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Cytoscape

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Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Gitter et al, Genome Res. 2013 Feb;23(2):365-76. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Linking the signaling cascades and dynamic regulatory networks controlling stress responses.
Gitter et al, Genome Res. 2013 Feb;23(2):365-76. 
 
Cytoscape cited!
Gene Regulation of Carbon Fixation, Storage, and Utilization in the Diatom Phaeodactylum tricornutum Acclimated to Light/Dark Cycles. Chauton et al, Plant Physiol. 2013 Feb;161(2):1034-48. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Gene Regulation of Carbon Fixation, Storage, and Utilization in the Diatom Phaeodactylum tricornutum Acclimated to Light/Dark Cycles.
Chauton et al, Plant Physiol. 2013 Feb;161(2):1034-48.
 
Cytoscape cited!
Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks. Matsui et al, Genome Biol Evol. 2013 Jan;5(2):267-82. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks.
Matsui et al, Genome Biol Evol. 2013 Jan;5(2):267-82.
 
Cytoscape cited!
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. Feldmann et al, Nucleic Acids Res. 2013 Feb 7. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells.
Feldmann et al, Nucleic Acids Res. 2013 Feb 7.
 
Cytoscape cited!
SIRT1 is a Highly Networked Protein That Mediates the Adaptation to Chronic Physiological Stress McBurney et al, Genes & Cancer February 7, 2013. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
SIRT1 is a Highly Networked Protein That Mediates the Adaptation to Chronic Physiological Stress
McBurney et al, Genes & Cancer February 7, 2013.
 
Cytoscape cited!
The Relationship Between Long-Range Chromatin Occupancy and Polymerization of the Drosophila ETS Family Transcriptional Repressor Yan. Webber et al, Genetics. 2013 Feb;193(2):633-49. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
The Relationship Between Long-Range Chromatin Occupancy and Polymerization of the Drosophila ETS Family Transcriptional Repressor Yan.
Webber et al, Genetics. 2013 Feb;193(2):633-49.
 
Cytoscape cited!
Saccharomyces cerevisiae Genetics Predicts Candidate Therapeutic Genetic Interactions at the Mammalian Replication Fork. van Pel et al, G3 (Bethesda). 2013 Feb;3(2):273-82. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Saccharomyces cerevisiae Genetics Predicts Candidate Therapeutic Genetic Interactions at the Mammalian Replication Fork.
van Pel et al, G3 (Bethesda). 2013 Feb;3(2):273-82.
 
Cytoscape cited!
Modeling temporal relationships in large scale clinical associations. Hanauer et al, J Am Med Inform Assoc. 2013 Mar 1;20(2):332-41. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Modeling temporal relationships in large scale clinical associations.
Hanauer et al, J Am Med Inform Assoc. 2013 Mar 1;20(2):332-41.
 
Cytoscape cited!
The Escherichia coli Peripheral Inner Membrane Proteome. Papanastasiou et al, Mol Cell Proteomics. 2013 Mar;12(3):599-610. - http://cytoscape-publications.tumblr.com/post...
The Escherichia coli Peripheral Inner Membrane Proteome.
Papanastasiou et al, Mol Cell Proteomics. 2013 Mar;12(3):599-610.
Cytoscape's February Bug Bounty Winners - http://groups.google.com/group...
Announcing the Cyni network inference toolbox for Cytoscape 3 - http://groups.google.com/group...
Proteomic and Functional Analyses Reveal the Role of Chromatin Reader SFMBT1 in Regulating Epigenetic Silencing and the Myogenic Gene Program. Lin  et al, J Biol Chem. 2013 Mar 1;288(9):6238-47. - http://cytoscape-publications.tumblr.com/post...
Proteomic and Functional Analyses Reveal the Role of Chromatin Reader SFMBT1 in Regulating Epigenetic Silencing and the Myogenic Gene Program.
Lin  et al, J Biol Chem. 2013 Mar 1;288(9):6238-47.
Centiscape available for Cytoscape 3.0! - http://groups.google.com/group...
Unexpected Diversity during Community Succession in the Apple Flower Microbiome. Shade  et al, MBio. 2013 Feb 26;4(2). Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Unexpected Diversity during Community Succession in the Apple Flower Microbiome.
Shade  et al, MBio. 2013 Feb 26;4(2).
 
Cytoscape cited!
Functional profiling discovers that the dieldrin organochlorinated pesticide affects leucine availability in yeast. Gaytan et al, Toxicol Sci. 2013 Jan 28. - http://cytoscape-publications.tumblr.com/post...
Functional profiling discovers that the dieldrin organochlorinated pesticide affects leucine availability in yeast.
Gaytan et al, Toxicol Sci. 2013 Jan 28.
TFEB regulates lysosomal proteostasis. Song et al, Hum Mol Genet. 2013 Feb 18. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
TFEB regulates lysosomal proteostasis.
Song et al, Hum Mol Genet. 2013 Feb 18.
 
