Medical Research Articles Published in January 2010

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01/01/2010
From QTL to candidate gene: genetical genomics of simple and complex traits in potato using a pooling strategy. (PubMedID: 20210995) BMC genomics
01/01/2010
Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs. (PubMedID: 20211033) BMC genomics
01/01/2010
Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans). (PubMedID: 20214793) BMC genomics
01/01/2010
Functional annotation of novel lineage-specific genes using co-expression and promoter analysis. (PubMedID: 20214810) BMC genomics
01/01/2010
Transcriptional and pathway analysis in the hypothalamus of newly hatched chicks during fasting and delayed feeding. (PubMedID: 20214824) BMC genomics
01/01/2010
Improvement of tissue preparation for laser capture microdissection: application for cell type-specific miRNA expression profiling in colorectal tumors. (PubMedID: 20219115) BMC genomics
01/01/2010
Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen. (PubMedID: 20219135) BMC genomics
01/01/2010
Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery. (PubMedID: 20222947) BMC genomics
01/01/2010
Distribution of candidate genes for experimentally induced arthritis in rats. (PubMedID: 20196835) BMC genomics
01/01/2010
Conservation and divergence of known apicomplexan transcriptional regulons. (PubMedID: 20199665) BMC genomics
01/01/2010
MicroRNAs of Bombyx mori identified by Solexa sequencing. (PubMedID: 20199675) BMC genomics
01/01/2010
Transcribed-ultra conserved region expression profiling from low-input total RNA. (PubMedID: 20199688) BMC genomics
01/01/2010
Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. (PubMedID: 20199690) BMC genomics
01/01/2010
Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements. (PubMedID: 20202189) BMC genomics
01/01/2010
Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents. (PubMedID: 20202191) BMC genomics
01/01/2010
Chemogenomic and transcriptome analysis identifies mode of action of the chemosensitizing agent CTBT (7-chlorotetrazolo[5,1-c]benzo[1,2,4]triazine). (PubMedID: 20202201) BMC genomics
01/01/2010
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon. (PubMedID: 20205726) BMC genomics
01/01/2010
Unified translation repression mechanism for microRNAs and upstream AUGs. (PubMedID: 20205738) BMC genomics
01/01/2010
Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. (PubMedID: 20181289) BMC genomics
01/01/2010
Escherichia coli infection induces distinct local and systemic transcriptome responses in the mammary gland. (PubMedID: 20184744) BMC genomics
01/01/2010
Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data. (PubMedID: 20184767) BMC genomics
01/01/2010
Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing. (PubMedID: 20184782) BMC genomics
01/01/2010
Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus. (PubMedID: 20187930) BMC genomics
01/01/2010
TobEA: an atlas of tobacco gene expression from seed to senescence. (PubMedID: 20187945) BMC genomics
01/01/2010
Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. (PubMedID: 20187961) BMC genomics
01/01/2010
Whole genome analysis of p38 SAPK-mediated gene expression upon stress. (PubMedID: 20187982) BMC genomics
01/01/2010
Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs. (PubMedID: 20193056) BMC genomics
01/01/2010
Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes. (PubMedID: 20175885) BMC genomics
01/01/2010
Comparative gene expression profiling between human cultured myotubes and skeletal muscle tissue. (PubMedID: 20175888) BMC genomics
01/01/2010
Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH). (PubMedID: 20175901) BMC genomics
01/01/2010
Expression profiling of mouse embryonic fibroblasts with a deletion in the helicase domain of the Werner Syndrome gene homologue treated with hydrogen peroxide. (PubMedID: 20175907) BMC genomics
01/01/2010
Defining species specific genome differences in malaria parasites. (PubMedID: 20175934) BMC genomics
01/01/2010
High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus. (PubMedID: 20178595) BMC genomics
01/01/2010
Identification and characterization of Tc1/mariner-like DNA transposons in genomes of the pathogenic fungi of the Paracoccidioides species complex. (PubMedID: 20178623) BMC genomics
01/01/2010
Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. (PubMedID: 20178641) BMC genomics
01/01/2010
Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations. (PubMedID: 20178649) BMC genomics
01/01/2010
Comparative analysis of fungal protein kinases and associated domains. (PubMedID: 20178650) BMC genomics
01/01/2010
Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles. (PubMedID: 20181233) BMC genomics
01/01/2010
A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs. (PubMedID: 20181260) BMC genomics
01/01/2010
Flux of transcript patterns during soybean seed development. (PubMedID: 20181280) BMC genomics
01/01/2010
Analysis of a normalised expressed sequence tag (EST) library from a key pollinator, the bumblebee Bombus terrestris. (PubMedID: 20156341) BMC genomics
01/01/2010
Identification of candidates for cyclotide biosynthesis and cyclisation by expressed sequence tag analysis of Oldenlandia affinis. (PubMedID: 20158917) BMC genomics
01/01/2010
Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility. (PubMedID: 20163706) BMC genomics
01/01/2010
SoyTEdb: a comprehensive database of transposable elements in the soybean genome. (PubMedID: 20163715) BMC genomics
01/01/2010
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. (PubMedID: 20163725) BMC genomics
01/01/2010
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum. (PubMedID: 20163733) BMC genomics
01/01/2010
Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus. (PubMedID: 20167051) BMC genomics
01/01/2010
General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species. (PubMedID: 20167053) BMC genomics
01/01/2010
Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. (PubMedID: 20167116) BMC genomics
01/01/2010
Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. (PubMedID: 20167119) BMC genomics
01/01/2010
High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. (PubMedID: 20167121) BMC genomics
01/01/2010
Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis. (PubMedID: 20167122) BMC genomics
01/01/2010
Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species. (PubMedID: 20170511) BMC genomics
01/01/2010
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. (PubMedID: 20170513) BMC genomics
01/01/2010
Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus. (PubMedID: 20146791) BMC genomics
01/01/2010
Identification and analysis of in planta expressed genes of Magnaporthe oryzae. (PubMedID: 20146797) BMC genomics
01/01/2010
Fungal secretome database: integrated platform for annotation of fungal secretomes. (PubMedID: 20146824) BMC genomics
01/01/2010
U12 type introns were lost at multiple occasions during evolution. (PubMedID: 20149226) BMC genomics
01/01/2010
Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate. (PubMedID: 20149241) BMC genomics
01/01/2010
Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication. (PubMedID: 20152025) BMC genomics
01/01/2010
Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. (PubMedID: 20152027) BMC genomics
01/01/2010
Mechanisms of chromosomal rearrangement in the human genome. (PubMedID: 20158866) BMC genomics
01/01/2010
Transposon identification using profile HMMs. (PubMedID: 20158867) BMC genomics
01/01/2010
Modeling neutral evolution of Alu elements using a branching process. (PubMedID: 20158868) BMC genomics
01/01/2010
Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome. (PubMedID: 20158869) BMC genomics
01/01/2010
Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction. (PubMedID: 20158870) BMC genomics
01/01/2010
Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases. (PubMedID: 20158871) BMC genomics
01/01/2010
Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset. (PubMedID: 20158872) BMC genomics
01/01/2010
Collective motions and specific effectors: a statistical mechanics perspective on biological regulation. (PubMedID: 20158873) BMC genomics
01/01/2010
Computational approaches for detecting protein complexes from protein interaction networks: a survey. (PubMedID: 20158874) BMC genomics
01/01/2010
Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. (PubMedID: 20158875) BMC genomics
01/01/2010
Differences in the transactivation domains of p53 family members: a computational study. (PubMedID: 20158876) BMC genomics
01/01/2010
Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha. (PubMedID: 20158877) BMC genomics
01/01/2010
Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction. (PubMedID: 20158878) BMC genomics
01/01/2010
Bimodal gene expression patterns in breast cancer. (PubMedID: 20158879) BMC genomics
01/01/2010
Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression. (PubMedID: 20158880) BMC genomics
01/01/2010
Transcriptional response of Burkholderia cenocepacia J2315 sessile cells to treatments with high doses of hydrogen peroxide and sodium hypochlorite. (PubMedID: 20137066) BMC genomics
01/01/2010
Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. (PubMedID: 20137072) BMC genomics
01/01/2010
Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. (PubMedID: 20137074) BMC genomics
01/01/2010
Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis. (PubMedID: 20137087) BMC genomics
01/01/2010
Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. (PubMedID: 20141623) BMC genomics
01/01/2010
Genome-wide analysis of rice ClpB/HSP100, ClpC and ClpD genes. (PubMedID: 20141629) BMC genomics
01/01/2010
Variability of gene expression profiles in human blood and lymphoblastoid cell lines. (PubMedID: 20141636) BMC genomics
01/01/2010
Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). (PubMedID: 20141639) BMC genomics
01/01/2010
Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs. (PubMedID: 20141640) BMC genomics
01/01/2010
Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics. (PubMedID: 20144183) BMC genomics
01/01/2010
Annotation and classification of the bovine T cell receptor delta genes. (PubMedID: 20144200) BMC genomics
01/01/2010
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. (PubMedID: 20144220) BMC genomics
01/01/2010
Homopolymeric tracts represent a general regulatory mechanism in prokaryotes. (PubMedID: 20144225) BMC genomics
01/01/2010
Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data. (PubMedID: 20113528) BMC genomics
01/01/2010
Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola. (PubMedID: 20122142) BMC genomics
01/01/2010
Comparative evolutionary analysis of protein complexes in E. coli and yeast. (PubMedID: 20122144) BMC genomics
01/01/2010
Tracking chromosomal positions of oligomers - a case study with Illumina's BovineSNP50 beadchip. (PubMedID: 20122154) BMC genomics
01/01/2010
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. (PubMedID: 20122162) BMC genomics
01/01/2010
Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome. (PubMedID: 20122165) BMC genomics
