Medical Research Articles Published in January 2011

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01/01/2011
Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. (PubMedID: 21679429) BMC genomics
01/01/2011
Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. (PubMedID: 21679437) BMC genomics
01/01/2011
Minimal regulatory spaces in yeast genomes. (PubMedID: 21679449) BMC genomics
01/01/2011
Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize. (PubMedID: 21679461) BMC genomics
01/01/2011
Implication of next-generation sequencing on association studies. (PubMedID: 21682891) BMC genomics
01/01/2011
Introduction: Validation methods for function genome annotation. (PubMedID: 21810202) BMC genomics
01/01/2011
Genome-wide protein localization prediction strategies for gram negative bacteria. (PubMedID: 21810203) BMC genomics
01/01/2011
Synergistic use of plant-prokaryote comparative genomics for functional annotations. (PubMedID: 21810204) BMC genomics
01/01/2011
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. (PubMedID: 21810205) BMC genomics
01/01/2011
Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. (PubMedID: 21810206) BMC genomics
01/01/2011
Filtering "genic" open reading frames from genomic DNA samples for advanced annotation. (PubMedID: 21810207) BMC genomics
01/01/2011
Improved genome annotation through untargeted detection of pathway-specific metabolites. (PubMedID: 21810208) BMC genomics
01/01/2011
A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans. (PubMedID: 21810209) BMC genomics
01/01/2011
Environment sensing and response mediated by ABC transporters. (PubMedID: 21810210) BMC genomics
01/01/2011
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny. (PubMedID: 21663614) BMC genomics
01/01/2011
Identification of SNP and SSR markers in eggplant using RAD tag sequencing. (PubMedID: 21663628) BMC genomics
01/01/2011
A tissue-specific landscape of sense/antisense transcription in the mouse intestine. (PubMedID: 21663663) BMC genomics
01/01/2011
Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling. (PubMedID: 21663664) BMC genomics
01/01/2011
Identification of novel soybean microRNAs involved in abiotic and biotic stresses. (PubMedID: 21663675) BMC genomics
01/01/2011
A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella. (PubMedID: 21663692) BMC genomics
01/01/2011
Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna. (PubMedID: 21668940) BMC genomics
01/01/2011
Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate. (PubMedID: 21668972) BMC genomics
01/01/2011
Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). (PubMedID: 21668978) BMC genomics
01/01/2011
Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi. (PubMedID: 21668986) BMC genomics
01/01/2011
Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. (PubMedID: 21669002) BMC genomics
01/01/2011
Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes. (PubMedID: 21672188) BMC genomics
01/01/2011
Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome. (PubMedID: 21645357) BMC genomics
01/01/2011
RNA-seq: technical variability and sampling. (PubMedID: 21645359) BMC genomics
01/01/2011
Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence. (PubMedID: 21645368) BMC genomics
01/01/2011
Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques. (PubMedID: 21645414) BMC genomics
01/01/2011
A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae. (PubMedID: 21649883) BMC genomics
01/01/2011
Dissecting gene expression in mosquito. (PubMedID: 21649884) BMC genomics
01/01/2011
De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. (PubMedID: 21649902) BMC genomics
01/01/2011
Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.). (PubMedID: 21649926) BMC genomics
01/01/2011
Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif. (PubMedID: 21649932) BMC genomics
01/01/2011
Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus. (PubMedID: 21651758) BMC genomics
01/01/2011
Single nucleotide polymorphism discovery in elite North American potato germplasm. (PubMedID: 21658273) BMC genomics
01/01/2011
The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium. (PubMedID: 21627782) BMC genomics
01/01/2011
Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes. (PubMedID: 21627783) BMC genomics
01/01/2011
The development and characterization of a 60K SNP chip for chicken. (PubMedID: 21627800) BMC genomics
01/01/2011
Global analysis of gene expression in response to L-Cysteine deprivation in the anaerobic protozoan parasite Entamoeba histolytica. (PubMedID: 21627801) BMC genomics
01/01/2011
MicroRNA profiling of rhesus macaque embryonic stem cells. (PubMedID: 21627802) BMC genomics
01/01/2011
Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. (PubMedID: 21627805) BMC genomics
01/01/2011
BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae). (PubMedID: 21627820) BMC genomics
01/01/2011
Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions. (PubMedID: 21627843) BMC genomics
01/01/2011
Seeds for effective oligonucleotide design. (PubMedID: 21627845) BMC genomics
01/01/2011
Polyomic profiling reveals significant hepatic metabolic alterations in glucagon-receptor (GCGR) knockout mice: implications on anti-glucagon therapies for diabetes. (PubMedID: 21631939) BMC genomics
01/01/2011
Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential. (PubMedID: 21631945) BMC genomics
01/01/2011
Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. (PubMedID: 21635727) BMC genomics
01/01/2011
Retraction. MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori). (PubMedID: 21635743) BMC genomics
01/01/2011
ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence. (PubMedID: 21635747) BMC genomics
01/01/2011
Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis. (PubMedID: 21635767) BMC genomics
01/01/2011
Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides. (PubMedID: 21635780) BMC genomics
01/01/2011
Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae. (PubMedID: 21635781) BMC genomics
01/01/2011
A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). (PubMedID: 21639890) BMC genomics
01/01/2011
A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues. (PubMedID: 21639908) BMC genomics
01/01/2011
Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity. (PubMedID: 21639920) BMC genomics
01/01/2011
Analysis of common bean expressed sequence tags identifies sulfur metabolic pathways active in seed and sulfur-rich proteins highly expressed in the absence of phaseolin and major lectins. (PubMedID: 21615926) BMC genomics
01/01/2011
The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation. (PubMedID: 21619626) BMC genomics
01/01/2011
Genomic features and computational identification of human microRNAs under long-range developmental regulation. (PubMedID: 21619633) BMC genomics
01/01/2011
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding. (PubMedID: 21619637) BMC genomics
01/01/2011
Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene. (PubMedID: 21605348) BMC genomics
01/01/2011
A canine model of Cohen syndrome: Trapped Neutrophil Syndrome. (PubMedID: 21605373) BMC genomics
01/01/2011
Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing. (PubMedID: 21605378) BMC genomics
01/01/2011
Novel transposable elements from Anopheles gambiae. (PubMedID: 21605407) BMC genomics
01/01/2011
Genes in the terminal regions of orthopoxvirus genomes experience adaptive molecular evolution. (PubMedID: 21605412) BMC genomics
01/01/2011
GiSAO.db: a database for ageing research. (PubMedID: 21609420) BMC genomics
01/01/2011
Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site. (PubMedID: 21609454) BMC genomics
01/01/2011
Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.). (PubMedID: 21609476) BMC genomics
01/01/2011
Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. (PubMedID: 21609489) BMC genomics
01/01/2011
A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population. (PubMedID: 21609492) BMC genomics
01/01/2011
Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: role of the LINE-encoded endonuclease. (PubMedID: 21612594) BMC genomics
01/01/2011
Organization and molecular evolution of a disease-resistance gene cluster in coffee trees. (PubMedID: 21575174) BMC genomics
01/01/2011
Genome-wide profiling of G protein-coupled receptors in cerebellar granule neurons using high-throughput, real-time PCR. (PubMedID: 21575240) BMC genomics
01/01/2011
Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon. (PubMedID: 21575266) BMC genomics
01/01/2011
Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing. (PubMedID: 21592371) BMC genomics
01/01/2011
Preferential regulation of miRNA targets by environmental chemicals in the human genome. (PubMedID: 21592377) BMC genomics
01/01/2011
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. (PubMedID: 21592414) BMC genomics
01/01/2011
454 sequencing of pooled BAC clones on chromosome 3H of barley. (PubMedID: 21592415) BMC genomics
01/01/2011
BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). (PubMedID: 21595870) BMC genomics
01/01/2011
Horizontal gene transfer in silkworm, Bombyx mori. (PubMedID: 21595916) BMC genomics
01/01/2011
Integration of Solexa sequences on an ultradense genetic map in Brassica rapa L. (PubMedID: 21595929) BMC genomics
01/01/2011
A simple Bayesian estimate of direct RNAi gene regulation events from differential gene expression profiles. (PubMedID: 21599879) BMC genomics
01/01/2011
An untargeted multi-technique metabolomics approach to studying intracellular metabolites of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin. (PubMedID: 21599895) BMC genomics
01/01/2011
Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. (PubMedID: 21599934) BMC genomics
01/01/2011
Understanding Streptococcus suis serotype 2 infection in pigs through a transcriptional approach. (PubMedID: 21599948) BMC genomics
01/01/2011
The aspartic proteinase family of three Phytophthora species. (PubMedID: 21599950) BMC genomics
01/01/2011
Genotype-specific responses in Atlantic salmon (Salmo salar) subject to dietary fish oil replacement by vegetable oil: a liver transcriptomic analysis. (PubMedID: 21599965) BMC genomics
01/01/2011
Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach. (PubMedID: 21599977) BMC genomics
01/01/2011
Identification of gene expression changes associated with the initiation of diapause in the brain of the cotton bollworm, Helicoverpa armigera. (PubMedID: 21569297) BMC genomics
01/01/2011
Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes. (PubMedID: 21569303) BMC genomics
01/01/2011
Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources. (PubMedID: 21569310) BMC genomics
01/01/2011
Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope. (PubMedID: 21569315) BMC genomics
01/01/2011
Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. (PubMedID: 21569327) BMC genomics
01/01/2011
Transcriptional double-autorepression feedforward circuits act for multicellularity and nervous system development. (PubMedID: 21569329) BMC genomics
01/01/2011
Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies. (PubMedID: 21569352) BMC genomics
01/01/2011
Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. (PubMedID: 21569359) BMC genomics
01/01/2011
The effect of measurement error of phenotypes on genome wide association studies. (PubMedID: 21569388) BMC genomics
