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jfr network [69 articles]

Recent papers added to jfr library classified by the tag network. You can also see everyone's network.
  • Identification of gene interactions associated with disease from gene expression data using synergy networks
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by John Watkinson, Xiaodong Wang, Tian Zheng, Dimitris Anastassiou
    posted to network interaction gene_expression by jfr on 2008-07-17 14:47:51 as *** along with 4 people balicea frohike barriot smgomez
  • The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data.
    Journal of biomedical informatics, Vol. 41, No. 4. (August 2008), pp. 530-543.
    by X Ruan, J Wang, H Li, RE Perozzi, EF Perozzi
    posted to progression pathway_analysis network gene_expression colon_cancer by jfr on 2008-07-17 14:36:18 as read along with 1 person balicea
  • Fast Network Component Analysis (FastNCA) for gene regulatory network reconstruction from microarray data.
    Bioinformatics (Oxford, England) (9 April 2008)
    by Chunqi Chang, Zhi Ding, Yeung Sam S Hung, Peter Chin Wan C Fung
    posted to network by jfr on 2008-06-17 16:42:35 as ** along with 3 people AbnerCYH roys jyuh
  • Protein networks in disease
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 644-652.
    by Trey Ideker, Roded Sharan
    posted to review protein_interaction network by jfr on 2008-05-16 10:33:51 as read along with 19 people zwang balicea raiyar ptrobajo brianb paolomarcatili thomaskelder gracio schuylrp jyuh tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl
  • A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
    Nature Genetics, Vol. 40, No. 2. (27 January 2008), pp. 181-188.
    by Insuk Lee, Ben Lehner, Catriona Crombie, Wendy Wong, Andrew G Fraser, Edward M Marcotte
    posted to network by jfr on 2008-05-05 10:46:20 as **** along with 7 people tmmurali balicea capitall roys jiny kintoki meiklej
  • 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 software network co-expression by jfr on 2008-05-04 22:58:45 as ** along with 1 person AlexanderPico
  • 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 network methodology meta-analysis by jfr on 2008-05-04 22:41:21 as **** along with 1 person AlexanderPico
  • What are artificial neural networks?
    Nature Biotechnology, Vol. 26, No. 2., pp. 195-197.
    by Anders Krogh
    posted to primer network by jfr on 2008-04-30 17:55:57 as ** along with 10 people mjoach ale adacier Yanno jyuh dullhunk zwang cabbagezs asddd sci91078
  • MetaReg: A platform for modeling, analysis and visualization of biological systems using large-scale experimental data
    Genome Biology, Vol. 9 (02 January 2008), R1.
    by Igor Ulitsky, Irit Gat-Viks, Ron Shamir
    posted to software network integration by jfr on 2008-04-30 11:23:17 as ** along with 4 people jyuh tmmurali waszak ptrobajo
  • Building pathway clusters from Random Forests classification using class votes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Herbert Pang, Hongyu Zhao
    posted to pathway_analysis network clustering by jfr on 2008-04-29 15:40:12 as **** along with 4 people AlexanderPico jyuh xtizon thomaskelder
  • The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
    BMC Bioinformatics, Vol. 9 (06 February 2008), 86.
    by Frederic Chalmel, Michael Primig
    posted to software network integration by jfr on 2008-04-29 15:25:15 as read along with 2 people jyuh maralena
  • Mixture models and exploratory analysis in networks.
    Proc Natl Acad Sci U S A (24 May 2007)
    by M E J E Newman, E A A Leicht
    posted to community network by jfr on 2008-04-22 08:59:17 as ** along with 5 people jyuh baronka sebastien_vigneau jaspervoskuilen stefanoallesina
  • 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 network software by jfr on 2008-04-22 08:54:57 as ** along with 5 people jyuh dullhunk grahamc sgoetz idonaldson
  • Reconstruction of genetic association networks from microarray data: A partial least squares approach.
    Bioinformatics (18 January 2008)
    by Vasyl Pihur, Somnath Datta, Susmita Datta
    posted to gene_expression methodology network by jfr on 2008-04-22 08:31:47 as ** along with 6 people winterschlaefer jyuh cannin shigepong aconesa sotacam
  • Reverse engineering cellular networks.
    Nat Protoc, Vol. 1, No. 2. (2006), pp. 662-671.
    by AA Margolin, K Wang, WK Lim, M Kustagi, I Nemenman, A Califano
    posted to network by jfr on 2008-04-17 14:02:28 as *** along with 3 people and 1 group jyuh cdawson natstreet GIG
  • Protein-protein interaction networks and biology—what's the connection?
