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Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol (2007) 2.72

Protein function annotation by homology-based inference. Genome Biol (2009) 2.20

Protein co-evolution, co-adaptation and interactions. EMBO J (2008) 1.65

Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol (2006) 1.60

DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res (2010) 1.59

DOMINE: a database of protein domain interactions. Nucleic Acids Res (2007) 1.54

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics (2007) 1.47

The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res (2009) 1.32

Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes. PLoS Comput Biol (2007) 1.29

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface (2008) 1.24

Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics (2006) 1.22

DIMA 3.0: Domain Interaction Map. Nucleic Acids Res (2010) 1.19

Reuse of structural domain-domain interactions in protein networks. BMC Bioinformatics (2007) 1.19

NetGrep: fast network schema searches in interactomes. Genome Biol (2008) 1.08

ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC Bioinformatics (2011) 1.00

Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. Bioinformatics (2009) 0.91

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens. BMC Genomics (2009) 0.87

Organization of physical interactomes as uncovered by network schemas. PLoS Comput Biol (2008) 0.87

Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biol (2007) 0.87

DIMA 2.0--predicted and known domain interactions. Nucleic Acids Res (2007) 0.87

Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics (2008) 0.86

Computational approaches for prediction of pathogen-host protein-protein interactions. Front Microbiol (2015) 0.80

Practical aspects of protein co-evolution. Front Cell Dev Biol (2014) 0.79

Protein annotation from protein interaction networks and Gene Ontology. J Biomed Inform (2011) 0.76

Mutual information and variants for protein domain-domain contact prediction. BMC Res Notes (2012) 0.75

Fungome: Annotating proteins implicated in fungal pathogenesis. Bioinformation (2010) 0.75

The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39

Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78

The MIPS mammalian protein-protein interaction database. Bioinformatics (2004) 4.66

Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06

Bace1 modulates myelination in the central and peripheral nervous system. Nat Neurosci (2006) 3.85

Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics (2008) 3.78

Elevated beta-secretase expression and enzymatic activity detected in sporadic Alzheimer disease. Nat Med (2003) 3.78

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res (2004) 3.71

Illuminating the evolutionary history of chlamydiae. Science (2004) 3.39

Amyloid beta peptide load is correlated with increased beta-secretase activity in sporadic Alzheimer's disease patients. Proc Natl Acad Sci U S A (2004) 2.88

Hepatic encephalopathy in chronic liver disease: 2014 Practice Guideline by the American Association for the Study of Liver Diseases and the European Association for the Study of the Liver. Hepatology (2014) 2.56

Phase 2 gene therapy trial of an anti-HIV ribozyme in autologous CD34+ cells. Nat Med (2009) 2.21

Protein function annotation by homology-based inference. Genome Biol (2009) 2.20

Management of chronic hepatitis C: consensus guidelines. Can J Gastroenterol (2007) 2.06

Pathogenicity determinants in smut fungi revealed by genome comparison. Science (2010) 2.03

Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. OMICS (2004) 1.92

The PEDANT genome database in 2005. Nucleic Acids Res (2005) 1.88

PEDANT covers all complete RefSeq genomes. Nucleic Acids Res (2008) 1.78

Management of chronic hepatitis B: consensus guidelines. Can J Gastroenterol (2007) 1.78

Ectopic varices. Gastrointest Endosc (2011) 1.75

Pharmacological response of human cardiomyocytes derived from virus-free induced pluripotent stem cells. Cardiovasc Res (2011) 1.67

CCancer: a bird's eye view on gene lists reported in cancer-related studies. Nucleic Acids Res (2010) 1.62

Mining sequence annotation databanks for association patterns. Bioinformatics (2005) 1.62

Sildenafil preserves intracorporeal smooth muscle after radical retropubic prostatectomy. J Urol (2004) 1.62

Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements. Plant Cell (2012) 1.61

Conservation of protein-protein interactions - lessons from ascomycota. Trends Genet (2004) 1.55

