A human functional protein interaction network and its application to cancer data analysis.

PubWeight™: 4.73‹?› | Rank: Top 1%

🔗 View Article (PMC 2898064)

Published in Genome Biol on May 19, 2010

Authors

Guanming Wu1, Xin Feng, Lincoln Stein

Author Affiliations

1: Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3, Canada. guanmingwu@gmail.com

Articles citing this

(truncated to the top 100)

The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91

Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23

The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19

The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56

Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22

Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39

Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep (2013) 3.92

GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64

Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. Cancer Cell (2011) 2.56

Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) (2012) 2.35

Visualizing multidimensional cancer genomics data. Genome Med (2013) 2.19

Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med (2012) 2.06

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res (2012) 1.95

A network module-based method for identifying cancer prognostic signatures. Genome Biol (2012) 1.61

Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol (2012) 1.49

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics (2012) 1.43

Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Mol Neurodegener (2016) 1.41

Host responses to melioidosis and tuberculosis are both dominated by interferon-mediated signaling. PLoS One (2013) 1.35

Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics (2014) 1.33

From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets. Nat Rev Cancer (2012) 1.32

Identification of cereblon-binding proteins and relationship with response and survival after IMiDs in multiple myeloma. Blood (2014) 1.22

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol (2012) 1.21

Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci. Nat Commun (2015) 1.18

Next-generation sequencing identifies rare variants associated with Noonan syndrome. Proc Natl Acad Sci U S A (2014) 1.17

ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. F1000Res (2014) 1.15

Cancer missense mutations alter binding properties of proteins and their interaction networks. PLoS One (2013) 1.14

Epistasis network centrality analysis yields pathway replication across two GWAS cohorts for bipolar disorder. Transl Psychiatry (2012) 1.13

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res (2011) 1.11

Identification of gene pathways implicated in Alzheimer's disease using longitudinal imaging phenotypes with sparse regression. Neuroimage (2012) 1.10

The systematic annotation of the three main GPCR families in Reactome. Database (Oxford) (2010) 1.09

Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics (2012) 1.08

Transcriptome landscape of the human placenta. BMC Genomics (2012) 1.05

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples. Genome Biol (2013) 1.03

Inference and validation of predictive gene networks from biomedical literature and gene expression data. Genomics (2014) 1.01

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. Elife (2014) 1.01

Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. BMC Genomics (2013) 0.98

DawnRank: discovering personalized driver genes in cancer. Genome Med (2014) 0.98

Systems biology in aging: linking the old and the young. Curr Genomics (2012) 0.97

Genetic Basis of Common Human Disease: Insight into the Role of Missense SNPs from Genome-Wide Association Studies. J Mol Biol (2015) 0.96

A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One (2011) 0.96

A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis. BMC Genomics (2012) 0.94

Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives. Hum Genet (2014) 0.94

GWAS and drug targets. BMC Genomics (2014) 0.93

Intrinsically disordered proteins and conformational noise: implications in cancer. Cell Cycle (2012) 0.92

Breast tumor subgroups reveal diverse clinical prognostic power. Sci Rep (2014) 0.92

Learning regulatory programs by threshold SVD regression. Proc Natl Acad Sci U S A (2014) 0.92

Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. Nat Commun (2015) 0.92

Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc (2014) 0.92

Combing the hairball with BioFabric: a new approach for visualization of large networks. BMC Bioinformatics (2012) 0.91

A systems biology analysis of the unique and overlapping transcriptional responses to caloric restriction and dietary methionine restriction in rats. FASEB J (2014) 0.91

Ets-1 global gene expression profile reveals associations with metabolism and oxidative stress in ovarian and breast cancers. Cancer Metab (2013) 0.90

Genome-wide association studies of refractive error and myopia, lessons learned, and implications for the future. Invest Ophthalmol Vis Sci (2014) 0.90

Bioinformatics for cancer immunology and immunotherapy. Cancer Immunol Immunother (2012) 0.90

Deep Sequencing the microRNA profile in rhabdomyosarcoma reveals down-regulation of miR-378 family members. BMC Cancer (2014) 0.89

