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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!
Protein profiles associated with context fear conditioning and their modulation by memantine. Ahmed MM, Dhanasekaran AR, Block A, Tong S, Costa AC, Gardiner KJ (2014) Mol. Cell Proteomics 4(13). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Protein profiles associated with context fear conditioning and their modulation by memantine.
Ahmed MM, Dhanasekaran AR, Block A, Tong S, Costa AC, Gardiner KJ (2014) Mol. Cell Proteomics 4(13).
 
Cytoscape cited!
Molecular characterization of the evolution of phagosomes. Boulais J, Trost M, Landry CR, Dieckmann R, Levy ED, Soldati T, Michnick SW, Thibault P, Desjardins M (2010) Mol. Syst. Biol. (6). - http://cytoscape-publications.tumblr.com/post...
Molecular characterization of the evolution of phagosomes.
Boulais J, Trost M, Landry CR, Dieckmann R, Levy ED, Soldati T, Michnick SW, Thibault P, Desjardins M (2010) Mol. Syst. Biol. (6).
Crtc1 activates a transcriptional program deregulated at early Alzheimer’s disease-related stages. Parra-Damas A, Valero J, Chen M, España J, Martín E, Ferrer I, Rodríguez-Alvarez J, Saura CA (2014) J. Neurosci. 17(34). ClueGO at the Cytoscape App Store - http://cytoscape-publications.tumblr.com/post...
Crtc1 activates a transcriptional program deregulated at early Alzheimer’s disease-related stages.
Parra-Damas A, Valero J, Chen M, España J, Martín E, Ferrer I, Rodríguez-Alvarez J, Saura CA (2014) J. Neurosci. 17(34).
 
ClueGO at the Cytoscape App Store
Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks. Swamidass SJ, Schillebeeckx CN, Matlock M, Hurle MR, Agarwal P (2014) J Biomol Screen 5(19). - http://cytoscape-publications.tumblr.com/post...
Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks.
Swamidass SJ, Schillebeeckx CN, Matlock M, Hurle MR, Agarwal P (2014) J Biomol Screen 5(19).
MicroRNA Regulation of Bovine Monocyte Inflammatory and Metabolic Networks in an In Vivo Infection Model. Lawless N, Reinhardt TA, Bryan K, Baker M, Pesch B, Zimmerman D, Zuelke K, Sonstegard T, O’Farrelly C, Lippolis JD, Lynn DJ (2014) G3 (Bethesda) 6(4). cytoHubba at the Cytoscape App Store jActiveModules at the Cytoscape App Store Cytoscape... - http://cytoscape-publications.tumblr.com/post...
MicroRNA Regulation of Bovine Monocyte Inflammatory and Metabolic Networks in an In Vivo Infection Model.
Lawless N, Reinhardt TA, Bryan K, Baker M, Pesch B, Zimmerman D, Zuelke K, Sonstegard T, O’Farrelly C, Lippolis JD, Lynn DJ (2014) G3 (Bethesda) 6(4).
 
cytoHubba at the Cytoscape App Store
jActiveModules at the Cytoscape App Store
Cytoscape cited!
Maritime route of colonization of Europe Paschou et al, PNAS, Jun 2014. - http://cytoscape-publications.tumblr.com/post...
Maritime route of colonization of Europe
Paschou et al, PNAS, Jun 2014.
A distinct set of long non-coding RNAs in childhood MLL-rearranged acute lymphoblastic leukemia: biology and epigenetic target. Fang K, Han BW, Chen ZH, Lin KY, Zeng CW, Li XJ, Li JH, Luo XQ, Chen YQ (2014) Hum. Mol. Genet. 12(23). BINGO at the Cytoscape App Store - http://cytoscape-publications.tumblr.com/post...
A distinct set of long non-coding RNAs in childhood MLL-rearranged acute lymphoblastic leukemia: biology and epigenetic target.
Fang K, Han BW, Chen ZH, Lin KY, Zeng CW, Li XJ, Li JH, Luo XQ, Chen YQ (2014) Hum. Mol. Genet. 12(23).
BINGO at the Cytoscape App Store
Leucine-Rich Repeat Kinase 2 Binds to Neuronal Vesicles through Protein Interactions Mediated by Its C-Terminal WD40 Domain. Piccoli G, Onofri F, Cirnaru MD, Kaiser CJ, Jagtap P, Kastenmüller A, Pischedda F, Marte A, von Zweydorf F, Vogt A, Giesert F, Pan L, Antonucci F, Kiel C, Zhang M, Weinkauf S, Sattler M, Sala C, Matteoli M, Ueffing M,... - http://cytoscape-publications.tumblr.com/post...
Leucine-Rich Repeat Kinase 2 Binds to Neuronal Vesicles through Protein Interactions Mediated by Its C-Terminal WD40 Domain.
Piccoli G, Onofri F, Cirnaru MD, Kaiser CJ, Jagtap P, Kastenmüller A, Pischedda F, Marte A, von Zweydorf F, Vogt A, Giesert F, Pan L, Antonucci F, Kiel C, Zhang M, Weinkauf S, Sattler M, Sala C, Matteoli M, Ueffing M, Gloeckner CJ (2014) Mol. Cell. Biol. 12(34).
 