01/01/2010
Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages. (PubMedID: 20122178) BMC genomics
01/01/2010
Gene prioritization in Type 2 Diabetes using domain interactions and network analysis. (PubMedID: 20122255) BMC genomics
01/01/2010
MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori. (PubMedID: 20122259) BMC genomics
01/01/2010
Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity. (PubMedID: 20122262) BMC genomics
01/01/2010
Systematic overrepresentation of DNA termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear DNA molecules. (PubMedID: 20122283) BMC genomics
01/01/2010
Whole-genome sequencing of a laboratory-evolved yeast strain. (PubMedID: 20128923) BMC genomics
01/01/2010
Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? (PubMedID: 20132532) BMC genomics
01/01/2010
Differences in the transcriptome signatures of two genetically related Entamoeba histolytica cell lines derived from the same isolate with different pathogenic properties. (PubMedID: 20102605) BMC genomics
01/01/2010
Changes in the genomic content of circulating Bordetella pertussis strains isolated from the Netherlands, Sweden, Japan and Australia: adaptive evolution or drift? (PubMedID: 20102608) BMC genomics
01/01/2010
Tungsten carbide cobalt nanoparticles exert hypoxia-like effects on the gene expression level in human keratinocytes. (PubMedID: 20105288) BMC genomics
01/01/2010
Re-examination of chimp protein kinases suggests "novel architectures" are gene prediction artifacts. (PubMedID: 20105302) BMC genomics
01/01/2010
Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching. (PubMedID: 20105305) BMC genomics
01/01/2010
The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. (PubMedID: 20105308) BMC genomics
01/01/2010
Transcriptome analysis reveals absence of unintended effects in drought-tolerant transgenic plants overexpressing the transcription factor ABF3. (PubMedID: 20105335) BMC genomics
01/01/2010
Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map. (PubMedID: 20109198) BMC genomics
01/01/2010
Relationship between operon preference and functional properties of persistent genes in bacterial genomes. (PubMedID: 20109203) BMC genomics
01/01/2010
Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques. (PubMedID: 20109224) BMC genomics
01/01/2010
Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses. (PubMedID: 20109239) BMC genomics
01/01/2010
Automated design of genomic Southern blot probes. (PubMedID: 20113467) BMC genomics
01/01/2010
Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells. (PubMedID: 20113474) BMC genomics
01/01/2010
Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis. (PubMedID: 20113487) BMC genomics
01/01/2010
DIGA--a database of improved gene annotation for phytopathogens. (PubMedID: 20089203) BMC genomics
01/01/2010
Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum. (PubMedID: 20092619) BMC genomics
01/01/2010
Genome-wide computational prediction of tandem gene arrays: application in yeasts. (PubMedID: 20092627) BMC genomics
01/01/2010
Gene expression profiling to identify eggshell proteins involved in physical defense of the chicken egg. (PubMedID: 20092629) BMC genomics
01/01/2010
Does replication groups scoring reduce false positive rate in SNP interaction discovery? (PubMedID: 20092660) BMC genomics
01/01/2010
Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation. (PubMedID: 20096118) BMC genomics
01/01/2010
Identical repeated backbone of the human genome. (PubMedID: 20096123) BMC genomics
01/01/2010
Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs. (PubMedID: 20100322) BMC genomics
01/01/2010
Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. (PubMedID: 20100350) BMC genomics
01/01/2010
Gene expression profiles in Atlantic salmon adipose-derived stromo-vascular fraction during differentiation into adipocytes. (PubMedID: 20078893) BMC genomics
01/01/2010
Sorting by reversals and block-interchanges with various weight assignments. (PubMedID: 19958558) BMC bioinformatics
01/01/2010
BiologicalNetworks 2.0--an integrative view of genome biology data. (PubMedID: 21190573) BMC bioinformatics
01/01/2010
SIDEKICK: Genomic data driven analysis and decision-making framework. (PubMedID: 21192813) BMC bioinformatics
01/01/2010
A two-step site and mRNA-level model for predicting microRNA targets. (PubMedID: 21194446) BMC bioinformatics
01/01/2010
The complexity of gene expression dynamics revealed by permutation entropy. (PubMedID: 21176199) BMC bioinformatics
01/01/2010
MBAT: a scalable informatics system for unifying digital atlasing workflows. (PubMedID: 21176225) BMC bioinformatics
01/01/2010
RISCI--Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes. (PubMedID: 21184688) BMC bioinformatics
01/01/2010
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels. (PubMedID: 21167019) BMC bioinformatics
01/01/2010
A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences. (PubMedID: 21167044) BMC bioinformatics
01/01/2010
Gene processing control loops suggested by sequencing, splicing, and RNA folding. (PubMedID: 21167075) BMC bioinformatics
01/01/2010
Content-based microarray search using differential expression profiles. (PubMedID: 21172034) BMC bioinformatics
01/01/2010
Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites. (PubMedID: 21172036) BMC bioinformatics
01/01/2010
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. (PubMedID: 21176124) BMC bioinformatics
01/01/2010
Kernel based methods for accelerated failure time model with ultra-high dimensional data. (PubMedID: 21176134) BMC bioinformatics
01/01/2010
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. (PubMedID: 21210976) BMC bioinformatics
01/01/2010
interPopula: a Python API to access the HapMap Project dataset. (PubMedID: 21210977) BMC bioinformatics
01/01/2010
An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators. (PubMedID: 21210978) BMC bioinformatics
01/01/2010
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. (PubMedID: 21210979) BMC bioinformatics
01/01/2010
IPRStats: visualization of the functional potential of an InterProScan run. (PubMedID: 21210980) BMC bioinformatics
01/01/2010
SeqWare Query Engine: storing and searching sequence data in the cloud. (PubMedID: 21210981) BMC bioinformatics
01/01/2010
Hybrid cloud and cluster computing paradigms for life science applications. (PubMedID: 21210982) BMC bioinformatics
01/01/2010
Galaxy CloudMan: delivering cloud compute clusters. (PubMedID: 21210983) BMC bioinformatics
01/01/2010
Community-driven computational biology with Debian Linux. (PubMedID: 21210984) BMC bioinformatics
01/01/2010
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. (PubMedID: 21210985) BMC bioinformatics
01/01/2010
SADI, SHARE, and the in silico scientific method. (PubMedID: 21210986) BMC bioinformatics
01/01/2010
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. (PubMedID: 21210987) BMC bioinformatics
01/01/2010
The Musite open-source framework for phosphorylation-site prediction. (PubMedID: 21210988) BMC bioinformatics
01/01/2010
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling. (PubMedID: 21144021) BMC bioinformatics
01/01/2010
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. (PubMedID: 21144022) BMC bioinformatics
01/01/2010
Initial steps towards a production platform for DNA sequence analysis on the grid. (PubMedID: 21156038) BMC bioinformatics
01/01/2010
A genome alignment algorithm based on compression. (PubMedID: 21159205) BMC bioinformatics
01/01/2010
Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. (PubMedID: 21172044) BMC bioinformatics
01/01/2010
Accurate HLA type inference using a weighted similarity graph. (PubMedID: 21172045) BMC bioinformatics
01/01/2010
MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features. (PubMedID: 21172046) BMC bioinformatics
01/01/2010
Detection and reconstruction of tandemly organized de novo copy number variations. (PubMedID: 21172047) BMC bioinformatics
01/01/2010
Revealing parasite influence in metabolic pathways in Apicomplexa infected patients. (PubMedID: 21172048) BMC bioinformatics
01/01/2010
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. (PubMedID: 21172049) BMC bioinformatics
01/01/2010
A novel parametric approach to mine gene regulatory relationship from microarray datasets. (PubMedID: 21172050) BMC bioinformatics
01/01/2010
Sorting out inherent features of head-to-head gene pairs by evolutionary conservation. (PubMedID: 21172051) BMC bioinformatics
01/01/2010
Improved protein surface comparison and application to low-resolution protein structure data. (PubMedID: 21172052) BMC bioinformatics
01/01/2010
Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology. (PubMedID: 21172053) BMC bioinformatics
01/01/2010
Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures. (PubMedID: 21172054) BMC bioinformatics
01/01/2010
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. (PubMedID: 21172055) BMC bioinformatics
01/01/2010
Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. (PubMedID: 21172056) BMC bioinformatics
01/01/2010
Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species. (PubMedID: 21172057) BMC bioinformatics
01/01/2010
RecMotif: a novel fast algorithm for weak motif discovery. (PubMedID: 21172058) BMC bioinformatics
01/01/2010
Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution. (PubMedID: 21172059) BMC bioinformatics
01/01/2010
An improved machine learning protocol for the identification of correct Sequest search results. (PubMedID: 21138573) BMC bioinformatics
01/01/2010
Haplotype association analyses in resources of mixed structure using Monte Carlo testing. (PubMedID: 21143908) BMC bioinformatics
01/01/2010
Application of Wavelet Packet Transform to detect genetic polymorphisms by the analysis of inter-Alu PCR patterns. (PubMedID: 21143911) BMC bioinformatics
01/01/2010
BIGSdb: Scalable analysis of bacterial genome variation at the population level. (PubMedID: 21143983) BMC bioinformatics
01/01/2010
Addressing the challenge of defining valid proteomic biomarkers and classifiers. (PubMedID: 21208396) BMC bioinformatics
01/01/2010
Merged consensus clustering to assess and improve class discovery with microarray data. (PubMedID: 21129181) BMC bioinformatics
01/01/2010
A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. (PubMedID: 21114815) BMC bioinformatics
01/01/2010
The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses. (PubMedID: 21114820) BMC bioinformatics
01/01/2010
Systematic integration of experimental data and models in systems biology. (PubMedID: 21114840) BMC bioinformatics
01/01/2010
Preprocessing of gene expression data by optimally robust estimators. (PubMedID: 21118506) BMC bioinformatics
01/01/2010
LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. (PubMedID: 21118513) BMC bioinformatics
01/01/2010
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. (PubMedID: 21118515) BMC bioinformatics
01/01/2010
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. (PubMedID: 21118522) BMC bioinformatics
01/01/2010
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. (PubMedID: 21118553) BMC bioinformatics
