Published in Nucleic Acids Res on May 28, 2008
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res (2009) 7.34
Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity (2014) 3.94
Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet (2012) 2.92
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Hum Genet (2009) 2.31
Bioinformatics challenges for personalized medicine. Bioinformatics (2011) 2.28
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database (Oxford) (2013) 1.92
The RNA-binding protein Elavl1/HuR is essential for placental branching morphogenesis and embryonic development. Mol Cell Biol (2009) 1.78
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol (2008) 1.58
NEK1 mutations cause short-rib polydactyly syndrome type majewski. Am J Hum Genet (2011) 1.56
Exome-sequencing confirms DNAJC5 mutations as cause of adult neuronal ceroid-lipofuscinosis. PLoS One (2011) 1.51
Bioinformatics for personal genome interpretation. Brief Bioinform (2012) 1.51
An integrative computational approach for prioritization of genomic variants. PLoS One (2014) 1.45
Predicting the effects of frameshifting indels. Genome Biol (2012) 1.33
PINTA: a web server for network-based gene prioritization from expression data. Nucleic Acids Res (2011) 1.16
Linking genes to diseases: it's all in the data. Genome Med (2009) 1.14
In silico gene prioritization by integrating multiple data sources. PLoS One (2011) 1.10
Chapter 15: disease gene prioritization. PLoS Comput Biol (2013) 1.05
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. BMC Syst Biol (2010) 1.03
Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Am J Med Genet A (2010) 1.01
Information encoded in a network of inflammation proteins predicts clinical outcome after myocardial infarction. BMC Med Genomics (2011) 1.01
CNV-WebStore: online CNV analysis, storage and interpretation. BMC Bioinformatics (2011) 0.98
Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics. Hum Genet (2010) 0.97
The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. Front Genet (2013) 0.96
Application of gene network analysis techniques identifies AXIN1/PDIA2 and endoglin haplotypes associated with bicuspid aortic valve. PLoS One (2010) 0.96
Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia. Hum Genet (2012) 0.96
A quick guide to large-scale genomic data mining. PLoS Comput Biol (2010) 0.93
Gene prioritization and clustering by multi-view text mining. BMC Bioinformatics (2010) 0.91
Integrating computational biology and forward genetics in Drosophila. PLoS Genet (2009) 0.91
Identifying proteins controlling key disease signaling pathways. Bioinformatics (2013) 0.90
The genetics of diabetic nephropathy. Genes (Basel) (2013) 0.90
Identification of novel therapeutics for complex diseases from genome-wide association data. BMC Med Genomics (2014) 0.90
Integration of multiple data sources to prioritize candidate genes using discounted rating system. BMC Bioinformatics (2010) 0.90
EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization. Nucleic Acids Res (2014) 0.89
Retracted Candidate gene prioritization. Mol Genet Genomics (2012) 0.88
Text mining in cancer gene and pathway prioritization. Cancer Inform (2014) 0.85
FAM5C contributes to aggressive periodontitis. PLoS One (2010) 0.85
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Brief Bioinform (2015) 0.84
Progress and challenges in the computational prediction of gene function using networks. F1000Res (2012) 0.84
Evidence for novel genetic loci associated with metabolic traits in Yup'ik people. Am J Hum Biol (2013) 0.84
Genome-wide analysis identifies 12 loci influencing human reproductive behavior. Nat Genet (2016) 0.84
Systems biology elucidates common pathogenic mechanisms between nonalcoholic and alcoholic-fatty liver disease. PLoS One (2013) 0.83
Candidate gene prioritization with Endeavour. Nucleic Acids Res (2016) 0.83
Combining heterogenous data for prediction of disease related and pharmacogenes. Pac Symp Biocomput (2014) 0.82
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. Nucleic Acids Res (2012) 0.82
Identification of novel genetic risk loci in Maltese dogs with necrotizing meningoencephalitis and evidence of a shared genetic risk across toy dog breeds. PLoS One (2014) 0.81
A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. Biol Direct (2011) 0.81
Fine mapping and candidate gene search of quantitative trait loci for growth and obesity using mouse intersubspecific subcongenic intercrosses and exome sequencing. PLoS One (2014) 0.80
Dysfunction of the Voltage-Gated K+ Channel β2 Subunit in a Familial Case of Brugada Syndrome. J Am Heart Assoc (2016) 0.80
A Single Amino Acid Deletion (ΔF1502) in the S6 Segment of CaV2.1 Domain III Associated with Congenital Ataxia Increases Channel Activity and Promotes Ca2+ Influx. PLoS One (2015) 0.79
Mind the dbGAP: the application of data mining to identify biological mechanisms. Mol Interv (2011) 0.79
Disease gene prioritization using network and feature. J Comput Biol (2015) 0.79
Gentrepid V2.0: a web server for candidate disease gene prediction. BMC Bioinformatics (2013) 0.79
Linkage and association analysis of obesity traits reveals novel loci and interactions with dietary n-3 fatty acids in an Alaska Native (Yup'ik) population. Metabolism (2015) 0.77
Multitask learning of signaling and regulatory networks with application to studying human response to flu. PLoS Comput Biol (2014) 0.77
Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update. F1000Res (2013) 0.77
Prioritization of candidate genes for attention deficit hyperactivity disorder by computational analysis of multiple data sources. Protein Cell (2012) 0.77
Genome-wide haplotype association study identify TNFRSF1A, CASP7, LRP1B, CDH1 and TG genes associated with Alzheimer's disease in Caribbean Hispanic individuals. Oncotarget (2015) 0.76