    Nature Biotechnology, Vol. 26, No. 1., pp. 69-72.
    by Luke Hakes, John W Pinney, David L Robertson, Simon C Lovell
    posted to network protein_interaction by jfr on 2008-04-11 16:31:00 as read along with 14 people and 1 group paolomarcatili Yanno jyuh tmmurali balicea dullhunk neils mikaelhuss cjeans nedwards biehl shikin mclarenv Yumyai GeneGo
  • Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases
    BMC Bioinformatics, Vol. 8 (04 October 2007), 372.
    by Seth I Berger, Jeremy M Posner, Avi Ma'ayan
    posted to annotation network software by jfr on 2008-04-09 15:29:32 as ** along with 2 people and 1 group jyuh shikin GeneGo
  • Uncovering the overlapping community structure of complex networks in nature and society
    Nature, Vol. 435, No. 7043., pp. 814-818.
    by Gergely Palla, Imre Derényi, Illés Farkas, Tamás Vicsek
    posted to community network by jfr on 2008-04-09 15:10:52 as *** along with 12 people and 2 groups betaparticle ellakat tmmurali kuhn lfriedl wilmegape gcalda ltabourier michaelmampaey Scis0000002 maralena lmichan kdl ADMiRes
  • From the Cover: Modularity and community structure in networks
    PNAS, Vol. 103, No. 23. (6 June 2006), pp. 8577-8582.
    by MEJ Newman
    posted to community module_detection network by jfr on 2008-04-09 15:06:59 as read along with 17 people and 3 groups jjray ellakat carlk aqeel ChaTo yas balicea ddahlem cmm fukken kubyaddi adriandefroment gcalda hannu marcio phreeza Diego_Prada T_lab FAB-lab ThinkTank
  • 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 network software by jfr on 2008-04-08 17:32:09 as * along with 5 people frohike jyuh kengg grahamc mclarenv
  • Network constrained clustering for gene microarray data
    Bioinformatics, Vol. 21, No. 21. (1 November 2005), pp. 4014-4020.
    by Dongxiao Zhu, Alfred O Hero, Hong Cheng, Ritu Khanna, Anand Swaroop
    posted to clustering module_detection network by jfr on 2008-02-05 12:12:19 as ** along with 2 people abhik wnpx
  • Drug[mdash]target network
    Nat Biotech, Vol. 25, No. 10. (October 2007), pp. 1119-1126.
    by Muhammed A Yildirim, Kwang-Il Goh, Michael E Cusick, Albert-Laszlo Barabasi, Marc Vidal
    posted to network therapy by jfr on 2008-02-04 11:41:06 as **** along with 9 people and 1 group Yanno jyuh cannin julius grahamc cjeans zwang dejori mingzhi libr
  • Extracting the hierarchical organization of complex systems
    Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15224-15229.
    by Marta Sales-Pardo, Roger Guimera, Andre A Moreira, Luis A Amaral
    posted to network by jfr on 2008-02-04 10:34:54 as *** along with 5 people and 1 group studentx zwang sobolevnrm niallhaslam arasbm baker-group
  • A graph-based approach to systematically reconstruct human transcriptional regulatory modules.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by X Yan, MR Mehan, Y Huang, MS Waterman, PS Yu, XJ Zhou
    posted to module_detection network regulation by jfr on 2008-02-04 10:32:43 as ** along with 1 person shigepong
  • Protein network inference from multiple genomic data: a supervised approach.
    Bioinformatics, Vol. 20 Suppl 1 (4 August 2004)
    by Y Yamanishi, JP Vert, M Kanehisa
    posted to integration motif network by jfr on 2008-01-28 16:05:54 as *** along with 2 people bioinfo iris_2001
  • Integrative molecular concept modeling of prostate cancer progression
    Nature Genetics, Vol. 39, No. 1. (17 December 2006), pp. 41-51.
    by Scott A Tomlins, Rohit Mehra, Daniel R Rhodes, Xuhong Cao, Lei Wang, Saravana M Dhanasekaran, Shanker Kalyana-Sundaram, John T Wei, Mark A Rubin, Kenneth J Pienta, Rajal B Shah, Arul M Chinnaiyan
    posted to network by jfr on 2008-01-24 17:08:34 as read along with 6 people ihpark srp33 kentsis shigepong xingxu daed
  • Network modeling links breast cancer susceptibility and centrosome dysfunction.
