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	Mixture models and exploratory analysis in networks [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 23. (5 June 2007), pp. 9564-9569. by M. E. J. Newman, E. A. Leicht posted to networks by carlk on 2009-09-22 20:52:10 as along with 12 people AaronMcDaid Kovanen conradlee stepapergroups cfelipesp guhjy jfr baronka sebastien_vigneau jaspervoskuilen stefanoallesina compbio
	Circuits through prescribed vertices in <I>k</I>-connected <I>k</I>-regular graphs [My Copy] Journal of Graph Theory, Vol. 39, No. 2. (2002), pp. 145-163. by Roland Häggkvist, Wolfgang Mader posted to networks graph_theory by carlk on 2009-09-19 18:06:10 as
	Learning signaling network structures with sparsely distributed data. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 16, No. 2. (February 2009), pp. 201-212. by K. Sachs, S. Itani, J. Carlisle, G. P. Nolan, D. Pe'er, D. A. Lauffenburger posted to linkprediction networks rgrg signaling by carlk on 2009-03-30 20:44:23 as along with 3 people mstumpf frohike brianb
	Protein complex identification by supervised graph local clustering [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i250-268. by Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph posted to community complex networks by carlk on 2009-01-22 23:55:36 as along with 3 people adking80 saket neils
	Evolution and dynamics of protein interactions and networks [My Copy] Current Opinion in Structural Biology, Vol. 18, No. 3. (June 2008), pp. 349-357. by E. Levy, J. Pereiraleal posted to dynamics networks review by carlk on 2008-11-21 20:37:05 as along with 8 people saket chica paolomarcatili guhjy neils cabbagesofdoom marck zdai
	Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length [My Copy] Journal of Computational Biology, Vol. 14, No. 6. (2007), pp. 817-838. by Benny Chor, Tamir Tuller posted to algorithms distance networks by carlk on 2008-11-19 23:02:19 as along with 2 people saket jiny
	Towards zoomable multidimensional maps of the cell [My Copy] 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 12 people Scis0000002 agonzale tmmurali kuhn cmmorel yas balajis thomaskelder dullhunk guhjy AlexanderPico Borelli
	Relating whole-genome expression data with protein-protein interactions. [My Copy] 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 10 people saket Robinder gurkanbebek gespim grahamc cjeans iris_2001 kintoki paolomarcatili nedwards
	Residue-rotamer-reduction algorithm for the protein side-chain conformation problem [My Copy] 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 4 people and 2 groups dfgreen bicko marcius bluvsh1 BioinfoCIPF SGU-CIPF
	Exploring conformational space using a mean field technique with MOLS sampling. [My Copy] Journal of biosciences, Vol. 32, No. 5. (August 2007), pp. 909-920. by P. A. 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 [My Copy] Bioinformatics, Vol. 18, No. suppl_1. (1 July 2002), pp. S145-154. by Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer posted to bicriteria clustering expression moduledetection modules networks by carlk on 2008-06-20 17:20:17 as along with 5 people meanerelk poirel saket chad_davis srp33
	Annotating pathways in interaction networks. [My Copy] 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 [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 31, No. 21. (1 November 2003), pp. 6283-6289. by Sabine Tornow, H. W. Mewes posted to bicriteria moduledetection modules networks by carlk on 2008-06-12 21:32:17 as along with 4 people yaredo saket bertelsen jiny
