CellMontage: Similar Expression Profile Search Server (2008)
Wataru Fujibuchi A, Larisa Kiseleva A, Takeaki Taniguchi B, Hajime Harada A, Paul Horton ∗a, Prof Martin Bishop
Summary: The establishment and rapid expansion of microarray databases has created a need for new search tools. Here we present CellMontage, the first server for expression profile similarity search...
Zongli Xu, Norman L. Kaplan, Jack A. Taylor, Prof Martin Bishop
Summary: Genetic association studies increasingly rely on the use of linkage disequilibrium (LD) tag SNPs to reduce genotyping costs. We developed a software package TAGster to select, evaluate, and...
Gene expression The High-level Similarity of Some Disparate Gene Expression Measures (2008)
Ini Raghavan, De Bondt, Willem Talloen, Dieder Moechars, Hinrich W. H, ...
Probe level data from Affymetrix GeneChips can be summarized in many ways to produce probe-set level gene expression measures. Disturbingly, the different approaches not only generate quite different...
Peter J Bradbury, Zhiwu Zhang, Dallas E Kroon, Terry M Casstevens, Yogesh Ramdoss, Edward S Buckler, ...
Summary: Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend...
Zongli Xu, Norman L. Kaplan, Jack A. Taylor, Prof Martin Bishop
Summary: Genetic association studies increasingly rely on the use of linkage disequilibrium (LD) tag SNPs to reduce genotyping costs. We developed a software package TAGster to select, evaluate, and...
Application Note GenABEL: an R library for genome-wide association analysis (2008)
Yurii S. Aulchenko, Stephan Ripke, Aaron Isaacs, Prof Martin Bishop
Here we describe an R library for genome-wide association (GWA) analysis. It implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of...
Application Note CTree: comparison of clusters between phylogenetic trees made easy (2008)
John Archer, David L. Robertson, Prof Martin Bishop
Summary: CTree has been designed for the quantification of clusters within viral phylogenetic tree topologies. Clusters are stored as individual data structures from which statistical data, such as...
Ali Torkamani, Nicholas J. Schork, Prof Martin Bishop
Motivation: Contemporary, high-throughput sequencing efforts have identified a rich source of naturally occurring single nucleotide polymorphisms (SNPs), a subset of which occur in the coding region...
Patricia Buendia, Giri Narasimhan, Prof Martin Bishop
Motivation: Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses....
Illumina Platform, Prof Joachim, L. Schultze, Daniela Eggle, Prof Martin Bishop
Summary: IlluminaGUI is a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform. All key components of a microarray experiment, including quality...
Phylocomposer and Phylodirector: Analysis and Visualization of Transducer Indel Models (2007)
Ian Holmes, Prof Martin Bishop
Summary: Finite-state string transducers are probabilistic tools similar to Hidden Markov Models that can be systematically extended to large numbers of sequences related by indel and substitution...
Four-Body Scoring Function for Mutagenesis (2007)
Chris Deutsch A, Bala Krishnamoorthy A, Prof Martin Bishop
Motivation: There is a need for an efficient and accurate computational method to identify the effects of single and multiple residue mutations on the stability and reactivity of proteins. Such a...