Medical Research Articles Published in January 2012

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01/01/2012
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. (PubMedID: 22817640) BMC genomics
01/01/2012
Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data. (PubMedID: 22817656) BMC genomics
01/01/2012
Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community. (PubMedID: 22823523) BMC genomics
01/01/2012
Burkholderia pseudomallei transcriptional adaptation in macrophages. (PubMedID: 22823543) BMC genomics
01/01/2012
Characterization of the small RNA component of leaves and fruits from four different cucurbit species. (PubMedID: 22823569) BMC genomics
01/01/2012
Differential gene expression profiling of porcine epithelial cells infected with three enterotoxigenic Escherichia coli strains. (PubMedID: 22823589) BMC genomics
01/01/2012
Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis. (PubMedID: 22823751) BMC genomics
01/01/2012
Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study. (PubMedID: 22823888) BMC genomics
01/01/2012
A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study. (PubMedID: 22823907) BMC genomics
01/01/2012
A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. (PubMedID: 22823934) BMC genomics
01/01/2012
A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome. (PubMedID: 22823938) BMC genomics
01/01/2012
Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. (PubMedID: 22823947) BMC genomics
01/01/2012
An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. (PubMedID: 22793670) BMC genomics
01/01/2012
Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. (PubMedID: 22793791) BMC genomics
01/01/2012
Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing. (PubMedID: 22799740) BMC genomics
01/01/2012
Comparative genomics of Shiga toxin encoding bacteriophages. (PubMedID: 22799768) BMC genomics
01/01/2012
Mapping the polysaccharide degradation potential of Aspergillus niger. (PubMedID: 22799883) BMC genomics
01/01/2012
Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification. (PubMedID: 22800085) BMC genomics
01/01/2012
Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis. (PubMedID: 22800176) BMC genomics
01/01/2012
Development and validation of genic-SSR markers in sesame by RNA-seq. (PubMedID: 22800194) BMC genomics
01/01/2012
A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation. (PubMedID: 22805527) BMC genomics
01/01/2012
Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. (PubMedID: 22805587) BMC genomics
01/01/2012
RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish. (PubMedID: 22805612) BMC genomics
01/01/2012
Differential microRNA response to a high-cholesterol, high-fat diet in livers of low and high LDL-C baboons. (PubMedID: 22809019) BMC genomics
01/01/2012
The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus). (PubMedID: 23025625) BMC genomics
01/01/2012
De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. (PubMedID: 22776250) BMC genomics
01/01/2012
Let-7b regulates the expression of the growth hormone receptor gene in deletion-type dwarf chickens. (PubMedID: 22781587) BMC genomics
01/01/2012
Cysteine peptidases and their inhibitors in Tetranychus urticae: a comparative genomic approach. (PubMedID: 22784002) BMC genomics
01/01/2012
Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. (PubMedID: 22768919) BMC genomics
01/01/2012
Oomycete Transcriptomics Database: a resource for oomycete transcriptomes. (PubMedID: 22768977) BMC genomics
01/01/2012
Technical and biological variance structure in mRNA-Seq data: life in the real world. (PubMedID: 22769017) BMC genomics
01/01/2012
PePPER: a webserver for prediction of prokaryote promoter elements and regulons. (PubMedID: 22747501) BMC genomics
01/01/2012
Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. (PubMedID: 22747568) BMC genomics
01/01/2012
Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis. (PubMedID: 22747707) BMC genomics
01/01/2012
Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis. (PubMedID: 22747754) BMC genomics
01/01/2012
Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration. (PubMedID: 22747785) BMC genomics
01/01/2012
Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation. (PubMedID: 22747837) BMC genomics
01/01/2012
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species. (PubMedID: 22747887) BMC genomics
01/01/2012
Computational identification and analysis of novel sugarcane microRNAs. (PubMedID: 22747909) BMC genomics
01/01/2012
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery. (PubMedID: 22747958) BMC genomics
01/01/2012
Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology. (PubMedID: 22747974) BMC genomics
01/01/2012
Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome. (PubMedID: 22747999) BMC genomics
01/01/2012
Identification of genes specifically or preferentially expressed in maize silk reveals similarity and diversity in transcript abundance of different dry stigmas. (PubMedID: 22748054) BMC genomics
01/01/2012
Transcriptional profile of Taxus chinensis cells in response to methyl jasmonate. (PubMedID: 22748077) BMC genomics
01/01/2012
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. (PubMedID: 22748112) BMC genomics
01/01/2012
Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism. (PubMedID: 22748146) BMC genomics
01/01/2012
Distinct and overlapping gene regulatory networks in BMP- and HDAC-controlled cell fate determination in the embryonic forebrain. (PubMedID: 22748179) BMC genomics
01/01/2012
Finding combinatorial histone code by semi-supervised biclustering. (PubMedID: 22759587) BMC genomics
01/01/2012
Transcriptome sequencing for SNP discovery across Cucumis melo. (PubMedID: 22726804) BMC genomics
01/01/2012
High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. (PubMedID: 22726880) BMC genomics
01/01/2012
NetWalker: a contextual network analysis tool for functional genomics. (PubMedID: 22732065) BMC genomics
01/01/2012
ATon, abundant novel nonautonomous mobile genetic elements in yellow fever mosquito (Aedes aegypti). (PubMedID: 22738224) BMC genomics
01/01/2012
Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct. (PubMedID: 22742208) BMC genomics
01/01/2012
Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. (PubMedID: 22712530) BMC genomics
01/01/2012
Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes. (PubMedID: 22712556) BMC genomics
01/01/2012
Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. (PubMedID: 22712577) BMC genomics
01/01/2012
Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens. (PubMedID: 22712610) BMC genomics
01/01/2012
On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer. (PubMedID: 22712622) BMC genomics
01/01/2012
The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum). (PubMedID: 22716167) BMC genomics
01/01/2012
Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum. (PubMedID: 22716200) BMC genomics
01/01/2012
The immune gene repertoire of an important viral reservoir, the Australian black flying fox. (PubMedID: 22716473) BMC genomics
01/01/2012
Whole genome sequencing analysis of Plasmodium vivax using whole genome capture. (PubMedID: 22721170) BMC genomics
01/01/2012
Transcription factor co-localization patterns affect human cell type-specific gene expression. (PubMedID: 22721266) BMC genomics
01/01/2012
Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice. (PubMedID: 22721355) BMC genomics
01/01/2012
The genomic basis for the evolution of a novel form of cellular reproduction in the bacterium Epulopiscium. (PubMedID: 22721417) BMC genomics
01/01/2012
De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. (PubMedID: 22721448) BMC genomics
01/01/2012
The WRKY transcription factor family in Brachypodium distachyon. (PubMedID: 22726208) BMC genomics
01/01/2012
Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida. (PubMedID: 22726260) BMC genomics
01/01/2012
Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae. (PubMedID: 22726298) BMC genomics
01/01/2012
A genome-wide detection of copy number variations using SNP genotyping arrays in swine. (PubMedID: 22726314) BMC genomics
01/01/2012
Defining new criteria for selection of cell-based intestinal models using publicly available databases. (PubMedID: 22726358) BMC genomics
01/01/2012
Visualizing spatiotemporal dynamics of apoptosis after G1 arrest by human T cell leukemia virus type 1 Tax and insights into gene expression changes using microarray-based gene expression analysis. (PubMedID: 22726420) BMC genomics
01/01/2012
The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera. (PubMedID: 22726496) BMC genomics
01/01/2012
Celiac disease T-cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation. (PubMedID: 22726570) BMC genomics
01/01/2012
Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers. (PubMedID: 22726614) BMC genomics
01/01/2012
Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus. (PubMedID: 22726727) BMC genomics
01/01/2012
Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. (PubMedID: 22727066) BMC genomics
01/01/2012
Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish. (PubMedID: 22727144) BMC genomics
01/01/2012
Gene expression and proteomic analysis of the formation of Phakopsora pachyrhizi appressoria. (PubMedID: 22727213) BMC genomics
01/01/2012
Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis. (PubMedID: 22697265) BMC genomics
01/01/2012
A reference linkage map for Eucalyptus. (PubMedID: 22702473) BMC genomics
01/01/2012
Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort. (PubMedID: 22702538) BMC genomics
01/01/2012
An elm EST database for identifying leaf beetle egg-induced defense genes. (PubMedID: 22702658) BMC genomics
01/01/2012
The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L. (PubMedID: 22702718) BMC genomics
01/01/2012
Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. (PubMedID: 22702806) BMC genomics
01/01/2012
Detection of horizontal transfer of individual genes by anomalous oligomer frequencies. (PubMedID: 22702893) BMC genomics
01/01/2012
Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications. (PubMedID: 22702965) BMC genomics
01/01/2012
Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. (PubMedID: 22703051) BMC genomics
01/01/2012
Larval midgut modifications associated with Bti resistance in the yellow fever mosquito using proteomic and transcriptomic approaches. (PubMedID: 22703117) BMC genomics
01/01/2012
IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. (PubMedID: 22703188) BMC genomics
01/01/2012
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology. (PubMedID: 22708644) BMC genomics
01/01/2012
Evolution of coding and non-coding genes in HOX clusters of a marsupial. (PubMedID: 22708672) BMC genomics
01/01/2012
A hemocyte gene expression signature correlated with predictive capacity of oysters to survive Vibrio infections. (PubMedID: 22708697) BMC genomics
01/01/2012
Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). (PubMedID: 22708723) BMC genomics
01/01/2012
SNP-SIG Meeting 2011: identification and annotation of SNPs in the context of structure, function, and disease. (PubMedID: 22759647) BMC genomics
