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Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008 Rouchka, Eric C; Krushkal, Julia; Goldowitz, Daniel Jul 8, 2008

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ralssBioMed CentBMC BioinformaticsOpen AcceMeeting reportProceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008Eric C Rouchka*1, Julia Krushkal2 and Daniel Goldowitz3Address: 1Department of Computer Engineering and Computer Science, University of Louisville, 123 JB Speed Building, Louisville, KY 40292, USA, 2Department of Preventive Medicine and Center of Genomics and Bioinformatics, University of Tennessee Health Science Center, 66 N. Pauline Street, Suite 633, Memphis, TN 38163, USA and 3Child and Family Research Institute, Center for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Room 2026, 850 West 28th Avenue, Vancouver, BC V5Z 4H4, CanadaEmail: Eric C Rouchka* - eric.rouchka@louisville.edu; Julia Krushkal - jkrushka@utmem.edu; Daniel Goldowitz - dang@cmmt.ubc.ca* Corresponding author    The University of Tennessee (UT), Oak Ridge NationalLaboratory (ORNL), and Kentucky Bioinformatics Net-work (KBRIN) have extensive research and educationalties in bioinformatics and have a long standing traditionof holding annual joint bioinformatics regional summitsthat bring together researchers, educators, and studentsinterested in bioinformatics. These summits provideunique opportunities for enhancing collaborative linksand integration of multidisciplinary research efforts andhave resulted in numerous new collaborative projects inbioinformatics research and education. The SeventhAnnual UT-ORNL-KBRIN Bioinformatics Summit washeld at Lake Barkley State Park in Cadiz, Kentucky onMarch 28–30, 2008. A total of 174 participants registeredfor the summit, with 81 from various Tennessee institu-tions, and 78 from Kentucky institutions. Eighty-two reg-istrants were faculty, while 45 were students, 33 staff, and7 post-docs with the remainder as invited speakers.The conference program included three days of presenta-tions, the first devoted to the National Center for Biotech-nology Information (NCBI) short courses, a discussion ofthe revolutionary changes in the concept of a gene in lightof recent data generated by the ENCODE project andother advances in molecular biology and genome analysis[1], and a presentation on educational opportunities atnary sessions: Pathways to Prediction; BiomedicalInformatics; and Regulatory Analysis as well as a keynotespeech given by Jeremy Smith of ORNL and a bioinfor-matics education workshop led by A. Malcolm Campbellof Davidson College.NCBI short coursesWayne Matten (NCBI) presented two of the NCBI mini-course modules, "Entrez Gene Quick Start" and "Correlat-ing Disease Genes and Phenotypes." Both of these mini-courses were 2.5 hours in length with a one and a halfhour lecture overview, followed by a one-hour interactiveproblem-based session. The first module concentrated onusing NCBI's resources for searching for gene-based infor-mation based on a RefSeq record, including sequenceinformation such as reference gene, isoforms, singlenucleotide polymorphisms and associated phenotypes,homologs, and protein structure. The second mini-coursefocused on associating a diseased gene with a correspond-ing change in phenotype using a number of NCBIresources [2].Pathways to predictionNitin Baliga (Institute for Systems Biology) started thefirst plenary session with an exciting presentation titled "APredictive Model for Transcriptional Control of Physiol-from UT-ORNL-KBRIN Bioinformatics Summit 2008Cadiz, KY, USA. 28–30 March 2008Published: 8 July 2008BMC Bioinformatics 2008, 9(Suppl 7):I1 doi:10.1186/1471-2105-9-S7-I1<supplement> <title> <p>UT-ORNL-KBRIN Bioinformatics Summit 2008</p> </title> <editor>Eric C Rouchka and Julia Krushkal</editor> <note>Meeting abstracts – A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/pdf/1471-2105-9-S7-full.pdf">here</a>.