Mass spectrometry is an important technique for chemical profiling and is a major tool in proteomics, a discipline interested in large-scale studies of proteins expressed by an organism. In this paper we propose using a sparse coding algorithm for classification of mass spectrometry serum protein profiles of colorectal ...

Numerous applications in Computational Biology process molecular structures and hence require not only reliable atomic cordinates, but also correct bond order information. Regrettably, this information is not always provided in molecular databases like the Cambridge Structural Database or the Protein Data Bank. Very ...

Resequencing microarrays are a common tool for fast monitoring of individual genetic variations. Applications include diagnosis of genetic and infectious diseases and SNP prediction. Base calling is the crucial step in the analysis of resequencing data. All current base calling algorithms produce ambiguous calls on parts ...

We present a software package for fast pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and SNPs. If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is ...

Array-based analysis of chromatin immunoprecipitation data (ChIP-chip) is a powerful technique for identifying DNA target regions of individual transcription factors. Here, we present three approaches, a standard log-fold-change analysis (LFC), a basic method based on a Hidden Markov Model (HMM), and an ex- tension of ...

We introduce small molecule rotamers into the rotamer search protocol used in Rosetta to model small molecule flexibility in docking. Rosetta, a premier protein modeling suite, models side chain flexibility using discrete conformations observed in the Protein Data Bank (PDB). We mimic this concept and build small molecule ...

Post-genomic data analysis represents a new challenge to link and interpret the vast amount of raw data obtained with transcriptomic or proteomic techniques in the context of metabolic pathways. We propose a new strategy with the help of a metabolic network graph to extend PathExpress, a web-based tool to interpret gene ...

An odorant stimulus given to a bee elicits a characteristic combinatorial pattern of activity in neuronal units called glomeruli. These patterns can be measured by optical imaging, however detecting and identifying the glomeruli is a laborious task and prone to errors. Here, we present an image analysis pipeline for the ...

MicroRNAs (miRNAs) have rapidly become the focus of many cancer research studies. These small non-coding RNAs have been shown to play important roles in the regulation of oncogenes and tumor suppressors. It has also been demonstrated that miRNA expression profiles differ significantly between normal and cancerous cells, ...