Cytoscape cited!
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. Leung A, Bader GD, Reimand J (2014) Bioinformatics (). HyperModules at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery.
Leung A, Bader GD, Reimand J (2014) Bioinformatics ().
 
HyperModules at the Cytoscape App Store 
Cytoscape cited!
Knockdown of a Zebrafish Aryl Hydrocarbon Receptor Repressor (AHRRa) Affects Expression of Genes Related to Photoreceptor Development and Hematopoiesis. Aluru N, Jenny MJ, Hahn ME (2014) Toxicol. Sci. 2(139). jActiveModules at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Knockdown of a Zebrafish Aryl Hydrocarbon Receptor Repressor (AHRRa) Affects Expression of Genes Related to Photoreceptor Development and Hematopoiesis.
Aluru N, Jenny MJ, Hahn ME (2014) Toxicol. Sci. 2(139).
 
jActiveModules at the Cytoscape App Store
 
Cytoscape cited!
Combinatorial therapy discovery using mixed integer linear programming. Pang K, Wan YW, Choi WT, Donehower LA, Sun J, Pant D, Liu Z (2014) Bioinformatics 10(30). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Combinatorial therapy discovery using mixed integer linear programming.
Pang K, Wan YW, Choi WT, Donehower LA, Sun J, Pant D, Liu Z (2014) Bioinformatics 10(30).
Cytoscape cited!
Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach. Li Y, Liang C, Wong KC, Jin K, Zhang Z (2014) Nucleic Acids Res. (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach.
Li Y, Liang C, Wong KC, Jin K, Zhang Z (2014) Nucleic Acids Res. ().
Cytoscape cited!
Network analysis of inflammatory genes and their transcriptional regulators in coronary artery disease. Nair J, Ghatge M, Kakkar VV, Shanker J (2014) PLoS ONE 4(9). NetworkAnalyzer at Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Network analysis of inflammatory genes and their transcriptional regulators in coronary artery disease.
Nair J, Ghatge M, Kakkar VV, Shanker J (2014) PLoS ONE 4(9).
 
NetworkAnalyzer at Cytoscape App Store 
Cytoscape cited!
Multiple Omics Uncovers Host–Gut Microbial Mutualism During Prebiotic Fructooligosaccharide Supplementation Kato T, Fukuda S, Fujiwara A, Suda W, Hattori M, Kikuchi J, Ohno H (2014) DNA Research Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Multiple Omics Uncovers Host–Gut Microbial Mutualism During Prebiotic Fructooligosaccharide Supplementation
Kato T, Fukuda S, Fujiwara A, Suda W, Hattori M, Kikuchi J, Ohno H (2014) DNA Research 
 
Cytoscape cited!
Modeling the Transcriptional Regulatory Network That Controls the Early Hypoxic Response in Candida albicans. Sellam A, van Het Hoog M, Tebbji F, Beaurepaire C, Whiteway M, Nantel A (2014) Eukaryotic Cell 5(13). EnrichmentMap at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Modeling the Transcriptional Regulatory Network That Controls the Early Hypoxic Response in Candida albicans.
Sellam A, van Het Hoog M, Tebbji F, Beaurepaire C, Whiteway M, Nantel A (2014) Eukaryotic Cell 5(13).
EnrichmentMap at the Cytoscape App Store
Cytoscape cited!
TRIM65 regulates microRNA activity by ubiquitination of TNRC6. Li S, Wang L, Fu B, Berman MA, Diallo A, Dorf ME (2014) Proc. Natl. Acad. Sci. U.S.A. 19(111). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
TRIM65 regulates microRNA activity by ubiquitination of TNRC6.
Li S, Wang L, Fu B, Berman MA, Diallo A, Dorf ME (2014) Proc. Natl. Acad. Sci. U.S.A. 19(111).
Cytoscape cited!
Evolutionary history of redox metal-binding domains across the tree of life. Harel A, Bromberg Y, Falkowski PG, Bhattacharya D (2014) Proc. Natl. Acad. Sci. U.S.A. 19(111). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Evolutionary history of redox metal-binding domains across the tree of life.
Harel A, Bromberg Y, Falkowski PG, Bhattacharya D (2014) Proc. Natl. Acad. Sci. U.S.A. 19(111).
Cytoscape cited!
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