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	Physical network models. [My Copy] J Comput Biol, Vol. 11, No. 2-3. (2004), pp. 243-262. by C. H. Yeang, T. Ideker, T. Jaakkola posted by 4 people tmmurali wnpx noano koller
	Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae [My Copy] Journal of Biology, Vol. 5, No. 4. (08 June 2006), 11. by Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, et al.Bobby J. Breitkreutz, Gary Hon, Chad Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga Troyanskya, Trey Ideker, Kara Dolinski, Nizar Batada, Mike Tyers posted by 22 people carlk snuppepuppan tmmurali lfriedl balajis wnpx nickluscombe egralla citecat noano koller grahamc iris_2001 sgoetz kdl EBI-regulation shikin s041629 GeneGo pmendes mtruksa chasmand
	A data integration methodology for systems biology. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 48. (29 November 2005), pp. 17296-17301. by D. Hwang, A. G. Rust, S. Ramsey, et al.J. J. Smith, D. M. Leslie, A. D. Weston, P. de Atauri, J. D. Aitchison, L. Hood, A. F. Siegel, H. Bolouri posted by 26 people daforerog shikin jimineep Jarman Lab ggallone brian tmmurali dragonrez okarsligil jfr lfriedl Schmidtc eweaver wnpx biosv Sharpshoot noano mbeautru reidy grahamc GeeSharpMinor nedwards kdl Bioinformatics JJJ athleem
	Modeling and Simulation of Genetic Regulatory Systems: A Literature Review [My Copy] Journal of Computational Biology, Vol. 9, No. 1. (January 2002), pp. 67-103. by Hidde de Jong posted by 34 people mjoach Borelli qluo antonkratz reyez smac tlse65 wangbo GEB dlobo jago behindtherabbit cswinburne Jarman Lab ggallone softsimu eldan tmmurali bayesian balicea Happybene wnpx kengg noano sstoma josepe dagmar jo_davies VirtualPlants Plantandetc compneur roys maburkitt phoenixzxl
	Validation and refinement of gene-regulatory pathways on a network of physical interactions. [My Copy] Genome Biol, Vol. 6, No. 7. (2005) by C. H. Yeang, H. C. Mak, S. McCuine, C. Workman, T. Jaakkola, T. Ideker posted by 16 people kaarsinogen isimpson hplatero snuppepuppan abhik tmmurali textoris wnpx noano koller ccr cdppublications CDP AlexanderPico carlk jago
	Predicting new molecular targets for known drugs [My Copy] Nature, Vol. 462, No. 7270. (01 November 2009), pp. 175-181. by Michael J. Keiser, Vincent Setola, John J. Irwin, et al.Christian Laggner, Atheir I. Abbas, Sandra J. Hufeisen, Niels H. Jensen, Michael B. Kuijer, Roberto C. Matos, Thuy B. Tran, Ryan Whaley, Richard A. Glennon, Jerome Hert, Kelan L. H. Thomas, Douglas D. Edwards, Brian K. Shoichet, Bryan L. Roth posted by 16 people venancio okapi Journal picks ahmetbakan zufar pablocarb zwang TRHvidsten phoenixzxl qshao Yanno mnishimu tmmurali sjcockell seb1 abhishek_tiwari
	Disease signatures are robust across tissues and experiments [My Copy] Molecular Systems Biology, Vol. 5 (15 September 2009) by Joel T. Dudley, Robert Tibshirani, Tarangini Deshpande, Atul J. Butte posted by 15 people phoenixzxl tmmurali giovanni grahamc renatomilani ptrobajo zufar jclau klo mingzhi ngehlenborg dswan winterschlaefer daforerog brianb
	Gene-set analysis and reduction [My Copy] Brief Bioinform, Vol. 10, No. 1. (1 January 2009), pp. 24-34. by Irina Dinu, John D. Potter, Thomas Mueller, et al.Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, Yutaka Yasui posted by 10 people zufar jfr ipark-kaist renatomilani shikin tmmurali guhjy ihpark nuin ptrobajo
	Identifying differentially expressed subnetworks with MMG. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 23. (1 December 2008), pp. 2792-2793. by J. Noirel, G. Sanguinetti, P. C. Wright posted by 12 people zufar pauldobson jfr sg45653 pengchy behindtherabbit roys jiayi369 tmmurali bertelsen guhjy rdiaz
	Network inference using informative priors [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (2008), pp. 14313-14318. by Sach Mukherjee, Terence P. Speed posted by 12 people zufar bertelsen Jarman Lab ggallone guhjy Borelli ptrobajo jfr markstoehr stringertheory roys tmmurali
	Geometric interpretation of gene coexpression network analysis. [My Copy] PLoS computational biology, Vol. 4, No. 8. (15 August 2008), e1000117. by Steve Horvath, Jun Dong posted by 23 people jeremymiller zufar dolchan sficklin isimpson rdiaz guhjy cswinburne jfr ptrobajo pengchy nolodie druvus aramesh2 kengg roys Ema tmmurali Borelli Totobox AbnerCYH davidchavalarias caseybrown
