Spectral affinity in protein networks.

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New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. Bioinformatics (2014) 1.16

MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. BMC Bioinformatics (2010) 1.09

A single source k-shortest paths algorithm to infer regulatory pathways in a gene network. Bioinformatics (2012) 0.96

Information flow in interaction networks II: channels, path lengths, and potentials. J Comput Biol (2012) 0.88

Prediction of protein interaction types based on sequence and network features. BMC Syst Biol (2013) 0.79

CytoITMprobe: a network information flow plugin for Cytoscape. BMC Res Notes (2012) 0.77

Network propagation: a universal amplifier of genetic associations. Nat Rev Genet (2017) 0.75

Collective dynamics of 'small-world' networks. Nature (1998) 98.45

Community structure in social and biological networks. Proc Natl Acad Sci U S A (2002) 29.77

Lethality and centrality in protein networks. Nature (2001) 29.64

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29

Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25

Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 24.12

BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41

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An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics (2003) 15.42

Uncovering the overlapping community structure of complex networks in nature and society. Nature (2005) 13.05

Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A (2003) 9.03

MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res (2004) 8.58

Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci U S A (2003) 4.53

Protein complex prediction via cost-based clustering. Bioinformatics (2004) 4.30

Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics (2006) 3.94

Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83

Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol (2003) 3.80

Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol (2004) 3.73

Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci U S A (2003) 2.63

Functional topology in a network of protein interactions. Bioinformatics (2004) 2.38

Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics (2006) 2.35

Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics (2006) 2.20

Finding local community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.86

Predicting protein complex membership using probabilistic network reliability. Genome Res (2004) 1.79

Clustering and embedding using commute times. IEEE Trans Pattern Anal Mach Intell (2007) 1.71

Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinformatics (2007) 1.70

Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics (2002) 1.58

Accurate extraction of functional associations between proteins based on common interaction partners and common domains. Bioinformatics (2005) 0.89

A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26

Relating three-dimensional structures to protein networks provides evolutionary insights. Science (2006) 5.50

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26

The serine protease TMPRSS6 is required to sense iron deficiency. Science (2008) 3.70

Printable ion-gel gate dielectrics for low-voltage polymer thin-film transistors on plastic. Nat Mater (2008) 3.22

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell (2007) 2.95

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol (2009) 2.43

Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33

Mutant DNA-binding domain of HSF4 is associated with autosomal dominant lamellar and Marner cataract. Nat Genet (2002) 2.21

Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol (2008) 2.07

The P4-type ATPase ATP11C is essential for B lymphopoiesis in adult bone marrow. Nat Immunol (2011) 1.96

Alternately pulsed nanoelectrospray ionization/atmospheric pressure chemical ionization for ion/ion reactions in an electrodynamic ion trap. Anal Chem (2006) 1.86

ATP-sensitive potassium channels mediate survival during infection in mammals and insects. Nat Genet (2007) 1.83

Lethal mitochondrial cardiomyopathy in a hypomorphic Med30 mouse mutant is ameliorated by ketogenic diet. Proc Natl Acad Sci U S A (2011) 1.59

Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. Genetics (2010) 1.56

Slc15a4, AP-3, and Hermansky-Pudlak syndrome proteins are required for Toll-like receptor signaling in plasmacytoid dendritic cells. Proc Natl Acad Sci U S A (2010) 1.55

Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol (2009) 1.53

The role of disorder in interaction networks: a structural analysis. Mol Syst Biol (2008) 1.50

Biochemical characterization, localization, and tissue distribution of the longer form of mouse SIRT3. Protein Sci (2009) 1.46

Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation. J Bacteriol (2005) 1.45

Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Environ Microbiol (2012) 1.41

An Slfn2 mutation causes lymphoid and myeloid immunodeficiency due to loss of immune cell quiescence. Nat Immunol (2010) 1.39

Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biol (2006) 1.33

Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Q Rev Biophys (2004) 1.31

ENU-induced phenovariance in mice: inferences from 587 mutations. BMC Res Notes (2012) 1.28

A forward genetic screen reveals roles for Nfkbid, Zeb1, and Ruvbl2 in humoral immunity. Proc Natl Acad Sci U S A (2012) 1.19

Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis. Bioresour Technol (2012) 1.16

Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res (2009) 1.15

Rapidly alternating transmission mode electron-transfer dissociation and collisional activation for the characterization of polypeptide ions. Anal Chem (2008) 1.15

Loss of T cell and B cell quiescence precedes the onset of microbial flora-dependent wasting disease and intestinal inflammation in Gimap5-deficient mice. J Immunol (2010) 1.13

Precis on forward genetics in mice. Nat Immunol (2007) 1.13

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. Nucleic Acids Res (2005) 1.12

Ion trap collisional activation of c and z* ions formed via gas-phase ion/ion electron-transfer dissociation. J Proteome Res (2007) 1.10

Printed, sub-3V digital circuits on plastic from aqueous carbon nanotube inks. ACS Nano (2010) 1.10

Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor. J Mol Biol (2004) 1.08

iRhom2 is required for the secretion of mouse TNFα. Blood (2012) 1.08

Finding local communities in protein networks. BMC Bioinformatics (2009) 1.05

Structural principles within the human-virus protein-protein interaction network. Proc Natl Acad Sci U S A (2011) 1.05

Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis. BMC Genomics (2011) 1.03

The Tpl2 mutation Sluggish impairs type I IFN production and increases susceptibility to group B streptococcal disease. J Immunol (2009) 1.03

Nanoelectrospray ionization of protein mixtures: solution pH and protein pI. Anal Chem (2004) 1.02

A mutation of Ikbkg causes immune deficiency without impairing degradation of IkappaB alpha. Proc Natl Acad Sci U S A (2010) 1.01

Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environ Microbiol (2014) 1.01

Mice with mutations of Dock7 have generalized hypopigmentation and white-spotting but show normal neurological function. Proc Natl Acad Sci U S A (2009) 1.01

Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over 4 years. Environ Microbiol Rep (2013) 1.01

Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants. Appl Microbiol Biotechnol (2014) 0.97

Flt3 permits survival during infection by rendering dendritic cells competent to activate NK cells. Proc Natl Acad Sci U S A (2010) 0.97

Positive ion transmission mode ion/ion reactions in a hybrid linear ion trap. Anal Chem (2004) 0.96

A pulsed triple ionization source for sequential ion/ion reactions in an electrodynamic ion trap. J Am Soc Mass Spectrom (2006) 0.96

Therapeutics of Ebola hemorrhagic fever: whole-genome transcriptional analysis of successful disease mitigation. J Infect Dis (2011) 0.96

Gain-of-function mutation of KIT ligand on melanin synthesis causes familial progressive hyperpigmentation. Am J Hum Genet (2009) 0.94

Discovering causal signaling pathways through gene-expression patterns. Nucleic Acids Res (2010) 0.94

Coronary artery bypass grafting with concomitant resection for carcinoma of lung. J Biomed Res (2010) 0.94

The Roles of Moonlighting Proteins in Bacteria. Curr Issues Mol Biol (2013) 0.94

Electron transfer dissociation (ETD) of peptides containing intrachain disulfide bonds. J Am Soc Mass Spectrom (2011) 0.94

Hypermorphic mutation of the voltage-gated sodium channel encoding gene Scn10a causes a dramatic stimulus-dependent neurobehavioral phenotype. Proc Natl Acad Sci U S A (2011) 0.93

Laparoscopic versus open right hemicolectomy for colon cancer: a meta-analysis. J Laparoendosc Adv Surg Tech A (2013) 0.91

Immune complexes activate human endothelium involving the cell-signaling HMGB1-RAGE axis in the pathogenesis of lupus vasculitis. Lab Invest (2013) 0.91

Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A (2013) 0.91

ZBTB1 is a determinant of lymphoid development. J Exp Med (2011) 0.91

Multiplexed fluorescence resonance energy transfer aptasensor between upconversion nanoparticles and graphene oxide for the simultaneous determination of mycotoxins. Anal Chem (2012) 0.91

Mutation of the gastric hydrogen-potassium ATPase alpha subunit causes iron-deficiency anemia in mice. Blood (2011) 0.90

The fine-tuning of thermosensitive and degradable polymer micelles for enhancing intracellular uptake and drug release in tumors. Biomaterials (2011) 0.90

Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Protein Sci (2002) 0.90

Beam-type collisional activation of polypeptide cations that survive ion/ion electron transfer. Rapid Commun Mass Spectrom (2007) 0.89

