Published in BMC Bioinformatics on August 06, 2007
A general modular framework for gene set enrichment analysis. BMC Bioinformatics (2009) 3.92
Fewer permutations, more accurate P-values. Bioinformatics (2009) 1.91
Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform (2011) 1.84
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics (2008) 1.77
A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res (2010) 1.54
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics (2008) 1.45
miRNA deregulation by epigenetic silencing disrupts suppression of the oncogene PLAG1 in chronic lymphocytic leukemia. Blood (2009) 1.25
Alterations in cardiac DNA methylation in human dilated cardiomyopathy. EMBO Mol Med (2013) 1.23
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics (2009) 1.17
Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. BMC Plant Biol (2011) 1.06
Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. Nucleic Acids Res (2010) 1.03
Chromatin signature of widespread monoallelic expression. Elife (2013) 1.03
Identification of high-copper-responsive target pathways in Atp7b knockout mouse liver by GSEA on microarray data sets. Mamm Genome (2011) 1.01
Changes in gene expression and cellular architecture in an ovarian cancer progression model. PLoS One (2011) 1.01
miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics (2012) 1.01
P58(IPK): a novel "CIHD" member of the host innate defense response against pathogenic virus infection. PLoS Pathog (2009) 0.99
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res (2011) 0.94
Differentially expressed miRNAs after GnRH treatment and their potential roles in FSH regulation in porcine anterior pituitary cell. PLoS One (2013) 0.88
Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets. BMC Bioinformatics (2010) 0.84
PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. J Proteome Res (2014) 0.81
miEAA: microRNA enrichment analysis and annotation. Nucleic Acids Res (2016) 0.79
Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. BMC Genomics (2014) 0.79
Comparison of Invariant NKT Cells with Conventional T Cells by Using Gene Set Enrichment Analysis (GSEA). Immune Netw (2011) 0.78
Pathway-based variant enrichment analysis on the example of dilated cardiomyopathy. Hum Genet (2015) 0.77
A Comparative Study of Mouse Hepatic and Intestinal Gene Expression Profiles under PPARα Knockout by Gene Set Enrichment Analysis. PPAR Res (2011) 0.76
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Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
MINT: a Molecular INTeraction database. FEBS Lett (2002) 17.21
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell (2003) 9.81
PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics (2005) 8.41
GeneTrail--advanced gene set enrichment analysis. Nucleic Acids Res (2007) 5.10
ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinformatics (2005) 4.98
Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol (2007) 4.40
Extensions to gene set enrichment. Bioinformatics (2006) 4.26
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics (2005) 2.82
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res (2006) 2.55
GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. Nucleic Acids Res (2005) 1.57
Circumventing the cut-off for enrichment analysis. Brief Bioinform (2006) 1.37
GeneTrail--advanced gene set enrichment analysis. Nucleic Acids Res (2007) 5.10
New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun (2012) 3.18
BNDB - the Biochemical Network Database. BMC Bioinformatics (2007) 2.75
Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PLoS One (2009) 2.14
Toward the blood-borne miRNome of human diseases. Nat Methods (2011) 2.14
A blood based 12-miRNA signature of Alzheimer disease patients. Genome Biol (2013) 1.99
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics (2008) 1.77
miRNAs in lung cancer - studying complex fingerprints in patient's blood cells by microarray experiments. BMC Cancer (2009) 1.61
GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. Nucleic Acids Res (2005) 1.57
Complex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets. Proc Natl Acad Sci U S A (2005) 1.56
A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res (2010) 1.54
Specific peripheral miRNA profiles for distinguishing lung cancer from COPD. Lung Cancer (2011) 1.38
High-throughput miRNA profiling of human melanoma blood samples. BMC Cancer (2010) 1.32
A combinatorial approach to protein docking with flexible side chains. J Comput Biol (2002) 1.29
Genome-wide miRNA signatures of human longevity. Aging Cell (2012) 1.21
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics (2009) 1.17
Comprehensive analysis of microRNA profiles in multiple sclerosis including next-generation sequencing. Mult Scler (2013) 1.16
Stable serum miRNA profiles as potential tool for non-invasive lung cancer diagnosis. RNA Biol (2011) 1.16
Genome-wide gene amplification during differentiation of neural progenitor cells in vitro. PLoS One (2012) 1.14
BALL--biochemical algorithms library 1.3. BMC Bioinformatics (2010) 1.12
Next-generation sequencing identifies novel microRNAs in peripheral blood of lung cancer patients. Mol Biosyst (2011) 1.10
Frequent overexpression of the genes FXR1, CLAPM1 and EIF4G located on amplicon 3q26-27 in squamous cell carcinoma of the lung. Int J Cancer (2007) 1.09
BALLView: a tool for research and education in molecular modeling. Bioinformatics (2005) 1.07
Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. BMC Plant Biol (2011) 1.06
Altered microRNA expression profiles of human spermatozoa in patients with different spermatogenic impairments. Fertil Steril (2013) 1.06
Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistence. Proteomics (2009) 1.05
A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors. BMC Bioinformatics (2006) 1.05
Amplicons on chromosome 12q13-21 in glioblastoma recurrences. Int J Cancer (2010) 1.01
Novel autoantigens immunogenic in COPD patients. Respir Res (2009) 1.01
miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics (2012) 1.01
Immunogenicity of autoantigens. BMC Genomics (2011) 0.97
Genome wide expression profiling identifies specific deregulated pathways in meningioma. Int J Cancer (2009) 0.96
The human miRNA repertoire of different blood compounds. BMC Genomics (2014) 0.95
Evidence for the mode of action of the highly cytotoxic Streptomyces polyketide kendomycin. Chembiochem (2007) 0.95
Whole miRNome-wide differential co-expression of microRNAs. Genomics Proteomics Bioinformatics (2012) 0.95
A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma. Mol Cancer Res (2008) 0.94
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res (2011) 0.94
A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J Comput Chem (2010) 0.93
Electrostatic potentials of proteins in water: a structured continuum approach. Bioinformatics (2007) 0.92
Toward an early diagnosis of lung cancer: an autoantibody signature for squamous cell lung carcinoma. Int J Cancer (2008) 0.92
Novel immunogenic antigens increase classification accuracy in meningioma to 93.84%. Int J Cancer (2011) 0.92
Identification of lung cancer with high sensitivity and specificity by blood testing. Respir Res (2010) 0.91
Automated bond order assignment as an optimization problem. Bioinformatics (2011) 0.90
Pattern of serum autoantibodies allows accurate distinction between a tumor and pathologies of the same organ. Clin Cancer Res (2008) 0.88
Circulating Biomarker Panels in Alzheimer's Disease. Gerontology (2015) 0.87
Is there a general autoantibody signature for cancer? Eur J Cancer (2012) 0.87
BALLView: an object-oriented molecular visualization and modeling framework. J Comput Aided Mol Des (2006) 0.87
MicroRNA expression changes after lung cancer resection: a follow-up study. RNA Biol (2012) 0.86
Increased seroreactivity to glioma-expressed antigen 2 in brain tumor patients under radiation. PLoS One (2008) 0.86
Treatment-independent miRNA signature in blood of Wilms tumor patients. BMC Genomics (2012) 0.86
Improving seroreactivity-based detection of glioma. Neoplasia (2009) 0.86
NetworkTrail--a web service for identifying and visualizing deregulated subnetworks. Bioinformatics (2013) 0.85
The Roche Cancer Genome Database (RCGDB). Hum Mutat (2010) 0.85
The blood-borne miRNA signature of lung cancer patients is independent of histology but influenced by metastases. Mol Cancer (2014) 0.85
Paleoproteomic study of the Iceman's brain tissue. Cell Mol Life Sci (2013) 0.84
Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing. J Virol (2013) 0.83
Proteomic study of human glioblastoma multiforme tissue employing complementary two-dimensional liquid chromatography- and mass spectrometry-based approaches. J Proteome Res (2009) 0.82
Computational modeling of the sugar-lectin interaction. Adv Drug Deliv Rev (2004) 0.82
GAS41 amplification results in overexpression of a new spindle pole protein. Genes Chromosomes Cancer (2012) 0.82
A consensus line search algorithm for molecular potential energy functions. J Comput Chem (2009) 0.80
Integrative analysis of cancer-related data using CAP. FASEB J (2004) 0.80
Autoantibody signature differentiates Wilms tumor patients from neuroblastoma patients. PLoS One (2011) 0.79
Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. BMC Genomics (2014) 0.79
The Roche Cancer Genome Database 2.0. BMC Med Genomics (2011) 0.79
The intestinal factor Tff3 and a miRNA network regulate murine caloric metabolism. RNA Biol (2011) 0.79
Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy. Brief Bioinform (2015) 0.79
A set of specific miRNAs is connected with murine and human gastric cancer. Genes Chromosomes Cancer (2012) 0.79
Lectin-sugar interaction. Calculated versus experimental binding energies. Eur J Biochem (2002) 0.78
Multicenter study identified molecular blood-born protein signatures for Wilms Tumor. Int J Cancer (2011) 0.76
NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction. BMC Bioinformatics (2013) 0.75
SePaCS--a web-based application for classification of seroreactivity profiles. Nucleic Acids Res (2007) 0.75
Protein- versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples. J Chromatogr A (2010) 0.75
Comparing genome versus proteome-based identification of clinical bacterial isolates. Brief Bioinform (2016) 0.75
A new method for the gradient-based optimization of molecular complexes. J Comput Chem (2009) 0.75
A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites. Brief Bioinform (2017) 0.75
Multiple sequence alignment with arbitrary gap costs: computing an optimal solution using polyhedral combinatorics. Bioinformatics (2002) 0.75