	A modular approach for integrative analysis of large-scale gene-expression and drug-response data [My Copy] Nat Biotech, Vol. 26, No. 5. (08 May 2008), pp. 531-539. by Zoltan Kutalik, Jacques S. Beckmann, Sven Bergmann posted by 11 people zufar TRHvidsten vingron mingzhi guhjy aviad_work jfr stringertheory tmmurali oelemento ptrobajo
	Protein networks in disease. [My Copy] Genome research, Vol. 18, No. 4. (1 April 2008), pp. 644-652. by Trey Ideker, Roded Sharan posted by 28 people shikin carlk isimpson chica saket zufar kaarsinogen giovenko guhjy balicea tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl brianb schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
	Biclustering algorithms for biological data analysis: a survey. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM In IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 1, No. 1. (r 2004), pp. 24-45. by Sara C. Madeira, Arlindo L. Oliveira posted by 16 people meanerelk marti socwangnan jurgenjanes zufar ilyashl saman_vp ihpark tvdbulck librain dps bozdagd ealloza carlk chrisamiller tmmurali
	The Genomic Landscapes of Human Breast and Colorectal Cancers. [My Copy] Science (11 October 2007) by Laura D D. Wood, D Williams W. Parsons, Siân Jones, et al.Jimmy Lin, Tobias Sjöblom, Rebecca J J. Leary, Dong Shen, Simina M M. Boca, Thomas Barber, Janine Ptak, Natalie Silliman, Steve Szabo, Zoltan Dezso, Vadim Ustyanksky, Tatiana Nikolskaya, Yuri Nikolsky, Rachel Karchin, Paul A A. Wilson, Joshua S S. Kaminker, Zemin Zhang, Randal Croshaw, Joseph Willis, Dawn Dawson, Michail Shipitsin, James K V K. Willson, Saraswati Sukumar, Kornelia Polyak, Ben Ho H. Park, Charit L L. Pethiyagoda, P V Krishna V. Pant, Dennis G G. Ballinger, Andrew B B. Sparks, James Hartigan, Douglas R R. Smith, Erick Suh, Nickolas Papadopoulos, Phillip Buckhaults, Sanford D D. Markowitz, Giovanni Parmigiani, Kenneth W W. Kinzler, Victor E E. Velculescu, Bert Vogelstein posted by 19 people zufar ssgong daed guhjy tmmurali jfr rdiaz eisei ramensky massivemayhem bioyang cabbagezs xingxu shikin renatomilani VUMCGenomics gwenknight cerami srp33
	A systems biology approach for pathway level analysis [My Copy] Genome Research, Vol. 17, No. 10. (4 October 2007), pp. 1537-1545. by Sorin Draghici, Purvesh Khatri, Adi L. Tarca, et al.Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero posted by 25 people zufar bertelsen tonamswish gbloeb cgaugain ptrobajo pengchy tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu Bioinformatics shikin idonaldson Pao-Yang OPIG thomaskelder heliopais AlexanderPico
	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 by 42 people Jporci beete tonamswish zufar nicholasflann icq242500260 guhjy Zephyrus antonkratz phoenixzxl bertelsen isimpson daforerog poirel agonzale roys Neeperando APRegier rdiaz klo Borelli Jarman Lab ggallone ptrobajo druvus cswinburne jfr eckart_bindewald wnpx nickluscombe kengg mikaelhuss jrbanga BIBLIOma RockHI lp2 natstreet EBI-regulation Plantandetc heliopais mariakmejia tmmurali
	Identifying differentially expressed genes using false discovery rate controlling procedures. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 3. (12 February 2003), pp. 368-375. by Anat Reiner, Daniel Yekutieli, Yoav Benjamini posted by 9 people ericrpaquet olberd zufar bertelsen maximilianh RMGraze maryee talponer shikin
	Oncogenic pathway signatures in human cancers as a guide to targeted therapies. [My Copy] Nature, Vol. 439, No. 7074. (19 January 2006), pp. 353-357. by Andrea H. Bild, Guang Yao, Jeffrey T. Chang, et al.Quanli Wang, Anil Potti, Dawn Chasse, Mary-Beth B. Joshi, David Harpole, Johnathan M. Lancaster, Andrew Berchuck, John A. Olson, Jeffrey R. Marks, Holly K. Dressman, Mike West, Joseph R. Nevins posted by 16 people bertelsen roys ipark-kaist zufar Yanno guhjy kentsis mfenner ajeffs tuck maryee eckart_bindewald frohike Ao_Li2007 waghsk srp33
	Genome-wide associations of gene expression variation in humans. [My Copy] PLoS Genet, Vol. 1, No. 6. (December 2005) by B. E. Stranger, M. S. Forrest, A. G. Clark, et al.M. J. Minichiello, S. Deutsch, R. Lyle, S. Hunt, B. Kahl, S. E. Antonarakis, S. Tavaré, P. Deloukas, E. T. Dermitzakis posted by 14 people zufar pengchy psique adepace rdiaz qfwills noano ashandanj jo_davies Bioinformatics EisenLab cisevol cis-regulatory-evolution shikin
	Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes [My Copy] Brief Bioinform, Vol. 10, No. 6. (1 November 2009), pp. 654-663. by Carol Soderlund posted by 2 people tmmurali kshameer
	The nature of cell-cycle checkpoints: facts and fallacies [My Copy] Journal of Biology, Vol. 8, No. 10. (2009), 88. by Alexey Khodjakov, Conly Rieder posted by 2 people tmmurali Zephyrus
	Edgetic perturbation models of human inherited disorders [My Copy] Molecular Systems Biology, Vol. 5 (03 November 2009) by Quan Zhong, Nicolas Simonis, Qian-Ru Li, et al.Benoit Charloteaux, Fabien Heuze, Niels Klitgord, Stanley Tam, Haiyuan Yu, Kavitha Venkatesan, Danny Mou, Venus Swearingen, Muhammed A. Yildirim, Han Yan, Amelie Dricot, David Szeto, Chenwei Lin, Tong Hao, Changyu Fan, Stuart Milstein, Denis Dupuy, Robert Brasseur, David E. Hill, Michael E. Cusick, Marc Vidal posted by 6 people mingzhi phoenixzxl tmmurali roys pedrobeltrao brianb
	Can literature analysis identify innovation drivers in drug discovery? [My Copy] Nature Reviews Drug Discovery, Vol. 8, No. 11. (01 November 2009), pp. 865-878. by Pankaj Agarwal, David B. Searls posted by 4 people lmichan tmmurali nicklynch dullhunk
	Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling [My Copy] Cell, Vol. 139, No. 3. (30 October 2009), pp. 610-622. by Shaohui Hu, Zhi Xie, Akishi Onishi, et al.Xueping Yu, Lizhi Jiang, Jimmy Lin, Hee-sool Rho, Crystal Woodard, Hong Wang, Jun-Seop Jeong posted by 4 people tmmurali renatomilani idonaldson maximilianh
	Genomics of Emerging Infectious Disease: A PLoS Collection [My Copy] PLoS Biol, Vol. 7, No. 10. (26 October 2009), e1000224. by Jonathan A. Eisen, Catriona J. MacCallum posted by 2 people tmmurali druvus
	Evolution of biomolecular networks \|[mdash]\| lessons from metabolic and protein interactions [My Copy] Nat Rev Mol Cell Biol, Vol. 10, No. 11. (01 November 2009), pp. 791-803. by Takuji Yamada, Peer Bork posted by 7 people venancio biomcgary colmryan pinney nzm pedrobeltrao tmmurali
	Decoding the multifaceted HIV-1 virus-host interactome [My Copy] Journal of Biology, Vol. 8, No. 9. (2009), 84. by Eric Chan, Marcus Korth, Michael Katze posted by 1 person tmmurali
	How to identify essential genes from molecular networks? [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 102. by Gabriel D. Rio, Dirk Koschutzki, Gerardo Coello posted by 8 people operon tmmurali kshameer phoenixzxl ptrobajo renatomilani druvus daforerog
	How to visually interpret biological data using networks [My Copy] Nature Biotechnology, Vol. 27, No. 10. (01 October 2009), pp. 921-924. by Daniele Merico, David Gfeller, Gary D. Bader posted by 15 people Geknitics perkeo Journal picks qayub mhamidi OliverHarriman AJCann grahamc rdiaz megraw tmmurali fgibson gotgenes druvus dullhunk
	Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics [My Copy] PLoS Biol, Vol. 7, No. 10. (6 October 2009), e1000213. by Zhihua Li, Insuk Lee, Emily Moradi, Nai-Jung Hung, Arlen W. Johnson, Edward M. Marcotte posted by 5 people carlk tmmurali djkt lp2 ptrobajo
	Coexpression network based on natural variation in human gene expression reveals gene interactions and functions [My Copy] Genome Research, Vol. 19, No. 11. (1 November 2009), pp. 1953-1962. by Renuka R. Nayak, Michael Kearns, Richard S. Spielman, Vivian G. Cheung posted by 11 people antonkratz nsc129psu iskathy Journal picks lp2 TRHvidsten megraw owhitney rdiaz tmmurali natstreet
	Joining forces in the quest for orthologs [My Copy] Genome Biology, Vol. 10, No. 9. (2009), 403. by Toni Gabaldon, Christophe Dessimoz, Julie H. Jones, Albert Vilella, Erik Sonnhammer, Suzanna Lewis posted by 8 people Orengo Group Journal Picks operon kshameer tmmurali bdessailly Journal picks ppgardne druvus
	Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 97. by Nicole Philippi, Dorothee Walter, Rebekka Schlatter, et al.Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar posted by 2 people tmmurali phoenixzxl
