saket's library 163 articles Export

	How and when should interactome-derived clusters be used to predict functional modules and protein function? [My Copy] Bioinformatics (Oxford, England) (21 September 2009) by Jimin Song, Mona Singh posted to survey networks modules functional_modules function_prediction clusterings by saket on 2009-10-03 07:37:28 as along with 3 people grahamc jsuchit carlk
	Scalable modeling of real graphs using Kronecker multiplication [My Copy] In ICML '07: Proceedings of the 24th international conference on Machine learning (2007), pp. 497-504. by Jure Leskovec, Christos Faloutsos posted to time_machine model_based by saket on 2009-09-22 07:53:46 as along with 1 person kohei-h
	The role mining problem: finding a minimal descriptive set of roles [My Copy] In SACMAT '07: Proceedings of the 12th ACM symposium on Access control models and technologies (2007), pp. 175-184. by Jaideep Vaidya, Vijayalakshmi Atluri, Qi Guo posted to summarize compression complexity by saket on 2009-09-21 05:20:46 as along with 2 people jfischer tmmurali
	Portraits of Complex Networks [My Copy] (28 Feb 2008) by J. P. Bagrow, E. M. Bollt, J. D. Skufca, D. ben-Avraham posted to visualization networks by saket on 2009-09-21 03:10:23 as along with 2 people jaspervoskuilen carlk
	Exploring genetic interactions and networks with yeast. [My Copy] Nature reviews. Genetics, Vol. 8, No. 6. (June 2007), pp. 437-449. by Charles Boone, Howard Bussey, Brenda J. Andrews posted to ssl genetic_interactions genetic_interaction by saket on 2009-09-17 01:14:29 as along with 12 people nzm sarahbates mtaschuk Petersarkies lp2 Annab balajis zwang carlk guhjy marck hryk
	Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network [My Copy] Genome Biology, Vol. 10, No. 9. (03 September 2009), R91. by Bolan Linghu, Evan Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi posted to human_diseases by saket on 2009-09-07 21:59:19 as along with 6 people and 1 group mchelen fstrozzi bdessailly farhat daforerog barriot Orengo Group Journal Picks
	Learning patterns in the dynamics of biological networks [My Copy] In KDD '09: Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining (2009), pp. 977-986. by Chang H. You, Lawrence B. Holder, Diane J. Cook posted to time_machine by saket on 2009-08-26 22:03:39 as
	The origins and evolution of functional modules: lessons from protein complexes. [My Copy] Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Vol. 361, No. 1467. (29 March 2006), pp. 507-517. by Jose B. Pereira-Leal, Emmanuel D. Levy, Sarah A. Teichmann posted to modules evolution duplication complexes by saket on 2009-08-24 18:14:55 as along with 6 people biomcgary agustinarce bicko choonpeng cjeans cmzmasek
	Evolutionary plasticity of genetic interaction networks [My Copy] Nat Genet, Vol. 40, No. 4. (April 2008), pp. 390-391. by Julia Tischler, Ben Lehner, Andrew G. Fraser posted to ssl pathways genetic_interactions by saket on 2009-08-20 16:27:57 as along with 7 people and 1 group dakelley aheilbut caseybrown smgomez ptrobajo emptyhb zwang GomezLab
	Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications [My Copy] BMC Evolutionary Biology, Vol. 4, No. 1. (27 November 2004), 51. by Johannes Berg, Michael Lassig, Andreas Wagner posted to evolution model_based networks time_machine by saket on 2009-08-06 17:39:44 as along with 8 people sergiun chica kaarsinogen diamantis phoenixzxl j3xucite timflutre iris_2001
	A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction [My Copy] Journal of Computational Biology, Vol. 13, No. 2. (March 2006), pp. 320-335. by Dannie Durand, Bjarni V. Halldorsson, Benjamin Vernot posted to phylogenetic_trees time_machine by saket on 2009-08-05 20:37:00 as along with 1 person parnell
	Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 51. (18 December 2007), pp. 20449-20453. by John W. Pinney, Grigoris D. Amoutzias, Magnus Rattray, David L. Robertson posted to phylogenetic_trees time_machine by saket on 2009-08-05 19:44:48 as along with 7 people carlk biomcgary tmmurali grahamc cjeans Pao-Yang hplatero
	The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 3. (22 January 2008), pp. 950-954. by Aviva Presser, Michael B. Elowitz, Manolis Kellis, Roy Kishony posted to time_machine by saket on 2009-08-05 18:55:07 as along with 10 people carlk ellarond leemond31 robfsouza loukialili pradiptaray cjeans zwang roys phoenixzxl
	Reverse engineering the evolution of protein interaction networks. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2009), pp. 190-202. by Todd A. Gibson, Debra S. Goldberg posted to phylogenetic_trees time_machine by saket on 2009-08-05 17:29:05 as
	Duplication-divergence model of protein interaction network [My Copy] (30 Nov 2004) by I. Ispolatov, P. L. Krapivsky, A. Yuryev posted to model_based time_machine by saket on 2009-08-05 16:23:29 as
	Identification of conserved protein complexes based on a model of protein network evolution [My Copy] Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. e170-176. by Eitan Hirsh, Roded Sharan posted to time_machine by saket on 2009-08-05 16:13:31 as
	Specificity and evolvability in eukaryotic protein interaction networks. [My Copy] PLoS computational biology, Vol. 3, No. 2. (16 February 2007), e25. by Pedro Beltrao, Luis Serrano posted to time_machine by saket on 2009-08-05 16:01:35 as along with 6 people chica kiekyon marti aalibes dylan77 aheilbut
	How the global structure of protein interaction networks evolves. [My Copy] Proceedings. Biological sciences / The Royal Society, Vol. 270, No. 1514. (7 March 2003), pp. 457-466. by Andreas Wagner posted to time_machine by saket on 2009-08-05 15:55:54 as along with 3 people chica yoh iris_2001
	Evolution at the system level: the natural history of protein interaction networks [My Copy] Trends in Ecology & Evolution, Vol. 22, No. 7. (30 July 2007), pp. 366-373. by M. Stumpf, W. Kelly, T. Thorne, C. Wiuf posted to survey time_machine by saket on 2009-08-05 15:51:50 as along with 2 people agustinarce balajis
	Unequal evolutionary conservation of human protein interactions in interologous networks. [My Copy] Genome biology, Vol. 8, No. 5. (29 May 2007), R95. by Kevin R. Brown, Igor Jurisica posted to time_machine by saket on 2009-08-05 15:47:17 as along with 6 people chica cerca diamantis grahamc zwang winterschlaefer
	Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution [My Copy] PLoS Comput Biol, Vol. 3, No. 7. (6 July 2007), e118. by Fereydoun Hormozdiari, Petra Berenbrink, Nataša Pržulj, S. Cenk Sahinalp posted to time_machine by saket on 2009-08-05 15:19:36 as along with 2 people babakap grahamc
	Molecular basis for evolving modularity in the yeast protein interaction network. [My Copy] PLoS computational biology, Vol. 3, No. 11. (1 November 2007), e226. by Ariel Fernández posted to time_machine by saket on 2009-08-05 14:58:03 as along with 6 people pradiptaray tomhebbron zwang niallhaslam Ema phoenixzxl
	Modeling protein network evolution under genome duplication and domain shuffling. [My Copy] BMC systems biology, Vol. 1 (2007) by Kirill Evlampiev, Hervé Isambert posted to time_machine by saket on 2009-08-05 14:47:39 as along with 2 people tomhebbron carlk
