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Group: Bioinformatics - with tag network [72 articles]

Recent papers posted by members of the Bioinformatics group with tag network
  • Integration of microarray and textual data improves the prognosis prediction of breast, lung and ovarian cancer patients.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 279-290.
    by O Gevaert, S Van Vooren, B de Moor
    posted to bayesian integration literature microarray network text by frohike to the group Bioinformatics on 2008-04-07 14:49:29 as ** along with 1 person jfr
  • A Framework for Elucidating Regulatory Networks Based on Prior Information and Expression Data
    Annals of the New York Academy of Sciences, Vol. 1115, No. 1. (December 2007), pp. 240-248.
    by Olivier Gevaert, VAN Vooren, N Steve, DE Moor, T Bar
    posted to bayesian dream integration microarray network prior protein by frohike to the group Bioinformatics on 2008-04-07 14:48:50 as ** along with 1 person jyuh
  • 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 cancer classification interaction network protein by frohike to the group Bioinformatics on 2008-03-05 17:20:01 as ** along with 12 people and 1 group jfr kengg mikaelhuss cjeans zwang cerami abhattac shikin oelemento roys ptrobajo dap5087 GeneGo
  • Current progress in network research: toward reference networks for key model organisms.
    Brief Bioinform (29 August 2007)
    by Balaji S S Srinivasan, Nigam H H Shah, Jason A A Flannick, Eduardo Abeliuk, Antal F F Novak, Serafim Batzoglou
    posted to network by sleepingcell to the group Bioinformatics on 2007-09-04 09:40:54 as ** along with 6 people marck daed jyuh grahamc nedwards roys
  • Integrating physical and genetic maps: from genomes to interaction networks
    Nature Reviews Genetics, Vol. 8, No. 9., pp. 699-710.
    by Andreas Beyer, Sourav Bandyopadhyay, Trey Ideker
    posted to network genomics by sleepingcell to the group Bioinformatics on 2007-08-20 12:08:12 as ** along with 11 people and 2 groups carlk cdeane jyuh balicea dchughes sebastien_vigneau grahamc joepickrell zwang shikin lh1 G4ID Genetics-of-Gambling
  • The human disease network
    PNAS, Vol. 104, No. 21. (22 May 2007), pp. 8685-8690.
    by Kwang-Il Goh, Michael E Cusick, David Valle, Barton Childs, Marc Vidal, Albert-Laszlo Barabasi
    posted to network by sleepingcell to the group Bioinformatics on 2007-07-30 09:04:47 as ***** along with 25 people and 7 groups yaredo shoshin carlk mingzhi Yanno jyuh aalibes cannin kuhn jfr yas balicea neveaire bundschu raiyar grahamc joepickrell leSyl henning dejori xingxu winterschlaefer naegele shikin nolodie GomezLab Biostatistics Computational-Genomics Neuroscience steinmetzlab ic4 generif_paper
  • 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 by sleepingcell to the group Bioinformatics on 2007-06-06 09:10:04 as ** along with 7 people and 1 group pinney jfr grahamc massivemayhem cjeans zwang cabbagezs ParkinsonLab_at_MaRS
  • Understanding Network Concepts in Modules
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Jun Dong, Steve Horvath
    posted to network by sleepingcell to the group Bioinformatics on 2007-06-05 05:41:43 as ** along with 4 people jfr kengg grahamc natstreet
  • SYSTEMS BIOLOGY: Less Is More in Modeling Large Genetic Networks
    Science, Vol. 310, No. 5747. (21 October 2005), pp. 449-451.
    by Stefan Bornholdt
    posted to network by sleepingcell to the group Bioinformatics on 2007-05-21 03:29:19 as ** along with 7 people snuppepuppan eldan jmeppley balajis wnpx biosv fishtank
  • Genetic reconstruction of a functional transcriptional regulatory network.
    Nat Genet (8 April 2007)
    by Zhanzhi Hu, Patrick J J Killion, Vishwanath R R Iyer
    posted to tfbs regulation prediction network by sleepingcell to the group Bioinformatics on 2007-04-11 07:25:32 as ** along with 9 people and 5 groups czeller dpollard xico nickluscombe zwang lizabeth dejori xingxu naegele EisenLab WetBiology EBI-regulation ic4 generif_paper
  • A network perspective on the topological importance of enzymes and their phylogenetic conservation
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Wei C Liu, Wen H Lin, Andrew Davis, Ferenc Jordan, Hsih T Yang, Ming J Hwang
    posted to network by sleepingcell to the group Bioinformatics on 2007-04-11 07:24:59 as ** along with 2 people ptrobajo mdstobbe
  • Functional cartography of complex metabolic networks
    Nature, Vol. 433, No. 7028. (24 February 2005), pp. 895-900.
    by Roger Guimera, LAN Luis
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:42:05 as *** along with 15 people and 3 groups carlk camster dbk BioGeek Borelli lfriedl balajis alexg eweaver tny wnpx cjeans kdang RobMills Diego_Prada streptomyces dbk-lab kdl
  • Motifs, modules and games in bacteria.