	Evolutionarily Conserved Herpesviral Protein Interaction Networks [My Copy] PLoS Pathog, Vol. 5, No. 9. (4 September 2009), e1000570. by Even Fossum, Caroline C. Friedel, Seesandra V. Rajagopala, et al.Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Thorsten Stellberger, Christiane Rutenberg, Silpa Suthram, Sourav Bandyopadhyay, Dietlind Rose, Albrecht von Brunn, Mareike Uhlmann, Christine Zeretzke, Yu-An Dong, Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz, Ralf Zimmer, Jürgen Haas posted by 3 people pauldobson tmmurali reyez
	Protein quantification across hundreds of experimental conditions [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15544-15548. by Zia Khan, Joshua S. Bloom, Benjamin A. Garcia, Mona Singh, Leonid Kruglyak posted by 6 people brianb nedwards bennos tmmurali roys GeeSharpMinor
	Next generation software for functional trend analysis [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 3043-3044. by Gabriel F. Berriz, John E. Beaver, Can Cenik, Murat Tasan, Frederick P. Roth posted by 6 people Orengo Group Journal Picks jperkins tmmurali kmdaily VGreiff guhjy
	Systems-Level Modeling of Cancer-Fibroblast Interaction [My Copy] PLoS ONE, Vol. 4, No. 9. (3 September 2009), e6888. by Raymond C. Wadlow, Ben S. Wittner, S. Aidan Finley, et al.Henry Bergquist, Rabi Upadhyay, Stephen Finn, Massimo Loda, Umar Mahmood, Sridhar Ramaswamy posted by 1 person tmmurali
	Parsing Social Network Survey Data from Hidden Populations Using Stochastic Context-Free Grammars [My Copy] PLoS ONE, Vol. 4, No. 9. (7 September 2009), e6777. by Art F. Y. Poon, Kimberly C. Brouwer, Steffanie A. Strathdee, et al.Michelle Firestone-Cruz, Remedios M. Lozada, Sergei L. Kosakovsky Pond, Douglas D. Heckathorn, Simon D. W. Frost posted by 1 person tmmurali
	Fusing Tissue Engineering and Systems Biology Toward Fulfilling Their Promise [My Copy] Cellular and Molecular Bioengineering, Vol. 1, No. 1. (1 March 2008), pp. 33-41. by Benjamin Cosgrove, Linda Griffith, Douglas Lauffenburger posted by 1 person tmmurali
	Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses [My Copy] Science, Vol. 326, No. 5950. (9 October 2009), pp. 257-263. by Ido Amit, Manuel Garber, Nicolas Chevrier, et al.Ana P. Leite, Yoni Donner, Thomas Eisenhaure, Mitchell Guttman, Jennifer K. Grenier, Weibo Li, Or Zuk, Lisa A. Schubert, Brian Birditt, Tal Shay, Alon Goren, Xiaolan Zhang, Zachary Smith, Raquel Deering, Rebecca C. McDonald, Moran Cabili, Bradley E. Bernstein, John L. Rinn, Alex Meissner, David E. Root, Nir Hacohen, Aviv Regev posted by 10 people xianjun inesdesantiago leliavski TRHvidsten agonzale gbloeb roys ptrobajo natgoodman tmmurali
	Mining gene functional networks to improve mass-spectrometry-based protein identification [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2955-2961. by Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. Penalva, Edward M. Marcotte, Daniel P. Miranker posted by 2 people tmmurali ptrobajo
	A genome-wide genetic screen for host factors required for hepatitis C virus propagation [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 38. (22 September 2009), pp. 16410-16415. by Qisheng Li, Abraham L. Brass, Aylwin Ng, et al.Zongyi Hu, Ramnik J. Xavier, T. Jake Liang, Stephen J. Elledge posted by 2 people tmmurali guhjy
	Strong Inference for Systems Biology [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000459. by Daniel A. Beard, Martin J. Kushmerick posted by 12 people sobolevnrm dagmar ajaymalik Borelli rdiaz ptrobajo coffeerv bertelsen jonathancooper abhishek_tiwari tmmurali jjray
	Incorporating Existing Network Information into Gene Network Inference [My Copy] PLoS ONE, Vol. 4, No. 8. (27 August 2009), e6799. by Scott Christley, Qing Nie, Xiaohui Xie posted by 6 people rdiaz coffeerv tmmurali TRHvidsten installe frohike
	Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms [My Copy] Nucl. Acids Res., Vol. 37, No. 18. (1 October 2009), pp. 5969-5980. by Kang Tu, Hui Yu, You-Jia Hua, et al.Yuan-Yuan Li, Lei Liu, Lu Xie, Yi-Xue Li posted by 9 people aaron_webber fpattyn microRNA heliopais tmmurali eshirdel pshuster guhjy valeriehilgers
	The human protein coevolution network. [My Copy] Genome research, Vol. 19, No. 10. (20 October 2009), pp. 1861-1871. by Elisabeth R. Tillier, Robert L. Charlebois posted by 8 people dfdong Garamonfok venancio jperkins TRHvidsten djkt phoenixzxl tmmurali