01/01/2012
Automated extraction and semantic analysis of mutation impacts from the biomedical literature. (PubMedID: 22759648) BMC genomics
01/01/2012
Disease-related mutations predicted to impact protein function. (PubMedID: 22759649) BMC genomics
01/01/2012
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. (PubMedID: 22759650) BMC genomics
01/01/2012
Prioritization of pathogenic mutations in the protein kinase superfamily. (PubMedID: 22759651) BMC genomics
01/01/2012
Predict impact of single amino acid change upon protein structure. (PubMedID: 22759652) BMC genomics
01/01/2012
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. (PubMedID: 22759653) BMC genomics
01/01/2012
Evaluating our ability to predict the structural disruption of RNA by SNPs. (PubMedID: 22759654) BMC genomics
01/01/2012
Large-scale computational identification of regulatory SNPs with rSNP-MAPPER. (PubMedID: 22759655) BMC genomics
01/01/2012
Predicting cancer-associated germline variations in proteins. (PubMedID: 22759656) BMC genomics
01/01/2012
Domain landscapes of somatic mutations in cancer. (PubMedID: 22759657) BMC genomics
01/01/2012
Comparative proteome analysis of Saccharomyces cerevisiae: a global overview of in vivo targets of the yeast activator protein 1. (PubMedID: 22681880) BMC genomics
01/01/2012
Differential transcript profiling through cDNA-AFLP showed complexity of rutin biosynthesis and accumulation in seeds of a nutraceutical food crop (Fagopyrum spp.). (PubMedID: 22686486) BMC genomics
01/01/2012
Transcriptome analysis of microRNAs in developing cerebral cortex of rat. (PubMedID: 22691069) BMC genomics
01/01/2012
A pursuit of lineage-specific and niche-specific proteome features in the world of archaea. (PubMedID: 22691113) BMC genomics
01/01/2012
A defect in dystrophin causes a novel porcine stress syndrome. (PubMedID: 22691118) BMC genomics
01/01/2012
Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species. (PubMedID: 22691139) BMC genomics
01/01/2012
Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack). (PubMedID: 22691168) BMC genomics
01/01/2012
Identification of metagenes and their interactions through large-scale analysis of Arabidopsis gene expression data. (PubMedID: 22694750) BMC genomics
01/01/2012
Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout. (PubMedID: 22694767) BMC genomics
01/01/2012
The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage. (PubMedID: 22759610) BMC genomics
01/01/2012
A LDA-based approach to promoting ranking diversity for genomics information retrieval. (PubMedID: 22759611) BMC genomics
01/01/2012
Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. (PubMedID: 22759612) BMC genomics
01/01/2012
A natural language interface plug-in for cooperative query answering in biological databases. (PubMedID: 22759613) BMC genomics
01/01/2012
Hypotheses generation as supervised link discovery with automated class labeling on large-scale biomedical concept networks. (PubMedID: 22759614) BMC genomics
01/01/2012
Multi-objective dynamic population shuffled frog-leaping biclustering of microarray data. (PubMedID: 22759615) BMC genomics
01/01/2012
Simultaneous prediction of RNA secondary structure and helix coaxial stacking. (PubMedID: 22759616) BMC genomics
01/01/2012
Discriminative application of string similarity methods to chemical and non-chemical names for biomedical abbreviation clustering. (PubMedID: 22759617) BMC genomics
01/01/2012
Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb). (PubMedID: 22672128) BMC genomics
01/01/2012
Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. (PubMedID: 22672192) BMC genomics
01/01/2012
Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. (PubMedID: 22672222) BMC genomics
01/01/2012
A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. (PubMedID: 22672252) BMC genomics
01/01/2012
Large-scale analysis of microRNA evolution. (PubMedID: 22672736) BMC genomics
01/01/2012
Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages. (PubMedID: 22676492) BMC genomics
01/01/2012
Genome-wide characterization of Vibrio phage fpp2 with unique arrangements of the mob-like genes. (PubMedID: 22676552) BMC genomics
01/01/2012
Probing the Xenopus laevis inner ear transcriptome for biological function. (PubMedID: 22676585) BMC genomics
01/01/2012
Comparative analysis of a plant pseudoautosomal region (PAR) in Silene latifolia with the corresponding S. vulgaris autosome. (PubMedID: 22681719) BMC genomics
01/01/2012
Horizontal transfer of expressed genes in a parasitic flowering plant. (PubMedID: 22681756) BMC genomics
01/01/2012
Genomic characterization of two Staphylococcus epidermidis bacteriophages with anti-biofilm potential. (PubMedID: 22681775) BMC genomics
01/01/2012
Anatomy and evolution of telomeric and subtelomeric regions in the human protozoan parasite Trypanosoma cruzi. (PubMedID: 22681854) BMC genomics
01/01/2012
MicroRNA-mRNA interactions in a murine model of hyperoxia-induced bronchopulmonary dysplasia. (PubMedID: 22646479) BMC genomics
01/01/2012
Comparison of Atlantic salmon individuals with different outcomes of cardiomyopathy syndrome (CMS). (PubMedID: 22646522) BMC genomics
01/01/2012
Limitations of the rhesus macaque draft genome assembly and annotation. (PubMedID: 22646658) BMC genomics
01/01/2012
Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. (PubMedID: 22646700) BMC genomics
01/01/2012
A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis. (PubMedID: 22646724) BMC genomics
01/01/2012
Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions. (PubMedID: 22646746) BMC genomics
01/01/2012
Genome-wide analysis of acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. (PubMedID: 22646801) BMC genomics
01/01/2012
Identification of chemosensory receptor genes in Manduca sexta and knockdown by RNA interference. (PubMedID: 22646846) BMC genomics
01/01/2012
High-throughput comparison of gene fitness among related bacteria. (PubMedID: 22646920) BMC genomics
01/01/2012
Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens. (PubMedID: 22646994) BMC genomics
01/01/2012
Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain. (PubMedID: 22651826) BMC genomics
01/01/2012
Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii. (PubMedID: 22651860) BMC genomics
01/01/2012
Insights into the evolution of mammalian telomerase: platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes. (PubMedID: 22655747) BMC genomics
01/01/2012
Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development. (PubMedID: 22655855) BMC genomics
01/01/2012
Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. (PubMedID: 22631220) BMC genomics
01/01/2012
RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. (PubMedID: 22607119) BMC genomics
01/01/2012
Exome sequencing generates high quality data in non-target regions. (PubMedID: 22607156) BMC genomics
01/01/2012
Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb. (PubMedID: 22607188) BMC genomics
01/01/2012
A neutral theory of genome evolution and the frequency distribution of genes. (PubMedID: 22613814) BMC genomics
01/01/2012
Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants. (PubMedID: 22613869) BMC genomics
01/01/2012
A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state. (PubMedID: 22613937) BMC genomics
01/01/2012
Overrepresentation of transcription factor families in the genesets underlying breast cancer subtypes. (PubMedID: 22616941) BMC genomics
01/01/2012
Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae. (PubMedID: 22616984) BMC genomics
01/01/2012
Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra). (PubMedID: 22621340) BMC genomics
01/01/2012
Comparing thousands of circular genomes using the CGView Comparison Tool. (PubMedID: 22621371) BMC genomics
01/01/2012
Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content. (PubMedID: 22587570) BMC genomics
01/01/2012
Genome-wide recruitment to Polycomb-modified chromatin and activity regulation of the synovial sarcoma oncogene SYT-SSX2. (PubMedID: 22594313) BMC genomics
01/01/2012
Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks. (PubMedID: 22594378) BMC genomics
01/01/2012
Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. (PubMedID: 22607086) BMC genomics
01/01/2012
De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). (PubMedID: 22607098) BMC genomics
01/01/2012
Improving the performance of true single molecule sequencing for ancient DNA. (PubMedID: 22574620) BMC genomics
01/01/2012
Improving ancient DNA read mapping against modern reference genomes. (PubMedID: 22574660) BMC genomics
01/01/2012
Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation. (PubMedID: 22574681) BMC genomics
01/01/2012
Genome wide response to dietary tetradecylthioacetic acid supplementation in the heart of Atlantic Salmon (Salmo salar L). (PubMedID: 22577878) BMC genomics
01/01/2012
Fast skeletal muscle transcriptome of the gilthead sea bream (Sparus aurata) determined by next generation sequencing. (PubMedID: 22577894) BMC genomics
01/01/2012
The dependence of expression of NF-?B-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR. (PubMedID: 22577947) BMC genomics
01/01/2012
Identification of avian W-linked contigs by short-read sequencing. (PubMedID: 22583744) BMC genomics
01/01/2012
Transcription profiling reveals stage- and function-dependent expression patterns in the filarial nematode Brugia malayi. (PubMedID: 22583769) BMC genomics
01/01/2012
Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). (PubMedID: 22583801) BMC genomics
01/01/2012
Estimating RNA-quality using GeneChip microarrays. (PubMedID: 22583818) BMC genomics
01/01/2012
Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit. (PubMedID: 22583865) BMC genomics
01/01/2012
Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. (PubMedID: 22559316) BMC genomics
01/01/2012
Expansion of CORE-SINEs in the genome of the Tasmanian devil. (PubMedID: 22559330) BMC genomics
01/01/2012
Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection. (PubMedID: 22559730) BMC genomics
01/01/2012
The footprint of metabolism in the organization of mammalian genomes. (PubMedID: 22568857) BMC genomics
01/01/2012
Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns. (PubMedID: 22568875) BMC genomics
01/01/2012
Construction of physical maps for the sex-specific regions of papaya sex chromosomes. (PubMedID: 22568889) BMC genomics
01/01/2012
MASiVEdb: the Sirevirus Plant Retrotransposon Database. (PubMedID: 22545773) BMC genomics
01/01/2012
Characterization of host microRNAs that respond to DNA virus infection in a crustacean. (PubMedID: 22545795) BMC genomics
01/01/2012
Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma. (PubMedID: 22549044) BMC genomics
01/01/2012
Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe. (PubMedID: 22554201) BMC genomics
01/01/2012
Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. (PubMedID: 22554235) BMC genomics
01/01/2012
Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (Macaca fascicularis) for biomedical research. (PubMedID: 22554259) BMC genomics
01/01/2012