Clostridium difficile colitis: increasing incidence, risk factors, and outcomes in solid organ transplant recipients. Transplantation (2012) 1.52

Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Pathog (2011) 1.52

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS (2014) 1.49

G-CSF for stem cell therapy in acute myocardial infarction: friend or foe? Cardiovasc Res (2010) 1.47

BACE1 deficiency causes altered neuronal activity and neurodegeneration. J Neurosci (2010) 1.45

Bioabsorbable vascular scaffold overexpansion: insights from in vitro post-expansion experiments. EuroIntervention (2016) 1.45

TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics (2010) 1.43

Ex vivo differentiation of human adult bone marrow stem cells into cardiomyocyte-like cells. Biochem Biophys Res Commun (2004) 1.43

Retracted Myoblast transplantation for cardiac repair: from automyoblast to allomyoblast transplantation. Ann Thorac Surg (2008) 1.39

In regard to RTOG sarcoma radiation oncologists reach consensus on gross tumor volume and clinical target volume on computed tomographic images for preoperative radiotherapy of primary soft tissue sarcoma of extremity in Radiation Therapy Oncology Group studies: in regard to Wang et al (Int J Radiat Oncol Biol Phys 2011;81:e525-e528). Int J Radiat Oncol Biol Phys (2012) 1.37

Pitfalls of supervised feature selection. Bioinformatics (2009) 1.33

Incomplete stent apposition causes high shear flow disturbances and delay in neointimal coverage as a function of strut to wall detachment distance: implications for the management of incomplete stent apposition. Circ Cardiovasc Interv (2014) 1.33

The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res (2009) 1.32

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res (2004) 1.31

PROMPT: a protein mapping and comparison tool. BMC Bioinformatics (2006) 1.31

GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists. Nucleic Acids Res (2009) 1.31

Will my protein crystallize? A sequence-based predictor. Proteins (2006) 1.30

SNAPper: gene order predicts gene function. Bioinformatics (2002) 1.27

Co-evolving residues in membrane proteins. Bioinformatics (2007) 1.25

Generation of patient-specific induced pluripotent stem cell-derived cardiomyocytes as a cellular model of arrhythmogenic right ventricular cardiomyopathy. Eur Heart J (2012) 1.24

Hepatitis E in new zealand. J Gastroenterol Hepatol (2007) 1.23

Protein solubility: sequence based prediction and experimental verification. Bioinformatics (2006) 1.23

TICL--a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics. FEBS J (2009) 1.21

PEDANT genome database: 10 years online. Nucleic Acids Res (2006) 1.20

DIMA 3.0: Domain Interaction Map. Nucleic Acids Res (2010) 1.19

MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res (2010) 1.19

Disrupted-in-Schizophrenia-1 expression is regulated by beta-site amyloid precursor protein cleaving enzyme-1-neuregulin cascade. Proc Natl Acad Sci U S A (2010) 1.18

Applying negative rule mining to improve genome annotation. BMC Bioinformatics (2007) 1.18

Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiol Lett (2006) 1.15

Electrophysiology of human cardiac atrial and ventricular telocytes. J Cell Mol Med (2014) 1.14

Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs. J Mol Biol (2007) 1.12

Modeling type 3 long QT syndrome with cardiomyocytes derived from patient-specific induced pluripotent stem cells. Int J Cardiol (2013) 1.11

One-step derivation of cardiomyocytes and mesenchymal stem cells from human pluripotent stem cells. Stem Cell Res (2012) 1.06

Pretreatment serum VEGF is associated with clinical response and overall survival in advanced melanoma patients treated with ipilimumab. Cancer Immunol Res (2014) 1.05

Current trends in diagnostic biomarkers of acute coronary syndrome. Ann Acad Med Singapore (2010) 1.05

Analysis and outcomes of right lobe hepatectomy in 101 consecutive living donors. Am J Transplant (2005) 1.04

