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Cytoscape

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The exocyst and regulatory GTPases in urinary exosomes. Chacon-Heszele MF, Choi SY, Zuo X, Baek JI, Ward C, Lipschutz JH (2014) Physiol Rep 8(2). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
The exocyst and regulatory GTPases in urinary exosomes.
Chacon-Heszele MF, Choi SY, Zuo X, Baek JI, Ward C, Lipschutz JH (2014) Physiol Rep 8(2).
Cytoscape cited!
Quantifying the underlying landscape and paths of cancer. Li C, Wang J (2014) J R Soc Interface 100(11). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Quantifying the underlying landscape and paths of cancer.
Li C, Wang J (2014) J R Soc Interface 100(11).
Cytoscape cited!
Gene expression profiles of entorhinal cortex in Alzheimer’s disease. Ding B, Xi Y, Gao M, Li Z, Xu C, Fan S, He W (2014) Am J Alzheimers Dis Other Demen 6(29). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Gene expression profiles of entorhinal cortex in Alzheimer’s disease.
Ding B, Xi Y, Gao M, Li Z, Xu C, Fan S, He W (2014) Am J Alzheimers Dis Other Demen 6(29).
Cytoscape cited!
cddApp: A Cytoscape App for Accessing the NCBI Conserved Domain Database. Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE (2014) Bioinformatics (). cddApp at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
cddApp: A Cytoscape App for Accessing the NCBI Conserved Domain Database.
Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE (2014) Bioinformatics ().
cddApp at the Cytoscape App Store 
Cytoscape cited!
Extracting patterns of database and software usage from the bioinformatics literature. Duck G, Nenadic G, Brass A, Robertson DL, Stevens R (2014) Bioinformatics 17(30). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Extracting patterns of database and software usage from the bioinformatics literature.
Duck G, Nenadic G, Brass A, Robertson DL, Stevens R (2014) Bioinformatics 17(30).
Cytoscape cited!
Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Jachiet PA, Colson P, Lopez P, Bapteste E (2014) Genome Biol Evol 9(6). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network.
Jachiet PA, Colson P, Lopez P, Bapteste E (2014) Genome Biol Evol 9(6).
Cytoscape cited!
Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks. Winterhalter C, Nicolle R, Louis A, To C, Radvanyi F, Elati M (2014) Bioinformatics (). Cytoscape cited! PEPPER at the Cytoscape App Store - http://cytoscape-publications.tumblr.com/post...
Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks.
Winterhalter C, Nicolle R, Louis A, To C, Radvanyi F, Elati M (2014) Bioinformatics ().
 
Cytoscape cited!
 
PEPPER at the Cytoscape App Store
Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB. Polito VA, Li H, Martini-Stoica H, Wang B, Yang L, Xu Y, Swartzlander DB, Palmieri M, di Ronza A, Lee VM, Sardiello M, Ballabio A, Zheng H (2014) EMBO Mol Med 9(6). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB.
Polito VA, Li H, Martini-Stoica H, Wang B, Yang L, Xu Y, Swartzlander DB, Palmieri M, di Ronza A, Lee VM, Sardiello M, Ballabio A, Zheng H (2014) EMBO Mol Med 9(6).
Cytoscape cited!
Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. Cheng F, Zhao Z (2014) J Am Med Inform Assoc (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties.
Cheng F, Zhao Z (2014) J Am Med Inform Assoc ().
Cytoscape cited!
Vitamin C deficiency improves somatic embryo development through distinct gene regulatory networks in Arabidopsis. Becker MG, Chan A, Mao X, Girard IJ, Lee S, Mohamed E, Stasolla C, Belmonte MF (2014) J. Exp. Bot. (). - http://cytoscape-publications.tumblr.com/post...
Vitamin C deficiency improves somatic embryo development through distinct gene regulatory networks in Arabidopsis.
Becker MG, Chan A, Mao X, Girard IJ, Lee S, Mohamed E, Stasolla C, Belmonte MF (2014) J. Exp. Bot. ().
DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal. Britton S, Dernoncourt E, Delteil C, Froment C, Schiltz O, Salles B, Frit P, Calsou P (2014) Nucleic Acids Res. 14(42). - http://cytoscape-publications.tumblr.com/post...
DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal.
Britton S, Dernoncourt E, Delteil C, Froment C, Schiltz O, Salles B, Frit P, Calsou P (2014) Nucleic Acids Res. 14(42).
The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington’s disease. Butland SL, Sanders SS, Schmidt ME, Riechers SP, Lin DT, Martin DD, Vaid K, Graham RK, Singaraja RR, Wanker EE, Conibear E, Hayden MR (2014) Hum. Mol. Genet. 15(23). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington’s disease.
Butland SL, Sanders SS, Schmidt ME, Riechers SP, Lin DT, Martin DD, Vaid K, Graham RK, Singaraja RR, Wanker EE, Conibear E, Hayden MR (2014) Hum. Mol. Genet. 15(23).
 