GeSICA: genome segmentation from intra-chromosomal associations. (PubMedID: 22559164) BMC genomics
01/01/2012
A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. (PubMedID: 22559199) BMC genomics
01/01/2012
Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex. (PubMedID: 22559219) BMC genomics
01/01/2012
Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension. (PubMedID: 22559237) BMC genomics
01/01/2012
AlliumMap-A comparative genomics resource for cultivated Allium vegetables. (PubMedID: 22559261) BMC genomics
01/01/2012
Genome organization and characteristics of soybean microRNAs. (PubMedID: 22559273) BMC genomics
01/01/2012
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. (PubMedID: 22559291) BMC genomics
01/01/2012
The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction. (PubMedID: 22533342) BMC genomics
01/01/2012
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. (PubMedID: 22537144) BMC genomics
01/01/2012
Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation. (PubMedID: 22537182) BMC genomics
01/01/2012
MicroRNA modulate alveolar epithelial response to cyclic stretch. (PubMedID: 22537220) BMC genomics
01/01/2012
Evolution of vertebrate interferon inducible transmembrane proteins. (PubMedID: 22537233) BMC genomics
01/01/2012
The stable traits of melanoma genetics: an alternate approach to target discovery. (PubMedID: 22537248) BMC genomics
01/01/2012
Metabolic classification of microbial genomes using functional probes. (PubMedID: 22537274) BMC genomics
01/01/2012
Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. (PubMedID: 22524407) BMC genomics
01/01/2012
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. (PubMedID: 22524439) BMC genomics
01/01/2012
Identification and expression analysis of methyl jasmonate responsive ESTs in paclitaxel producing Taxus cuspidata suspension culture cells. (PubMedID: 22530557) BMC genomics
01/01/2012
Characterization of the transcriptome of an ecologically important avian species, the Vinous-throated Parrotbill Paradoxornis webbianus bulomachus (Paradoxornithidae; Aves). (PubMedID: 22530590) BMC genomics
01/01/2012
Functional organization and its implication in evolution of the human protein-protein interaction network. (PubMedID: 22530615) BMC genomics
01/01/2012
Genome-wide host responses against infectious laryngotracheitis virus vaccine infection in chicken embryo lung cells. (PubMedID: 22530940) BMC genomics
01/01/2012
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. (PubMedID: 22530965) BMC genomics
01/01/2012
Comparing the mitochondrial genomes of Wolbachia-dependent and independent filarial nematode species. (PubMedID: 22530989) BMC genomics
01/01/2012
Meta-analysis of chicken--salmonella infection experiments. (PubMedID: 22531008) BMC genomics
01/01/2012
Genome-wide analysis of Pax8 binding provides new insights into thyroid functions. (PubMedID: 22531031) BMC genomics
01/01/2012
A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. (PubMedID: 22507374) BMC genomics
01/01/2012
Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. (PubMedID: 22507400) BMC genomics
01/01/2012
Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. (PubMedID: 22507456) BMC genomics
01/01/2012
A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea. (PubMedID: 22507536) BMC genomics
01/01/2012
A transcriptome map of perennial ryegrass (Lolium perenne L.). (PubMedID: 22513206) BMC genomics
01/01/2012
De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. (PubMedID: 22494814) BMC genomics
01/01/2012
Gene expression analysis of Drosophilaa Manf mutants reveals perturbations in membrane traffic and major metabolic changes. (PubMedID: 22494833) BMC genomics
01/01/2012
A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation. (PubMedID: 22500940) BMC genomics
01/01/2012
Gene expression in Atlantic salmon skin in response to infection with the parasitic copepod Lepeophtheirus salmonis, cortisol implant, and their combination. (PubMedID: 22480234) BMC genomics
01/01/2012
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. (PubMedID: 22480257) BMC genomics
01/01/2012
Transcriptome-wide identification and characterization of miRNAs from Pinus densata. (PubMedID: 22480283) BMC genomics
01/01/2012
De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. (PubMedID: 22462805) BMC genomics
01/01/2012
Unravelling the molecular basis for light modulated cellulase gene expression - the role of photoreceptors in Neurospora crassa. (PubMedID: 22462823) BMC genomics
01/01/2012
A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains. (PubMedID: 22475007) BMC genomics
01/01/2012
Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. (PubMedID: 22475018) BMC genomics
01/01/2012
The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing. (PubMedID: 22448618) BMC genomics
01/01/2012
Transcriptome landscape of the human placenta. (PubMedID: 22448651) BMC genomics
01/01/2012
RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts. (PubMedID: 22452724) BMC genomics
01/01/2012
Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation. (PubMedID: 22452797) BMC genomics
01/01/2012
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. (PubMedID: 22452820) BMC genomics
01/01/2012
Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. (PubMedID: 22453055) BMC genomics
01/01/2012
Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures. (PubMedID: 22453064) BMC genomics
01/01/2012
Identification of bovine leukemia virus tax function associated with host cell transcription, signaling, stress response and immune response pathway by microarray-based gene expression analysis. (PubMedID: 22455445) BMC genomics
01/01/2012
Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. (PubMedID: 22455456) BMC genomics
01/01/2012
Epigenetic features are significantly associated with alternative splicing. (PubMedID: 22455468) BMC genomics
01/01/2012
Comparative modular analysis of gene expression in vertebrate organs. (PubMedID: 22458817) BMC genomics
01/01/2012
Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). (PubMedID: 22458863) BMC genomics
01/01/2012
Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures. (PubMedID: 22435851) BMC genomics
01/01/2012
Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria. (PubMedID: 22435897) BMC genomics
01/01/2012
Evolutionary forces shaping genomic islands of population differentiation in humans. (PubMedID: 22439654) BMC genomics
01/01/2012
Characterization and differential expression of microRNAs elicited by sulfur deprivation in Chlamydomonas reinhardtii. (PubMedID: 22439676) BMC genomics
01/01/2012
Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. (PubMedID: 22439699) BMC genomics
01/01/2012
Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria. (PubMedID: 22439737) BMC genomics
01/01/2012
Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers. (PubMedID: 22443094) BMC genomics
01/01/2012
Variation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans. (PubMedID: 22443515) BMC genomics
01/01/2012
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. (PubMedID: 22443545) BMC genomics
01/01/2012
A low protein diet during pregnancy provokes a lasting shift of hepatic expression of genes related to cell cycle throughout ontogenesis in a porcine model. (PubMedID: 22424151) BMC genomics
01/01/2012
Genome wide expression profiling of two accession of G. herbaceum L. in response to drought. (PubMedID: 22424186) BMC genomics
01/01/2012
The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don. (PubMedID: 22424262) BMC genomics
01/01/2012
Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). (PubMedID: 22424280) BMC genomics
01/01/2012
Sequence signatures involved in targeting the Male-Specific Lethal complex to X-chromosomal genes in Drosophila melanogaster. (PubMedID: 22424303) BMC genomics
01/01/2012
Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice. (PubMedID: 22429805) BMC genomics
01/01/2012
Quantitative molecular assessment of chimerism across tissues in marmosets and tamarins. (PubMedID: 22429831) BMC genomics
01/01/2012
A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. (PubMedID: 22429863) BMC genomics
01/01/2012
Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency. (PubMedID: 22433273) BMC genomics
01/01/2012
Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq. (PubMedID: 22433311) BMC genomics
01/01/2012
Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades. (PubMedID: 22433423) BMC genomics
01/01/2012
Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. (PubMedID: 22433453) BMC genomics
01/01/2012
Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC. (PubMedID: 22404855) BMC genomics
01/01/2012
Genomic variation in Salmonella enterica core genes for epidemiological typing. (PubMedID: 22409488) BMC genomics
01/01/2012
Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association. (PubMedID: 22409516) BMC genomics
01/01/2012
De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). (PubMedID: 22409576) BMC genomics
01/01/2012
Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons. (PubMedID: 22413862) BMC genomics
01/01/2012
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. (PubMedID: 22417298) BMC genomics
01/01/2012
Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. (PubMedID: 22394504) BMC genomics
01/01/2012
C57Bl/6 N mice on a western diet display reduced intestinal and hepatic cholesterol levels despite a plasma hypercholesterolemia. (PubMedID: 22394543) BMC genomics
01/01/2012
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. (PubMedID: 22397531) BMC genomics
01/01/2012
Comparative genomics reveals evidence of marine adaptation in Salinispora species. (PubMedID: 22401625) BMC genomics
01/01/2012
Altered gene expression profiles in the hippocampus and prefrontal cortex of type 2 diabetic rats. (PubMedID: 22369239) BMC genomics
01/01/2012
Stepwise kinetic equilibrium models of quantitative polymerase chain reaction. (PubMedID: 22897900) BMC bioinformatics
01/01/2012
Enabling dynamic network analysis through visualization in TVNViewer. (PubMedID: 22897913) BMC bioinformatics
01/01/2012
Reconstructing DNA copy number by joint segmentation of multiple sequences. (PubMedID: 22897923) BMC bioinformatics
01/01/2012
CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes. (PubMedID: 22901030) BMC bioinformatics
01/01/2012
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. (PubMedID: 22901054) BMC bioinformatics
01/01/2012
Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data. (PubMedID: 22873695) BMC bioinformatics
01/01/2012
RNA-Seq quantification of the human small airway epithelium transcriptome. (PubMedID: 22375630) BMC genomics
01/01/2012
A minimal model of peptide binding predicts ensemble properties of serum antibodies. (PubMedID: 22353141) BMC genomics
01/01/2012
High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. (PubMedID: 22356647) BMC genomics
01/01/2012
High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. (PubMedID: 22336032) BMC genomics
01/01/2012
GemSIM: general, error-model based simulator of next-generation sequencing data. (PubMedID: 22336055) BMC genomics
01/01/2012
