Published in BMC Bioinformatics on May 28, 2010
RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinformatics (2011) 1.08
Markov Chain Ontology Analysis (MCOA). BMC Bioinformatics (2012) 0.97
Novel search method for the discovery of functional relationships. Bioinformatics (2011) 0.84
Exact score distribution computation for ontological similarity searches. BMC Bioinformatics (2011) 0.84
An integrative approach to inferring biologically meaningful gene modules. BMC Syst Biol (2011) 0.83
PhenUMA: a tool for integrating the biomedical relationships among genes and diseases. BMC Bioinformatics (2014) 0.77
Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica. Front Microbiol (2016) 0.75
TopoICSim: a new semantic similarity measure based on gene ontology. BMC Bioinformatics (2016) 0.75
Protein complex discovery by interaction filtering from protein interaction networks using mutual rank coexpression and sequence similarity. Biomed Res Int (2015) 0.75
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The human disease network. Proc Natl Acad Sci U S A (2007) 19.58
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol (2004) 15.61
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics (2003) 9.47
Coexpression analysis of human genes across many microarray data sets. Genome Res (2004) 9.38
A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell (2006) 8.61
A module map showing conditional activity of expression modules in cancer. Nat Genet (2004) 8.57
A probabilistic functional network of yeast genes. Science (2004) 8.35
The presentation and use of height and weight data for comparing the nutritional status of groups of children under the age of 10 years. Bull World Health Organ (1977) 7.57
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res (2009) 7.34
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet (2006) 6.10
A new method to measure the semantic similarity of GO terms. Bioinformatics (2007) 5.91
An in vivo map of the yeast protein interactome. Science (2008) 5.52
Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol (2009) 5.41
Semantic similarity in biomedical ontologies. PLoS Comput Biol (2009) 5.05
Use and misuse of the gene ontology annotations. Nat Rev Genet (2008) 5.01
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol (2009) 4.65
The modular nature of genetic diseases. Clin Genet (2007) 4.06
Finding function in novel targets: C. elegans as a model organism. Nat Rev Drug Discov (2006) 3.64
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell (2004) 3.26
A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics (2002) 3.04
Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics (2005) 2.99
SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics (2006) 2.96
Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics (2008) 2.87
From syndrome families to functional genomics. Nat Rev Genet (2004) 2.86
Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol (2008) 2.46
A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics (2003) 2.42
Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics (2007) 2.15
Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics (2008) 2.10
A network biology approach to prostate cancer. Mol Syst Biol (2007) 2.07
Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res (2006) 1.93
Phenome connections. Trends Genet (2008) 1.84
Comparison of human protein-protein interaction maps. Bioinformatics (2007) 1.79
Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion. Conf Proc IEEE Eng Med Biol Soc (2006) 1.67
A computational system to select candidate genes for complex human traits. Bioinformatics (2007) 1.60
G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nucleic Acids Res (2009) 1.55
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics (2007) 1.54
A pathway-based view of human diseases and disease relationships. PLoS One (2009) 1.52
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. Bioinformatics (2007) 1.50
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. BMC Bioinformatics (2008) 1.47
Combining functional and topological properties to identify core modules in protein interaction networks. Proteins (2006) 1.36
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol (2008) 1.35
Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships. Proc IEEE Symp Comput Intell Bioinforma Comput Biol (2004) 1.29
A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinformatics (2007) 1.29
Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. Bioinformatics (2008) 1.28
Modularity in the genetic disease-phenotype network. FEBS Lett (2008) 1.27
