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	Models and computational strategies linking physiological response to molecular networks from large-scale data. [My Copy] Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, Vol. 366, No. 1878. (13 September 2008), pp. 3067-3089. by Fernando Ortega, Katrin Sameith, Nil Turan, et al.Russell Compton, Victor Trevino, Marina Vannucci, Francesco Falciani posted to inference modelling networks by aviad_work on 2008-12-15 22:58:43 as along with 2 people bertelsen cswinburne
	Unequal group variances in microarray data analyses. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 9. (1 May 2008), pp. 1168-1174. by Meaza Demissie, Barbara Mascialino, Stefano Calza, Yudi Pawitan posted to differential_genes microarray_analysis statistics by aviad_work on 2008-04-29 18:54:23 as along with 5 people and 1 group GeeSharpMinor dswan guhjy shigepong jfr Bioinformatics
	Mapping normal and cancer cell signalling networks: towards single-cell proteomics [My Copy] Nat Rev Cancer, Vol. 6, No. 2. (February 2006), pp. 146-155. by Jonathan M. Irish, Nikesh Kotecha, Garry P. Nolan posted to networks proteomics signaling by aviad_work on 2008-12-11 16:16:22 as along with 1 person and 1 group julius SysbioMPI-TCells
	Tight Clustering: A Resampling-Based Approach for Identifying Stable and Tight Patterns in Data [My Copy] Biometrics, Vol. 61, No. 1. (March 2005), pp. 10-16. by George C. Tseng, Wing H. Wong posted to clustering resampling by aviad_work on 2008-12-01 15:02:56 as along with 1 person jfr
	Diagnosis of multiple cancer types by shrunken centroids of gene expression. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 10. (14 May 2002), pp. 6567-6572. by Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Gilbert Chu posted to centroids classification gene_expression gene_selection shrunken by aviad_work on 2008-10-28 13:17:29 as along with 9 people and 1 group akastrin daed kliger jfr archroad giovanni frohike GeeSharpMinor jjrodriguez GeschwindLab
	New resampling method for evaluating stability of clusters [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Irina G. Dresen, Tanja Boes, Johannes Huesing, Markus Neuhaeuser, Karl H. Joeckel posted to clustering evaluation resampling stability by aviad_work on 2008-08-21 16:24:02 as along with 7 people and 2 groups ghattem Dori2008 derwisch sobolevnrm RamuAnandakrishnan jfr guhjy SIMR bioinformatics baker-group
	LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by G. Wang, A. V. Kossenkov, M. F. Ochs posted to nmf by aviad_work on 2008-08-19 16:50:21 as along with 3 people dragonrez jfr pliz
	Microarray data analysis: from disarray to consolidation and consensus. [My Copy] Nature reviews. Genetics, Vol. 7, No. 1. (01 January 2006), pp. 55-65. by David B. Allison, Xiangqin Cui, Grier P. Page, Mahyar Sabripour posted to microarray microarray_analysis pathways review by aviad_work on 2008-07-14 22:08:51 as along with 31 people and 3 groups stharward antonkratz ipark-kaist svozil bertelsen Stew daforerog winterschlaefer verdicchio guhjy barry textoris jfr Ayest balicea sterovetta lhonigberg acidwizard ronaldozhou vpschulz rmk schuylrp Garamonfok debasis GeeSharpMinor dimatura heliopais shikin minostro giovenko jo_davies Bioinformatics - CRUK structural_bioinformatics Bioinformatics
	Jointly analyzing gene expression and copy number data in breast cancer using data reduction models. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 3, No. 1. (January 2006), pp. 2-16. by John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra, Jaakko Astola posted to cdna copy_number_alterations gene_expression snp by aviad_work on 2008-04-02 21:55:10 as along with 1 person rdiaz
	Cluster-wise assessment of cluster stability [My Copy] Computational Statistics & Data Analysis, Vol. 52, No. 1. (15 September 2007), pp. 258-271. by Christian Hennig posted to clustering cluster_validation pattern_recognition by aviad_work on 2008-03-06 15:29:39 as
