Session Slides & Details

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Wednesday, March 10, 2010

(S01) Deriving Meaning from Data

• Assessing Temporal Correlation of Significant Gene Pathways Using String Edit Distance. Y. Huang, A. Hero, University of Michigan
• Mapping Transcription Mechanisms from Multimodal Genomic Data. H. Chang, M. McGeachie, M. Ramoni, Harvard Medical School
• Stromal Microenvironment Processes Unveiled by Biological Component Analysis of Gene Expression in Xenograft Tumor Models. X. Yang, Sect. Genetic Medicine, Y. Lee, Y. Huang, University of Chicago; J. Chen, University of Chicago Medical Center; H. Xing, Y. Lussier, University of Chicago

(S02) Networks of Researchers

• VIVO: A Semantic Approach to Creating a National Network of Researchers. Part I. Approach and Dissemination. M. Devare, Cornell University; V. Davis, University of Florida; K. Holmes, Washington University in St. Louis School of Medicine; S. Russell Gonzalez, M. Tennant, M. Conlon, University of Florida; VIVO Collaboration
• VIVO: A Semantic Approach to Creating a National Network of Researchers. Part II. Technical Design. J. Corson-Rikert, Cornell University; M. Conlon, University of Florida; B. Lowe, B. Caruso, Cornell University; K. Börner, Y. Ding, Indiana University; D. Krafft, Cornell University; L. McIntosh, Washington University School of Medicine; VIVO Collaboration
• The Gene Wiki: Community Intelligence Applied to Human Gene Annotation. J. Huss III, Genomics Institute of the Novartis Research Foundation; P. Lindenbaum, CEPH/Fondation Jean-Dausset; M. Martone, Rush University Medical College; D. Roberts, San Diego State University; A. Pizarro, University of Pennsylvania School of Medicine; F. Valafar, San Diego State University; J. Hogenesch, University of Pennsylvania School of Medicine; A. Su, Genomics Institute of the Novartis Research Foundation
• Harvard Catalyst Profiles: Discovering and Visualizing Connections in Research. G. Weber, Harvard Medical School

(S03) Panel: The Electronic Medical Records & Genomics (eMERGE) Network

• P. Tarczy-Hornoch (Chair), University of Washington
• C. Chute, Mayo Clinic
• J. Starren, Marshfield Clinic
• L. Rasmussen, Marshfield Clinic

(S04) National Centers for Biomedical Computing (NCBC) and Translational Bioinformatics: National Alliance for Medical Imaging Computing (NA-MIC) and Informatics for Integrating Biology and the Bedside (i2b2)

• R. Kikinis, Brigham and Women's Hospital (NA-MIC, Part 1)
• I. Kohane, Brigham and Women's Hospital (i2b2, Part 2)

Thursday, March 11, 2010

(S05) Personalized Medicine

• Empowering the Patient: Recommendation System for Prospective Healthcare. N. Chawla, D. Davis, University of Notre Dame; N. Christakis, Harvard; A. Barabasi, Northeastern
• Translational Medicine: Using Systems of Differential Equations to Identify Patterns in Symptom Remission in Response to Treatment and the Underlying Dynamics of the Interactions. J. Luciano, Predictive Medicine, Inc.; M. Cohen, Boston University; J. Samson, Harvard Medical School and McLean Hospital
• Feasibility of Incorporating Genomic Knowledge into Electronic Medical Records for Pharmacogenomic Clinical Decision Support. C. Overby, P. Tarczy-Hornoch, J. Hoath, I. Kalet, D. Veenstra, University of Washington

(S06) Mining the Medical Record

• EHR Dynamics and Stratification. D. Albers, G. Hripcsak, Columbia University
• Latent Physiological Factors of Complex Human Diseases Revealed by Independent Component Analysis of Clinarrays. D. Chen, J. Dudley, A. Butte, Stanford University
• Architecture of an Analytic Information Warehouse for Discovering Risk Factor Models of Disease in Quality Improvement and Research. A. Post, T. Kurc, Emory University; J. Butler, Emory Healthcare; J. Saltz, Emory University
• Integrating Pre-clinical and Clinical Data Sets to Enable Translational Science Queries and Comparisons of Multiple Biological Result Types. J. Shon, R. Varma, V. Mahuvakar, J. Vig, N. Gonzaludo, S. Chiu, Roche

