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	Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease. [My Copy] BMC medical genomics, Vol. 1, No. 1. (20 October 2008) by Jessica D. Tenenbaum, Michael G. Walker, Paul J. Utz, Atul J. Butte posted to signature pathway mining epsa disease analysis by dolchan on 2009-10-29 17:15:35 as along with 9 people ipark-kaist jfr zufar daforerog imina guhjy huiminC ptrobajo oelemento
	Differential Dependency Network Analysis to Identify Condition-Specific Topological Changes in Biological Networks [My Copy] Bioinformatics (26 December 2008), btn660. by Bai Zhang, Huai Li, Rebecca B. Riggins, et al.Ming Zhan, Jianhua Xuan, Zhen Zhang, Eric P. Hoffman, Robert Clarke, Yue Wang posted to biology condition context networks regulatory specific systems by dolchan on 2009-02-13 17:24:59 as along with 7 people southo bertelsen lptolik mstumpf imina grahamc roys
	Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. [My Copy] Bioinformatics, Vol. 19, No. 15. (12 October 2003), pp. 1917-1926. by J. Qian, J. Lin, N. M. Luscombe, H. Yu, M. Gerstein posted to no-tag by dolchan on 2008-09-17 16:41:03 as along with 1 person koller
	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 specificity protein network interaction context by dolchan on 2009-10-29 17:14:03 as along with 13 people jfr balicea poirel tmmurali diamantis phoenixzxl coela frohike Kubke renatomilani TRHvidsten grahamc sjung
	Discerning static and causal interactions in genome-wide reverse engineering problems [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. 1510-1515. by Mattia Zampieri, Nicola Soranzo, Claudio Altafini posted to static network inference causal by dolchan on 2009-10-29 17:12:51 as along with 7 people meanerelk rdiaz roys guhjy tmmurali verdicchio balicea
	Benchmarking regulatory network reconstruction with GRENDEL [My Copy] Bioinformatics, Vol. 25, No. 6. (15 March 2009), pp. 801-807. by Brian C. Haynes, Michael R. Brent posted to regulation network inference grendel gene benchmark by dolchan on 2009-10-29 17:11:32 as along with 7 people tmarscha tonamswish TRHvidsten APRegier roys rdiaz imina
	PathBuilder--open source software for annotating and developing pathway resources [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2860-2862. by Kumaran Kandasamy, Shivakumar Keerthikumar, Rajesh Raju, et al.T. S. Keshava Prasad, Y. L. Ramachandra, Sujatha Mohan, Akhilesh Pandey posted to no-tag by dolchan on 2009-10-23 17:59:35 as along with 5 people druvus dullhunk kshameer guhjy renatomilani
	integrOmics: an R package to unravel relationships between two omics datasets. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 21. (1 November 2009), pp. 2855-2856. by Kim-Anh A. Lê Cao, Ignacio González, Sébastien Déjean posted to no-tag by dolchan on 2009-10-23 17:50:51 as along with 18 people and 1 group guhjy molnet-mna jperkins tonamswish dswan mayercd operon kshameer heliopais nuin ptrobajo sebastien_vigneau rdiaz cassj brianb neils natstreet druvus Orengo Group Journal Picks
	iBioSim: A Tool for the Analysis and Design of Genetic Circuits. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 21. (23 July 2009), pp. 2848-2849. by Chris J. Myers, Nathan Barker, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam-Phuong P. Nguyen posted to no-tag by dolchan on 2009-10-23 17:48:41 as along with 2 people grahamc sebastien_vigneau
	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 to no-tag by dolchan on 2009-10-23 17:47:29 as along with 5 people tmmurali rdiaz pkonings guhjy nuin
	Bi-correlation clustering algorithm for determining a set of co-regulated genes [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2795-2801. by Anindya Bhattacharya, Rajat K. De posted to no-tag by dolchan on 2009-10-23 17:46:43 as along with 7 people bsamal colm meanerelk TRHvidsten barriot kevinzheng1983 rdiaz
