Tag organization_paper [33 articles] Export

Recent papers classified by the tag organization_paper.

	A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling [My Copy] Bioinformatics, Vol. 17, No. 12. (1 December 2001), pp. 1113-1122. by Gert Thijs, Magali Lescot, Kathleen Marchal, et al.Stephane Rombauts, Bart De Moor, Pierre Rouze, Yves Moreau posted to organization_paper by lusk on 2009-05-04 18:16:52 as along with 7 people raylim Mehlhorn lyongu dquest natstreet nklee xili03
	PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000156. by Rahul Siddharthan posted to organization_paper by lusk on 2009-05-02 03:49:38 as along with 4 people and 1 group malcook nuin sabahkadri emptyhb BenosLab
	Big Genomes Facilitate the Comparative Identification of Regulatory Elements [My Copy] PLoS ONE, Vol. 4, No. 3. (4 March 2009), e4688. by Brant K. Peterson, Emily E. Hare, Venky N. Iyer, et al.Steven Storage, Laura Conner, Daniel R. Papaj, Rick Kurashima, Eric Jang, Michael B. Eisen posted to organization_paper by lusk on 2009-05-02 03:47:37 as along with 8 people and 2 groups natstreet dpollard JustinCrocker daveGerrard emmahe maximilianh trfield idoerg RockmanLab BergmanLab
	Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster [My Copy] PLoS Comput Biol, Vol. 3, No. 1. (19 January 2007), e7. by Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard posted to organization_paper by lusk on 2009-05-02 03:46:09 as along with 11 people and 1 group daveGerrard ychromosome timhubbard wowalz indigoviolet dpollard dquest SeungjoonOh nklee emptyhb isimpson EisenLab
	Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. [My Copy] BMC bioinformatics, Vol. 6 (2005) by C. T. Brown, Y. Xie, E. H. Davidson, R. A. Cameron posted to organization_paper by lusk on 2009-05-01 19:12:35 as
	The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. [My Copy] Developmental biology, Vol. 318, No. 2. (15 June 2008), pp. 366-377. by Sepand Rastegar, Isabell Hess, Thomas Dickmeis, et al.Jean Christophe C. Nicod, Raymond Ertzer, Yavor Hadzhiev, Wolf-Gerolf G. Thies, Gerd Scherer, Uwe Strähle posted to organization_paper by lusk on 2009-05-01 19:05:13 as along with 3 people and 1 group maximilianh brant cisevol cis-regulatory-evolution
	Identification of Nucleic Acid High-Affinity Binding Sequences of Proteins by SELEX [My Copy] DNA-Protein Interactions (2009), pp. 139-150. by Philippe Bouvet posted to organization_paper by lusk on 2009-05-01 19:01:42 as
	Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. [My Copy] BMC genomics, Vol. 10 (21 January 2009), 37. by Philippe Lefrançois, Ghia M. Euskirchen, Raymond K. Auerbach, et al.Joel Rozowsky, Theodore Gibson, Christopher M. Yellman, Mark Gerstein, Michael Snyder posted to organization_paper by lusk on 2009-05-01 18:59:59 as along with 5 people Vincent_Rouilly guhjy emptyhb WanderingAengus abizar
	DNA microarray technologies for measuring protein-DNA interactions [My Copy] Current Opinion in Biotechnology In Protein technologies, Vol. 17, No. 4. (August 2006), pp. 422-430. by Martha L. Bulyk posted to organization_paper by lusk on 2009-05-01 18:55:41 as along with 3 people and 2 groups dchughes blobbybirdman kristallreiner G4ID Genetics-of-Gambling
	High-throughput methods of regulatory element discovery. [My Copy] BioTechniques, Vol. 41, No. 6. (December 2006) by M. E. Hudson, M. Snyder posted to organization_paper by lusk on 2009-05-01 18:55:00 as along with 1 person cam-swarmers