	A boosting approach to structure learning of graphs with and without prior knowledge [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2929-2936. by Shahzia Anjum, Arnaud Doucet, Chris C. Holmes posted by 7 people hughitt1 tmmurali fastjoe23 TRHvidsten rdiaz phoenixzxl frohike
	Geometric De-noising of Protein-Protein Interaction Networks [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (7 August 2009), e1000454. by Oleksii Kuchaiev, Marija Rašajski, Desmond J. Higham, Nataša Pržulj posted by 10 people Orengo Group Journal Picks CorinYeats klexa tmmurali roys grahamc zwang robfsouza phoenixzxl kiekyon
	A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2831-2838. by Ze Tian, TaeHyun Hwang, Rui Kuang posted by 6 people tmmurali dolchan rdiaz pkonings guhjy nuin
	Distinguishing direct versus indirect transcription factorâDNA interactions [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca GordÃ¢n, Alexander J. Hartemink, Martha L. Bulyk posted by 12 people oannes nklee djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	Recovering time-varying networks of dependencies in social and biological studies [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 29. (21 July 2009), pp. 11878-11883. by Amr Ahmed, Eric P. Xing posted by 7 people rdiaz Borelli maximzhao pinney zwang friendpine tmmurali
	Systems biology: Untangling the protein web [My Copy] Nature, Vol. 460, No. 7253. (15 July 2009), pp. 415-418. by Nathan Blow posted by 16 people Orengo Group Journal Picks robertrentzsch pekrau apocapoc psique leemond31 colmryan reyez carlk guhjy saket tmmurali dswan dullhunk renatomilani agonzale
	Assessing the relevance of node features for network structure [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 28. (14 July 2009), pp. 11433-11438. by Ginestra Bianconi, Paolo Pin, Matteo Marsili posted by 13 people rdiaz daforerog Kovanen zwang apocapoc Diego_Prada winterstream trfield deanmalmgren tomt21 roys tmmurali statnet
	The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction [My Copy] Bioinformatics, Vol. 25, No. 18. (15 September 2009), pp. 2404-2410. by Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Amy A. Caudy, David C. Hess, Olga G. Troyanskaya posted by 4 people wilbur tmmurali TRHvidsten phoenixzxl
	Large-Scale Assessment of the Effect of Popularity on the Reliability of Research [My Copy] PLoS ONE, Vol. 4, No. 6. (24 June 2009), e5996. by Thomas Pfeiffer, Robert Hoffmann posted by 6 people radagabriel nellapower sriesenfeld bpcusack rdiaz dullhunk
	Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. [My Copy] PLoS biology, Vol. 7, No. 6. (16 June 2009), e1000134. by Pedro Beltrao, Jonathan C. Trinidad, Dorothea Fiedler, et al.Assen Roguev, Wendell A. Lim, Kevan M. Shokat, Alma L. Burlingame, Nevan J. Krogan posted by 15 people psique dakelley robfsouza emptyhb mingzhi leemond31 chica tmmurali biomcgary kiekyon neils bpcusack djkt renatomilani ematsen
	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 by 13 people carlk chica saket dakelley Orengo Group Journal Picks tomhebbron davidalee leemond31 druvus kiekyon neils tmmurali grahamc
	Functional Equivalency Inferred from “Authoritative Sources” in Networks of Homologous Proteins [My Copy] PLoS ONE, Vol. 4, No. 6. (12 June 2009), e5898. by Shreedhar Natarajan, Eric Jakobsson posted by 1 person tmmurali
	A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series [My Copy] Algorithms for Molecular Biology, Vol. 4, No. 1. (04 June 2009), 8. by Sara Madeira, Arlindo Oliveira posted by 4 people meanerelk Bioinformatics dswan tmmurali
	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 by 6 people memerman Oxford Virology wsjames poirel dansullivanblk tmmurali
	Modulated modularity clustering as an exploratory tool for functional genomic inference. [My Copy] PLoS genetics, Vol. 5, No. 5. (8 May 2009), e1000479. by Eric A. Stone, Julien F. Ayroles posted by 6 people carlk rdiaz Morgan Lab-KSU theodorejmorgan roys tmmurali
	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 by 12 people rdiaz ptrobajo poirel apocapoc trfield uuh danmaclean fgibson dswan tmmurali Borelli shikin