01/01/2010
IntelliGO: a new vector-based semantic similarity measure including annotation origin. (PubMedID: 21122125) BMC bioinformatics
01/01/2010
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation. (PubMedID: 21122127) BMC bioinformatics
01/01/2010
Peptide binding predictions for HLA DR, DP and DQ molecules. (PubMedID: 21092157) BMC bioinformatics
01/01/2010
Knowledge-based biomedical word sense disambiguation: comparison of approaches. (PubMedID: 21092226) BMC bioinformatics
01/01/2010
Reticular alignment: a progressive corner-cutting method for multiple sequence alignment. (PubMedID: 21092255) BMC bioinformatics
01/01/2010
Probabilistic principal component analysis for metabolomic data. (PubMedID: 21092268) BMC bioinformatics
01/01/2010
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. (PubMedID: 21092284) BMC bioinformatics
01/01/2010
DeltaProt: a software toolbox for comparative genomics. (PubMedID: 21092291) BMC bioinformatics
01/01/2010
iGTP: a software package for large-scale gene tree parsimony analysis. (PubMedID: 21092314) BMC bioinformatics
01/01/2010
Sampling the conformation of protein surface residues for flexible protein docking. (PubMedID: 21092317) BMC bioinformatics
01/01/2010
Validation and characterization of DNA microarray gene expression data distribution and associated moments. (PubMedID: 21092329) BMC bioinformatics
01/01/2010
Speeding up tandem mass spectrometry-based database searching by longest common prefix. (PubMedID: 21108792) BMC bioinformatics
01/01/2010
Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays. (PubMedID: 21110835) BMC bioinformatics
01/01/2010
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. (PubMedID: 21110866) BMC bioinformatics
01/01/2010
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency. (PubMedID: 21083935) BMC bioinformatics
01/01/2010
Comparative study of unsupervised dimension reduction techniques for the visualization of microarray gene expression data. (PubMedID: 21087509) BMC bioinformatics
01/01/2010
Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study. (PubMedID: 21087464) BMC bioinformatics
01/01/2010
Assessment and optimisation of normalisation methods for dual-colour antibody microarrays. (PubMedID: 21073702) BMC bioinformatics
01/01/2010
Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. (PubMedID: 21073706) BMC bioinformatics
01/01/2010
Leukocyte nucleus segmentation and nucleus lobe counting. (PubMedID: 21073711) BMC bioinformatics
01/01/2010
Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture model and statistical model selection. (PubMedID: 21073736) BMC bioinformatics
01/01/2010
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs. (PubMedID: 21078174) BMC bioinformatics
01/01/2010
A factorization method for the classification of infrared spectra. (PubMedID: 21078178) BMC bioinformatics
01/01/2010
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. (PubMedID: 21078182) BMC bioinformatics
01/01/2010
TESTLoc: protein subcellular localization prediction from EST data. (PubMedID: 21078192) BMC bioinformatics
01/01/2010
Empirical bayes analysis of sequencing-based transcriptional profiling without replicates. (PubMedID: 21080965) BMC bioinformatics
01/01/2010
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. (PubMedID: 21059217) BMC bioinformatics
01/01/2010
The Text-mining based PubChem Bioassay neighboring analysis. (PubMedID: 21059237) BMC bioinformatics
01/01/2010
Localizing triplet periodicity in DNA and cDNA sequences. (PubMedID: 21059240) BMC bioinformatics
01/01/2010
Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes. (PubMedID: 20078895) BMC genomics
01/01/2010
Deletions of immunoglobulin heavy chain and T cell receptor gene regions are uniquely associated with lymphoid blast transformation of chronic myeloid leukemia. (PubMedID: 20082691) BMC genomics
01/01/2010
Evolution and diversity of secretome genes in the apicomplexan parasite Theileria annulata. (PubMedID: 20082698) BMC genomics
01/01/2010
Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). (PubMedID: 20082721) BMC genomics
01/01/2010
Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes. (PubMedID: 20085626) BMC genomics
01/01/2010
Novel OBP genes similar to hamster Aphrodisin in the bank vole, Myodes glareolus. (PubMedID: 20085627) BMC genomics
01/01/2010
Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. (PubMedID: 20085629) BMC genomics
01/01/2010
Expression profiling of prospero in the Drosophila larval chemosensory organ: Between growth and outgrowth. (PubMedID: 20085633) BMC genomics
01/01/2010
Intergenic, gene terminal, and intragenic CpG islands in the human genome. (PubMedID: 20085634) BMC genomics
01/01/2010
Identification of interacting transcription factors regulating tissue gene expression in human. (PubMedID: 20085649) BMC genomics
01/01/2010
Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data. (PubMedID: 20089164) BMC genomics
01/01/2010
An insight into the sialotranscriptome of the West Nile mosquito vector, Culex tarsalis. (PubMedID: 20089177) BMC genomics
01/01/2010
Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. (PubMedID: 20089182) BMC genomics
01/01/2010
Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array. (PubMedID: 20089193) BMC genomics
01/01/2010
Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana. (PubMedID: 20064227) BMC genomics
01/01/2010
Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background. (PubMedID: 20064228) BMC genomics
01/01/2010
Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates. (PubMedID: 20064230) BMC genomics
01/01/2010
Acetylation of p65 at lysine 314 is important for late NF-kappaB-dependent gene expression. (PubMedID: 20064247) BMC genomics
01/01/2010
Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development. (PubMedID: 20064253) BMC genomics
01/01/2010
Comparison of clastogen-induced gene expression profiles in wild-type and DNA repair-deficient Rad54/Rad54B cells. (PubMedID: 20067618) BMC genomics
01/01/2010
High-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation. (PubMedID: 20067632) BMC genomics
01/01/2010
1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1. (PubMedID: 20070897) BMC genomics
01/01/2010
Genomics Portals: integrative web-platform for mining genomics data. (PubMedID: 20070909) BMC genomics
01/01/2010
Regional regulation of transcription in the chicken genome. (PubMedID: 20074332) BMC genomics
01/01/2010
Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens. (PubMedID: 20074338) BMC genomics
01/01/2010
Variable structure motifs for transcription factor binding sites. (PubMedID: 20074339) BMC genomics
01/01/2010
Temperature increase prevails over acidification in gene expression modulation of amastigote differentiation in Leishmania infantum. (PubMedID: 20074347) BMC genomics
01/01/2010
Integrative analysis of the heat shock response in Aspergillus fumigatus. (PubMedID: 20074381) BMC genomics
01/01/2010
New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome. (PubMedID: 20078849) BMC genomics
01/01/2010
In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum. (PubMedID: 20078850) BMC genomics
01/01/2010
Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum. (PubMedID: 20078859) BMC genomics
01/01/2010
The proteolytic system of lactic acid bacteria revisited: a genomic comparison. (PubMedID: 20078865) BMC genomics
01/01/2010
A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes--an open access resource for neuroscience and evolutionary biology. (PubMedID: 20078875) BMC genomics
01/01/2010
High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. (PubMedID: 20078886) BMC genomics
01/01/2010
An integrated functional genomic study of acute phenobarbital exposure in the rat. (PubMedID: 20053287) BMC genomics
01/01/2010
The dynamic architecture of the metabolic switch in Streptomyces coelicolor. (PubMedID: 20053288) BMC genomics
01/01/2010
Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501. (PubMedID: 20053297) BMC genomics
01/01/2010
The Zur regulon of Corynebacterium glutamicum ATCC 13032. (PubMedID: 20055984) BMC genomics
01/01/2010
Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos. (PubMedID: 20055996) BMC genomics
01/01/2010
Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution. (PubMedID: 20055998) BMC genomics
01/01/2010
Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. (PubMedID: 20056002) BMC genomics
01/01/2010
Analysis of the heat shock response in mouse liver reveals transcriptional dependence on the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARalpha). (PubMedID: 20059764) BMC genomics
01/01/2010
Glutamate, aspartate and nucleotide transporters in the SLC17 family form four main phylogenetic clusters: evolution and tissue expression. (PubMedID: 20059771) BMC genomics
01/01/2010
Comparative transcriptomic analysis of follicle-enclosed oocyte maturational and developmental competence acquisition in two non-mammalian vertebrates. (PubMedID: 20059772) BMC genomics
01/01/2010
Proceedings of The International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS), August 3-8, 2009, Shanghai, China. (PubMedID: 21476224) BMC genomics
01/01/2010
Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis. (PubMedID: 20044946) BMC genomics
01/01/2010
Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity. (PubMedID: 20047678) BMC genomics
01/01/2010
Extensive analysis of D-J-C arrangements allows the identification of different mechanisms enhancing the diversity in sheep T cell receptor beta-chain repertoire. (PubMedID: 20047680) BMC genomics
01/01/2010
Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish. (PubMedID: 20047682) BMC genomics
01/01/2010
Normal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease. (PubMedID: 20047688) BMC genomics
01/01/2010
An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure? (PubMedID: 20051121) BMC genomics
01/01/2010
Decoding pooled RNAi screens by means of barcode tiling arrays. (PubMedID: 20051122) BMC genomics
01/01/2010
Detecting positive selection from genome scans of linkage disequilibrium. (PubMedID: 20051139) BMC genomics
01/01/2010
Proceedings from the International Workshop on Computational Systems Biology Approaches to Analysis of Genome Complexity and Regulatory Gene Networks, Singapore, 20-25 November 2008. (PubMedID: 20364452) BMC genomics
01/01/2010
Next generation models for storage and representation of microbial biological annotation. (PubMedID: 20946598) BMC bioinformatics
01/01/2010
HPIDB--a unified resource for host-pathogen interactions. (PubMedID: 20946599) BMC bioinformatics
01/01/2010
Promoter prediction in E. coli based on SIDD profiles and Artificial Neural Networks. (PubMedID: 20946600) BMC bioinformatics
01/01/2010
Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective. (PubMedID: 20946601) BMC bioinformatics
01/01/2010
Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks. (PubMedID: 20946602) BMC bioinformatics
01/01/2010
Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate. (PubMedID: 20946603) BMC bioinformatics
01/01/2010
