Motivation: Although metabolic reactions are unquestionably shaped by evolutionary processes, the degree to which the overall structure and complexity of their interconnections are linked to the phylogeny of species has not been evaluated in depth. Here,...

Motivation: Gene-set enrichment analysis (GSEA) can be greatly enhanced by linear model (regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential samples, and also to evaluate model fit and explore model expansion.

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Motivation: We present PCIT, an algorithm for the reconstruction of gene co-expression networks (GCN) that combines the concept partial correlation coefficient with information theory to identify significant gene to gene associations defining edges ...

Motivation: Analysis of the distribution of alleles across populations is a useful tool for examining population diversity and relationships. However, sample sizes often differ across populations, sometimes making it difficult to assess allelic ...

Motivation: DNA microarrays are routinely applied to study diseased or drug-treated cell populations. A critical challenge is distinguishing the genes directly affected by these perturbations from the hundreds of genes that are indirectly affected. ...

Motivation: At the center of computational systems biology are mathematical models that capture the dynamics of biological systems and offer novel insights. The bottleneck in the construction of these models is presently the identification of model ...

Motivation: Each protein performs its functions within some specific locations in a cell. This subcellular location is important for understanding protein function and for facilitating its purification. There are now many computational techniques for ...

Motivation: Most of the protein tyrosine kinases found in bacteria have been recently classified in a new family, termed BY-kinase. Indeed, they share no sequence homology with their eukaryotic counterparts and have no known eukaryotic homologues. They ...

Motivation: Finding protein-coding genes in a newly determined genomic sequence is the first step toward understanding the content written in the genome. Sequences of transcripts of homologous genes, if available, can considerably improve accuracy of ...

Motivation: The next generation sequencing technologies are generating billions of short reads daily. Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare ...

Motivation: There is a growing interest in extracting statistical patterns from gene expression time-series data, in which a key challenge is the development of stable and accurate probabilistic models. Currently popular models, however, would be ...

Summary: There are thousands of strongly conserved non-coding elements (CNEs) in vertebrate genomes, and their functions remain largely unknown. However, without biologically relevant criteria for prioritizing them, selecting a particular CNE sequences ...

Motivation: Epistatic or genetic interactions, representing the effects of mutating one gene on the phenotypes caused by mutations in one or moredistinct genes, can be very helpful for uncovering functional relationships between genes. Recently, the ...

Motivation: Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use ...

spolTools is a collection of online programs designed to manipulate and analyze spoligotype datasets of the Mycobacterium tuberculosis complex. These tools are integrated into a repository currently containing 1179 spoligotypes and 6278 isolates across ...

The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous residues across chains. A ...

We present a novel computational method for predicting which proteins from highly and abnormally expressed genes in diseased human tissues, such as cancers, can be secreted into the bloodstream, suggesting possible marker proteins for follow-up serum ...

Summary: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled ...

Summary: Recent developments in high-throughput sequencing technologies have generated considerable demand for tools to analyse large datasets of small RNA sequences. Here, we describe a suite of web-based tools for processing plant small RNA datasets. ...