    Curr Opin Microbiol, Vol. 6, No. 2. (April 2003), pp. 125-134.
    by DM Wolf, AP Arkin
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:41:17 as ** along with 2 people rklancer heliopais
  • Conservation of regulatory elements between two species of Drosophila.
    BMC Bioinformatics, Vol. 4 (20 November 2003)
    by E Emberly, N Rajewsky, ED Siggia
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:41:05 as ** along with 2 people dquest emptyhb
  • Structure and evolution of transcriptional regulatory networks.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 283-291.
    by MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:40:45 as ** along with 6 people and 1 group tny kengg koller tvdbulck cjeans karfunkel Plantandetc
  • Genome evolution reveals biochemical networks and functional modules.
    Proc Natl Acad Sci U S A, Vol. 100, No. 26. (23 December 2003), pp. 15428-15433.
    by C von Mering, EM Zdobnov, S Tsoka, FD Ciccarelli, JB Pereira-Leal, CA Ouzounis, P Bork
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:39:46 as ** along with 2 people and 1 group ujh lfriedl kdl
  • Modularity and evolutionary constraint on proteins
    Nature Genetics, Vol. 37, No. 4. (06 March 2005), pp. 351-352.
    by Hunter B Fraser
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:39:22 as ** along with 1 person rklancer
  • Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.
    Proc Natl Acad Sci U S A, Vol. 102, No. 20. (17 May 2005), pp. 7203-7208.
    by A Tanay, A Regev, R Shamir
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:39:03 as ** along with 2 people carlk Schmidtc
  • Methods to reveal domain networks
    Drug Discovery Today, Vol. 10, No. 16. (15 August 2005), pp. 1111-1117.
    by Elena Santonico, Luisa Castagnoli, Gianni Cesareni
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:38:42 as ** along with 3 people wnpx eukfn cjeans
  • Gene annotation and network inference by phylogenetic profiling.
    BMC Bioinformatics, Vol. 7 (2006)
    by J Wu, Z Hu, C DeLisi
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:38:26 as **
  • Differential evolutionary conservation of motif modes in the yeast protein interaction network.
    BMC Genomics, Vol. 7 (2006)
    by WP Lee, BC Jeng, TW Pai, CP Tsai, CY Yu, WS Tzou
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:33:59 as **
  • The outcomes of pathway database computations depend on pathway ontology
    Nucl. Acids Res., Vol. 34, No. 13. (7 August 2006), pp. 3687-3697.
    by ML Green, PD Karp
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:32:56 as ** along with 2 people kuhn eweaver
  • Graemlin: general and robust alignment of multiple large interaction networks.
    Genome Res, Vol. 16, No. 9. (September 2006), pp. 1169-1181.
    by J Flannick, A Novak, BS Srinivasan, HH McAdams, S Batzoglou
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 17:12:23 as * along with 3 people jfr balajis mdstobbe
  • Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.
    PLoS Comput Biol, Vol. 2, No. 11. (24 November 2006)
    by K Xia, H Xue, D Dong, S Zhu, J Wang, Q Zhang, L Hou, H Chen, R Tao, Z Huang, Z Fu, YG Chen, JD Han
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 16:35:20 as ** along with 2 people tmmurali jfr
  • Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems.
    PLoS Comput Biol, Vol. 2, No. 12. (1 December 2006)
    by Duccio Medini, Antonello Covacci, Claudio Donati
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 16:33:27 as *** along with 2 people bjorns mloewer
  • Detecting conserved interaction patterns in biological networks.
    J Comput Biol, Vol. 13, No. 7. (September 2006), pp. 1299-1322.
    by M Koyutürk, Y Kim, S Subramaniam, W Szpankowski, A Grama
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 16:32:18 as * along with 3 people balajis massivemayhem mirzazadeh
  • Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate
    Nature Cell Biology, Vol. 9, No. 3. (18 February 2007), pp. 324-330.
    by Silvia DM Santos, Peter J Verveer, Philippe IH Bastiaens
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 16:23:57 as ** along with 2 people pmendes balabu
  • The potential for signal integration and processing in interacting MAP kinase cascades.
    J Theor Biol (14 January 2007)
    by John H H Schwacke, Eberhard O O Voit
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 16:23:39 as ** along with 1 person jyuh
  • Regulation of metabolic networks by small molecule metabolites
    BMC Bioinformatics, Vol. 8 (13 March 2007), 88.
    by Alex Gutteridge, Minoru Kanehisa, Susumu Goto
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 16:12:47 as **** along with 2 people aswin shung
  • Extraction of phylogenetic network modules from the metabolic network.
    BMC Bioinformatics, Vol. 7 (2006)
    by T Yamada, M Kanehisa, S Goto
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 14:03:43 as ****
  • Extraction of phylogenetic network modules from prokayrote metabolic pathways.
    Genome Inform Ser Workshop Genome Inform, Vol. 15, No. 1. (2004), pp. 249-258.
    by T Yamada, S Goto, M Kanehisa
    posted to network module by sleepingcell to the group Bioinformatics on 2007-04-05 14:03:06 as * along with 1 person alexg
  • An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
    Nature Biotechnology, Vol. 25, No. 3. (25 February 2007), pp. 345-352.
    by Oliver Rinner, Lukas N Mueller, Martin Hubálek, Markus Müller, Matthias Gstaiger, Ruedi Aebersold
    posted to ms network protein by okarsligil to the group Bioinformatics on 2007-03-19 13:10:19 as ** along with 5 people jyuh jfr Dualsystems nedwards mingzhi
  • Classes of complex networks defined by role-to-role connectivity profiles
    Nat Phys, Vol. 3, No. 1. (January 2007), pp. 63-69.
    by Roger Guimera, Marta Sales-Pardo, Luis A Amaral
    posted to network connectivity by okarsligil to the group Bioinformatics on 2007-01-11 14:29:43 as ** along with 4 people AbnerCYH aalibes jaspervoskuilen biehl
  • The regulatory architecture of the human genome.
    Asia Pac J Clin Nutr, Vol. 13, No. Suppl. (2004)
    by JS Mattick
    posted to genomics network regulation by bsmagic to the group Bioinformatics on 2006-11-16 13:26:01 as ** along with 1 person and 1 group snuppepuppan bioinplant
  • Principles of microRNA regulation of a human cellular signaling network.
    Mol Syst Biol, Vol. 2 (2006)
    by Q Cui, Z Yu, EO Purisima, E Wang
    posted to network regulation signaling by okarsligil to the group Bioinformatics on 2006-10-17 14:54:47 as ** along with 7 people and 2 groups bootsy jfr marcius tardigrade mtagaya ealloza maralena BioinfoCIPF SGU-CIPF
  • Functional annotation and network reconstruction through cross-platform integration of microarray data
    Nature Biotechnology, Vol. 23, No. 2. (16 January 2005), pp. 238-243.
    by Xianghong J Zhou, Ming-Chih J Kao, Haiyan Huang, Angela Wong, Juan Nunez-Iglesias, Michael Primig, Oscar M Aparicio, Caleb E Finch, Todd E Morgan, Wing H Wong
    posted to algorithm expression microarray modeling network networks omics reconstruction regulatory by bsmagic to the group Bioinformatics on 2006-08-11 03:26:26 as ** along with 6 people and 1 group setar andytseng imouthesmp lyongu wnpx rdiaz bioinplant
  • A gene fusion network in human neoplasia
    Oncogene, Vol. aop, No. current.
    by M Höglund, A Frigyesi, F Mitelman
    posted to cancer fusion gene hubs human network by bsmagic to the group Bioinformatics on 2006-08-11 03:03:15 as ** along with 2 people and 2 groups ealloza Garamonfok BioinfoCIPF bioinplant
  • Modeling Lactococcus lactis using a genome-scale flux model.
    BMC Microbiol, Vol. 5 (2005)
    by AP Oliveira, J Nielsen, J Förster
    posted to flux metabolic microbe model network reconstruction by bsmagic to the group Bioinformatics on 2006-08-01 21:32:20 as ** along with 1 person and 2 groups athleem bioinplant JJJ
  • Reconstructing the metabolic network of a bacterium from its genome
    Trends in Microbiology, Vol. 13, No. 11. (November 2005), pp. 550-558.
    by Christof Francke, Roland J Siezen, Bas Teusink
    posted to bacterium genome metabolic network reconstruction template by bsmagic to the group Bioinformatics on 2006-08-01 21:27:02 as ** along with 5 people and 1 group kuhn jmeppley JeremyZucker gurkanbebek shung bioinplant
  • metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella
    Nucleic Acids Research, Vol. 33, No. 4., pp. 1399-1409.
    by W Pinney, W Shirley, A Mcconkey, R Westhead
    posted to metabolic network prediction reconstruction sequence software systems by bsmagic to the group Bioinformatics on 2006-08-01 21:24:10 as ** along with 4 people and 1 group hryk jmeppley eweaver shung bioinplant
  • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
    Genome Res, Vol. 13, No. 2. (February 2003), pp. 244-253.
    by J Förster, I Famili, P Fu, BØ Palsson, J Nielsen
    posted to biology genome genome-scale metabolic model network organism reconstruction systems template yeast by bsmagic to the group Bioinformatics on 2006-08-01 21:13:46 as ** along with 7 people and 2 groups opheliav wnpx nirfriedman JeremyZucker gcalda jpoyatos edwardmorrissey bioinplant MetabolicModeling
  • Advances in flux balance analysis.
    Curr Opin Biotechnol, Vol. 14, No. 5. (October 2003), pp. 491-496.
    by KJ Kauffman, P Prakash, JS Edwards
    posted to advance algorithm balance biochemical flux gene metabolic method network review by bsmagic to the group Bioinformatics on 2006-07-28 20:00:56 as ** along with 4 people and 4 groups beapen wnpx nirfriedman edwardmorrissey Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics bioinplant
  • Searching RNA motifs and their intermolecular contacts with constraint networks.
    Bioinformatics (4 July 2006)
    by P Thébault, S de Givry, T Schiex, C Gaspin
    posted to algorithm constraint intermolecular motif network rna search structure by bsmagic to the group Bioinformatics on 2006-07-28 06:12:09 as ** along with 3 people and 3 groups marcius tardigrade dquest BioinfoCIPF bioinplant SGU-CIPF
  • Origins of fractality in the growth of complex networks
    Nat Phys, Vol. 2, No. 4. (April 2006), pp. 275-281.
    by Chaoming Song, Shlomo Havlin, Hernan A Makse
    posted to complex fractal network by okarsligil to the group Bioinformatics on 2006-04-11 20:36:33 as **** along with 2 people gane5h muraken
  • Chance and necessity in the evolution of minimal metabolic networks
    Nature, Vol. 440, No. 7084., pp. 667-670.
    by Csaba Pã¡l, Balã¡zs Papp, Martin J Lercher, Pã©ter Csermely, Stephen G Oliver, Laurence D Hurst
    posted to evolution metabolic network by okarsligil to the group Bioinformatics on 2006-04-04 20:52:08 as *** along with 8 people and 1 group michaelbarton icases Borelli ccots nirfriedman rabu mikaelhuss edwardmorrissey TNT
  • Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks
    Mol Syst Biol, Vol. 2, No. 1. (31 January 2006), pp. msb4100047-E1-msb4100047-E14.
    by Noam Slonim, Olivier Elemento, Saeed Tavazoie
    posted to genotype network phenotype by okarsligil to the group Bioinformatics on 2006-03-22 20:58:30 as **** along with 5 people and 1 group ccots balajis cmm koller dylan77 FAB-lab
  • Gene network shaping of inherent noise spectra
    Nature, Vol. 439, No. 7076., pp. 608-611.
    by DW Austin, MS Allen, JM Mccollum, RD Dar, JR Wilgus, GS Sayler, NF Samatova, CD Cox, ML Simpson
    posted to gene network noise regulation spectra by okarsligil to the group Bioinformatics on 2006-02-02 16:23:09 as *** along with 4 people dylanwalker madhadron balabu margaritis
  • Creation and implications of a phenome-genome network
    Nature Biotechnology, Vol. 24, No. 1. (10 January 2006), pp. 55-62.
    by Atul J Butte, Isaac S Kohane
    posted to genome network phenome by okarsligil to the group Bioinformatics on 2006-01-12 16:13:37 as *** along with 8 people and 1 group jyuh BioGeek bpb balajis wnpx tag elsiatcase eukfn metric_embeddings
  • Inference in Bayesian networks
    Nature Biotechnology, Vol. 24, No. 1., pp. 51-53.
    by Chris J Needham, James R Bradford, Andrew J Bulpitt, David R Westhead
    posted to bayesian inference network by okarsligil to the group Bioinformatics on 2006-01-12 16:10:32 as **** along with 10 people and 2 groups Pragmatist quianominorleo Yanno jrw garyfeng Borelli ddahlem lujiec kozlak jo_davies ReadingLab ThinkBridge
  • A quantitative protein interaction network for the ErbB receptors using protein microarrays
    Nature (06 November 2005)
    by Richard B Jones, Andrew Gordus, Jordan A Krall, Gavin Macbeath
    posted to interaction network protein by okarsligil to the group Bioinformatics on 2006-01-11 22:02:29 as ** along with 6 people and 3 groups jfr marcius tny julius koller pjasper SysbioMPI-TCells BioinfoCIPF SGU-CIPF
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