	Preferential protection of protein interaction network hubs in yeast: evolved functionality of genetic redundancy. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 4. (29 January 2008), pp. 1243-1248. by Ran Kafri, Orna Dahan, Jonathan Levy, Yitzhak Pilpel posted to duplication time_machine by saket on 2009-08-04 22:41:02 as along with 5 people and 1 group cjeans zwang janek04 wsjames mclarenv Oxford Virology
	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 evolution modules networks time_machine by saket on 2009-08-04 22:08:23 as along with 8 people chica carlk paolomarcatili guhjy neils cabbagesofdoom marck zdai
	Unraveling Protein Networks with Power Graph Analysis [My Copy] PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000108. by Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder posted to compression modules networks summarize by saket on 2009-08-04 22:02:47 as along with 24 people and 2 groups colmryan carlk diamantis yyby jfr jiny aramesh2 AbnerCYH jmuhlich MatthiasReimann royerloic Ema lptolik kengg roys reyez tmmurali nuin Borelli askrajiv renatomilani stajich sebk rsantana Mycology OPIG
	The evolution of protein interaction networks in regulatory proteins. [My Copy] Comparative and functional genomics, Vol. 5, No. 1. (2004), pp. 79-84. by Gregory D. Amoutzias, David L. Robertson, Erich Bornberg-Bauer posted to time_machine by saket on 2009-08-04 21:49:18 as
	Conservation and topology of protein interaction networks under duplication-divergence evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 29. (22 July 2008), pp. 9863-9868. by Kirill Evlampiev, Hervé Isambert posted to evolution model_based motifs time_machine by saket on 2009-08-04 21:41:32 as along with 3 people winterschlaefer Garamonfok bpcusack
	Protein evolution on a human signaling network [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 21. by Qinghua Cui, Enrico Purisima, Edwin Wang posted to time_machine by saket on 2009-08-04 20:58:43 as along with 3 people MaxH renatomilani druvus
	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 complexes evolution modules time_machine by saket on 2009-08-04 20:44:21 as along with 11 people and 1 group carlk chica dakelley tomhebbron davidalee leemond31 druvus kiekyon neils tmmurali grahamc Orengo Group Journal Picks
	Evidence of Interaction Network Evolution by Whole-Genome Duplications: A Case Study in MADS-Box Proteins [My Copy] Mol Biol Evol, Vol. 24, No. 3. (1 March 2007), pp. 670-678. by Amelie S. Veron, Kerstin Kaufmann, Erich Bornberg-Bauer posted to time_machine by saket on 2009-08-04 20:24:28 as along with 3 people and 3 groups dpollard dchughes TaqSys EisenLab G4ID Genetics-of-Gambling
	Model criticism based on likelihood-free inference, with an application to protein network evolution. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 26. (30 June 2009), pp. 10576-10581. by Oliver Ratmann, Christophe Andrieu, Carsten Wiuf, Sylvia Richardson posted to evolution model_based time_machine by saket on 2009-08-04 19:53:49 as along with 2 people guhjy TRHvidsten
	Comparison of protein interaction networks reveals species conservation and divergence [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (17 October 2006), 457. by Zhi Liang, Meng Xu, Maikun Teng, Liwen Niu posted to conserved_modules evolution networks time_machine by saket on 2009-08-04 19:36:58 as along with 7 people and 1 group thegoose thegoose2 tharris balajis biehl cerca carlk C. elegans / WormBase
	Replaying the evolutionary tape: biomimetic reverse engineering of gene networks. [My Copy] Annals of the New York Academy of Sciences, Vol. 1158, No. 1. (March 2009), pp. 234-245. by Daniel Marbach, Claudio Mattiussi, Dario Floreano posted to evolution gene_expression time_machine by saket on 2009-08-04 19:13:15 as
	Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (27 May 2009), 119. by Bjorn von Reumont, Karen Meusemann, Nikolaus Szucsich, et al.Emiliano Dell'ampio, Vivek G. Shankar, Daniela Bartel, Sabrina Simon, Harald Letsch, Roman Stocsits, Yun X. Luan, Johann Wagele, Gunther Pass, Heike Hadrys, Bernhard Misof posted to evolution phylogenetic_trees time_machine by saket on 2009-08-04 19:08:10 as
	Clustering by common friends finds locally significant proteins mediating modules [My Copy] Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1124-1131. by Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, Michael Schroeder posted to function_prediction hierarchical inter_modules by saket on 2009-07-23 15:52:11 as along with 2 people carlk zwang
	Deciphering the connectivity structure of biological networks using MixNet [My Copy] BMC Bioinformatics, Vol. 10, No. Suppl 6. (2009), S17. by Franck Picard, Vincent Miele, Jean J. Daudin, Ludovic Cottret, Stephane Robin posted to inter_modules model_based modules by saket on 2009-07-23 15:15:56 as along with 1 person and 1 group sillitoe Orengo Group Journal Picks
	Community detection in graphs [My Copy] (3 Jun 2009) by Santo Fortunato posted to clusterings hierarchical model_based modularity modules survey by saket on 2009-07-21 21:35:33 as along with 14 people ecome AaronMcDaid pdlug dpf Bolozna lawraga Kovanen marinari Diego_Prada juhop janpaniev acrmartins aheilbut deanmalmgren
	Computing communities in large networks using random walks (long version) [My Copy] (12 Dec 2005) by Pascal Pons, Matthieu Latapy posted to clusterings modules random_walks by saket on 2009-07-21 21:27:53 as along with 3 people cgaugain ansobol ltabourier
	Hierarchical structure and the prediction of missing links in networks [My Copy] Nature, Vol. 453, No. 7191. (01 May 2008), pp. 98-101. by Aaron Clauset, Cristopher Moore, M. E. J. Newman posted to hierarchical link_prediction model_based by saket on 2009-07-21 20:47:57 as along with 46 people ipark-kaist carlk gtgt15 wei_tang Kovanen diamantis cfelipesp orahcio rcrane kubyaddi pbull Ema jago cmor balicea kengg jjray soramame_0518 deanmalmgren briordan hryk tny AbnerCYH cactus tmmurali akshat bryanhughes gagliol margaritis guhjy craigwilson06 cmmorel eyliu markusd elsantosneto pinney i-stevenson fbaroni nedwards apwesolowski Borelli ptrobajo dpf rds lfriedl sen_cheng
	Statistical properties of community structure in large social and information networks [My Copy] In WWW '08: Proceeding of the 17th international conference on World Wide Web (2008), pp. 695-704. by Jure Leskovec, Kevin J. Lang, Anirban Dasgupta, Michael W. Mahoney posted to modularity social_networks validating_clusterings by saket on 2009-07-21 17:38:19 as along with 6 people dschafer laurobeltrao agulli tnhh ChaTo beete
	Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 69. by Antonio Marco, Ignacio Marin posted to function_prediction gene_ontology go_cut hierarchical by saket on 2009-07-21 02:18:37 as along with 4 people fgibson kiekyon sjcockell barriot
	Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 74. by Roland Pache, M. Babu, Patrick Aloy posted to complexes core_attachment by saket on 2009-07-21 01:59:10 as
	CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure [My Copy] Bioinformatics, Vol. 23, No. 14. (15 July 2007), pp. 1801-1806. by Mattias Jakobsson, Noah A. Rosenberg posted to clusterings comparing_clusterings module_ensembles by saket on 2009-07-20 23:39:45 as along with 3 people carlk scryrps ryanraaum
