Published in Bioinformatics on February 25, 2010
Integrative approaches for finding modular structure in biological networks. Nat Rev Genet (2013) 2.19
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. Bioinformatics (2011) 1.29
An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. Sci Rep (2013) 1.26
Defining the transcriptional and cellular landscape of type 1 diabetes in the NOD mouse. PLoS One (2013) 1.21
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. Nat Protoc (2015) 1.17
Patient-specific data fusion defines prognostic cancer subtypes. PLoS Comput Biol (2011) 1.16
GenRev: exploring functional relevance of genes in molecular networks. Genomics (2011) 1.07
Concerted perturbation observed in a hub network in Alzheimer's disease. PLoS One (2012) 1.00
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res (2011) 0.94
LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes. Evol Bioinform Online (2011) 0.91
Network-based functional enrichment. BMC Bioinformatics (2011) 0.91
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. Sci Rep (2015) 0.89
Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines. Cell Commun Signal (2015) 0.88
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Integration of 'omics' data in aging research: from biomarkers to systems biology. Aging Cell (2015) 0.88
Systems analysis of high-throughput data. Adv Exp Med Biol (2014) 0.87
Genome-Wide Association Analyses Point to Candidate Genes for Electric Shock Avoidance in Drosophila melanogaster. PLoS One (2015) 0.85
Steiner tree methods for optimal sub-network identification: an empirical study. BMC Bioinformatics (2013) 0.83
Increased expression of c-Jun in nonalcoholic fatty liver disease. Lab Invest (2014) 0.83
Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection. Sci Rep (2012) 0.82
Identification of rifampin-regulated functional modules and related microRNAs in human hepatocytes based on the protein interaction network. BMC Genomics (2016) 0.81
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Syst Biol (2012) 0.81
Profiling the human response to physical exercise: a computational strategy for the identification and kinetic analysis of metabolic biomarkers. J Clin Bioinforma (2011) 0.81
Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure. PLoS One (2014) 0.81
Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. BMC Med Genomics (2012) 0.81
Correlation of clinical features and genetic profiles of stromal interaction molecule 1 (STIM1) in colorectal cancers. Oncotarget (2015) 0.80
Proteomics for systems toxicology. Comput Struct Biotechnol J (2014) 0.79
Assessment of subnetwork detection methods for breast cancer. Cancer Inform (2014) 0.79
KeyPathwayMinerWeb: online multi-omics network enrichment. Nucleic Acids Res (2016) 0.79
Broad DNA methylation changes of spermatogenesis, inflammation and immune response-related genes in a subgroup of sperm samples for assisted reproduction. Andrology (2013) 0.79
Network representations of immune system complexity. Wiley Interdiscip Rev Syst Biol Med (2015) 0.78
Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation. PLoS Genet (2016) 0.78
A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology. BMC Genomics (2013) 0.77
A systems biology analysis of brain microvascular endothelial cell lipotoxicity. BMC Syst Biol (2014) 0.77
Efficient randomization of biological networks while preserving functional characterization of individual nodes. BMC Bioinformatics (2016) 0.77
Associations of maternal BMI and insulin resistance with the maternal metabolome and newborn outcomes. Diabetologia (2016) 0.77
On the performance of de novo pathway enrichment. NPJ Syst Biol Appl (2017) 0.76
Robust de novo pathway enrichment with KeyPathwayMiner 5. F1000Res (2016) 0.76
Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping. Sci Rep (2016) 0.76
Algorithms for modeling global and context-specific functional relationship networks. Brief Bioinform (2015) 0.76
Identification of genes and pathways associated with pancreatic ductal adenocarcinoma by bioinformatics analyses. Oncol Lett (2015) 0.76
Pathway deregulation and expression QTLs in response to Actinobacillus pleuropneumoniae infection in swine. Mamm Genome (2014) 0.76
Reconciling differential gene expression data with molecular interaction networks. Bioinformatics (2013) 0.76
Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. PLoS One (2017) 0.75
Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women. PLoS One (2016) 0.75
GWAS of self-reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune-related predisposition loci. Hum Mol Genet (2017) 0.75
Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma. PLoS Comput Biol (2015) 0.75
NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data. Bioinformatics (2013) 0.75
Identification of genes and signaling pathways associated with squamous cell carcinoma by bioinformatics analysis. Oncol Lett (2015) 0.75