(S07) Applications of Text Mining

• Cytochrome P450 Drug-drug Interactions in FDA Adverse Event Reports. H. Enchin, Oregon Health & Science University
• Mining Multi-item Drug Adverse Effect Associations in Spontaneous Reporting Systems. R. Harpaz, H. Chase, C. Friedman, Columbia University
• Peeling Away the Black Box Label: Clinical Validation of a MaxEnt Machine Learning Character N-gram Feature Set for Acute Lung Injury. I. Solti, University of Washington; C. Cooke, University of Michigan; F. Xia, M. Wurfel, University of Washington
• Statistical Extraction of Medication Information from Clinical Records. S. Halgrim, F. Xia, I. Solti, E. Cadag, University of Washington; O. Uzuner, SUNY at Albany

(S08) National Centers for Biomedical Computing (NCBC) and Translational Bioinformatics: National Center for Biomedical Ontology (NCBO) and National Center for Integrative Biomedical Informatics (NCIBI)

• M. Musen, Stanford University (NCBO, Part 1)
• B. Athey, University of Michigan (NCIBI, Part 2)

(S09) Drugs and Biomarkers

• Chem_BLAST - A Rule-based Method to Develop Advanced Structural Ontologies for Chemical Bioinformatics. T. Bhat, NIST
• Shared Genomics: Developing an Accessible Integrated Analysis Platform for Genome-wide Association Studies. D. Hoyle, M. Delderfield, L. Kitching, G. Smith, I. Buchan, University of Manchester
• Predicting Biomarkers for Chronic Lymphocytic Leukemia Using Gene Co-expression Network Analyses for ZAP70. J. Zhang, L. Ding, Ohio State University; K. Circle, Mount Carmel College of Nursing; T. Borlawsky, Y. Xiang, H. Ozer, Ohio State University; R. Jin, Kent State University; P. Payne, K. Huang, Ohio State University
• MicroRNA Signatures of Cytotoxicity Unveils Molecular Underpinnings of Chemotherapeutic Drug Classes. W. Zhang, E. Gamazon, R. Huang, University of Chicago; S. Duan, Singapore Institute for Clinical Sciences; W. Bleibel, M. Welsh, Y. Lussier, M. Dolan, University of Chicago

(S10) Disease Gene Discoveries

• An Integrative Method for Scoring Candidate Genes from Association Studies: Application to Warfarin Dosing. N. Tatonetti, J. Dudley, H. Sagreiya, R. Altman, Stanford University
• Tests for Category Enrichment Identifies a Novel Set of Cancer Genes with Genome-wide Significance in Autism. M. Banos, D. Wall, Harvard Medical School
• Candidate Gene Prioritization Using Network Based Probabilistic Models. S. Wang, M. Hauskrecht, S. Visweswaran, University of Pittsburgh

(S11) Panel: Cooperative Research Initiatives on Biomedical Informatics in Europe

• F. Martin-Sanchez, National Institute of Health Carlos III
• F. Sanz, IMIM, Universitat Pompeu Fabra, Barcelona
• J. van der Lei, Erasmus Medical Center Rotterdam

(S12) Late Breaking Presentations

• Gene Expression Meta-analysis Supports Existence of Molecular Apocrine Breast Cancer with a Role for Androgen Receptor and Implies Interactions with ErbB Family. S. Sanga, University of Texas at Austin; B. Broom, University of Texas; V. Cristini, University of Texas Health Science Center; M. Edgerton, University of Texas M.D. Anderson Cancer Center
• An Integrative Approach to Reveal Driver Gene Fusions from Paired-End Sequencing Data in Cancer. X. Wang, J. Prensner, Michigan Center for Translational Pathology; G. Chen, University of Michigan; Q. Cao, B. Han, S. Dhanasekaran, R. Ponnala, X. Cao, S. Varambally, Michigan Center for Translational Pathology; D. Thomas, T. Giordano, D. Beer, University of Michigan; N. Palanisamy, Michigan Center for Translational Pathology; M. Sartor, G. Omenn, National Center for Integrative Biomedical Informatics; A. Chinnaiyan, Michigan Center for Translational Pathology
• Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis. Y. Lee, X. Yang, Y. Huang, H Fan, Q. Zhang, Y. Wu, J. Li, R. Hasina, University of Chicago; C. Cheng, Yale University School of Medicine; M. Lingen, University of Chicago; M. Gerstein, Yale University School of Medicine; R. Weichselbaum, H. Rosie Xing, Y. Lussier, University of Chicago

(S13) Panel: Using Ontologies to Drive Biomedical Research

• M. Musen, Stanford University (chair)
• N. Baker, Washington University
• D. Paik, Stanford University
• I. Sim, UCSF
• S. Twigger, Medical College of Wisconsin
• R. Winslow, Johns Hopkins University School of Medicine

(S14) Systems Biology

• Context-constrained Molecular Interaction Networks Uncover Shared Biological Pathways among Breast Cancer Signatures. J. Chen, Y. Lussier, L. Sam, Y. Lee, J. Li, Y. Huang, Y. Liu, H. Xing, University of Chicago
• Tissue-tissue Gene Co-expression Network for Tumor Microenvironment Study. K. Huang, The Ohio State University; A. Leung, Oregon State University; J. Zhang, The Ohio State University; C. Zhang, West Virginia University
• Comparative Network Analysis of Specific Host-pathogen Interactions. J. McDermott, M. Costa, B. Thrall, K. Waters, J. Adkins, L. Shi, Pacific Northwest National Laboratory; F. Heffron, Oregon Health & Sciences University

(S15) Panel: Linking Clinical and Genomic Data: Opportunities to Achieve Personalized Healthcare

• Lewis Frey (Moderator)
• C. Chute, Mayo Clinic
• G. Downing, HHS
• J. Starren, Marshfield Clinic
• M. Yandell, University of Utah

(S16) Late Breaking Presentations

• Novel Sequence Feature Variant Type Analysis of the HLA Genetic Association in Systemic Sclerosis. D. Karp, N. Marthandan, U.T. Southwestern Medical Center; S. Marsh, Anthony Nolan Research Institute, R. Scheuermann, U.T. Southwestern Medical Center, et al
• Autoimmune Disease Classification by Inverse Association with SNP Alleles. M. Sirota, M. Schaub, S. Batzoglou, W. Robinson, A. Butte, Stanford University
• Computational Phenomics and Thorough Biological Characterization Uncovers a Tumor Suppressor microRNA and its Regulatory Network. Y. Lee, X. Yang, Y. Huang, H. Fan, Q. Zhang, Y. Wu, J. Li, R. Hasina, University of Chicago; C. Cheng, Yale University School of Medicine; M. Lingen, University of Chicago; M. Gerstein, Yale University School of Medicine; R. Weichselbaum, H. Xing, Y. Lussier, University of Chicago

Keynote Presentation: Getting from Heterogeneous Data to Actionable Shared Models of Biology. Andrew Kasarskis, Sage Bionetworks

Friday, March 12, 2010

(S17) Methods in Text Mining

• A Knowledge Extraction Framework for BioMedical Pathways. S. Harabagiu, C. Bejan, University of Texas at Dallas
• Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine. T. Borlawsky, The Ohio State University; J. Li, University of Chicago; L. Shagina, Columbia University; M. Crowson, Y. Liu, University of Chicago; C. Friedman, Columbia University; Y. Lussier, University of Chicago
• NCIBI NLP Tools: Foundation for Integration. J. Cavalcoli, A. Ade, B. Mirel, H. Jagadish, G. Omenn, B. Athey, University of Michigan
• Concept Discovery for Pathology Reports using an N-gram Model. V. Yip, University of Arkansas for Medical Sciences; M. Mete, Texas A&M University-Commerce; U. Topaloglu, University of Arkansas for Medical Sciences; S. Kockara, University of Central Arkansas

(S18) Mutations and Variations

• Machine-learning Classification of RET Mutation Severity. D. Crockett, S. Piccolo, S. Narus, J. Mitchell, J. Facelli, University of Utah
• Assessment of Genetic Variation for the LINE1 Retrotransposon from Next Generation Sequence Data. E. Rouchka, Speed School of Engineering; D. Montoya, V. Stribinskis, K. Ramos, T. Kalbfleisch, University of Louisville
• Predicting Molecular Functions Disrupted by Mutations Using Protein Functional Information. P. Radivojac, Indiana University; M. Mort, Cardiff University; B. Li, Indiana University; U. Evani, V. Krishnan, K. Kamati, Buck Institute for Age Research; P. Baenziger, Indiana University; Y. Sun, M. Kann, University of Maryland Baltimore County; D. Cooper, Cardiff University; S. Mooney, Buck Institute for Age Research
• Tracking Viral Sequence Mutations. J. Shon, R. Varma, E. Scott, Y. Ji, D. Chin, K. Klumpp, Roche Pharmaceuticals

(S19) Genome Wide Association Studies

• Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology. Y. Lee, J. Li, E. Gamazon, J. Chen, A. Tikhomirov, N. Cox, Y. Lussier, University of Chicago
• A Grid-based framework for Genome-wide Studies. L. Torterolo, University of Genoa; A. Nuzzo, University of Pavia; A. Malovini, A. Puca, IRCCS Multimedica; M. Fato, University of Genoa; R. Bellazzi, Università di Pavia
• Identify Polygenetic Disease Models from an Ontology Fingerprints Derived Gene Network for Genome Wide Association Study. T. Qin, L. Tsoi, A. Lawson, J. Zheng, Medical University of South Carolina

