poirel's library 47 articles Export

	Prediction of protein binding sites in protein structures using hidden Markov support vector machine [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 381. by Bin Liu, Xiaolong Wang, Lei Lin, Buzhou Tang, Qiwen Dong, Xuan Wang posted to no-tag by poirel on 2009-11-20 16:28:30 as
	Algorithms for effective querying of compound graph-based pathway databases [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 376. by Ugur Dogrusoz, Ahmet Cetintas, Emek Demir, Ozgun Babur posted to no-tag by poirel on 2009-11-20 16:26:51 as along with 3 people operon calderonv dullhunk
	Identification of genes involved in the same pathways using a Hidden Markov Model-based approach [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2945-2954. by Alexander Senf, Xue-wen Chen posted to no-tag by poirel on 2009-11-13 19:57:34 as along with 2 people and 1 group TRHvidsten ptrobajo Orengo Group Journal Picks
	The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes [My Copy] Nucl. Acids Res., Vol. 32, No. 18. (14 October 2004), pp. 5539-5545. by Andreas Ruepp, Alfred Zollner, Dieter Maier, et al.Kaj Albermann, Jean Hani, Martin Mokrejs, Igor Tetko, Ulrich Guldener, Gertrud Mannhaupt, Martin Munsterkotter, H. Werner Mewes posted to no-tag by poirel on 2009-11-05 02:30:06 as along with 6 people and 1 group thegoose udivi tsoumakas gurkanbebek ichbins81 carlk Multilabel Classification
	Structural classification of zinc fingers: survey and summary. [My Copy] Nucleic acids research, Vol. 31, No. 2. (15 January 2003), pp. 532-550. by Sri S. Krishna, Indraneel Majumdar, Nick V. Grishin posted to no-tag by poirel on 2009-11-05 01:28:46 as along with 1 person ca3295
	The Death Domain Superfamily in Intracellular Signaling of Apoptosis and Inflammation [My Copy] Annual Review of Immunology, Vol. 25, No. 1. (2007), pp. 561-586. by Hyun H. Park, Yu C. Lo, Su C. Lin, Liwei Wang, Jin K. Yang, Hao Wu posted to no-tag by poirel on 2009-11-04 22:51:39 as
	Structure of Protein Interaction Networks and Their Implications on Drug Design [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (30 October 2009), e1000550. by Takeshi Hase, Hiroshi Tanaka, Yasuhiro Suzuki, So Nakagawa, Hiroaki Kitano posted to no-tag by poirel on 2009-10-30 12:30:13 as along with 9 people and 1 group kiekyon nickolay kshameer zwang phoenixzxl venancio CorinYeats ess30 jbesnard Orengo Group Journal Picks
	Network biology: understanding the cell's functional organization [My Copy] Nature Reviews Genetics, Vol. 5, No. 2. (01 February 2004), pp. 101-113. by Albert-Laszlo Barabasi, Zoltan N. Oltvai posted to no-tag by poirel on 2009-10-28 19:24:33 as along with 26 people and 1 group ess30 tonamswish asadrahman tmarscha cn_honjyo behindtherabbit yangjustinc lawraga sschurer hadesnumb cswinburne babakap carlk pkm daforerog diamantis okarsligil bayesian tny mmt grahamc mirzazadeh lpfernandes karfunkel vietanh0 nolodie Bioinformatics
	Toward accurate reconstruction of functional protein networks. [My Copy] Molecular systems biology, Vol. 5 (17 March 2009) by Nir Yosef, Lior Ungar, Einat Zalckvar, et al.Adi Kimchi, Martin Kupiec, Eytan Ruppin, Roded Sharan posted to no-tag by poirel on 2009-10-27 14:12:42 as along with 6 people jfr zwang roys renatomilani phoenixzxl biomcgary
	A Markov Blanket-Based Model for Gene Regulatory Network Inference [My Copy] IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 99, No. 1. (5555) by Ramesh Ram, Madhu Chetty posted to no-tag by poirel on 2009-10-15 23:13:49 as
	Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics [My Copy] PLoS ONE, Vol. 4, No. 10. (6 October 2009), e7310. by Mihaela E. Sardiu, Joshua M. Gilmore, Michael J. Carrozza, et al.Bing Li, Jerry L. Workman, Laurence Florens, Michael P. Washburn posted to no-tag by poirel on 2009-10-07 02:26:09 as along with 1 person brianb
	Kavosh: a new algorithm for finding network motifs [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 318. by Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabian, Elahe Elahi, et al.Abbas N. Dalini, Elnaz S. Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber, Ali M. Nejad posted to no-tag by poirel on 2009-10-04 17:10:49 as along with 1 person ashishanand