Identification and localisation of the NB-LRR gene family within the potato genome. (PubMedID: 22336098) BMC genomics
01/01/2012
Sexual and asexual oogenesis require the expression of unique and shared sets of genes in the insect Acyrthosiphon pisum. (PubMedID: 22336141) BMC genomics
01/01/2012
Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method. (PubMedID: 22340203) BMC genomics
01/01/2012
Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. (PubMedID: 22340285) BMC genomics
01/01/2012
Transcriptome profiling of low temperature-treated cassava apical shoots showed dynamic responses of tropical plant to cold stress. (PubMedID: 22321773) BMC genomics
01/01/2012
Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data. (PubMedID: 22325056) BMC genomics
01/01/2012
Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands. (PubMedID: 22325062) BMC genomics
01/01/2012
Aluminum tolerance association mapping in triticale. (PubMedID: 22330691) BMC genomics
01/01/2012
Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis. (PubMedID: 22330747) BMC genomics
01/01/2012
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC. (PubMedID: 22333191) BMC genomics
01/01/2012
Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus. (PubMedID: 22333217) BMC genomics
01/01/2012
Identification of common genetic modifiers of neurodegenerative diseases from an integrative analysis of diverse genetic screens in model organisms. (PubMedID: 22333271) BMC genomics
01/01/2012
Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. (PubMedID: 22333298) BMC genomics
01/01/2012
Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters. (PubMedID: 22309450) BMC genomics
01/01/2012
Ac/Ds-transposon activation tagging in poplar: a powerful tool for gene discovery. (PubMedID: 22309468) BMC genomics
01/01/2012
Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter. (PubMedID: 22309491) BMC genomics
01/01/2012
Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages. (PubMedID: 22321740) BMC genomics
01/01/2012
Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice. (PubMedID: 22289642) BMC genomics
01/01/2012
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages. (PubMedID: 22292898) BMC genomics
01/01/2012
Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR. (PubMedID: 22296850) BMC genomics
01/01/2012
Microgravity simulation by diamagnetic levitation: effects of a strong gradient magnetic field on the transcriptional profile of Drosophila melanogaster. (PubMedID: 22296880) BMC genomics
01/01/2012
Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution. (PubMedID: 22296923) BMC genomics
01/01/2012
Zonation related function and ubiquitination regulation in human hepatocellular carcinoma cells in dynamic vs. static culture conditions. (PubMedID: 22296956) BMC genomics
01/01/2012
Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics. (PubMedID: 22300585) BMC genomics
01/01/2012
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. (PubMedID: 22300633) BMC genomics
01/01/2012
Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis. (PubMedID: 22300648) BMC genomics
01/01/2012
Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes. (PubMedID: 22305460) BMC genomics
01/01/2012
Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens. (PubMedID: 22305654) BMC genomics
01/01/2012
Identification of differentially expressed genes in SHSY5Y cells exposed to okadaic acid by suppression subtractive hybridization. (PubMedID: 22284234) BMC genomics
01/01/2012
Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome. (PubMedID: 22289472) BMC genomics
01/01/2012
Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle. (PubMedID: 22289501) BMC genomics
01/01/2012
Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida. (PubMedID: 22272603) BMC genomics
01/01/2012
Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. (PubMedID: 22272658) BMC genomics
01/01/2012
The core and unique proteins of haloarchaea. (PubMedID: 22272718) BMC genomics
01/01/2012
Genetic diversity of human RNase 8. (PubMedID: 22272736) BMC genomics
01/01/2012
The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis. (PubMedID: 22272770) BMC genomics
01/01/2012
An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies. (PubMedID: 22276688) BMC genomics
01/01/2012
Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis. (PubMedID: 22276739) BMC genomics
01/01/2012
miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. (PubMedID: 22276777) BMC genomics
01/01/2012
Transcriptional profiling of bovine milk using RNA sequencing. (PubMedID: 22276848) BMC genomics
01/01/2012
Quantification and accurate normalisation of small RNAs through new custom RT-qPCR arrays demonstrates Salmonella-induced microRNAs in human monocytes. (PubMedID: 22248082) BMC genomics
01/01/2012
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression. (PubMedID: 22251276) BMC genomics
01/01/2012
Postmortem cardiac tissue maintains gene expression profile even after late harvesting. (PubMedID: 22251372) BMC genomics
01/01/2012
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. (PubMedID: 22251412) BMC genomics
01/01/2012
Estimation of linkage disequilibrium in four US pig breeds. (PubMedID: 22252454) BMC genomics
01/01/2012
Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA. (PubMedID: 22257641) BMC genomics
01/01/2012
Centromere-associated repeat arrays on Trypanosoma brucei chromosomes are much more extensive than predicted. (PubMedID: 22257693) BMC genomics
01/01/2012
Microarray analysis on germfree mice elucidates the primary target of a traditional Japanese medicine juzentaihoto: acceleration of IFN-a response via affecting the ISGF3-IRF7 signaling cascade. (PubMedID: 22257721) BMC genomics
01/01/2012
Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes. (PubMedID: 22257742) BMC genomics
01/01/2012
IntegromeDB: an integrated system and biological search engine. (PubMedID: 22260095) BMC genomics
01/01/2012
High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach. (PubMedID: 22260654) BMC genomics
01/01/2012
Transcriptional ontogeny of the developing liver. (PubMedID: 22260730) BMC genomics
01/01/2012
Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. (PubMedID: 22260749) BMC genomics
01/01/2012
A metabolomic strategy defines the regulation of lipid content and global metabolism by ?9 desaturases in Caenorhabditis elegans. (PubMedID: 22264337) BMC genomics
01/01/2012
Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples. (PubMedID: 22235840) BMC genomics
01/01/2012
Lipopolysaccharide priming enhances expression of effectors of immune defence while decreasing expression of pro-inflammatory cytokines in mammary epithelia cells from cows. (PubMedID: 22235868) BMC genomics
01/01/2012
Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing. (PubMedID: 22239826) BMC genomics
01/01/2012
Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. (PubMedID: 22244270) BMC genomics
01/01/2012
Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome. (PubMedID: 22244314) BMC genomics
01/01/2012
Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome. (PubMedID: 22244352) BMC genomics
01/01/2012
Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds. (PubMedID: 22244367) BMC genomics
01/01/2012
RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug. (PubMedID: 22226239) BMC genomics
01/01/2012
Rootstock-regulated gene expression patterns associated with fire blight resistance in apple. (PubMedID: 22229964) BMC genomics
01/01/2012
Transcriptome changes during fruit development and ripening of sweet orange (Citrus sinensis). (PubMedID: 22230690) BMC genomics
01/01/2012
Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits. (PubMedID: 22230737) BMC genomics
01/01/2012
Quantitative Interactor Screening with next-generation Sequencing (QIS-Seq) identifies Arabidopsis thaliana MLO2 as a target of the Pseudomonas syringae type III effector HopZ2. (PubMedID: 22230763) BMC genomics
01/01/2012
SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. (PubMedID: 22233093) BMC genomics
01/01/2012
Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation. (PubMedID: 22233127) BMC genomics
01/01/2012
Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. (PubMedID: 22233149) BMC genomics
01/01/2012
Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development. (PubMedID: 22233483) BMC genomics
01/01/2012
A searchable cross-platform gene expression database reveals connections between drug treatments and disease. (PubMedID: 22233519) BMC genomics
01/01/2012
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. (PubMedID: 22214261) BMC genomics
01/01/2012
Yeast-based assay identifies novel Shh/Gli target genes in vertebrate development. (PubMedID: 22214306) BMC genomics
01/01/2012
RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. (PubMedID: 22214349) BMC genomics
01/01/2012
Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel. (PubMedID: 22216965) BMC genomics
01/01/2012
Controversies in modern evolutionary biology: the imperative for error detection and quality control. (PubMedID: 22217008) BMC genomics
01/01/2012
Quantification and clustering of phenotypic screening data using time-series analysis for chemotherapy of schistosomiasis. (PubMedID: 22369037) BMC genomics
01/01/2012
Learning generative models of molecular dynamics. (PubMedID: 22369071) BMC genomics
01/01/2012
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. (PubMedID: 22369122) BMC genomics
01/01/2012
A mixture framework for inferring ancestral gene orders. (PubMedID: 22369143) BMC genomics
01/01/2012
A model for biased fractionation after whole genome duplication. (PubMedID: 22369177) BMC genomics
01/01/2012
Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB). (PubMedID: 22369214) BMC genomics
01/01/2012
The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). Introduction. (PubMedID: 22369290) BMC genomics
01/01/2012
Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information. (PubMedID: 22369349) BMC genomics
01/01/2012
Identification of gene-oriented exon orthology between human and mouse. (PubMedID: 22369432) BMC genomics
01/01/2012
A study on promoter characteristics of head-to-head genes in Saccharomyces cerevisiae. (PubMedID: 22369481) BMC genomics
01/01/2012
An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems. (PubMedID: 22369509) BMC genomics
01/01/2012
miRNA arm selection and isomiR distribution in gastric cancer. (PubMedID: 22369582) BMC genomics
01/01/2012
CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications. (PubMedID: 22369626) BMC genomics
01/01/2012
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. (PubMedID: 22369646) BMC genomics
01/01/2012
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. (PubMedID: 22369666) BMC genomics
01/01/2012
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. (PubMedID: 22369687) BMC genomics
01/01/2012
Analysis of composition-based metagenomic classification. (PubMedID: 23095761) BMC genomics
01/01/2012
Comparing the reconstruction of regulatory pathways with distinct Bayesian networks inference methods. (PubMedID: 23095805) BMC genomics
01/01/2012
MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques. (PubMedID: 23095859) BMC genomics
01/01/2012
Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer. (PubMedID: 23095915) BMC genomics
01/01/2012
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome. (PubMedID: 23095951) BMC genomics
01/01/2012
Searching joint association signals in CATIE schizophrenia genome-wide association studies through a refined integrative network approach. (PubMedID: 23134571) BMC genomics
01/01/2012
Effective normalization for copy number variation detection from whole genome sequencing. (PubMedID: 23134596) BMC genomics
01/01/2012
C²Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships. (PubMedID: 23134618) BMC genomics
01/01/2012
Atlas2 Cloud: a framework for personal genome analysis in the cloud. (PubMedID: 23134663) BMC genomics
01/01/2012
A systematic model of the LC-MS proteomics pipeline. (PubMedID: 23134670) BMC genomics
01/01/2012
A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles. (PubMedID: 23134689) BMC genomics
01/01/2012
Mathematical modeling and stability analysis of macrophage activation in left ventricular remodeling post-myocardial infarction. (PubMedID: 23134700) BMC genomics
01/01/2012
Selected articles from the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'2011). (PubMedID: 23134705) BMC genomics
01/01/2012
Integrative genome-wide chromatin signature analysis using finite mixture models. (PubMedID: 23134707) BMC genomics
01/01/2012
Efficient calculation of steady state probability distribution for stochastic biochemical reaction network. (PubMedID: 23134718) BMC genomics
01/01/2012
Boolean modeling and fault diagnosis in oxidative stress response. (PubMedID: 23134720) BMC genomics
01/01/2012
Assessing the efficacy of molecularly targeted agents on cell line-based platforms by using system identification. (PubMedID: 23134733) BMC genomics
01/01/2012
Application of Max-SAT-based ATPG to optimal cancer therapy design. (PubMedID: 23134738) BMC genomics
01/01/2012
Adaptive reference update (ARU) algorithm. A stochastic search algorithm for efficient optimization of multi-drug cocktails. (PubMedID: 23134742) BMC genomics
01/01/2012
A modulator based regulatory network for ERa signaling pathway. (PubMedID: 23134758) BMC genomics
01/01/2012
Assessing the gain of biological data integration in gene networks inference. (PubMedID: 23134775) BMC genomics
01/01/2012
Methods for high-throughput MethylCap-Seq data analysis. (PubMedID: 23134780) BMC genomics
01/01/2012
A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis. (PubMedID: 23134806) BMC genomics
01/01/2012
Boolean network inference from time series data incorporating prior biological knowledge. (PubMedID: 23134816) BMC genomics
01/01/2012
A UML profile for the OBO relation ontology. (PubMedID: 23095840) BMC genomics
01/01/2012
Pathway Distiller - multisource biological pathway consolidation. (PubMedID: 23134636) BMC genomics
01/01/2012
Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer. (PubMedID: 23134756) BMC genomics
01/01/2012
Analysis of high-throughput RNAi screening data in identifying genes mediating sensitivity to chemotherapeutic drugs: statistical approaches and perspectives. (PubMedID: 23281588) BMC genomics
01/01/2012
Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs. (PubMedID: 23281599) BMC genomics
01/01/2012
snpTree--a web-server to identify and construct SNP trees from whole genome sequence data. (PubMedID: 23281601) BMC genomics
01/01/2012
Genomic sequence analysis and characterization of Sneathia amnii sp. nov. (PubMedID: 23281612) BMC genomics
01/01/2012
A computational tool for the design of live attenuated virus vaccine based on microRNA-mediated gene silencing. (PubMedID: 23281624) BMC genomics
01/01/2012
Redistribution of H3K4me2 on neural tissue specific genes during mouse brain development. (PubMedID: 23281639) BMC genomics
01/01/2012
C-mii: a tool for plant miRNA and target identification. (PubMedID: 23281648) BMC genomics
01/01/2012
Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes. (PubMedID: 23281662) BMC genomics
01/01/2012
MicroRNA-centric measurement improves functional enrichment analysis of co-expressed and differentially expressed microRNA clusters. (PubMedID: 23281707) BMC genomics
01/01/2012
Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. (PubMedID: 23281708) BMC genomics
01/01/2012
Comprehensive analysis of microRNAs in breast cancer. (PubMedID: 23281739) BMC genomics
01/01/2012
Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. (PubMedID: 23281772) BMC genomics
01/01/2012
The parasite specific substitution matrices improve the annotation of apicomplexan proteins. (PubMedID: 23281791) BMC genomics
01/01/2012
BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data. (PubMedID: 23281802) BMC genomics
01/01/2012
Feasibility of using 454 pyrosequencing for studying quasispecies of the whole dengue viral genome. (PubMedID: 23281804) BMC genomics
01/01/2012
iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies. (PubMedID: 23281813) BMC genomics
01/01/2012
Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs). (PubMedID: 23281827) BMC genomics
01/01/2012
Blocking protein kinase C signaling pathway: mechanistic insights into the anti-leishmanial activity of prospective herbal drugs from Withania somnifera. (PubMedID: 23281834) BMC genomics
01/01/2012
Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets. (PubMedID: 23281852) BMC genomics
01/01/2012
FastAnnotator--an efficient transcript annotation web tool. (PubMedID: 23281853) BMC genomics
01/01/2012
Genomics in 2012: challenges and opportunities in the next generation sequencing era. (PubMedID: 23281891) BMC genomics
01/01/2012
In silico engineering of aggregation-prone recombinant proteins for substrate recognition by the chaperonin GroEL. (PubMedID: 23281895) BMC genomics
01/01/2012
Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. (PubMedID: 23281921) BMC genomics
01/01/2012
An approach to identifying drug resistance associated mutations in bacterial strains. (PubMedID: 23281931) BMC genomics
01/01/2012
DFI: gene feature discovery in RNA-seq experiments from multiple sources. (PubMedID: 23281963) BMC genomics
01/01/2012
Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era. (PubMedID: 23281970) BMC genomics
01/01/2012
Combining multiple ChIP-seq peak detection systems using combinatorial fusion. (PubMedID: 23282014) BMC genomics
01/01/2012
Discovering pathway cross-talks based on functional relations between pathways. (PubMedID: 23282018) BMC genomics
01/01/2012
Comparison and evaluation of pathway-level aggregation methods of gene expression data. (PubMedID: 23282027) BMC genomics
01/01/2012
A Bayesian decision fusion approach for microRNA target prediction. (PubMedID: 23282032) BMC genomics
01/01/2012
Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data. (PubMedID: 23282070) BMC genomics
01/01/2012
Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma. (PubMedID: 23282077) BMC genomics
01/01/2012
Advances in translational bioinformatics and population genomics in the Asia-Pacific. (PubMedID: 23282089) BMC genomics
01/01/2012
A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework. (PubMedID: 23282094) BMC genomics
01/01/2012
Automatically clustering large-scale miRNA sequences: methods and experiments. (PubMedID: 23282099) BMC genomics
01/01/2012
An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications. (PubMedID: 23282110) BMC genomics
01/01/2012
Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand. (PubMedID: 23282134) BMC genomics
01/01/2012
Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study. (PubMedID: 23282140) BMC genomics
01/01/2012
A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription. (PubMedID: 23282148) BMC genomics
01/01/2012
Bayesian prediction of bacterial growth temperature range based on genome sequences. (PubMedID: 23282160) BMC genomics
01/01/2012
Species-level classification of the vaginal microbiome. (PubMedID: 23282177) BMC genomics
01/01/2012
Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates. (PubMedID: 23282184) BMC genomics
01/01/2012
Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes. (PubMedID: 23282187) BMC genomics
01/01/2012
CTF: a CRF-based transcription factor binding sites finding system. (PubMedID: 23282203) BMC genomics
01/01/2012
Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs. (PubMedID: 23282220) BMC genomics
01/01/2012
Quantitative assessment of mitochondrial DNA copies from whole genome sequencing. (PubMedID: 23282223) BMC genomics
01/01/2012
Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics. (PubMedID: 23282225) BMC genomics
01/01/2012
RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia. (PubMedID: 23282246) BMC genomics
01/01/2012
GLAD4U: deriving and prioritizing gene lists from PubMed literature. (PubMedID: 23282288) BMC genomics
01/01/2012
Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. (PubMedID: 23282337) BMC genomics
01/01/2012
New methods for separating causes from effects in genomics data. (PubMedID: 23282373) BMC genomics
01/01/2012
Literature aided determination of data quality and statistical significance threshold for gene expression studies. (PubMedID: 23282414) BMC genomics
01/01/2012
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation. (PubMedID: 23442169) BMC genomics
01/01/2012
An assessment on epitope prediction methods for protozoa genomes. (PubMedID: 23170965) BMC bioinformatics
01/01/2012
Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data. (PubMedID: 23171000) BMC bioinformatics
01/01/2012
Bioinformatics Resource Manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools. (PubMedID: 23174015) BMC bioinformatics
01/01/2012
Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search. (PubMedID: 23174036) BMC bioinformatics
01/01/2012
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. (PubMedID: 23176036) BMC bioinformatics
01/01/2012
Local functional descriptors for surface comparison based binding prediction. (PubMedID: 23176080) BMC bioinformatics
01/01/2012
Improving protein coreference resolution by simple semantic classification. (PubMedID: 23157272) BMC bioinformatics
01/01/2012
Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. (PubMedID: 23157288) BMC bioinformatics
01/01/2012
Gains of ubiquitylation sites in highly conserved proteins in the human lineage. (PubMedID: 23157318) BMC bioinformatics
01/01/2012
Multiple graph regularized protein domain ranking. (PubMedID: 23157331) BMC bioinformatics
01/01/2012
Estimating relative abundances of proteins from shotgun proteomics data. (PubMedID: 23164367) BMC bioinformatics
01/01/2012
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. (PubMedID: 23146171) BMC bioinformatics
01/01/2012
iMS2Flux--a high-throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis. (PubMedID: 23146204) BMC bioinformatics
01/01/2012
Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation. (PubMedID: 23148417) BMC bioinformatics
01/01/2012
Oculus: faster sequence alignment by streaming read compression. (PubMedID: 23148484) BMC bioinformatics
01/01/2012