	Linking oncogenic pathways with therapeutic opportunities [My Copy] Nature Reviews Cancer, Vol. 6, No. 9. (17 August 2006), pp. 735-741. by Andrea H. Bild, Anil Potti, Joseph R. Nevins posted to cancer gsea pathways src therapeutic by aviad_work on 2008-02-15 22:59:26 as along with 4 people jackjackjjj frohike srp33 jfr
	High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. [My Copy] Cancer Cell, Vol. 9, No. 4. (April 2006), pp. 313-325. by D. R. Carrasco, G. Tonon, Y. Huang, et al.Y. Zhang, R. Sinha, B. Feng, J. P. Stewart, F. Zhan, D. Khatry, M. Protopopova, A. Protopopov, K. Sukhdeo, I. Hanamura, O. Stephens, B. Barlogie, K. C. Anderson, L. Chin, J. D. Shaughnessy, C. Brennan, R. A. Depinho posted to cancer copy_number_alterations microarray_analysis nmf by aviad_work on 2008-01-23 16:05:38 as along with 1 person ma_ko
	Wnt/Wingless pathway activation and chromosome 6 loss characterize a distinct molecular sub-group of medulloblastomas associated with a favorable prognosis. [My Copy] Cell Cycle, Vol. 5, No. 22. (November 2006), pp. 2666-2670. by S. C. Clifford, M. E. Lusher, J. C. Lindsey, et al.J. A. Langdon, R. J. Gilbertson, D. Straughton, D. W. Ellison posted to cancer medulloblastoma wnt_pathway by aviad_work on 2007-12-18 18:00:06 as along with 1 person jlangdon
	Estimating the number of clusters in a dataset via the gap statistic [My Copy] (2000) by R. Tibshirani, G. Walther, T. Hastie posted to clustering number_of_clusters validity by aviad_work on 2007-12-14 21:29:57 as along with 6 people saket balajis archroad sugarexpletive ykuoka frohike
	Summaries of Affymetrix GeneChip probe level data. [My Copy] Nucleic acids research In Nucl. Acids Res., Vol. 31, No. 4. (15 February 2003), e15. by Rafael A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs, Terence P. Speed posted to microarray normalization rma by aviad_work on 2007-12-06 21:05:29 as along with 18 people frohike jperkins daforerog lwaldron shikin dswan huiminC pcahan1 RMGraze vplagnol ghattem talponer heliopais wirawan waszak rschulz bertelsen srp33
	Clustering Validity Based on the Improved Hubert Γ Statistic and the Separation of Clusters [My Copy] In ICICIC '06: Proceedings of the First International Conference on Innovative Computing, Information and Control (2006), pp. 539-543. by Heng Zhao, Jimin Liang, Haihong Hu posted to clustering hubert validation by aviad_work on 2007-12-05 16:54:47 as
	Computational cluster validation in post-genomic data analysis [My Copy] Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3201-3212. by Julia Handl, Joshua Knowles, Douglas B. Kell posted to clustering validation by aviad_work on 2007-12-05 16:54:12 as along with 6 people srp33 gangcai santiago isimpson saket frohike
	Improving molecular cancer class discovery through sparse non-negative matrix factorization [My Copy] Bioinformatics, Vol. 21, No. 21. (1 November 2005), pp. 3970-3975. by Yuan Gao, George Church posted to cancer classification gene_expression nmf by aviad_work on 2007-10-15 21:41:41 as along with 6 people zufar Scis0000002 kentsis dragonrez jfr yama_tah
	High-throughput oncogene mutation profiling in human cancer [My Copy] Nature Genetics, Vol. 39, No. 3. (11 February 2007), pp. 347-351. by Roman K. Thomas, Alissa C. Baker, Ralph M. Debiasi, et al.Wendy Winckler, Thomas Laframboise, William M. Lin, Meng Wang, Whei Feng, Thomas Zander, Laura E. Macconnaill, Jeffrey C. Lee, Rick Nicoletti, Charlie Hatton, Mary Goyette, Luc Girard, Kuntal Majmudar, Liuda Ziaugra, Kwok-Kin Wong, Stacey Gabriel, Rameen Beroukhim, Michael Peyton, Jordi Barretina, Amit Dutt, Caroline Emery, Heidi Greulich, Kinjal Shah, Hidefumi Sasaki, Adi Gazdar, John Minna, Scott A. Armstrong, Ingo K. Mellinghoff, Stephen F. Hodi, Glenn Dranoff, Paul S. Mischel, Tim F. Cloughesy, Stan F. Nelson, Linda M. Liau, Kirsten Mertz, Mark A. Rubin, Holger Moch, Massimo Loda, William Catalona, Jonathan Fletcher, Sabina Signoretti, Frederic Kaye, Kenneth C. Anderson, George D. Demetri, Reinhard Dummer, Stephan Wagner, Meenhard Herlyn, William R. Sellers, Matthew Meyerson, Levi A. Garraway posted to cancer snp by aviad_work on 2007-10-11 19:43:33 as along with 7 people and 1 group allmensch huiminC oelemento jfr ealloza xingxu cerami BioinfoCIPF
