Merging two gene-expression studies via cross-platform normalization

Merging two gene-expression studies via cross-platform normalization - Motivation: Gene-expression microarrays are currently being applied in a variety of biomedical applications.

Optimizing the size of the sequence profiles

Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms - Motivation: Profile-based protein homology detection algorithms are valuable tools in genome annotation and protein classification.

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the m

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm - Motivation: Reliable structural modelling of protein–protein complexes has widespread application, from drug design to advancing our knowledg

A nearest neighbor approach for automated transporter prediction and categorization from protein sequences

A nearest neighbor approach for automated transporter prediction and categorization from protein sequences - Motivation: Membrane transport proteins play a crucial role in the import and export of ions, small molecules or macromolecules across biological membranes.

W-AlignACE: improved Gibbs algorithm based on more accurate position weight matrices from sequence and gene expression data

W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data - Motivation: Position weight matrices (PWMs) are widely used to depict the DNA binding preferences of transcription factors (TFs) in computational

Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DN

Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection - DNA methylation changes that are recurrent in cancer have generated great interest as potential biomarkers for the early detection and monitoring of cancer.

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data - Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1000 to several million base pairs.

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells - Only few selected cancer cells drive tumor progression and are responsible for therapy resistance.

Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays

Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays - Motivation: Oligonucleotide arrays such as Affymetrix GeneChips use multiple probes, or a probe set, to measure the abundance of mRNA of every gene of interest.