01/01/2011
QTL underlying resistance to two HG types of Heterodera glycines found in soybean cultivar 'L-10'. (PubMedID: 21569389) BMC genomics
01/01/2011
Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. (PubMedID: 21569398) BMC genomics
01/01/2011
Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. (PubMedID: 21569405) BMC genomics
01/01/2011
Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues. (PubMedID: 21569431) BMC genomics
01/01/2011
Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae). (PubMedID: 21569439) BMC genomics
01/01/2011
Escherichia coli genome-wide promoter analysis: identification of additional AtoC binding target elements. (PubMedID: 21569465) BMC genomics
01/01/2011
A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly. (PubMedID: 21569561) BMC genomics
01/01/2011
A comprehensive platform for highly multiplexed mammalian functional genetic screens. (PubMedID: 21548937) BMC genomics
01/01/2011
Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties. (PubMedID: 21548945) BMC genomics
01/01/2011
Eukaryotic protein kinases (ePKs) of the helminth parasite Schistosoma mansoni. (PubMedID: 21548963) BMC genomics
01/01/2011
Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. (PubMedID: 21554708) BMC genomics
01/01/2011
Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. (PubMedID: 21554714) BMC genomics
01/01/2011
The impact of oxygen on the transcriptome of recombinant S. cerevisiae and P. pastoris - a comparative analysis. (PubMedID: 21554735) BMC genomics
01/01/2011
Probing genomic diversity and evolution of Streptococcus suis serotype 2 by NimbleGen tiling arrays. (PubMedID: 21554741) BMC genomics
01/01/2011
Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways. (PubMedID: 21569240) BMC genomics
01/01/2011
Transcriptional profiling of fetal hypothalamic TRH neurons. (PubMedID: 21569245) BMC genomics
01/01/2011
The midgut transcriptome of Phlebotomus (Larroussius) perniciosus, a vector of Leishmania infantum: comparison of sugar fed and blood fed sand flies. (PubMedID: 21569254) BMC genomics
01/01/2011
The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects. (PubMedID: 21569260) BMC genomics
01/01/2011
Evolution of an endofungal lifestyle: Deductions from the Burkholderia rhizoxinica genome. (PubMedID: 21539752) BMC genomics
01/01/2011
Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. (PubMedID: 21542930) BMC genomics
01/01/2011
Characterization of age-related gene expression profiling in bone marrow and epididymal adipocytes. (PubMedID: 21545734) BMC genomics
01/01/2011
Novel simple sequence repeats (SSRs) detected by ND-FISH in heterochromatin of Drosophila melanogaster. (PubMedID: 21521504) BMC genomics
01/01/2011
Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome. (PubMedID: 21521529) BMC genomics
01/01/2011
Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element. (PubMedID: 21524285) BMC genomics
01/01/2011
Transcriptomic analysis of milk somatic cells in mastitis resistant and susceptible sheep upon challenge with Staphylococcus epidermidis and Staphylococcus aureus. (PubMedID: 21527017) BMC genomics
01/01/2011
The testosterone-dependent and independent transcriptional networks in the hypothalamus of Gpr54 and Kiss1 knockout male mice are not fully equivalent. (PubMedID: 21527035) BMC genomics
01/01/2011
Nucleosome DNA sequence structure of isochores. (PubMedID: 21510861) BMC genomics
01/01/2011
Recent acquisition of imprinting at the rodent Sfmbt2 locus correlates with insertion of a large block of miRNAs. (PubMedID: 21510876) BMC genomics
01/01/2011
Interactions of a pesticide/heavy metal mixture in marine bivalves: a transcriptomic assessment. (PubMedID: 21496282) BMC genomics
01/01/2011
Identification of novel target genes of nerve growth factor (NGF) in human mastocytoma cell line (HMC-1 (V560G c-Kit)) by transcriptome analysis. (PubMedID: 21501463) BMC genomics
01/01/2011
First complete genome sequence of infectious laryngotracheitis virus. (PubMedID: 21501528) BMC genomics
01/01/2011
Characterization and genome sequencing of two Propionibacterium acnes phages displaying pseudolysogeny. (PubMedID: 21504575) BMC genomics
01/01/2011
Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. (PubMedID: 21504589) BMC genomics
01/01/2011
Gene expression patterns in four brain areas associate with quantitative measure of estrous behavior in dairy cows. (PubMedID: 21504592) BMC genomics
01/01/2011
Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains. (PubMedID: 21507216) BMC genomics
01/01/2011
Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. (PubMedID: 21507250) BMC genomics
01/01/2011
Gene expression profiles in rat mesenteric lymph nodes upon supplementation with conjugated linoleic acid during gestation and suckling. (PubMedID: 21481241) BMC genomics
01/01/2011
Copy number variation of microRNA genes in the human genome. (PubMedID: 21486463) BMC genomics
01/01/2011
Accurate and exact CNV identification from targeted high-throughput sequence data. (PubMedID: 21486468) BMC genomics
01/01/2011
Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements. (PubMedID: 21486474) BMC genomics
01/01/2011
A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs. (PubMedID: 21486491) BMC genomics
01/01/2011
Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model. (PubMedID: 21489287) BMC genomics
01/01/2011
Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences. (PubMedID: 21492448) BMC genomics
01/01/2011
A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. (PubMedID: 21492453) BMC genomics
01/01/2011
Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars. (PubMedID: 21492454) BMC genomics
01/01/2011
De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing. (PubMedID: 21492485) BMC genomics
01/01/2011
FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens. (PubMedID: 21496229) BMC genomics
01/01/2011
Differences in TCDD-elicited gene expression profiles in human HepG2, mouse Hepa1c1c7 and rat H4IIE hepatoma cells. (PubMedID: 21496263) BMC genomics
01/01/2011
Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes. (PubMedID: 21496274) BMC genomics
01/01/2011
Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize. (PubMedID: 21473768) BMC genomics
01/01/2011
Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing. (PubMedID: 21473771) BMC genomics
01/01/2011
A first generation integrated map of the rainbow trout genome. (PubMedID: 21473775) BMC genomics
01/01/2011
Nuclear factor I revealed as family of promoter binding transcription activators. (PubMedID: 21473784) BMC genomics
01/01/2011
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. (PubMedID: 21457549) BMC genomics
01/01/2011
Comparative genomic analyses identify common molecular pathways modulated upon exposure to low doses of arsenic and cadmium. (PubMedID: 21457566) BMC genomics
01/01/2011
A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. (PubMedID: 21457569) BMC genomics
01/01/2011
Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes. (PubMedID: 21463507) BMC genomics
01/01/2011
Deep sequencing analysis of the developing mouse brain reveals a novel microRNA. (PubMedID: 21466694) BMC genomics
01/01/2011
Expansion and functional diversification of a leucyl aminopeptidase family that encodes the major protein constituents of Drosophila sperm. (PubMedID: 21466698) BMC genomics
01/01/2011
A cell spot microarray method for production of high density siRNA transfection microarrays. (PubMedID: 21443765) BMC genomics
01/01/2011
Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line. (PubMedID: 21443807) BMC genomics
01/01/2011
Taxonomically restricted genes are associated with the evolution of sociality in the honey bee. (PubMedID: 21447185) BMC genomics
01/01/2011
Rice-Map: a new-generation rice genome browser. (PubMedID: 21450055) BMC genomics
01/01/2011
RS-SNP: a random-set method for genome-wide association studies. (PubMedID: 21450072) BMC genomics
01/01/2011
Stochastic variation of transcript abundance in C57BL/6J mice. (PubMedID: 21450099) BMC genomics
01/01/2011
Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals. (PubMedID: 21453472) BMC genomics
01/01/2011
High-throughput sequencing of Astrammina rara: sampling the giant genome of a giant foraminiferan protist. (PubMedID: 21453490) BMC genomics
01/01/2011
Reliability analysis of the Ahringer Caenorhabditis elegans RNAi feeding library: a guide for genome-wide screens. (PubMedID: 21453524) BMC genomics
01/01/2011
Modulation of gene expression in heart and liver of hibernating black bears (Ursus americanus). (PubMedID: 21453527) BMC genomics
01/01/2011
Alu distribution and mutation types of cancer genes. (PubMedID: 21429208) BMC genomics
01/01/2011
Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing. (PubMedID: 21435219) BMC genomics
01/01/2011
Proteomic analysis of the marine diatom Thalassiosira pseudonana upon exposure to benzo(a)pyrene. (PubMedID: 21435224) BMC genomics
01/01/2011
Comparative transcriptome profiling of amyloid precursor protein family members in the adult cortex. (PubMedID: 21435241) BMC genomics
01/01/2011
Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi. (PubMedID: 21435244) BMC genomics
01/01/2011
Rhythms and synchronization patterns in gene expression in the Aedes aegypti mosquito. (PubMedID: 21414217) BMC genomics
01/01/2011
Identification and characterization of maize microRNAs involved in the very early stage of seed germination. (PubMedID: 21414237) BMC genomics
01/01/2011
Development of the piggyBac transposable system for Plasmodium berghei and its application for random mutagenesis in malaria parasites. (PubMedID: 21418605) BMC genomics
01/01/2011
RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. (PubMedID: 21418615) BMC genomics
01/01/2011
Moult cycle specific differential gene expression profiling of the crab Portunus pelagicus. (PubMedID: 21396120) BMC genomics
01/01/2011
Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels. (PubMedID: 21401935) BMC genomics
01/01/2011
Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice. (PubMedID: 21406116) BMC genomics
01/01/2011
Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). (PubMedID: 21410945) BMC genomics
01/01/2011
Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation. (PubMedID: 21410957) BMC genomics
01/01/2011
Cross species comparison of C/EBPa and PPAR? profiles in mouse and human adipocytes reveals interdependent retention of binding sites. (PubMedID: 21410980) BMC genomics
01/01/2011
Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization. (PubMedID: 21385342) BMC genomics
01/01/2011
Genome wide analysis of the bovine mucin genes and their gastrointestinal transcription profile. (PubMedID: 21385362) BMC genomics
01/01/2011
Gene expression analyses of immune responses in Atlantic salmon during early stages of infection by salmon louse (Lepeophtheirus salmonis) revealed bi-phasic responses coinciding with the copepod-chalimus transition. (PubMedID: 21385383) BMC genomics
01/01/2011
Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. (PubMedID: 21385395) BMC genomics
01/01/2011
Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle. (PubMedID: 21385442) BMC genomics
01/01/2011