A framework for automated enrichment of functionally significant inverted repeats in whole genomes. (PubMedID: 20946604) BMC bioinformatics
01/01/2010
A predictive model for secondary RNA structure using graph theory and a neural network. (PubMedID: 20946605) BMC bioinformatics
01/01/2010
Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function. (PubMedID: 20946606) BMC bioinformatics
01/01/2010
Lesion detection in demoscopy images with novel density-based and active contour approaches. (PubMedID: 20946607) BMC bioinformatics
01/01/2010
Dynamics of protofibril elongation and association involved in Aß42 peptide aggregation in Alzheimer's disease. (PubMedID: 20946608) BMC bioinformatics
01/01/2010
Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize. (PubMedID: 20946609) BMC bioinformatics
01/01/2010
Analysis of density based and fuzzy c-means clustering methods on lesion border extraction in dermoscopy images. (PubMedID: 20946610) BMC bioinformatics
01/01/2010
Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing mechanism. (PubMedID: 20946611) BMC bioinformatics
01/01/2010
IView: introgression library visualization and query tool. (PubMedID: 20946612) BMC bioinformatics
01/01/2010
GOModeler--a tool for hypothesis-testing of functional genomics datasets. (PubMedID: 20946613) BMC bioinformatics
01/01/2010
Assessing constancy of substitution rates in viruses over evolutionary time. (PubMedID: 20946614) BMC bioinformatics
01/01/2010
An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays. (PubMedID: 20946615) BMC bioinformatics
01/01/2010
The EDKB: an established knowledge base for endocrine disrupting chemicals. (PubMedID: 20946616) BMC bioinformatics
01/01/2010
Two new ArrayTrack libraries for personalized biomedical research. (PubMedID: 20946617) BMC bioinformatics
01/01/2010
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. (PubMedID: 20946618) BMC bioinformatics
01/01/2010
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. (PubMedID: 20946619) BMC bioinformatics
01/01/2010
Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences. (PubMedID: 20946620) BMC bioinformatics
01/01/2010
A semi-nonparametric mixture model for selecting functionally consistent proteins. (PubMedID: 20920204) BMC bioinformatics
01/01/2010
Analysis of lifestyle and metabolic predictors of visceral obesity with Bayesian Networks. (PubMedID: 20920208) BMC bioinformatics
01/01/2010
A global optimization algorithm for protein surface alignment. (PubMedID: 20920230) BMC bioinformatics
01/01/2010
Computationally efficient flux variability analysis. (PubMedID: 20920235) BMC bioinformatics
01/01/2010
BPDA - a Bayesian peptide detection algorithm for mass spectrometry. (PubMedID: 20920238) BMC bioinformatics
01/01/2010
Non-coding RNA detection methods combined to improve usability, reproducibility and precision. (PubMedID: 20920260) BMC bioinformatics
01/01/2010
The structural and content aspects of abstracts versus bodies of full text journal articles are different. (PubMedID: 20920264) BMC bioinformatics
01/01/2010
A systematic study of genome context methods: calibration, normalization and combination. (PubMedID: 20920312) BMC bioinformatics
01/01/2010
A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer. (PubMedID: 20860844) BMC bioinformatics
01/01/2010
Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development. (PubMedID: 20860850) BMC bioinformatics
01/01/2010
Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome. (PubMedID: 20863374) BMC bioinformatics
01/01/2010
Using diffusion distances for flexible molecular shape comparison. (PubMedID: 20868474) BMC bioinformatics
01/01/2010
Predicting phenotypic traits of prokaryotes from protein domain frequencies. (PubMedID: 20868492) BMC bioinformatics
01/01/2010
MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. (PubMedID: 20868497) BMC bioinformatics
01/01/2010
Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. (PubMedID: 20875095) BMC bioinformatics
01/01/2010
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. (PubMedID: 20875130) BMC bioinformatics
01/01/2010
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. (PubMedID: 20875133) BMC bioinformatics
01/01/2010
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. (PubMedID: 20854660) BMC bioinformatics
01/01/2010
SeqAnt: a web service to rapidly identify and annotate DNA sequence variations. (PubMedID: 20854673) BMC bioinformatics
01/01/2010
GPFrontend and GPGraphics: graphical analysis tools for genetic association studies. (PubMedID: 20858257) BMC bioinformatics
01/01/2010
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. (PubMedID: 20858292) BMC bioinformatics
01/01/2010
ModuleOrganizer: detecting modules in families of transposable elements. (PubMedID: 20860790) BMC bioinformatics
01/01/2010
FragViz: visualization of fragmented networks. (PubMedID: 20860802) BMC bioinformatics
01/01/2010
Improving performance of mammalian microRNA target prediction. (PubMedID: 20860840) BMC bioinformatics
01/01/2010
Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks. (PubMedID: 20840745) BMC bioinformatics
01/01/2010
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. (PubMedID: 20840752) BMC bioinformatics
01/01/2010
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. (PubMedID: 20843356) BMC bioinformatics
01/01/2010
Context dependent substitution biases vary within the human genome. (PubMedID: 20843365) BMC bioinformatics
01/01/2010
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model. (PubMedID: 20846408) BMC bioinformatics
01/01/2010
Parallel multiplicity and error discovery rate (EDR) in microarray experiments. (PubMedID: 20846437) BMC bioinformatics
01/01/2010
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. (PubMedID: 20846443) BMC bioinformatics
01/01/2010
ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment. (PubMedID: 20849574) BMC bioinformatics
01/01/2010
Multivariate meta-analysis of proteomics data from human prostate and colon tumours. (PubMedID: 20849579) BMC bioinformatics
01/01/2010
MetNetGE: interactive views of biological networks and ontologies. (PubMedID: 20849585) BMC bioinformatics
01/01/2010
Simple and flexible classification of gene expression microarrays via Swirls and Ripples. (PubMedID: 20825641) BMC bioinformatics
01/01/2010
A multifactorial analysis of obesity as CVD risk factor: use of neural network based methods in a nutrigenetics context. (PubMedID: 20825661) BMC bioinformatics
01/01/2010
On the choice and number of microarrays for transcriptional regulatory network inference. (PubMedID: 20825684) BMC bioinformatics
01/01/2010
Next generation tools for genomic data generation, distribution, and visualization. (PubMedID: 20828407) BMC bioinformatics
01/01/2010
Multivariate Hawkes process models of the occurrence of regulatory elements. (PubMedID: 20828413) BMC bioinformatics
01/01/2010
An algorithm for automated closure during assembly. (PubMedID: 20831800) BMC bioinformatics
01/01/2010
The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems. (PubMedID: 20831831) BMC bioinformatics
01/01/2010
Fast and accurate protein substructure searching with simulated annealing and GPUs. (PubMedID: 20813068) BMC bioinformatics
01/01/2010
Sample size and statistical power considerations in high-dimensionality data settings: a comparative study of classification algorithms. (PubMedID: 20815881) BMC bioinformatics
01/01/2010
Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. (PubMedID: 20815925) BMC bioinformatics
01/01/2010
Consistency, comprehensiveness, and compatibility of pathway databases. (PubMedID: 20819233) BMC bioinformatics
01/01/2010
Filtering, FDR and power. (PubMedID: 20822518) BMC bioinformatics
01/01/2010
VIGOR, an annotation program for small viral genomes. (PubMedID: 20822531) BMC bioinformatics
01/01/2010
Relations as patterns: bridging the gap between OBO and OWL. (PubMedID: 20807438) BMC bioinformatics
01/01/2010
Forward-time simulation of realistic samples for genome-wide association studies. (PubMedID: 20809983) BMC bioinformatics
01/01/2010
Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. (PubMedID: 20809988) BMC bioinformatics
01/01/2010
Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. (PubMedID: 20813045) BMC bioinformatics
01/01/2010
Automatic detection of anchor points for multiple sequence alignment. (PubMedID: 20813050) BMC bioinformatics
01/01/2010
Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics. (PubMedID: 20796299) BMC bioinformatics
01/01/2010
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. (PubMedID: 20796314) BMC bioinformatics
01/01/2010
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation. (PubMedID: 20796320) BMC bioinformatics
01/01/2010
An exploratory data analysis method to reveal modular latent structures in high-throughput data. (PubMedID: 20799972) BMC bioinformatics
01/01/2010
Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. (PubMedID: 20727159) BMC bioinformatics
01/01/2010
A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis. (PubMedID: 20727194) BMC bioinformatics
01/01/2010
CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. (PubMedID: 20731828) BMC bioinformatics
01/01/2010
A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra. (PubMedID: 20731867) BMC bioinformatics
01/01/2010
TOPSAN: a collaborative annotation environment for structural genomics. (PubMedID: 20716366) BMC bioinformatics
01/01/2010
An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data. (PubMedID: 20716381) BMC bioinformatics
01/01/2010
Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets. (PubMedID: 20718947) BMC bioinformatics
01/01/2010
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. (PubMedID: 20718956) BMC bioinformatics
01/01/2010
Coverage statistics for sequence census methods. (PubMedID: 20718980) BMC bioinformatics
01/01/2010
Hidden Markov model speed heuristic and iterative HMM search procedure. (PubMedID: 20718988) BMC bioinformatics
01/01/2010
rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. (PubMedID: 20718989) BMC bioinformatics
01/01/2010
FACT: functional annotation transfer between proteins with similar feature architectures. (PubMedID: 20696036) BMC bioinformatics
01/01/2010
eGIFT: mining gene information from the literature. (PubMedID: 20696046) BMC bioinformatics
01/01/2010
TAM: a method for enrichment and depletion analysis of a microRNA category in a list of microRNAs. (PubMedID: 20696049) BMC bioinformatics
01/01/2010
An improved classification of G-protein-coupled receptors using sequence-derived features. (PubMedID: 20696050) BMC bioinformatics
01/01/2010
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. (PubMedID: 20698961) BMC bioinformatics
01/01/2010
baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. (PubMedID: 20698981) BMC bioinformatics
01/01/2010
Ranked retrieval of Computational Biology models. (PubMedID: 20701772) BMC bioinformatics
01/01/2010
Computing H/D-exchange rates of single residues from data of proteolytic fragments. (PubMedID: 20701784) BMC bioinformatics
01/01/2010
TF-finder: a software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base. (PubMedID: 20704747) BMC bioinformatics