	Algorithms for Non-negative Matrix Factorization [My Copy] In NIPS (2000), pp. 556-562. by Daniel D. Lee, Sebastian H. Seung posted to clustering factorization nmf by aviad_work on 2006-07-10 16:19:13 as along with 17 people and 2 groups zufar bcao sainsworth pprett ppeeling anar yas luispedro pliz walkking atbrew sugarexpletive phlow vsree007 dragonrez vlachmore cager T_lab Computer_Graphics
	Data clustering: a review [My Copy] ACM Computing Surveys, Vol. 31, No. 3. (1999), pp. 264-323. by A. K. Jain, M. N. Murty, P. J. Flynn posted to clustering review by aviad_work on 2006-07-10 13:43:28 as along with 26 people and 3 groups vingron meanerelk marquisdesade jmenche doitian radical V pdlug stanley jelsas sona gangli macowell mhaller ali grimm numata carueda microserf rahul rchauhan sugarexpletive stewi2 MortMan nklee shinichi3 tulip SRL BUiGEM
	Effects of filtering by Present call on analysis of microarray experiments. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by J. N. McClintick, H. J. Edenberg posted to probes present gene_expression filtering call by aviad_work on 2009-12-01 15:13:42 as along with 6 people jfr bertelsen heliopais ghattem waszak yevishere
	The properties of high-dimensional data spaces: implications for exploring gene and protein expression data [My Copy] Nat Rev Cancer, Vol. 8, No. 1. (01 January 2008), pp. 37-49. by Robert Clarke, Habtom W. Ressom, Antai Wang, et al.Jianhua Xuan, Minetta C. Liu, Edmund A. Gehan, Yue Wang posted to no-tag by aviad_work on 2009-09-24 15:22:56 as along with 17 people and 1 group Zephyrus ipark-kaist isimpson Scis0000002 baizhang bertelsen ptrobajo jfr guhjy tmmurali dwf frohike cjeans nedwards shikin blackm0k brianb Bioinformatics
	NCBI GEO: mining tens of millions of expression profilesdatabase and tools update [My Copy] Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D760-D765. by Barrett, Tanya, Troup, et al.B. Dennis, Wilhite, E. Stephen, Ledoux, Pierre, Rudnev, Dmitry, Evangelista, Carlos, Kim, F. Irene, Soboleva, Alexandra, Tomashevsky, Maxim, Edgar, Ron posted to dataset expression_data geo ncbi by aviad_work on 2009-05-26 01:48:03 as along with 5 people frohike Borelli akastrin giovenko minostro
	The cancer genome [My Copy] Nature In Nature, Vol. 458, No. 7239. (09 April 2009), pp. 719-724. by Michael R. Stratton, Peter J. Campbell, P. Andrew Futreal posted to cancer nature review by aviad_work on 2009-05-26 01:47:35 as along with 13 people and 1 group heliopais jfr suizifish guhjy jessopher ilyashl frohike pkonings reyez Zephyrus rdiaz renatomilani kristen Roswell Cancer Crosstalk
	A general modular framework for gene set enrichment analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (03 February 2009), 47. by Marit Ackermann, Korbinian Strimmer posted to enrichment genesets gsea pathway-analysis review by aviad_work on 2009-04-14 22:51:03 as along with 18 people and 1 group bertelsen ptrobajo zufar srp33 vingron dipenps shikin arjun_citeulike guhjy pk506 thomaskelder ydhwang rdiaz kshameer renatomilani dswan cmzmasek RamuAnandakrishnan Bioinformatics
	On testing the significance of sets of genes [My Copy] (4 Sep 2007) by Bradley Efron, Robert Tibshirani posted to enrichment genesets gsea pathways statistics by aviad_work on 2009-04-14 22:49:40 as along with 1 person jgilbert
	Modeling Cancer Progression via Pathway Dependencies [My Copy] PLoS Comput Biol, Vol. 4, No. 2. (15 February 2008), e28. by Elena J. Edelman, Justin Guinney, Jen-Tsan Chi, Phillip G. Febbo, Sayan Mukherjee posted to cancer pathway-analysis by aviad_work on 2009-04-14 22:28:34 as along with 6 people bertelsen ptrobajo wei ipark-kaist bootsy jfr
	Powerful goodness-of-fit tests based on the likelihood ratio [My Copy] Journal of the Royal Statistical Society: Series B (Statistical Methodology), Vol. 64, No. 2. (2002), pp. 281-294. by Jin Zhang posted to goodness-of-fit likelihood_ratio statistics by aviad_work on 2009-04-03 22:23:13 as