</note> <url>http://www.kbrin.louisville.edu/summit/</url> </supplement>This article is available from: http://www.biomedcentral.com/1471-2105/9/S7/I1© 2008 Rouchka et al; licensee BioMed Central Ltd. Page 1 of 4(page number not for citation purposes)UT-Knoxville and ORNL. The last day and a half was ded-icated to scientific presentations divided into three ple-ogy in a Free Living Cell." What followed was a discussionof systems biology approaches incorporating transcrip-BMC Bioinformatics 2008, 9(Suppl 7):I1 http://www.biomedcentral.com/1471-2105/9/S7/I1tion, translation, and interactions to derive dynamic tem-poral relationships that allow for organisms to thrive inextreme conditions. The main focus of this session was themolecular mechanisms of response of Archea to extremetemperature, radiation, pH levels, and high salinity andthe wealth of systems biology methods and approaches toinvestigate this response [3-6].Biomedical informaticsDan Masys (Vanderbilt University) led the second plenarysession on Biomedical Informatics. Dr Masys, along withPaul Harris of Vanderbilt, presented an overview of theClinical and Translational Science Awards (CTSA) pro-gram at NIH. Vanderbilt's CTSA program, the VanderbiltInstitute for Clinical and Translational Research (VICTR),was discussed. In order to efficiently process the largeinflux of patient information and tissue samples into theVanderbilt DNA Databank, VICTR has implemented aresearch portal, StarBRITE. StarBRITE offers clinicalresearchers a number of tools for conducting patient-based research, including regulatory support, patientrecruitment support, data management, and clinical sys-tems integration for electronic medical record (EMR) sup-port. The VICTR Informatics Core is involved in theconsortium developing the REDCap (Research ElectronicData Capture) http://www.iwg-online.org/projects/redcap/index.php data collection project as a portion of theEMR functionality of StarBRITE.Mikael Benson (Göteborg University, Sweden) was anadditional plenary speaker for this session. He discusseddetection of markers for personalized medicine specifi-cally targeted for allergies, including locating epigeneticmarkers using hay fever as a disease model. Potentialmarkers could emerge from systems biology analysis ofdecomposed transcriptional networks using DNA micro-arrays [7-9]. Genes identified in these networks are furtheranalyzed for polymorphisms, which may eventually beused as diagnostic markers.Regulatory analysisThe final plenary session, Regulatory Analysis, was led byZiv Bar-Joseph (Carnegie Mellon University) with his plat-form presentation "Reconstructing Dynamic RegulatoryNetworks in Multiple Species." Dr. Bar-Joseph discussedcurrent limitations of common approaches to analysis oftime series gene expression data, including dealing withpopulations of cells instead of single cells and the use ofstatic data for the study of dynamic time course responses.In order to better address these limitations and to incor-porate temporal features of such data, he presented anapproach known as STEM [10] that aligns time courseexpression data to pre-determined sets of expression pro-together expression patterns of genes, a hidden Markovmodel approach for bifurcating profiles of dynamic regu-latory events (DREM) [11] was presented, with evidenceof experimental studies from yeast [12] and E. coli [13].David Galas, (Institute for Systems Biology and BattelleMemorial), was the second speaker for the RegulatoryAnalysis session providing an intriguing closing talk in hispresentation "Grappling with Complexity: Key Problemsin Computational Biology." Dr. Galas discussed the cur-rent and future issues in computational biology, particu-larly in relationship to the massive explosion of availablegenome information and technical breakthroughs such asNextGen sequencing [14]. The importance of these issuesis dictated by the fact that available biological data aregrowing exponentially rather than linearly, thus outpac-ing the rate at which the data can be handled by thegrowth of processor speed as dictated by Moore's Law[15]. He discussed how the Institute for Systems Biologyis approaching this issue by looking at a thorough under-standing of subsets of data in order to aid in P4 (Predic-tive, Personalized, Preventative, and Participatory)Medicine, particularly through their innovative Personal-ized Genome and Blood Organ Fingerprint projects.Keynote speakerJeremy Smith, director of the ORNL Center for MolecularPhysics, was the keynote speaker for the summit, giving atalk titled "Computer Simulation of MolecularMachines." Dr. Smith discussed numerous examples ofhow physical principles drive various processes at amolecular level, including protein folding [16] and mus-cular contraction. He also discussed the computationalresources available at ORNL for bio-computing, includingthe 119-teraflop Cray XT3/XT4 Jaguar supercomputer,which currently ranks as the second most powerful super-computer in the world and will provide a significant boostto computing power of Tennessee bioinformaticians andbiology researches.Bioinformatics education presentation and workshopDr. Cynthia Petersen, the director of UT/ORNL GraduateSchool of