Cytoscape cited!
Influence of DNA extraction methods, 16S rRNA targeted hypervariable regions and sample origins on the microbial diversity detected by 454 pyrosequencing in marine chemosynthetic ecosystems. Cruaud P, Vigneron A, Lucchetti-Miganeh C, Ciron PE, Godfroy A, Cambon-Bonavita MA (2014) Appl. Environ. Microbiol. (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Influence of DNA extraction methods, 16S rRNA targeted hypervariable regions and sample origins on the microbial diversity detected by 454 pyrosequencing in marine chemosynthetic ecosystems.
Cruaud P, Vigneron A, Lucchetti-Miganeh C, Ciron PE, Godfroy A, Cambon-Bonavita MA (2014) Appl. Environ. Microbiol. ().
Cytoscape cited!
Cellulolytic Streptomyces strains associated with herbivorous insects share a phylogenetically-linked capacity for the degradation of lignocellulose. Book AJ, Lewin GR, McDonald BR, Takasuka TE, Doering DT, Adams AS, Blodgett JA, Clardy J, Raffa KF, Fox BG, Currie CR (2014) Appl. Environ. Microbiol. (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Cellulolytic Streptomyces strains associated with herbivorous insects share a phylogenetically-linked capacity for the degradation of lignocellulose.
Book AJ, Lewin GR, McDonald BR, Takasuka TE, Doering DT, Adams AS, Blodgett JA, Clardy J, Raffa KF, Fox BG, Currie CR (2014) Appl. Environ. Microbiol. ().
Cytoscape cited!
Early Targets of miR-34a in Neuroblastoma. De Antonellis P, Carotenuto M, Vandenbussche J, De Vita G, Ferrucci V, Medaglia C, Boffa I, Galiero A, Di Somma S, Magliulo D, Aiese N, Alonzi A, Spano D, Liguori L, Chiarolla C, Verrico A, Schulte JH, Mestdagh P, Vandesompele J, Gevaert K, Zollo M (2014) Mol. Cell Proteomics 8(13). Cytoscape cited! MiMI... - http://cytoscape-publications.tumblr.com/post...
Early Targets of miR-34a in Neuroblastoma.
De Antonellis P, Carotenuto M, Vandenbussche J, De Vita G, Ferrucci V, Medaglia C, Boffa I, Galiero A, Di Somma S, Magliulo D, Aiese N, Alonzi A, Spano D, Liguori L, Chiarolla C, Verrico A, Schulte JH, Mestdagh P, Vandesompele J, Gevaert K, Zollo M (2014) Mol. Cell Proteomics 8(13).
 
Cytoscape cited!
 
MiMI App at the Cytoscape App Store
Systems-level perspective of sudden infant death syndrome. Salomonis, Pediatr Res. 2014 Jun 25. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Systems-level perspective of sudden infant death syndrome.
Salomonis, Pediatr Res. 2014 Jun 25.
 
Cytoscape cited!
The intra viral protein interaction network of hepatitis C virus. Hagen N, Bayer K, Roesch K, Schindler M (2014) Mol. Cell Proteomics (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
The intra viral protein interaction network of hepatitis C virus.
Hagen N, Bayer K, Roesch K, Schindler M (2014) Mol. Cell Proteomics ().
Cytoscape cited!
Meta-Analysis of Retrograde Signaling in Arabidopsis thaliana Reveals a Core Module of Genes Embedded in Complex Cellular Signaling Networks. Gläßer C, Haberer G, Finkemeier I, Pfannschmidt T, Kleine T, Leister D, Dietz KJ, Häusler RE, Grimm B, Mayer KF (2014) Mol Plant 7(7). - http://cytoscape-publications.tumblr.com/post...
Meta-Analysis of Retrograde Signaling in Arabidopsis thaliana Reveals a Core Module of Genes Embedded in Complex Cellular Signaling Networks.
Gläßer C, Haberer G, Finkemeier I, Pfannschmidt T, Kleine T, Leister D, Dietz KJ, Häusler RE, Grimm B, Mayer KF (2014) Mol Plant 7(7).
Correcting for link loss in causal network inference caused by regulator interference. Wang Y, Penfold CA, Hodgson DA, Gifford ML, Burroughs NJ (2014) Bioinformatics (). - http://cytoscape-publications.tumblr.com/post...
Correcting for link loss in causal network inference caused by regulator interference.
Wang Y, Penfold CA, Hodgson DA, Gifford ML, Burroughs NJ (2014) Bioinformatics ().
A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation. Tomaru Y, Hasegawa R, Suzuki T, Sato T, Kubosaki A, Suzuki M, Kawaji H, Forrest AR, Hayashizaki Y, , Shin JW, Suzuki H (2014) Nucleic Acids Res. (). - http://cytoscape-publications.tumblr.com/post...
A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.
Tomaru Y, Hasegawa R, Suzuki T, Sato T, Kubosaki A, Suzuki M, Kawaji H, Forrest AR, Hayashizaki Y, , Shin JW, Suzuki H (2014) Nucleic Acids Res. ().
GeneMANIA: Fast gene network construction and function prediction for Cytoscape Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q   F1000Research 2014, 3:153 GeneMANIA at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q   F1000Research 2014, 3:153
 