Improving accuracy for cancer classification with a new algorithm for genes selection. (PubMedID: 23148517) BMC bioinformatics
01/01/2012
Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence. (PubMedID: 23148531) BMC bioinformatics
01/01/2012
Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects. (PubMedID: 23151154) BMC bioinformatics
01/01/2012
NRE: a tool for exploring neutral loci in the human genome. (PubMedID: 23151206) BMC bioinformatics
01/01/2012
PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides. (PubMedID: 23151233) BMC bioinformatics
01/01/2012
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. (PubMedID: 23151247) BMC bioinformatics
01/01/2012
mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines. (PubMedID: 23130999) BMC bioinformatics
01/01/2012
Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching. (PubMedID: 23137144) BMC bioinformatics
01/01/2012
Effective inter-residue contact definitions for accurate protein fold recognition. (PubMedID: 23140471) BMC bioinformatics
01/01/2012
The tree alignment problem. (PubMedID: 23140486) BMC bioinformatics
01/01/2012
Combing the hairball with BioFabric: a new approach for visualization of large networks. (PubMedID: 23102059) BMC bioinformatics
01/01/2012
Coral: an integrated suite of visualizations for comparing clusterings. (PubMedID: 23102108) BMC bioinformatics
01/01/2012
Simple binary segmentation frameworks for identifying variation in DNA copy number. (PubMedID: 23107320) BMC bioinformatics
01/01/2012
Bayesian semiparametric regression models to characterize molecular evolution. (PubMedID: 23107360) BMC bioinformatics
01/01/2012
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. (PubMedID: 23110596) BMC bioinformatics
01/01/2012
Multi-scale RNA comparison based on RNA triple vector curve representation. (PubMedID: 23110635) BMC bioinformatics
01/01/2012
Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors. (PubMedID: 23110660) BMC bioinformatics
01/01/2012
Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer. (PubMedID: 23110677) BMC bioinformatics
01/01/2012
Denoising PCR-amplified metagenome data. (PubMedID: 23113967) BMC bioinformatics
01/01/2012
A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies. (PubMedID: 23113980) BMC bioinformatics
01/01/2012
Gene expression anti-profiles as a basis for accurate universal cancer signatures. (PubMedID: 23088656) BMC bioinformatics
01/01/2012
Exploiting protein flexibility to predict the location of allosteric sites. (PubMedID: 23095452) BMC bioinformatics
01/01/2012
A quantitative genetic and epigenetic model of complex traits. (PubMedID: 23102025) BMC bioinformatics
01/01/2012
Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data. (PubMedID: 23075381) BMC bioinformatics
01/01/2012
dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. (PubMedID: 23083219) BMC bioinformatics
01/01/2012
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. (PubMedID: 23061897) BMC bioinformatics
01/01/2012
Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods. (PubMedID: 23061930) BMC bioinformatics
01/01/2012
Tissue-based Alzheimer gene expression markers-comparison of multiple machine learning approaches and investigation of redundancy in small biomarker sets. (PubMedID: 23066814) BMC bioinformatics
01/01/2012
MetNet Online: a novel integrated resource for plant systems biology. (PubMedID: 23066841) BMC bioinformatics
01/01/2012
Simple regression models as a threshold for selecting AFLP loci with reduced error rates. (PubMedID: 23072295) BMC bioinformatics
01/01/2012
Gene Fusion Markup Language: a prototype for exchanging gene fusion data. (PubMedID: 23072312) BMC bioinformatics
01/01/2012
Frnakenstein: multiple target inverse RNA folding. (PubMedID: 23043260) BMC bioinformatics
01/01/2012
Semantic similarity in the biomedical domain: an evaluation across knowledge sources. (PubMedID: 23046094) BMC bioinformatics
01/01/2012
Cluster-based assessment of protein-protein interaction confidence. (PubMedID: 23050565) BMC bioinformatics
01/01/2012
Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis. (PubMedID: 23057711) BMC bioinformatics
01/01/2012
VarioML framework for comprehensive variation data representation and exchange. (PubMedID: 23031277) BMC bioinformatics
01/01/2012
Normalized N50 assembly metric using gap-restricted co-linear chaining. (PubMedID: 23031320) BMC bioinformatics
01/01/2012
A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. (PubMedID: 23033843) BMC bioinformatics
01/01/2012
Coalescent: an open-source and scalable framework for exact calculations in coalescent theory. (PubMedID: 23033878) BMC bioinformatics
01/01/2012
DMET-analyzer: automatic analysis of Affymetrix DMET data. (PubMedID: 23035929) BMC bioinformatics
01/01/2012
Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment. (PubMedID: 23039758) BMC bioinformatics
01/01/2012
HIDEN: Hierarchical decomposition of regulatory networks. (PubMedID: 23016513) BMC bioinformatics
01/01/2012
Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). (PubMedID: 23017167) BMC bioinformatics
01/01/2012
The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. (PubMedID: 23020215) BMC bioinformatics
01/01/2012
QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data. (PubMedID: 23020243) BMC bioinformatics
01/01/2012
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. (PubMedID: 23020263) BMC bioinformatics
01/01/2012
Regulatory network operations in the Pathway Tools software. (PubMedID: 22998532) BMC bioinformatics
01/01/2012
The LO-BaFL method and ALS microarray expression analysis. (PubMedID: 23006766) BMC bioinformatics
01/01/2012
An algorithm for chemical genomic profiling that minimizes batch effects: bucket evaluations. (PubMedID: 23009392) BMC bioinformatics
01/01/2012
ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. (PubMedID: 23009561) BMC bioinformatics
01/01/2012
ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing. (PubMedID: 23009593) BMC bioinformatics
01/01/2012
The simulation of meiosis in diploid and tetraploid organisms using various genetic models. (PubMedID: 23013469) BMC bioinformatics
01/01/2012
Correlation analysis of the side-chains conformational distribution in bound and unbound proteins. (PubMedID: 22984947) BMC bioinformatics
01/01/2012
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach. (PubMedID: 22984983) BMC bioinformatics
01/01/2012
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. (PubMedID: 22988817) BMC bioinformatics
01/01/2012
SNP calling by sequencing pooled samples. (PubMedID: 22992255) BMC bioinformatics
01/01/2012
The Ruby UCSC API: accessing the UCSC genome database using Ruby. (PubMedID: 22994508) BMC bioinformatics
01/01/2012
Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. (PubMedID: 22998471) BMC bioinformatics
01/01/2012
Quality assessment of protein model-structures based on structural and functional similarities. (PubMedID: 22998498) BMC bioinformatics
01/01/2012
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. (PubMedID: 22967011) BMC bioinformatics
01/01/2012
Highly improved homopolymer aware nucleotide-protein alignments with 454 data. (PubMedID: 22971057) BMC bioinformatics
01/01/2012
Quick, "imputation-free" meta-analysis with proxy-SNPs. (PubMedID: 22971100) BMC bioinformatics
01/01/2012
Ranked retrieval of segmented nuclei for objective assessment of cancer gene repositioning. (PubMedID: 22971117) BMC bioinformatics
01/01/2012
Automatic classification of protein structures relying on similarities between alignments. (PubMedID: 22974051) BMC bioinformatics
01/01/2012
Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling). (PubMedID: 22974078) BMC bioinformatics
01/01/2012
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. (PubMedID: 22978315) BMC bioinformatics
01/01/2012
ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs. (PubMedID: 22958836) BMC bioinformatics
01/01/2012
Improved model quality assessment using ProQ2. (PubMedID: 22963006) BMC bioinformatics
01/01/2012
Coupled mutation finder: a new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations. (PubMedID: 22963049) BMC bioinformatics
01/01/2012
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. (PubMedID: 22966941) BMC bioinformatics
01/01/2012
The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules. (PubMedID: 22966958) BMC bioinformatics
01/01/2012
Protein-DNA docking with a coarse-grained force field. (PubMedID: 22966980) BMC bioinformatics
01/01/2012
Proceedings of the NETTAB 2011 Workshop on Clinical Bioinformatics Pavia, Italy. 12-14 October 2011. (PubMedID: 23046162) BMC bioinformatics
01/01/2012
CerealsDB 2.0: an integrated resource for plant breeders and scientists. (PubMedID: 22943283) BMC bioinformatics
01/01/2012
TFinDit: transcription factor-DNA interaction data depository. (PubMedID: 22943312) BMC bioinformatics
01/01/2012
ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. (PubMedID: 22946927) BMC bioinformatics
01/01/2012
Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray. (PubMedID: 22950634) BMC bioinformatics
01/01/2012
GenNon-h: generating multiple sequence alignments on nonhomogeneous phylogenetic trees. (PubMedID: 22928840) BMC bioinformatics
01/01/2012
Process attributes in bio-ontologies. (PubMedID: 22928880) BMC bioinformatics
01/01/2012
Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: incorporating EGFR signaling pathway and angiogenesis. (PubMedID: 22935054) BMC bioinformatics
01/01/2012
Sampling issues in quantitative analysis of dendritic spines morphology. (PubMedID: 22920322) BMC bioinformatics
01/01/2012
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. (PubMedID: 22920415) BMC bioinformatics
01/01/2012
FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry. (PubMedID: 22906155) BMC bioinformatics
01/01/2012
Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. (PubMedID: 22909249) BMC bioinformatics
01/01/2012
A support vector machine based test for incongruence between sets of trees in tree space. (PubMedID: 22909268) BMC bioinformatics
01/01/2012
NetiNeti: discovery of scientific names from text using machine learning methods. (PubMedID: 22913485) BMC bioinformatics
01/01/2012
Screening of selective histone deacetylase inhibitors by proteochemometric modeling. (PubMedID: 22913517) BMC bioinformatics
01/01/2012
Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds. (PubMedID: 22888776) BMC bioinformatics
01/01/2012
SDAR: a practical tool for graphical analysis of two-dimensional data. (PubMedID: 22892030) BMC bioinformatics
01/01/2012
An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters. (PubMedID: 22897887) BMC bioinformatics
01/01/2012
Web tools for large-scale 3D biological images and atlases. (PubMedID: 22676296) BMC bioinformatics
01/01/2012
Quartet decomposition server: a platform for analyzing phylogenetic trees. (PubMedID: 22676320) BMC bioinformatics
01/01/2012
BioWord: a sequence manipulation suite for Microsoft Word. (PubMedID: 22676326) BMC bioinformatics
01/01/2012
PollenCALC: software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species. (PubMedID: 22676372) BMC bioinformatics
01/01/2012