    Nat Genet (7 October 2007)
    by Miguel Angel A Pujana, Jing-Dong J D Han, Lea M M Starita, Kristen N N Stevens, Muneesh Tewari, Jin Sook S Ahn, Gad Rennert, Víctor Moreno, Tomas Kirchhoff, Bert Gold, Volker Assmann, Wael M M Elshamy, Jean-François F Rual, Douglas Levine, Laura S S Rozek, Rebecca S S Gelman, Kristin C C Gunsalus, Roger A A Greenberg, Bijan Sobhian, Nicolas Bertin, Kavitha Venkatesan, Nono Ayivi-Guedehoussou, Xavier Solé, Pilar Hernández, Conxi Lázaro, Katherine L L Nathanson, Barbara L L Weber, Michael E E Cusick, David E E Hill, Kenneth Offit, David M M Livingston, Stephen B B Gruber, Jeffrey D D Parvin, Marc Vidal
    posted to brca breast_cancer network by jfr on 2008-01-23 15:35:57 as read along with 6 people and 1 group chrisamiller ealloza cjeans nedwards jdiezperezj phoenixzxl BioinfoCIPF
  • Combining functional and topological properties to identify core modules in protein interaction networks
    Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 4. (2006), pp. 948-959.
    by Zelmina Lubovac, Jonas Gamalielsson, Björn Olsson
    posted to integration motif network by jfr on 2008-01-23 15:12:18 as ** along with 1 person conkymacro
  • Defining and identifying communities in networks.
    Proc Natl Acad Sci U S A, Vol. 101, No. 9. (2 March 2004), pp. 2658-2663.
    by F Radicchi, C Castellano, F Cecconi, V Loreto, D Parisi
    posted to community graphs motif network by jfr on 2008-01-23 15:07:19 as read along with 8 people and 1 group tnhh carlk shivaram yas merazzle gcalda ltabourier sparikh T_lab
  • Modular organization of protein interaction networks.
    Bioinformatics (8 November 2006)
    by Feng Luo, Yunfeng Yang, Chin-Fu F Chen, Roger Chang, Jizhong Zhou, Richard H H Scheuermann
    posted to motif network protein_interaction by jfr on 2008-01-23 15:00:49 as ** along with 3 people and 1 group grahamc massivemayhem maralena ParkinsonLab_at_MaRS
  • A Gibbs sampler for the identification of gene expression and network connectivity consistency.
    Bioinformatics (23 October 2006)
    by Mark P P Brynildsen, Linh M M Tran, James C C Liao
    posted to integration network protein_interaction by jfr on 2008-01-09 12:09:17 as *** along with 1 person gpalidwor
  • Detecting functional modules in the yeast proteinprotein interaction network
    Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2283-2290.
    by Chen, Jingchun, Yuan, Bo
    posted to module_detection network protein_interaction by jfr on 2008-01-09 12:07:50 as *** along with 3 people ellakat tmmurali maralena
  • A novel functional module detection algorithm for protein-protein interaction network
    Algorithms for Molecular Biology, Vol. 1 (05 December 2006), 24.
    by Woochang Hwang, Young-Rae Cho, Aidong Zhang, Murali Ramanathan
    posted to module_detection network protein_interaction by jfr on 2008-01-09 11:55:03 as *** along with 1 person laughcry
  • Evaluation of clustering algorithms for protein-protein interaction networks
    BMC Bioinformatics, Vol. 7 (06 November 2006), 488.
    by Sylvain Brohee, Jacques van Helden
    posted to clustering network protein_interaction by jfr on 2008-01-09 11:53:43 as ** along with 13 people and 1 group AbnerCYH Borelli carlk pdelosri chad_davis balajis nirfriedman dquest grahamc cjeans hpaces Pao-Yang oktie EPFL_SB_ITP_LBS
  • In Search of the Biological Significance of Modular Structures in Protein Networks
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e107.
    by Zhi Wang, Jianzhi Zhang
    posted to network protein_interaction by jfr on 2008-01-09 11:52:23 as *** along with 6 people and 2 groups pinney grahamc massivemayhem cjeans zwang cabbagezs Bioinformatics ParkinsonLab_at_MaRS
  • 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 integration network software by jfr on 2008-01-09 11:46:14 as read along with 5 people and 1 group AlexanderPico jyuh shikin shung thomaskelder GeneGo
  • Discovering molecular pathways from protein interaction and gene expression data.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by E Segal, H Wang, D Koller
    posted to integration network by jfr on 2008-01-09 11:42:50 as read along with 6 people and 1 group lfriedl wnpx noano bhaddow edwardmorrissey jiny kdl
  • Making the most of high-throughput protein-interaction data
    Genome Biology, Vol. 8 (02 November 2007), 112.
    by Robert Gentleman, Wolfgang Huber
    posted to network protein_interaction review by jfr on 2008-01-09 11:41:50 as read along with 1 person cjeans
  • Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy.
