Bioinformatics - recent issues
Sun May 9 22:44:09 EDT 2010
Home: http://bioinformatics.oxfordjournals.org
Feed: http://bioinformatics.oxfordjournals.org/rss/recent.xml

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

Correction of sequencing errors in a mixed set of reads

Structural variation analysis with strobe reads

Quality assessment of protein model-structures using evolutionary conservation

Supervised normalization of microarrays

Meta-analysis for pathway enrichment analysis when combining multiple genomic studies

Streamlining the construction of large-scale dynamic models using generic kinetic equations

An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells

Permutation importance: a corrected feature importance measure

A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval

partDSA: deletion/substitution/addition algorithm for partitioning the covariate space in prediction

ACCUSA--accurate SNP calling on draft genomes

CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs

Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures

Studying the co-evolution of protein families with the Mirrortree web server

DensiTree: making sense of sets of phylogenetic trees

VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters

Modular analysis of gene expression data with R

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks

Payao: a community platform for SBML pathway model curation

SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology

An extended IUPAC nomenclature code for polymorphic nucleic acids

Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?

LOTUS, a new domain associated with small RNA pathways in the germline

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

Localized motif discovery in gene regulatory sequences

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking

Alignment-free local structural search by writhe decomposition

Reducing the algorithmic variability in transcriptome-based inference

Integrative mixture of experts to combine clinical factors and gene markers

A signal-noise model for significance analysis of ChIP-seq with negative control

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations

Pathway discovery in metabolic networks by subgraph extraction

Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network

PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways

Going from where to why--interpretable prediction of protein subcellular localization

Identification of genetic network dynamics with unate structure

Building a high-quality sense inventory for improved abbreviation disambiguation

EuGene-maize: a web site for maize gene prediction

PanCGHweb: a web tool for genotype calling in pangenome CGH data

SeSAW: balancing sequence and structural information in protein functional mapping

ArchSchema: a tool for interactive graphing of related Pfam domain architectures

WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data

HALO--a Java framework for precise transcript half-life determination

CoP: a database for characterizing co-expressed gene modules with biological information in plants

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations

TopoGSA: network topological gene set analysis

TiSGeD: a database for tissue-specific genes

Curators of the world unite: the International Society of Biocuration

Biased hosting of intronic microRNA genes

Composition bias and the origin of ORFan genes

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations

A min-cut algorithm for the consistency problem in multiple sequence alignment

Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules

High quality SNP calling using Illumina data at shallow coverage

SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank

Statistical expression deconvolution from mixed tissue samples

Post hoc power estimation in large-scale multiple testing problems

The power of protein interaction networks for associating genes with diseases

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison

Inferring cluster-based networks from differently stimulated multiple time-course gene expression data

Cross-species common regulatory network inference without requirement for prior gene affiliation

A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems

Domain adaptation for semantic role labeling in the biomedical domain

SPICi: a fast clustering algorithm for large biological networks

Modeling sample variables with an Experimental Factor Ontology

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

An Ergatis-based prokaryotic genome annotation web server

ScripTree: scripting phylogenetic graphics

ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules

BioNet: an R-Package for the functional analysis of biological networks

CPFP: a central proteomics facilities pipeline

SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses