Bioinformatics - recent issues
Sun Jan 24 11:53:16 EST 2010
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CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes

Joint estimation of DNA copy number from multiple platforms

MIRAGAA--a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer

Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae

Target prediction and a statistical sampling algorithm for RNA-RNA interaction

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials

Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis

Co-expression networks: graph properties and topological comparisons

Bayesian variable selection for disease classification using gene expression data

mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets

A personalized microRNA microarray normalization method using a logistic regression model

Bayesian model selection for characterizing genomic imprinting effects and patterns

Quantifying uncertainty in genotype calls

Pathway analysis using random forests with bivariate node-split for survival outcomes

SCAN: SNP and copy number annotation

AQUA: automated quality improvement for multiple sequence alignments

PyNAST: a flexible tool for aligning sequences to a template alignment

MADS+: discovery of differential splicing events from Affymetrix exon junction array data

MAVEN: a tool for visualization and functional analysis of genome-wide association results

CMap3D: a 3D visualization tool for comparative genetic maps

PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks

Expertomica Cells: analysis of cell monolayer development

VIBE 2.0: Visual Integration for Bayesian Evaluation

The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis

EGAN: exploratory gene association networks

hPDI: a database of experimental human protein-DNA interactions

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

Accurate confidence aware clustering of array CGH tumor profiles

Identification of non-Hodgkin's lymphoma prognosis signatures using the CTGDR method

Annotation confidence score for genome annotation: a genome comparison approach

Predictive rule inference for epistatic interaction detection in genome-wide association studies

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere

Automatic clustering of docking poses in virtual screening process using self-organizing map

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

Reporting bias when using real data sets to analyze classification performance

Computational protein profile similarity screening for quantitative mass spectrometry experiments

ARH: predicting splice variants from genome-wide data with modified entropy

Identification of microRNA activity by Targets' Reverse EXpression

Methods for combining peptide intensities to estimate relative protein abundance

Simulation-based model selection for dynamical systems in systems and population biology

Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D

Targeted interrogation of copy number variation using SCIMMkit

MicroRazerS: rapid alignment of small RNA reads

NGSView: an extensible open source editor for next-generation sequencing data

inGAP: an integrated next-generation genome analysis pipeline

Ancestors 1.0: a web server for ancestral sequence reconstruction

MATICCE: mapping transitions in continuous character evolution

The gputools package enables GPU computing in R

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks

GATE: software for the analysis and visualization of high-dimensional time series expression data

Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations

GeneE: Gene and protein query expansion with disambiguation

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

A Bayesian approach to the alignment of mass spectra

Efficient estimation of pairwise distances between genomes

Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

Inferring relative proportions of DNA variants from sequencing electropherograms

Significant speedup of database searches with HMMs by search space reduction with PSSM family models

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

Detailing regulatory networks through large scale data integration

INTERSNP: genome-wide interaction analysis guided by a priori information

Pathway identification by network pruning in the metabolic network of Escherichia coli

Model aggregation: a building-block approach to creating large macromolecular regulatory networks

Estimating population haplotype frequencies from pooled SNP data using incomplete database information

Predicting citation count of Bioinformatics papers within four years of publication

A novel method for mining highly imbalanced high-throughput screening data in PubChem

CRISPI: a CRISPR interactive database

ABWGAT: anchor-based whole genome analysis tool

G-compass: a web-based comparative genome browser between human and other vertebrate genomes

Exon Array Analyzer: a web interface for Affymetrix exon array analysis

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'