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Upcoming challenges for multiple sequence alignment methods in the high-throughput era
Network analyses in systems pharmacology
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster
An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication
Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks
Benchmarking homology detection procedures with low complexity filters
A new method for revealing correlated mutations under the structural and functional constraints in proteins
PerM
A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance
Improving phylogenetic analyses by incorporating additional information from genetic sequence databases
Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks
FRODOCK
Methyl side-chain dynamics prediction based on protein structure
Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments
aGEM
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition
Reconstructing spatiotemporal gene expression data from partial observations
Testing the hypothesis of tissue selectivity
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases–schizophrenia as a case
DiProGB
CEAS
ShortRead
PineSAP—sequence alignment and SNP identification pipeline
PhyloDet
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite
RNA-MATE
Genoscape
metahdep
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
Erratum