	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 no-tag by poirel on 2009-10-03 18:28:03 as along with 4 people saket chad_davis srp33 carlk
	The Modular Organization of Protein Interactions in Escherichia coli [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (2 October 2009), e1000523. by José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson posted to no-tag by poirel on 2009-10-03 17:30:44 as along with 6 people and 2 groups venancio CorinYeats biomcgary grahamc kiekyon dswan Orengo Group Journal Picks Bioinformatics
	Pre-processing of microarray data and analysis of differential expression. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 89-110. by Steffen Durinck posted to no-tag by poirel on 2009-10-01 23:54:19 as along with 3 people shikin jmcdonou klo
	Microarray data analysis for differential expression: a tutorial. [My Copy] Puerto Rico health sciences journal, Vol. 28, No. 2. (June 2009), pp. 89-104. by Erick Suárez, Ana Burguete, Geoffrey J. Mclachlan posted to springer_survey_active_networks by poirel on 2009-10-01 23:53:55 as
	Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. [My Copy] FEBS letters, Vol. 470, No. 2. (24 March 2000), pp. 156-160. by J. DeRisi, B. van den Hazel, P. Marc, et al.E. Balzi, P. Brown, C. Jacq, A. Goffeau posted to no-tag by poirel on 2009-10-01 22:10:25 as
	A Model for Measurement Error for Gene Expression Arrays [My Copy] Journal of Computational Biology, Vol. 8 (2001), pp. 557-569. by David M. Rocke, Blythe Durbin posted to no-tag by poirel on 2009-10-01 22:01:04 as
	Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 16. (31 July 2001), pp. 8961-8965. by M. Kathleen Kerr, Gary A. Churchill posted to no-tag by poirel on 2009-10-01 22:00:42 as along with 6 people and 1 group nuin textoris ghattem pbellec briordan klo SIMR bioinformatics
	A Model for Measurement Error for Gene Expression Arrays [My Copy] Journal of Computational Biology, Vol. 8 (2001), pp. 557-569. by David M. Rocke, Blythe Durbin posted to no-tag by poirel on 2009-10-01 22:00:06 as
	Network Motifs: Simple Building Blocks of Complex Networks [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 824-827. by R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon posted to no-tag by poirel on 2009-09-30 22:00:25 as along with 71 people and 10 groups jaspervoskuilen Sergey_gerbek nurban balabu ocs mjoach makrehchi schwartzjmc tomhebbron arsyed vtraag sergiun fierykylin Akimasa operon dlobo daforerog chasmand wei_tang darian orahcio babakap brewbooks phoenixzxl Md_2007 mtagaya heliopais kaarsinogen galyardt cswinburne mullonc camster korakot aalibes ChaTo imouthesmp Borelli lfriedl alexg balicea tny ssb wnpx ddahlem cmm donade neveaire griota gurkanbebek jtaylor josepe iris_2001 michaelmampaey rebeccamancy karfunkel lenov Evangelia roys tfogal zibuyu maralena stefanoallesina pbull cmor renatomilani shikin carlk applesnow subhacom i-stevenson ethkim complex networks GEB Philosophy_of_Information dbk-lab Blog_and_Wiki_Research kdl FAB-lab ColDyn ADMiRes GeneGo
	Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values [My Copy] Bioinformatics, Vol. 19, No. 10. (1 July 2003), pp. 1236-1242. by Stan Pounds, Stephan W. Morris posted to no-tag by poirel on 2009-09-20 22:33:39 as along with 2 people czeller ugengma
	An Algorithmic Framework for the Exact Solution of the Prize-Collecting Steiner Tree Problem [My Copy] Mathematical Programming, Vol. 105, No. 2. (1 February 2006), pp. 427-449. by Ivana Ljubić, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, Matteo Fischetti posted to no-tag by poirel on 2009-09-20 19:58:27 as
	Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture [My Copy] Molecular Systems Biology, Vol. 5 (18 August 2009) by Raja Jothi, S. Balaji, Arthur Wuster, et al.Joshua A. Grochow, Jorg Gsponer, Teresa M. Przytycka, L. Aravind, Madan M. Babu posted to no-tag by poirel on 2009-09-17 16:49:05 as along with 12 people ashishanand apocapoc brianb dswan sjcockell zwang fenghezi rdiaz megraw TRHvidsten jjray biomcgary
