Volume 10 Supplement 9

Proceedings of the 2009 AMIA Summit on Translational Bioinformatics

Proceedings

2009 AMIA Summit on Translational Bioinformatics.

San Francisco, CA, USA

15-17 March 2009

  1. Introduction

    Transcriptional network classifiers

    Gene interactions play a central role in transcriptional networks. Many studies have performed genome-wide expression analysis to reconstruct regulatory networks to investigate disease processes. Since biologi...

    Hsun-Hsien Chang and Marco F Ramoni

    BMC Bioinformatics 2009 10(Suppl 9):S1

    Published on: 17 September 2009

  2. Proceedings

    Analysis of AML genes in dysregulated molecular networks

    Identifying disease causing genes and understanding their molecular mechanisms are essential to developing effective therapeutics. Thus, several computational methods have been proposed to prioritize candidate...

    Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim and Doheon Lee

    BMC Bioinformatics 2009 10(Suppl 9):S2

    Published on: 17 September 2009

  3. Proceedings

    Network analysis of genes regulated in renal diseases: implications for a molecular-based classification

    Chronic renal diseases are currently classified based on morphological similarities such as whether they produce predominantly inflammatory or non-inflammatory responses. However, such classifications do not r...

    Suresh K Bhavnani, Felix Eichinger, Sebastian Martini, Paul Saxman, HV Jagadish and Matthias Kretzler

    BMC Bioinformatics 2009 10(Suppl 9):S3

    Published on: 17 September 2009

  4. Proceedings

    Infection in the intensive care unit alters physiological networks

    Physicians use clinical and physiological data to treat patients every day, and it is essential for treating a patient appropriately. However, medical sources of clinical physiological data are only now starti...

    Adam D Grossman, Mitchell J Cohen, Geoffrey T Manley and Atul J Butte

    BMC Bioinformatics 2009 10(Suppl 9):S4

    Published on: 17 September 2009

  5. Proceedings

    Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia

    Current outcome predictors based on "molecular profiling" rely on gene lists selected without consideration for their molecular mechanisms. This study was designed to demonstrate that we could learn about gene...

    Xinan Yang, Yong Huang, James L Chen, Jianming Xie, Xiao Sun and Yves A Lussier

    BMC Bioinformatics 2009 10(Suppl 9):S6

    Published on: 17 September 2009

  6. Proceedings

    PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment

    The decision environment for cancer care is becoming increasingly complex due to the discovery and development of novel genomic tests that offer information regarding therapy response, prognosis and monitoring...

    Angel Janevski, Sitharthan Kamalakaran, Nilanjana Banerjee, Vinay Varadan and Nevenka Dimitrova

    BMC Bioinformatics 2009 10(Suppl 9):S7

    Published on: 17 September 2009

  7. Proceedings

    The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers

    Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to ...

    Casey Lynnette Overby, Peter Tarczy-Hornoch and Dina Demner-Fushman

    BMC Bioinformatics 2009 10(Suppl 9):S8

    Published on: 17 September 2009

  8. Proceedings

    Towards large-scale sample annotation in gene expression repositories

    Large repositories of biomedical research data are most useful to translational researchers if their data can be aggregated for efficient queries and analyses. However, inconsistent or non-existent annotations...

    Erik Pitzer, Ronilda Lacson, Christian Hinske, Jihoon Kim, Pedro AF Galante and Lucila Ohno-Machado

    BMC Bioinformatics 2009 10(Suppl 9):S9

    Published on: 17 September 2009

  9. Proceedings

    Evaluation of a large-scale biomedical data annotation initiative

    This study describes a large-scale manual re-annotation of data samples in the Gene Expression Omnibus (GEO), using variables and values derived from the National Cancer Institute thesaurus. A framework is des...

    Ronilda Lacson, Erik Pitzer, Christian Hinske, Pedro Galante and Lucila Ohno-Machado

    BMC Bioinformatics 2009 10(Suppl 9):S10

    Published on: 17 September 2009

  10. Proceedings

    Evaluating the accuracy of a functional SNP annotation system

    Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to under...

    Terry H Shen, Christopher S Carlson and Peter Tarczy-Hornoch

    BMC Bioinformatics 2009 10(Suppl 9):S11

    Published on: 17 September 2009

  11. Proceedings

    Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease

    Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for trans...

    Brett R South, Shuying Shen, Makoto Jones, Jennifer Garvin, Matthew H Samore, Wendy W Chapman and Adi V Gundlapalli

    BMC Bioinformatics 2009 10(Suppl 9):S12

    Published on: 17 September 2009

  12. Proceedings

    Comparison of concept recognizers for building the Open Biomedical Annotator

    The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources. The system's indexing workflow processes the text metadata of dive...

    Nigam H Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P Chiang and Mark A Musen

    BMC Bioinformatics 2009 10(Suppl 9):S14

    Published on: 17 September 2009

  13. Proceedings

    Feature selection for fMRI-based deception detection

    Functional magnetic resonance imaging (fMRI) is a technology used to detect brain activity. Patterns of brain activation have been utilized as biomarkers for various neuropsychiatric applications. Detecting de...

    Bo Jin, Alvin Strasburger, Steven J Laken, F Andrew Kozel, Kevin A Johnson, Mark S George and Xinghua Lu

    BMC Bioinformatics 2009 10(Suppl 9):S15

    Published on: 17 September 2009

  14. Proceedings

    Knowledge-based variable selection for learning rules from proteomic data

    The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in ...

    Jonathan L Lustgarten, Shyam Visweswaran, Robert P Bowser, William R Hogan and Vanathi Gopalakrishnan

    BMC Bioinformatics 2009 10(Suppl 9):S16

    Published on: 17 September 2009

  15. Proceedings

    Structural similarity assessment for drug sensitivity prediction in cancer

    The ability to predict drug sensitivity in cancer is one of the exciting promises of pharmacogenomic research. Several groups have demonstrated the ability to predict drug sensitivity by integrating chemo-sens...

    Pavithra Shivakumar and Michael Krauthammer

    BMC Bioinformatics 2009 10(Suppl 9):S17

    Published on: 17 September 2009