Interactome mapping reveals important pathways in skeletal muscle development of pigs. Int J Mol Sci (2014) 0.75
Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data. Mol Cell Proteomics (2014) 0.75
Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PLoS Genet (2016) 0.75
Identification of the key genes connected with plasma cells of multiple myeloma using expression profiles. Onco Targets Ther (2015) 0.75
Gene expression profiling analysis of ovarian cancer. Oncol Lett (2016) 0.75
Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis. PLoS One (2017) 0.75
SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformatics (2017) 0.75
SLICE: determining cell differentiation and lineage based on single cell entropy. Nucleic Acids Res (2017) 0.75
Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BMC Genomics (2017) 0.75
Prior knowledge guided active modules identification: an integrated multi-objective approach. BMC Syst Biol (2017) 0.75
Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network. BMC Bioinformatics (2017) 0.75
Identification of genes associated with methotrexate resistance in methotrexate-resistant osteosarcoma cell lines. J Orthop Surg Res (2015) 0.75
Identification of genes associated with tongue cancer in patients with a history of tobacco and/or alcohol use. Oncol Lett (2016) 0.75
RNA-seq based gene expression analysis of ovarian granulosa cells exposed to zearalenone in vitro: significance to steroidogenesis. Oncotarget (2017) 0.75
IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nat Genet (2009) 13.03
Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics (2008) 3.00
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA (2005) 2.75
On the power of profiles for transcription factor binding site detection. Stat Appl Genet Mol Biol (2003) 2.52
5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene (2008) 2.51
Combined effects of different interleukin-28B gene variants on the outcome of dual combination therapy in chronic hepatitis C virus type 1 infection. Hepatology (2012) 2.42
A Variegated Squirrel Bornavirus Associated with Fatal Human Encephalitis. N Engl J Med (2015) 2.34
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics (2006) 2.24
Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol Mol Biol Rev (2004) 2.19
Mitochondrial changes in skeletal muscle in amyotrophic lateral sclerosis and other neurogenic atrophies. Brain (2005) 2.18
Graft-versus-host disease is enhanced by extracellular ATP activating P2X7R. Nat Med (2010) 2.17
Evaluation of liver disease progression in the German hepatitis C virus (1b)-contaminated anti-D cohort at 35 years after infection. Hepatology (2013) 2.13
Polymorphisms in melanoma differentiation-associated gene 5 link protein function to clearance of hepatitis C virus. Hepatology (2015) 2.11
Importance of IL28B gene polymorphisms in hepatitis C virus genotype 2 and 3 infected patients. J Hepatol (2010) 2.09
Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. Proc Natl Acad Sci U S A (2008) 2.06
Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nat Rev Microbiol (2010) 2.04
The ITS2 Database III--sequences and structures for phylogeny. Nucleic Acids Res (2009) 2.04
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA (2005) 1.94
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res (2006) 1.92
Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat Genet (2013) 1.83
Distinguishing species. RNA (2007) 1.74
Platelet protein interactions: map, signaling components, and phosphorylation groundstate. Arterioscler Thromb Vasc Biol (2008) 1.71
Local application of FTY720 to the lung abrogates experimental asthma by altering dendritic cell function. J Clin Invest (2006) 1.67
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J (2010) 1.66
L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res (2005) 1.57
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res Notes (2008) 1.54
Distinct, alcohol-modulated effects of PNPLA3 genotype on progression of chronic hepatitis C. J Hepatol (2011) 1.52
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics (2007) 1.51
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evol Biol (2004) 1.51
Metabolites: a helping hand for pathway evolution? Trends Biochem Sci (2003) 1.50
Production of serotonin by tryptophan hydroxylase 1 and release via platelets contribute to allergic airway inflammation. Am J Respir Crit Care Med (2013) 1.49
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol (2006) 1.48
Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res (2004) 1.47
The serotoninergic receptors of human dendritic cells: identification and coupling to cytokine release. J Immunol (2004) 1.44
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biol Direct (2010) 1.44
The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'. BMC Genomics (2008) 1.42
The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res (2007) 1.41
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In Silico Biol (2005) 1.39