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol (2007) 1.27
Suppression of apoptosis by bcl-2 overexpression in lymphoid cells of transgenic zebrafish. Blood (2004) 1.26
Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. PLoS One (2009) 1.26
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics (2006) 1.23
Fast gene ontology based clustering for microarray experiments. BioData Min (2008) 1.21
Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics (2007) 1.12
A functional network module for Smith-Magenis syndrome. Clin Genet (2009) 1.10
A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes. BMC Evol Biol (2009) 1.08
Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics (2006) 1.05
Towards a pathway definition of Parkinson's disease: a complex disorder with links to cancer, diabetes and inflammation. Neurogenetics (2008) 1.04
Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities. Gene (2006) 0.99
Physical protein-protein interactions predicted from microarrays. Bioinformatics (2008) 0.94
Discovering gene annotations in biomedical text databases. BMC Bioinformatics (2008) 0.89
Evaluation of high-throughput functional categorization of human disease genes. BMC Bioinformatics (2007) 0.89
A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge. BMC Bioinformatics (2008) 0.88
Co-evolutionary rates of functionally related yeast genes. Evol Bioinform Online (2006) 0.88
Protein function assignment through mining cross-species protein-protein interactions. PLoS One (2008) 0.85
Learnability-based further prediction of gene functions in Gene Ontology. Genomics (2004) 0.81
Create and assess protein networks through molecular characteristics of individual proteins. Bioinformatics (2006) 0.76
Aligned single-crystalline Si nanowire arrays for photovoltaic applications. Small (2005) 2.98
Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics (2005) 2.01
Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases. Sci Signal (2013) 1.73
Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics (2007) 1.69
Metal-particle-induced, highly localized site-specific etching of Si and formation of single-crystalline Si nanowires in aqueous fluoride solution. Chemistry (2006) 1.64
A pilot study in non-human primates shows no adverse response to intravenous injection of quantum dots. Nat Nanotechnol (2012) 1.57
Function and molecular mechanism of acetylation in autophagy regulation. Science (2012) 1.56
The use of allograft shell with intramedullary vascularized fibula graft for intercalary reconstruction after diaphyseal resection for lower extremity bony malignancy. J Surg Oncol (2010) 1.50
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. Bioinformatics (2007) 1.50
Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics (2008) 1.48
Uniform, axial-orientation alignment of one-dimensional single-crystal silicon nanostructure arrays. Angew Chem Int Ed Engl (2005) 1.41
Comment on "Preparation of superparamagnetic ribonuclease a surface-imprinted submicrometer particles for protein recognition in aqueous media". Anal Chem (2008) 1.39
Composite organic-inorganic nanoparticles as Raman labels for tissue analysis. Nano Lett (2007) 1.39
GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology. BMC Genomics (2007) 1.39
Enhanced photoluminescence and field-emission behavior of vertically well aligned arrays of In-doped ZnO Nanowires. ACS Appl Mater Interfaces (2011) 1.32
A robust hybrid between genetic algorithm and support vector machine for extracting an optimal feature gene subset. Genomics (2005) 1.30
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes. Bioinformatics (2009) 1.29
Caesium europium(III) polyphosphate, CsEu(PO(3))(4). Acta Crystallogr Sect E Struct Rep Online (2009) 1.29
A novel method for detection of phosphorylation in single cells by surface enhanced Raman scattering (SERS) using composite organic-inorganic nanoparticles (COINs). PLoS One (2009) 1.24
Fabrication of slantingly-aligned silicon nanowire arrays for solar cell applications. Nanotechnology (2008) 1.24
Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene (2005) 1.23
Brain tumour necrosis factor-alpha modulates neurotransmitters in hypothalamic paraventricular nucleus in heart failure. Cardiovasc Res (2009) 1.21
Synthesis, structure and antibacterial activity of new 2-(1-(2-(substituted-phenyl)-5-methyloxazol-4-yl)-3-(2-substitued-phenyl)-4,5-dihydro-1H-pyrazol-5-yl)-7-substitued-1,2,3,4-tetrahydroisoquinoline derivatives. Bioorg Med Chem (2008) 1.20