01/01/2010
The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data. (PubMedID: 20684785) BMC bioinformatics
01/01/2010
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data. (PubMedID: 20684787) BMC bioinformatics
01/01/2010
Global parameter estimation methods for stochastic biochemical systems. (PubMedID: 20691037) BMC bioinformatics
01/01/2010
PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. (PubMedID: 20691053) BMC bioinformatics
01/01/2010
Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-censored data. (PubMedID: 20691091) BMC bioinformatics
01/01/2010
RuleMonkey: software for stochastic simulation of rule-based models. (PubMedID: 20673321) BMC bioinformatics
01/01/2010
OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data. (PubMedID: 20673335) BMC bioinformatics
01/01/2010
MS4--Multi-Scale Selector of Sequence Signatures: an alignment-free method for classification of biological sequences. (PubMedID: 20673356) BMC bioinformatics
01/01/2010
Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures. (PubMedID: 20673368) BMC bioinformatics
01/01/2010
Comparison study of microarray meta-analysis methods. (PubMedID: 20678237) BMC bioinformatics
01/01/2010
Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. (PubMedID: 20682040) BMC bioinformatics
01/01/2010
A method for automatically extracting infectious disease-related primers and probes from the literature. (PubMedID: 20682041) BMC bioinformatics
01/01/2010
Extracting the abstraction pyramid from complex networks. (PubMedID: 20682075) BMC bioinformatics
01/01/2010
CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies. (PubMedID: 20663186) BMC bioinformatics
01/01/2010
Quantized correlation coefficient for measuring reproducibility of ChIP-chip data. (PubMedID: 20663215) BMC bioinformatics
01/01/2010
Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes. (PubMedID: 20663218) BMC bioinformatics
01/01/2010
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). (PubMedID: 20667077) BMC bioinformatics
01/01/2010
Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. (PubMedID: 20667087) BMC bioinformatics
01/01/2010
Data reduction for spectral clustering to analyze high throughput flow cytometry data. (PubMedID: 20667133) BMC bioinformatics
01/01/2010
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. (PubMedID: 20646284) BMC bioinformatics
01/01/2010
VIPR: A probabilistic algorithm for analysis of microbial detection microarrays. (PubMedID: 20646301) BMC bioinformatics
01/01/2010
Applications of a formal approach to decipher discrete genetic networks. (PubMedID: 20646302) BMC bioinformatics
01/01/2010
Efficiency clustering for low-density microarrays and its application to QPCR. (PubMedID: 20646303) BMC bioinformatics
01/01/2010
S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. (PubMedID: 20646315) BMC bioinformatics
01/01/2010
Deriving enzymatic and taxonomic signatures of metagenomes from short read data. (PubMedID: 20649951) BMC bioinformatics
01/01/2010
Robust test method for time-course microarray experiments. (PubMedID: 20649954) BMC bioinformatics
01/01/2010
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks. (PubMedID: 20649980) BMC bioinformatics
01/01/2010
Compartmentalization of the Edinburgh Human Metabolic Network. (PubMedID: 20649990) BMC bioinformatics
01/01/2010
A comparison of internal validation techniques for multifactor dimensionality reduction. (PubMedID: 20650002) BMC bioinformatics
01/01/2010
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. (PubMedID: 20650010) BMC bioinformatics
01/01/2010
Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. (PubMedID: 20653935) BMC bioinformatics
01/01/2010
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. (PubMedID: 20653963) BMC bioinformatics
01/01/2010
A comparative study of conservation and variation scores. (PubMedID: 20663120) BMC bioinformatics
01/01/2010
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. (PubMedID: 20663121) BMC bioinformatics
01/01/2010
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. (PubMedID: 20633259) BMC bioinformatics
01/01/2010
MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics. (PubMedID: 20633263) BMC bioinformatics
01/01/2010
R-Gada: a fast and flexible pipeline for copy number analysis in association studies. (PubMedID: 20637081) BMC bioinformatics
01/01/2010
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. (PubMedID: 20637083) BMC bioinformatics
01/01/2010
Integration and visualization of systems biology data in context of the genome. (PubMedID: 20642854) BMC bioinformatics
01/01/2010
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. (PubMedID: 20624289) BMC bioinformatics
01/01/2010
KID--an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes. (PubMedID: 20626859) BMC bioinformatics
01/01/2010
The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets. (PubMedID: 20626915) BMC bioinformatics
01/01/2010
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. (PubMedID: 20630057) BMC bioinformatics
01/01/2010
Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL isoelectric focussing. (PubMedID: 20602788) BMC bioinformatics
01/01/2010
Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. (PubMedID: 20609242) BMC bioinformatics
01/01/2010
Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images. (PubMedID: 20615231) BMC bioinformatics
01/01/2010
Interaction prediction and classification of PDZ domains. (PubMedID: 20591147) BMC bioinformatics
01/01/2010
MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. (PubMedID: 20591175) BMC bioinformatics
01/01/2010
On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence. (PubMedID: 20591178) BMC bioinformatics
01/01/2010
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. (PubMedID: 20594316) BMC bioinformatics
01/01/2010
Scanner calibration revisited. (PubMedID: 20594322) BMC bioinformatics
01/01/2010
Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse. (PubMedID: 20594327) BMC bioinformatics
01/01/2010
Robust probabilistic superposition and comparison of protein structures. (PubMedID: 20594332) BMC bioinformatics
01/01/2010
Automatic structure classification of small proteins using random forest. (PubMedID: 20594334) BMC bioinformatics
01/01/2010
Knowledge-based annotation of small molecule binding sites in proteins. (PubMedID: 20594344) BMC bioinformatics
01/01/2010
Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. (PubMedID: 20594356) BMC bioinformatics
01/01/2010
A flexible R package for nonnegative matrix factorization. (PubMedID: 20598126) BMC bioinformatics
01/01/2010
A factor model to analyze heterogeneity in gene expression. (PubMedID: 20598132) BMC bioinformatics
01/01/2010
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. (PubMedID: 20598134) BMC bioinformatics
01/01/2010
Predicting changes in protein thermostability brought about by single- or multi-site mutations. (PubMedID: 20598148) BMC bioinformatics
01/01/2010
Metamotifs--a generative model for building families of nucleotide position weight matrices. (PubMedID: 20579334) BMC bioinformatics
01/01/2010
Modular composition predicts kinase/substrate interactions. (PubMedID: 20579376) BMC bioinformatics
01/01/2010
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. (PubMedID: 20584269) BMC bioinformatics
01/01/2010
Identifying differentially regulated subnetworks from phosphoproteomic data. (PubMedID: 20584295) BMC bioinformatics
01/01/2010
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. (PubMedID: 20584304) BMC bioinformatics
01/01/2010
ScreenMill: a freely available software suite for growth measurement, analysis and visualization of high-throughput screen data. (PubMedID: 20584323) BMC bioinformatics
01/01/2010
Nonparametric methods for the analysis of single-color pathogen microarrays. (PubMedID: 20584331) BMC bioinformatics
01/01/2010
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. (PubMedID: 20587029) BMC bioinformatics
01/01/2010
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. (PubMedID: 20587065) BMC bioinformatics
01/01/2010
PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms. (PubMedID: 20565932) BMC bioinformatics
01/01/2010
Identifying interactions in the time and frequency domains in local and global networks - A Granger Causality Approach. (PubMedID: 20565962) BMC bioinformatics
01/01/2010
svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification. (PubMedID: 20565989) BMC bioinformatics
01/01/2010
Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques. (PubMedID: 20569422) BMC bioinformatics
01/01/2010
A high-throughput pipeline for the design of real-time PCR signatures. (PubMedID: 20573238) BMC bioinformatics
01/01/2010
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. (PubMedID: 20573248) BMC bioinformatics
01/01/2010
TabSQL: a MySQL tool to facilitate mapping user data to public databases. (PubMedID: 20573251) BMC bioinformatics
01/01/2010
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. (PubMedID: 20573270) BMC bioinformatics
01/01/2010
Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays. (PubMedID: 20576120) BMC bioinformatics
01/01/2010
SOPRA: Scaffolding algorithm for paired reads via statistical optimization. (PubMedID: 20576136) BMC bioinformatics
01/01/2010
Predicting nucleosome positioning using a duration Hidden Markov Model. (PubMedID: 20576140) BMC bioinformatics
01/01/2010
Local alignment of generalized k-base encoded DNA sequence. (PubMedID: 20576157) BMC bioinformatics
01/01/2010
Pripper: prediction of caspase cleavage sites from whole proteomes. (PubMedID: 20546630) BMC bioinformatics
01/01/2010
An integrated Bayesian analysis of LOH and copy number data. (PubMedID: 20550648) BMC bioinformatics
01/01/2010
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. (PubMedID: 20550657) BMC bioinformatics
01/01/2010
A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy. (PubMedID: 20550692) BMC bioinformatics
01/01/2010
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. (PubMedID: 20550700) BMC bioinformatics
01/01/2010
Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm. (PubMedID: 20550715) BMC bioinformatics
01/01/2010
PPLook: an automated data mining tool for protein-protein interaction. (PubMedID: 20550717) BMC bioinformatics
01/01/2010
FRASS: the web-server for RNA structural comparison. (PubMedID: 20553602) BMC bioinformatics
01/01/2010
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. (PubMedID: 21059262) BMC bioinformatics
01/01/2010
Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies. (PubMedID: 21062443) BMC bioinformatics
01/01/2010
Algorithm-driven artifacts in median Polish summarization of microarray data. (PubMedID: 21070630) BMC bioinformatics
01/01/2010
FITBAR: a web tool for the robust prediction of prokaryotic regulons. (PubMedID: 21070640) BMC bioinformatics
01/01/2010
The LabelHash algorithm for substructure matching. (PubMedID: 21070651) BMC bioinformatics
01/01/2010
CaGrid Workflow Toolkit: a Taverna based workflow tool for cancer grid. (PubMedID: 21044328) BMC bioinformatics
01/01/2010
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. (PubMedID: 21044337) BMC bioinformatics
01/01/2010
Clustering metagenomic sequences with interpolated Markov models. (PubMedID: 21044341) BMC bioinformatics
01/01/2010
Bioactive conformational generation of small molecules: a comparative analysis between force-field and multiple empirical criteria based methods. (PubMedID: 21050454) BMC bioinformatics
01/01/2010
Optimizing transformations for automated, high throughput analysis of flow cytometry data. (PubMedID: 21050468) BMC bioinformatics
01/01/2010
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems. (PubMedID: 21054868) BMC bioinformatics
01/01/2010
Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots. (PubMedID: 21029427) BMC bioinformatics
01/01/2010
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. (PubMedID: 21034461) BMC bioinformatics
01/01/2010
Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. (PubMedID: 21034480) BMC bioinformatics
01/01/2010
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. (PubMedID: 21034504) BMC bioinformatics
01/01/2010
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. (PubMedID: 21034510) BMC bioinformatics
01/01/2010
Circadian signatures in rat liver: from gene expression to pathways. (PubMedID: 21040584) BMC bioinformatics
01/01/2010
Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support. (PubMedID: 21044357) BMC bioinformatics
01/01/2010
Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. (PubMedID: 21044358) BMC bioinformatics
01/01/2010
Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. (PubMedID: 21044359) BMC bioinformatics
01/01/2010
Mapping transcription mechanisms from multimodal genomic data. (PubMedID: 21044360) BMC bioinformatics
01/01/2010
Multi-dimensional discovery of biomarker and phenotype complexes. (PubMedID: 21044361) BMC bioinformatics
01/01/2010
Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. (PubMedID: 21044362) BMC bioinformatics
01/01/2010
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia. (PubMedID: 21044363) BMC bioinformatics
01/01/2010
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. (PubMedID: 21044364) BMC bioinformatics
01/01/2010
Mining multi-item drug adverse effect associations in spontaneous reporting systems. (PubMedID: 21044365) BMC bioinformatics
01/01/2010
Assessing the quality of annotations in asthma gene expression experiments. (PubMedID: 21044366) BMC bioinformatics
01/01/2010
An integrative method for scoring candidate genes from association studies: application to warfarin dosing. (PubMedID: 21044367) BMC bioinformatics
01/01/2010
Selected proceedings of the 2010 Summit on Translational Bioinformatics. (PubMedID: 21044356) BMC bioinformatics
01/01/2010
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. (PubMedID: 20973947) BMC bioinformatics
01/01/2010
BALL--biochemical algorithms library 1.3. (PubMedID: 20973958) BMC bioinformatics
01/01/2010
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model. (PubMedID: 20973976) BMC bioinformatics
01/01/2010
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. (PubMedID: 20977780) BMC bioinformatics
01/01/2010
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. (PubMedID: 20979641) BMC bioinformatics
01/01/2010
Efficient motif finding algorithms for large-alphabet inputs. (PubMedID: 21034426) BMC bioinformatics
01/01/2010
Graphical models for inferring single molecule dynamics. (PubMedID: 21034427) BMC bioinformatics
01/01/2010
A machine learning pipeline for quantitative phenotype prediction from genotype data. (PubMedID: 21034428) BMC bioinformatics
01/01/2010
Classifying and scoring of molecules with the NGN: new datasets, significance tests, and generalization. (PubMedID: 21034429) BMC bioinformatics
01/01/2010
Inferring latent task structure for Multitask Learning by Multiple Kernel Learning. (PubMedID: 21034430) BMC bioinformatics
01/01/2010
Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models. (PubMedID: 21034431) BMC bioinformatics
01/01/2010
Exploiting physico-chemical properties in string kernels. (PubMedID: 21034432) BMC bioinformatics
01/01/2010
Infinite mixture-of-experts model for sparse survival regression with application to breast cancer. (PubMedID: 21034433) BMC bioinformatics
01/01/2010
Statistical analysis and molecular dynamics simulations of ambivalent a-helices. (PubMedID: 20955581) BMC bioinformatics
01/01/2010
Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks. (PubMedID: 20955620) BMC bioinformatics
01/01/2010
Discover protein complexes in protein-protein interaction networks using parametric local modularity. (PubMedID: 20958996) BMC bioinformatics
01/01/2010
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. (PubMedID: 20961418) BMC bioinformatics
01/01/2010
Class prediction for high-dimensional class-imbalanced data. (PubMedID: 20961420) BMC bioinformatics
01/01/2010
A genetic ensemble approach for gene-gene interaction identification. (PubMedID: 20961462) BMC bioinformatics
01/01/2010
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. (PubMedID: 20964836) BMC bioinformatics
01/01/2010
A statistical approach to finding overlooked genetic associations. (PubMedID: 20964847) BMC bioinformatics
01/01/2010
CCRaVAT and QuTie-enabling analysis of rare variants in large-scale case control and quantitative trait association studies. (PubMedID: 20964851) BMC bioinformatics
01/01/2010
PathEx: a novel multi factors based datasets selector web tool. (PubMedID: 20969778) BMC bioinformatics
01/01/2010
Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers. (PubMedID: 20969788) BMC bioinformatics
01/01/2010
Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm. (PubMedID: 20942913) BMC bioinformatics
01/01/2010
Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets. (PubMedID: 20942918) BMC bioinformatics
01/01/2010
Trimming of mammalian transcriptional networks using network component analysis. (PubMedID: 20942926) BMC bioinformatics
01/01/2010
Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data. (PubMedID: 20942945) BMC bioinformatics
01/01/2010
Booly: a new data integration platform. (PubMedID: 20942966) BMC bioinformatics
01/01/2010
Data structures and compression algorithms for high-throughput sequencing technologies. (PubMedID: 20946637) BMC bioinformatics
01/01/2010
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: transcriptional dynamics and regulatory structures. (PubMedID: 20946642) BMC bioinformatics
01/01/2010
QTLminer: identifying genes regulating quantitative traits. (PubMedID: 20950438) BMC bioinformatics
01/01/2010
Inferring gene regression networks with model trees. (PubMedID: 20950452) BMC bioinformatics
01/01/2010
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies. (PubMedID: 20950483) BMC bioinformatics
01/01/2010
InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. (PubMedID: 21106116) BMC bioinformatics
01/01/2010
Analysis and verification of the HMGB1 signaling pathway. (PubMedID: 21106117) BMC bioinformatics
01/01/2010
Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis. (PubMedID: 21106118) BMC bioinformatics
01/01/2010
Sensitivity analysis of dynamic biological systems with time-delays. (PubMedID: 21106119) BMC bioinformatics
01/01/2010
Modeling the competition between lung metastases and the immune system using agents. (PubMedID: 21106120) BMC bioinformatics
01/01/2010
DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences. (PubMedID: 21106121) BMC bioinformatics
01/01/2010
IKKß inhibitor identification: a multi-filter driven novel scaffold. (PubMedID: 21106122) BMC bioinformatics
01/01/2010
Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis. (PubMedID: 21106123) BMC bioinformatics
01/01/2010
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. (PubMedID: 21106124) BMC bioinformatics
01/01/2010
Robust and accurate prediction of noncoding RNAs from aligned sequences. (PubMedID: 21106125) BMC bioinformatics
01/01/2010
T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. (PubMedID: 21106126) BMC bioinformatics
01/01/2010
A quantitatively-modeled homozygosity mapping algorithm, qHomozygosityMapping, utilizing whole genome single nucleotide polymorphism genotyping data. (PubMedID: 21106127) BMC bioinformatics
01/01/2010
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection. (PubMedID: 21106128) BMC bioinformatics
01/01/2010
Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins. (PubMedID: 21106129) BMC bioinformatics
01/01/2010
Integrating diverse biological and computational sources for reliable protein-protein interactions. (PubMedID: 21106130) BMC bioinformatics
01/01/2010
Network analysis of human protein location. (PubMedID: 21106131) BMC bioinformatics
01/01/2010
Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering. (PubMedID: 20932281) BMC bioinformatics
01/01/2010
Predicting enzyme targets for cancer drugs by profiling human metabolic reactions in NCI-60 cell lines. (PubMedID: 20932284) BMC bioinformatics
01/01/2010
Misty Mountain clustering: application to fast unsupervised flow cytometry gating. (PubMedID: 20932336) BMC bioinformatics
01/01/2010
Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering. (PubMedID: 20937082) BMC bioinformatics
01/01/2010
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. (PubMedID: 20939868) BMC bioinformatics
01/01/2010
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. (PubMedID: 20939873) BMC bioinformatics
01/01/2010
Geoseq: a tool for dissecting deep-sequencing datasets. (PubMedID: 20939882) BMC bioinformatics
01/01/2010
Proteome scanning to predict PDZ domain interactions using support vector machines. (PubMedID: 20939902) BMC bioinformatics
01/01/2010
GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing. (PubMedID: 20939910) BMC bioinformatics
01/01/2010
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage. (PubMedID: 20923564) BMC bioinformatics
01/01/2010
An integrated analysis of molecular aberrations in NCI-60 cell lines. (PubMedID: 20925909) BMC bioinformatics
01/01/2010
MetAssimulo: simulation of realistic NMR metabolic profiles. (PubMedID: 20925910) BMC bioinformatics
01/01/2010
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. (PubMedID: 20925918) BMC bioinformatics
01/01/2010
Automatic, context-specific generation of Gene Ontology slims. (PubMedID: 20929524) BMC bioinformatics
01/01/2010
Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome. (PubMedID: 20929581) BMC bioinformatics
01/01/2010
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. (PubMedID: 20946592) BMC bioinformatics
01/01/2010
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. (PubMedID: 20946593) BMC bioinformatics
01/01/2010
Mixed reality simulation of rasping procedure in artificial cervical disc replacement (ACDR) surgery. (PubMedID: 20946594) BMC bioinformatics
01/01/2010
Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum. (PubMedID: 20946595) BMC bioinformatics
01/01/2010
Quail Genomics: a knowledgebase for Northern bobwhite. (PubMedID: 20946596) BMC bioinformatics
01/01/2010
Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization). (PubMedID: 20946597) BMC bioinformatics
01/01/2010