	Using GOstats to test gene lists for GO term association [My Copy] Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. 257-258. by S. Falcon, R. Gentleman posted to enrichment go gostats package r by aviad_work on 2009-03-20 20:38:15 as along with 8 people schwalb srp33 heliopais jfr jandot guhjy macavity1g mcgannd
	Network-based classification of breast cancer metastasis. [My Copy] Molecular systems biology, Vol. 3 (16 October 2007) by Han-Yu Y. Chuang, Eunjung Lee, Yu-Tsueng T. Liu, Doheon Lee, Trey Ideker posted to breast cancer classification metastasis by aviad_work on 2009-03-13 15:18:32 as along with 30 people and 4 groups gowtham yaredo fesousa ipark-kaist AbnerCYH zufar provero jmuhlich Zephyrus ggallone giovenko winterschlaefer isimpson ihpark bertelsen jfr kengg frohike mikaelhuss cjeans zwang cerami abhattac shikin oelemento roys ptrobajo dap5087 saman_vp verdicchio Complex Networks Jarman Lab Bioinformatics GeneGo
	Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists [My Copy] Nucl. Acids Res., Vol. 37, No. 1. (1 January 2009), pp. 1-13. by Da W. Huang, Brad T. Sherman, Richard A. Lempicki posted to enrichment_analysis pathway-analysis by aviad_work on 2009-03-04 19:17:49 as along with 49 people and 2 groups bsamal icecrown natstreet provero psique darian chasmand hzoltan ipark-kaist giovenko lwaldron jcaddy antonkratz Zephyrus shikin yaredo tonamswish ddunbar robfsouza Keywan daforerog ptrobajo rdiaz bertelsen Stew inesdesantiago heliopais AlexanderPico ekotelnikova frohike aramesh2 jfr zufar ilyashl dolchan paszkows lptolik thomaskelder AbnerCYH neils tmmurali ealloza barriot druvus renatomilani pengchy phoenixzxl guhjy sjcockell Bioinformatics - CRUK ConklinLab
	Inferring Pathway Activity toward Precise Disease Classification [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000217. by Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee posted to class_discovery gene_expression pathway-analysis by aviad_work on 2009-03-04 17:55:54 as along with 13 people frohike rschulz isimpson yaredo ipark-kaist jfr ajbattle zufar carlk renatomilani dragonrez tmmurali ptrobajo
	Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach. [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. 1607-1615. by V. Pihur, S. Datta, S. Datta posted to cluster_validation by aviad_work on 2009-03-04 17:49:52 as along with 2 people fer jfr
	Clustering gene-expression data with repeated measurements [My Copy] Genome Biology, Vol. 4, No. 5. (2003) by Ka Yeung, Mario Medvedovic, Roger Bumgarner posted to clustering gene_expression replicates by aviad_work on 2009-02-27 15:30:47 as along with 1 person and 1 group ghattem SIMR bioinformatics
	Improving gene set analysis of microarray data by SAM-GS [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007), 242. by Irina Dinu, John Potter, Thomas Mueller, et al.Qi Liu, Adeniyi Adewale, Gian Jhangri, Gunilla Einecke, Konrad Famulski, Philip Halloran, Yutaka Yasui posted to gene_expression gsea sam by aviad_work on 2009-02-19 18:00:50 as along with 12 people and 1 group tonamswish aramesh2 zufar jfr ealloza shigepong ghattem GeeSharpMinor waghsk LuigiAugugliaro heliopais renatomilani BioinfoCIPF
	A modular approach for integrative analysis of large-scale gene-expression and drug-response data [My Copy] Nature Biotechnology In Nat Biotech, Vol. 26, No. 5. (08 May 2008), pp. 531-539. by Zoltan Kutalik, Jacques S. Beckmann, Sven Bergmann posted to gene_expression integration isa pingpong by aviad_work on 2009-02-11 19:30:09 as along with 13 people frohike mysickova meanerelk zufar TRHvidsten vingron mingzhi guhjy jfr stringertheory tmmurali oelemento ptrobajo
	Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 18. (2000), pp. 9834-9839. by Mei-Ling T. Lee, Frank C. Kuo, G. A. Whitmore, Jeffrey Sklar posted to gene_expression microarray replicates statistics by aviad_work on 2009-01-21 17:23:42 as