Discovery of Time-Delayed Gene Regulatory Networks based on temporal gene expression profiling. BMC Bioinformatics (2006) 1.18
Prognostic values of the miR-17-92 cluster and its paralogs in colon cancer. J Surg Oncol (2011) 1.13
Alkylation damage by lipid electrophiles targets functional protein systems. Mol Cell Proteomics (2014) 1.13
Glycosylation affects the protein stability and cell surface expression of Kv1.4 but Not Kv1.1 potassium channels. A pore region determinant dictates the effect of glycosylation on trafficking. J Biol Chem (2003) 1.12
Glycosylation affects rat Kv1.1 potassium channel gating by a combined surface potential and cooperative subunit interaction mechanism. J Physiol (2003) 1.10
Activation of RXR and RAR signaling promotes myogenic differentiation of myoblastic C2C12 cells. Differentiation (2009) 1.09
Surgical technique: Unicondylar osteoallograft prosthesis composite in tumor limb salvage surgery. Clin Orthop Relat Res (2012) 1.07
Upregulation of miR-195 increases the sensitivity of breast cancer cells to Adriamycin treatment through inhibition of Raf-1. Oncol Rep (2013) 1.07
Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules. Bioinformatics (2006) 1.07
Irregular osteotomy in limb salvage for juxta-articular osteosarcoma under computer-assisted navigation. J Surg Oncol (2012) 1.06
Artificial lamellar mesostructures to WS(2) nanotubes. J Am Chem Soc (2002) 1.05
dbCRID: a database of chromosomal rearrangements in human diseases. Nucleic Acids Res (2010) 1.04
The glycosylation state of Kv1.2 potassium channels affects trafficking, gating, and simulated action potentials. Brain Res (2007) 1.04
Simultaneous optimization of charge-carrier balance and luminous efficacy in highly efficient white polymer light-emitting devices. Adv Mater (2011) 1.03
Attenuation of Streptococcus suis virulence by the alteration of bacterial surface architecture. Sci Rep (2012) 1.03
Contributions of O island 48 to adherence of enterohemorrhagic Escherichia coli O157:H7 to epithelial cells in vitro and in ligated pig ileal loops. Appl Environ Microbiol (2009) 1.01
Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. BMC Syst Biol (2013) 1.01
GO-function: deriving biologically relevant functions from statistically significant functions. Brief Bioinform (2011) 1.01
Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities. Gene (2006) 0.99
Quantum factorization of 143 on a dipolar-coupling nuclear magnetic resonance system. Phys Rev Lett (2012) 0.99
Implant failure of Bryan cervical disc due to broken polyurethane sheath: a case report. Spine (Phila Pa 1976) (2012) 0.98
An amperometric NO2 sensor based on La10Si5NbO27.5 electrolyte and nano-structured CuO sensing electrode. J Hazard Mater (2013) 0.97
Hypoxia inducible factor 1α-mediated LOX expression correlates with migration and invasion in epithelial ovarian cancer. Int J Oncol (2013) 0.97
Four-and-a-half LIM protein 2 promotes invasive potential and epithelial-mesenchymal transition in colon cancer. Carcinogenesis (2010) 0.96
Does Microwave Ablation of the Tumor Edge Allow for Joint-sparing Surgery in Patients With Osteosarcoma of the Proximal Tibia? Clin Orthop Relat Res (2015) 0.96
Secreted protein acidic and rich in cysteine (SPARC) suppresses angiogenesis by down-regulating the expression of VEGF and MMP-7 in gastric cancer. PLoS One (2012) 0.95
Comparing crystal structures of Ca(2+) -ATPase in the presence of different lipids. FEBS J (2014) 0.95
Synthesis of ternary CuInS(2)/ZnS quantum dot bioconjugates and their applications for targeted cancer bioimaging. Integr Biol (Camb) (2010) 0.95
Rapid and sensitive detection of H7N9 avian influenza virus by use of reverse transcription-loop-mediated isothermal amplification. J Clin Microbiol (2013) 0.95
Separate enrichment analysis of pathways for up- and downregulated genes. J R Soc Interface (2013) 0.95
Dynamic effect of di-2-(ethylhexyl) phthalate on testicular toxicity: epigenetic changes and their impact on gene expression. Int J Toxicol (2010) 0.95
Electrical breakdown of nanowires. Nano Lett (2011) 0.95
Incomplete beta-ketone processing as a mechanism for polyene structural variation in the FR-008/candicidin complex. Chem Biol (2008) 0.95
Associations of polymorphisms in the apolipoprotein APOA1-C3-A5 gene cluster with acute coronary syndrome. J Biomed Biotechnol (2012) 0.95
Identification of Cys255 in HIF-1α as a novel site for development of covalent inhibitors of HIF-1α/ARNT PasB domain protein-protein interaction. Protein Sci (2012) 0.94
Dynamic epigenetic changes involved in testicular toxicity induced by di-2-(ethylhexyl) phthalate in mice. Basic Clin Pharmacol Toxicol (2009) 0.94
