR Telephone:507-280-4647

    Jim ClausenProgram Management Consultantfor Bioscience, UMR


    BICB Web

    A Match Made in . . . Rochester

    Over the history of scientific inquiry, some of the most fertilecollaborations have arisen by chance, as investigators from differentdisciplines or different institutions discover connections between theirefforts during casual conversation. But chance is slow, too slow for fast-evolving, interdisciplinary endeavors such as biomedical informatics andcomputational biology. That is why last spring BICB gave chance a handup by giving researchers from IBM, Mayo Clinic, the University ofMinnesota Twin Cities, and the Hormel Institute the opportunity toexplore opportunities for future collaboration.

    Modeled after speed dating, the first such effort brought togetherapproximately 40 scientists and researchers in March 2007 in Rochester tomeet and discuss how their interests and investigations might dovetail.Afterwards, the BICB program provided seed funding for fivecollaborations involving 25 researchers (see page 4) and for 10 graduatetraineeship projects.

    I found the BICB symposium beneficial, commented participant CarlosSosa, Ph.D., of IBM. It provided an opportunity to present some of theresearch that is funded through BICB grants and also served as a catalystfor researchers to discuss potential collaborations among the differentgroups. It provided a valuable forum for this type of interaction.

    The next speed collaboration session is scheduled for June 20, 2008, witha focus on collaborative, interdisciplinary biomedical research in the areasof medical imaging informatics, biomedical informatics and bioinformatics,computational biology, computational approaches to genomics andproteomics, and integration of data types with genomic emphasis.


    BICB Seed Grant Updates

    Multi-modality Data Mining:Accelerating DiscoveryKelvin Lim, M.D. (UM); Vipin Kumar, Ph.D. (UM);Monica Luciana, Ph.D. (UM); Tim Mullins (IBM),Richard Mushlin, Ph.D. (IBM); Michael Steinbach,Ph.D. (UM), Tushar Garg (UM), and Ben Mayer (UM)

    In order todiscover patternsthat can lead tothe developmentof hypothesesaboutrelationshipsamong genetics,brain structure,and cognition inadolescents, thisseed grant aimsto develop new computational tools to analyze massiveamounts of neuroimaging, cognitive, and genotype data,collected from roughly 200 subjects who are part of afederally funded research project. The investigators havemade encouraging progress towards accelerating theprocessing of brain images by reengineering existing open-source image processing software for IBMs Cell processor.In addition, the application of high-powered computationaltools to data analysis has begun to reveal intriguingcorrelations among cognitive and neuroimaging features,which provide preliminary evidence for interestingdifferences due to ge


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