lusk's library 258 articles Export

	Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. [My Copy] Current opinion in genetics & development (11 November 2009) by Antonio Ca C. Meireles-Filho, Alexander Stark posted to organization_paper null by lusk on 2009-11-18 19:05:07 as along with 1 person maximilianh
	Insertion-deletion biases and the evolution of genome size. [My Copy] Gene, Vol. 324 (7 January 2004), pp. 15-34. by T. Ryan Gregory posted to insertion deletion by lusk on 2009-11-02 23:08:56 as along with 2 people aprasad brant
	Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome [My Copy] Cell, Vol. 128, No. 6. (23 March 2007), pp. 1231-1245. by T. Kim, Z. Abdullaev, A. Smith, et al.K. Ching, D. Loukinov, R. Green, M. Zhang, V. Lobanenkov, B. Ren posted to turnover_rate by lusk on 2009-10-21 18:57:55 as along with 6 people suizifish clearbluespring caseybrown sebastien_vigneau rschulz xingxu
	Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. [My Copy] Genome biology, Vol. 8, No. 10. (24 October 2007), R225. by Weichun Huang, Joseph R. Nevins, Uwe Ohler posted to turnover_rate by lusk on 2009-10-21 18:35:43 as along with 5 people and 2 groups dpollard djkt stajich Garamonfok maximilianh EisenLab cis-regulatory-evolution
	A phylogenetic analysis of indel dynamics in the cotton genus. [My Copy] Molecular biology and evolution, Vol. 25, No. 7. (9 July 2008), pp. 1415-1428. by Corrinne E. Grover, Yeisoo Yu, Rod A. Wing, Andrew H. Paterson, Jonathan F. Wendel posted to plant deletion by lusk on 2009-10-20 19:59:00 as along with 2 people druvus aprasad
	Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (7 October 2009) by Jennifer S. Hawkins, Stephen R. Proulx, Ryan A. Rapp, Jonathan F. Wendel posted to plants deletion by lusk on 2009-10-20 19:54:39 as along with 1 person bpcusack
	Constructing a meaningful evolutionary average at the phylogenetic center of mass [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (26 June 2007), 222. by Eric Stone, Arend Sidow posted to weighted_average by lusk on 2009-10-09 01:38:05 as
	A -Defensin Mutation Causes Black Coat Color in Domestic Dogs [My Copy] Science, Vol. 318, No. 5855. (30 November 2007), pp. 1418-1423. by Sophie I. Candille, Christopher B. Kaelin, Bruce M. Cattanach, et al.Bin Yu, Darren A. Thompson, Matthew A. Nix, Julie A. Kerns, Sheila M. Schmutz, Glenn L. Millhauser, Gregory S. Barsh posted to 290 by lusk on 2009-09-20 20:05:20 as along with 3 people melissa21 dchughes caseybrown
	Molecular and Evolutionary History of Melanism in North American Gray Wolves [My Copy] Science, Vol. 323, No. 5919. (6 March 2009), pp. 1339-1343. by Tovi M. Anderson, Bridgett M. vonHoldt, Sophie I. Candille, et al.Marco Musiani, Claudia Greco, Daniel R. Stahler, Douglas W. Smith, Badri Padhukasahasram, Ettore Randi, Jennifer A. Leonard, Carlos D. Bustamante, Elaine A. Ostrander, Hua Tang, Robert K. Wayne, Gregory S. Barsh posted to 290 by lusk on 2009-09-20 20:03:07 as along with 5 people biomcgary quesada smit2jam djkt dlhoyt
	Pseudocounts for transcription factor binding sites. [My Copy] Nucleic acids research, Vol. 37, No. 3. (23 February 2009), pp. 939-944. by Keishin Nishida, Martin C. Frith, Kenta Nakai posted to pseudocounts by lusk on 2009-08-14 17:42:58 as along with 4 people and 1 group Stew jkim63 fpattyn nuin Bioinformatics - CRUK
	Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. [My Copy] Cell, Vol. 133, No. 7. (27 June 2008), pp. 1277-1289. by M. B. Noyes, R. G. Christensen, A. Wakabayashi, G. D. Stormo, M. H. Brodsky, S. A. Wolfe posted to next_project by lusk on 2009-05-08 19:25:35 as along with 6 people austin_mcdonald maximilianh_otx maximilianh emptyhb isimpson icq242500260
	A comparison of transplantable bicoid activity and partial bicoid homeobox sequences in several Drosophila and blowfly species (Calliphoridae) [My Copy] Development Genes and Evolution, Vol. 203, No. 1. (1 January 1993), pp. 34-43. by R. Schröder, K. Sander posted to next_project transplantation by lusk on 2009-05-06 19:57:12 as along with 1 person emptyhb
	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 17 people and 2 groups hzoltan 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
	GENE REGULATION: A Paradigm for Precision [My Copy] Science, Vol. 293, No. 5532. (10 August 2001), pp. 1054-1055. by Kevin Struhl posted to impact by lusk on 2009-02-17 19:51:59 as along with 1 person maximilianh
	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
	High local protein concentrations at promoters: Strategies in prokaryotic and eukaryotic cells [My Copy] BioEssays, Vol. 23, No. 2. (2001), pp. 179-183. by Peter Dröge, Benno Müller-Hill posted to impact by lusk on 2009-02-17 19:48:26 as
	On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses [My Copy] Journal of Molecular Evolution, Vol. 44, No. 6. (24 June 1997), pp. 625-631. by Angelo Pavesi, Bettina De Iaco, Maria I. Granero, Alfredo Porati posted to impact information by lusk on 2009-02-16 22:09:39 as
