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Tag cytoscape [37 articles]

Articoli recentemente classificati sotto il tag cytoscape.
  • Integration of biological networks and gene expression data using Cytoscape.
    Nat Protoc, Vol. 2, No. 10. (2007), pp. 2366-2382.
    by MS Cline, M Smoot, E Cerami, A Kuchinsky, N Landys, C Workman, R Christmas, I Avila-Campilo, M Creech, B Gross, K Hanspers, R Isserlin, R Kelley, S Killcoyne, S Lotia, S Maere, J Morris, K Ono, V Pavlovic, AR Pico, A Vailaya, PL Wang, A Adler, BR Conklin, L Hood, M Kuiper, C Sander, I Schmulevich, B Schwikowski, GJ Warner, T Ideker, GD Bader
    posted to cytoscape networks by thomaskelder on 2008-02-21 11:53:31 as read along with 5 people and 1 group jyuh jfr shikin shung AlexanderPico GeneGo
  • An architecture for biological information extraction and representation
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 430-438.
    by Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael Creech, Annette Adler
    posted to cytoscape textmining by thomaskelder on 2008-02-21 11:47:42 as **** along with 5 people and 1 group irenas eweaver kt t11 kemo dbk-lab
  • NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression.
    In silico biology, Vol. 8, No. 1. (2008), pp. 47-52.
    by L Yang, JR Walker, JB Hogenesch, RS Thomas
    posted to cytoscape microarray pathway by jyuh on 2008-05-10 09:37:16 as **
  • NetMatch: a Cytoscape Plugin for Searching Biological Networks.
    Bioinformatics (3 February 2007)
    by A Ferro, R Giugno, G Pigola, A Pulvirenti, D Skripin, G D D Bader, D Shasha
    posted to cytoscape interactions visualization by grahamc to the group ParkinsonLab_at_MaRS on 2007-02-16 03:56:38 as ** along with 1 person jyuh
  • APID2NET: unified interactome graphic analyzer.
    Bioinformatics (21 July 2007)
    by Juan Hernandez H Toro, Carlos Prieto, Javier De Las D Rivas
    posted to tools cytoscape by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 18:04:58 as ** along with 1 person jyuh
  • Integrating Expression Data with Domain Interaction Networks
    Bioinformatics (19 August 2008), btn437.
    by Dorothea Emig, Melissa S Cline, Thomas Lengauer, Mario Albrecht
    posted to cytoscape domains interactions protein-protein by grahamc on 2008-08-28 00:28:27 as ** along with 1 person zimbo1
  • Computing topological parameters of biological networks.
    Bioinformatics (15 November 2007)
    by Yassen Assenov, Fidel Ramírez, Sven-Eric E Schelhorn, Thomas Lengauer, Mario Albrecht
    posted to cytoscape network_statistics network_topology tools by grahamc on 2007-12-14 04:18:26 as ** along with 5 people jyuh jfr kengg mclarenv frohike
  • BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
    Bioinformatics (16 November 2007), btm553.
    by Andrei Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot
    posted to cytoscape network_properties network_statistics network_topology tools by grahamc on 2007-12-14 04:12:56 as ** along with 5 people jyuh jfr dullhunk sgoetz idonaldson
  • Cytoscape ESP: simple search of complex biological networks.
    Bioinformatics (Oxford, England) (28 April 2008)
    by Maital Ashkenazi, Gary D D Bader, Allan Kuchinsky, Menachem Moshelion, David J J States
    posted to cytoscape tools by grahamc on 2008-05-28 01:58:26 as ** along with 4 people jyuh maralena kengg renatomilani
  • BioNetBuilder, an automatic network interface.
    Bioinformatics (30 November 2006)
    by Iliana Avila-Campillo, Kevin Drew, John Lin, David J J Reiss, Richard Bonneau
    posted to cytoscape network software by frohike on 2006-12-11 10:10:56 as ***** along with 1 person jyuh
  • BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.
    Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3448-3449.
    by S Maere, K Heymans, M Kuiper
    posted to bingo cytoscape gene ontology statistics by frohike on 2007-09-24 12:02:04 as read along with 1 person natstreet
  • Cytoscape: a software environment for integrated models of biomolecular interaction networks.
    Genome Res, Vol. 13, No. 11. (November 2003), pp. 2498-2504.
    by P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang, D Ramage, N Amin, B Schwikowski, T Ideker
    posted to cytoscape networks tool visualisation by Borelli on 2008-08-16 17:30:31 as ** along with 12 people and 3 groups dragonrez balajis tvdbulck frohike carmaus dagmar natstreet jlh64 Evangelia pmendes yggdrasil carlk dIEMoSIRIS MoSi-Rostock compneur
  • Gene-set approach for expression pattern analysis
    Brief Bioinform (17 January 2008), bbn001.
    by Dougu Nam, Seon-Young Kim
    posted to cytoscape genmapp pathway_analysis by AlexanderPico on 2008-05-19 22:58:59 as ** along with 9 people seemu thomaskelder lp2 giovenko heliopais tmmurali yas beete klo
  • A search engine to identify pathway genes from expression data on multiple organisms
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Chunnuan Chen, Matthew Weirauch, Corey Powell, Alexander Zambon, Joshua Stuart
    posted to cytoscape pathway_analysis tool by AlexanderPico on 2008-05-19 22:35:05 as ** along with 5 people jyuh tmmurali jfr rsandie waszak
  • Tools for Visually Exploring Biological Networks.