	Greedily building protein networks with confidence. [My Copy] Bioinformatics, Vol. 19, No. 15. (12 October 2003), pp. 1869-1874. by J. S. Bader posted to complexes networks steiner by carlk on 2008-06-12 18:24:48 as along with 2 people anf iris_2001
	An automated method for finding molecular complexes in large protein interaction networks. [My Copy] BMC Bioinformatics, Vol. 4, No. 1. (13 January 2003) by G. D. Bader, C. W. Hogue posted to moduledetection modules networks by carlk on 2008-06-12 18:15:53 as along with 10 people and 2 groups zufar dswan waqaralikeble cswinburne jiny dragonrez lfriedl nirfriedman massivemayhem ethkim Bioinformatics kdl
	Functional evaluation of domain-domain interactions and human protein interaction networks [My Copy] 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 [My Copy] 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. [My Copy] 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. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008), 50. by A. del Pozo, F. Pazos, A. Valencia posted to go by carlk on 2008-06-03 16:08:36 as along with 10 people and 2 groups biomcgary MarcoAlvarez sgoetz wilbur barry tny grahamc sobolevnrm barriot guhjy Bioinformatics baker-group
	Use and misuse of the gene ontology annotations [My Copy] Nature Reviews Genetics, Vol. 9, No. 7. (13 May 2008), pp. 509-515. 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 41 people and 3 groups lisa1 singhsh epigenetics davidmam Thaverkamp druvus dullhunk suizan dolchan Borelli Zephyrus VGreiff klo thomaskelder ilyashl phoenixzxl MarcoAlvarez isakemal bertelsen daforerog jfr djkt guhjy aheilbut mariakmejia cmzmasek A_Olympia realzhang roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck rvosa bpcusack 8_01 logics of knowledge FAB-lab
	Computing Communities in Large Networks Using Random Walks [My Copy] 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 along with 1 person studentx
	Hierarchical multi-label prediction of gene function [My Copy] 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 2 people and 1 group egibaja jread82 Multilabel Classification
	NetworKIN: a resource for exploring cellular phosphorylation networks. [My Copy] Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008) by R. Linding, L. J. Jensen, A. Pasculescu, et al.M. Olhovsky, K. Colwill, P. Bork, M. B. Yaffe, T. Pawson posted to networks signaling by carlk on 2008-05-23 18:08:17 as along with 6 people hryk coela larsjuhljensen brianb guhjy bouncingbudha
	Discovering regulatory and signalling circuits in molecular interaction networks. [My Copy] Bioinformatics (Oxford, England), Vol. 18 Suppl 1, No. suppl_1. (1 July 2002), pp. S233-240. by Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel posted to networks regulation signaling by carlk on 2008-05-23 18:03:43 as along with 15 people and 2 groups myzhang tmmurali akshayk wilbur arne junehlee cswinburne isimpson yaredo dragonrez okarsligil lfriedl noano koller frohike kdl Bioinformatics
	A complex-centric view of protein network evolution. [My Copy] Nucleic acids research, Vol. 37, No. 12. (1 July 2009), e88. by Nir Yosef, Martin Kupiec, Eytan Ruppin, Roded Sharan posted to protein ppi networks complexes complex by carlk on 2009-10-07 19:08:57 as along with 11 people and 1 group chica saket dakelley tomhebbron davidalee leemond31 druvus kiekyon neils tmmurali grahamc Orengo Group Journal Picks
	Modular decomposition of protein-protein interaction networks. [My Copy] Genome Biol, Vol. 5, No. 8. (2004) by J. Gagneur, R. Krause, T. Bouwmeester, G. Casari posted to moduledetection modules networks by carlk on 2009-04-25 23:31:09 as along with 4 people schwartzjmc ezotenko AbnerCYH tmmurali
