Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
Published in Bioinformatics
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Ev...
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...
Into the heart of darkness: large-scale clustering of human non-coding DNA.
Published in Bioinformatics
Efficient approximations for learning phylogenetic HMM models from data.
Published in Bioinformatics
Support vector machine classification and validation of cancer tissue samples using microarray expression data.
Published in Bioinformatics
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
Published in Bioinformatics
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.
Published in Bioinformatics
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Published in Bioinformatics
The variant call format and VCFtools.
...Published in Bioinformatics (Oxford, England)
The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was develop...
