Issue navigation
Volume 30, Issue 9, 1 May 2014
Discovery Note
Genome analysis
Characterization of the SOS meta-regulon in the human gut microbiome
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1193–1197, https://doi.org/10.1093/bioinformatics/btt753
Original Papers
Genome analysis
Subclonal variant calling with multiple samples and prior knowledge
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1198–1204, https://doi.org/10.1093/bioinformatics/btt750
Sequence analysis
Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1205–1213, https://doi.org/10.1093/bioinformatics/btu009
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1214–1219, https://doi.org/10.1093/bioinformatics/btu010
Prediction of nuclear export signals using weighted regular expressions (Wregex)
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1220–1227, https://doi.org/10.1093/bioinformatics/btu016
Exploring genome characteristics and sequence quality without a reference
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1228–1235, https://doi.org/10.1093/bioinformatics/btu023
InterProScan 5: genome-scale protein function classification
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1236–1240, https://doi.org/10.1093/bioinformatics/btu031
Phylogenetics
Evolutionary footprint of coevolving positions in genes
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1241–1249, https://doi.org/10.1093/bioinformatics/btu012
Structural bioinformatics
Evolutionary solution for the RNA design problem
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1250–1258, https://doi.org/10.1093/bioinformatics/btu001
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1259–1265, https://doi.org/10.1093/bioinformatics/btu020
Genetics and population analysis
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1266–1272, https://doi.org/10.1093/bioinformatics/btu014
Systems biology
Characterizing cancer subtypes as attractors of Hopfield networks
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1273–1279, https://doi.org/10.1093/bioinformatics/btt773
Data and text mining
Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1280–1286, https://doi.org/10.1093/bioinformatics/btu022
APPLICATIONS NOTES
GENOME ANALYSIS
PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1287–1289, https://doi.org/10.1093/bioinformatics/btt743
CGAT: computational genomics analysis toolkit
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1290–1291, https://doi.org/10.1093/bioinformatics/btt756
estMOI: estimating multiplicity of infection using parasite deep sequencing data
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1292–1294, https://doi.org/10.1093/bioinformatics/btu005
CGARS: cancer genome analysis by rank sums
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1295–1296, https://doi.org/10.1093/bioinformatics/btu011
PanGP: A tool for quickly analyzing bacterial pan-genome profile
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1297–1299, https://doi.org/10.1093/bioinformatics/btu017
SEQUENCE ANALYSIS
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1300–1301, https://doi.org/10.1093/bioinformatics/btt731
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1302–1304, https://doi.org/10.1093/bioinformatics/btt774
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1305–1307, https://doi.org/10.1093/bioinformatics/btu018
PHYLOGENETICS
PhyloJIVE: Integrating biodiversity data with the Tree of Life
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1308–1309, https://doi.org/10.1093/bioinformatics/btu024
jmodeltest.org: selection of nucleotide substitution models on the cloud
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1310–1311, https://doi.org/10.1093/bioinformatics/btu032
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1312–1313, https://doi.org/10.1093/bioinformatics/btu033
STRUCTURAL BIOINFORMATICS
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1314–1315, https://doi.org/10.1093/bioinformatics/btu002
GENE EXPRESSION
MAGIC: access portal to a cross-platform gene expression compendium for maize
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1316–1318, https://doi.org/10.1093/bioinformatics/btt739
myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1319–1321, https://doi.org/10.1093/bioinformatics/btu007
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1322–1324, https://doi.org/10.1093/bioinformatics/btu013
netClass: an R-package for network based, integrative biomarker signature discovery
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1325–1326, https://doi.org/10.1093/bioinformatics/btu025
SYSTEMS BIOLOGY
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1327–1328, https://doi.org/10.1093/bioinformatics/btt758
Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1329–1330, https://doi.org/10.1093/bioinformatics/btt770
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1331–1332, https://doi.org/10.1093/bioinformatics/btt772
INCA: a computational platform for isotopically non-stationary metabolic flux analysis
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1333–1335, https://doi.org/10.1093/bioinformatics/btu015
ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1336–1337, https://doi.org/10.1093/bioinformatics/btu019
DATABASES AND ONTOLOGIES
The EBI RDF platform: linked open data for the life sciences
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1338–1339, https://doi.org/10.1093/bioinformatics/btt765
Ontodog: a web-based ontology community view generation tool
Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1340–1342, https://doi.org/10.1093/bioinformatics/btu008
Advertisement
Advertisement