alokm's library 48 articles Export

	A genomic code for nucleosome positioning [My Copy] Nature, Vol. 442, No. 7104. (17 August 2006), pp. 772-778. by Eran Segal, Yvonne Fondufe-Mittendorf, Lingyi Chen, et al.Annchristine Thastrom, Yair Field, Irene K. Moore, Ji-Ping Z. Wang, Jonathan Widom posted to no-tag by alokm on 2007-01-14 18:17:41 as along with 19 people and 10 groups TRHvidsten hagechouchin443 natstreet dakelley kentsis aalibes marcius indigoviolet dchughes cconboy neveaire kengg johncumbers joshuashen joepickrell GustavoLacerda rschulz inesdesantiago sonjadaniela Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience G4ID BioinfoCIPF SGU-CIPF Plantandetc Genetics-of-Gambling
	Transcriptional Regulatory Networks in Saccharomyces cerevisiae [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804. by Tong I. Lee, Nicola J. Rinaldi, Francois Robert, et al.Duncan T. Odom, Ziv Bar-Joseph, Georg K. Gerber, Nancy M. Hannett, Christopher T. Harbison, Craig M. Thompson, Itamar Simon, Julia Zeitlinger, Ezra G. Jennings, Heather L. Murray, D. Benjamin Gordon, Bing Ren, John J. Wyrick, Jean-Bosco Tagne, Thomas L. Volkert, Ernest Fraenkel, David K. Gifford, Richard A. Young posted to no-tag by alokm on 2006-11-30 19:26:37 as along with 32 people and 2 groups viren4388 mjoach kmdaily kinop junehlee lillo80 camster snuppepuppan icases forluvoft ggrot opheliav samal sameetmehta cconboy koller jguinney franklin timflutre jpoyatos lusk nklee karfunkel mimulus_99 roys njcitulike brant kristallreiner Borelli Takayuki dquest siebert dbk-lab TNT
	Transcriptional regulatory code of a eukaryotic genome [My Copy] Nature, Vol. 431, No. 7004. (02 September 2004), pp. 99-104. by Christopher T. Harbison, D. Benjamin Gordon, Tong I. Lee, et al.Nicola J. Rinaldi, Kenzie D. Macisaac, Timothy W. Danford, Nancy M. Hannett, Jean-Bosco Tagne, David B. Reynolds, Jane Yoo, Ezra G. Jennings, Julia Zeitlinger, Dmitry K. Pokholok, Manolis Kellis, P. Alex Rolfe, Ken T. Takusagawa, Eric S. Lander, David K. Gifford, Ernest Fraenkel, Richard A. Young posted to no-tag by alokm on 2006-11-30 19:14:22 as along with 29 people and 8 groups viren4388 daveGerrard Dulce talponer wowalz siebert tuck lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 brant mariakmejia kristallreiner snow_dragon aalibes Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
	Navigating gene expression using microarrays [mdash] a technology review [My Copy] Nat Cell Biol, Vol. 3, No. 8. (August 2001), pp. E190-E195. by Almut Schulze, Julian Downward posted to no-tag by alokm on 2006-11-30 15:55:54 as along with 8 people and 2 groups kentz ziquje numata balicea dchughes jo_davies ale mcox G4ID Genetics-of-Gambling
	Computational approaches to analysis of DNA microarray data. [My Copy] Methods Inf Med, Vol. 45 Suppl 1 (2006), pp. 91-103. by J. Quackenbush posted to no-tag by alokm on 2006-11-30 15:45:15 as along with 2 people maldi heliopais
	Microarray data normalization and transformation [My Copy] Nature Genetics, Vol. 32 Suppl (01 December 2002), pp. 496-501. by John Quackenbush posted to microarray review by alokm on 2006-11-30 15:32:44 as along with 10 people seb1 stharward surajitray daforerog textoris chad_davis schuylrp heliopais frohike bertelsen
	Inferring transcriptional modules from ChIP-chip, motif and microarray data. [My Copy] Genome biology, Vol. 7, No. 5. (2006) by Karen Lemmens, Thomas Dhollander, Tijl De Bie, et al.Pieter Monsieurs, Kristof Engelen, Bart Smets, Joris Winderickx, Bart De Moor, Kathleen Marchal posted to no-tag by alokm on 2006-11-27 21:37:35 as along with 4 people roys bozdagd jfr kristallreiner