	RRW: repeated random walks on genome-scale protein networks for local cluster discovery [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (9 September 2009), 283. by Kathy Macropol, Tolga Can, Ambuj Singh posted to no-tag by poirel on 2009-09-10 03:00:17 as along with 3 people and 1 group sillitoe barriot phoenixzxl Orengo Group Journal Picks
	Optimization by Simulated Annealing. [My Copy] Science (New York, N.Y.), Vol. 220, No. 4598. (13 May 1983), pp. 671-680. by S. Kirkpatrick, C. D. Gelatt, M. P. Vecchi posted to no-tag by poirel on 2009-09-07 21:17:46 as along with 15 people duelines chrisfischer brothers vtraag rtsade jstephens kentz eskay czeller gale82 ddahlem Bc91 naegele ywlin newton1234
	Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data [My Copy] Journal of Computational Biology, Vol. 7, No. 6. (December 2000), pp. 805-817. by Trey Ideker, Vesteinn Thorsson, Andrew F. Siegel, Leroy E. Hood posted to no-tag by poirel on 2009-09-07 04:30:43 as along with 1 person baldigroup
	The worst-case time complexity for generating all maximal cliques and computational experiments [My Copy] Theoretical Computer Science, Vol. 363, No. 1. (25 October 2006), pp. 28-42. by E. Tomita, A. Tanaka, H. Takahashi posted to no-tag by poirel on 2009-07-30 20:28:20 as along with 2 people conservatism renatocarmo
	Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles [My Copy] Research in Computational Molecular Biology (2008), pp. 347-359. by Igor Ulitsky, Richard Karp, Ron Shamir posted to no-tag by poirel on 2009-07-25 19:38:36 as along with 2 people ptrobajo akshayk
	Complex discovery from weighted PPI networks. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1891-1897. by Guimei Liu, Limsoon Wong, Hon Nian N. Chua posted to no-tag by poirel on 2009-07-23 04:00:57 as along with 7 people kgutwin kiekyon zwang friendpine neils tmmurali grahamc
	Selecting the right interestingness measure for association patterns [My Copy] In KDD '02: Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining (2002), pp. 32-41. by Pang N. Tan, Vipin Kumar, Jaideep Srivastava posted to no-tag by poirel on 2009-07-22 18:13:30 as along with 2 people paulovn onasraou
	A clustering algorithm based on graph connectivity [My Copy] Information Processing Letters, Vol. 76, No. 4-6. (31 December 2000), pp. 175-181. by E. Hartuv posted to no-tag by poirel on 2009-07-17 05:17:08 as along with 2 people and 1 group tmmurali lfriedl kdl
	From molecular to modular cell biology [My Copy] Nature, Vol. 402, No. 6761 Suppl. (02 December 1999), pp. C47-C52. by Leland H. Hartwell, John J. Hopfield, Stanislas Leibler, Andrew W. Murray posted to no-tag by poirel on 2009-07-15 15:51:01 as along with 26 people and 8 groups dagmar biomcgary bertelsen Scis0000002 daforerog jporternj chihchun_chen babakap AurelienMazurie rhem1224 balajis nuke2005 rubendrr wnpx i41m adepace javierFellow mmt mirzazadeh carmaus dejori carlk awooga tvdbulck vsausg dragonrez EisenLab TCR_Signaling cytoskeleton-and-afm SysbioMPI-TCells dIEMoSIRIS ic4 generif_paper MoSi-Rostock
	CORUM: the comprehensive resource of mammalian protein complexes. [My Copy] Nucleic acids research, Vol. 36, No. Database issue. (11 January 2008), pp. D646-650. by Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, et al.Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou N. Doudieu, Volker Stümpflen, H. Werner Mewes posted to no-tag by poirel on 2009-07-13 18:12:17 as along with 6 people dragonrez carlk tmmurali chad_davis guhjy shung
	The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists [My Copy] Cell, Vol. 92, No. 3. (6 February 1998), pp. 291-294. by B. Alberts posted to no-tag by poirel on 2009-07-13 17:43:47 as along with 1 person timg
	Evaluating functional network inference using simulations of complex biological systems [My Copy] Bioinformatics, Vol. 18, No. suppl_1. (1 July 2002), pp. S216-224. by V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink posted to no-tag by poirel on 2009-07-13 16:58:11 as along with 2 people BioGeek wnpx