Quantitative miRNA expression analysis using fluidigm microfluidics dynamic arrays. (PubMedID: 21388556) BMC genomics
01/01/2011
QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. (PubMedID: 21392393) BMC genomics
01/01/2011
Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. (PubMedID: 21396108) BMC genomics
01/01/2011
Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. (PubMedID: 21375742) BMC genomics
01/01/2011
Identification of microRNA-mRNA modules using microarray data. (PubMedID: 21375780) BMC genomics
01/01/2011
Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4a. (PubMedID: 21352552) BMC genomics
01/01/2011
Discovery of barley miRNAs through deep sequencing of short reads. (PubMedID: 21352554) BMC genomics
01/01/2011
In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis. (PubMedID: 21352611) BMC genomics
01/01/2011
Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. (PubMedID: 21356090) BMC genomics
01/01/2011
Gene expression throughout a vertebrate's embryogenesis. (PubMedID: 21356103) BMC genomics
01/01/2011
A proteomics approach to decipher the molecular nature of planarian stem cells. (PubMedID: 21356107) BMC genomics
01/01/2011
ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. (PubMedID: 21356108) BMC genomics
01/01/2011
Identification of surface proteins in Enterococcus faecalis V583. (PubMedID: 21362161) BMC genomics
01/01/2011
A further insight into the sialome of the tropical bont tick, Amblyomma variegatum. (PubMedID: 21362191) BMC genomics
01/01/2011
Distinct colonization patterns and cDNA-AFLP transcriptome profiles in compatible and incompatible interactions between melon and different races of Fusarium oxysporum f. sp. melonis. (PubMedID: 21338485) BMC genomics
01/01/2011
Comparative tissue transcriptomics reveal prompt inter-organ communication in response to local bacterial kidney infection. (PubMedID: 21338499) BMC genomics
01/01/2011
Alteration of gene expression by alcohol exposure at early neurulation. (PubMedID: 21338521) BMC genomics
01/01/2011
Consistency of gene starts among Burkholderia genomes. (PubMedID: 21342528) BMC genomics
01/01/2011
Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions. (PubMedID: 21342532) BMC genomics
01/01/2011
Genomic characteristics of cattle copy number variations. (PubMedID: 21345189) BMC genomics
01/01/2011
Characterization of statistical features for plant microRNA prediction. (PubMedID: 21324149) BMC genomics
01/01/2011
Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins. (PubMedID: 21324157) BMC genomics
01/01/2011
Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1. (PubMedID: 21324158) BMC genomics
01/01/2011
Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows. (PubMedID: 21324170) BMC genomics
01/01/2011
Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality. (PubMedID: 21324179) BMC genomics
01/01/2011
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. (PubMedID: 21324190) BMC genomics
01/01/2011
Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective. (PubMedID: 21324191) BMC genomics
01/01/2011
The living microarray: a high-throughput platform for measuring transcription dynamics in single cells. (PubMedID: 21324195) BMC genomics
01/01/2011
High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum. (PubMedID: 21324207) BMC genomics
01/01/2011
Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). (PubMedID: 21329497) BMC genomics
01/01/2011
Applicability of RNA standards for evaluating RT-qPCR assays and platforms. (PubMedID: 21332979) BMC genomics
01/01/2011
RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum. (PubMedID: 21332983) BMC genomics
01/01/2011
Identification, variation and transcription of pneumococcal repeat sequences. (PubMedID: 21333003) BMC genomics
01/01/2011
TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. (PubMedID: 21333005) BMC genomics
01/01/2011
Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. (PubMedID: 21310019) BMC genomics
01/01/2011
Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). (PubMedID: 21310031) BMC genomics
01/01/2011
Functional genomics of the horn fly, Haematobia irritans (Linnaeus, 1758). (PubMedID: 21310032) BMC genomics
01/01/2011
Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. (PubMedID: 21310087) BMC genomics
01/01/2011
The genetic interaction network of CCW12, a Saccharomyces cerevisiae gene required for cell wall integrity during budding and formation of mating projections. (PubMedID: 21320323) BMC genomics
01/01/2011
Bimodal distribution of RNA expression levels in human skeletal muscle tissue. (PubMedID: 21299892) BMC genomics
01/01/2011
De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. (PubMedID: 21303537) BMC genomics
01/01/2011
Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.). (PubMedID: 21303556) BMC genomics
01/01/2011
Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa. (PubMedID: 21306613) BMC genomics
01/01/2011
Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. (PubMedID: 21306619) BMC genomics
01/01/2011
The mining of toxin-like polypeptides from EST database by single residue distribution analysis. (PubMedID: 21281459) BMC genomics
01/01/2011
A unified framework for multi-locus association analysis of both common and rare variants. (PubMedID: 21281506) BMC genomics
01/01/2011
GC content around splice sites affects splicing through pre-mRNA secondary structures. (PubMedID: 21281513) BMC genomics
01/01/2011
General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq. (PubMedID: 21284834) BMC genomics
01/01/2011
Exome localization of complex disease association signals. (PubMedID: 21284873) BMC genomics
01/01/2011
Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018. (PubMedID: 21284892) BMC genomics
01/01/2011
Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries. (PubMedID: 21291514) BMC genomics
01/01/2011
Differential gene expression in liver and small intestine from lactating rats compared to age-matched virgin controls detects increased mRNA of cholesterol biosynthetic genes. (PubMedID: 21291544) BMC genomics
01/01/2011
Obesity resistant mechanisms in the Lean polygenic mouse model as indicated by liver transcriptome and expression of selected genes in skeletal muscle. (PubMedID: 21291556) BMC genomics
01/01/2011
Independent component and pathway-based analysis of miRNA-regulated gene expression in a model of type 1 diabetes. (PubMedID: 21294859) BMC genomics
01/01/2011
Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. (PubMedID: 21266089) BMC genomics
01/01/2011
Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing. (PubMedID: 21269450) BMC genomics
01/01/2011
Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library. (PubMedID: 21269452) BMC genomics
01/01/2011
Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations. (PubMedID: 21269469) BMC genomics
01/01/2011
Gene set enrichment analysis of microarray data from Pimephales promelas (Rafinesque), a non-mammalian model organism. (PubMedID: 21269471) BMC genomics
01/01/2011
Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology. (PubMedID: 21269493) BMC genomics
01/01/2011
Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide. (PubMedID: 21269496) BMC genomics
01/01/2011
Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis. (PubMedID: 21269501) BMC genomics
01/01/2011
Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates. (PubMedID: 21269504) BMC genomics
01/01/2011
Characterization of the past and current duplication activities in the human 22q11.2 region. (PubMedID: 21269513) BMC genomics
01/01/2011
Analysis of nucleosome positioning determined by DNA helix curvature in the human genome. (PubMedID: 21269520) BMC genomics
01/01/2011
Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies. (PubMedID: 21269523) BMC genomics
01/01/2011
PNAC: a protein nucleolar association classifier. (PubMedID: 21272300) BMC genomics
01/01/2011
Comparative genomics allowed the identification of drug targets against human fungal pathogens. (PubMedID: 21272313) BMC genomics
01/01/2011
Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. (PubMedID: 21272351) BMC genomics
01/01/2011
Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. (PubMedID: 21272354) BMC genomics
01/01/2011
Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region. (PubMedID: 21272357) BMC genomics
01/01/2011
Eukaryote-wide sequence analysis of mitochondrial ß-barrel outer membrane proteins. (PubMedID: 21272379) BMC genomics
01/01/2011
Evolution of major milk proteins in Mus musculus and Mus spretus mouse species: a genoproteomic analysis. (PubMedID: 21276224) BMC genomics
01/01/2011
Population transcriptomics of Drosophila melanogaster females. (PubMedID: 21276238) BMC genomics
01/01/2011
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti. (PubMedID: 21276245) BMC genomics
01/01/2011
ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. (PubMedID: 21276248) BMC genomics
01/01/2011
Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals. (PubMedID: 21276253) BMC genomics
01/01/2011
Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements. (PubMedID: 21276256) BMC genomics
01/01/2011
An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research. (PubMedID: 21276261) BMC genomics
01/01/2011
Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae. (PubMedID: 21276262) BMC genomics
01/01/2011
Development of a novel multiplex DNA microarray for Fusarium graminearum and analysis of azole fungicide responses. (PubMedID: 21255412) BMC genomics
01/01/2011
Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. (PubMedID: 21255432) BMC genomics
01/01/2011
Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription. (PubMedID: 21255435) BMC genomics
01/01/2011
Selective phenotyping, entropy reduction, and the mastermind game. (PubMedID: 22014271) BMC bioinformatics
01/01/2011
Dual channel rank-based intensity weighting for quantitative co-localization of microscopy images. (PubMedID: 22017789) BMC bioinformatics
01/01/2011
A motif-independent metric for DNA sequence specificity. (PubMedID: 22017798) BMC bioinformatics
01/01/2011
HOMER: a human organ-specific molecular electronic repository. (PubMedID: 22165817) BMC bioinformatics
01/01/2011
An efficient and extensible approach for compressing phylogenetic trees. (PubMedID: 22165819) BMC bioinformatics
01/01/2011
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. (PubMedID: 22165852) BMC bioinformatics
01/01/2011
Scenario driven data modelling: a method for integrating diverse sources of data and data streams. (PubMedID: 22165854) BMC bioinformatics
01/01/2011
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. (PubMedID: 22165903) BMC bioinformatics
01/01/2011
First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA. (PubMedID: 22165905) BMC bioinformatics
01/01/2011
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction. (PubMedID: 22165918) BMC bioinformatics
01/01/2011
Constructing a robust protein-protein interaction network by integrating multiple public databases. (PubMedID: 22165958) BMC bioinformatics
01/01/2011
Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets. (PubMedID: 22165960) BMC bioinformatics
01/01/2011
A CoD-based stationary control policy for intervening in large gene regulatory networks. (PubMedID: 22165980) BMC bioinformatics
01/01/2011
Analysis of cancer metabolism with high-throughput technologies. (PubMedID: 22166000) BMC bioinformatics