An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach. Plant Cell (2006) 1.37
IL28B, HLA-C, and KIR variants additively predict response to therapy in chronic hepatitis C virus infection in a European Cohort: a cross-sectional study. PLoS Med (2011) 1.36
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics (2007) 1.32
5-Hydroxytryptamine modulates cytokine and chemokine production in LPS-primed human monocytes via stimulation of different 5-HTR subtypes. Int Immunol (2005) 1.30
Extracellular adenosine triphosphate and chronic obstructive pulmonary disease. Am J Respir Crit Care Med (2010) 1.30
Interactions of methylene blue with human disulfide reductases and their orthologues from Plasmodium falciparum. Antimicrob Agents Chemother (2007) 1.28
ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies. Mol Phylogenet Evol (2012) 1.28
Genome-wide mapping of foamy virus vector integrations into a human cell line. J Gen Virol (2006) 1.28
P2X7 receptor signaling in the pathogenesis of smoke-induced lung inflammation and emphysema. Am J Respir Cell Mol Biol (2010) 1.27
Toward computer-based cleavage site prediction of cysteine endopeptidases. Biol Chem (2003) 1.27
ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments. Bioinformatics (2008) 1.25
Lack of the purinergic receptor P2X(7) results in resistance to contact hypersensitivity. J Exp Med (2010) 1.25
Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy. J Biol Chem (2006) 1.25
Metabolic programming of MEST DNA methylation by intrauterine exposure to gestational diabetes mellitus. Diabetes (2012) 1.25
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics (2005) 1.24
13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA. Proc Natl Acad Sci U S A (2006) 1.21
The highly attenuated oncolytic recombinant vaccinia virus GLV-1h68: comparative genomic features and the contribution of F14.5L inactivation. Mol Genet Genomics (2009) 1.20
Serotoninergic receptors on human airway epithelial cells. Am J Respir Cell Mol Biol (2006) 1.18
The transcriptional landscape of Chlamydia pneumoniae. Genome Biol (2011) 1.16
Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int J Syst Evol Microbiol (2004) 1.16
Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens. Nat Commun (2013) 1.15
Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest. PLoS One (2013) 1.15
The PNPLA3 rs738409 148M/M genotype is a risk factor for liver cancer in alcoholic cirrhosis but shows no or weak association in hepatitis C cirrhosis. PLoS One (2011) 1.13
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics (2005) 1.13
Shared components of protein complexes--versatile building blocks or biochemical artefacts? Bioessays (2004) 1.13
Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome. PLoS One (2011) 1.12
Purinergic receptor inhibition prevents the development of smoke-induced lung injury and emphysema. J Immunol (2010) 1.11
CLEVER: clique-enumerating variant finder. Bioinformatics (2012) 1.10
Analysis of SAGE data in human platelets: features of the transcriptome in an anucleate cell. Thromb Haemost (2006) 1.10
Use of functional highly purified human platelets for the identification of new proteins of the IPP signaling pathway. Thromb Res (2007) 1.07
A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer. PLoS One (2012) 1.06
RIP death domain structural interactions implicated in TNF-mediated proliferation and survival. Proteins (2006) 1.06
Purinergic receptor type 6 contributes to airway inflammation and remodeling in experimental allergic airway inflammation. Am J Respir Crit Care Med (2011) 1.05
A genetic validation study reveals a role of vitamin D metabolism in the response to interferon-alfa-based therapy of chronic hepatitis C. PLoS One (2012) 1.05
Perforin-like protein PPLP2 permeabilizes the red blood cell membrane during egress of Plasmodium falciparum gametocytes. Cell Microbiol (2014) 1.02
Subgroups of refusers in a disability prevention trial in older adults: baseline and follow-up analysis. Am J Public Health (2002) 1.02
Integrated systems view on networking by hormones in Arabidopsis immunity reveals multiple crosstalk for cytokinin. Plant Cell (2012) 1.01
The toll-like receptor 2 (TLR2) -196 to -174 del/ins polymorphism affects viral loads and susceptibility to hepatocellular carcinoma in chronic hepatitis C. Int J Cancer (2011) 1.00
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evol Biol (2008) 1.00
A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst (2011) 0.99
Molecular mechanisms of tolerance in tardigrades: new perspectives for preservation and stabilization of biological material. Biotechnol Adv (2009) 0.99
Mitochondrial respiratory rates and activities of respiratory chain complexes correlate linearly with heteroplasmy of deleted mtDNA without threshold and independently of deletion size. Biochim Biophys Acta (2002) 0.98
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. BMC Genomics (2009) 0.98