Expression profiling during mammary epithelial cell three-dimensional morphogenesis identifies PTPRO as a novel regulator of morphogenesis and ErbB2-mediated transformation. Mol Cell Biol (2012) 0.89

A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. BMC Bioinformatics (2014) 0.89

Determining effects of non-synonymous SNPs on protein-protein interactions using supervised and semi-supervised learning. PLoS Comput Biol (2014) 0.88

Predicting cancer prognosis using functional genomics data sets. Cancer Inform (2014) 0.88

Serglycin: at the crossroad of inflammation and malignancy. Front Oncol (2014) 0.87

A Systems Biology Approach to Characterize Biomarkers for Blood Stasis Syndrome of Unstable Angina Patients by Integrating MicroRNA and Messenger RNA Expression Profiling. Evid Based Complement Alternat Med (2013) 0.87

Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Stat Appl Genet Mol Biol (2012) 0.87

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst Biol (2012) 0.86

Pathprinting: An integrative approach to understand the functional basis of disease. Genome Med (2013) 0.86

Proteomics: from single molecules to biological pathways. Cardiovasc Res (2012) 0.86

Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes. Nat Commun (2015) 0.86

Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res (2016) 0.85

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles. Nucleic Acids Res (2015) 0.85

atBioNet--an integrated network analysis tool for genomics and biomarker discovery. BMC Genomics (2012) 0.85

Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells. Breast Cancer Res (2012) 0.85

Identification of aberrant pathways and network activities from high-throughput data. Brief Bioinform (2012) 0.85

Small molecule-induced mitochondrial disruption directs prostate cancer inhibition via UPR signaling. Oncotarget (2013) 0.84

Prediction of novel drug indications using network driven biological data prioritization and integration. J Cheminform (2014) 0.84

Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. BMC Syst Biol (2013) 0.84

A minimal connected network of transcription factors regulated in human tumors and its application to the quest for universal cancer biomarkers. PLoS One (2012) 0.84

Genome-Wide Analysis of DNA Methylation and Fine Particulate Matter Air Pollution in Three Study Populations: KORA F3, KORA F4, and the Normative Aging Study. Environ Health Perspect (2016) 0.83

Molecular profiling and computational network analysis of TAZ-mediated mammary tumorigenesis identifies actionable therapeutic targets. Oncotarget (2014) 0.83

Gene target specificity of the Super Elongation Complex (SEC) family: how HIV-1 Tat employs selected SEC members to activate viral transcription. Nucleic Acids Res (2015) 0.83

Pathway databases: making chemical and biological sense of the genomic data flood. Chem Biol (2013) 0.83

Genomics and bioinformatics of Parkinson's disease. Cold Spring Harb Perspect Med (2012) 0.82

Advanced systems biology methods in drug discovery and translational biomedicine. Biomed Res Int (2013) 0.82

Cancer module genes ranking using kernelized score functions. BMC Bioinformatics (2012) 0.82

Endogenous molecular network reveals two mechanisms of heterogeneity within gastric cancer. Oncotarget (2015) 0.82

Protein interaction networks as metric spaces: a novel perspective on distribution of hubs. BMC Syst Biol (2014) 0.82

Characterization of breast cancer interstitial fluids by TmT labeling, LTQ-Orbitrap Velos mass spectrometry, and pathway analysis. J Proteome Res (2012) 0.81

Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization. PLoS One (2015) 0.81

Identification of collaborative driver pathways in breast cancer. BMC Genomics (2014) 0.81

A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation. Breast Cancer Res (2015) 0.81

A vertex similarity-based framework to discover and rank orphan disease-related genes. BMC Syst Biol (2012) 0.81

An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. Artif Intell Med (2014) 0.81

Treatment-induced cell cycle kinetics dictate tumor response to chemotherapy. Oncotarget (2015) 0.81

IL-10 and integrin signaling pathways are associated with head and neck cancer progression. BMC Genomics (2016) 0.81