	Network Features of the Mammalian Circadian Clock [My Copy] PLoS Biol, Vol. 7, No. 3. (10 March 2009), e1000052. by Julie E. Baggs, Tom S. Price, Luciano Ditacchio, Satchidananda Panda, Garret A. Fitzgerald, John B. Hogenesch posted to dynamics networks by carlk on 2009-04-25 22:09:21 as along with 4 people newgene sherdim kieran101 biomcgary
	Genome-wide atlas of gene expression in the adult mouse brain. [My Copy] Nature, Vol. 445, No. 7124. (11 January 2007), pp. 168-176. by Ed S. Lein, Michael J. Hawrylycz, Nancy Ao, et al.Mikael Ayres, Amy Bensinger, Amy Bernard, Andrew F. Boe, Mark S. Boguski, Kevin S. Brockway, Emi J. Byrnes, Lin Chen, Li Chen, Tsuey-Ming M. Chen, Mei Chi C. Chin, Jimmy Chong, Brian E. Crook, Aneta Czaplinska, Chinh N. Dang, Suvro Datta, Nick R. Dee, Aimee L. Desaki, Tsega Desta, Ellen Diep, Tim A. Dolbeare, Matthew J. Donelan, Hong-Wei W. Dong, Jennifer G. Dougherty, Ben J. Duncan, Amanda J. Ebbert, Gregor Eichele, Lili K. Estin, Casey Faber, Benjamin A. Facer, Rick Fields, Shanna R. Fischer, Tim P. Fliss, Cliff Frensley, Sabrina N. Gates, Katie J. Glattfelder, Kevin R. Halverson, Matthew R. Hart, John G. Hohmann, Maureen P. Howell, Darren P. Jeung, Rebecca A. Johnson, Patrick T. Karr, Reena Kawal, Jolene M. Kidney, Rachel H. Knapik, Chihchau L. Kuan, James H. Lake, Annabel R. Laramee, Kirk D. Larsen, Christopher Lau, Tracy A. Lemon, Agnes J. Liang, Ying Liu, Lon T. Luong, Jesse Michaels, Judith J. Morgan, Rebecca J. Morgan, Marty T. Mortrud, Nerick F. Mosqueda, Lydia L. Ng, Randy Ng, Geralyn J. Orta, Caroline C. Overly, Tu H. Pak, Sheana E. Parry, Sayan D. Pathak, Owen C. Pearson, Ralph B. Puchalski, Zackery L. Riley, Hannah R. Rockett, Stephen A. Rowland, Joshua J. Royall, Marcos J. Ruiz, Nadia R. Sarno, Katherine Schaffnit, Nadiya V. Shapovalova, Taz Sivisay, Clifford R. Slaughterbeck, Simon C. Smith, Kimberly A. Smith, Bryan I. Smith, Andy J. Sodt, Nick N. Stewart, Kenda-Ruth R. Stumpf, Susan M. Sunkin, Madhavi Sutram, Angelene Tam, Carey D. Teemer, Christina Thaller, Carol L. Thompson, Lee R. Varnam, Axel Visel, Ray M. Whitlock, Paul E. Wohnoutka, Crissa K. Wolkey, Victoria Y. Wong, Matthew Wood, Murat B. Yaylaoglu, Rob C. Young, Brian L. Youngstrom, Xu Feng F. Yuan, Bin Zhang, Theresa A. Zwingman, Allan R. Jones posted to brain databases by carlk on 2008-12-13 22:45:52 as along with 17 people and 4 groups brianb booker daforerog rupachile jfr dchughes adepace jclau mgaldzic nm JBEgwa01 cjeans N0131826 cmor rschulz dlmace jeremymiller EisenLab G4ID CHIP Genetics-of-Gambling
	Resolution limit in community detection [My Copy] 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. [My Copy] 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. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 13. (1 July 2007) by I. Georgiev, B. R. Donald posted to scp structure by carlk on 2008-06-26 18:31:28 as along with 1 person dfgreen
	Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. [My Copy] Proteins, Vol. 26, No. 4. (December 1996), pp. 363-376. by R. W. 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. [My Copy] 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. [My Copy] BMC bioinformatics, Vol. 9 (2008) by J. G. Kim, D. Park, B. C. Kim, et al.S. W. Cho, Y. T. Kim, Y. J. Park, H. J. Cho, H. Park, K. B. Kim, K. O. Yoon, S. J. Park, B. M. 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. [My Copy] Bioinformation, Vol. 2, No. 5. (2007), pp. 194-196. by J. O. Yang, P. Charny, B. Lee, S. Kim, J. Bhak, H. G. 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. [My Copy] BMC bioinformatics, Vol. 9 Suppl 5 (2008) by D. P. Hill, B. Smith, M. S. McAndrews-Hill, J. A. Blake posted to go by carlk on 2008-06-03 16:07:03 as along with 8 people and 1 group vkwn guhjy dchughes mariakmejia lmichan grahamc dullhunk sabinaleo e-research en ciencias médicas y biológicas