    Bioinformatics (25 August 2007)
    by Matthew Suderman, Michael Hallett
    posted to cytoscape networks by AlexanderPico on 2008-05-19 23:27:02 as read along with 12 people and 3 groups jyuh icases dullhunk sebastien_vigneau grahamc sgoetz cabbagezs cerami loopback007 Pao-Yang schuylrp hryk ParkinsonLab_at_MaRS TNT Cancer_Stem_Cells
  • Extending pathways based on gene lists using InterPro domain signatures
    BMC Bioinformatics, Vol. 9 (04 January 2008), 3.
    by Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beissbarth
    posted to cytoscape pathways wikipathways by AlexanderPico on 2008-05-19 23:14:42 as *** along with 4 people and 1 group ealloza frohike renatomilani jyuh Bioinformatics
  • PaLS: filtering common literature, biological terms and pathway information
    Nucl. Acids Res. (8 May 2008), gkn251.
    by Andreu Alibes, Andres Canada, Ramon Diaz-Uriarte
    posted to cytoscape pathway_analysis tool wikipathways by AlexanderPico on 2008-05-19 22:43:37 as **** along with 3 people jyuh aalibes daed
  • notes A systems biology approach for pathway level analysis
    Genome Res. (4 September 2007), gr.6202607.
    by Sorin Draghici, Purvesh Khatri, Adi L Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero
    posted to cytoscape genmapp overview pathway_analysis by AlexanderPico on 2008-05-19 22:27:53 as read along with 15 people and 3 groups tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu shikin idonaldson Pao-Yang thomaskelder heliopais Bioinformatics ParkinsonLab_at_MaRS OPIG
  • A Global Pathway Crosstalk Network
    Bioinformatics (23 April 2008), btn200.
    by Yong Li, Pankaj Agarwal, Dilip Rajagopalan
    posted to cytoscape networks pathway_analysis pathways wikipathways by AlexanderPico on 2008-05-19 22:54:19 as ** along with 6 people thomaskelder maralena bootsy renatomilani jyuh balicea
  • Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasets.
    Journal of biomedical informatics (6 February 2008)
    by Emma Steele, Allan Tucker
    posted to cytoscape genmapp by AlexanderPico on 2008-05-19 22:17:00 as ** along with 1 person jfr
  • Mining pathway signatures from microarray data and relevant biological knowledge.
    J Biomed Inform, Vol. 40, No. 6. (December 2007), pp. 698-706.
    by E Panteris, S Swift, A Payne, X Liu
    posted to cytoscape pathway_analysis wikipathways by AlexanderPico on 2008-05-19 22:31:08 as **** along with 2 people jyuh jfr
  • Extracting biology from high-dimensional biological data.
    J Exp Biol, Vol. 210, No. Pt 9. (May 2007), pp. 1507-1517.
    by J Quackenbush
    posted to cytoscape genmapp overview by AlexanderPico on 2008-05-19 22:23:04 as **** along with 6 people jyuh frohike balicea Sharpshoot jo_davies jfr
  • SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays
    Genome Biology, Vol. 9 (29 February 2008), R46.
    by Miguel A Anton, Dorleta Gorostiaga, Elizabeth Guruceaga, Victor Segura, Pedro Carmona-Saez, Alberto Pascual-Montano, Ruben Pio, Luis M Montuenga, Angel Rubio
    posted to cytoscape genmapp by AlexanderPico on 2008-05-19 22:18:23 as * along with 5 people and 1 group jfr stajich huali Baten jyuh Berkeley Mycology
  • Towards zoomable multidimensional maps of the cell
    Nature Biotechnology, Vol. 25, No. 5. (04 May 2007), pp. 547-554.
    by Zhenjun Hu, Joe Mellor, Jie Wu, Minoru Kanehisa, Joshua M Stuart, Charles Delisi
    posted to cytoscape networks pathways by AlexanderPico on 2008-05-19 23:48:16 as read along with 10 people tmmurali kuhn cmmorel yas balajis thomaskelder dullhunk jyuh carlk Borelli
  • Eigengene networks for studying the relationships between co-expression modules
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Peter Langfelder, Steve Horvath
    posted to cytoscape by AlexanderPico on 2008-05-19 22:15:14 as ** along with 1 person jfr
  • VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by Z Hu, DM Ng, T Yamada, C Chen, S Kawashima, J Mellor, B Linghu, M Kanehisa, JM Stuart, C DeLisi
    posted to cytoscape genmapp pathway_analysis software by AlexanderPico on 2008-05-19 22:29:02 as read along with 1 person jfr
  • Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases.