	A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2787-2794. by Andreas Keller, Christina Backes, Andreas Gerasch, et al.Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, Hans-Peter Lenhof posted to no-tag by dolchan on 2009-10-23 17:45:54 as along with 10 people and 1 group shikin bertelsen jperkins tonamswish heliopais greg zufar rdiaz ptrobajo brianb Orengo Group Journal Picks
	Statistical methods for gene set co-expression analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2780-2786. by YounJeong Choi, Christina Kendziorski posted to no-tag by dolchan on 2009-10-23 17:43:54 as along with 8 people and 1 group zchen jperkins ptrobajo natstreet heliopais zufar rdiaz neils Orengo Group Journal Picks
	Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2735-2743. by Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka posted to no-tag by dolchan on 2009-10-23 17:43:05 as along with 8 people and 1 group inesdesantiago operon daforerog klo kshameer kevinzheng1983 pkonings rdiaz 8_01
	Model-based clustering of array CGH data [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i30-38. by Sohrab P. Shah, K-John Cheung, Nathalie A. Johnson, et al.Guillaume Alain, Randy D. Gascoyne, Douglas E. Horsman, Raymond T. Ng, Kevin P. Murphy posted to tool number hidden_markov_model dna_copy copy clustering change cgh bioinformatics by dolchan on 2009-10-13 18:48:12 as along with 5 people jfr jonilaserson rdiaz kdpreter nuin
	From bytes to bedside: data integration and computational biology for translational cancer research. [My Copy] PLoS computational biology, Vol. 3, No. 2. (23 February 2007), e12. by Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, et al.Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra posted to data integration research review translational by dolchan on 2009-07-20 06:52:44 as along with 8 people nicklynch dansullivanblk guhjy jfr kynn frohike oelemento srp33
	FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions [My Copy] Genome Biology, Vol. 10, No. 4. (2009), R39. by Jessica Severin, Andrew Waterhouse, Hideya Kawaji, et al.Timo Lassmann, Erik van Nimwegen, Piotr Balwierz, Michiel de Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten Daub, Alistair Forrest posted to biological database expression gene networks by dolchan on 2009-04-20 03:55:33 as along with 10 people jfr Garamonfok rdiaz bertelsen YukaH ealloza guhjy pengchy natstreet druvus
	Genome-Scale Reconstruction of <italic>Escherichia coli</italic>'s Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (13 March 2009), e1000312. by Ines Thiele, Neema Jamshidi, Ronan M. Fleming, Bernhard Palsson posted to e-coli knowledgebase modeling regulation transcriptional translational by dolchan on 2009-03-13 19:33:31 as along with 3 people TRHvidsten pablocarb trfield
	Biological context networks: a mosaic view of the interactome [My Copy] Molecular Systems Biology, Vol. 2 (28 November 2006) by John Rachlin, Dikla D. Cohen, Charles Cantor, Simon Kasif posted to biology context networks systems by dolchan on 2009-02-24 20:56:40 as along with 6 people ashishanand aramesh2 rdiaz massivemayhem mingzhi roys
	Reactome: a knowledge base of biologic pathways and processes [My Copy] Genome Biology, Vol. 8, No. 3. (16 March 2007), R39. by Imre Vastrik, Peter D'Eustachio, Esther Schmidt, et al.Geeta J. Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein posted to biological knowledgebase pathways processes reactome by dolchan on 2009-02-23 03:56:02 as along with 15 people ipark-kaist neilswainston peterli bertelsen aramesh2 shikin fgibson reyez guhjy dragonrez jfr balajis raiyar toshiaki_katayama AlexanderPico
	Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster [My Copy] Genome Research, Vol. 17 (2007), pp. 1236-1243. by Ming Zhan, Haruyoshi Yamaza, Yu Sun, Jason Sinclair, Huai Li, Sige Zou posted to aging data expression gene by dolchan on 2008-09-10 16:45:39 as
	Accurate and reliable cancer classification based on probabilistic inference of pathway activity. [My Copy] PloS one In PLoS ONE, Vol. 4, No. 12. (7 December 2009), e8161. by Junjie Su, Byung-Jun J. Yoon, Edward R. Dougherty posted to pathways knowledge-based integration classification by dolchan on 2009-12-17 18:23:59 as along with 2 people dglane001 ptrobajo
	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 ontology misuse gene by dolchan on 2009-10-29 17:27:41 as along with 41 people and 3 groups lisa1 singhsh epigenetics davidmam Thaverkamp druvus dullhunk suizan Borelli Zephyrus VGreiff klo thomaskelder ilyashl phoenixzxl MarcoAlvarez isakemal bertelsen daforerog jfr djkt guhjy aheilbut mariakmejia cmzmasek A_Olympia realzhang carlk roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck rvosa bpcusack 8_01 logics of knowledge FAB-lab
	Bayesian biclustering of gene expression data. [My Copy] BMC genomics, Vol. 9 Suppl 1, No. Suppl 1. (2008), S4. by Jiajun Gu, Jun S. Liu posted to gene expression biclustering bayesian by dolchan on 2009-10-29 17:23:55 as along with 9 people meanerelk marti tonamswish bertelsen imina tvdbulck jfr yangc dragonrez
	An in silico method for detecting overlapping functional modules from composite biological networks [My Copy] BMC Systems Biology, Vol. 2, No. 1. (2008) by Ioannis Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos posted to networks modules functional composite biological by dolchan on 2009-10-29 17:19:54 as along with 7 people jfr diamantis imina saket renatomilani lptolik jonesn
	A comprehensive functional analysis of tissue specificity of human gene expression. [My Copy] BMC biology, Vol. 6, No. 1. (2008) by Z. Dezso, Y. Nikolsky, E. Sviridov, et al.W. Shi, T. Serebriyskaya, D. Dosymbekov, A. Bugrim, E. Rakhmatulin, R. J. Brennan, A. Guryanov, K. Li, J. Blake, R. R. Samaha, T. Nikolskaya posted to tissue specificity gene expression by dolchan on 2009-10-29 17:19:01 as along with 8 people and 1 group grahamc shikin jfr guhjy acanario inesdesantiago imina GeeSharpMinor GeneGo
	Boolean implication networks derived from large scale, whole genome microarray datasets [My Copy] Genome Biology, Vol. 9 (30 October 2008), R157. by Debashis Sahoo, David L. Dill, Andrew J. Gentles, Robert Tibshirani, Sylvia K. Plevritis posted to scale networks microarray large boolean by dolchan on 2009-10-29 17:05:59 as along with 8 people zufar jfr rdiaz imina pengchy guhjy mdperry bcondon
	Identifying differential correlation in gene/pathway combinations [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (18 November 2008), 488. by Rosemary Braun, Leslie Cope, Giovanni Parmigiani posted to pathways expression differential correlation by dolchan on 2009-10-29 17:04:54 as along with 11 people dipenps zufar jfr shikin mdstobbe imina rdiaz renatomilani lptolik barriot ptrobajo
	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 to network expression analysis by dolchan on 2009-10-29 17:03:39 as along with 22 people jeremymiller zufar sficklin isimpson rdiaz guhjy cswinburne jfr ptrobajo pengchy nolodie druvus aramesh2 kengg roys Ema tmmurali Borelli Totobox AbnerCYH davidchavalarias caseybrown
	Arabidopsis gene co-expression network and its functional modules. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 346. by Linyong Mao, John L. Van Hemert, Sudhansu Dash, Julie A. Dickerson posted to networks interaction graph gene clustering by dolchan on 2009-10-26 22:35:12 as along with 6 people hchuang icecrown zchen venancio Borelli druvus