PoGO: Prediction of Gene Ontology terms for fungal proteins. (PubMedID: 20429880) BMC bioinformatics
01/01/2010
TassDB2 - A comprehensive database of subtle alternative splicing events. (PubMedID: 20429909) BMC bioinformatics
01/01/2010
ParallABEL: an R library for generalized parallelization of genome-wide association studies. (PubMedID: 20429914) BMC bioinformatics
01/01/2010
Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes. (PubMedID: 20429923) BMC bioinformatics
01/01/2010
WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. (PubMedID: 20429928) BMC bioinformatics
01/01/2010
Integration of open access literature into the RCSB Protein Data Bank using BioLit. (PubMedID: 20429930) BMC bioinformatics
01/01/2010
GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. (PubMedID: 20429936) BMC bioinformatics
01/01/2010
Fine-tuning structural RNA alignments in the twilight zone. (PubMedID: 20433706) BMC bioinformatics
01/01/2010
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. (PubMedID: 20433708) BMC bioinformatics
01/01/2010
Cgaln: fast and space-efficient whole-genome alignment. (PubMedID: 20433723) BMC bioinformatics
01/01/2010
SeqRate: sequence-based protein folding type classification and rates prediction. (PubMedID: 20438647) BMC bioinformatics
01/01/2010
Bacillus anthracis genome organization in light of whole transcriptome sequencing. (PubMedID: 20438648) BMC bioinformatics
01/01/2010
Exploratory analysis of protein translation regulatory networks using hierarchical random graphs. (PubMedID: 20438649) BMC bioinformatics
01/01/2010
Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins. (PubMedID: 20438650) BMC bioinformatics
01/01/2010
A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages. (PubMedID: 20438651) BMC bioinformatics
01/01/2010
A Markov blanket-based method for detecting causal SNPs in GWAS. (PubMedID: 20438652) BMC bioinformatics
01/01/2010
Towards reliable isoform quantification using RNA-SEQ data. (PubMedID: 20438653) BMC bioinformatics
01/01/2010
Detection of gene orthology from gene co-expression and protein interaction networks. (PubMedID: 20438654) BMC bioinformatics
01/01/2010
Application of kernel functions for accurate similarity search in large chemical databases. (PubMedID: 20438655) BMC bioinformatics
01/01/2010
Learning biological network using mutual information and conditional independence. (PubMedID: 20438656) BMC bioinformatics
01/01/2010
Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets. (PubMedID: 20409339) BMC bioinformatics
01/01/2010
BioPhysConnectoR: Connecting sequence information and biophysical models. (PubMedID: 20412558) BMC bioinformatics
01/01/2010
Conditional random pattern model for copy number aberration detection. (PubMedID: 20412592) BMC bioinformatics
01/01/2010
A model-independent approach to infer hierarchical codon substitution dynamics. (PubMedID: 20412602) BMC bioinformatics
01/01/2010
Systematic calibration of a cell signaling network model. (PubMedID: 20416044) BMC bioinformatics
01/01/2010
BS Seeker: precise mapping for bisulfite sequencing. (PubMedID: 20416082) BMC bioinformatics
01/01/2010
Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design. (PubMedID: 20398384) BMC bioinformatics
01/01/2010
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction. (PubMedID: 20398404) BMC bioinformatics
01/01/2010
Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. (PubMedID: 20398407) BMC bioinformatics
01/01/2010
Properties and identification of antibiotic drug targets. (PubMedID: 20406434) BMC bioinformatics
01/01/2010
Shared probe design and existing microarray reanalysis using PICKY. (PubMedID: 20406469) BMC bioinformatics
01/01/2010
Missing value imputation for epistatic MAPs. (PubMedID: 20406472) BMC bioinformatics
01/01/2010
Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents. (PubMedID: 20406499) BMC bioinformatics
01/01/2010
Linear predictive coding representation of correlated mutation for protein sequence alignment. (PubMedID: 20406500) BMC bioinformatics
01/01/2010
MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge. (PubMedID: 20406501) BMC bioinformatics
01/01/2010
Multivariate classification of urine metabolome profiles for breast cancer diagnosis. (PubMedID: 20406502) BMC bioinformatics
01/01/2010
Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. (PubMedID: 20406503) BMC bioinformatics
01/01/2010
Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS. (PubMedID: 20406504) BMC bioinformatics
01/01/2010
Learning an enriched representation from unlabeled data for protein-protein interaction extraction. (PubMedID: 20406505) BMC bioinformatics
01/01/2010
Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. (PubMedID: 20380738) BMC bioinformatics
01/01/2010
A robust method for estimating gene expression states using Affymetrix microarray probe level data. (PubMedID: 20380745) BMC bioinformatics
01/01/2010
FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods. (PubMedID: 20385005) BMC bioinformatics
01/01/2010
web cellHTS2: a web-application for the analysis of high-throughput screening data. (PubMedID: 20385013) BMC bioinformatics
01/01/2010
Shape based kinetic outlier detection in real-time PCR. (PubMedID: 20385019) BMC bioinformatics
01/01/2010
Artificial and natural duplicates in pyrosequencing reads of metagenomic data. (PubMedID: 20388221) BMC bioinformatics
01/01/2010
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. (PubMedID: 20398246) BMC bioinformatics
01/01/2010
JISTIC: identification of significant targets in cancer. (PubMedID: 20398270) BMC bioinformatics
01/01/2010
PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. (PubMedID: 20398296) BMC bioinformatics
01/01/2010
Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. (PubMedID: 20398334) BMC bioinformatics
01/01/2010
Using jackknife to assess the quality of gene order phylogenies. (PubMedID: 20370914) BMC bioinformatics
01/01/2010
A highly efficient multi-core algorithm for clustering extremely large datasets. (PubMedID: 20370922) BMC bioinformatics
01/01/2010
Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. (PubMedID: 20370926) BMC bioinformatics
01/01/2010
Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates. (PubMedID: 20370931) BMC bioinformatics
01/01/2010
Directionality in protein fold prediction. (PubMedID: 20374616) BMC bioinformatics
01/01/2010
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. (PubMedID: 20377871) BMC bioinformatics
01/01/2010
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. (PubMedID: 20377884) BMC bioinformatics
01/01/2010
Protein sequences classification by means of feature extraction with substitution matrices. (PubMedID: 20377887) BMC bioinformatics
01/01/2010
Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays. (PubMedID: 20377890) BMC bioinformatics
01/01/2010
A Bayesian network approach to feature selection in mass spectrometry data. (PubMedID: 20377906) BMC bioinformatics
01/01/2010
An overview of the CellML API and its implementation. (PubMedID: 20377909) BMC bioinformatics
01/01/2010
The value of position-specific priors in motif discovery using MEME. (PubMedID: 20380693) BMC bioinformatics
01/01/2010
Optimization algorithms for functional deimmunization of therapeutic proteins. (PubMedID: 20380721) BMC bioinformatics
01/01/2010
Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study. (PubMedID: 20380733) BMC bioinformatics
01/01/2010
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. (PubMedID: 20356413) BMC bioinformatics
01/01/2010
GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. (PubMedID: 20359363) BMC bioinformatics
01/01/2010
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. (PubMedID: 20361868) BMC bioinformatics
01/01/2010
CDK-Taverna: an open workflow environment for cheminformatics. (PubMedID: 20346188) BMC bioinformatics
01/01/2010
Identification of NAD interacting residues in proteins. (PubMedID: 20353553) BMC bioinformatics
01/01/2010
ProbFAST: Probabilistic functional analysis system tool. (PubMedID: 20353576) BMC bioinformatics
01/01/2010
Knowledge-guided gene ranking by coordinative component analysis. (PubMedID: 20353603) BMC bioinformatics
01/01/2010
New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. (PubMedID: 20356373) BMC bioinformatics
01/01/2010
Multiconstrained gene clustering based on generalized projections. (PubMedID: 20356386) BMC bioinformatics
01/01/2010
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. (PubMedID: 20307279) BMC bioinformatics
01/01/2010
Identification of recurrent regions of Copy-Number Variants across multiple individuals. (PubMedID: 20307285) BMC bioinformatics
01/01/2010
In silico fragmentation for computer assisted identification of metabolite mass spectra. (PubMedID: 20307295) BMC bioinformatics
01/01/2010
Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis. (PubMedID: 20307305) BMC bioinformatics
01/01/2010
Identifying common prognostic factors in genomic cancer studies: a novel index for censored outcomes. (PubMedID: 20334636) BMC bioinformatics
01/01/2010
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function. (PubMedID: 20334658) BMC bioinformatics
01/01/2010
permGPU: Using graphics processing units in RNA microarray association studies. (PubMedID: 20553619) BMC bioinformatics
01/01/2010
MimoSA: a system for minimotif annotation. (PubMedID: 20565705) BMC bioinformatics
01/01/2010
Computing and visually analyzing mutual information in molecular co-evolution. (PubMedID: 20565748) BMC bioinformatics
01/01/2010
CGHpower: exploring sample size calculations for chromosomal copy number experiments. (PubMedID: 20565750) BMC bioinformatics
01/01/2010
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. (PubMedID: 20565810) BMC bioinformatics
01/01/2010
MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane. (PubMedID: 20565847) BMC bioinformatics
01/01/2010
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking. (PubMedID: 20565873) BMC bioinformatics
01/01/2010
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. (PubMedID: 20565884) BMC bioinformatics
01/01/2010
Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. (PubMedID: 20537135) BMC bioinformatics
01/01/2010
A boosting method for maximizing the partial area under the ROC curve. (PubMedID: 20537139) BMC bioinformatics
01/01/2010
mu-CS: an extension of the TM4 platform to manage Affymetrix binary data. (PubMedID: 20537149) BMC bioinformatics
01/01/2010
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. (PubMedID: 20537162) BMC bioinformatics
01/01/2010
Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. (PubMedID: 20540779) BMC bioinformatics
01/01/2010
CONAN: copy number variation analysis software for genome-wide association studies. (PubMedID: 20546565) BMC bioinformatics
01/01/2010
Accessing the SEED genome databases via Web services API: tools for programmers. (PubMedID: 20546611) BMC bioinformatics
01/01/2010
Beyond rotamers: a generative, probabilistic model of side chains in proteins. (PubMedID: 20525384) BMC bioinformatics
01/01/2010
Rule-based spatial modeling with diffusing, geometrically constrained molecules. (PubMedID: 20529264) BMC bioinformatics