(S20) National Centers for Biomedical Computing (NCBC) and Translational Bionformatics: National Center for the Multi-Scale Analysis of Genomic and Cellular Networks (MAGNet) and Physics-based Simulation of Biological Structures (Simbios)

• R. Rabadan, Columbia University (MAGNet, Part 1)
• R. Altman, Stanford University (Simbios, Part 2)

(S21) Integrating Data I

• tranSMART: A Data Warehouse Platform for Pharmaceutical R&D. D. Housman, J. Adler, J. Liu, Recombinant Data Corp; S. Szalma, J. Smart, Centocor R&D, Inc.
• Multi-scale, Integrative Study of Brain Tumor: In Silico Brain Tumor Research Center. J. Saltz, T. Kurc, S. Cholleti, J. Kong, C. Moreno, A. Sharma, T. Pan, L. Cooper, E. Van Meir, Emory University; T. Mikkelsen, Henry Ford Hospital; A. Flanders, Thomas Jefferson University; D. Rubin, Stanford University; D. Brat, Emory University
• MIDR 1.0: The MURDOCK Integrated Data Repository. J. Tenenbaum, Duke University; S. Chakraborty, Duke Clinical Research Institute; C. Blach, M. Gardner, Duke University; B. McCourt, Duke Clinical Research Institute; M. Nahm, R. Califf, Duke University

(S22) Annotation

• Automated Ontological Gene Annotation for Computing Disease Similarity. D. Dinakarpandian, S. Mathur, University of Missouri-Kansas City
• PositionMatcher: A Fast Custom-annotation Tool for Short DNA Sequences. E. Pitzer, Upper Austria University of Applied Sciences; J. Kim, University of California San Diego; P. Galante, Ludwig Institute for Cancer Research; K. Patel, L. Ohno-Machado, University of California San Diego
• Assessing the Quality of Annotations in Asthma Gene Expression Experiments. R. Lacson, Brigham and Women's Hospital; M. Mbagwu, Ohio State University; H. Yousif, The University of Arizona; L. Ohno-Machado, University of California San Diego

(S23) Clinical Analysis of a Complete Human Genome: A Glimpse of the Future

• R. Altman, A. Butte, Stanford University

(S24) Late Breaking Presentations

• Extracting Cell-Type-Specific Gene Expression Differences from Complex Tissues. S. Shen-Orr, R. Tibshirani, P. Khatri, Stanford University School of Medicine; D. Bodian, Novartis Pharmaceuticals Corp; F. Staedtler, Novartis Institutes for BioMedical Research; N. Perry, T. Hastie, M. Sarwal, M. Davis, A. Butte, Stanford University School of Medicine
• Geographic Dependence, Surveillance, and Origins of the 2009 Influenza A (H1N1) Virus. V. Trifonov, H. Khiabanian, R. Rabadan, Columbia University
• Biogps: An Extensible and Customizable Portal for Querying and Organizing Gene Annotation Resources. C. Wu, C. Orozco, J. Boyer, M. Leglise, J. Goodale, S. Batalov, C. Hodge, J. Haase, J. Janes, J. Huss III, A. Su, Genomics Institute of the Novartis Research Foundation
• Genotype-to-Phenotype and Bioinformatics Open-Source Toolkits: A Case Study. P. Elkin, J. Lee, W. Zhang, M. Tuttle, H. Sampson, Mount Sinai School of Medicine

(S25) Integrating Data II

• A Case Study of Goal-directed User-centered Design for an Interactive, Integrated Bioinformatics Information Retrieval System. J. Bartlett, McGill University
• Defining the Neural Circuitry of Depression using Integrated Brain Imaging Modalities. D. Gutman, J. Saltz, P. Holtzheimer, H. Mayberg, Emory University
• Comparison of Multiplex Meta-analysis Techniques for Understanding the Acute Rejection of Solid Organ Transplants. A. Morgan, P. Khatri, R. Jones, M. Sarwal, A. Butte, Stanford University
• Multi-dimensional Discovery of Biomarker and Phenotype Complexes. P. Payne, K. Huang, Ohio State University; K. Circle, Mount Carmel College of Nursing; A. Kundu, J. Zhang, T. Borlawsky, Ohio State University

Closing Keynote Presentation: Translational Bioinformatics Year in Review. Russ Altman, Stanford University

 

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