	Selective pressures on genomes in molecular evolution [My Copy] Journal of Theoretical Biology (25 March 2003) by C. Ofria posted to impact information by lusk on 2009-02-16 22:09:31 as
	Evolution of biological information [My Copy] Nucl. Acids Res., Vol. 28, No. 14. (15 July 2000), pp. 2794-2799. by Thomas D. Schneider posted to impact information by lusk on 2009-02-16 22:06:54 as along with 3 people kumar_physics itmeson vkwn
	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
	Information display by transcriptional enhancers [My Copy] Development, Vol. 130, No. 26. (29 December 2003), pp. 6569-6575. by Meghana M. Kulkarni, David N. Arnosti posted to impact by lusk on 2009-02-13 21:52:16 as along with 1 person emptyhb
	Coordinate enhancers share common organizational features in the Drosophila genome. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 11. (16 March 2004), pp. 3851-3856. by A. Erives, M. Levine posted to impact by lusk on 2009-02-13 17:54:26 as
	Evidence for stabilizing selection in a eukaryotic enhancer element [My Copy] Nature, Vol. 403, No. 6769. (3 February 2000), pp. 564-567. by Michael Z. Ludwig, Casey Bergman, Nipam H. Patel, Martin Kreitman posted to impact by lusk on 2009-02-13 17:53:01 as along with 5 people and 1 group gderwin ranb cisevol emptyhb brant cis-regulatory-evolution
	Drosophila Paired regulates late even-skipped expression through a composite binding site for the paired domain and the homeodomain [My Copy] Development, Vol. 122, No. 9. (1 September 1996), pp. 2697-2707. by M. Fujioka, P. Miskiewicz, L. Raj, A. A. Gulledge, M. Weir, T. Goto posted to impact by lusk on 2009-02-13 17:51:43 as
	Evolution of developmental genes: molecular microevolution of enhancer sequences at the Ubx locus in Drosophila and its impact on developmental phenotypes. [My Copy] Molecular biology and evolution, Vol. 21, No. 2. (February 2004), pp. 348-363. by J. Phinchongsakuldit, S. MacArthur, J. F. Brookfield posted to impact by lusk on 2009-02-13 17:46:57 as along with 4 people and 2 groups Stew adepace cisevol emptyhb EisenLab cis-regulatory-evolution
	Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster [My Copy] Evolution & Development, Vol. 8, No. 1. (January 2006), pp. 6-15. by Naomi S. Wratten, Alistair P. Mcgregor, Philip J. Shaw, Gabriel A. Dover posted to impact by lusk on 2009-02-13 17:45:41 as along with 1 person and 1 group adepace EisenLab
	Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. [My Copy] Development, Vol. 125, No. 5. (March 1998), pp. 949-958. by M. Z. Ludwig, N. H. Patel, M. Kreitman posted to impact by lusk on 2009-02-13 17:41:23 as along with 4 people and 2 groups adepace cisevol emptyhb brant EisenLab cis-regulatory-evolution
	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
	A discriminative model for identifying spatial cis-regulatory modules. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 12, No. 6. (g 2005), pp. 822-834. by E. Segal, R. Sharan posted to impact by lusk on 2009-02-13 06:01:19 as
	Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells [My Copy] Genome Res. (15 May 2008), gr.072769.107. by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong posted to impact by lusk on 2009-02-13 05:46:20 as along with 7 people dandaman maximilianh idonaldson isimpson GustavoLacerda phoenixzxl yoonk
	Competition for overlapping sites in the regulatory region of the Drosophila gene Krüppel. [My Copy] Science (New York, N.Y.), Vol. 256, No. 5053. (3 April 1992), pp. 94-97. by M. Hoch, N. Gerwin, H. Taubert, H. Jäckle posted to impact by lusk on 2009-02-13 05:41:18 as

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outside	69
inside	55
organization_paper	34
review	30
impact	25
methods	23
eisen_journal_club	18
specificity	15
affin_cut	12
cutoff_model	11
proteomic	11
round_robin	10
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sm_mol	5
cancer	4
deletion	4
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regulon	4
rich_presented	4
stuart_presented	4
colin_presented	3
cooperativity	3
devin_presented	3
e3	3
flies	3
information	3
motif	3
next_project	3
nucleosome	3
null	3
290	2
angela_presented	2
brant_presented	2
danr_presented	2
drosophila	2
eve	2
gam1	2
g_protein	2
in_depth	2
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mcm1	2
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skn7	2
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genny	1
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rap1	1
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ryan_presented	1
sea_urchin	1
segmentation	1
selection	1
senescence	1
stewart_presented	1
tfbs	1
theory	1
transplantation	1
tss	1
weighted_average	1
yap1	1

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