01/01/2010
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation. (PubMedID: 20529327) BMC bioinformatics
01/01/2010
L2-norm multiple kernel learning and its application to biomedical data fusion. (PubMedID: 20529363) BMC bioinformatics
01/01/2010
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. (PubMedID: 20529369) BMC bioinformatics
01/01/2010
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. (PubMedID: 20534127) BMC bioinformatics
01/01/2010
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. (PubMedID: 20534164) BMC bioinformatics
01/01/2010
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. (PubMedID: 20513238) BMC bioinformatics
01/01/2010
EnvMine: a text-mining system for the automatic extraction of contextual information. (PubMedID: 20515448) BMC bioinformatics
01/01/2010
Bayesian integrated modeling of expression data: a case study on RhoG. (PubMedID: 20515463) BMC bioinformatics
01/01/2010
Super-sparse principal component analyses for high-throughput genomic data. (PubMedID: 20525176) BMC bioinformatics
01/01/2010
A classification model for distinguishing copy number variants from cancer-related alterations. (PubMedID: 20525196) BMC bioinformatics
01/01/2010
An interaction-motif-based scoring function for protein-ligand docking. (PubMedID: 20525216) BMC bioinformatics
01/01/2010
poolMC: smart pooling of mRNA samples in microarray experiments. (PubMedID: 20525223) BMC bioinformatics
01/01/2010
UFFizi: a generic platform for ranking informative features. (PubMedID: 20525252) BMC bioinformatics
01/01/2010
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information. (PubMedID: 20525281) BMC bioinformatics
01/01/2010
Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. (PubMedID: 20525291) BMC bioinformatics
01/01/2010
Detecting internally symmetric protein structures. (PubMedID: 20525292) BMC bioinformatics
01/01/2010
Scaffold filling, contig fusion and comparative gene order inference. (PubMedID: 20525342) BMC bioinformatics
01/01/2010
Prediction of epigenetically regulated genes in breast cancer cell lines. (PubMedID: 20525369) BMC bioinformatics
01/01/2010
Importance of replication in analyzing time-series gene expression data: corticosteroid dynamics and circadian patterns in rat liver. (PubMedID: 20500897) BMC bioinformatics
01/01/2010
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. (PubMedID: 20504309) BMC bioinformatics
01/01/2010
A comparison of probe-level and probeset models for small-sample gene expression data. (PubMedID: 20504334) BMC bioinformatics
01/01/2010
An eScience-Bayes strategy for analyzing omics data. (PubMedID: 20504364) BMC bioinformatics
01/01/2010
Optimal contact definition for reconstruction of contact maps. (PubMedID: 20507547) BMC bioinformatics
01/01/2010
JCoDA: a tool for detecting evolutionary selection. (PubMedID: 20507581) BMC bioinformatics
01/01/2010
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. (PubMedID: 20507584) BMC bioinformatics
01/01/2010
Conserved residue clusters at protein-protein interfaces and their use in binding site identification. (PubMedID: 20507585) BMC bioinformatics
01/01/2010
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. (PubMedID: 20509870) BMC bioinformatics
01/01/2010
GWAMA: software for genome-wide association meta-analysis. (PubMedID: 20509871) BMC bioinformatics
01/01/2010
Spatio-structural granularity of biological material entities. (PubMedID: 20509878) BMC bioinformatics
01/01/2010
Revealing and avoiding bias in semantic similarity scores for protein pairs. (PubMedID: 20509916) BMC bioinformatics
01/01/2010
Washing scaling of GeneChip microarray expression. (PubMedID: 20509934) BMC bioinformatics
01/01/2010
TargetSpy: a supervised machine learning approach for microRNA target prediction. (PubMedID: 20509939) BMC bioinformatics
01/01/2010
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. (PubMedID: 20492656) BMC bioinformatics
01/01/2010
A high-level 3D visualization API for Java and ImageJ. (PubMedID: 20492697) BMC bioinformatics
01/01/2010
HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data. (PubMedID: 20492700) BMC bioinformatics
01/01/2010
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. (PubMedID: 20500820) BMC bioinformatics
01/01/2010
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. (PubMedID: 20500821) BMC bioinformatics
01/01/2010
Semantic annotation of morphological descriptions: an overall strategy. (PubMedID: 20500882) BMC bioinformatics
01/01/2010
PhenoFam-gene set enrichment analysis through protein structural information. (PubMedID: 20478033) BMC bioinformatics
01/01/2010
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. (PubMedID: 20478034) BMC bioinformatics
01/01/2010
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. (PubMedID: 20478076) BMC bioinformatics
01/01/2010
Detecting microRNA activity from gene expression data. (PubMedID: 20482775) BMC bioinformatics
01/01/2010
Cloud computing for comparative genomics. (PubMedID: 20482786) BMC bioinformatics
01/01/2010
Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities. (PubMedID: 20482787) BMC bioinformatics
01/01/2010
vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments. (PubMedID: 20482791) BMC bioinformatics
01/01/2010
The Protein-DNA Interface database. (PubMedID: 20482798) BMC bioinformatics
01/01/2010
The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. (PubMedID: 20482811) BMC bioinformatics
01/01/2010
CNstream: a method for the identification and genotyping of copy number polymorphisms using Illumina microarrays. (PubMedID: 20482829) BMC bioinformatics
01/01/2010
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. (PubMedID: 20482861) BMC bioinformatics
01/01/2010
FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data. (PubMedID: 20482883) BMC bioinformatics
01/01/2010
Retraction: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase. (PubMedID: 20482900) BMC bioinformatics
01/01/2010
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. (PubMedID: 20487530) BMC bioinformatics
01/01/2010
Characterization of phylogenetic networks with NetTest. (PubMedID: 20487540) BMC bioinformatics
01/01/2010
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. (PubMedID: 20487544) BMC bioinformatics
01/01/2010
sdef: an R package to synthesize lists of significant features in related experiments. (PubMedID: 20487547) BMC bioinformatics
01/01/2010
Incorporating gene co-expression network in identification of cancer prognosis markers. (PubMedID: 20487548) BMC bioinformatics
01/01/2010
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. (PubMedID: 20487560) BMC bioinformatics
01/01/2010
Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. (PubMedID: 20459766) BMC bioinformatics
01/01/2010
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. (PubMedID: 20459804) BMC bioinformatics
01/01/2010
A database and API for variation, dense genotyping and resequencing data. (PubMedID: 20459810) BMC bioinformatics
01/01/2010
Using caching and optimization techniques to improve performance of the Ensembl website. (PubMedID: 20459812) BMC bioinformatics
01/01/2010
eHive: an artificial intelligence workflow system for genomic analysis. (PubMedID: 20459813) BMC bioinformatics
01/01/2010
Error margin analysis for feature gene extraction. (PubMedID: 20459827) BMC bioinformatics
01/01/2010
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. (PubMedID: 20459833) BMC bioinformatics
01/01/2010
MOTIPS: automated motif analysis for predicting targets of modular protein domains. (PubMedID: 20459839) BMC bioinformatics
01/01/2010
Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective. (PubMedID: 20462403) BMC bioinformatics
01/01/2010
TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. (PubMedID: 20462408) BMC bioinformatics
01/01/2010
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems. (PubMedID: 20462443) BMC bioinformatics
01/01/2010
Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data. (PubMedID: 20462459) BMC bioinformatics
01/01/2010
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. (PubMedID: 20465797) BMC bioinformatics
01/01/2010
Gene bi-targeting by viral and human miRNAs. (PubMedID: 20465802) BMC bioinformatics
01/01/2010
In-silico prediction of blood-secretory human proteins using a ranking algorithm. (PubMedID: 20465853) BMC bioinformatics
01/01/2010
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH. (PubMedID: 20470364) BMC bioinformatics
01/01/2010
Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data. (PubMedID: 20470414) BMC bioinformatics
01/01/2010
Selection of optimal reference genes for normalization in quantitative RT-PCR. (PubMedID: 20470420) BMC bioinformatics
01/01/2010
GOAL: a software tool for assessing biological significance of genes groups. (PubMedID: 20459620) BMC bioinformatics
01/01/2010
BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. (PubMedID: 20459626) BMC bioinformatics
01/01/2010
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. (PubMedID: 20459631) BMC bioinformatics
01/01/2010
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. (PubMedID: 20459641) BMC bioinformatics
01/01/2010
Odefy--from discrete to continuous models. (PubMedID: 20459647) BMC bioinformatics
01/01/2010
A semi-parametric Bayesian model for unsupervised differential co-expression analysis. (PubMedID: 20459663) BMC bioinformatics
01/01/2010
MTRAP: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues. (PubMedID: 20459682) BMC bioinformatics
01/01/2010
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. (PubMedID: 20438625) BMC bioinformatics
01/01/2010
Partitioning of copy-number genotypes in pedigrees. (PubMedID: 20438641) BMC bioinformatics
01/01/2010
A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling. (PubMedID: 20441598) BMC bioinformatics
01/01/2010
Learning gene regulatory networks from only positive and unlabeled data. (PubMedID: 20444264) BMC bioinformatics
01/01/2010
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. (PubMedID: 20420672) BMC bioinformatics
01/01/2010
Predicting conserved protein motifs with Sub-HMMs. (PubMedID: 20420695) BMC bioinformatics
01/01/2010
Comparative performances of DNA barcoding across insect orders. (PubMedID: 20420717) BMC bioinformatics
01/01/2010
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. (PubMedID: 20423484) BMC bioinformatics
01/01/2010
Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. (PubMedID: 20423502) BMC bioinformatics
01/01/2010
Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. (PubMedID: 20423512) BMC bioinformatics
01/01/2010
AMS 3.0: prediction of post-translational modifications. (PubMedID: 20423529) BMC bioinformatics
01/01/2010
Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays. (PubMedID: 20426803) BMC bioinformatics
01/01/2010
Concept-based query expansion for retrieving gene related publications from MEDLINE. (PubMedID: 20426836) BMC bioinformatics
01/01/2010
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. (PubMedID: 20426874) BMC bioinformatics
01/01/2010
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. (PubMedID: 20426876) BMC bioinformatics