	A critical assessment of Mus musculus gene function prediction using integrated genomic evidence [My Copy] Genome Biology, Vol. 9, No. Suppl 1. (2008), S2. by Lourdes P. Castillo, Murat Tasan, Chad Myers, et al.Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Lin, Gabriel Berriz, Francis Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David Hill, David W. Farley, Chris Grouios, Debajyoti Ray, Judith Blake, Minghua Deng, Michael Jordan, William Noble, Quaid Morris, Judith K. Seetharaman, Ziv B. Joseph, Ting Chen, Fengzhu Sun, Olga Troyanskaya, Edward Marcotte, Dong Xu, Timothy Hughes, Frederick Roth posted to function_prediction ml survey by saket on 2009-07-20 22:01:26 as along with 6 people phoenixzxl carlk kgutwin ptrobajo guhjy aconesa
	Systems biology: Untangling the protein web [My Copy] Nature, Vol. 460, No. 7253. (15 July 2009), pp. 415-418. by Nathan Blow posted to experimental survey by saket on 2009-07-17 21:21:49 as along with 14 people and 1 group robertrentzsch pekrau apocapoc psique leemond31 colmryan reyez carlk guhjy tmmurali dswan dullhunk renatomilani agonzale Orengo Group Journal Picks
	Detection of functional modules from protein interaction networks [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 54, No. 1. (1 January 2004), pp. 49-57. by Jose B. Pereira-Leal, Anton J. Enright, Christos A. Ouzounis posted to modules networks by saket on 2009-07-15 22:38:03 as along with 4 people carlk ujh opheliav wnpx
	Using diversity in cluster ensembles [My Copy] Systems, Man and Cybernetics, 2004 IEEE International Conference on In Systems, Man and Cybernetics, 2004 IEEE International Conference on, Vol. 2 (2004), pp. 1214-1219 vol.2. by L. I. Kuncheva, S. T. Hadjitodorov posted to module_ensembles modules by saket on 2009-07-13 00:00:41 as
	Model-based clustering for social networks [My Copy] Journal of the Royal Statistical Society: Series A (Statistics in Society), Vol. 170, No. 2. (March 2007), pp. 301-354. by Mark S. Handcock, Adrian E. Raftery, Jeremy M. Tantrum posted to model_based by saket on 2009-07-10 17:13:53 as along with 4 people and 2 groups makrehchi galyardt ctacmo Pao-Yang Statistics_and_Social_Science Biostatistics
	Information-based clustering [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 51. (20 December 2005), pp. 18297-18302. by Noam Slonim, Gurinder S. Atwal, Gašper Tkačik, William Bialek posted to model_based by saket on 2009-07-10 17:10:06 as along with 11 people and 1 group carlk tmmurali kuhn textoris okarsligil bayesian balicea jdiggans dylan77 nklee quianominorleo Bioinformatics

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networks	34
human_disease	31
time_machine	30
clusterings	25
evolution	23
modules	21
survey	14
microarray	13
algorithms	12
function_prediction	12
model_based	10
modularity	10
ml	8
complexes	7
compression	7
domains	6
hierarchical	5
phylogenetic_trees	5
software	5
validating_clusterings	5
ddi	4
gene_ontology	4
lp	4
motifs	4
overlapping_modules	4
semi_supervised	4
brain	3
choosing_k	3
conserved_modules	3
core_attachment	3
local_clustering	3
metabolic_networks	3
ppigexp	3
ppi_prediction	3
random_walks	3
summarize	3
trees	3
yeast	3
boolean_networks	2
duplication	2
evolutionary_biology	2
genetic_interactions	2
inter_modules	2
limit_clusterings	2
module_ensembles	2
pathways	2
protein_structure	2
small_world	2
social_networks	2
ssl	2
basketball	1
blogs	1
comparing_clusterings	1
complexity	1
cover_time	1
dag	1
diffusion	1
dynamics	1
enrichment	1
essentiality	1
experimental	1
fly	1
fmri	1
functional_modules	1
game_theory	1
gene_expression	1
genetic_interaction	1
go_cut	1
human_diseases	1
intra_modules	1
link_prediction	1
myers_terms	1
orthologs	1
parismony	1
social_animals	1
steiner_tree	1
uniprot	1
visualization	1
women	1
worm	1

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