01/01/2011
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. (PubMedID: 22166002) BMC bioinformatics
01/01/2011
Mining FDA drug labels using an unsupervised learning technique--topic modeling. (PubMedID: 22166012) BMC bioinformatics
01/01/2011
Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. (PubMedID: 22166046) BMC bioinformatics
01/01/2011
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. (PubMedID: 22166047) BMC bioinformatics
01/01/2011
An improved border detection in dermoscopy images for density based clustering. (PubMedID: 22166058) BMC bioinformatics
01/01/2011
The NTD Nanoscope: potential applications and implementations. (PubMedID: 22166072) BMC bioinformatics
01/01/2011
A modified Stokes-Einstein equation for Aß aggregation. (PubMedID: 22166081) BMC bioinformatics
01/01/2011
Leveraging domain information to restructure biological prediction. (PubMedID: 22166097) BMC bioinformatics
01/01/2011
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments. (PubMedID: 22166114) BMC bioinformatics
01/01/2011
Selecting a single model or combining multiple models for microarray-based classifier development?--a comparative analysis based on large and diverse datasets generated from the MAQC-II project. (PubMedID: 22166133) BMC bioinformatics
01/01/2011
Validation of an arterial tortuosity measure with application to hypertension collection of clinical hypertensive patients. (PubMedID: 22166145) BMC bioinformatics
01/01/2011
SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds. (PubMedID: 21992011) BMC bioinformatics
01/01/2011
Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. (PubMedID: 21995452) BMC bioinformatics
01/01/2011
MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures. (PubMedID: 21999117) BMC bioinformatics
01/01/2011
Comparison of lists of genes based on functional profiles. (PubMedID: 21999355) BMC bioinformatics
01/01/2011
An empirical Bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry. (PubMedID: 21985394) BMC bioinformatics
01/01/2011
Enriching a biomedical event corpus with meta-knowledge annotation. (PubMedID: 21985429) BMC bioinformatics
01/01/2011
Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences. (PubMedID: 21985453) BMC bioinformatics
01/01/2011
Phamerator: a bioinformatic tool for comparative bacteriophage genomics. (PubMedID: 21991981) BMC bioinformatics
01/01/2011
Techniques for analysing pattern formation in populations of stem cells and their progeny. (PubMedID: 21991994) BMC bioinformatics
01/01/2011
The BioLexicon: a large-scale terminological resource for biomedical text mining. (PubMedID: 21992002) BMC bioinformatics
01/01/2011
Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations. (PubMedID: 21966893) BMC bioinformatics
01/01/2011
Biblio-MetReS: a bibliometric network reconstruction application and server. (PubMedID: 21975133) BMC bioinformatics
01/01/2011
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. (PubMedID: 21975162) BMC bioinformatics
01/01/2011
ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples. (PubMedID: 21977986) BMC bioinformatics
01/01/2011
Classification of microarrays; synergistic effects between normalization, gene selection and machine learning. (PubMedID: 21982277) BMC bioinformatics
01/01/2011
Microarray-based cancer prediction using single genes. (PubMedID: 21982331) BMC bioinformatics
01/01/2011
A method for computing an inventory of metazoan mitochondrial gene order rearrangements. (PubMedID: 22151086) BMC bioinformatics
01/01/2011
Multi-stage gene normalization for full-text articles with context-based species filtering for dynamic dictionary entry selection. (PubMedID: 22151087) BMC bioinformatics
01/01/2011
Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree. (PubMedID: 22151151) BMC bioinformatics
01/01/2011
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. (PubMedID: 22151178) BMC bioinformatics
01/01/2011
Genomic distance under gene substitutions. (PubMedID: 22151231) BMC bioinformatics
01/01/2011
Classifying protein-protein interaction articles using word and syntactic features. (PubMedID: 22151252) BMC bioinformatics
01/01/2011
Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index. (PubMedID: 22151279) BMC bioinformatics
01/01/2011
The rise and fall of breakpoint reuse depending on genome resolution. (PubMedID: 22151330) BMC bioinformatics
01/01/2011
The evolution of the tape measure protein: units, duplications and losses. (PubMedID: 22151602) BMC bioinformatics
01/01/2011
Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes. (PubMedID: 22151646) BMC bioinformatics
01/01/2011
Overview of the BioCreative III Workshop. (PubMedID: 22151647) BMC bioinformatics
01/01/2011
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. (PubMedID: 22151701) BMC bioinformatics
01/01/2011
Efficient algorithms for reconstructing gene content by co-evolution. (PubMedID: 22151715) BMC bioinformatics
01/01/2011
Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature. (PubMedID: 22151769) BMC bioinformatics
01/01/2011
On the weight of indels in genomic distances. (PubMedID: 22151784) BMC bioinformatics
01/01/2011
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. (PubMedID: 22151823) BMC bioinformatics
01/01/2011
Origin and evolution of gene families in Bacteria and Archaea. (PubMedID: 22151831) BMC bioinformatics
01/01/2011
Detection of interaction articles and experimental methods in biomedical literature. (PubMedID: 22151872) BMC bioinformatics
01/01/2011
STELLAR: fast and exact local alignments. (PubMedID: 22151882) BMC bioinformatics
01/01/2011
The gene normalization task in BioCreative III. (PubMedID: 22151901) BMC bioinformatics
01/01/2011
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development. (PubMedID: 22151910) BMC bioinformatics
01/01/2011
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. (PubMedID: 22151929) BMC bioinformatics
01/01/2011
Approximating the double-cut-and-join distance between unsigned genomes. (PubMedID: 22151948) BMC bioinformatics
01/01/2011
BioCreative III interactive task: an overview. (PubMedID: 22151968) BMC bioinformatics
01/01/2011
Identification of conserved gene clusters in multiple genomes based on synteny and homology. (PubMedID: 22151970) BMC bioinformatics
01/01/2011
Cross-species gene normalization by species inference. (PubMedID: 22151999) BMC bioinformatics
01/01/2011
Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes. (PubMedID: 22152004) BMC bioinformatics
01/01/2011
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization. (PubMedID: 22152021) BMC bioinformatics
01/01/2011
Evolution of orthologous tandemly arrayed gene clusters. (PubMedID: 22152029) BMC bioinformatics
01/01/2011
Genome dedoubling by DCJ and reversal. (PubMedID: 22152053) BMC bioinformatics
01/01/2011
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. (PubMedID: 22152084) BMC bioinformatics
01/01/2011
The genomic features that affect the lengths of 5' untranslated regions in multicellular eukaryotes. (PubMedID: 22152105) BMC bioinformatics
01/01/2011
Fast and accurate methods for phylogenomic analyses. (PubMedID: 22152123) BMC bioinformatics
01/01/2011
Fractionation statistics. (PubMedID: 22152148) BMC bioinformatics
01/01/2011
Mulcom: a multiple comparison statistical test for microarray data in Bioconductor. (PubMedID: 21955789) BMC bioinformatics
01/01/2011
caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts. (PubMedID: 21957981) BMC bioinformatics
01/01/2011
Multilocus association mapping using generalized ridge logistic regression. (PubMedID: 21958005) BMC bioinformatics
01/01/2011
Interactive metagenomic visualization in a Web browser. (PubMedID: 21961884) BMC bioinformatics
01/01/2011
Top scoring pairs for feature selection in machine learning and applications to cancer outcome prediction. (PubMedID: 21939564) BMC bioinformatics
01/01/2011
EnzymeDetector: an integrated enzyme function prediction tool and database. (PubMedID: 21943292) BMC bioinformatics
01/01/2011
A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype. (PubMedID: 21943316) BMC bioinformatics
01/01/2011
Prediction of protein-binding areas by small-world residue networks and application to docking. (PubMedID: 21943333) BMC bioinformatics
01/01/2011
GOmotif: A web server for investigating the biological role of protein sequence motifs. (PubMedID: 21943350) BMC bioinformatics
01/01/2011
iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks. (PubMedID: 21943367) BMC bioinformatics
01/01/2011
Discovering biological connections between experimental conditions based on common patterns of differential gene expression. (PubMedID: 21951600) BMC bioinformatics
01/01/2011
Toponomics method for the automated quantification of membrane protein translocation. (PubMedID: 21929784) BMC bioinformatics
01/01/2011
The representation of protein complexes in the Protein Ontology (PRO). (PubMedID: 21929785) BMC bioinformatics
01/01/2011
Significance testing in ridge regression for genetic data. (PubMedID: 21929786) BMC bioinformatics
01/01/2011
Quantification of protein group coherence and pathway assignment using functional association. (PubMedID: 21929787) BMC bioinformatics
01/01/2011
Hierarchical parallelization of gene differential association analysis. (PubMedID: 21936916) BMC bioinformatics
01/01/2011
MetaboLab--advanced NMR data processing and analysis for metabolomics. (PubMedID: 21914187) BMC bioinformatics
01/01/2011
Methodology and software to detect viral integration site hot-spots. (PubMedID: 21914224) BMC bioinformatics
01/01/2011
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. (PubMedID: 21920038) BMC bioinformatics
01/01/2011
Thawing Frozen Robust Multi-array Analysis (fRMA). (PubMedID: 21923903) BMC bioinformatics
01/01/2011
Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute. (PubMedID: 21906284) BMC bioinformatics
01/01/2011
Integrating GPCR-specific information with full text articles. (PubMedID: 21910883) BMC bioinformatics
01/01/2011
Selection of organisms for the co-evolution-based study of protein interactions. (PubMedID: 21910884) BMC bioinformatics
01/01/2011
Characterizing genetic interactions in human disease association studies using statistical epistasis networks. (PubMedID: 21910885) BMC bioinformatics
01/01/2011
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns. (PubMedID: 21910886) BMC bioinformatics
01/01/2011
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. (PubMedID: 21878105) BMC bioinformatics
01/01/2011
An integrative approach to ortholog prediction for disease-focused and other functional studies. (PubMedID: 21880147) BMC bioinformatics
01/01/2011
Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis. (PubMedID: 21884583) BMC bioinformatics
01/01/2011
Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data. (PubMedID: 21884587) BMC bioinformatics
01/01/2011
GO-based functional dissimilarity of gene sets. (PubMedID: 21884611) BMC bioinformatics
01/01/2011
Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment. (PubMedID: 21867510) BMC bioinformatics
01/01/2011
Parallelized short read assembly of large genomes using de Bruijn graphs. (PubMedID: 21867511) BMC bioinformatics
01/01/2011
Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts. (PubMedID: 21871110) BMC bioinformatics