	The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process [My Copy] Genome Biology, Vol. 10, No. 5. (2009), R58. by Erick Antezana, Mikel Egana, Ward Blonde, et al.Aitzol Illarramendi, Inaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper posted by 9 people druvus Orengo Group Journal Picks bdessailly guhjy tmmurali daforerog behindtherabbit fgibson dullhunk
	Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. [My Copy] PLoS genetics, Vol. 5, No. 3. (20 March 2009), e1000407. by David C. Hess, Chad L. Myers, Curtis Huttenhower, et al.Matthew A. Hibbs, Alicia P. Hayes, Jadine Paw, John J. Clore, Rosa M. Mendoza, Bryan San S. Luis, Corey Nislow, Guri Giaever, Michael Costanzo, Olga G. Troyanskaya, Amy A. Caudy posted by 2 people tmmurali raiyar
	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 by 8 people kgutwin kiekyon zwang friendpine poirel neils tmmurali grahamc
	Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. [My Copy] BMC medical genomics, Vol. 2, No. 1. (18 May 2009) by Perry Evans, William Dampier, Lyle Ungar, Aydin Tozeren posted by 4 people tmmurali niallhaslam zwang friendpine
	DIANA-mirPath: Integrating human and mouse microRNAs in pathways. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1991-1993. by G. L. Papadopoulos, P. Alexiou, M. Maragkakis, M. Reczko, A. G. Hatzigeorgiou posted by 12 people microRNA jfr ealloza megraw Bioinformatics - CRUK Stew Bioinformatics dswan daforerog tmmurali guhjy pengchy
	Diversity and Complexity in DNA Recognition by Transcription Factors [My Copy] Science, Vol. 324, No. 5935. (26 June 2009), pp. 1720-1723. by Gwenael Badis, Michael F. Berger, Anthony A. Philippakis, et al.Shaheynoor Talukder, Andrew R. Gehrke, Savina A. Jaeger, Esther T. Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen, Hanna Kuznetsov, Chi-Fong Wang, David Coburn, Daniel E. Newburger, Quaid Morris, Timothy R. Hughes, Martha L. Bulyk posted by 24 people nklee sconlan isimpson jbhiatt daforerog absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts RockmanLab dpollard siebert JustinCrocker burak aalibes dipenps roys emptyhb tmmurali
	A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (1 May 2009), e1000382. by Nicholas J. Hudson, Antonio Reverter, Brian P. Dalrymple posted by 11 people rdiaz guhjy tmmurali Borelli giovanni cabbagesofdoom roys chrisamiller dswan ptrobajo dolchan
	In Silico Generation of Alternative Hypotheses Using Causal Mapping (CMAP) [My Copy] PLoS ONE, Vol. 4, No. 4. (29 April 2009), e5378. by Gabriel E. Weinreb, Maryna T. Kapustina, Ken Jacobson, Timothy C. Elston posted by 3 people rdiaz bertelsen tmmurali
	Redefining microRNA targets. [My Copy] Current biology : CB, Vol. 19, No. 10. (26 May 2009), pp. 870-873. by Hervé Seitz posted by 7 people guhjy tmmurali ealloza microRNA tonamswish ilyashl valeriehilgers
	Listen to Genes: Dealing with Microarray Data in the Frequency Domain [My Copy] PLoS ONE, Vol. 4, No. 4. (6 April 2009), e5098. by Jianfeng Feng, Dongyun Yi, Ritesh Krishna, Shuixia Guo, Vicky Buchanan-Wollaston posted by 3 people Borelli rdiaz tmmurali
	Tissue specificity and the human protein interaction network. [My Copy] Molecular systems biology, Vol. 5 (7 April 2009) by Alice Bossi, Ben Lehner posted by 14 people jfr dolchan balicea poirel tmmurali diamantis phoenixzxl coela frohike Kubke renatomilani TRHvidsten grahamc sjung
	The automation of science. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5923. (3 April 2009), pp. 85-89. by Ross D. King, Jem Rowland, Stephen G. Oliver, et al.Michael Young, Wayne Aubrey, Emma Byrne, Maria Liakata, Magdalena Markham, Pinar Pir, Larisa N. Soldatova, Andrew Sparkes, Kenneth E. Whelan, Amanda Clare posted by 59 people singhsh Sergey_gerbek schwartzjmc yyfwuhan antonkratz CulCog ckai1 jcaddy thegoose tommcdonagh tonamswish qwermish axeltan ocs TobiasAbenius CameronNeylon guhjy davidcsterratt bcondon Scis0000002 kevinemamy TRHvidsten emiko Zephyrus arne muraken vagoskar katiehumphry NaCTeM Effie robertknight acrmartins psique dbikard tyrell_turing Tomste renatomilani subhacom druvus ramanuja sen_cheng coela VGreiff hagechouchin443 Benja austin stober rdiaz Fortran napvasconcelos mikel_egana allysonlister dullhunk fgibson pkonings MetabolicModeling JeremyZucker jbhiatt tmmurali
