Published in In Silico Biol on January 01, 2002
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
XML-based approaches for the integration of heterogeneous bio-molecular data. BMC Bioinformatics (2009) 1.12
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. BMC Bioinformatics (2004) 1.06
Databases and QSAR for cancer research. Cancer Inform (2007) 0.79
ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33
ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics (2005) 6.12
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (2005) 5.95
Computing topological parameters of biological networks. Bioinformatics (2007) 5.36
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
RelEx--relation extraction using dependency parse trees. Bioinformatics (2006) 4.81
Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet (2005) 4.23
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A (2002) 3.46
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet (2004) 3.19
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA (2008) 3.13
A simple approach for protein name identification: prospects and limits. BMC Bioinformatics (2005) 3.12
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe (2011) 3.05
Playing biology's name game: identifying protein names in scientific text. Pac Symp Biocomput (2003) 3.03
CpG island mapping by epigenome prediction. PLoS Comput Biol (2007) 3.02
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet (2011) 2.98
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther (2007) 2.49
Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol (2004) 2.48
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res (2003) 2.37
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res (2009) 2.26
The HIN domain of IFI-200 proteins consists of two OB folds. Biochem Biophys Res Commun (2005) 2.25
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19
A DNA methylation fingerprint of 1628 human samples. Genome Res (2011) 2.16
Large-scale gene expression profiling reveals major pathogenetic pathways of cartilage degeneration in osteoarthritis. Arthritis Rheum (2006) 2.13
Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12
Computational epigenetics. Bioinformatics (2007) 1.92
Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe (2010) 1.91
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res (2011) 1.90
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88
NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol (2009) 1.83
Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer. Nucleic Acids Res (2010) 1.80
Profile-profile alignment: a powerful tool for protein structure prediction. Pac Symp Biocomput (2003) 1.76
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol (2006) 1.75
Learning multiple evolutionary pathways from cross-sectional data. J Comput Biol (2005) 1.74
Recco: recombination analysis using cost optimization. Bioinformatics (2006) 1.68
Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog (2009) 1.67
Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics (2007) 1.65
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics (2010) 1.57
Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinformatics (2006) 1.54
Computational analysis of human protein interaction networks. Proteomics (2007) 1.53
Gene and protein nomenclature in public databases. BMC Bioinformatics (2006) 1.52
Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. J Comput Biol (2009) 1.51
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS One (2007) 1.42
Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics (2005) 1.41
Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathog (2012) 1.40
EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol (2012) 1.40
Inferring gene regulatory networks by ANOVA. Bioinformatics (2012) 1.39
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol (2007) 1.39
Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. FEBS Lett (2004) 1.38
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37
Alternative splicing and protein structure evolution. Nucleic Acids Res (2007) 1.35
Permutation importance: a corrected feature importance measure. Bioinformatics (2010) 1.32
Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors. J Virol (2006) 1.28
Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics (2005) 1.27
An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol (2004) 1.26
Survey on the PABC recognition motif PAM2. Biochem Biophys Res Commun (2004) 1.26
BioWeka--extending the Weka framework for bioinformatics. Bioinformatics (2007) 1.26
Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. Mol Biosyst (2007) 1.25
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res (2012) 1.24
Structural and functional analysis of ataxin-2 and ataxin-3. Eur J Biochem (2004) 1.24
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family. Proc Natl Acad Sci U S A (2005) 1.23
Confirmation of human protein interaction data by human expression data. BMC Bioinformatics (2005) 1.23
Decomposing protein networks into domain-domain interactions. Bioinformatics (2005) 1.22
Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways. Hum Mol Genet (2005) 1.21
Identification of PatL1, a human homolog to yeast P body component Pat1. Biochim Biophys Acta (2007) 1.21
Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. J Infect Dis (2005) 1.19
Microarrays: how many do you need? J Comput Biol (2003) 1.19
Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer (2012) 1.19
Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinformatics (2005) 1.18
DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics (2006) 1.18
New methods for joint analysis of biological networks and expression data. Bioinformatics (2004) 1.17
Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antivir Ther (2007) 1.17
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics (2004) 1.16
Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis. BMC Struct Biol (2009) 1.16
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics (2011) 1.15
Vorolign--fast structural alignment using Voronoi contacts. Bioinformatics (2007) 1.14
The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. PLoS Pathog (2011) 1.14
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics (2005) 1.11
Tenofovir resistance and resensitization. Antimicrob Agents Chemother (2003) 1.10
Protein structure alignment considering phenotypic plasticity. Bioinformatics (2008) 1.09
Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics (2012) 1.08
Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis (2009) 1.07
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS One (2009) 1.07
Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy. PLoS One (2008) 1.07
Contextual analysis of RNAi-based functional screens using interaction networks. Bioinformatics (2011) 1.07
Microarray analyses of transdifferentiated mesenchymal stem cells. J Cell Biochem (2008) 1.06
ProCope--protein complex prediction and evaluation. Bioinformatics (2008) 1.05
Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening. Chemistry (2007) 1.05
Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics (2005) 1.05