Efficient approximations for learning phylogenetic HMM models from data.
Published in Bioinformatics
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
Published in Bioinformatics
Support vector machine classification and validation of cancer tissue samples using microarray expression data.
Published in Bioinformatics
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Ev...
Published in Bioinformatics
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.
Published in Bioinformatics
The UCSC Known Genes.
Published in Bioinformatics
The University of California Santa Cruz (UCSC) Known Genes dataset is constructed by a fully automated process, based on protein data from Swiss-Prot/TrEMBL (UniProt) and the associated mRNA data from Genbank. The detailed steps of this process are described. Extensive cross-references from this dataset to other genomic and proteomic data were cons...
HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Published in Bioinformatics
Gene structure-based splice variant deconvolution using a microarray platform.
...Published in Bioinformatics
Classifying G-protein coupled receptors with support vector machines.
Published in Bioinformatics
Motivation: The enormous amount of protein sequence data uncovered by genome research has increased the demand for computer software that can automate the recognition of new proteins. We discuss the relative merits of various automated methods for recognizing G-Protein Coupled Receptors (GPCRs), a superfamily of cell membrane proteins. GPCRs are fo...
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Published in Bioinformatics