	Computation of recurrent minimal genomic alterations from array-CGH data [My Copy] Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 849-856. by C. Rouveirol, N. Stransky, Ph Hupe, et al.Ph Rosa, E. Viara, E. Barillot, F. Radvanyi posted to tool pattern mining dna_copy data cgh bioinformatics analysis by dolchan on 2009-10-13 18:58:14 as along with 1 person stharward
	Inferring the role of transcription factors in regulatory networks [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (06 May 2008), 228. by Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel posted to gene inference networks regulation regulatory transcriptional by dolchan on 2009-07-26 05:13:53 as along with 6 people guhjy idonaldson renatomilani heliopais maralena isimpson
	Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. [My Copy] Genome biology, Vol. 10, No. 7. (22 July 2009), R79. by Piotr J. Balwierz, Piero Carninci, Carsten O. Daub, et al.Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen posted to deep expression human mouse promoterome sequencing by dolchan on 2009-07-23 08:26:54 as along with 8 people mamitamura vingron orzenil ptrobajo maximilianh inesdesantiago djkt guhjy
	Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. [My Copy] PLoS computational biology, Vol. 5, No. 5. (15 May 2009), e1000387. by Li Xie, Jerry Li, Lei Xie, Philip E. Bourne posted to bioinformatics biology discovery drug interaction protein-protein sysems by dolchan on 2009-05-18 19:35:45 as along with 5 people and 1 group ubcg08l flbarroso jmccammon reyez barry McCammon
	KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 11. (1 June 2009), pp. 1470-1471. by Jitao David D. Zhang, Stefan Wiemann posted to analysis graph kegg pathway by dolchan on 2009-05-17 06:57:13 as along with 16 people jfr Thaverkamp daforerog Vincent_Rouilly kiara coela guhjy neils VGreiff nuin chrisamiller renatomilani jmeppley natstreet phoenixzxl druvus
	Bioinformatics for next generation sequencing. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 4. (15 February 2009), pp. 429-429. by Alex Bateman, John Quackenbush posted to bioinformatics nextgene sequencing by dolchan on 2009-05-06 21:10:19 as along with 8 people seb1 n00c svenrahmann idoerg orzenil druvus floatingpoint djkt
	High-resolution DNA-binding specificity analysis of yeast transcription factors. [My Copy] Genome research, Vol. 19, No. 4. (21 April 2009), pp. 556-566. by Cong Zhu, Kelsey J. Byers, Rachel Patton P. McCord, et al.Zhenwei Shi, Michael F. Berger, Daniel E. Newburger, Katrina Saulrieta, Zachary Smith, Mita V. Shah, Mathangi Radhakrishnan, Anthony A. Philippakis, Yanhui Hu, Federico De Masi, Marcin Pacek, Andreas Rolfs, Tal Murthy, Joshua Labaer, Martha L. Bulyk posted to factor transcription yeast by dolchan on 2009-04-29 18:29:26 as along with 9 people matted austin_mcdonald siebert rpatward xwbcn absterga djkt kristallreiner aalibes
	Transcriptional features of genomic regulatory blocks [My Copy] Genome Biology, Vol. 10, No. 4. (2009), R38. by Altuna Akalin, David Fredman, Erik Arner, et al.Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten Daub, Yoshihide Hayashizaki, Boris Lenhard posted to gene regulation transcription by dolchan on 2009-04-20 03:57:10 as along with 3 people xianjun djkt JustinCrocker
	The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation [My Copy] Genome Biology, Vol. 10, No. 4. (2009), R40. by Hideya Kawaji, Jessica Severin, Marina Lizio, et al.Andrew Waterhouse, Shintaro Katayama, Katharine Irvine, David Hume, Alistair Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten Daub posted to dynamics gene networks regulation transcription by dolchan on 2009-04-20 03:56:32 as along with 7 people jfr rdiaz YukaH tonamswish guhjy natstreet druvus
	Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (20 March 2009), e1000311. by Chun Ye, Simon J. Galbraith, James C. Liao, Eleazar Eskin posted to analysis component factor network networks regulatory transcription yeast by dolchan on 2009-03-27 18:49:50 as along with 5 people TRHvidsten svenrahmann idonaldson rdiaz roys
	Inferring connectivity of genetic regulatory networks using information-theoretic criteria. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 5, No. 2. (n 2008), pp. 262-274. by W. Zhao, E. Serpedin, E. R. Dougherty posted to boolean inference information network by dolchan on 2009-03-25 18:50:45 as
	Inferring regulatory networks. [My Copy] Frontiers in bioscience : a journal and virtual library, Vol. 13 (2008), pp. 263-275. by H. Li, J. Xuan, Y. Wang, M. Zhan posted to gene inference networks regulatory by dolchan on 2009-03-25 18:49:34 as along with 4 people agonzale jago tvdbulck bertelsen
	Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1999), pp. 17-28. by T. Akutsu, S. Miyano, S. Kuhara posted to boolean inference network by dolchan on 2009-03-25 18:48:44 as along with 1 person and 1 group dlobo GEB
	Reveal, a general reverse engineering algorithm for inference of genetic network architectures. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1998), pp. 18-29. by S. Liang, S. Fuhrman, R. Somogyi posted to boolean inference network reveal by dolchan on 2009-03-25 18:47:56 as
	Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007) by Peng Li, Chaoyang Zhang, Edward Perkins, Ping Gong, Youping Deng posted to bayesian boolean dynamic network pbn probabilistic by dolchan on 2009-03-25 18:45:59 as along with 2 people ivokwee heliopais
	TFCat: the curated catalog of mouse and human transcription factors. [My Copy] Genome biology, Vol. 10, No. 3. (2009) by Debra L. Fulton, Saravanan Sundararajan, Gwenael Badis, et al.Timothy R. Hughes, Wyeth W. Wasserman, Jared C. Roach, Rob Sladek posted to curated database factor transcription by dolchan on 2009-03-14 07:27:36 as along with 8 people and 1 group bsamal maximilianh megraw natstreet idonaldson bmajoros cisevol druvus BergmanLab
	DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. [My Copy] Genome biology, Vol. 10, No. 3. (06 March 2009), R27. by Karen Lemmens, Tijl De Bie, Thomas Dhollander, et al.Sigrid C. De Keersmaecker, Inge M. Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal posted to condition gene network regulation specific by dolchan on 2009-03-14 07:20:06 as along with 6 people enelkinsan frohike druvus natstreet tvdbulck biomcgary
	Canalization of Gene Expression and Domain Shifts in the <italic>Drosophila</italic> Blastoderm by Dynamical Attractors [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (13 March 2009), e1000303. by Manu, Svetlana Surkova, Alexander V. Spirov, et al.Vitaly V. Gursky, Hilde Janssens, Ah-Ram Kim, Ovidiu Radulescu, Carlos E. Vanario-Alonso, David H. Sharp, Maria Samsonova, John Reinitz posted to attractors drosophila dynamical expression gene modeling by dolchan on 2009-03-13 19:34:29 as along with 2 people balabu JustinCrocker
	Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (6 March 2009), e1000298. by Jeremy E. Purvis, Ravi Radhakrishnan, Scott L. Diamond posted to dynamic kinetic model steady-state by dolchan on 2009-03-06 16:51:57 as along with 3 people abhishek_tiwari schwartzjmc ulfliebal
	Cancer Genomes: From Chaos Comes Order? [My Copy] Sci. Signal., Vol. 1, No. 39. (30 September 2008), ec340. by Paula A. Kiberstis posted to cancer genome science by dolchan on 2009-02-23 04:17:06 as along with 1 person ajaymalik

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