01/01/2011
Statistical methods for analyzing immunosignatures. (PubMedID: 21854615) BMC bioinformatics
01/01/2011
Haplo2Ped: a tool using haplotypes as markers for linkage analysis. (PubMedID: 21854652) BMC bioinformatics
01/01/2011
Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case. (PubMedID: 21859449) BMC bioinformatics
01/01/2011
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. (PubMedID: 21861881) BMC bioinformatics
01/01/2011
PChopper: high throughput peptide prediction for MRM/SRM transition design. (PubMedID: 21838934) BMC bioinformatics
01/01/2011
Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization. (PubMedID: 21846353) BMC bioinformatics
01/01/2011
Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature. (PubMedID: 21846404) BMC bioinformatics
01/01/2011
A comparison of the functional modules identified from time course and static PPI network data. (PubMedID: 21849017) BMC bioinformatics
01/01/2011
Recent human evolution has shaped geographical differences in susceptibility to disease. (PubMedID: 21261943) BMC genomics
01/01/2011
Pyrosequencing the transcriptome of the greenhouse whitefly, Trialeurodes vaporariorum reveals multiple transcripts encoding insecticide targets and detoxifying enzymes. (PubMedID: 21261962) BMC genomics
01/01/2011
Transcriptome dynamics and molecular cross-talk between bovine oocyte and its companion cumulus cells. (PubMedID: 21261964) BMC genomics
01/01/2011
The Trypanosoma cruzi Sylvio X10 strain maxicircle sequence: the third musketeer. (PubMedID: 21261994) BMC genomics
01/01/2011
Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. (PubMedID: 21266061) BMC genomics
01/01/2011
Characterization of the Conus bullatus genome and its venom-duct transcriptome. (PubMedID: 21266071) BMC genomics
01/01/2011
The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. (PubMedID: 21266083) BMC genomics
01/01/2011
Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level. (PubMedID: 21241472) BMC genomics
01/01/2011
Global gene expression of Poncirus trifoliata, Citrus sunki and their hybrids under infection of Phytophthora parasitica. (PubMedID: 21241495) BMC genomics
01/01/2011
Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin. (PubMedID: 21241518) BMC genomics
01/01/2011
The Zea mays mutants opaque-2 and opaque-7 disclose extensive changes in endosperm metabolism as revealed by protein, amino acid, and transcriptome-wide analyses. (PubMedID: 21241522) BMC genomics
01/01/2011
Next-generation sequencing for HLA typing of class I loci. (PubMedID: 21244689) BMC genomics
01/01/2011
MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms. (PubMedID: 21244711) BMC genomics
01/01/2011
Ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast. (PubMedID: 21247416) BMC genomics
01/01/2011
Comparative analysis of information contents relevant to recognition of introns in many species. (PubMedID: 21247441) BMC genomics
01/01/2011
Conserved generation of short products at piRNA loci. (PubMedID: 21247452) BMC genomics
01/01/2011
Identification of Schistosoma mansoni microRNAs. (PubMedID: 21247453) BMC genomics
01/01/2011
A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae. (PubMedID: 21247459) BMC genomics
01/01/2011
Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses. (PubMedID: 21247492) BMC genomics
01/01/2011
False negative rates in Drosophila cell-based RNAi screens: a case study. (PubMedID: 21251254) BMC genomics
01/01/2011
Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae. (PubMedID: 21251255) BMC genomics
01/01/2011
Complete genome sequencing and analysis of a Lancefield group G Streptococcus dysgalactiae subsp. equisimilis strain causing streptococcal toxic shock syndrome (STSS). (PubMedID: 21223537) BMC genomics
01/01/2011
Analysis of the unexplored features of rrs (16S rDNA) of the Genus Clostridium. (PubMedID: 21223548) BMC genomics
01/01/2011
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. (PubMedID: 21223577) BMC genomics
01/01/2011
Global gene expression profile progression in Gaucher disease mouse models. (PubMedID: 21223590) BMC genomics
01/01/2011
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. (PubMedID: 21223593) BMC genomics
01/01/2011
A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation. (PubMedID: 21226900) BMC genomics
01/01/2011
Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle. (PubMedID: 21226902) BMC genomics
01/01/2011
The epigenetic regulator Histone Deacetylase 1 promotes transcription of a core neurogenic programme in zebrafish embryos. (PubMedID: 21226904) BMC genomics
01/01/2011
Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942. (PubMedID: 21226929) BMC genomics
01/01/2011
Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents. (PubMedID: 21226930) BMC genomics
01/01/2011
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. (PubMedID: 21226956) BMC genomics
01/01/2011
Identification of genes differentially expressed in a resistant reaction to Mycosphaerella pinodes in pea using microarray technology. (PubMedID: 21226971) BMC genomics
01/01/2011
Gene expression profiling of rat spermatogonia and Sertoli cells reveals signaling pathways from stem cells to niche and testicular cancer cells to surrounding stroma. (PubMedID: 21232125) BMC genomics
01/01/2011
De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). (PubMedID: 21232141) BMC genomics
01/01/2011
Regulation and expression of sexual differentiation factors in embryonic and extragonadal tissues of Atlantic salmon. (PubMedID: 21232142) BMC genomics
01/01/2011
Genomic fluidity: an integrative view of gene diversity within microbial populations. (PubMedID: 21232151) BMC genomics
01/01/2011
Recent and historical recombination in the admixed Norwegian Red cattle breed. (PubMedID: 21232164) BMC genomics
01/01/2011
Divergent responses to peptidoglycans derived from different E. coli serotypes influence inflammatory outcome in trout, Oncorhynchus mykiss, macrophages. (PubMedID: 21235753) BMC genomics
01/01/2011
Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination. (PubMedID: 21235758) BMC genomics
01/01/2011
Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation. (PubMedID: 21235772) BMC genomics
01/01/2011
The sex-biased brain: sexual dimorphism in gene expression in two species of songbirds. (PubMedID: 21235773) BMC genomics
01/01/2011
The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. (PubMedID: 21208457) BMC genomics
01/01/2011
Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array. (PubMedID: 21211017) BMC genomics
01/01/2011
The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis. (PubMedID: 21211035) BMC genomics
01/01/2011
Mesenteric lymph node transcriptome profiles in BALB/c mice sensitized to three common food allergens. (PubMedID: 21211037) BMC genomics
01/01/2011
ZNF280BY and ZNF280AY: autosome derived Y-chromosome gene families in Bovidae. (PubMedID: 21214936) BMC genomics
01/01/2011
Expression of G protein-coupled receptors and related proteins in HEK293, AtT20, BV2, and N18 cell lines as revealed by microarray analysis. (PubMedID: 21214938) BMC genomics
01/01/2011
Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadense. (PubMedID: 21214949) BMC genomics
01/01/2011
Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes. (PubMedID: 21194499) BMC genomics
01/01/2011
Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering. (PubMedID: 21205307) BMC genomics
01/01/2011
Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis. (PubMedID: 21205313) BMC genomics
01/01/2011
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. (PubMedID: 21205322) BMC genomics
01/01/2011
The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits. (PubMedID: 21208403) BMC genomics
01/01/2011
An iterative workflow for mining the human intestinal metaproteome. (PubMedID: 21208423) BMC genomics
01/01/2011
Association genetics in Solanum tuberosum provides new insights into potato tuber bruising and enzymatic tissue discoloration. (PubMedID: 21208436) BMC genomics
01/01/2011
Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.]. (PubMedID: 21208448) BMC genomics
01/01/2011
Sublineage structure analysis of Mycobacterium tuberculosis complex strains using multiple-biomarker tensors. (PubMedID: 21988942) BMC genomics
01/01/2011
Correlating CpG islands, motifs, and sequence variants in human chromosome 21. (PubMedID: 21989037) BMC genomics
01/01/2011
Dynamic biclustering of microarray data by multi-objective immune optimization. (PubMedID: 21989068) BMC genomics
01/01/2011
Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters. (PubMedID: 21989079) BMC genomics
01/01/2011
FluReF, an automated flu virus reassortment finder based on phylogenetic trees. (PubMedID: 21989112) BMC genomics
01/01/2011
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. (PubMedID: 21989143) BMC genomics
01/01/2011
Building interpretable fuzzy models for high dimensional data analysis in cancer diagnosis. (PubMedID: 21989191) BMC genomics
01/01/2011
CAMBer: an approach to support comparative analysis of multiple bacterial strains. (PubMedID: 21989220) BMC genomics
01/01/2011
?-RA: a parallel sparse index for genomic read alignment. (PubMedID: 21989248) BMC genomics
01/01/2011
Evaluation of short read metagenomic assembly. (PubMedID: 21989307) BMC genomics
01/01/2011
bNEAT: a Bayesian network method for detecting epistatic interactions in genome-wide association studies. (PubMedID: 21989368) BMC genomics
01/01/2011
A new strategy for better genome assembly from very short reads. (PubMedID: 22208765) BMC bioinformatics
01/01/2011
Identifying elemental genomic track types and representing them uniformly. (PubMedID: 22208806) BMC bioinformatics
01/01/2011
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. (PubMedID: 22208852) BMC bioinformatics
01/01/2011
A mixture model with a reference-based automatic selection of components for disease classification from protein and/or gene expression levels. (PubMedID: 22208882) BMC bioinformatics
01/01/2011
Partition decoupling for multi-gene analysis of gene expression profiling data. (PubMedID: 22208906) BMC bioinformatics
01/01/2011
Predicting RNA-protein interactions using only sequence information. (PubMedID: 22192482) BMC bioinformatics
01/01/2011
"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis. (PubMedID: 22192526) BMC bioinformatics
01/01/2011
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. (PubMedID: 22192575) BMC bioinformatics
01/01/2011
Structural measures for network biology using QuACN. (PubMedID: 22195644) BMC bioinformatics
01/01/2011
GC-content normalization for RNA-Seq data. (PubMedID: 22177264) BMC bioinformatics
01/01/2011
U-Compare bio-event meta-service: compatible BioNLP event extraction services. (PubMedID: 22177292) BMC bioinformatics
01/01/2011
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. (PubMedID: 22182279) BMC bioinformatics
01/01/2011
Supervised regularized canonical correlation analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery. (PubMedID: 22182303) BMC bioinformatics
01/01/2011
Normalizing for individual cell population context in the analysis of high-content cellular screens. (PubMedID: 22185194) BMC bioinformatics
01/01/2011
Constructing a semantic predication gold standard from the biomedical literature. (PubMedID: 22185221) BMC bioinformatics