The path to routine use of genomic biomarkers in the cancer clinic. Genome Res (2015) 0.81

Signaling pathway switch in breast cancer. Cancer Cell Int (2013) 0.80

Glucocorticoid-induced reversal of interleukin-1β-stimulated inflammatory gene expression in human oviductal cells. PLoS One (2014) 0.80

High expression of Zinc-finger protein X-linked promotes tumor growth and predicts a poor outcome for stage II/III colorectal cancer patients. Oncotarget (2016) 0.79

Current advances in systems and integrative biology. Comput Struct Biotechnol J (2014) 0.79

Impaired extracellular matrix structure resulting from malnutrition in ovariectomized mature rats. Histochem Cell Biol (2015) 0.79

Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery. BMC Syst Biol (2014) 0.79

Detecting cancer outlier genes with potential rearrangement using gene expression data and biological networks. Adv Bioinformatics (2012) 0.79

Articles cited by this

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46

The hallmarks of cancer. Cell (2000) 113.05

Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76

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

Emergence of scaling in random networks Science (1999) 89.38

Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature (2008) 75.40

The consensus coding sequences of human breast and colorectal cancers. Science (2006) 60.02

The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05

An integrated genomic analysis of human glioblastoma multiforme. Science (2008) 51.36

[''R"--project for statistical computing]. Ugeskr Laeger (2008) 41.69

The genomic landscapes of human breast and colorectal cancers. Science (2007) 38.12

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science (2008) 36.02

Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83

Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02

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

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

Cancer genes and the pathways they control. Nat Med (2004) 24.22

GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63

The human disease network. Proc Natl Acad Sci U S A (2007) 19.58

TGFbeta in Cancer. Cell (2008) 17.44

Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02

IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82

Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36

Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet (2007) 12.27

Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18

The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83

Ensembl's 10th year. Nucleic Acids Res (2009) 10.82

Coexpression analysis of human genes across many microarray data sets. Genome Res (2004) 9.38

Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16

The small world inside large metabolic networks. Proc Biol Sci (2001) 7.63

An empirical framework for binary interactome mapping. Nat Methods (2008) 6.59

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res (2006) 6.20

Human F-box protein hCdc4 targets cyclin E for proteolysis and is mutated in a breast cancer cell line. Nature (2001) 5.07

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform (2004) 4.57

The KLF4 tumour suppressor is a transcriptional repressor of p53 that acts as a context-dependent oncogene. Nat Cell Biol (2005) 4.29

Functional copy-number alterations in cancer. PLoS One (2008) 4.27

Global topological features of cancer proteins in the human interactome. Bioinformatics (2006) 4.17

Protein interaction mapping: a Drosophila case study. Genome Res (2005) 4.15

A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res (2007) 4.09

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79

Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins (2006) 3.78

A phosphoserine-regulated docking site in the protein kinase RSK2 that recruits and activates PDK1. EMBO J (2000) 3.70

Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64

Inferring cellular networks--a review. BMC Bioinformatics (2007) 3.49

The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep (2004) 2.75

TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res (2007) 2.67

Regulation of T cell receptor signaling by tyrosine phosphatase SYP association with CTLA-4. Science (1996) 2.56

A map of human cancer signaling. Mol Syst Biol (2007) 2.50

Signaling of transforming growth factor-beta family members through Smad proteins. Eur J Biochem (2000) 2.39

Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics (2006) 2.36

A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet (2009) 2.24

Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One (2008) 2.09

Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics (2004) 2.00

The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics (2005) 1.97

A GLI1-p53 inhibitory loop controls neural stem cell and tumour cell numbers. EMBO J (2009) 1.95

Phosphorylation of the cell cycle inhibitor p21Cip1/WAF1 by Pim-1 kinase. Biochim Biophys Acta (2002) 1.86

Defects in energy homeostasis in Leigh syndrome French Canadian variant through PGC-1alpha/LRP130 complex. Genes Dev (2006) 1.85

A proteome resource of ovarian cancer ascites: integrated proteomic and bioinformatic analyses to identify putative biomarkers. J Proteome Res (2007) 1.80