	New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites. [My Copy] Genome research, Vol. 19, No. 7. (31 July 2009), pp. 1175-1183. by Inhan Lee, Subramanian S. Ajay, Jong In I. Yook, et al.Hyun Sil S. Kim, Su Hyung H. Hong, Nam Hee H. Kim, Saravana M. Dhanasekaran, Arul M. Chinnaiyan, Brian D. Athey posted by 22 people danaiancu hzoltan ebcgantman jfr ashkelon13 heliopais megraw fenghezi Neuroblastoma fpattyn tmmurali Journal picks ppgardne microRNA tonamswish Mycology stajich Einat cube_and_beyond daforerog valeriehilgers ealloza
	Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks [My Copy] Nature Genetics, Vol. 41, No. 4. (08 March 2009), pp. 415-423. by Xia Yang, Joshua L. Deignan, Hongxiu Qi, et al.Jun Zhu, Su Qian, Judy Zhong, Gevork Torosyan, Sana Majid, Brie Falkard, Robert R. Kleinhanz, Jenny Karlsson, Lawrence W. Castellani, Sheena Mumick, Kai Wang, Tao Xie, Michael Coon, Chunsheng Zhang, Daria Estrada-Smith, Charles R. Farber, Susanna S. Wang, Atila van Nas, Anatole Ghazalpour, Bin Zhang, Douglas J. MacNeil, John R. Lamb, Katrina M. Dipple, Marc L. Reitman, Margarete Mehrabian, Pek Y. Lum, Eric E. Schadt, Aldons J. Lusis, Thomas A. Drake posted by 7 people ipark-kaist sameersoi tonamswish renatomilani guhjy tmmurali bertrandservin
	Experimental advances in the characterization of metazoan gene regulatory networks [My Copy] Brief Funct Genomic Proteomic, Vol. 8, No. 1. (1 January 2009), pp. 12-27. by Bart Deplancke posted by 3 people BergmanLab cisevol tmmurali
	The Cartographers toolbox: building bigger and better human protein interaction networks [My Copy] Brief Funct Genomic Proteomic, Vol. 8, No. 1. (1 January 2009), pp. 1-11. by Christopher M. Sanderson posted by 2 people renatomilani tmmurali
	Reverse Engineering Time Discrete Finite Dynamical Systems: A Feasible Undertaking? [My Copy] PLoS ONE, Vol. 4, No. 3. (19 March 2009), e4939. by Edgar Delgado-Eckert posted by 2 people rdiaz tmmurali
	Directing experimental biology: a case study in mitochondrial biogenesis. [My Copy] PLoS computational biology, Vol. 5, No. 3. (20 March 2009), e1000322. by Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, et al.David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya posted by 5 people tmmurali bertelsen Marcotte_Lab biomcgary ptrobajo
	Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity [My Copy] Nature Genetics, Vol. 41, No. 3. (22 February 2009), pp. 316-323. by Esti Yeger-Lotem, Laura Riva, Linhui J. Su, et al.Aaron D. Gitler, Anil G. Cashikar, Oliver D. King, Pavan K. Auluck, Melissa L. Geddie, Julie S. Valastyan, David R. Karger, Susan Lindquist, Ernest Fraenkel posted by 6 people tmmurali stasaki roys absterga provero psique
	A roadmap of clustering algorithms: finding a match for a biomedical application [My Copy] Brief Bioinform, Vol. 10, No. 3. (1 May 2009), pp. 297-314. by Bill Andreopoulos, Aijun An, Xiaogang Wang, Michael Schroeder posted by 17 people jfr mhamidi eliasman Gorzomagnificent reyez brianb nuin m509396 jmeppley tmmurali tonamswish VGreiff baker-group sobolevnrm Bioinformatics barry svozil
	Early and sustained innate immune response defines pathology and death in nonhuman primates infected by highly pathogenic influenza virus. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (13 February 2009) by Carole R R. Baskin, Helle Bielefeldt-Ohmann, Terrence M M. Tumpey, et al.Patrick J J. Sabourin, James P P. Long, Adolfo García-Sastre, Airn-E E. Tolnay, Randy Albrecht, John A A. Pyles, Pam H H. Olson, Lauri D D. Aicher, Elizabeth R R. Rosenzweig, Kaja Murali-Krishna, Edward A A. Clark, Mark S S. Kotur, Jamie L L. Fornek, Sean Proll, Robert E E. Palermo, Carol L L. Sabourin, Michael G G. Katze posted by 2 people tmmurali zwang
	Influenza viruses and the NF-kappaB signaling pathway - towards a novel concept of antiviral therapy. [My Copy] Biological chemistry, Vol. 389, No. 10. (October 2008), pp. 1307-1312. by S. Ludwig, O. Planz posted by 1 person tmmurali
	SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 4. (15 February 2009), pp. 541-542. by Daniel M. Gatti, Myroslav Sypa, Ivan Rusyn, Fred A. Wright, William T. Barry posted by 5 people jfr tmmurali guhjy Bioinformatics dswan