01/01/2011
Morphometic analysis of TCGA glioblastoma multiforme. (PubMedID: 22185703) BMC bioinformatics
01/01/2011
New concepts for building vocabulary for cell image ontologies. (PubMedID: 22188658) BMC bioinformatics
01/01/2011
Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer. (PubMedID: 22188670) BMC bioinformatics
01/01/2011
SNPInterForest: a new method for detecting epistatic interactions. (PubMedID: 22151604) BMC bioinformatics
01/01/2011
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. (PubMedID: 22165866) BMC bioinformatics
01/01/2011
MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature. (PubMedID: 22168213) BMC bioinformatics
01/01/2011
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. (PubMedID: 22168237) BMC bioinformatics
01/01/2011
Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows. (PubMedID: 22168258) BMC bioinformatics
01/01/2011
Jetset: selecting the optimal microarray probe set to represent a gene. (PubMedID: 22172014) BMC bioinformatics
01/01/2011
Performance analysis of novel methods for detecting epistasis. (PubMedID: 22172045) BMC bioinformatics
01/01/2011
Phylogenetically informed logic relationships improve detection of biological network organization. (PubMedID: 22172058) BMC bioinformatics
01/01/2011
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. (PubMedID: 22172090) BMC bioinformatics
01/01/2011
Survival models with preclustered gene groups as covariates. (PubMedID: 22177110) BMC bioinformatics
01/01/2011
NanoStriDE: normalization and differential expression analysis of NanoString nCounter data. (PubMedID: 22177214) BMC bioinformatics
01/01/2011
Development, evaluation and application of 3D QSAR Pharmacophore model in the discovery of potential human renin inhibitors. (PubMedID: 22372967) BMC bioinformatics
01/01/2011
Integrative analysis workflow for the structural and functional classification of C-type lectins. (PubMedID: 22372988) BMC bioinformatics
01/01/2011
iGepros: an integrated gene and protein annotation server for biological nature exploration. (PubMedID: 22373022) BMC bioinformatics
01/01/2011
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. (PubMedID: 22373054) BMC bioinformatics
01/01/2011
Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs. (PubMedID: 22373085) BMC bioinformatics
01/01/2011
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. (PubMedID: 22373099) BMC bioinformatics
01/01/2011
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. (PubMedID: 22373367) BMC bioinformatics
01/01/2011
A protein-dependent side-chain rotamer library. (PubMedID: 22373394) BMC bioinformatics
01/01/2011
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. (PubMedID: 22373417) BMC bioinformatics
01/01/2011
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. (PubMedID: 22373441) BMC bioinformatics
01/01/2011
Accelerated large-scale multiple sequence alignment. (PubMedID: 22151470) BMC bioinformatics
01/01/2011
Empirical comparison of cross-platform normalization methods for gene expression data. (PubMedID: 22151536) BMC bioinformatics
01/01/2011
openBIS: a flexible framework for managing and analyzing complex data in biology research. (PubMedID: 22151573) BMC bioinformatics
01/01/2011
From hybridization theory to microarray data analysis: performance evaluation. (PubMedID: 22136743) BMC bioinformatics
01/01/2011
Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. (PubMedID: 22142146) BMC bioinformatics
01/01/2011
Semantic annotation of biological concepts interplaying microbial cellular responses. (PubMedID: 22122862) BMC bioinformatics
01/01/2011
A unified framework for managing provenance information in translational research. (PubMedID: 22126369) BMC bioinformatics
01/01/2011
Segmentation and intensity estimation for microarray images with saturated pixels. (PubMedID: 22129216) BMC bioinformatics
01/01/2011
Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems. (PubMedID: 22132775) BMC bioinformatics
01/01/2011
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. (PubMedID: 22111509) BMC bioinformatics
01/01/2011
miREE: miRNA recognition elements ensemble. (PubMedID: 22115078) BMC bioinformatics
01/01/2011
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. (PubMedID: 22115179) BMC bioinformatics
01/01/2011
Unintended consequences of existential quantifications in biomedical ontologies. (PubMedID: 22115278) BMC bioinformatics
01/01/2011
A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships. (PubMedID: 22115330) BMC bioinformatics
01/01/2011
Multiple-input multiple-output causal strategies for gene selection. (PubMedID: 22118187) BMC bioinformatics
01/01/2011
Integrative set enrichment testing for multiple omics platforms. (PubMedID: 22118224) BMC bioinformatics
01/01/2011
Discovery of error-tolerant biclusters from noisy gene expression data. (PubMedID: 22168285) BMC bioinformatics
01/01/2011
Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. (PubMedID: 22168340) BMC bioinformatics
01/01/2011
FEPI-MB: identifying SNPs-disease association using a Markov Blanket-based approach. (PubMedID: 22168374) BMC bioinformatics
01/01/2011
Combining active learning and semi-supervised learning techniques to extract protein interaction sentences. (PubMedID: 22168401) BMC bioinformatics
01/01/2011
Planning combinatorial disulfide cross-links for protein fold determination. (PubMedID: 22168447) BMC bioinformatics
01/01/2011
A new method for identifying bivariate differential expression in high dimensional microarray data using quadratic discriminant analysis. (PubMedID: 22168481) BMC bioinformatics
01/01/2011
New threats to health data privacy. (PubMedID: 22168526) BMC bioinformatics
01/01/2011
Random KNN feature selection - a fast and stable alternative to Random Forests. (PubMedID: 22093447) BMC bioinformatics
01/01/2011
Identification and correction of systematic error in high-throughput sequence data. (PubMedID: 22099972) BMC bioinformatics
01/01/2011
eXframe: reusable framework for storage, analysis and visualization of genomics experiments. (PubMedID: 22103807) BMC bioinformatics
01/01/2011
Exact score distribution computation for ontological similarity searches. (PubMedID: 22078312) BMC bioinformatics
01/01/2011
Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria. (PubMedID: 22078363) BMC bioinformatics
01/01/2011
SIGNATURE: a workbench for gene expression signature analysis. (PubMedID: 22078435) BMC bioinformatics
01/01/2011
Correlated mutations via regularized multinomial regression. (PubMedID: 22082126) BMC bioinformatics
01/01/2011
Validating clustering of molecular dynamics simulations using polymer models. (PubMedID: 22082218) BMC bioinformatics
01/01/2011
POPISK: T-cell reactivity prediction using support vector machines and string kernels. (PubMedID: 22085524) BMC bioinformatics
01/01/2011
OmniMapFree: a unified tool to visualise and explore sequenced genomes. (PubMedID: 22085540) BMC bioinformatics
01/01/2011
A flexible framework for sparse simultaneous component based data integration. (PubMedID: 22085701) BMC bioinformatics
01/01/2011
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. (PubMedID: 22087737) BMC bioinformatics
01/01/2011
A parallel method for enumerating amino acid compositions and masses of all theoretical peptides. (PubMedID: 22059886) BMC bioinformatics
01/01/2011
Analyzing 2D gel images using a two-component empirical Bayes model. (PubMedID: 22067142) BMC bioinformatics
01/01/2011
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. (PubMedID: 22070167) BMC bioinformatics
01/01/2011
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. (PubMedID: 22070195) BMC bioinformatics
01/01/2011
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. (PubMedID: 22070249) BMC bioinformatics
01/01/2011
An iterative approach of protein function prediction. (PubMedID: 22074332) BMC bioinformatics
01/01/2011
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. (PubMedID: 22078224) BMC bioinformatics
01/01/2011
SCFIA: a statistical corresponding feature identification algorithm for LC/MS. (PubMedID: 22078262) BMC bioinformatics
01/01/2011
Efficient a, ß-motif finder for identification of phenotype-related functional modules. (PubMedID: 22078292) BMC bioinformatics
01/01/2011
Fast MCMC sampling for hidden Markov Models to determine copy number variations. (PubMedID: 22047014) BMC bioinformatics
01/01/2011
Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform. (PubMedID: 22050630) BMC bioinformatics
01/01/2011
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. (PubMedID: 22051375) BMC bioinformatics
01/01/2011
AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations. (PubMedID: 22054122) BMC bioinformatics
01/01/2011
Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation. (PubMedID: 22024143) BMC bioinformatics
01/01/2011
PMS5: an efficient exact algorithm for the (l, d)-motif finding problem. (PubMedID: 22024209) BMC bioinformatics
01/01/2011
EPEPT: a web service for enhanced P-value estimation in permutation tests. (PubMedID: 22024252) BMC bioinformatics
01/01/2011
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. (PubMedID: 22026390) BMC bioinformatics
01/01/2011
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features. (PubMedID: 22026913) BMC bioinformatics
01/01/2011
Impact of the spotted microarray preprocessing method on fold-change compression and variance stability. (PubMedID: 22026942) BMC bioinformatics
01/01/2011
Exploratory analysis of genomic segmentations with Segtools. (PubMedID: 22029426) BMC bioinformatics
01/01/2011
SegMine workflows for semantic microarray data analysis in Orange4WS. (PubMedID: 22029475) BMC bioinformatics
01/01/2011
BioNØT: a searchable database of biomedical negated sentences. (PubMedID: 22032181) BMC bioinformatics
01/01/2011
Automated NMR relaxation dispersion data analysis using NESSY. (PubMedID: 22032230) BMC bioinformatics
01/01/2011
Predicting protein ligand binding motions with the conformation explorer. (PubMedID: 22032721) BMC bioinformatics
01/01/2011
Improving ontologies by automatic reasoning and evaluation of logical definitions. (PubMedID: 22032770) BMC bioinformatics
01/01/2011
MAPI: towards the integrated exploitation of bioinformatics Web Services. (PubMedID: 22032807) BMC bioinformatics
01/01/2011
Mitochondrial genome sequence analysis: a custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy. (PubMedID: 22011106) BMC bioinformatics
01/01/2011
DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference. (PubMedID: 22011170) BMC bioinformatics
01/01/2011
pcrEfficiency: a Web tool for PCR amplification efficiency prediction. (PubMedID: 22014212) BMC bioinformatics
01/01/2011
An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. (PubMedID: 22014236) BMC bioinformatics
01/01/2011
RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples. (PubMedID: 21682879) BMC bioinformatics
01/01/2011
HomPPI: a class of sequence homology based protein-protein interface prediction methods. (PubMedID: 21682895) BMC bioinformatics
01/01/2011
In-silico prediction of disorder content using hybrid sequence representation. (PubMedID: 21682902) BMC bioinformatics
01/01/2011
Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. (PubMedID: 21682921) BMC bioinformatics
01/01/2011
