Bioinformatics - recent issues
Sun Apr 24 04:38:55 EDT 2011
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aCGH.Spline--an R package for aCGH dye bias normalization

PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies

Histogram-based DNA analysis for the visualization of chromosome, genome and species information

SplamiR--prediction of spliced miRNAs in plants

MemLoci: predicting subcellular localization of membrane proteins in eukaryotes

Identifying discriminative classification-based motifs in biological sequences

A probabilistic model of nuclear import of proteins

Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map

MrBayes on a Graphics Processing Unit

Structure-based de novo prediction of zinc-binding sites in proteins of unknown function

Mixtures of common t-factor analyzers for clustering high-dimensional microarray data

Large-scale learning of combinatorial transcriptional dynamics from gene expression

A wholly defined Agilent microarray spike-in dataset

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

Customizable views on semantically integrated networks for systems biology

Comparative visualization of genetic and physical maps with Strudel

GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments

GeCo++: a C++ library for genomic features computation and annotation in the presence of variants

TEQC: an R package for quality control in target capture experiments

Agos--a universal web tool for GW Argonaute-binding domain prediction

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics

Rapid membrane protein topology prediction

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins

Rigid substructure search

SC2ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

ogaraK: a population genetics simulator for malaria

High-throughput feature counting and measurement of roots

AStream: an R package for annotating LC/MS metabolomic data

Compounds In Literature (CIL): screening for compounds and relatives in PubMed

UniCarb-DB: a database resource for glycomic discovery

eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study

Performance assessment of copy number microarray platforms using a spike-in experiment

Topological entropy of DNA sequences

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

Topology and prediction of RNA pseudoknots

All-atom knowledge-based potential for RNA structure prediction and assessment

Defining an informativeness metric for clustering gene expression data

Automatically identifying and annotating mouse embryo gene expression patterns

Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets

The effects of feedback loops on disease comorbidity in human signaling networks

Interactive, multiscale navigation of large and complicated biological networks

Assigning spectrum-specific P-values to protein identifications by mass spectrometry

Connectedness of PPI network neighborhoods identifies regulatory hub proteins

Condensing biomedical journal texts through paragraph ranking

eGOB: eukaryotic Gene Order Browser

ACT: aggregation and correlation toolbox for analyses of genome tracks

Human variation database: an open-source database template for genomic discovery

Improving SNP discovery by base alignment quality

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data

ProtTest 3: fast selection of best-fit models of protein evolution

libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data

SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

SiGN-SSM: open source parallel software for estimating gene networks with state space models

BiC: a web server for calculating bimodality of coexpression between gene and protein networks

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

FNV: light-weight flash-based network and pathway viewer

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows

AGRA: analysis of gene ranking algorithms

Gene List significance at-a-glance with GeneValorization

A comprehensive protein-centric ID mapping service for molecular data integration

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures

Comments on 'Bayesian variable selection for disease classification using gene expression data'

Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome

Phage display can select over-hydrophobic sequences that may impair prediction of natural domain-peptide interactions

Conveyor: a workflow engine for bioinformatic analyses

Modeling and comparing the organization of circular genomes

B2G-FAR, a species-centered GO annotation repository

GOSSIP: a method for fast and accurate global alignment of protein structures

FISH Finder: a high-throughput tool for analyzing FISH images

Entropy-accelerated exact clustering of protein decoys

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions

Cross-platform comparison of microarray data using order restricted inference

Automated analysis of biological oscillator models using mode decomposition

HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

Annotating genes and genomes with DNA sequences extracted from biomedical articles

SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists

Network clustering: probing biological heterogeneity by sparse graphical models

A common layer of interoperability for biomedical ontologies based on OWL EL

Easyfig: a genome comparison visualizer

SHRiMP2: Sensitive yet Practical Short Read Mapping

A Ruby API to query the Ensembl database for genomic features

Gobe: an interactive, web-based tool for comparative genomic visualization

FIMO: scanning for occurrences of a given motif

uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application

fconv: format conversion, manipulation and feature computation of molecular data

LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data

tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models

PiNGO: a Cytoscape plugin to find candidate genes in biological networks

GeneTUKit: a software for document-level gene normalization

GeneReporter--sequence-based document retrieval and annotation

DDN: a caBIG(R) analytical tool for differential network analysis

ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins

Flower: extracting information from pyrosequencing data

BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID