Published in Bioinformatics on March 12, 2010
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Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. Bioinformatics (2013) 0.75
A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning. BMC Syst Biol (2016) 0.75
Inferring host gene subnetworks involved in viral replication. PLoS Comput Biol (2014) 0.75
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Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics (2004) 1.92
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Inferring meaningful pathways in weighted metabolic networks. J Mol Biol (2005) 1.28
Representing and analysing molecular and cellular function using the computer. Biol Chem (2001) 1.24
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Metabolic pathfinding using RPAIR annotation. J Mol Biol (2009) 1.13
Automated extraction of meaningful pathways from quantitative proteomics data. Brief Funct Genomic Proteomic (2008) 0.79
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
Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics (2006) 4.85
RSAT: regulatory sequence analysis tools. Nucleic Acids Res (2008) 3.93
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Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics (2009) 2.66
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc (2008) 2.17
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res (2008) 1.99
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res (2011) 1.79
Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res (2010) 1.59
Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae. Mol Cell Biol (2007) 1.50
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. Nucleic Acids Res (2010) 1.47
Network Analysis Tools: from biological networks to clusters and pathways. Nat Protoc (2008) 1.40
The powerful law of the power law and other myths in network biology. Mol Biosyst (2009) 1.29
Inferring meaningful pathways in weighted metabolic networks. J Mol Biol (2005) 1.28
Algorithms for Design of Continuum Robots Using the Concentric Tubes Approach: A Neurosurgical Example. IEEE Int Conf Robot Autom (2011) 1.26
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics (2008) 1.22
Regional differences in adipose tissue metabolism in women: minor effect of obesity and body fat distribution. Diabetes (2006) 1.20
Transcriptional regulation of protein complexes in yeast. Genome Biol (2004) 1.20
Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res (2005) 1.19
Ovarian hormone status and abdominal visceral adipose tissue metabolism. J Clin Endocrinol Metab (2004) 1.19
Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat Protoc (2008) 1.17
Metabolic pathfinding using RPAIR annotation. J Mol Biol (2009) 1.13
Passive markers for ultrasound tracking of surgical instruments. Med Image Comput Comput Assist Interv (2005) 1.13
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc (2012) 1.07
Subdivision of the subcutaneous adipose tissue compartment and lipid-lipoprotein levels in women. Obes Res (2003) 1.06
An overview of data models for the analysis of biochemical pathways. Brief Bioinform (2003) 1.06
Discovery of conserved motifs in promoters of orthologous genes in prokaryotes. Methods Mol Biol (2007) 1.03
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinformatics (2009) 1.02
Discovery of motifs in promoters of coregulated genes. Methods Mol Biol (2007) 1.00
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinformatics (2009) 0.99
Modularity of the transcriptional response of protein complexes in yeast. J Mol Biol (2006) 0.98
Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res (2011) 0.96
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PLoS One (2007) 0.95
In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis. Plant Physiol (2003) 0.92
Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data. Nat Protoc (2008) 0.91
Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol (2009) 0.90
Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics (2005) 0.90
In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC Bioinformatics (2007) 0.87
Molecular characterization of a new Tetratrichomonas species in a patient with empyema. J Clin Microbiol (2009) 0.85
Local androgen inactivation in abdominal visceral adipose tissue. J Clin Endocrinol Metab (2003) 0.83
Expression and activity of steroid aldoketoreductases 1C in omental adipose tissue are positive correlates of adiposity in women. Am J Physiol Endocrinol Metab (2004) 0.82
Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae. BMC Proc (2008) 0.82
Hypoxia integration in the serological proteome analysis unmasks tumor antigens and fosters the identification of anti-phospho-eEF2 antibodies as potential cancer biomarkers. PLoS One (2013) 0.81
Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems (2011) 0.79
Predicting metabolic pathways by sub-network extraction. Methods Mol Biol (2012) 0.79
Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis. BMC Genomics (2013) 0.78
Expression and activity of 20alpha-hydroxysteroid dehydrogenase (AKR1C1) in abdominal subcutaneous and omental adipose tissue in women. J Clin Endocrinol Metab (2004) 0.78
Endoscopic findings in case of incidental colonic uptake in PET-CT how to improve PET-CT specificity? Acta Gastroenterol Belg (2014) 0.76
In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinformatics (2009) 0.76