    Bioinformatics (28 June 2007)
    by Duccio Cavalieri, Cinzia Castagnini, Simona Toti, Karolina Maciag, Thomas Kelder, Luca Gambineri, Samuele Angioli, Piero Dolara
    posted to cytoscape pathway_analysis software wikipathways by AlexanderPico on 2008-05-19 22:37:10 as read along with 6 people jyuh tmmurali jfr aviad_work waszak thomaskelder
  • PathExpress: a web-based tool to identify relevant pathways in gene expression data
    Nucl. Acids Res. (22 June 2007), gkm261.
    by Nicolas Goffard, Georg Weiller
    posted to cytoscape genmapp pathway_analysis software tool by AlexanderPico on 2008-05-19 22:29:34 as read along with 3 people and 1 group jyuh jfr ealloza BioinfoCIPF
  • Pathway recognition and augmentation by computational analysis of microarray expression data.
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 233-241.
    by BA Novak, AN Jain
    posted to cytoscape genmapp pathway_analysis by AlexanderPico on 2008-05-19 22:40:21 as ** along with 1 person jfr
  • Pathway mapping tools for analysis of high content data.
    Methods in molecular biology (Clifton, N.J.), Vol. 356 (2007), pp. 319-350.
    by S Ekins, Y Nikolsky, A Bugrim, E Kirillov, T Nikolskaya
    posted to cytoscape genmapp overview pathway_analysis software tool wikipathways by AlexanderPico on 2008-05-19 22:56:52 as ** along with 2 people and 1 group thomaskelder shikin GeneGo
  • Pathway analysis using random forests classification and regression.
    Bioinformatics (29 June 2006)
    by Herbert Pang, Aiping Lin, Matthew Holford, Bradley E E Enerson, Bin Lu, Michael P P Lawton, Eugenia Floyd, Hongyu Zhao
    posted to cytoscape pathway_analysis by AlexanderPico on 2008-05-19 22:41:01 as ** along with 5 people and 2 groups jfr tabu ealloza giovanni ptrobajo BioinfoCIPF GeschwindLab
  • Systems biology and new technologies enable predictive and preventative medicine.
    Science, Vol. 306, No. 5696. (22 October 2004), pp. 640-643.
    by L Hood, JR Heath, ME Phelps, B Lin
    posted to cytoscape medicine networks technology by AlexanderPico on 2008-05-19 23:50:32 as read along with 6 people and 1 group wnpx cconboy maburkitt shikin megraw raiyar GeneGo
  • Pathway and gene ontology based analysis of gene expression in a rat model of cerebral ischemic tolerance
    Brain Research, Vol. 1177 (26 October 2007), pp. 103-123.
    by Zheng Feng, Daniel P Davis, Roman Sásik, Hemal H Patel, John C Drummond, Piyush M Patel
    posted to cytoscape ontology pathway_analysis by AlexanderPico on 2008-05-19 23:43:11 as read
  • SPIKE - a database, visualization and analysis tool of cellular signaling pathways
    BMC Bioinformatics, Vol. 9 (20 February 2008), 110.
    by Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, Ron Shamir
    posted to cytoscape database genmapp pathway_analysis pathways software wikipathways by AlexanderPico on 2008-05-19 22:59:41 as read along with 4 people jyuh renatomilani maralena thomaskelder
  • The PANTHER database of protein families, subfamilies, functions and pathways.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by H Mi, B Lazareva-Ulitsky, R Loo, A Kejariwal, J Vandergriff, S Rabkin, N Guo, A Muruganujan, O Doremieux, MJ Campbell, H Kitano, PD Thomas
    posted to cytoscape database genmapp pathway_analysis pathways tool wikipathways by AlexanderPico on 2008-05-19 22:52:42 as read along with 3 people and 2 groups Cortel yas xico T_lab WetBiology
  • Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biol, Vol. 6, No. 7. (2005)
    by CH Yeang, HC Mak, S McCuine, C Workman, T Jaakkola, T Ideker
    posted to cytoscape networks pathway_analysis by AlexanderPico on 2008-05-19 23:00:49 as ** along with 11 people and 1 group snuppepuppan abhik tmmurali textoris wnpx noano koller ccr cdppublications carlk jago CDP
  • Design Logic of a Cannabinoid Receptor Signaling Network That Triggers Neurite Outgrowth
    Science, Vol. 320, No. 5878. (16 May 2008), pp. 903-909.
    by Kenneth D Bromberg, Avi Ma'ayan, Susana R Neves, Ravi Iyengar
    posted to brain cytoscape networks pathway_analysis transcription_factors by AlexanderPico on 2008-06-02 22:17:40 as read along with 3 people waszak caseybrown oelemento
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