	Use of high-density tiling microarrays to globally identify mutations and elucidate mechanisms of drug resistance in Plasmodium falciparum [My Copy] Genome Biology, Vol. 10, No. 2. (2009) by Neekesh Dharia, Amar, Maria B. Cassera, et al.Scott Westenberger, Selina Bopp, Rich Eastman, David Plouffe, Serge Batalov, Daniel Park, Sarah Volkman, Dyann Wirth, Yingyao Zhou, David Fidock, Elizabeth Winzeler posted by 5 people JoeDunckley tmmurali GeeSharpMinor neils behindtherabbit
	Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. [My Copy] Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, Vol. 4 (2004), pp. 2881-2884. by T. Joshi, Y. Chen, N. Alexandrov, D. Xu posted by 1 person tmmurali
	Gene expression trends and protein features effectively complement each other in gene function prediction [My Copy] Bioinformatics, Vol. 25, No. 3. (1 February 2009), pp. 322-330. by Krzysztof Wabnik, Torgeir R. Hvidsten, Anna Kedzierska, et al.Jelle Van Leene, Geert De Jaeger, Gerrit T. S. Beemster, Jan Komorowski, Martin T. R. Kuiper posted by 7 people grimplet TRHvidsten jfr guhjy Bioinformatics dswan tmmurali
	Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation [My Copy] Mol Syst Biol, Vol. 5 (20 January 2009) by Attila Csikasz-Nagy, Orsolya Kapuy, Attila Toth, et al.Csaba Pal, Lars J. Jensen, Frank Uhlmann, John J. Tyson, Bela Novak posted by 4 people tmmurali shikin larsjuhljensen renatomilani
	CUR matrix decompositions for improved data analysis [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 3. (20 January 2009), pp. 697-702. by Michael W. Mahoney, Petros Drineas posted by 4 people jzujovic rdiaz nurban tmmurali
	Precision and recall estimates for two-hybrid screens. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 3. (1 February 2009), pp. 372-378. by Hailiang Huang, Joel S. Bader posted by 9 people anf guhjy mariap3636 roys phoenixzxl mstumpf tmmurali sjcockell grahamc
	Cataloguing the HIV Type 1 Human Protein Interaction Network [My Copy] AIDS Research and Human Retroviruses, Vol. 24, No. 12. (2008), pp. 1497-1502. by Roger G. Ptak, William Fu, Brigitte, et al.Jonathan E. Dickerson, John W. Pinney, David L. Robertson, Mikhail N. Rozanov, Kenneth S. Katz, Donna R. Maglott, Kim D. Pruitt, Carl W. Dieffenbach posted by 1 person tmmurali
	MicroRNA target prediction by expression analysis of host genes [My Copy] Genome Research, Vol. 19, No. 3. (16 March 2009), pp. 481-490. by Vincenzo A. Gennarino, Marco Sardiello, Raffaella Avellino, et al.Nicola Meola, Vincenza Maselli, Santosh Anand, Luisa Cutillo, Andrea Ballabio, Sandro Banfi posted by 19 people danaiancu gbloeb ptrobajo guhjy tonamswish gennarino heliopais megraw tmmurali microRNA jfr samgj valeriehilgers Roswell Cancer Crosstalk Zephyrus pengchy giovenko daforerog ealloza
	Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy [My Copy] Genome Biology, Vol. 9 (16 December 2008), R174. by Li, Chen Ting posted by 2 people tmmurali natstreet
	Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model [My Copy] Bioinformatics, Vol. 25, No. 3. (1 February 2009), pp. 387-393. by Je-Gun Joung, Zhangjun Fei posted by 9 people tonamswish TRHvidsten microRNA jfr megraw tmmurali mhamada natstreet druvus
	Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (28 November 2008), e1000237. by Shubhada R. Hegde, Palanisamy Manimaran, Shekhar C. Mande posted by 2 people kristen tmmurali
	Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (28 November 2008), e1000232. by Wan K. Kim, Edward M. Marcotte posted by 8 people wangbo dakelley biomcgary cabbagesofdoom chad_davis grahamc bpcusack tmmurali
	A general framework for multiple testing dependence [My Copy] Proceedings of the National Academy of Sciences (24 November 2008) by Jeffrey T. Leek, John D. Storey posted by 12 people SIMR bioinformatics ghattem TRHvidsten guhjy briordan dbk stringertheory jiqiu fpattyn barriot tmmurali jjray
	Dynamic Proteomics of Individual Cancer Cells in Response to a Drug [My Copy] Science, Vol. 322, No. 5907. (5 December 2008), pp. 1511-1516. by A. A. Cohen, N. Geva-Zatorsky, E. Eden, et al.M. Frenkel-Morgenstern, I. Issaeva, A. Sigal, R. Milo, C. Cohen-Saidon, Y. Liron, Z. Kam, L. Cohen, T. Danon, N. Perzov, U. Alon posted by 15 people agonzale VGreiff tjchen myzhang brianb Borelli lflorez jessopher reyez jbhiatt caseybrown winterschlaefer sjcockell renatomilani pengchy