Estimation of allele frequency and association mapping using next-generation sequencing data. (PubMedID: 21663684) BMC bioinformatics
01/01/2011
Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3D segmentation algorithms. (PubMedID: 21668958) BMC bioinformatics
01/01/2011
Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities. (PubMedID: 21668997) BMC bioinformatics
01/01/2011
Evaluating methods for ranking differentially expressed genes applied to microArray quality control data. (PubMedID: 21639945) BMC bioinformatics
01/01/2011
Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics. (PubMedID: 21649912) BMC bioinformatics
01/01/2011
Towards an Age-Phenome Knowledge-base. (PubMedID: 21651792) BMC bioinformatics
01/01/2011
NeurphologyJ: an automatic neuronal morphology quantification method and its application in pharmacological discovery. (PubMedID: 21651810) BMC bioinformatics
01/01/2011
Topics in machine learning for biomedical literature analysis and text retrieval. (PubMedID: 21658287) BMC bioinformatics
01/01/2011
Building a biomedical tokenizer using the token lattice design pattern and the adapted Viterbi algorithm. (PubMedID: 21658288) BMC bioinformatics
01/01/2011
A system for de-identifying medical message board text. (PubMedID: 21658289) BMC bioinformatics
01/01/2011
A context-blocks model for identifying clinical relationships in patient records. (PubMedID: 21658290) BMC bioinformatics
01/01/2011
Collocation analysis for UMLS knowledge-based word sense disambiguation. (PubMedID: 21658291) BMC bioinformatics
01/01/2011
Improving a gold standard: treating human relevance judgments of MEDLINE document pairs. (PubMedID: 21658292) BMC bioinformatics
01/01/2011
Machine learning with naturally labeled data for identifying abbreviation definitions. (PubMedID: 21658293) BMC bioinformatics
01/01/2011
A structural SVM approach for reference parsing. (PubMedID: 21658294) BMC bioinformatics
01/01/2011
RAG: an update to the RNA-As-Graphs resource. (PubMedID: 21627789) BMC bioinformatics
01/01/2011
Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform. (PubMedID: 21627824) BMC bioinformatics
01/01/2011
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. (PubMedID: 21631914) BMC bioinformatics
01/01/2011
Kernel density weighted loess normalization improves the performance of detection within asymmetrical data. (PubMedID: 21631915) BMC bioinformatics
01/01/2011
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. (PubMedID: 21635749) BMC bioinformatics
01/01/2011
Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis. (PubMedID: 21635750) BMC bioinformatics
01/01/2011
Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences. (PubMedID: 21635751) BMC bioinformatics
01/01/2011
StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase. (PubMedID: 21635786) BMC bioinformatics
01/01/2011
A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data. (PubMedID: 21612662) BMC bioinformatics
01/01/2011
New methods to measure residues coevolution in proteins. (PubMedID: 21612664) BMC bioinformatics
01/01/2011
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information. (PubMedID: 21612668) BMC bioinformatics
01/01/2011
NCACO-score: an effective main-chain dependent scoring function for structure modeling. (PubMedID: 21612673) BMC bioinformatics
01/01/2011
Multiple testing for gene sets from microarray experiments. (PubMedID: 21615889) BMC bioinformatics
01/01/2011
A novel and well-defined benchmarking method for second generation read mapping. (PubMedID: 21615913) BMC bioinformatics
01/01/2011
Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping. (PubMedID: 21615941) BMC bioinformatics
01/01/2011
Exploring subdomain variation in biomedical language. (PubMedID: 21619603) BMC bioinformatics
01/01/2011
Identifier mapping performance for integrating transcriptomics and proteomics experimental results. (PubMedID: 21619611) BMC bioinformatics
01/01/2011
Structator: fast index-based search for RNA sequence-structure patterns. (PubMedID: 21619640) BMC bioinformatics
01/01/2011
A beta-mixture model for dimensionality reduction, sample classification and analysis. (PubMedID: 21619656) BMC bioinformatics
01/01/2011
miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM. (PubMedID: 21619662) BMC bioinformatics
01/01/2011
Conotoxin protein classification using free scores of words and support vector machines. (PubMedID: 21619696) BMC bioinformatics
01/01/2011
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. (PubMedID: 21619703) BMC bioinformatics
01/01/2011
Normalization and centering of array-based heterologous genome hybridization based on divergent control probes. (PubMedID: 21600029) BMC bioinformatics
01/01/2011
SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation. (PubMedID: 21600033) BMC bioinformatics
01/01/2011
GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models. (PubMedID: 21605354) BMC bioinformatics
01/01/2011
Extension of the bayesian alphabet for genomic selection. (PubMedID: 21605355) BMC bioinformatics
01/01/2011
Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library. (PubMedID: 21605356) BMC bioinformatics
01/01/2011
The biomedical discourse relation bank. (PubMedID: 21605399) BMC bioinformatics
01/01/2011
Enriching for correct prediction of biological processes using a combination of diverse classifiers. (PubMedID: 21605426) BMC bioinformatics
01/01/2011
Stereochemical errors and their implications for molecular dynamics simulations. (PubMedID: 21605430) BMC bioinformatics
01/01/2011
MINE: Module Identification in Networks. (PubMedID: 21605434) BMC bioinformatics
01/01/2011
Bacterial syntenies: an exact approach with gene quorum. (PubMedID: 21605461) BMC bioinformatics
01/01/2011
Inference of chromosome-specific copy numbers using population haplotypes. (PubMedID: 21605463) BMC bioinformatics
01/01/2011
Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs. (PubMedID: 21605466) BMC bioinformatics
01/01/2011
Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface. (PubMedID: 21609434) BMC bioinformatics
01/01/2011
Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in breast cancer. (PubMedID: 21609452) BMC bioinformatics
01/01/2011
HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors. (PubMedID: 21609463) BMC bioinformatics
01/01/2011
MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries. (PubMedID: 21609501) BMC bioinformatics
01/01/2011
rnaSeqMap: a Bioconductor package for RNA sequencing data exploration. (PubMedID: 21612622) BMC bioinformatics
01/01/2011
CAPL: an efficient association software package using family and case-control data and accounting for population stratification. (PubMedID: 21612626) BMC bioinformatics
01/01/2011
Qxpak.5: old mixed model solutions for new genomics problems. (PubMedID: 21612630) BMC bioinformatics
01/01/2011
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. (PubMedID: 21612636) BMC bioinformatics
01/01/2011
Tree edit distance for leaf-labelled trees on free leafset and its comparison with frequent subsplit dissimilarity and popular distance measures. (PubMedID: 21612645) BMC bioinformatics
01/01/2011
A network of SCOP hidden Markov models and its analysis. (PubMedID: 21635719) BMC bioinformatics
01/01/2011
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. (PubMedID: 21575183) BMC bioinformatics
01/01/2011
PRIN: a predicted rice interactome network. (PubMedID: 21575196) BMC bioinformatics
01/01/2011
NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq. (PubMedID: 21575225) BMC bioinformatics
01/01/2011
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method. (PubMedID: 21575263) BMC bioinformatics
01/01/2011
Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure. (PubMedID: 21575268) BMC bioinformatics
01/01/2011
A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data. (PubMedID: 21586113) BMC bioinformatics
01/01/2011
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. (PubMedID: 21586134) BMC bioinformatics
01/01/2011
More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs. (PubMedID: 21586147) BMC bioinformatics
01/01/2011
Predicting drug side-effect profiles: a chemical fragment-based approach. (PubMedID: 21586169) BMC bioinformatics
01/01/2011
Objective identification of residue ranges for the superposition of protein structures. (PubMedID: 21592348) BMC bioinformatics
01/01/2011
TAFFEL: Independent Enrichment Analysis of gene sets. (PubMedID: 21592412) BMC bioinformatics
01/01/2011
Genotype calling in tetraploid species from bi-allelic marker data using mixture models. (PubMedID: 21595880) BMC bioinformatics
01/01/2011
An analysis of single amino acid repeats as use case for application specific background models. (PubMedID: 21595908) BMC bioinformatics
01/01/2011
Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge. (PubMedID: 21595926) BMC bioinformatics
01/01/2011
Toward an interactive article: integrating journals and biological databases. (PubMedID: 21595960) BMC bioinformatics
01/01/2011
Web-based metabolic network visualization with a zooming user interface. (PubMedID: 21595965) BMC bioinformatics
01/01/2011
An application of kernel methods to variety identification based on SSR markers genetic fingerprinting. (PubMedID: 21595989) BMC bioinformatics
01/01/2011
TreeRipper web application: towards a fully automated optical tree recognition software. (PubMedID: 21599881) BMC bioinformatics
01/01/2011
Brunn: an open source laboratory information system for microplates with a graphical plate layout design process. (PubMedID: 21599898) BMC bioinformatics
01/01/2011
A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression. (PubMedID: 21599902) BMC bioinformatics
01/01/2011
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs. (PubMedID: 21599912) BMC bioinformatics
01/01/2011
CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. (PubMedID: 21599929) BMC bioinformatics
01/01/2011
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. (PubMedID: 21849035) BMC bioinformatics
01/01/2011
A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants. (PubMedID: 21849042) BMC bioinformatics
01/01/2011
A novel method to compare protein structures using local descriptors. (PubMedID: 21849047) BMC bioinformatics
01/01/2011
BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection. (PubMedID: 21849049) BMC bioinformatics
01/01/2011
ProbPS: a new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity. (PubMedID: 21849060) BMC bioinformatics
01/01/2011
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. (PubMedID: 21851598) BMC bioinformatics
01/01/2011
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. (PubMedID: 21851628) BMC bioinformatics
01/01/2011
Development of a classification scheme for disease-related enzyme information. (PubMedID: 21827651) BMC bioinformatics
01/01/2011
Randomization techniques for assessing the significance of gene periodicity results. (PubMedID: 21827656) BMC bioinformatics
01/01/2011
Genome-wide algorithm for detecting CNV associations with diseases. (PubMedID: 21827692) BMC bioinformatics
01/01/2011
Classifying short genomic fragments from novel lineages using composition and homology. (PubMedID: 21827705) BMC bioinformatics
01/01/2011
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs. (PubMedID: 21831265) BMC bioinformatics
01/01/2011
Efficient counting of k-mers in DNA sequences using a bloom filter. (PubMedID: 21831268) BMC bioinformatics