Cytoscape cited!
Complementary detection of embryotoxic properties of substances in the neural and cardiac embryonic stem cell tests. Theunissen et al, Toxicol Sci. 2013 Mar;132(1):118-30. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Complementary detection of embryotoxic properties of substances in the neural and cardiac embryonic stem cell tests.
Theunissen et al, Toxicol Sci. 2013 Mar;132(1):118-30.
 
Cytoscape cited!
MosaicFinder: Identification of fused gene families in sequence similarity networks. Jachiet et al, Bioinformatics. 2013 Jan 30. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
MosaicFinder: Identification of fused gene families in sequence similarity networks.
Jachiet et al, Bioinformatics. 2013 Jan 30.
 
Cytoscape cited!
Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana. Giorgi et al, Bioinformatics. 2013 Feb 1. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana.
Giorgi et al, Bioinformatics. 2013 Feb 1.
 
Cytoscape cited!
Host Cell Factors Necessary for Influenza A Infection: Meta-Analysis of Genome Wide Studies. Capitanio et al, Quantitative Biology, Cell Behavior. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Host Cell Factors Necessary for Influenza A Infection: Meta-Analysis of Genome Wide Studies. 
Capitanio et al, Quantitative Biology, Cell Behavior. 
 
Cytoscape cited!
Host Cell Factors Necessary for Influenza A Infection: Meta-Analysis of Genome Wide Studies. Capitanio et al, Quantitative Biology, Cell Behavior. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Host Cell Factors Necessary for Influenza A Infection: Meta-Analysis of Genome Wide Studies. 
Capitanio et al, Quantitative Biology, Cell Behavior. 
 
Cytoscape cited!
An information-gain approach to detecting three-way epistatic interactions in genetic association studies. Hu et al, J Am Med Inform Assoc. 2013 Feb 8. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
An information-gain approach to detecting three-way epistatic interactions in genetic association studies.
Hu et al, J Am Med Inform Assoc. 2013 Feb 8.
 
Cytoscape cited!
X-linked dystonia parkinsonism syndrome (XDP, lubag): disease-specific sequence change DSC3 in TAF1/DYT3 affects genes in vesicular transport and dopamine metabolism. Herzfeld et al, Hum Mol Genet. 2013 Mar 1;22(5):941-51. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
X-linked dystonia parkinsonism syndrome (XDP, lubag): disease-specific sequence change DSC3 in TAF1/DYT3 affects genes in vesicular transport and dopamine metabolism.
Herzfeld et al, Hum Mol Genet. 2013 Mar 1;22(5):941-51.
 
Cytoscape cited!
Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection Stewart et al, mBio Feb 5, 2013. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection
Stewart et al, mBio Feb 5, 2013.
 
Cytoscape cited!
Identification of Novel in vivo MAP Kinase Substrates in Arabidopsis thaliana Through Use of Tandem Metal Oxide Affinity Chromatography. Hoehenwarter et al, Mol Cell Proteomics. 2013 Feb 1. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Identification of Novel in vivo MAP Kinase Substrates in Arabidopsis thaliana Through Use of Tandem Metal Oxide Affinity Chromatography.
Hoehenwarter et al, Mol Cell Proteomics. 2013 Feb 1.
 
Cytoscape cited!
Cytoscape core projects are now hosted at GitHub - http://groups.google.com/group...
Unbiased label-free quantitative proteomic profiling and enriched proteomic pathways in seminal plasma of adult men before and after varicocelectomy. Camargo et al, Hum Reprod. 2013 Jan;28(1):33-46. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Unbiased label-free quantitative proteomic profiling and enriched proteomic pathways in seminal plasma of adult men before and after varicocelectomy.
Camargo et al, Hum Reprod. 2013 Jan;28(1):33-46.
 
Cytoscape cited!
Visualizing multidimensional cancer genomics data. Schroeder et al, Genome Med. 2013 Jan 31;5(1):9. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
Visualizing multidimensional cancer genomics data.
Schroeder et al, Genome Med. 2013 Jan 31;5(1):9.
 
Cytoscape cited!
BIG NEWS ABOUT CYTOSCAPE -- v3.0 is released! - http://groups.google.com/group...
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bindea et al, Bioinformatics. 2013 Jan 16. Cytoscape cited! - http://cytoscape-publications.tumblr.com/post...
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data.
Bindea et al, Bioinformatics. 2013 Jan 16.
 
Cytoscape cited!
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