	Artificial gene networks for objective comparison of analysis algorithms [My Copy] Bioinformatics, Vol. 19, No. suppl_2. (27 September 2003), pp. ii122-129. by Pedro Mendes, Wei Sha, Keying Ye posted to no-tag by poirel on 2009-07-13 16:40:48 as along with 9 people and 2 groups meanerelk fastjoe23 tonamswish kaarsinogen camster tmmurali dragonrez lfriedl pmendes dbk-lab kdl
	BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes [My Copy] Nucl. Acids Res., Vol. 33, No. suppl_2. (1 July 2005), pp. W324-325. by Jason Mcdermott, Michal Guerquin, Zach Frazier, Aaron N. Chang, Ram Samudrala posted to sequencing by poirel on 2009-07-13 16:21:34 as along with 1 person aelef
	Bioverse: functional, structural and contextual annotation of proteins and proteomes [My Copy] Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3736-3737. by Jason Mcdermott, Ram Samudrala posted to sequencing by poirel on 2009-07-13 16:20:54 as
	SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (2006), 43. by Tim Van den Bulcke, Koenraad Van Leemput, Bart Naudts, et al.Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor, Kathleen Marchal posted to data-simulation by poirel on 2009-07-08 19:12:45 as along with 6 people tonamswish ptrobajo Ayest tvdbulck frohike ajgentles
	Tissue specificity and the human protein interaction network. [My Copy] Molecular systems biology, Vol. 5 (7 April 2009) by Alice Bossi, Ben Lehner posted to no-tag by poirel on 2009-07-07 21:35:45 as along with 13 people jfr dolchan balicea tmmurali diamantis phoenixzxl coela frohike Kubke renatomilani TRHvidsten grahamc sjung
	Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1831-1832. by Aziz Mithani, Gail M. Preston, Jotun Hein posted to hypergraph by poirel on 2009-07-06 19:20:56 as along with 3 people JeremyZucker dquest renatomilani
	Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis [My Copy] Bioinformatics, Vol. 23, No. 22. (15 November 2007), pp. 3024-3031. by Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron posted to no-tag by poirel on 2009-06-30 01:40:37 as along with 8 people cmzmasek dandaman tmmurali sgoetz grahamc heliopais RamuAnandakrishnan marck
	How to infer gene networks from expression profiles [My Copy] Molecular Systems Biology, Vol. 3 (13 February 2007) by Mukesh Bansal, Vincenzo Belcastro, Alberto Ambesi-Impiombato, Diego di Bernardo posted to gene-networks reverse-egineering by poirel on 2009-06-19 17:04:32 as along with 38 people and 3 groups Jporci beete tonamswish zufar nicholasflann icq242500260 guhjy Zephyrus antonkratz phoenixzxl bertelsen isimpson daforerog agonzale roys Neeperando APRegier rdiaz klo Borelli ggallone ptrobajo druvus cswinburne jfr eckart_bindewald wnpx nickluscombe kengg mikaelhuss jrbanga BIBLIOma RockHI lp2 natstreet heliopais mariakmejia tmmurali Jarman Lab EBI-regulation Plantandetc
	Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data [My Copy] Science, Vol. 308, No. 5721. (22 April 2005), pp. 523-529. by Karen Sachs, Omar Perez, Dana Pe'er, Douglas A. Lauffenburger, Garry P. Nolan posted to bayesian-networks reverse-engineering by poirel on 2009-06-17 17:03:25 as along with 23 people and 1 group pkm phoenixzxl sameersoi abhishek_tiwari roys frohike aviad_work czeller emptyhb kentsis kaarsinogen balajis rand_bayes ryang wnpx os252 j3xucite noano koller jhatrimatri cdppublications lp2 saman_vp CDP
	Hypergraphs and Cellular Networks [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (29 May 2009), e1000385. by Steffen Klamt, Utz-Uwe Haus, Fabian Theis posted to cellular-network hypergraph by poirel on 2009-06-08 02:38:04 as along with 11 people rdiaz ptrobajo apocapoc trfield uuh danmaclean fgibson dswan tmmurali Borelli shikin
	Host cell factors in HIV replication: meta-analysis of genome-wide studies. [My Copy] PLoS pathogens, Vol. 5, No. 5. (29 May 2009), e1000437. by Frederic D. Bushman, Nirav Malani, Jason Fernandes, et al.Iván D'Orso, Gerard Cagney, Tracy L. Diamond, Honglin Zhou, Daria J. Hazuda, Amy S. Espeseth, Renate König, Sourav Bandyopadhyay, Trey Ideker, Stephen P. Goff, Nevan J. Krogan, Alan D. Frankel, John A. Young, Sumit K. Chanda posted to no-tag by poirel on 2009-06-08 02:36:38 as along with 4 people and 1 group memerman wsjames dansullivanblk tmmurali Oxford Virology

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