01/01/2011
Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. (PubMedID: 21831299) BMC bioinformatics
01/01/2011
Predicting receptor-ligand pairs through kernel learning. (PubMedID: 21834994) BMC bioinformatics
01/01/2011
Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana. (PubMedID: 21834997) BMC bioinformatics
01/01/2011
IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches. (PubMedID: 21838867) BMC bioinformatics
01/01/2011
The volatile compound BinBase mass spectral database. (PubMedID: 21816034) BMC bioinformatics
01/01/2011
Strategies for aggregating gene expression data: the collapseRows R function. (PubMedID: 21816037) BMC bioinformatics
01/01/2011
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. (PubMedID: 21816040) BMC bioinformatics
01/01/2011
rapmad: Robust analysis of peptide microarray data. (PubMedID: 21816082) BMC bioinformatics
01/01/2011
A regression system for estimation of errors introduced by confocal imaging into gene expression data in situ. (PubMedID: 21816093) BMC bioinformatics
01/01/2011
How the gene ontology evolves. (PubMedID: 21819553) BMC bioinformatics
01/01/2011
Domain architecture conservation in orthologs. (PubMedID: 21819573) BMC bioinformatics
01/01/2011
NETGEM: Network Embedded Temporal GEnerative Model for gene expression data. (PubMedID: 21824426) BMC bioinformatics
01/01/2011
Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. (PubMedID: 21806838) BMC bioinformatics
01/01/2011
GSV: a web-based genome synteny viewer for customized data. (PubMedID: 21810250) BMC bioinformatics
01/01/2011
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. (PubMedID: 21812952) BMC bioinformatics
01/01/2011
Mining for genotype-phenotype relations in Saccharomyces using partial least squares. (PubMedID: 21812956) BMC bioinformatics
01/01/2011
RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences. (PubMedID: 21813013) BMC bioinformatics
01/01/2011
miRTar: an integrated system for identifying miRNA-target interactions in human. (PubMedID: 21791068) BMC bioinformatics
01/01/2011
Deterministic and stochastic population-level simulations of an artificial lac operon genetic network. (PubMedID: 21791088) BMC bioinformatics
01/01/2011
Bayesian semi-supervised classification of bacterial samples using MLST databases. (PubMedID: 21791094) BMC bioinformatics
01/01/2011
Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. (PubMedID: 21791100) BMC bioinformatics
01/01/2011
Applications of the pipeline environment for visual informatics and genomics computations. (PubMedID: 21791102) BMC bioinformatics
01/01/2011
IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data. (PubMedID: 21794104) BMC bioinformatics
01/01/2011
Expression cartography of human tissues using self organizing maps. (PubMedID: 21794127) BMC bioinformatics
01/01/2011
The projection score--an evaluation criterion for variable subset selection in PCA visualization. (PubMedID: 21798031) BMC bioinformatics
01/01/2011
Visualizing meta-features in proteomic maps. (PubMedID: 21798033) BMC bioinformatics
01/01/2011
Application of an efficient Bayesian discretization method to biomedical data. (PubMedID: 21798039) BMC bioinformatics
01/01/2011
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. (PubMedID: 21798043) BMC bioinformatics
01/01/2011
Rigorous assessment and integration of the sequence and structure based features to predict hot spots. (PubMedID: 21798070) BMC bioinformatics
01/01/2011
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. (PubMedID: 21801404) BMC bioinformatics
01/01/2011
Open-target sparse sensing of biological agents using DNA microarray. (PubMedID: 21801424) BMC bioinformatics
01/01/2011
Dimension reduction with gene expression data using targeted variable importance measurement. (PubMedID: 21849016) BMC bioinformatics
01/01/2011
Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study. (PubMedID: 21774796) BMC bioinformatics
01/01/2011
ADAM: analysis of discrete models of biological systems using computer algebra. (PubMedID: 21774817) BMC bioinformatics
01/01/2011
Differential C3NET reveals disease networks of direct physical interactions. (PubMedID: 21777411) BMC bioinformatics
01/01/2011
BioIMAX: a Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data. (PubMedID: 21777450) BMC bioinformatics
01/01/2011
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. (PubMedID: 21777475) BMC bioinformatics
01/01/2011
Ranking insertion, deletion and nonsense mutations based on their effect on genetic information. (PubMedID: 21781308) BMC bioinformatics
01/01/2011
Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes. (PubMedID: 21756370) BMC bioinformatics
01/01/2011
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. (PubMedID: 21767381) BMC bioinformatics
01/01/2011
Bias detection and correction in RNA-Sequencing data. (PubMedID: 21771300) BMC bioinformatics
01/01/2011
Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. (PubMedID: 21771315) BMC bioinformatics
01/01/2011
Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. (PubMedID: 21771321) BMC bioinformatics
01/01/2011
FAAST: Flow-space Assisted Alignment Search Tool. (PubMedID: 21771335) BMC bioinformatics
01/01/2011
Detection of fused genes in eukaryotic genomes using gene deFuser: analysis of the Tetrahymena thermophila genome. (PubMedID: 21745395) BMC bioinformatics
01/01/2011
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. (PubMedID: 21745398) BMC bioinformatics
01/01/2011
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. (PubMedID: 21749690) BMC bioinformatics
01/01/2011
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. (PubMedID: 21749710) BMC bioinformatics
01/01/2011
Improving the performance of ß-turn prediction using predicted shape strings and a two-layer support vector machine model. (PubMedID: 21749732) BMC bioinformatics
01/01/2011
Modeling measurement error in tumor characterization studies. (PubMedID: 21752297) BMC bioinformatics
01/01/2011
S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. (PubMedID: 21756325) BMC bioinformatics
01/01/2011
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview. (PubMedID: 21756334) BMC bioinformatics
01/01/2011
Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments. (PubMedID: 21756356) BMC bioinformatics
01/01/2011
AlignHUSH: alignment of HMMs using structure and hydrophobicity information. (PubMedID: 21729312) BMC bioinformatics
01/01/2011
Quantitative characterization and analysis of the dynamic NF-?B response in microglia. (PubMedID: 21729324) BMC bioinformatics
01/01/2011
An integrated ChIP-seq analysis platform with customizable workflows. (PubMedID: 21736739) BMC bioinformatics
01/01/2011
ReadDB provides efficient storage for mapped short reads. (PubMedID: 21736741) BMC bioinformatics
01/01/2011
New words in human mutagenesis. (PubMedID: 21718472) BMC bioinformatics
01/01/2011
Network-based group variable selection for detecting expression quantitative trait loci (eQTL). (PubMedID: 21718480) BMC bioinformatics
01/01/2011
Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology. (PubMedID: 21718515) BMC bioinformatics
01/01/2011
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. (PubMedID: 21718538) BMC bioinformatics
01/01/2011
Improving pan-genome annotation using whole genome multiple alignment. (PubMedID: 21718539) BMC bioinformatics
01/01/2011
Gene set analysis for longitudinal gene expression data. (PubMedID: 21722407) BMC bioinformatics
01/01/2011
Detection of lineage-specific evolutionary changes among primate species. (PubMedID: 21726447) BMC bioinformatics
01/01/2011
PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity. (PubMedID: 21703007) BMC bioinformatics
01/01/2011
A mutation degree model for the identification of transcriptional regulatory elements. (PubMedID: 21708002) BMC bioinformatics
01/01/2011
Characterization of a Bayesian genetic clustering algorithm based on a Dirichlet process prior and comparison among Bayesian clustering methods. (PubMedID: 21708038) BMC bioinformatics
01/01/2011
MAVENs: motion analysis and visualization of elastic networks and structural ensembles. (PubMedID: 21711533) BMC bioinformatics
01/01/2011
phenosim--A software to simulate phenotypes for testing in genome-wide association studies. (PubMedID: 21714868) BMC bioinformatics
01/01/2011
DOSim: an R package for similarity between diseases based on Disease Ontology. (PubMedID: 21714896) BMC bioinformatics
01/01/2011
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. (PubMedID: 21714929) BMC bioinformatics
01/01/2011
Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. (PubMedID: 21689388) BMC bioinformatics
01/01/2011
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome. (PubMedID: 21689434) BMC bioinformatics
01/01/2011
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. (PubMedID: 21693013) BMC bioinformatics
01/01/2011
NORMA-Gene: a simple and robust method for qPCR normalization based on target gene data. (PubMedID: 21693017) BMC bioinformatics
01/01/2011
Determinants of antigenicity and specificity in immune response for protein sequences. (PubMedID: 21693021) BMC bioinformatics
01/01/2011
Computational study of noise in a large signal transduction network. (PubMedID: 21693049) BMC bioinformatics
01/01/2011
Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. (PubMedID: 21693065) BMC bioinformatics
01/01/2011
Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis. (PubMedID: 21696593) BMC bioinformatics
01/01/2011
Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and structure. (PubMedID: 21699684) BMC bioinformatics
01/01/2011
Semantic inference using chemogenomics data for drug discovery. (PubMedID: 21699718) BMC bioinformatics
01/01/2011
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. (PubMedID: 21702939) BMC bioinformatics
01/01/2011
Cell subset prediction for blood genomic studies. (PubMedID: 21702940) BMC bioinformatics
01/01/2011
AMDORAP: non-targeted metabolic profiling based on high-resolution LC-MS. (PubMedID: 21702951) BMC bioinformatics
01/01/2011
Computable visually observed phenotype ontological framework for plants. (PubMedID: 21702966) BMC bioinformatics
01/01/2011
PI: an open-source software package for validation of the SEQUEST result and visualization of mass spectrum. (PubMedID: 21672262) BMC bioinformatics
01/01/2011
Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry. (PubMedID: 21676240) BMC bioinformatics
01/01/2011
FFCA: a feasibility-based method for flux coupling analysis of metabolic networks. (PubMedID: 21676263) BMC bioinformatics
01/01/2011
Semi-automatic segmentation of multiple mouse embryos in MR images. (PubMedID: 21679425) BMC bioinformatics
01/01/2011
MotifClick: prediction of cis-regulatory binding sites via merging cliques. (PubMedID: 21679436) BMC bioinformatics
01/01/2011
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. (PubMedID: 21679454) BMC bioinformatics
01/01/2011
LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures. (PubMedID: 21679460) BMC bioinformatics
01/01/2011
PeptX: using genetic algorithms to optimize peptides for MHC binding. (PubMedID: 21679477) BMC bioinformatics
01/01/2011
Querying large read collections in main memory: a versatile data structure. (PubMedID: 21682852) BMC bioinformatics