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Volume 26, Issue 1, January 2010
DISCOVERY NOTE
SEQUENCE ANALYSIS
Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 1–5, https://doi.org/10.1093/bioinformatics/btp609
ORIGINAL PAPERS
GENOME ANALYSIS
Accurate confidence aware clustering of array CGH tumor profiles
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 6–14, https://doi.org/10.1093/bioinformatics/btp603
Identification of non-Hodgkin's lymphoma prognosis signatures using the CTGDR method
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 15–21, https://doi.org/10.1093/bioinformatics/btp604
Annotation confidence score for genome annotation: a genome comparison approach
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 22–29, https://doi.org/10.1093/bioinformatics/btp613
Predictive rule inference for epistatic interaction detection in genome-wide association studies
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 30–37, https://doi.org/10.1093/bioinformatics/btp622
SEQUENCE ANALYSIS
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 38–45, https://doi.org/10.1093/bioinformatics/btp614
STRUCTURAL BIOINFORMATICS
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 46–52, https://doi.org/10.1093/bioinformatics/btp599
Automatic clustering of docking poses in virtual screening process using self-organizing map
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 53–60, https://doi.org/10.1093/bioinformatics/btp623
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 61–67, https://doi.org/10.1093/bioinformatics/btp627
GENE EXPRESSION
Reporting bias when using real data sets to analyze classification performance
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 68–76, https://doi.org/10.1093/bioinformatics/btp605
Computational protein profile similarity screening for quantitative mass spectrometry experiments
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 77–83, https://doi.org/10.1093/bioinformatics/btp607
ARH: predicting splice variants from genome-wide data with modified entropy
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 84–90, https://doi.org/10.1093/bioinformatics/btp626
SYSTEMS BIOLOGY
Identification of microRNA activity by Targets' Reverse EXpression
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 91–97, https://doi.org/10.1093/bioinformatics/btp598
Methods for combining peptide intensities to estimate relative protein abundance
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 98–103, https://doi.org/10.1093/bioinformatics/btp610
Simulation-based model selection for dynamical systems in systems and population biology
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 104–110, https://doi.org/10.1093/bioinformatics/btp619
DATA AND TEXT MINING
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 111–119, https://doi.org/10.1093/bioinformatics/btp602
APPLICATIONS NOTE
GENOME ANALYSIS
Targeted interrogation of copy number variation using SCIMMkit
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 120–122, https://doi.org/10.1093/bioinformatics/btp606
SEQUENCE ANALYSIS
MicroRazerS: rapid alignment of small RNA reads
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 123–124, https://doi.org/10.1093/bioinformatics/btp601
NGSView: an extensible open source editor for next-generation sequencing data
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 125–126, https://doi.org/10.1093/bioinformatics/btp611
inGAP: an integrated next-generation genome analysis pipeline
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 127–129, https://doi.org/10.1093/bioinformatics/btp615
PHYLOGENETICS
Ancestors 1.0: a web server for ancestral sequence reconstruction
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 130–131, https://doi.org/10.1093/bioinformatics/btp600
MATICCE: mapping transitions in continuous character evolution
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 132–133, https://doi.org/10.1093/bioinformatics/btp625
GENE EXPRESSION
The gputools package enables GPU computing in R
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 134–135, https://doi.org/10.1093/bioinformatics/btp608
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 136–138, https://doi.org/10.1093/bioinformatics/btp612
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 139–140, https://doi.org/10.1093/bioinformatics/btp616
SYSTEMS BIOLOGY
SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 141–142, https://doi.org/10.1093/bioinformatics/btp617
GATE: software for the analysis and visualization of high-dimensional time series expression data
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 143–144, https://doi.org/10.1093/bioinformatics/btp628
DATA AND TEXT MINING
Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 145–146, https://doi.org/10.1093/bioinformatics/btp618
GeneE: Gene and protein query expansion with disambiguation
Bioinformatics, Volume 26, Issue 1, January 2010, Pages 147–148, https://doi.org/10.1093/bioinformatics/btp597