Identifying dysregulated pathways in cancers from pathway interaction networks. (PubMedID: 22676414) BMC bioinformatics
01/01/2012
The language of gene ontology: a Zipf's law analysis. (PubMedID: 22676436) BMC bioinformatics
01/01/2012
ROCS: a reproducibility index and confidence score for interaction proteomics studies. (PubMedID: 22682516) BMC bioinformatics
01/01/2012
MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. (PubMedID: 22646090) BMC bioinformatics
01/01/2012
Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. (PubMedID: 22646858) BMC bioinformatics
01/01/2012
Molecular ecological network analyses. (PubMedID: 22646978) BMC bioinformatics
01/01/2012
Detection and correction of probe-level artefacts on microarrays. (PubMedID: 22647057) BMC bioinformatics
01/01/2012
PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. (PubMedID: 22647087) BMC bioinformatics
01/01/2012
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features. (PubMedID: 22651691) BMC bioinformatics
01/01/2012
Multiple structure alignment with msTALI. (PubMedID: 22607234) BMC bioinformatics
01/01/2012
Natural product-likeness score revisited: an open-source, open-data implementation. (PubMedID: 22607271) BMC bioinformatics
01/01/2012
Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval. (PubMedID: 22621237) BMC bioinformatics
01/01/2012
Extracting semantically enriched events from biomedical literature. (PubMedID: 22621266) BMC bioinformatics
01/01/2012
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. (PubMedID: 22621308) BMC bioinformatics
01/01/2012
TreeSnatcher plus: capturing phylogenetic trees from images. (PubMedID: 22624611) BMC bioinformatics
01/01/2012
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. (PubMedID: 22624656) BMC bioinformatics
01/01/2012
The partitioned LASSO-patternsearch algorithm with application to gene expression data. (PubMedID: 22587526) BMC bioinformatics
01/01/2012
Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data. (PubMedID: 22591016) BMC bioinformatics
01/01/2012
MELTING, a flexible platform to predict the melting temperatures of nucleic acids. (PubMedID: 22591039) BMC bioinformatics
01/01/2012
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. (PubMedID: 22591066) BMC bioinformatics
01/01/2012
Workflows for microarray data processing in the Kepler environment. (PubMedID: 22594911) BMC bioinformatics
01/01/2012
rCUR: an R package for CUR matrix decomposition. (PubMedID: 22594948) BMC bioinformatics
01/01/2012
Profile-based short linear protein motif discovery. (PubMedID: 22607209) BMC bioinformatics
01/01/2012
SparSNP: fast and memory-efficient analysis of all SNPs for phenotype prediction. (PubMedID: 22574887) BMC bioinformatics
01/01/2012
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. (PubMedID: 22574904) BMC bioinformatics
01/01/2012
Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems. (PubMedID: 22574924) BMC bioinformatics
01/01/2012
GeVaDSs - decision support system for novel Genetic Vaccine development process. (PubMedID: 22574945) BMC bioinformatics
01/01/2012
A comparative evaluation of sequence classification programs. (PubMedID: 22574964) BMC bioinformatics
01/01/2012
An in silico platform for the design of heterologous pathways in nonnative metabolite production. (PubMedID: 22578364) BMC bioinformatics
01/01/2012
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. (PubMedID: 22578440) BMC bioinformatics
01/01/2012
3DMolNavi: a web-based retrieval and navigation tool for flexible molecular shape comparison. (PubMedID: 22583488) BMC bioinformatics
01/01/2012
SIS: a program to generate draft genome sequence scaffolds for prokaryotes. (PubMedID: 22583530) BMC bioinformatics
01/01/2012
Exploration of multivariate analysis in microbial coding sequence modeling. (PubMedID: 22583558) BMC bioinformatics
01/01/2012
False discovery rate control in two-stage designs. (PubMedID: 22559038) BMC bioinformatics
01/01/2012
Readjoiner: a fast and memory efficient string graph-based sequence assembler. (PubMedID: 22559072) BMC bioinformatics
01/01/2012
Detecting long tandem duplications in genomic sequences. (PubMedID: 22568762) BMC bioinformatics
01/01/2012
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny. (PubMedID: 22568790) BMC bioinformatics
01/01/2012
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. (PubMedID: 22568821) BMC bioinformatics
01/01/2012
DIPSBC--data integration platform for systems biology collaborations. (PubMedID: 22568834) BMC bioinformatics
01/01/2012
DNA methylation arrays as surrogate measures of cell mixture distribution. (PubMedID: 22568884) BMC bioinformatics
01/01/2012
Introduction: Advanced intelligent computing theories and their applications in bioinformatics. (PubMedID: 22594994) BMC bioinformatics
01/01/2012
Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity. (PubMedID: 22594995) BMC bioinformatics
01/01/2012
Modeling the interactions of Alzheimer-related genes from the whole brain microarray data and diffusion tensor images of human brain. (PubMedID: 22594996) BMC bioinformatics
01/01/2012
Pattern-driven neighborhood search for biclustering of microarray data. (PubMedID: 22594997) BMC bioinformatics
01/01/2012
Genovar: a detection and visualization tool for genomic variants. (PubMedID: 22594998) BMC bioinformatics
01/01/2012
ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval. (PubMedID: 22594999) BMC bioinformatics
01/01/2012
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration. (PubMedID: 22595000) BMC bioinformatics
01/01/2012
An overlapping module identification method in protein-protein interaction networks. (PubMedID: 22595001) BMC bioinformatics
01/01/2012
Prediction of protein-protein interactions between viruses and human by an SVM model. (PubMedID: 22595002) BMC bioinformatics
01/01/2012
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. (PubMedID: 22595003) BMC bioinformatics
01/01/2012
Exploring drug combinations in genetic interaction network. (PubMedID: 22595004) BMC bioinformatics
01/01/2012
Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method. (PubMedID: 22595005) BMC bioinformatics
01/01/2012
Comparison of data-merging methods with SVM attribute selection and classification in breast cancer gene expression. (PubMedID: 22595006) BMC bioinformatics
01/01/2012
The MULTICOM toolbox for protein structure prediction. (PubMedID: 22545707) BMC bioinformatics
01/01/2012
T3DB: an integrated database for bacterial type III secretion system. (PubMedID: 22545727) BMC bioinformatics
01/01/2012
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. (PubMedID: 22548871) BMC bioinformatics
01/01/2012
Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. (PubMedID: 22548918) BMC bioinformatics
01/01/2012
Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. (PubMedID: 22548963) BMC bioinformatics
01/01/2012
A unified computational model for revealing and predicting subtle subtypes of cancers. (PubMedID: 22548981) BMC bioinformatics
01/01/2012
Cancer bioinformatics: a new approach to systems clinical medicine. (PubMedID: 22549015) BMC bioinformatics
01/01/2012
Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis. (PubMedID: 22554139) BMC bioinformatics
01/01/2012
A Bayesian variable selection procedure to rank overlapping gene sets. (PubMedID: 22554182) BMC bioinformatics
01/01/2012
Inferring high-confidence human protein-protein interactions. (PubMedID: 22558947) BMC bioinformatics
01/01/2012
Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses. (PubMedID: 22559006) BMC bioinformatics
01/01/2012
Metaprotein expression modeling for label-free quantitative proteomics. (PubMedID: 22559859) BMC bioinformatics
01/01/2012
Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis. (PubMedID: 22559876) BMC bioinformatics
01/01/2012
EpiFire: An open source C++ library and application for contact network epidemiology. (PubMedID: 22559915) BMC bioinformatics
01/01/2012
Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support. (PubMedID: 22559942) BMC bioinformatics
01/01/2012
EnzML: multi-label prediction of enzyme classes using InterPro signatures. (PubMedID: 22533924) BMC bioinformatics
01/01/2012
CBDB: the codon bias database. (PubMedID: 22536831) BMC bioinformatics
01/01/2012
Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation. (PubMedID: 22540951) BMC bioinformatics
01/01/2012
Comprehensive comparison of graph based multiple protein sequence alignment strategies. (PubMedID: 22540977) BMC bioinformatics
01/01/2012
F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks. (PubMedID: 22524245) BMC bioinformatics
01/01/2012
Methods for visual mining of genomic and proteomic data atlases. (PubMedID: 22524279) BMC bioinformatics
01/01/2012
A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform. (PubMedID: 22524302) BMC bioinformatics
01/01/2012
Is EC class predictable from reaction mechanism? (PubMedID: 22530800) BMC bioinformatics
01/01/2012
'maskBAD'--a package to detect and remove Affymetrix probes with binding affinity differences. (PubMedID: 22507266) BMC bioinformatics
01/01/2012
Exploiting sparseness in de novo genome assembly. (PubMedID: 22537038) BMC bioinformatics
01/01/2012
Early classification of multivariate temporal observations by extraction of interpretable shapelets. (PubMedID: 22873729) BMC bioinformatics
01/01/2012
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. (PubMedID: 22876807) BMC bioinformatics
01/01/2012
GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network. (PubMedID: 22876834) BMC bioinformatics
01/01/2012
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions. (PubMedID: 22883815) BMC bioinformatics
01/01/2012
Normalization of ChIP-seq data with control. (PubMedID: 22883957) BMC bioinformatics
01/01/2012
Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis. (PubMedID: 22870920) BMC bioinformatics
01/01/2012
Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data. (PubMedID: 22870940) BMC bioinformatics
01/01/2012
Estimation of sequencing error rates in short reads. (PubMedID: 22846331) BMC bioinformatics
01/01/2012
Integrated QSAR study for inhibitors of Hedgehog Signal Pathway against multiple cell lines:a collaborative filtering method. (PubMedID: 22849868) BMC bioinformatics
01/01/2012
ParsEval: parallel comparison and analysis of gene structure annotations. (PubMedID: 22852583) BMC bioinformatics
01/01/2012
A resource for benchmarking the usefulness of protein structure models. (PubMedID: 22856649) BMC bioinformatics
01/01/2012
AGORA: Assembly Guided by Optical Restriction Alignment. (PubMedID: 22856673) BMC bioinformatics
01/01/2012
A web-based multi-genome synteny viewer for customized data. (PubMedID: 22856879) BMC bioinformatics
01/01/2012
Abstracts of the 11th Annual UT-ORNL-KBRIN Bioinformatics Summit 2012. Louisville, Kentucky, USA. March 30-April 1, 2012. (PubMedID: 22873757) BMC bioinformatics
01/01/2012
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. (PubMedID: 22827163) BMC bioinformatics
01/01/2012
Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data. (PubMedID: 22827252) BMC bioinformatics
01/01/2012