Genome Science and Technology, provided anexciting brief overview of new educational initiatives inbioinformatics aiming to raise computationally-enabledbioscientists. She discussed the new SCALE-IT (Scalablecomputing and leading-edge innovative technologies)program, the availability of TeraGrid portals for biology,and educational opportunities for undergraduate andgraduate students.Malcolm Campbell (Davidson College) presented aPage 2 of 4(page number not for citation purposes)files, allowing for comparisons of significant profilesfound across time course experiments. To better grouphands-on guide to teaching bioinformatics education atan undergraduate level through his workshop "FunctionalBMC Bioinformatics 2008, 9(Suppl 7):I1 http://www.biomedcentral.com/1471-2105/9/S7/I1Genomics Cafeteria Style." His workshop was dividedinto Part I: Introducing Genomics and BioinformaticsEarly; Part II: Meshing Mathematics with Biology; and PartIII: A Fun Way to Integrate Biology, Math, CS, and Engi-neering. In Part I, he introduced the notion of teachingmicroarrays at the undergraduate level, through wet labsimulations [17] and creation of synthetic microarrayswith known expression levels [18]. Part II focused on theuse of MAGIC Tool for statistical analysis of microarrays[19,20]. Part III focused on facilitating interdisciplinaryresearch at the undergraduate level by breaking downdepartmental boundaries and encouraging creativitythrough the International Genetically EngineeredMachine Competition (iGEM).Additional discussions of the role of bioinformaticians instudent education and K-12 educational outreach wereheld throughout the summit.Poster sessionA total of 44 posters were presented during a 3-hourposter session on Saturday afternoon. These posterabstracts, a number of which are published in this supple-ment, were grouped in the topics of Bioimaging, Bioinfor-matics Infrastructure, Bioinformatics of Health andDisease, Comparative Genomics, Databases, FunctionalGenomics, Gene Regulation, Genomics, Machine Learn-ing and Algorithms, Microarrays, Ontologies and TextMining, Proteomics, Structure and Function Prediction,and Systems Biology.Seven of the poster abstracts were selected for inclusion inthe Summit program as short 15-minute platform presen-tations. Those posters presented as platform presentationswere "Impact of sequence variants on the genetic analysisof expression" (Daniel Ciobanu); "Evaluation of pooledallelotyping versus individual genotyping for genome-wide association analysis of complex disease" (SiddharthPratap); "Using spacings to infer regions of loss-of-hetero-zygosity from paired genotype array data" (StanleyPounds); "Integrated bioinformatics platform for differ-ential proteomics" (Xiang Zhang); "Towards ultimatequantification – recent advances in statistical analysis ofreal-time PCR data with linear models" (Joshua Yuan);"Geometric databases of protein structures" (Di Wu); and"Extracting putative gene networks from microarray datausing graph theoretical algorithms" (Sudhir Naswa).Future plansThe 2009 Bioinformatics Summit will return to Fall CreekFalls State Park, Tennessee in the Spring of 2009. Potentialfocus areas for next year may include translational infor-matics, epigenetics, and current technological advancesAcknowledgementsWe would like to thank the additional Conference Program Committee members Nigel Cooper (University of Louisville), Jack Dongarra (Univer-sity of Tennessee), Ramin Homayouni (University of Memphis), Mike Lang-ston (University of Tennessee), Terry Mark-Major (University of Tennessee-Memphis), Dan Masys (Vanderbilt University), Terry Moore (University of Tennessee), Jay Snoddy (Vanderbilt University), Chuck Sta-ben (University of Kentucky), Arnold Stromberg (University of Kentucky), Bruce Whitehead (University of Tennessee Space Institute) and Rob Wil-liams (University of Tennessee-Memphis) for putting together a well received scientific program. In addition, we wish to thank Bethany Coates, Stephanie Dearing, Terry Mark-Major, and Michelle Padgett for all of their efforts in putting together all of the details that allowed for the meeting to proceed. We would also like to thank Kerry Allen and the delightful staff of Lake Barkley State Park, who helped to make our stay as pleasant and smooth as possible. Funding for the UT-ORNL-KBRIN Summit is provided in part by The Kentucky Biomedical Research Infrastructure Network (KBRIN), The University of Tennessee Center for Information Technology Research, the University of Tennessee Molecular Resource Center, The UT-ORNL Science Alliance, The University of Tennessee Health Science Campus Research Center of Genomics and Bioinformatics, and NIH grants P20RR16481 and R13LM009315.References1. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR,Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al.:Identification and analysis of functional elements in 1% of thehuman genome by the ENCODE pilot project.  Nature 2007,447:799-816.2. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K,Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, et al.:Database resources of the National Center for Biotechnol-ogy Information.  Nucleic Acids Res 2008, 36:D13-D21.3. Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC,Hood L, Diruggiero J: Systems level insights into the stressresponse to UV radiation in the halophilic archaeon Halo-bacterium NRC-1.  Genome Res 2004, 14:1025-1035.4. Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thors-son V, Shannon P, Johnson MH, Bare JC, et al.: A predictive modelfor transcriptional control of physiology in a free living cell.Cell 2007, 131:1354-1365.5. Kaur A, Pan M, Meislin M, Facciotti MT, El-Gewely R, Baliga NS: Asystems view of haloarchaeal strategies to withstand stressfrom transition metals.  Genome Res 2006, 16:841-854.6. Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L,Diruggiero J, Baliga NS: An integrated systems approach forunderstanding cellular responses to gamma radiation.  MolSyst Biol 2006, 2:47.7. Benson M, Carlsson L, Guillot G, Jernas M, Langston MA, Rudemo M,Andersson B: A network-based analysis of allergen-challengedCD4+ T cells from patients with allergic rhinitis.  Genes Immun2006, 7:514-521.8. Benson M, Langston MA, Adner M, Andersson B, Torinssson-NaluaiA, Cardell LO: A network-based analysis of the late-phasereaction of the skin.  J Allergy Clin Immunol 2006, 118:220-225.9. Benson M, Cardell LO, Hohmann S, Jirstrand M, Langston M, MobiniR, Nerman O: [Systems biology can radically change healthcare. Basis for individualized prediction, prevention andtreatment].  Lakartidningen 2007, 104:3037-3041.10. Ernst J, Bar-Joseph Z: STEM: a tool for the analysis of short timeseries gene expression data.  BMC Bioinformatics 2006, 7:191.11. Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z: Reconstruct-ing dynamic regulatory maps.  Mol Syst Biol 2007, 3:74.12. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK,Hannett NM, Harbison CT, Thompson CM, Simon I, et al.: Tran-scriptional regulatory networks in Saccharomyces cerevi-siae.  Science 2002, 298:799-804.13. Ernst J, Beg QK, Kay KA, Balazsi G, Oltvai ZN, Bar-Joseph Z: APage 3 of 4(page number not for citation purposes)for generating biological data. Semi-Supervised Method for Predicting Transcription Fac-tor-Gene Interactions in Escherichia coli.  PLoS Comput Biol2008, 4:e1000044.Publish with BioMed Central   and  every scientist can read your work free of charge"BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime."Sir Paul Nurse, Cancer Research UKYour research papers will be:available free of charge to the entire biomedical communitypeer reviewed and published immediately upon acceptancecited in PubMed and archived on PubMed Central BMC Bioinformatics 2008, 9(Suppl 7):I1 http://www.biomedcentral.com/1471-2105/9/S7/I114. Mardis ER: The impact of next-generation sequencing tech-nology on genetics.  Trends Genet 2008, 24:133-141.15. Moore GE: Cramming more components onto integrated cir-cuits.  Electronics 1965, 38:.16. Daidone I, Ulmschneider MB, Di NA, Amadei A, Smith JC: Dehydra-tion-driven solvent exposure of hydrophobic surfaces as adriving force in peptide folding.  Proc Natl Acad Sci USA 2007,104:15230-15235.17. Campbell AM, Zanta CA, Heyer LJ, Kittinger B, Gabric KM, Adler L,Schulz B: DNA microarray wet lab simulation brings genom-ics into the high school curriculum.  CBE Life Sci Educ 2006,5:332-339.18. Campbell AM, Hatfield WT, Heyer LJ: Make microarray data withknown ratios.  CBE Life Sci Educ 2007, 6:196-197.19. Campbell AM, Ledbetter ML, Hoopes LL, Eckdahl TT, Heyer LJ,Rosenwald A, Fowlks E, Tonidandel S, Bucholtz B, Gottfried G:Genome Consortium for Active Teaching: meeting the goalsof BIO2010.  CBE Life Sci Educ 2007, 6:109-118.20. Heyer LJ, Moskowitz DZ, Abele JA, Karnik P, Choi D, Campbell AM,Oldham EE, Akin BK: MAGIC Tool: integrated microarray dataanalysis.  Bioinformatics 2005, 21:2114-2115.yours — you keep the copyrightSubmit your manuscript here:http://www.biomedcentral.com/info/publishing_adv.aspBioMedcentralPage 4 of 4(page number not for citation purposes)

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