	Applications of next-generation sequencing technologies in functional genomics [My Copy] Genomics, Vol. 92, No. 5. (11 November 2008), pp. 255-264. by O. Morozova, M. Marra posted to organization_paper by lusk on 2009-05-01 18:39:30 as along with 16 people and 2 groups heliopais viren4388 fishtank jandot natstreet druvus floatingpoint usagi-kirin malcook abizar reyez dchughes xingxu giovenko GeeSharpMinor guhjy Journal picks SIMR bioinformatics
	A self-organizing system of repressor gradients establishes segmental complexity in Drosophila. [My Copy] Nature, Vol. 426, No. 6968. (18 December 2003), pp. 849-853. by D. E. Clyde, M. S. Corado, X. Wu, A. Paré, D. Papatsenko, S. Small posted to organization_paper by lusk on 2009-05-01 18:23:22 as along with 1 person and 1 group adepace EisenLab
	Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter [My Copy] Development, Vol. 119, No. 3. (1 November 1993), pp. 767-772. by S. Small, D. N. Arnosti, M. Levine posted to organization_paper by lusk on 2009-05-01 18:16:18 as along with 1 person and 1 group emilyhare EisenLab
	Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. [My Copy] Pac Symp Biocomput (2008), pp. 489-500. by R. W. Lusk, M. B. Eisen posted to organization_paper by lusk on 2009-04-30 23:28:55 as along with 3 people and 2 groups dpollard maximilianh caseybrown EisenLab cis-regulatory-evolution
	On the probability of fixation of mutant genes in a population. [My Copy] Genetics, Vol. 47 (June 1962), pp. 713-719. by M. KIMURA posted to organization_paper by lusk on 2009-04-30 22:28:30 as along with 1 person timflutre
	Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (13 March 2009), e1000299. by Xin He, Xu Ling, Saurabh Sinha posted to organization_paper by lusk on 2009-04-30 18:31:50 as along with 9 people roys megraw TRHvidsten kieran101 nuin djkt mhamada maximilianh druvus
	Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation [My Copy] PLoS Genet, Vol. 4, No. 6. (27 June 2008), e1000106. by Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolf Meier, Michael B. Eisen posted to organization_paper by lusk on 2009-04-30 18:00:59 as along with 8 people and 2 groups maximilianh Stew emptyhb djkt stajich pradiptaray cisevol caseybrown Mycology cis-regulatory-evolution
	A survey of DNA motif finding algorithms. [My Copy] BMC bioinformatics, Vol. 8 Suppl 7, No. Suppl 7. (2007) by Modan K. Das, Ho-Kwok K. Dai posted to organization_paper by lusk on 2009-04-30 17:48:50 as along with 17 people and 2 groups Dulce wowalz svenrahmann isimpson daveGerrard coldmeadow druvus Stew emptyhb dquest nklee maximilianh yevishere csdhwang brant xili03 pradiptaray BergmanLab Bioinformatics - CRUK
	Parsing regulatory DNA: General tasks,techniques,and the PhyloGibbs approach. [My Copy] J Biosci, Vol. 32, No. 5. (August 2007), pp. 863-870. by R. Siddharthan posted to organization_paper by lusk on 2009-04-30 02:30:48 as along with 3 people isimpson druvus maximilianh
	CtBP-independent repression in the Drosophila embryo. [My Copy] Molecular and cellular biology, Vol. 23, No. 11. (June 2003), pp. 3990-3999. by Y. Nibu, K. Senger, M. Levine posted to organization_paper by lusk on 2009-04-30 02:11:39 as
	Enhanceosomes [My Copy] Current Opinion in Genetics & Development, Vol. 11, No. 2. (1 April 2001), pp. 205-208. by M. Merika posted to impact organization_paper by lusk on 2009-02-17 19:49:54 as along with 1 person afenley
	Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? [My Copy] Journal of Cellular Biochemistry, Vol. 94, No. 5. (2005), pp. 890-898. by David N. Arnosti, Meghana M. Kulkarni posted to impact organization_paper by lusk on 2009-02-13 21:52:56 as along with 2 people raylim olympos
	A rationale for the enhanceosome and other evolutionarily constrained enhancers [My Copy] Current Biology, Vol. 17, No. 22. (20 November 2007), pp. R955-R957. by Dmitri Papatsenko, Mike Levine posted to impact organization_paper by lusk on 2009-02-13 17:22:24 as along with 1 person oelemento
	Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 37. (13 September 2005), pp. 13176-13181. by D. Lebrecht, M. Foehr, E. Smith, et al.F. J. Lopes, C. E. Vanario-Alonso, J. Reinitz, D. S. Burz, S. D. Hanes posted to impact organization_paper by lusk on 2009-02-13 05:36:42 as along with 3 people maximilianh_otx TOchi emptyhb
	Analysis of combinatorial cis-regulation in synthetic and genomic promoters [My Copy] Nature, Vol. 457, No. 7226. (23 November 2008), pp. 215-218. by Jason Gertz, Eric D. Siggia, Barak A. Cohen posted to impact organization_paper by lusk on 2009-02-13 05:35:10 as along with 17 people and 4 groups Vincent_Rouilly pcarbo emptyhb TRHvidsten rpatward jbhiatt maximilianh roys dpollard druvus sebastien_vigneau pengchy sandersl djkt siebert isimpson xianjun TranscriptionalRegulationWithThermodynamicModels RockmanLab cis-regulatory-evolution microbiology_nijmegen
	Frequent Gain and Loss of Functional Transcription Factor Binding Sites [My Copy] PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e99. by Scott W. Doniger, Justin C. Fay posted to impact organization_paper by lusk on 2009-02-13 05:32:52 as along with 11 people and 2 groups fenghezi JustinCrocker pradiptaray brant dpollard sebastien_vigneau zwang maximilianh cisevol xili03 emptyhb EisenLab cis-regulatory-evolution
	Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 34. (26 August 2008), pp. 12376-12381. by Ville Mustonen, Justin Kinney, Curtis G. Callan, Michael LÃ¤ssig posted to neutral organization_paper by lusk on 2009-02-12 23:47:21 as along with 5 people marck emptyhb bmajoros bpcusack zwang
	Modeling Promoter Grammars with Evolving Hidden Markov Models. [My Copy] Bioinformatics (Oxford, England) (5 June 2008) by Kyoung-Jae J. Won, Albin Sandelin, Troels Torben T. Marstrand, Anders Krogh posted to module_inference organization_paper spacing by lusk on 2008-06-19 19:25:37 as along with 2 people maximilianh niallhaslam
	Sequence Context affects the rate of short insertions and deletions in flies and primates [My Copy] Genome Biology, Vol. 9 (21 February 2008), R37. by Amos Tanay, Eric D. Siggia posted to deletion insertion inside organization_paper by lusk on 2008-04-15 02:02:12 as along with 8 people emptyhb timflutre bpcusack djkt biomcgary gjuggler brant aprasad
	Position specific variation in the rate of evolution in transcription factor binding sites. [My Copy] BMC Evol Biol, Vol. 3, No. 1. (28 August 2003) by A. M. Moses, D. Y. Chiang, M. Kellis, E. S. Lander, M. B. Eisen posted to inside organization_paper by lusk on 2007-05-03 17:46:18 as along with 6 people and 2 groups briann dpollard adepace nklee cisevol emptyhb EisenLab cis-regulatory-evolution
	Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. [My Copy] J Mol Evol, Vol. 22, No. 2. (1985), pp. 160-174. by M. Hasegawa, H. Kishino, T. Yano posted to hky inside organization_paper by lusk on 2007-05-03 17:45:03 as along with 4 people aprasad alexeid AaronDarling Natasha
	Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. [My Copy] Mol Biol Evol, Vol. 15, No. 7. (July 1998), pp. 910-917. by A. L. Halpern, W. J. Bruno posted to inside organization_paper by lusk on 2007-05-03 17:42:54 as along with 2 people and 1 group emptyhb dpollard EisenLab
	cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. [My Copy] Mol Cell Biol, Vol. 25, No. 9. (May 2005), pp. 3411-3420. by M. M. Kulkarni, D. N. Arnosti posted to inside organization_paper by lusk on 2007-04-21 18:30:27 as along with 2 people and 1 group adepace olympos EisenLab