An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics (2008) 1.03

Coevolution predicts direct interactions between mtDNA-encoded and nDNA-encoded subunits of oxidative phosphorylation complex i. J Mol Biol (2010) 1.02

Specificity in substrate and cofactor recognition by the N-terminal domain of the chaperone ClpX. Proc Natl Acad Sci U S A (2006) 1.02

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. Nucleic Acids Res (2013) 1.01

Correlated mutations: a hallmark of phenotypic amino acid substitutions. PLoS Comput Biol (2010) 1.00

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res (2006) 0.99

Phosphorylation variation during the cell cycle scales with structural propensities of proteins. PLoS Comput Biol (2013) 0.99

Noninvasive diagnosis of liver fibrosis: The importance of being reimbursed. Can J Gastroenterol Hepatol (2015) 0.97

Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN). Gene (2008) 0.97

Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks. Proteins (2009) 0.97

The DIMA web resource--exploring the protein domain network. Bioinformatics (2006) 0.96

PLIPS, an automatically collected database of protein lists reported by proteomics studies. J Proteome Res (2009) 0.96

Importance of mRNA secondary structural elements for the expression of influenza virus genes. OMICS (2009) 0.96

Cell delivery and tracking in post-myocardial infarction cardiac stem cell therapy: an introduction for clinical researchers. Heart Fail Rev (2010) 0.93

Hemodynamic contribution of stem cell scaffolding in acute injured myocardium. Tissue Eng Part A (2012) 0.92

Early changes in kidney function predict long-term chronic kidney disease and mortality in patients after liver transplantation. Transplantation (2011) 0.91

Designability, aggregation propensity and duplication of disease-associated proteins. Protein Eng Des Sel (2005) 0.91

Identification and characterization of calcium sparks in cardiomyocytes derived from human induced pluripotent stem cells. PLoS One (2013) 0.90

PROSO II--a new method for protein solubility prediction. FEBS J (2012) 0.90

Assignment of isochores for all completely sequenced vertebrate genomes using a consensus. Genome Biol (2008) 0.89

Differential effect of myocardial matrix and integrins on cardiac differentiation of human mesenchymal stem cells. Differentiation (2010) 0.88

Current status of membrane protein structure classification. Proteins (2010) 0.88

QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis. Nucleic Acids Res (2013) 0.87

Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus. RNA Biol (2012) 0.87

DIMA 2.0--predicted and known domain interactions. Nucleic Acids Res (2007) 0.87

Sequence-structure relationships in yeast mRNAs. Nucleic Acids Res (2011) 0.86

Hepatitis B and the infected health care worker: public safety at what cost? Can J Gastroenterol (2012) 0.85

Pharmacoelectrophysiology of viral-free induced pluripotent stem cell-derived human cardiomyocytes. Toxicol Sci (2012) 0.85

Liquid chromatography/tandem mass spectrometry for the determination of carbamazepine and its main metabolite in rat plasma utilizing an automated blood sampling system. J Pharm Biomed Anal (2005) 0.85

iPSC-derived human mesenchymal stem cells improve myocardial strain of infarcted myocardium. J Cell Mol Med (2014) 0.85

Complex principal component and correlation structure of 16 yeast genomic variables. Mol Biol Evol (2011) 0.84

RNAtips: Analysis of temperature-induced changes of RNA secondary structure. Nucleic Acids Res (2013) 0.84

Critical path in cardiac stem cell therapy: an update on cell delivery. Cytotherapy (2013) 0.84

Hydrogen sulphide suppresses human atrial fibroblast proliferation and transformation to myofibroblasts. J Cell Mol Med (2013) 0.83

Characterization of hepatitis B virus genotypes and quantitative hepatitis B surface antigen titres in North American tertiary referral liver centres. Liver Int (2013) 0.83

Antioxidant therapy in nonalcoholic steatohepatitis. Hepat Res Treat (2012) 0.83