Seqcrawler: biological data indexing and browsing platform. (PubMedID: 22827839) BMC bioinformatics
01/01/2012
Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification. (PubMedID: 22830977) BMC bioinformatics
01/01/2012
A Bayesian method for comparing and combining binary classifiers in the absence of a gold standard. (PubMedID: 22838505) BMC bioinformatics
01/01/2012
Optimal experiment selection for parameter estimation in biological differential equation models. (PubMedID: 22838836) BMC bioinformatics
01/01/2012
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. (PubMedID: 22838965) BMC bioinformatics
01/01/2012
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. (PubMedID: 22839106) BMC bioinformatics
01/01/2012
Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants. (PubMedID: 22839202) BMC bioinformatics
01/01/2012
An image classification approach to analyze the suppression of plant immunity by the human pathogen Salmonella Typhimurium. (PubMedID: 22812426) BMC bioinformatics
01/01/2012
A text-mining system for extracting metabolic reactions from full-text articles. (PubMedID: 22823282) BMC bioinformatics
01/01/2012
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. (PubMedID: 22823337) BMC bioinformatics
01/01/2012
A novel hierarchical clustering algorithm for gene sequences. (PubMedID: 22823405) BMC bioinformatics
01/01/2012
SNP interaction detection with Random Forests in high-dimensional genetic data. (PubMedID: 22793366) BMC bioinformatics
01/01/2012
Network-enabled gene expression analysis. (PubMedID: 22799258) BMC bioinformatics
01/01/2012
Integrative prescreening in analysis of multiple cancer genomic studies. (PubMedID: 22799431) BMC bioinformatics
01/01/2012
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. (PubMedID: 22800292) BMC bioinformatics
01/01/2012
Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation. (PubMedID: 22800377) BMC bioinformatics
01/01/2012
Detecting pore-lining regions in transmembrane protein sequences. (PubMedID: 22805427) BMC bioinformatics
01/01/2012
Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms. (PubMedID: 22808927) BMC bioinformatics
01/01/2012
OLSVis: an animated, interactive visual browser for bio-ontologies. (PubMedID: 22646023) BMC bioinformatics
01/01/2012
Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures. (PubMedID: 22776037) BMC bioinformatics
01/01/2012
ParticleCall: a particle filter for base calling in next-generation sequencing systems. (PubMedID: 22776067) BMC bioinformatics
01/01/2012
Concept annotation in the CRAFT corpus. (PubMedID: 22776079) BMC bioinformatics
01/01/2012
Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study. (PubMedID: 22783946) BMC bioinformatics
01/01/2012
A graph-based approach for designing extensible pipelines. (PubMedID: 22788675) BMC bioinformatics
01/01/2012
Protein-protein binding site identification by enumerating the configurations. (PubMedID: 22768846) BMC bioinformatics
01/01/2012
TAPDANCE: an automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data. (PubMedID: 22748055) BMC bioinformatics
01/01/2012
A fast tool for minimum hybridization networks. (PubMedID: 22748099) BMC bioinformatics
01/01/2012
Genes2FANs: connecting genes through functional association networks. (PubMedID: 22748121) BMC bioinformatics
01/01/2012
Minimalist ensemble algorithms for genome-wide protein localization prediction. (PubMedID: 22759391) BMC bioinformatics
01/01/2012
Identifying mutation regions for closely related individuals without a known pedigree. (PubMedID: 22731852) BMC bioinformatics
01/01/2012
Arrow plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups. (PubMedID: 22734592) BMC bioinformatics
01/01/2012
Surprising results on phylogenetic tree building methods based on molecular sequences. (PubMedID: 22738078) BMC bioinformatics
01/01/2012
PREMIM and EMIM: tools for estimation of maternal, imprinting and interaction effects using multinomial modelling. (PubMedID: 22738121) BMC bioinformatics
01/01/2012
A statistical approach to selecting and confirming validation targets in -omics experiments. (PubMedID: 22738145) BMC bioinformatics
01/01/2012
Towards a theoretical understanding of false positives in DNA motif finding. (PubMedID: 22738169) BMC bioinformatics
01/01/2012
Detecting sequence dependent transcriptional pauses from RNA and protein number time series. (PubMedID: 22741547) BMC bioinformatics
01/01/2012
Molecular evolution of dihydrouridine synthases. (PubMedID: 22741570) BMC bioinformatics
01/01/2012
Guest editors' introduction. (PubMedID: 22759414) BMC bioinformatics
01/01/2012
Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation. (PubMedID: 22759415) BMC bioinformatics
01/01/2012
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. (PubMedID: 22759416) BMC bioinformatics
01/01/2012
Consensus properties for the deep coalescence problem and their application for scalable tree search. (PubMedID: 22759417) BMC bioinformatics
01/01/2012
Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution. (PubMedID: 22759418) BMC bioinformatics
01/01/2012
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. (PubMedID: 22759419) BMC bioinformatics
01/01/2012
Comparative evaluation of set-level techniques in predictive classification of gene expression samples. (PubMedID: 22759420) BMC bioinformatics
01/01/2012
Exploring biological interaction networks with tailored weighted quasi-bicliques. (PubMedID: 22759421) BMC bioinformatics
01/01/2012
Gene network modular-based classification of microarray samples. (PubMedID: 22759422) BMC bioinformatics
01/01/2012
A methodology for detecting the orthology signal in a PPI network at a functional complex level. (PubMedID: 22759423) BMC bioinformatics
01/01/2012
Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks. (PubMedID: 22759424) BMC bioinformatics
01/01/2012
Computing the protein binding sites. (PubMedID: 22759425) BMC bioinformatics
01/01/2012
Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study. (PubMedID: 22759426) BMC bioinformatics
01/01/2012
Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search. (PubMedID: 22759427) BMC bioinformatics
01/01/2012
High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs. (PubMedID: 22759428) BMC bioinformatics
01/01/2012
The maximum clique enumeration problem: algorithms, applications, and implementations. (PubMedID: 22759429) BMC bioinformatics
01/01/2012
Efficient error correction for next-generation sequencing of viral amplicons. (PubMedID: 22759430) BMC bioinformatics
01/01/2012
A systematic comparison of genome-scale clustering algorithms. (PubMedID: 22759431) BMC bioinformatics
01/01/2012
Genome plasticity and systems evolution in Streptomyces. (PubMedID: 22759432) BMC bioinformatics
01/01/2012
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes. (PubMedID: 22759433) BMC bioinformatics
01/01/2012
The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011. (PubMedID: 22759455) BMC bioinformatics
01/01/2012
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. (PubMedID: 22759456) BMC bioinformatics
01/01/2012
BioNLP Shared Task--The Bacteria Track. (PubMedID: 22759457) BMC bioinformatics
01/01/2012
University of Turku in the BioNLP'11 Shared Task. (PubMedID: 22759458) BMC bioinformatics
01/01/2012
Biomedical event extraction from abstracts and full papers using search-based structured prediction. (PubMedID: 22759459) BMC bioinformatics
01/01/2012
Semantically linking molecular entities in literature through entity relationships. (PubMedID: 22759460) BMC bioinformatics
01/01/2012
Biological event composition. (PubMedID: 22759461) BMC bioinformatics
01/01/2012
Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach. (PubMedID: 22759462) BMC bioinformatics
01/01/2012
Combining joint models for biomedical event extraction. (PubMedID: 22759463) BMC bioinformatics
01/01/2012
A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels. (PubMedID: 22712439) BMC bioinformatics
01/01/2012
ß-empirical Bayes inference and model diagnosis of microarray data. (PubMedID: 22713095) BMC bioinformatics
01/01/2012
Down-weighting overlapping genes improves gene set analysis. (PubMedID: 22713124) BMC bioinformatics
01/01/2012
EGNAS: an exhaustive DNA sequence design algorithm. (PubMedID: 22716030) BMC bioinformatics
01/01/2012
Comparative study of classification algorithms for immunosignaturing data. (PubMedID: 22720696) BMC bioinformatics
01/01/2012
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. (PubMedID: 22720726) BMC bioinformatics
01/01/2012
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. (PubMedID: 22720753) BMC bioinformatics
01/01/2012
Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization. (PubMedID: 22720789) BMC bioinformatics
01/01/2012
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. (PubMedID: 22726705) BMC bioinformatics
01/01/2012
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. (PubMedID: 22726767) BMC bioinformatics
01/01/2012
Error-correcting properties of the SOLiD Exact Call Chemistry. (PubMedID: 22726842) BMC bioinformatics
01/01/2012
Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2. (PubMedID: 22698142) BMC bioinformatics
01/01/2012
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling. (PubMedID: 22702410) BMC bioinformatics
01/01/2012
Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. (PubMedID: 22708584) BMC bioinformatics
01/01/2012
Fast and robust multiple sequence alignment with phylogeny-aware gap placement. (PubMedID: 22694311) BMC bioinformatics
01/01/2012
Bayesian model to detect phenotype-specific genes for copy number data. (PubMedID: 22694346) BMC bioinformatics
01/01/2012
Gene regulatory network modeling via global optimization of high-order dynamic Bayesian network. (PubMedID: 22694481) BMC bioinformatics
01/01/2012
Inferring transcript phylogenies. (PubMedID: 22831154) BMC bioinformatics
01/01/2012
Modeling and mining term association for improving biomedical information retrieval performance. (PubMedID: 22901087) BMC bioinformatics
01/01/2012
Inference of gene regulatory subnetworks from time course gene expression data. (PubMedID: 22901088) BMC bioinformatics
01/01/2012
Discovering patterns in drug-protein interactions based on their fingerprints. (PubMedID: 22901089) BMC bioinformatics
01/01/2012
A novel method to identify high order gene-gene interactions in genome-wide association studies: gene-based MDR. (PubMedID: 22901090) BMC bioinformatics
01/01/2012
Bayesian probabilistic network modeling from multiple independent replicates. (PubMedID: 22901091) BMC bioinformatics
01/01/2012
DTome: a web-based tool for drug-target interactome construction. (PubMedID: 22901092) BMC bioinformatics
01/01/2012
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. (PubMedID: 22901093) BMC bioinformatics
01/01/2012
Biomine: predicting links between biological entities using network models of heterogeneous databases. (PubMedID: 22672646) BMC bioinformatics
01/01/2012
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. (PubMedID: 22672667) BMC bioinformatics
01/01/2012
Detection of identity by descent using next-generation whole genome sequencing data. (PubMedID: 22672699) BMC bioinformatics