	Integrated Assessment and Prediction of Transcription Factor Binding [My Copy] PLoS Computational Biology, Vol. preprint, No. 2006. (1 May 2006) by Andreas Beyer, Christopher Workman, Jens Hollunder, et al.Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey G. Ideker posted to no-tag by alokm on 2006-11-27 21:31:54 as along with 2 people brixtonmc ranb
	Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks [My Copy] Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2523-2531. by Werhli, V. Adriano, Grzegorczyk, Marco, Husmeier, Dirk posted to bayesian comparison ggm network by alokm on 2006-11-27 21:26:49 as along with 3 people czeller Borelli roys
	Incorporating gene functions as priors in model-based clustering of microarray gene expression data [My Copy] Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 795-801. by Wei Pan posted to bayesian knowledge net prior by alokm on 2006-11-27 21:23:47 as along with 2 people akastrin dps
	Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 16. (April 2004), pp. 5934-5939. by Yeger E. Lotem, S. Sattath, N. Kashtan, et al.S. Itzkovitz, R. Milo, R. Y. Pinter, U. Alon, H. Margalit posted to interaction network protein-protein bibtex-import by alokm on 2006-11-27 15:02:40 as
	Revealing modular organization in the yeast transcriptional network [My Copy] Nature Genet, Vol. 31 (2002), pp. 370-377. by James Ihmels, Gilgi Friedlander, Sven Bergmann, Ofer Sarig, Yaniv Ziv, Naama Barkai posted to bibtex-import by alokm on 2006-11-27 15:02:40 as
	Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks [My Copy] Bioinformatics, Vol. 19, No. 17. (2003), pp. 2271-2282. by Dirk Husmeier posted to bibtex-import by alokm on 2006-11-27 15:02:40 as
	Using Bayesian networks to analyze expression data [My Copy] Journal of Computational Biology, Vol. 7, No. 3. (August 2000), pp. 601-620. by Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe'er posted to bibtex-import by alokm on 2006-11-27 15:02:40 as
	Kernel k-means: spectral clustering and normalized cuts [My Copy] In KDD '04: Proceedings of the tenth ACM SIGKDD international conference on Knowledge discovery and data mining (2004), pp. 551-556. by Inderjit S. Dhillon, Yuqiang Guan, Brian Kulis posted to bibtex-import by alokm on 2006-11-27 15:02:40 as
	A tutorial on spectral clustering [My Copy] No. 149. (August 2006) by U. von Luxburg posted to bibtex-import by alokm on 2006-11-27 15:02:40 as along with 1 person zibuyu
	Kernel Methods for Pattern Analysis [My Copy] (June 2004) by John S. Taylor, Nello Cristianini posted to bibtex-import by alokm on 2006-11-27 15:02:40 as
	Clustering Under Prior Knowledge with Application to Image Segmentation [My Copy] In Advances in Neural Information Processing Systems 19 (2007) by Mario Figueiredo, Dong S. Cheng, Vittorio Murino edited by B. Scholkopf, J. C. Platt, T. Hofmann posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Validation and functional annotation of expression-based clusters based on gene ontology [My Copy] BMC Bioinformatics, Vol. 7 (2006) by Ralf Steuer, Peter Humburg, Joachim Selbig posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Unsupervised and Semi-supervised Clustering:a Brief Survey [My Copy] (2005) by Nizar Grira, Michel Crucianu, Nozha Boujemaa posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Semi-Supervised Learning Literature Survey [My Copy] (2005) by Xiaojin Zhu posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Molecular biology for computer scientists [My Copy] (1993) by L. Hunter posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Kernel Methods in Computational Biology [My Copy] (2004) edited by B. Schã¶lkopf, K. Tsuda, J. P. Vert posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Semi-supervised graph clustering: a kernel approach [My Copy] In ICML '05: Proceedings of the 22nd international conference on Machine learning (2005), pp. 457-464. by Brian Kulis, Sugato Basu, Inderjit Dhillon, Raymond Mooney posted to spectral bibtex-import by alokm on 2006-11-27 15:02:39 as