Adherence of Escherichia coli O157:H7 mutants in vitro and in ligated pig intestines. Appl Environ Microbiol (2009) 0.94
Gemcitabine eliminates double minute chromosomes from human ovarian cancer cells. PLoS One (2013) 0.94
Extracting consistent knowledge from highly inconsistent cancer gene data sources. BMC Bioinformatics (2010) 0.94
Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis. BMC Syst Biol (2010) 0.93
BRCA1 mRNA expression as a predictive and prognostic marker in advanced esophageal squamous cell carcinoma treated with cisplatin- or docetaxel-based chemotherapy/chemoradiotherapy. PLoS One (2013) 0.93
Electron-beam-induced elastic-plastic transition in Si nanowires. Nano Lett (2012) 0.93
Ethanol and its metabolites induce histone lysine 9 acetylation and an alteration of the expression of heart development-related genes in cardiac progenitor cells. Cardiovasc Toxicol (2010) 0.93
Metformin inhibits the development and metastasis of ovarian cancer. Oncol Rep (2012) 0.92
Comparison of dexmedetomidine and propofol for conscious sedation in awake craniotomy: a prospective, double-blind, randomized, and controlled clinical trial. Ann Pharmacother (2013) 0.92
Human retinal progenitor cell transplantation preserves vision. J Biol Chem (2014) 0.92
Sustained delivery of VEGF from designer self-assembling peptides improves cardiac function after myocardial infarction. Biochem Biophys Res Commun (2012) 0.92
In situ electrical measurements of polytypic silver nanowires. Nanotechnology (2008) 0.91
Limb salvage surgery for calcaneal malignancy. J Surg Oncol (2010) 0.91
Trichostatin a promotes cardiomyocyte differentiation of rat mesenchymal stem cells after 5-azacytidine induction or during coculture with neonatal cardiomyocytes via a mechanism independent of histone deacetylase inhibition. Cell Transplant (2011) 0.91
Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol (2009) 0.91
Bis[2-bromo-4-(2-hy-droxy-eth-yl)phenol] monohydrate. Acta Crystallogr Sect E Struct Rep Online (2011) 0.91
Fingertip replantation: determinants of survival. Plast Reconstr Surg (2008) 0.91
The catalase C-262T gene polymorphism and cancer risk: a systematic review and meta-analysis. Medicine (Baltimore) (2015) 0.90
Critical limitations of prognostic signatures based on risk scores summarized from gene expression levels: a case study for resected stage I non-small-cell lung cancer. Brief Bioinform (2015) 0.90
Synthesis of transferrin (Tf) conjugated liposomes via Staudinger ligation. Int J Pharm (2010) 0.90
Inhibition of the transcription factor Sp1 suppresses colon cancer stem cell growth and induces apoptosis in vitro and in nude mouse xenografts. Oncol Rep (2013) 0.90
Suberoylanilide hydroxamic acid promotes cardiomyocyte differentiation of rat mesenchymal stem cells. Exp Cell Res (2009) 0.90
Downregulation of SPARC expression decreases gastric cancer cellular invasion and survival. J Exp Clin Cancer Res (2010) 0.90
MicroRNA-19a targets tissue factor to inhibit colon cancer cells migration and invasion. Mol Cell Biochem (2013) 0.90
A role for Gcn5 in cardiomyocyte differentiation of rat mesenchymal stem cells. Mol Cell Biochem (2010) 0.90
Additional bedtime H2-receptor antagonist for the control of nocturnal gastric acid breakthrough. Cochrane Database Syst Rev (2004) 0.89
An automatic and quantitative on-chip cell migration assay using self-assembled monolayers combined with real-time cellular impedance sensing. Lab Chip (2008) 0.89
Tissue factor/activated factor VIIa induces matrix metalloproteinase-7 expression through activation of c-Fos via ERK1/2 and p38 MAPK signaling pathways in human colon cancer cell. Int J Colorectal Dis (2011) 0.89
Porous titanium-6 aluminum-4 vanadium cage has better osseointegration and less micromotion than a poly-ether-ether-ketone cage in sheep vertebral fusion. Artif Organs (2013) 0.89
TGFbeta receptor saxophone non-autonomously regulates germline proliferation in a Smox/dSmad2-dependent manner in Drosophila testis. Dev Biol (2007) 0.89
An epitaxial ferroelectric tunnel junction on silicon. Adv Mater (2014) 0.89
Inhibition of p300-HAT results in a reduced histone acetylation and down-regulation of gene expression in cardiac myocytes. Life Sci (2010) 0.89
Rapid visual detection of highly pathogenic Streptococcus suis serotype 2 isolates by use of loop-mediated isothermal amplification. J Clin Microbiol (2013) 0.89
The new age of carbon nanotubes: an updated review of functionalized carbon nanotubes in electrochemical sensors. Nanoscale (2012) 0.89