GeneMANIA at the Cytoscape App Store
 
Cytoscape cited!
KEGGscape: a Cytoscape app for pathway data integration Nishida K, Ono K, Kanaya S, Takahashi K  F1000Research 2014, 3:144 KEGGscape at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
KEGGscape: a Cytoscape app for pathway data integration
Nishida K, Ono K, Kanaya S, Takahashi K  F1000Research 2014, 3:144
 
KEGGscape at the Cytoscape App Store
 
Cytoscape cited!
ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysisWu G, Eric Dawson, Duong A, Haw R, Stein L  F1000Research 2014, 3:146 ReactomeFIViz at the Cytoscape App Store - http://cytoscape-publications.tumblr.com/post...
ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysisWu G, Eric Dawson, Duong A, Haw R, Stein L  
F1000Research 2014, 3:146
 
ReactomeFIViz at the Cytoscape App Store
WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization Kutmon M, Lotia S, Evelo CT, Pico AR  F1000Research 2014, 3:151 WikiPathways at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization
Kutmon M, Lotia S, Evelo CT, Pico AR  F1000Research 2014, 3:151
 
WikiPathways at the Cytoscape App Store
 
Cytoscape cited!
MetaImprint: an information repository of mammalian imprinted genes. Wei Y, Su J, Liu H, Lv J, Wang F, Yan H, Wen Y, Liu H, Wu Q, Zhang Y (2014) Development 12(141). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
MetaImprint: an information repository of mammalian imprinted genes.
Wei Y, Su J, Liu H, Lv J, Wang F, Yan H, Wen Y, Liu H, Wu Q, Zhang Y (2014) Development 12(141).
 
Cytoscape cited!
Supertrees Based on the Subtree Prune-and-Regraft Distance. Whidden C, Zeh N, Beiko RG (2014) Syst. Biol. 4(63). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Supertrees Based on the Subtree Prune-and-Regraft Distance.
Whidden C, Zeh N, Beiko RG (2014) Syst. Biol. 4(63).
 
Cytoscape cited!
Steady-state hydrogen peroxide induces glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa. Deng X, Liang H, Ulanovskaya OA, Ji Q, Zhou T, Sun F, Lu Z, Hutchison AL, Lan L, Wu M, Cravatt BF, He C (2014) J. Bacteriol. (). EnrichmentMap at the Cytoscape App Store - http://cytoscape-publications.tumblr.com/post...
Steady-state hydrogen peroxide induces glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa.
Deng X, Liang H, Ulanovskaya OA, Ji Q, Zhou T, Sun F, Lu Z, Hutchison AL, Lan L, Wu M, Cravatt BF, He C (2014) J. Bacteriol. ().
 
EnrichmentMap at the Cytoscape App Store
Asymmetric Evolution of Human Transcription Factor Regulatory Networks. Zhou Z, Zhou J, Su Z, Gu X (2014) Mol. Biol. Evol. (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Asymmetric Evolution of Human Transcription Factor Regulatory Networks.
Zhou Z, Zhou J, Su Z, Gu X (2014) Mol. Biol. Evol. ().
 
Cytoscape cited!
Comparative Genomics of Mammalian Hibernators Using Gene Networks. Villanueva-Cañas JL, Faherty SL, Yoder AD, Albà MM (2014) Integr. Comp. Biol. (). GeneMANIA app at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Comparative Genomics of Mammalian Hibernators Using Gene Networks.
Villanueva-Cañas JL, Faherty SL, Yoder AD, Albà MM (2014) Integr. Comp. Biol. ().
 
GeneMANIA app at the Cytoscape App Store 
Cytoscape cited!
A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana. Lindemose S, Jensen MK, de Velde JV, O’Shea C, Heyndrickx KS, Workman CT, Vandepoele K, Skriver K, Masi FD (2014) Nucleic Acids Res. (). nodeCharts app at the Cytoscape AppStore Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana.
Lindemose S, Jensen MK, de Velde JV, O’Shea C, Heyndrickx KS, Workman CT, Vandepoele K, Skriver K, Masi FD (2014) Nucleic Acids Res. ().
 
nodeCharts app at the Cytoscape AppStore 
Cytoscape cited!
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