Epidermal growth factor (EGF)-like repeats of human tenascin-C as ligands for EGF receptor. J Cell Biol (2001) 1.74

Transforming growth factor-beta and breast cancer: Tumor promoting effects of transforming growth factor-beta. Breast Cancer Res (2000) 1.54

E2F transcriptional activation requires TRRAP and GCN5 cofactors. J Biol Chem (2001) 1.44

An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality. Bioinformatics (2006) 1.37

Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT). Mol Biosyst (2008) 1.37

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics (2007) 1.27

Transforming growth factor-beta and breast cancer: Mammary gland development. Breast Cancer Res (2000) 1.26

Annexins--modulators of EGF receptor signalling and trafficking. Cell Signal (2009) 1.25

CREB-binding protein/p300 co-activation of crystallin gene expression. J Biol Chem (2002) 1.20

Low duplicability and network fragility of cancer genes. Trends Genet (2008) 1.18

hGTSE-1 expression stimulates cytoplasmic localization of p53. J Biol Chem (2004) 1.18

A factor graph nested effects model to identify networks from genetic perturbations. PLoS Comput Biol (2009) 1.14

CD46 is phosphorylated at tyrosine 354 upon infection of epithelial cells by Neisseria gonorrhoeae. J Cell Biol (2002) 1.14

Transforming growth factor-beta and breast cancer: Transforming growth factor-beta/SMAD signaling defects and cancer. Breast Cancer Res (2000) 1.11

Transforming growth factor-beta and breast cancer: Cell cycle arrest by transforming growth factor-beta and its disruption in cancer. Breast Cancer Res (2000) 1.07

Epidermal growth factor stimulation of the ACK1/Dbl pathway in a Cdc42 and Grb2-dependent manner. Biochem Biophys Res Commun (2001) 1.07

Transcriptional activation of the insulin-like growth factor I receptor gene by the Kruppel-like factor 6 (KLF6) tumor suppressor protein: potential interactions between KLF6 and p53. Endocrinology (2004) 1.03

Cyclin E-mediated elimination of p27 requires its interaction with the nuclear pore-associated protein mNPAP60. EMBO J (2000) 1.02

Transforming growth factor-beta and breast cancer: Lessons learned from genetically altered mouse models. Breast Cancer Res (2000) 1.02

Modulation of DNA topoisomerase I activity by p53. Biochemistry (1996) 1.00

Src family kinases directly regulate JIP1 module dynamics and activation. Mol Cell Biol (2007) 0.97

Genetic investigation of DNA-repair pathway genes PMS2, MLH1, MSH2, MSH6, MUTYH, OGG1 and MTH1 in sporadic colon cancer. Int J Cancer (2007) 0.91

Essential roles of caspases and their upstream regulators in rotenone-induced apoptosis. Biochem Biophys Res Commun (2008) 0.90

NGF-dependent and tissue-specific transcription of vgf is regulated by a CREB-p300 and bHLH factor interaction. FEBS Lett (2002) 0.89

Comparative analysis of protein-protein interactions in cancer-associated genes. Genomics Proteomics Bioinformatics (2009) 0.88

Protein kinase C and guanosine triphosphate combine to potentiate calcium-dependent membrane fusion driven by annexin 7. J Biol Chem (2002) 0.86

Articles by these authors

The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20

Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69

Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36

Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39

Unlocking the secrets of the genome. Nature (2009) 11.80

Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78

The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56

A standard variation file format for human genome sequences. Genome Biol (2010) 7.83

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res (2002) 6.65

A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet (2003) 5.34

Gramene: a growing plant comparative genomics resource. Nucleic Acids Res (2007) 4.59

The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci (2011) 4.16

WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87

Gramene: a resource for comparative grass genomics. Nucleic Acids Res (2002) 3.72

Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res (2006) 3.47

A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet (2010) 3.25

Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. Cancer Cell (2011) 2.56

Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics (2005) 2.48

WormBase 2014: new views of curated biology. Nucleic Acids Res (2013) 2.39

Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) (2012) 2.35

SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics (2005) 2.34

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res (2008) 2.28

Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genomics (2002) 2.16

Gramene 2013: comparative plant genomics resources. Nucleic Acids Res (2013) 2.08

CMap 1.01: a comparative mapping application for the Internet. Bioinformatics (2009) 2.03

Evolution of Arabidopsis microRNA families through duplication events. Genome Res (2006) 1.96

Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet (2005) 1.93

Recommendations of the 2006 Human Variome Project meeting. Nat Genet (2007) 1.90

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol (2005) 1.84

Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform (2008) 1.80

Cancer genomics: technology, discovery, and translation. J Clin Oncol (2012) 1.70

Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69

Towards patient-based cancer therapeutics. Nat Biotechnol (2010) 1.63

Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinformatics (2014) 1.62

Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res (2006) 1.62

A network module-based method for identifying cancer prognostic signatures. Genome Biol (2012) 1.61

PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics (2011) 1.44

Bile exposure inhibits expression of squamous differentiation genes in human esophageal epithelial cells. Ann Surg (2012) 1.40

Maize-targeted mutagenesis: A knockout resource for maize. Proc Natl Acad Sci U S A (2003) 1.35

Subthreshold symptoms of depression in preadolescent girls are stable and predictive of depressive disorders. J Am Acad Child Adolesc Psychiatry (2008) 1.33

Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol (2006) 1.31

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement). DNA Res (2002) 1.29

CD14(high)CD16(+) rather than CD14(low)CD16(+) monocytes correlate with disease progression in chronic HIV-infected patients. J Acquir Immune Defic Syndr (2009) 1.29

Gramene QTL database: development, content and applications. Database (Oxford) (2009) 1.25

InterMOD: integrated data and tools for the unification of model organism research. Sci Rep (2013) 1.23

The PANE1 gene encodes a novel human minor histocompatibility antigen that is selectively expressed in B-lymphoid cells and B-CLL. Blood (2006) 1.17

PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol (2015) 1.17

Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics (2011) 1.17

Irradiation stability and cytotoxicity of gold nanoparticles for radiotherapy. Int J Nanomedicine (2009) 1.15

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol (2008) 1.14

A method for generation phage cocktail with great therapeutic potential. PLoS One (2012) 1.12

Impact of oppositional defiant disorder dimensions on the temporal ordering of conduct problems and depression across childhood and adolescence in girls. J Child Psychol Psychiatry (2011) 1.10

Species trees from highly incongruent gene trees in rice. Syst Biol (2009) 1.10

The systematic annotation of the three main GPCR families in Reactome. Database (Oxford) (2010) 1.09

Improving the chemical stability of amorphous solid dispersion with cocrystal technique by hot melt extrusion. Pharm Res (2011) 1.09

ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Res (2003) 1.08

Depression begets depression: comparing the predictive utility of depression and anxiety symptoms to later depression. J Child Psychol Psychiatry (2009) 1.08

LysGH15, a novel bacteriophage lysin, protects a murine bacteremia model efficiently against lethal methicillin-resistant Staphylococcus aureus infection. J Clin Microbiol (2010) 1.07

Evidence-based gene predictions in plant genomes. Genome Res (2009) 1.06

Comparison of genes among cereals. Curr Opin Plant Biol (2003) 1.05

SOD1, ANG, TARDBP and FUS mutations in amyotrophic lateral sclerosis: a United States clinical testing lab experience. Amyotroph Lateral Scler (2012) 0.99

Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiol (2004) 0.98

Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J (2010) 0.97

Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans. J Biol Chem (2005) 0.96

Linkage disequilibrium mapping of the replicated type 2 diabetes linkage signal on chromosome 1q. Diabetes (2009) 0.95

Early G₁ cyclin-dependent kinases as prognostic markers and potential therapeutic targets in esophageal adenocarcinoma. Clin Cancer Res (2011) 0.94

Complete genome sequence of Staphylococcus aureus bacteriophage GH15. J Virol (2012) 0.94

