Volume 9 Supplement 1

Quantitative inference of gene function from diverse large-scale datasets


Edited by Timothy R Hughes and Frederick P Roth

  1. Research

    A critical assessment of Mus musculusgene function prediction using integrated genomic evidence

    Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help...

    Lourdes Peña-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin…

    Genome Biology 2008 9(Suppl 1):S2

    Published on: 27 June 2008

  2. Research

    Predicting gene function in a hierarchical context with an ensemble of classifiers

    The wide availability of genome-scale data for several organisms has stimulated interest in computational approaches to gene function prediction. Diverse machine learning methods have been applied to unicellul...

    Yuanfang Guan, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy and Olga G Troyanskaya

    Genome Biology 2008 9(Suppl 1):S3

    Published on: 27 June 2008

  3. Method

    Consistent probabilistic outputs for protein function prediction

    In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate...

    Guillaume Obozinski, Gert Lanckriet, Charles Grant, Michael I Jordan and William Stafford Noble

    Genome Biology 2008 9(Suppl 1):S6

    Published on: 27 June 2008

  4. Method

    Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiaegene function

    Learning the function of genes is a major goal of computational genomics. Methods for inferring gene function have typically fallen into two categories: 'guilt-by-profiling', which exploits correlation between...

    Weidong Tian, Lan V Zhang, Murat Taşan, Francis D Gibbons, Oliver D King, Julie Park, Zeba Wunderlich, J Michael Cherry and Frederick P Roth

    Genome Biology 2008 9(Suppl 1):S7

    Published on: 27 June 2008

  5. Research

    An en masse phenotype and function prediction system for Mus musculus

    Individual researchers are struggling to keep up with the accelerating emergence of high-throughput biological data, and to extract information that relates to their specific questions. Integration of accumula...

    Murat Taşan, Weidong Tian, David P Hill, Francis D Gibbons, Judith A Blake and Frederick P Roth

    Genome Biology 2008 9(Suppl 1):S8

    Published on: 27 June 2008