Identification of candidate regulatory SNPs by combination of TFBS prediction, SNP genotyping and haploChIP

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP - Disease-associated SNPs detected in large-scale association studies are frequently located in non-coding genomic regions, suggesting that they may be involved in transcriptional re

ESG: extended similarity group method for automated protein function prediction

ESG: extended similarity group method for automated protein function prediction - Motivation: Importance of accurate automatic protein function prediction is ever increasing in the face of a large number of newly sequenced genomes and proteomics data that are awaiting biological interpretation.

Data structures and compression algorithms for genomic sequence data

Data structures and compression algorithms for genomic sequence data - Motivation: The continuing exponential accumulation of full genome data, including full diploid human genomes, creates new challenges not only for understanding genomic structure, function and evolution, but also for the storage,

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences - Motivation:One of the first steps in metagenomic analysis is the assignment of reads/contigs obtained from various sequencing technologies to their correct taxonomic bins.

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data - Motivation: Chromatin immunoprecipitation (ChIP) experiments followed by array hybridization, or ChIP-chip, is a powerful approach for identifying transcription factor binding sites (TFBS) and has be

Text-based over-representation analysis of microarray gene lists with annotation bias

Text-based over-representation analysis of microarray gene lists with annotation bias - A major challenge in microarray data analysis is the functional interpretation of gene lists.

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences - Gene families compose a large proportion of eukaryotic genomes. The rapidly expanding genomic sequence database provides a good opportunity to study gene family evolution and function.

Textual data compression in computational biology: a synopsis

Textual data compression in computational biology: a synopsis - Motivation: Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner - Motivation: The most accurate way to determine the intron–exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines.