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carlks library [303 articles]

Neue Artikel in carlks ordered by to_read.
  • 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 visualization by carlk on 2008-08-24 00:51:34 as ***** along with 10 people tmmurali kuhn cmmorel yas balajis thomaskelder dullhunk guhjy AlexanderPico Borelli
  • Relating whole-genome expression data with protein-protein interactions.
    Genome Res, Vol. 12, No. 1. (January 2002), pp. 37-46.
    by R Jansen, D Greenbaum, M Gerstein
    posted to bicriteria expression linkprediction moduledetection modules networks by carlk on 2008-06-26 22:01:37 as ***** along with 9 people Robinder gurkanbebek gespim grahamc cjeans iris_2001 kintoki paolomarcatili nedwards
  • Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 188-194.
    by Wei Xie, Nikolaos V Sahinidis
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:26:40 as ***** along with 3 people and 2 groups bicko marcius bluvsh1 BioinfoCIPF SGU-CIPF
  • Exploring conformational space using a mean field technique with MOLS sampling.
    Journal of biosciences, Vol. 32, No. 5. (August 2007), pp. 909-920.
    by PA Prasad, V Kanagasabai, J Arunachalam, N Gautham
    posted to algorithms energy protein scp structure by carlk on 2008-06-26 18:25:42 as *****
  • Co-clustering of biological networks and gene expression data.
    Bioinformatics, Vol. 18 Suppl 1 (2002)
    by D Hanisch, A Zien, R Zimmer, T Lengauer
    posted to bicriteria clustering expression moduledetection modules networks by carlk on 2008-06-20 17:20:17 as ***** along with 2 people chad_davis srp33
  • Annotating pathways in interaction networks.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 153-165.
    by J Pandey, M Koyutürk, W Szpankowski, A Grama
    posted to functionprediction networks by carlk on 2008-06-15 17:52:58 as ***** along with 1 person cswinburne
  • Functional modules by relating protein interaction networks and gene expression
    Nucl. Acids Res., Vol. 31, No. 21. (1 November 2003), pp. 6283-6289.
    by Sabine Tornow, HW Mewes
    posted to bicriteria moduledetection modules networks by carlk on 2008-06-12 21:32:17 as ***** along with 1 person jiny
  • Greedily building protein networks with confidence.
    Bioinformatics, Vol. 19, No. 15. (12 October 2003), pp. 1869-1874.
    by JS Bader
    posted to complexes networks steiner by carlk on 2008-06-12 18:24:48 as ***** along with 1 person iris_2001
  • An automated method for finding molecular complexes in large protein interaction networks.
    BMC Bioinformatics, Vol. 4, No. 1. (13 January 2003)
    by GD Bader, CW Hogue
    posted to moduledetection modules networks by carlk on 2008-06-12 18:15:53 as ***** along with 9 people and 2 groups dswan waqaralikeble cswinburne jiny dragonrez lfriedl nirfriedman massivemayhem ethkim Bioinformatics kdl
  • Functional evaluation of domain-domain interactions and human protein interaction networks
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 859-865.
    by Andreas Schlicker, Carola Huthmacher, Fidel Ramirez, Thomas Lengauer, Mario Albrecht
    posted to domains human networks by carlk on 2008-06-11 06:16:14 as ***** along with 1 person zwang
  • Reuse of structural domain-domain interactions in protein networks
    BMC Bioinformatics, Vol. 8 (18 July 2007), 259.
    by Benjamin Schuster-Bockler, Alex Bateman
    posted to domains networks by carlk on 2008-06-10 20:43:05 as ***** along with 2 people zwang saket
  • The MoVIN server for the analysis of protein interaction networks.
    BMC bioinformatics, Vol. 9 Suppl 2 (2008)
    by P Marcatili, G Bussotti, A Tramontano
    posted to databases domains networks yeast by carlk on 2008-06-10 16:47:57 as ***** along with 3 people kluck maralena guhjy
  • Defining functional distances over Gene Ontology
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Angela D Pozo, Florencio Pazos, Alfonso Valencia
    posted to go by carlk on 2008-06-03 16:08:36 as ***** along with 6 people and 2 groups barry tny grahamc sobolevnrm barriot guhjy Bioinformatics baker-group
  • Use and misuse of the gene ontology annotations.
    Nature reviews. Genetics (13 May 2008)
    by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici
    posted to go by carlk on 2008-06-03 16:06:02 as ***** along with 22 people and 2 groups daforerog jfr djkt guhjy aheilbut mariakmejia cmzmasek A_Olympia realzhang roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck rvosa bpcusack logics of knowledge FAB-lab
  • Computing Communities in Large Networks Using Random Walks
    Computer and Information Sciences - ISCIS 2005 (2005), pp. 284-293.
    by Pascal Pons, Matthieu Latapy
    posted to algorithms modules networks by carlk on 2008-06-01 03:33:10 as *****
  • Hierarchical multi-label prediction of gene function
    Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 830-836.
    by Zafer Barutcuoglu, Robert E Schapire, Olga G Troyanskaya
    posted to functionprediction go networks by carlk on 2008-05-29 19:58:58 as ***** along with 1 person jread82
  • NetworKIN: a resource for exploring cellular phosphorylation networks.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    by R Linding, LJ Jensen, A Pasculescu, M Olhovsky, K Colwill, P Bork, MB Yaffe, T Pawson
    posted to networks signaling by carlk on 2008-05-23 18:08:17 as ***** along with 4 people larsjuhljensen brianb guhjy bouncingbudha
  • Discovering regulatory and signalling circuits in molecular interaction networks.
    Bioinformatics, Vol. 18 Suppl 1 (2002)
    by T Ideker, O Ozier, B Schwikowski, AF Siegel
    posted to networks regulation signaling by carlk on 2008-05-23 18:03:43 as ***** along with 9 people and 2 groups cswinburne isimpson yaredo dragonrez okarsligil lfriedl noano koller frohike kdl Bioinformatics
  • Resolution limit in community detection
    Proc. Natl. Acad. Sci. USA, Vol. 104, No. 1. (2 January 2007), pp. 36-41.
    by Santo Fortunato, Marc Barthelemy
    edited by David O Siegmund
    posted to moduledetection modules by carlk on 2008-08-01 21:13:14 as ****
  • A tree-decomposition approach to protein structure prediction.
    Proc IEEE Comput Syst Bioinform Conf (2005), pp. 247-256.
    by J Xu, F Jiao, B Berger
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:49:50 as **** along with 1 person j3xucite
  • Dead-end elimination with backbone flexibility.
    Bioinformatics (Oxford, England), Vol. 23, No. 13. (1 July 2007)
    by I Georgiev, BR Donald
    posted to scp structure by carlk on 2008-06-26 18:31:28 as ****
  • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures.
    Proteins, Vol. 26, No. 4. (December 1996), pp. 363-376.
    by RW Hooft, C Sander, G Vriend
    posted to scp structure by carlk on 2008-06-26 18:21:59 as **** along with 1 person lna
  • Side chain substitution benchmark for peptide/MHC interaction.
    Protein science : a publication of the Protein Society, Vol. 17, No. 6. (June 2008), pp. 977-982.
    by B Knapp, U Omasits, W Schreiner
    posted to scp structure by carlk on 2008-06-26 16:20:59 as ****
  • Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service.
    BMC bioinformatics, Vol. 9 (2008)
    by JG Kim, D Park, BC Kim, SW Cho, YT Kim, YJ Park, HJ Cho, H Park, KB Kim, KO Yoon, SJ Park, BM Lee, J Bhak
    posted to databases linkprediction networks by carlk on 2008-06-10 16:52:23 as ****
  • GS2PATH: A web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data.
    Bioinformation, Vol. 2, No. 5. (2007), pp. 194-196.
    by JO Yang, P Charny, B Lee, S Kim, J Bhak, HG Woo
    posted to go by carlk on 2008-06-03 16:07:41 as **** along with 1 person guhjy
  • Gene Ontology annotations: what they mean and where they come from.
    BMC bioinformatics, Vol. 9 Suppl 5 (2008)
    by DP Hill, B Smith, MS McAndrews-Hill, JA Blake
    posted to go by carlk on 2008-06-03 16:07:03 as **** along with 7 people and 1 group guhjy dchughes mariakmejia lmichan grahamc dullhunk sabinaleo e-research en ciencias médicas y biológicas
  • On Steiner Versions of (bi)Connectivity in Network Problems
    Graphs and Combinatorics, Vol. 20, No. 2. (1 June 2004), pp. 263-273.
    by A Volgenant, CW Duin
    posted to functionprediction networks steiner by carlk on 2008-05-30 17:32:34 as ****
  • PDZ Domain Binding Selectivity Is Optimized Across the Mouse Proteome
    Science, Vol. 317, No. 5836. (20 July 2007), pp. 364-369.
    by Michael A Stiffler, Jiunn R Chen, Viara P Grantcharova, Ying Lei, Daniel Fuchs, John E Allen, Lioudmila A Zaslavskaia, Gavin Macbeath
    posted to domains evolution networks by carlk on 2008-05-23 18:15:17 as **** along with 2 people zwang phoenixzxl
  • Identification and analysis of evolutionarily cohesive functional modules in protein networks.
    Genome Res (31 January 2006)
    by Mónica Campillos, Christian von Mering, Lars Juhl J Jensen, Peer Bork
    posted to functionprediction modules networks by carlk on 2008-05-23 18:10:32 as **** along with 7 people and 2 groups lfriedl balajis nirfriedman nickluscombe koller dbgoodman larsjuhljensen kdl EBI-regulation
  • How biologically relevant are interaction-based modules in protein networks?
    Genome Biol, Vol. 5, No. 11. (2004)
    by JF Poyatos, LD Hurst
    posted to networks protein by carlk on 2008-05-20 19:46:04 as **** along with 4 people and 1 group ggallone jfr bpcusack yoonk Jarman Lab
  • A domain-based approach to predict protein-protein interactions
    BMC Bioinformatics, Vol. 8 (13 June 2007), 199.
    by Mudita Singhal, Haluk Resat
    posted to domains linkprediction networks by carlk on 2008-06-11 06:13:59 as *** along with 3 people and 2 groups yas grahamc phoenixzxl T_lab ParkinsonLab_at_MaRS
  • The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation.
    In silico biology, Vol. 7, No. 6. (2007), pp. 575-582.
    by YA Kourmpetis, A van der Burgt, MC Bink, CJ Ter Braak, RC van Ham
    posted to go by carlk on 2008-06-03 16:06:47 as ***
  • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    Nature, Vol. 430, No. 6995. (01 July 2004), pp. 88-93.
    by Jing-Dong J Han, Nicolas Bertin, Tong Hao, Debra S Goldberg, Gabriel F Berriz, Lan V Zhang, Denis Dupuy, Albertha JM Walhout, Michael E Cusick, Frederick P Roth, Marc Vidal
    posted to moduledetection networks protein yeast by carlk on 2008-05-23 17:42:09 as *** along with 27 people and 2 groups saket lawraga diamantis davidecellai dragonrez lfriedl balajis yoh j3xucite kintoki koller mikaelhuss ruvido gcalda grahamc iris_2001 lpfernandes winterschlaefer Evangelia cdeane shung phoenixzxl stefanoallesina ellakat frohike shikin ksiek kdl GeneGo
  • Information-theoretic approach to network modularity
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 71, No. 4. (2005)
    by Etay Ziv, Manuel Middendorf, Chris H Wiggins
    posted to moduledetection modules by carlk on 2008-05-20 20:32:42 as *** along with 1 person jwhitney
  • 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 moduledetection modules networks tmpcite1 by carlk on 2008-05-20 20:30:48 as *** along with 16 people and 1 group kaarsinogen pdelosri jfr chad_davis balajis nirfriedman dquest grahamc cjeans hpaces Pao-Yang oktie Borelli AbnerCYH cerca ethkim EPFL_SB_ITP_LBS
  • Predicting protein complex membership using probabilistic network reliability.
    Genome Res, Vol. 14, No. 6. (June 2004), pp. 1170-1175.
    by S Asthana, OD King, FD Gibbons, FP Roth
    posted to complex linkprediction networks noise by carlk on 2008-05-20 20:12:00 as *** along with 1 person iris_2001
  • Predicting gene function from patterns of annotation.
    Genome research, Vol. 13, No. 5. (May 2003), pp. 896-904.
    by OD King, RE Foulger, SS Dwight, JV White, FP Roth
    posted to functionprediction networks by carlk on 2008-05-20 20:08:00 as ***
  • Predicting phenotype from patterns of annotation.
    Bioinformatics (Oxford, England), Vol. 19 Suppl 1 (2003)
    by OD King, JC Lee, AM Dudley, DM Janse, GM Church, FP Roth
    posted to linkprediction networks by carlk on 2008-05-20 20:05:33 as ***
  • Functional maps of protein complexes from quantitative genetic interaction data.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by S Bandyopadhyay, R Kelley, NJ Krogan, T Ideker
    posted to networks transcription by carlk on 2008-05-20 19:57:58 as *** along with 4 people roys giovenko emmackinnon guhjy
  • Evolution and dynamics of protein interactions and networks
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Emmanuel D Levy, Jose B Pereira-Leal
    posted to review networks dynamics by carlk on 2008-11-21 20:37:05 as ** along with 6 people paolomarcatili guhjy neils cabbagesofdoom marck zdai
  • metaTIGER: a metabolic evolution resource.
    Nucleic acids research (25 October 2008)
    by John W W Whitaker, Ivica Letunic, Glenn A A McConkey, David R R Westhead
    posted to metabolic by carlk on 2008-11-19 23:07:25 as **
  • Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.
    by Morgan N Price, Paramvir S Dehal, Adam P Arkin
    posted to transcription regulation networks alignment by carlk on 2008-11-19 23:04:20 as ** along with 10 people and 3 groups druvus treangen operon dpollard dquest djkt zwang cabbagezs heliopais blobbybirdman EisenLab cis-regulatory-evolution Myxo group
  • The Shapley value of phylogenetic trees.
    Journal of mathematical biology, Vol. 56, No. 4. (April 2008), pp. 479-497.
    by CJ Haake, A Kashiwada, FE Su
    posted to phylogeny by carlk on 2008-11-19 23:03:15 as **
  • Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length
    Journal of Computational Biology, Vol. 14, No. 6. (2007), pp. 817-838.
    by Benny Chor, Tamir Tuller
    posted to networks distance algorithms by carlk on 2008-11-19 23:02:19 as ** along with 1 person jiny
  • A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules
    Science, Vol. 302, No. 5643. (10 October 2003), pp. 249-255.
    by Joshua M Stuart, Eran Segal, Daphne Koller, Stuart K Kim
    posted to regulatory regulation networks expression by carlk on 2008-11-19 21:47:35 as ** along with 20 people and 7 groups saket pengchy nolodie jeremymiller tharris dragonrez textoris lfriedl balajis nuke2005 maryee tardigrade opheliav wnpx neveaire macle raylim lp2 karfunkel vertikalist C. elegans / WormBase kdl Biostatistics Computational-Genomics Bioinformatics Neuroscience BTS-PT-AS-CS
  • Evolution of genetic potential.
    PLoS Comput Biol, Vol. 1, No. 3. (August 2005)
    by L Ancel Meyers, FD Ancel, M Lachmann
    posted to evolution by carlk on 2008-11-19 21:47:10 as ** along with 2 people and 1 group rklancer livingthingdan livingthing
  • A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons
    PLoS Comput Biol, Vol. 4, No. 11. (14 November 2008), e1000219.
    by Roxana A Stefanescu, Viktor K Jirsa
    posted to networks brain by carlk on 2008-11-19 21:46:10 as ** along with 1 person fbaroni
  • A Hierarchy of Time-Scales and the Brain
    PLoS Comput Biol, Vol. 4, No. 11. (14 November 2008), e1000209.
    by Stefan J Kiebel, Jean Daunizeau, Karl J Friston
    posted to network brain by carlk on 2008-11-19 21:45:46 as ** along with 4 people nishiokov j-ito ocs DNAcombo
  • CGI: a new approach for prioritizing genes by combining gene expression and proteinprotein interaction data
    Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. 215-221.
    by Ma, Xiaotu, Lee, Hyunju, Sun, Fengzhu
    posted to ranking networks disease alzheimer by carlk on 2008-11-14 21:11:47 as ** along with 3 people yyby jiny nedwards
  • Changes in connectivity profiles define functionally distinct regions in human medial frontal cortex.
    Proc Natl Acad Sci U S A, Vol. 101, No. 36. (7 September 2004), pp. 13335-13340.
    by H Johansen-Berg, TE Behrens, MD Robson, I Drobnjak, MF Rushworth, JM Brady, SM Smith, DJ Higham, PM Matthews
    posted to networks functionprediction brain by carlk on 2008-10-28 03:04:21 as ** along with 1 person memphisphil
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