Systematic prioritization and integrative analysis of copy number variations in schizophrenia reveal key schizophrenia susceptibility genes. Schizophr Bull (2014) 0.76
Ehlers-Danlos Syndrome, Hypermobility Type, Is Linked to Chromosome 8p22-8p21.1 in an Extended Belgian Family. Dis Markers (2015) 0.76
GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles. Bioinformatics (2015) 0.76
Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis. PLoS One (2013) 0.76
SoftPanel: a website for grouping diseases and related disorders for generation of customized panels. BMC Bioinformatics (2016) 0.76
Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice. BMC Genomics (2016) 0.75
Mining the literature: new methods to exploit keyword profiles. Genome Med (2012) 0.75
CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments. Biol Direct (2016) 0.75
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PLoS One (2014) 0.75
A large-scale benchmark of gene prioritization methods. Sci Rep (2017) 0.75
Decoding the complex genetic causes of heart diseases using systems biology. Biophys Rev (2014) 0.75
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PLoS One (2016) 0.75
Beegle: from literature mining to disease-gene discovery. Nucleic Acids Res (2015) 0.75
EnRICH: Extraction and Ranking using Integration and Criteria Heuristics. BMC Syst Biol (2013) 0.75
DDK Promotes Tumor Chemoresistance and Survival via Multiple Pathways. Neoplasia (2017) 0.75
Understanding the molecular mechanisms of human microtia via a pig model of HOXA1 syndrome. Dis Model Mech (2015) 0.75
Linkage and association analysis of circulating vitamin D and parathyroid hormone identifies novel loci in Alaska Native Yup'ik people. Genes Nutr (2016) 0.75
Identification of p53-target genes in Danio rerio. Sci Rep (2016) 0.75
Finding genetic overlaps among diseases based on ranked gene lists. J Comput Biol (2015) 0.75
Genome-wide haplotype association study identify the FGFR2 gene as a risk gene for acute myeloid leukemia. Oncotarget (2016) 0.75
Identifying new targets in leukemogenesis using computational approaches. Saudi J Biol Sci (2015) 0.75
Clinical Applicability of Whole-Exome Sequencing Exemplified by a Study in Young Adults with the Advanced Cryptogenic Cholestatic Liver Diseases. Gastroenterol Res Pract (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet (2008) 25.83
Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A (2002) 25.47
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2007) 22.53
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet (2008) 20.73
Ensembl 2008. Nucleic Acids Res (2007) 20.67
The human disease network. Proc Natl Acad Sci U S A (2007) 19.58
Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet (2008) 17.65
ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res (2003) 17.39
Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet (2008) 15.43
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82
Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics (2004) 13.46
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90
BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res (2001) 11.74
BLAST: improvements for better sequence analysis. Nucleic Acids Res (2006) 9.77
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res (2002) 9.50
Newly identified genetic risk variants for celiac disease related to the immune response. Nat Genet (2008) 7.63
Gene prioritization through genomic data fusion. Nat Biotechnol (2006) 7.48
Common variants in the GDF5-UQCC region are associated with variation in human height. Nat Genet (2008) 7.31
Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet (2008) 6.10
Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Nat Genet (2008) 6.06
Human disease genes. Nature (2001) 5.31
Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus. Nat Genet (2008) 5.00
The modular nature of genetic diseases. Clin Genet (2007) 4.06
A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet (2008) 3.71
MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res (2006) 3.68
Using literature-based discovery to identify disease candidate genes. Int J Med Inform (2005) 3.16
Impaired glycosylation and cutis laxa caused by mutations in the vesicular H+-ATPase subunit ATP6V0A2. Nat Genet (2007) 3.02
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
POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol (2003) 2.93
Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res (2004) 2.86
Canonical Wnt signaling is required for development of embryonic stem cell-derived mesoderm. Development (2006) 2.82
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res (2005) 2.68
Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis. Nat Genet (2007) 2.63
Chymotrypsin C (CTRC) variants that diminish activity or secretion are associated with chronic pancreatitis. Nat Genet (2007) 2.48
Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res (2005) 2.46
Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus. Nat Genet (2007) 2.38
Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Res (2006) 2.30
Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice. Nature (2005) 2.29
A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss. Hum Genet (2006) 2.27
Database of mRNA gene expression profiles of multiple human organs. Genome Res (2005) 2.11
Applications of a rat multiple tissue gene expression data set. Genome Res (2004) 2.01
Human disease genes: patterns and predictions. Gene (2003) 1.99
G2D: a tool for mining genes associated with disease. BMC Genet (2005) 1.85
TXTGate: profiling gene groups with text-based information. Genome Biol (2004) 1.72
The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Development (2005) 1.68
Comparative expression profiling in pulmonary fibrosis suggests a role of hypoxia-inducible factor-1alpha in disease pathogenesis. Am J Respir Crit Care Med (2007) 1.67
A computational system to select candidate genes for complex human traits. Bioinformatics (2007) 1.60
CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics (2006) 1.55
Candidate gene identification approach: progress and challenges. Int J Biol Sci (2007) 1.51
In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics. Mol Cell Proteomics (2007) 1.45
Identification of novel candidate genes associated with cleft lip and palate using array comparative genomic hybridisation. J Med Genet (2007) 1.40
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. Nucleic Acids Res (2005) 1.38
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics (2006) 1.35
TOM: a web-based integrated approach for identification of candidate disease genes. Nucleic Acids Res (2006) 1.15
A strategy to search for common obesity and type 2 diabetes genes. Trends Endocrinol Metab (2006) 0.96
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
The landscape of cancer genes and mutational processes in breast cancer. Nature (2012) 11.24
Mutational processes molding the genomes of 21 breast cancers. Cell (2012) 11.22
The life history of 21 breast cancers. Cell (2012) 10.59
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet (2009) 7.61
Gene prioritization through genomic data fusion. Nat Biotechnol (2006) 7.48
Clinical and biological implications of driver mutations in myelodysplastic syndromes. Blood (2013) 6.50
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res (2002) 6.43
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol (2002) 4.05
Chromosome instability is common in human cleavage-stage embryos. Nat Med (2009) 3.85
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80
Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res (2003) 3.68
Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Res (2009) 3.22
Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res (2009) 3.09
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
Computational detection of cis -regulatory modules. Bioinformatics (2003) 2.89
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics (2006) 2.82
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res (2005) 2.68
Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia. Nat Genet (2012) 2.64
Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet (2003) 2.54
Polysomy 17 in breast cancer: clinicopathologic significance and impact on HER-2 testing. J Clin Oncol (2008) 2.36
Biomarkers of endometriosis. Fertil Steril (2013) 2.28
INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics (2002) 2.13
Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nat Biotechnol (2011) 2.10
Using ribosomal protein genes as reference: a tale of caution. PLoS One (2008) 2.06
Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis. J Histochem Cytochem (2005) 2.05
Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks. Bioinformatics (2006) 1.95
Biclustering microarray data by Gibbs sampling. Bioinformatics (2003) 1.82
Molecular response to cetuximab and efficacy of preoperative cetuximab-based chemoradiation in rectal cancer. J Clin Oncol (2009) 1.82
Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A (2011) 1.78
Single-cell chromosomal imbalances detection by array CGH. Nucleic Acids Res (2006) 1.78
Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res (2013) 1.77
Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis. Plant Physiol (2005) 1.76
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation. BMC Genomics (2012) 1.74
TXTGate: profiling gene groups with text-based information. Genome Biol (2004) 1.72
arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics (2005) 1.71
Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. Nat Genet (2012) 1.70
A guide to web tools to prioritize candidate genes. Brief Bioinform (2010) 1.70
PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability. Mol Microbiol (2005) 1.69
Adaptive quality-based clustering of gene expression profiles. Bioinformatics (2002) 1.68
Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics (2004) 1.68
Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1. Neuron (2013) 1.67
Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol (2006) 1.64
A tutorial on support vector machine-based methods for classification problems in chemometrics. Anal Chim Acta (2010) 1.60
Whole exome sequencing of adenoid cystic carcinoma. J Clin Invest (2013) 1.58
Hypoxia-driven gene expression is an independent prognostic factor in stage II and III colon cancer patients. Clin Cancer Res (2014) 1.55
INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res (2003) 1.55
Alteration of the microRNA network during the progression of Alzheimer's disease. EMBO Mol Med (2013) 1.54
The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models. Genome Biol (2013) 1.54
Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience. Hum Mutat (2012) 1.51
eXtasy: variant prioritization by genomic data fusion. Nat Methods (2013) 1.48
Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma. Nat Genet (2013) 1.45
Kernel-based data fusion for gene prioritization. Bioinformatics (2007) 1.44
Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. J Mol Evol (2005) 1.41
LRP1B deletion in high-grade serous ovarian cancers is associated with acquired chemotherapy resistance to liposomal doxorubicin. Cancer Res (2012) 1.39
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol (2009) 1.36
Cleavage of NIK by the API2-MALT1 fusion oncoprotein leads to noncanonical NF-kappaB activation. Science (2011) 1.30
Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. Bioinformatics (2008) 1.28
Importing MAGE-ML format microarray data into BioConductor. Bioinformatics (2004) 1.28
A kernel-based integration of genome-wide data for clinical decision support. Genome Med (2009) 1.26
An unbiased evaluation of gene prioritization tools. Bioinformatics (2012) 1.25
L2-norm multiple kernel learning and its application to biomedical data fusion. BMC Bioinformatics (2010) 1.24