    J Clin Oncol, Vol. 23, No. 15. (20 May 2005), pp. 3614-3621.
    by EF Petricoin, VE Bichsel, VS Calvert, V Espina, M Winters, L Young, C Belluco, BJ Trock, M Lippman, DA Fishman, DC Sgroi, PJ Munson, LJ Esserman, LA Liotta
    posted to network proteomics review treatment by jfr on 2008-01-09 11:40:50 as ** along with 1 person jyuh
  • Graphs in molecular biology.
    BMC Bioinformatics, Vol. 8 Suppl 6 (2007)
    by W Huber, VJ Carey, L Long, S Falcon, R Gentleman
    posted to graphs network by jfr on 2008-01-09 11:34:54 as read along with 3 people girschick bertelsen jyuh
  • Comparison of Human Protein-Protein Interaction Maps.
    Bioinformatics (19 January 2007)
    by Matthias E E Futschik, Gautam Chaurasia, Hanspeter Herzel
    posted to network protein_interaction by jfr on 2007-12-18 13:11:50 as ** along with 4 people and 1 group frohike jyuh bicko grahamc ParkinsonLab_at_MaRS
  • Module-based outcome prediction using breast cancer compendia.
    PLoS ONE, Vol. 2, No. 10. (2007)
    by MH van Vliet, CN Klijn, LF Wessels, MJ Reinders
    posted to meta-analysis breast_cancer network by jfr on 2007-12-18 13:02:32 as read along with 2 people macavity1g ptrobajo
  • Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data
    PLoS Computational Biology, Vol. 3, No. 10. (1 October 2007), e206.
    by Tom C Freeman, Leon Goldovsky, Markus Brosch, Stijn van Dongen, Pierre Mazière, Russell J Grocock, Shiri Freilich, Janet Thornton, Anton J Enright
    posted to network regulation software by jfr on 2007-12-18 12:55:38 as *** along with 6 people jyuh sebastien_vigneau giovanni shigepong heliopais waszak
  • Network-based classification of breast cancer metastasis
    Mol Syst Biol, Vol. 3 (16 October 2007)
    by Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee, Trey Ideker
    posted to breast_cancer classification network by jfr on 2007-12-17 12:07:52 as read along with 12 people and 2 groups kengg frohike mikaelhuss cjeans zwang cerami abhattac shikin oelemento roys ptrobajo dap5087 Bioinformatics GeneGo
  • Cancer systems biology: exploring cancer-associated genes on cellular networks.
    Cell Mol Life Sci, Vol. 64, No. 14. (July 2007), pp. 1752-1762.
    by E Wang, A Lenferink, M O'Connor-McCourt
    posted to network review systems_biology by jfr on 2007-12-07 10:47:15 as *** along with 2 people and 2 groups diging_data ealloza BTS-PT-AS-CS BioinfoCIPF
  • Human disease classification in the postgenomic era: A complex systems approach to human pathobiology
    Mol Syst Biol, Vol. 3 (10 July 2007)
    by Joseph Loscalzo, Isaac Kohane, Albert-Laszlo Barabasi
    posted to network review systems_biology by jfr on 2007-12-06 10:22:50 as **** along with 6 people and 2 groups Yanno kentsis yas dchughes zwang nolodie G4ID Genetics-of-Gambling
  • A Primer on Learning in Bayesian Networks for Computational Biology
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e129.
    by Chris J Needham, James R Bradford, Andrew J Bulpitt, David R Westhead
    posted to network review by jfr on 2007-12-06 10:01:25 as ** along with 11 people and 2 groups isimpson jyuh brian balicea grahamc zwang bertelsen cabbagezs groepl ppark idonaldson Bioinformatics BergmanLab
  • Integrating molecular and network biology to decode endocytosis
    Nature, Vol. 448, No. 7156. (2007), pp. 883-888.
    by Eva M Schmid, Harvey T Mcmahon
    posted to network integration by jfr on 2007-12-04 15:20:24 as *** along with 7 people dullhunk lechristophe zwang cactus ryanraaum lonettma wiedehopf
  • Protein interactions and disease: computational approaches to uncover the etiology of diseases
    Brief Bioinform (16 July 2007), bbm031.
    by Maricel G Kann
    posted to network protein_interaction review by jfr on 2007-12-03 17:39:13 as **** along with 4 people jyuh tmmurali AbnerCYH barriot
  • Understanding Network Concepts in Modules
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Jun Dong, Steve Horvath
    posted to network by jfr on 2007-11-28 11:09:25 as **** along with 3 people and 1 group kengg grahamc natstreet Bioinformatics
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