Published in BMC Genomics on June 18, 2015
VarI-SIG 2014--From SNPs to variants: interpreting different types of genetic variants. BMC Genomics (2015) 0.81
From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data. EURASIP J Bioinform Syst Biol (2017) 0.75
eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes. BMC Genomics (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res (2001) 24.45
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
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
PID: the Pathway Interaction Database. Nucleic Acids Res (2008) 12.92
MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
Inflammatory mechanisms in obesity. Annu Rev Immunol (2011) 9.83
WikiPathways: pathway editing for the people. PLoS Biol (2008) 8.13
MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res (2006) 7.75
A systems biology approach for pathway level analysis. Genome Res (2007) 6.95
A novel signaling pathway impact analysis. Bioinformatics (2008) 5.06
PINA v2.0: mining interactome modules. Nucleic Acids Res (2011) 2.23
Molecular mechanism for a gateway drug: epigenetic changes initiated by nicotine prime gene expression by cocaine. Sci Transl Med (2011) 1.97
Beta-Adrenergic receptors, diet-induced thermogenesis, and obesity. J Biol Chem (2003) 1.95
EnrichNet: network-based gene set enrichment analysis. Bioinformatics (2012) 1.92
Analysis of gene sets based on the underlying regulatory network. J Comput Biol (2009) 1.67
Apoptotic mechanisms in the control of erythropoiesis. Leukemia (2004) 1.59
Cyclic AMP, PKA, and the physiological regulation of adiposity. Recent Prog Horm Res (1998) 1.38
Reduced GABA concentration in attention-deficit/hyperactivity disorder. Arch Gen Psychiatry (2012) 1.35
Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol (2010) 1.25
Chapter 4: Protein interactions and disease. PLoS Comput Biol (2012) 1.10
Morbidly obese human subjects have increased peripheral blood CD4+ T cells with skewing toward a Treg- and Th2-dominated phenotype. Diabetes (2012) 1.09
Knowledge-based analysis of proteomics data. BMC Bioinformatics (2012) 1.03
PathNet: a tool for pathway analysis using topological information. Source Code Biol Med (2012) 1.01
Bile acids, obesity, and the metabolic syndrome. Best Pract Res Clin Gastroenterol (2014) 0.94
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks. Bioinformatics (2013) 0.90
SANTA: quantifying the functional content of molecular networks. PLoS Comput Biol (2014) 0.88
Steiner tree methods for optimal sub-network identification: an empirical study. BMC Bioinformatics (2013) 0.83
Altered tryptophan and alanine transport in fibroblasts from boys with attention-deficit/hyperactivity disorder (ADHD): an in vitro study. Behav Brain Funct (2011) 0.81
Associations of sodium intake with obesity, body mass index, waist circumference, and weight. Am J Prev Med (2014) 0.81
THINK Back: KNowledge-based Interpretation of High Throughput data. BMC Bioinformatics (2012) 0.80
Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis. Proteomics (2015) 0.79
Brain Serotonin, Carbohydrate-craving, obesity and depression. Adv Exp Med Biol (1996) 0.79
Network-based Pathway Enrichment Analysis. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2013) 0.79
FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks. Genomics Proteomics Bioinformatics (2014) 0.77
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res (2005) 4.32
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics (2004) 3.50
Transglutaminases: nature's biological glues. Biochem J (2002) 3.42
Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat (2009) 3.14
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics (2003) 3.10
Prediction of coordination number and relative solvent accessibility in proteins. Proteins (2002) 2.66
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23
A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics (2004) 2.16
BaCelLo: a balanced subcellular localization predictor. Bioinformatics (2006) 2.14
PredGPI: a GPI-anchor predictor. BMC Bioinformatics (2008) 1.86
Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem (2002) 1.74
A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics (2008) 1.73
SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. J Natl Cancer Inst (2011) 1.53
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics (2005) 1.49
Predicting protein stability changes from sequences using support vector machines. Bioinformatics (2005) 1.46
Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform (2009) 1.44
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics (2003) 1.44
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29
CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype. Blood (2013) 1.28
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network. Proteomics (2004) 1.20
An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics (2010) 1.18
WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics (2013) 1.14
In silico prediction of the structure of membrane proteins: is it feasible? Brief Bioinform (2003) 1.13
Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans. Hum Mutat (2008) 1.11
Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. PLoS One (2011) 1.11
eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res (2006) 1.10
Reconstruction of 3D structures from protein contact maps. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.10
The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation. Brief Funct Genomic Proteomic (2008) 1.10
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinformatics (2005) 1.09
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. Protein Eng (2002) 1.09
Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria. Protein Sci (2003) 1.08
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. Bioinformatics (2008) 1.08
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinformatics (2003) 1.07
EX-HOM (EXome HOMozygosity): a proof of principle. Hum Hered (2011) 1.06
A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes. BMC Genomics (2012) 1.05
New Escherichia coli outer membrane proteins identified through prediction and experimental verification. Protein Sci (2006) 1.00
Preprotein translocase of the outer mitochondrial membrane: reconstituted Tom40 forms a characteristic TOM pore. J Mol Biol (2005) 1.00
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res (2010) 0.99
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res (2011) 0.99
Substitution in the murine nectin1 receptor of a single conserved amino acid at a position distal from the herpes simplex virus gD binding site confers high-affinity binding to gD. J Virol (2002) 0.98
The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis. J Proteome Res (2009) 0.96
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. Bioinformatics (2011) 0.94
Correlating disease-related mutations to their effect on protein stability: a large-scale analysis of the human proteome. Hum Mutat (2011) 0.94
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinformatics (2009) 0.91
Hierarchical mechanochemical switches in angiostatin. Chembiochem (2006) 0.90
Predicting protein thermostability changes from sequence upon multiple mutations. Bioinformatics (2008) 0.89
Expression of IGF-1 receptor in KIT/PDGF receptor-α wild-type gastrointestinal stromal tumors with succinate dehydrogenase complex dysfunction. Future Oncol (2013) 0.88
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. BMC Genomics (2012) 0.87
The pros and cons of predicting protein contact maps. Methods Mol Biol (2008) 0.87