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Cytoscape

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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!
Serum metabolomics identifies citrulline as a predictor of adverse outcomes in an equine model of gut-derived sepsis. Steelman SM, Johnson P, Jackson A, Schulze J, Chowdhary BP (2014) Physiol. Genomics 10(46). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Serum metabolomics identifies citrulline as a predictor of adverse outcomes in an equine model of gut-derived sepsis.
Steelman SM, Johnson P, Jackson A, Schulze J, Chowdhary BP (2014) Physiol. Genomics 10(46).
Cytoscape cited!
Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections. Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S (2014) J. Virol. 11(88). CyTargetLinker at the Cytoscape App Store... - http://cytoscape-publications.tumblr.com/post...
Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections.
Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S (2014) J. Virol. 11(88).
 
CyTargetLinker at the Cytoscape App Store
 
Cytoscape cited!
Disease Risk Factors Identified Through Shared Genetic Architecture and Electronic Medical Records Li et al, Science Translational Medicine, 30 April 2014 Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Disease Risk Factors Identified Through Shared Genetic Architecture and Electronic Medical Records
 
Li et al, Science Translational Medicine, 30 April 2014
Cytoscape cited!
A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection. Siddle KJ, Deschamps M, Tailleux L, Nédélec Y, Pothlichet J, Lugo-Villarino G, Libri V, Gicquel B, Neyrolles O, Laval G, Patin E, Barreiro LB, Quintana-Murci L (2014) Genome Res. (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection.
Siddle KJ, Deschamps M, Tailleux L, Nédélec Y, Pothlichet J, Lugo-Villarino G, Libri V, Gicquel B, Neyrolles O, Laval G, Patin E, Barreiro LB, Quintana-Murci L (2014) Genome Res. ().
Cytoscape cited!
A Second-generation Protein-Protein Interaction Network of Helicobacter pylori. Häuser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P (2014) Mol. Cell Proteomics (). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
A Second-generation Protein-Protein Interaction Network of Helicobacter pylori.
Häuser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P (2014) Mol. Cell Proteomics ().
Cytoscape cited!
Phenol Soluble Modulin Variants of Community-Associated Methicillin-Resistant Staphylococcus aureus Captured Using Mass Spectrometry-Based Molecular Networking. Gonzalez DJ, Vuong L, Gonzalez IS, Keller N, McGrosso D, Hwang HK, Hung J, Zinkernagel AS, Dixon JE, Dorrestein PC, Nizet V (2014) Mol. Cell Proteomics (). - http://cytoscape-publications.tumblr.com/post...
Phenol Soluble Modulin Variants of Community-Associated Methicillin-Resistant Staphylococcus aureus Captured Using Mass Spectrometry-Based Molecular Networking.
Gonzalez DJ, Vuong L, Gonzalez IS, Keller N, McGrosso D, Hwang HK, Hung J, Zinkernagel AS, Dixon JE, Dorrestein PC, Nizet V (2014) Mol. Cell Proteomics ().
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!
MetDisease—connecting metabolites to diseases via literature. Duren W, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A (2014) Bioinformatics (). MetDisease at the Cytoscape App Store Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
MetDisease—connecting metabolites to diseases via literature.
Duren W, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A (2014) Bioinformatics ().
MetDisease at the Cytoscape App Store
Cytoscape cited!
Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates. Shi L, Ji B, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E, Mijakovic I (2014) Genome Biol Evol 4(6). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.
Shi L, Ji B, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E, Mijakovic I (2014) Genome Biol Evol 4(6).
Cytoscape cited!
A systems biology approach identifies effective tumor-stroma common targets for oral squamous cell carcinoma. Meng W, Wu Y, He X, Liu C, Gao Q, Ge L, Wu L, Liu Y, Guo Y, Li X, Liu Y, Chen S, Kong X, Liang Z, Zhou H (2014) Cancer Res. 8(74). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
A systems biology approach identifies effective tumor-stroma common targets for oral squamous cell carcinoma.
Meng W, Wu Y, He X, Liu C, Gao Q, Ge L, Wu L, Liu Y, Guo Y, Li X, Liu Y, Chen S, Kong X, Liang Z, Zhou H (2014) Cancer Res. 8(74).
Cytoscape cited!
Metabolic characterization of hepatocellular carcinoma using nontargeted tissue metabolomics. Huang Q, Tan Y, Yin P, Ye G, Gao P, Lu X, Wang H, Xu G (2013) Cancer Res. 16(73). - http://cytoscape-publications.tumblr.com/post...
Metabolic characterization of hepatocellular carcinoma using nontargeted tissue metabolomics.
Huang Q, Tan Y, Yin P, Ye G, Gao P, Lu X, Wang H, Xu G (2013) Cancer Res. 16(73).
SIRT1 is a Highly Networked Protein That Mediates the Adaptation to Chronic Physiological Stress. McBurney MW, Clark-Knowles KV, Caron AZ, Gray DA (2013) Genes Cancer 3-4(4). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
SIRT1 is a Highly Networked Protein That Mediates the Adaptation to Chronic Physiological Stress.
McBurney MW, Clark-Knowles KV, Caron AZ, Gray DA (2013) Genes Cancer 3-4(4).
Cytoscape cited!
The gene vitellogenin affects microRNA regulation in honey bee (Apis mellifera) fat body and brain. Nunes FM, Ihle KE, Mutti NS, Simões ZL, Amdam GV (2013) J. Exp. Biol. Pt 19(216). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
The gene vitellogenin affects microRNA regulation in honey bee (Apis mellifera) fat body and brain.
Nunes FM, Ihle KE, Mutti NS, Simões ZL, Amdam GV (2013) J. Exp. Biol. Pt 19(216).
 
Cytoscape cited!
Shrinking the FadE Proteome of Mycobacterium tuberculosis: Insights into Cholesterol Metabolism through Identification of an α2β2 Heterotetrameric Acyl Coenzyme A Dehydrogenase Family. Wipperman MF, Yang M, Thomas ST, Sampson NS (2013) J. Bacteriol. 19(195). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Shrinking the FadE Proteome of Mycobacterium tuberculosis: Insights into Cholesterol Metabolism through Identification of an α2β2 Heterotetrameric Acyl Coenzyme A Dehydrogenase Family.
Wipperman MF, Yang M, Thomas ST, Sampson NS (2013) J. Bacteriol. 19(195).
 
Cytoscape cited!
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