Published in Genome Inform on January 01, 2004
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Res (2013) 0.82
Systematic reconstruction of TRANSPATH data into cell system markup language. BMC Syst Biol (2008) 0.80
ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics (2005) 6.12
RelEx--relation extraction using dependency parse trees. Bioinformatics (2006) 4.81
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
Playing biology's name game: identifying protein names in scientific text. Pac Symp Biocomput (2003) 3.03
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res (2009) 2.26
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
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
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
Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog (2009) 1.67
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
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
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
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics (2003) 1.40
Inferring gene regulatory networks by ANOVA. Bioinformatics (2012) 1.39
Alternative splicing and protein structure evolution. Nucleic Acids Res (2007) 1.35
Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc Natl Acad Sci U S A (2007) 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
Microarrays: how many do you need? J Comput Biol (2003) 1.19
New methods for joint analysis of biological networks and expression data. Bioinformatics (2004) 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
The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. PLoS Pathog (2011) 1.14
Vorolign--fast structural alignment using Voronoi contacts. Bioinformatics (2007) 1.14
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics (2005) 1.11
Protein structure alignment considering phenotypic plasticity. Bioinformatics (2008) 1.09
Contextual analysis of RNAi-based functional screens using interaction networks. Bioinformatics (2011) 1.07
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS One (2009) 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
Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst Biol (2010) 1.05
Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics (2005) 1.05
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinformatics (2007) 0.99
MIRTFnet: analysis of miRNA regulated transcription factors. PLoS One (2011) 0.99
Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog (2012) 0.98
Petri Nets with Fuzzy Logic (PNFL): reverse engineering and parametrization. PLoS One (2010) 0.98
Gene expression profiling of serum- and interleukin-1 beta-stimulated primary human adult articular chondrocytes--a molecular analysis based on chondrocytes isolated from one donor. Cytokine (2005) 0.98
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PLoS Pathog (2013) 0.98
Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics (2006) 0.97
Identifying active transcription factors and kinases from expression data using pathway queries. Bioinformatics (2005) 0.96
WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics (2006) 0.95
ToPNet--an application for interactive analysis of expression data and biological networks. Bioinformatics (2004) 0.95
ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Res (2007) 0.95
Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set. BMC Biotechnol (2013) 0.93
Mining RNA-seq data for infections and contaminations. PLoS One (2013) 0.93
Gene expression in chondrocytes assessed with use of microarrays. J Bone Joint Surg Am (2003) 0.92
Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integr Biol (Camb) (2012) 0.92
Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum. PLoS Comput Biol (2009) 0.91
Rigorous assessment of gene set enrichment tests. Bioinformatics (2012) 0.91
Colored Petri net modeling and simulation of signal transduction pathways. Metab Eng (2005) 0.91
Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9. PLoS Pathog (2013) 0.90
Patterned assembly of genetically modified viral nanotemplates via nucleic acid hybridization. Nano Lett (2005) 0.90
Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics (2010) 0.89
PARma: identification of microRNA target sites in AGO-PAR-CLIP data. Genome Biol (2013) 0.88
A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics (2012) 0.88
Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses. Clin Orthop Relat Res (2004) 0.88
Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics (2007) 0.87
Toward the complete interactome. Nat Biotechnol (2006) 0.87
Identifying the topology of protein complexes from affinity purification assays. Bioinformatics (2009) 0.87
FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics (2008) 0.86
Multiobjective flux balancing using the NISE method for metabolic network analysis. Biotechnol Prog (2009) 0.86
Characterization of silica-coated tobacco mosaic virus. J Colloid Interface Sci (2006) 0.86
MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Inform (2003) 0.86
Comprehensive analysis of varicella-zoster virus proteins using a new monoclonal antibody collection. J Virol (2013) 0.85
ProML--the protein markup language for specification of protein sequences, structures and families. In Silico Biol (2002) 0.85
Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis. PLoS Comput Biol (2010) 0.85
Complementary identification of multiple flux distributions and multiple metabolic pathways. Metab Eng (2005) 0.85
Estimation of zeta potential by electrokinetic analysis of ionic fluid flows through a divergent microchannel. J Colloid Interface Sci (2003) 0.84
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics (2008) 0.82
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Res (2013) 0.82
Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis. Methods Mol Med (2004) 0.82
HALO--a Java framework for precise transcript half-life determination. Bioinformatics (2010) 0.81
Improving fold recognition of protein threading by experimental distance constraints. In Silico Biol (2002) 0.81
Complementing the Eukaryotic Protein Interactome. PLoS One (2013) 0.81
Detecting outlier peptides in quantitative high-throughput mass spectrometry data. J Proteomics (2012) 0.81
Comparison of electrical properties of viruses studied by AC capacitance scanning probe microscopy. J Am Chem Soc (2007) 0.80
Web servicing the biological office. Bioinformatics (2005) 0.80
Normalization and gene p-value estimation: issues in microarray data processing. Bioinform Biol Insights (2008) 0.80
RIP-chip enrichment analysis. Bioinformatics (2012) 0.79
Detection and correction of probe-level artefacts on microarrays. BMC Bioinformatics (2012) 0.79
Biotemplated aqueous-phase palladium crystallization in the absence of external reducing agents. Nano Lett (2010) 0.79
A Turing test for artificial expression data. Bioinformatics (2013) 0.78
Functional genomics of osteoarthritis. Pharmacogenomics (2002) 0.78
Serial intravascular ultrasound analysis of the main and side branches in bifurcation lesions treated with the T-stenting technique. J Am Coll Cardiol (2009) 0.77
Carbonic anhydrase-mimetic bolaamphiphile self-assembly for CO2 hydration and sequestration. Chemistry (2014) 0.77
Quantitative study of Au(III) and Pd(II) ion biosorption on genetically engineered Tobacco mosaic virus. J Colloid Interface Sci (2009) 0.77
Confidence measures for protein fold recognition. Bioinformatics (2002) 0.76
A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation. Lipids Health Dis (2013) 0.75