IL-33 signaling contributes to the pathogenesis of myeloproliferative neoplasms. J Clin Invest (2015) 0.89

Pinpointing double bonds in lipids by Paternò-Büchi reactions and mass spectrometry. Angew Chem Int Ed Engl (2014) 0.89

The promotion of siRNA delivery to breast cancer overexpressing epidermal growth factor receptor through anti-EGFR antibody conjugation by immunoliposomes. Biomaterials (2011) 0.88

A novel locus for maternally inherited human gingival fibromatosis at chromosome 11p15. Hum Genet (2006) 0.88

Self-assembled supramolecular nano vesicles for safe and highly efficient gene delivery to solid tumors. Int J Nanomedicine (2012) 0.87

Selective PDE5A inhibition with sildenafil rescues left ventricular dysfunction, inflammatory immune response and cardiac remodeling in angiotensin II-induced heart failure in vivo. Basic Res Cardiol (2012) 0.87

Serum withdrawal up-regulates human SIRT1 gene expression in a p53-dependent manner. J Cell Mol Med (2009) 0.87

Transition metal complex cations as reagents for gas-phase transformation of multiply deprotonated polypeptides. J Am Soc Mass Spectrom (2009) 0.86

Exploring the structure and function of Thermotoga maritima CorA reveals the mechanism of gating and ion selectivity in Co2+/Mg2+ transport. Biochem J (2013) 0.86

How are the non-classically secreted bacterial proteins released into the extracellular milieu? Curr Microbiol (2013) 0.86

Birch reduction of benzene in a low-temperature plasma. Angew Chem Int Ed Engl (2009) 0.86

A method of coupling the Paternò-Büchi reaction with direct infusion ESI-MS/MS for locating the C[double bond, length as m-dash]C bond in glycerophospholipids. Analyst (2016) 0.86

Bis-huperzine B: highly potent and selective acetylcholinesterase inhibitors. J Med Chem (2005) 0.86

High plasma fibrinogen is correlated with poor response to trastuzumab treatment in HER2 positive breast cancer. Medicine (Baltimore) (2015) 0.85

Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PLoS One (2012) 0.85

High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics (2008) 0.85

Selection and characterization of aptamers against Salmonella typhimurium using whole-bacterium Systemic Evolution of Ligands by Exponential Enrichment (SELEX). J Agric Food Chem (2013) 0.85

Toward a three-dimensional view of protein networks between species. Front Microbiol (2012) 0.85

Yip1 domain family, member 6 (Yipf6) mutation induces spontaneous intestinal inflammation in mice. Proc Natl Acad Sci U S A (2012) 0.85

Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. PLoS One (2011) 0.85

Study of discontinuous atmospheric pressure interfaces for mass spectrometry instrumentation development. Anal Chem (2010) 0.84

Independent effects of protein core size and expression on residue-level structure-evolution relationships. PLoS One (2012) 0.84

MicroRNA-155 regulates T cell proliferation through targeting GSK3β in cardiac allograft rejection in a murine transplantation model. Cell Immunol (2013) 0.84

Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res (2010) 0.84

Genome reconstruction and gene expression of "Candidatus Accumulibacter phosphatis" Clade IB performing biological phosphorus removal. Environ Sci Technol (2014) 0.84

Exoprotein production correlates with morphotype changes of nonmotile Shewanella oneidensis mutants. J Bacteriol (2013) 0.84

Mutation analysis of 20 SARS virus genome sequences: evidence for negative selection in replicase ORF1b and spike gene. Acta Pharmacol Sin (2003) 0.83

Selection and identification of ssDNA aptamers recognizing zearalenone. Anal Bioanal Chem (2013) 0.83

Medial versus lateral approach in laparoscopic colorectal resection: a systematic review and meta-analysis. World J Surg (2013) 0.83

Identification of Annexin A1 protein expression in human gastric adenocarcinoma using proteomics and tissue microarray. World J Gastroenterol (2013) 0.83

Dialkoxybithiazole: a new building block for head-to-head polymer semiconductors. J Am Chem Soc (2013) 0.82

Radical induced disulfide bond cleavage within peptides via ultraviolet irradiation of an electrospray plume. Analyst (2013) 0.82

Injectable hydrogel as stem cell scaffolds from the thermosensitive terpolymer of NIPAAm/AAc/HEMAPCL. Int J Nanomedicine (2012) 0.82