	Nutritional Homeostasis in Batch and Steady-State Culture of Yeast [My Copy] Mol. Biol. Cell, Vol. 15, No. 9. (2004), pp. 4089-4104. by Alok J. Saldanha, Matthew J. Brauer, David Botstein posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Genomic expression programs in the response of yeast cells to environmental changes. [My Copy] Mol Biol Cell, Vol. 11, No. 12. (December 2000), pp. 4241-4257. by A. P. Gasch, P. T. Spellman, C. M. Kao, et al.Carmel O. Harel, M. B. Eisen, G. Storz, D. Botstein, P. O. Brown posted to bio high_throughput_dataset bibtex-import by alokm on 2006-11-27 15:02:39 as
	Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium [My Copy] Molecular Systems Biology, Vol. 1, No. 1. (March 2005) by Amos Tanay, Israel Steinfeld, Martin Kupiec, Ron Shamir posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Modeling and simulation of genetic regulatory systems: a literature review. [My Copy] J Comput Biol, Vol. 9, No. 1. (2002), pp. 67-103. by H. de Jong posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Functional Discovery via a Compendium of Expression Profiles [My Copy] Cell, Vol. 102 (July 2000), pp. 109-126. by Timothy R. Hughes, Matthew J. Marton, Allan R. Jones, et al.Christopher J. Roberts, Roland Stoughton, Christopher D. Armour, Holly A. Bennett, Ernest Coffey, Hongyue Dai, Yudong D. He, Matthew J. Kidd, Amy M. King, Michael R. Meyer, David Slade, Pek Y. Lum, Sergey B. Stepaniants, Daniel D. Shoemaker, Daniel Gachotte, Kalpana Chakraburtty, Julian Simon, Martin Bard, Stephen H. Friend posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	A statistical framework for genomic data fusion. [My Copy] Bioinformatics, Vol. 20, No. 16. (November 2004), pp. 2626-2635. by G. R. Lanckriet, T. De Bie, N. Cristianini, M. I. Jordan, W. S. Noble posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Kernel-based data fusion and its application to protein function prediction in yeast [My Copy] Proceedings of the Pacific Symposium on Biocomputing (January 2004), pp. 300-311. by G. R. Lanckriet, M. Deng, N. Cristianini, M. I. Jordan, W. S. Noble posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	An examination of procedures for determining the number of clusters in a data set [My Copy] Psychometrika (1985) by G. W. Milligan, M. C. Cooper posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	Comparing Partitions [My Copy] Journal of Classification (1985) by L. Hubert, P. Arabie posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	A systematic comparison and evaluation of biclustering methods for gene expression data [My Copy] Bioinformatics, Vol. 22, No. 9. (2006), pp. 1122-1129. by Amela Prelic, Stefan Bleuler, Philip Zimmermann, et al.Anja Wille, Peter Buhlmann, Wilhelm Gruissem, Lars Hennig, Lothar Thiele, Eckart Zitzler posted to bibtex-import by alokm on 2006-11-27 15:02:39 as
	A module map showing conditional activity of expression modules in cancer. [My Copy] Nat Genet, Vol. 36, No. 10. (Oct 2004), pp. 1090-8. by Eran Segal, Nir Friedman, Daphne Koller, Aviv Regev posted to 15448693 analysis array databases expression family female gene genetic govt humans male multigene neoplasms non-phs non-us oligonucleotide oncogenes organ profiling research sequence specificity support us bibtex-import by alokm on 2006-11-27 15:02:37 as