	On Steiner Versions of (bi)Connectivity in Network Problems [My Copy] Graphs and Combinatorics, Vol. 20, No. 2. (1 June 2004), pp. 263-273. by A. Volgenant, C. W. 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. [My Copy] Science (New York, N.Y.), Vol. 317, No. 5836. (20 July 2007), pp. 364-369. by Michael A. Stiffler, Jiunn R. Chen, Viara P. Grantcharova, et al.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 3 people HawkinsJohnC zwang phoenixzxl
	Identification and analysis of evolutionarily cohesive functional modules in protein networks. [My Copy] 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 8 people and 2 groups Garamonfok lfriedl balajis nirfriedman nickluscombe koller dbgoodman larsjuhljensen kdl EBI-regulation
	How biologically relevant are interaction-based modules in protein networks? [My Copy] Genome Biol, Vol. 5, No. 11. (2004) by J. F. Poyatos, L. D. 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
	Phylogenetic analysis of modularity in protein interaction networks [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (14 October 2009), 333. by Sinan Erten, Xin Li, Gurkan Bebek, Jing Li, Mehmet Koyuturk posted to phylogenetics paleodiktyology networks by carlk on 2009-12-07 15:12:26 as along with 9 people and 2 groups saket sillitoe biomcgary ppgardne grahamc zwang druvus barriot phoenixzxl Orengo Group Journal Picks Journal picks
	Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. [My Copy] PLoS pathogens, Vol. 4, No. 2. (15 February 2008) by M. I. Nelson, C. Viboud, L. Simonsen, et al.R. T. Bennett, S. B. Griesemer, K. St George, J. Taylor, D. J. Spiro, N. A. Sengamalay, E. Ghedin, J. K. Taubenberger, E. C. Holmes posted to flu reassortment by carlk on 2009-03-16 19:39:03 as
	A domain-based approach to predict protein-protein interactions [My Copy] 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 1 group yas grahamc phoenixzxl T_lab
	The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation. [My Copy] In silico biology, Vol. 7, No. 6. (2007), pp. 575-582. by Y. A. Kourmpetis, A. van der Burgt, M. C. Bink, C. J. Ter Braak, R. C. van Ham posted to go by carlk on 2008-06-03 16:06:47 as
	Evidence for dynamically organized modularity in the yeast protein\|[ndash]\|protein interaction network [My Copy] Nature, Vol. 430, No. 6995. (09 June 2004), pp. 88-93. by Jing-Dong J. Han, Nicolas Bertin, Tong Hao, et al.Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J. M. 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 31 people and 2 groups aceol daveGerrard colmryan mgomes 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 [My Copy] 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 [My Copy] 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. [My Copy] Genome Res, Vol. 14, No. 6. (June 2004), pp. 1170-1175. by S. Asthana, O. D. King, F. D. Gibbons, F. P. 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. [My Copy] Genome research, Vol. 13, No. 5. (May 2003), pp. 896-904. by O. D. King, R. E. Foulger, S. S. Dwight, J. V. White, F. P. Roth posted to functionprediction networks by carlk on 2008-05-20 20:08:00 as along with 1 person kimbie
	Predicting phenotype from patterns of annotation. [My Copy] Bioinformatics (Oxford, England), Vol. 19 Suppl 1 (2003) by O. D. King, J. C. Lee, A. M. Dudley, D. M. Janse, G. M. Church, F. P. Roth posted to linkprediction networks by carlk on 2008-05-20 20:05:33 as

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