	Comparison of various statistical methods for identifying differential gene expression in replicated microarray data [My Copy] Statistical Methods in Medical Research, Vol. 15, No. 1. (February 2006), pp. 3-20. by Seo Y. Kim, Jae W. Lee, In S. Sohn posted to gene_expression microarray replicates statistics by aviad_work on 2009-01-21 17:18:02 as
	Genomics Identifies Medulloblastoma Subgroups That Are Enriched for Specific Genetic Alterations [My Copy] J Clin Oncol, Vol. 24, No. 12. (20 April 2006), pp. 1924-1931. by Margaret C. Thompson, Christine Fuller, Twala L. Hogg, et al.James Dalton, David Finkelstein, Ching C. Lau, Murali Chintagumpala, Adekunle Adesina, David M. Ashley, Stewart J. Kellie, Michael D. Taylor, Tom Curran, Amar Gajjar, Richard J. Gilbertson posted to medulloblastoma by aviad_work on 2009-01-08 21:23:12 as
	Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets [My Copy] PLoS ONE, Vol. 2, No. 11. (21 November 2007), e1195. by Yujin Hoshida, Jean-Philippe Brunet, Pablo Tamayo, Todd R. Golub, Jill P. Mesirov posted to gsea mapping subclass by aviad_work on 2009-01-06 20:50:26 as along with 3 people zufar laral jfr
	Finding regulatory modules through large-scale gene-expression data analysis [My Copy] Bioinformatics In Bioinformatics, Vol. 21, No. 7. (1 April 2005), pp. 1172-1179. by M. Kloster, C. Tang, N. S. Wingreen posted to bi-clustering gene_expression isa pisa by aviad_work on 2009-01-05 22:15:16 as along with 2 people bsamal tvdbulck
	Challenges and prospects in the analysis of large-scale gene expression data [My Copy] Brief Bioinform, Vol. 5, No. 4. (1 January 2004), pp. 313-327. by Jan H. Ihmels, Sven Bergmann posted to bi-clustering gene_expression review by aviad_work on 2009-01-05 21:54:46 as
	Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. [My Copy] J Mol Biol, Vol. 360, No. 1. (30 June 2006), pp. 204-212. by S. Balaji, L. M. Iyer, L. Aravind, M. M. Babu posted to networks regulatory statistics systems by aviad_work on 2008-12-18 15:21:11 as along with 4 people behindtherabbit kaarsinogen mmt koller
	Defining transcription modules using large-scale gene expression data. [My Copy] Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 1993-2003. by J. Ihmels, S. Bergmann, N. Barkai posted to bi-clustering gene_expression by aviad_work on 2008-12-17 20:51:13 as along with 5 people and 3 groups marcius adepace natstreet tvdbulck siebert EisenLab BioinfoCIPF SGU-CIPF
	Gene module level analysis: identification to networks and dynamics [My Copy] Current Opinion in Biotechnology, Vol. 19, No. 5. (October 2008), pp. 482-491. by X. Wang, E. Dalkic, M. Wu, C. Chan posted to modules networks by aviad_work on 2008-12-15 23:04:25 as along with 1 person pengchy
	Understanding biological functions through molecular networks [My Copy] Cell Research, Vol. 18, No. 2. (01 February 2008), pp. 224-237. by Jing-Dong J. Han posted to networks review by aviad_work on 2008-12-15 23:03:14 as along with 11 people and 1 group Katieleonard rdiaz cmmorel cabbagezs jo_davies shikin mingzhi giorgiofotia maralena phoenixzxl guhjy GeneGo
	Current approaches to gene regulatory network modelling [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 6. (2007), S9. by Thomas Schlitt, Alvis Brazma posted to modelling networks regulatory review by aviad_work on 2008-12-15 23:00:55 as along with 7 people antonkratz Borelli kengg shigepong ramakris nicholasflann bertelsen
	Eigengene networks for studying the relationships between co-expression modules. [My Copy] BMC systems biology, Vol. 1, No. 1. (2007) by Peter Langfelder, Steve Horvath posted to modules networks by aviad_work on 2008-12-15 22:59:51 as along with 7 people jeremymiller tonamswish ptrobajo druvus isimpson jfr AlexanderPico
	Cell-signalling dynamics in time and space [My Copy] Nature Reviews Molecular Cell Biology, Vol. 7, No. 3. (15 February 2006), pp. 165-176. by Boris N. Kholodenko posted to modelling networks review signaling by aviad_work on 2008-12-15 22:56:43 as along with 9 people and 1 group citemyface cmetzner fierykylin mhellmann agonzale julius balabu rmk karfunkel SysbioMPI-TCells

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