	Computational discovery of gene modules and regulatory networks [My Copy] Nature Biotechnology, Vol. 21, No. 11. (2003), pp. 1337-1342. by Ziv B. Joseph, Georg K. Gerber, Tong I. Lee, et al.Nicola J. Rinaldi, Jane Y. Yoo, Franã§ois Robert, Benjamin D. Gordon, Ernest Fraenkel, Tommi S. Jaakkola, Richard A. Young, David K. Gifford posted to bibtex-import by alokm on 2006-11-27 15:02:37 as
	Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data [My Copy] PNAS, Vol. 101, No. 9. (2004), pp. 2981-2986. by Amos Tanay, Roded Sharan, Martin Kupiec, Ron Shamir posted to bibtex-import by alokm on 2006-11-27 15:02:37 as
	From co-expression to co-regulation: how many microarray experiments do we need? [My Copy] Genome Biology, Vol. 5, No. 7. (2004) by Ka Yeung, Mario Medvedovic, Roger Bumgarner posted to bibtex-import by alokm on 2006-11-27 15:02:37 as
	A Unified Theory of Gene Expression [My Copy] Cell, Vol. 108, No. 4. (February 2002), pp. 439-451. by George Orphanides, Danny Reinberg posted to bibtex-import by alokm on 2006-11-27 15:02:37 as
	Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. [My Copy] Nature Genetics, Vol. 34, No. 2. (2003), pp. 166-176. by Eran Segal, Michael Shapira, Aviv Regev, et al.Dana Pe'er, David Botstein, Daphne Koller, Nir Friedman posted to bibtex-import by alokm on 2006-11-27 15:02:37 as
	From signatures to models: understanding cancer using microarrays. [My Copy] Nat Genet, Vol. 37 Suppl (Jun 2005), pp. S38-45. by Eran Segal, Nir Friedman, Naftali Kaminski, Aviv Regev, Daphne Koller posted to 15920529 algorithms analysis animals array biological biology computational expression extramural gene genetic govt humans models neoplasms nih non-phs non-us oligonucleotide phs profiling regulation research sequence support transcription us bibtex-import by alokm on 2006-11-27 15:02:35 as
	Learning Module Networks [My Copy] Journal of Machine Learing Research, Vol. 6, No. Apr. (2005), pp. 557-588. by Eran Segal, Dana Pe'er, Aviv Regev, Daphne Koller, Nir Friedman posted to bibtex-import by alokm on 2006-11-27 15:02:35 as
	Inferring Cellular Networks Using Probabilistic Graphical Models [My Copy] Science, Vol. 303, No. 5659. (2004), pp. 799-805. by Nir Friedman posted to bibtex-import by alokm on 2006-11-27 15:02:35 as
	Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. [My Copy] Mol Biol Cell, Vol. 9, No. 12. (Dec 1998), pp. 3273-97. by P. T. Spellman, G. Sherlock, M. Q. Zhang, et al.V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, B. Futcher posted to 9843569 acid b base binding cell cerevisiae cycle cyclin cyclins dna expression family fungal gene genes genetic govt hybridization messenger multigene non-phs non-us nucleic phs primers proteins regulation repair replication research rna saccharomyces sequence sites support transcription us bibtex-import by alokm on 2006-11-27 15:02:31 as
	Estimating genomic coexpression networks using first-order conditional independence. [My Copy] Genome Biol, Vol. 5, No. 12. (2004) by Paul M. Magwene, Junhyong Kim posted to 15575966 bibtex-import by alokm on 2006-11-27 15:02:30 as
	An empirical Bayes approach to inferring large-scale gene association networks. [My Copy] Bioinformatics, Vol. 21, No. 6. (Mar 2005), pp. 754-64. by Juliane Schäfer, Korbinian Strimmer posted to bibtex-import by alokm on 2006-11-27 15:02:30 as
	Discovery of meaningful associations in genomic data using partial correlation coefficients [My Copy] Bioinformatics, Vol. 20, No. 18. (2004), pp. 3565-3574. by Alberto, Nan Bing, Ina Hoeschele, Pedro Mendes posted to bibtex-import by alokm on 2006-11-27 15:02:30 as
	A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics [My Copy] Statistical Applications in Genetics and Molecular Biology, Vol. 4, No. 1. (2005) by Juliane Schäfer, Korbinian Strimmer posted to bibtex-import by alokm on 2006-11-27 15:02:30 as

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