Panzea: an update on new content and features. Nucleic Acids Res (2007) 0.94

Potential of a suite of robot/computer-assisted motivating systems for personalized, home-based, stroke rehabilitation. J Neuroeng Rehabil (2007) 0.94

Using the reactome database. Curr Protoc Bioinformatics (2012) 0.93

Persistent homology for the quantitative prediction of fullerene stability. J Comput Chem (2014) 0.93

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics (2006) 0.93

Dantrolene: effects on abnormal intracellular Ca(2+) handling and inotropy in postinfarcted rat myocardium. Eur J Pharmacol (2003) 0.92

A novel approach for high-quality microarray processing using third-dye array visualization technology. IEEE Trans Nanobioscience (2003) 0.90

LysGH15 reduces the inflammation caused by lethal methicillin-resistant Staphylococcus aureus infection in mice. Bioeng Bugs (2011) 0.89

Overexpression of Na+/Ca2+ exchanger gene attenuates postinfarction myocardial dysfunction. Am J Physiol Heart Circ Physiol (2002) 0.88

Force-generation capacity of single vastus lateralis muscle fibers and physical function decline with age in African green vervet monkeys. J Gerontol A Biol Sci Med Sci (2012) 0.88

Selection of serotype-specific vaccine candidate genes in Actinobacillus pleuropneumoniae and heterologous immunization with Propionibacterium acnes. Vaccine (2008) 0.87

Chemoselective asymmetric N-allylic alkylation of indoles with Morita-Baylis-Hillman carbonates. Angew Chem Int Ed Engl (2009) 0.86

Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells. Breast Cancer Res (2012) 0.85

Children's affect expression and frontal EEG asymmetry: transactional associations with mothers' depressive symptoms. J Abnorm Child Psychol (2007) 0.85

Epidemiological survey and risk factor analysis of fatty liver disease of adult residents, Beijing, China. J Gastroenterol Hepatol (2013) 0.85

Fetal functional capabilities in response to maternal hypertonicity associated with altered central and peripheral angiotensinogen mRNA in rats. Peptides (2007) 0.84

Maternal quercetin administration during gestation and lactation decrease endoplasmic reticulum stress and related inflammation in the adult offspring of obese female rats. Eur J Nutr (2014) 0.83

Lack of assertion, peer victimization, and risk for depression in girls: testing a diathesis-stress model. J Adolesc Health (2010) 0.83

Identification of critical genes in microarray experiments by a Neuro-Fuzzy approach. Comput Biol Chem (2006) 0.83

Continuous production of fenofibrate solid lipid nanoparticles by hot-melt extrusion technology: a systematic study based on a quality by design approach. AAPS J (2014) 0.82

Expression of recombinant human lysozyme-tachyplesin I (hLYZ-TP I) in Pichia pastoris and analysis of antibacterial activity. Biomed Environ Sci (2013) 0.82

A semimetal bismuth element as a direct plasmonic photocatalyst. Chem Commun (Camb) (2014) 0.82

Multiscale geometric modeling of macromolecules I: Cartesian representation. J Comput Phys (2014) 0.81

Fructus Ligustri Lucidi (FLL) ethanol extract increases bone mineral density and improves bone properties in growing female rats. J Bone Miner Metab (2013) 0.81

Different transcriptional profiles of RAW264.7 infected with Mycobacterium tuberculosis H37Rv and BCG identified via deep sequencing. PLoS One (2012) 0.81

Geometries and electronic structures of metastable C2N4 and its ions. Spectrochim Acta A Mol Biomol Spectrosc (2006) 0.81

Genomic characterization of lytic Staphylococcus aureus phage GH15: providing new clues to intron shift in phages. J Gen Virol (2012) 0.80

Subtractive screening with the Mycobacterium tuberculosis surface protein phage display library. Tuberculosis (Edinb) (2011) 0.80

Specific humoral immune response induced by propionibacterium acnes can prevent Actinobacillus pleuropneumoniae infection in mice. Clin Vaccine Immunol (2014) 0.80