Bin HE's Top Recommendations

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	Functional variation and evolution of non-coding DNA [My Copy] Current Opinion in Genetics & Development In Genomes and evolution, Vol. 16, No. 6. (December 2006), pp. 559-564. by C. Bird, B. Stranger, E. Dermitzakis posted by 14 people jrhill jameswasmuth dpollard dchughes adepace lusk sujaikumar candypmcg Stew EisenLab G4ID Genetics-of-Gambling cisevol cis-regulatory-evolution
	Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans. [My Copy] Genome Biology, Vol. 8 (02 February 2007), R15. by Tanya Vavouri, Klaudia Walter, Walter R. Gilks, Ben Lehner, Greg Elgar posted by 10 people indigoviolet dpollard adepace djkt sujaikumar Stew EisenLab cisevol cis-regulatory-evolution smbe2008
	Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both. [My Copy] Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402. by T. Vavouri, G. Elgar posted by 9 people troels_marstrand kaspermunch dpollard adepace lusk Stew Bioinformatics EisenLab brant
	Evolutionary changes in cis and trans gene regulation. [My Copy] Nature, Vol. 430, No. 6995. (1 July 2004), pp. 85-88. by Patricia J. Wittkopp, Belinda K. Haerum, Andrew G. Clark posted by 15 people mox ajbattle athma balabu lyongu dpollard balicea tabu adepace emmahe emarker mimulus_99 EisenLab cisevol cis-regulatory-evolution
	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 by 38 people viren4388 daveGerrard Dulce talponer wowalz siebert alokm tuck lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling cisevol BergmanLab njcitulike xili03 brant mariakmejia kristallreiner snow_dragon aalibes
	Functional conservation of Rel binding sites in drosophilid genomes [My Copy] Genome Res., Vol. 17, No. 9. (1 September 2007), pp. 1327-1335. by Richard R. Copley, Maxim Totrov, Jane Linnell, Simon Field, Jiannis Ragoussis, Irina A. Udalova posted by 6 people dpollard Stew EisenLab cisevol cis-regulatory-evolution yevishere
	Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. [My Copy] Proc Natl Acad Sci U S A (29 March 2007) by Alona Sosinsky, Barry Honig, Richard S S. Mann, Andrea Califano posted by 7 people dpollard Stew EisenLab maximilianh cisevol cis-regulatory-evolution isimpson
	Expected rates and modes of evolution of enhancer sequences. [My Copy] Molecular biology and evolution, Vol. 21, No. 6. (June 2004), pp. 1064-1073. by S. MacArthur, J. F. Brookfield posted by 5 people Stew adepace EisenLab cisevol cis-regulatory-evolution
	Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. [My Copy] Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050. by A. Siepel, G. Bejerano, J. S. Pedersen, et al.A. S. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. W. Hillier, S. Richards, G. M. Weinstock, R. K. Wilson, R. A. Gibbs, W. J. Kent, W. Miller, D. Haussler posted by 25 people thegoose2 farhat skembel alessandroparini C. elegans / WormBase tharris bpb aprasad balajis eckart_bindewald indigoviolet brant pradiptaray adepace djkt olympos sujaikumar Stew EisenLab cisevol cis-regulatory-evolution dmc elfar AlexanderPico ConklinLab
	Pre-Steady-State Decoding of the Bicoid Morphogen Gradient [My Copy] PLoS Biology, Vol. 5, No. 2. (1 February 2007), e46. by Sven Bergmann, Oded Sandler, Hila Sberro, et al.Sara Shnider, Eyal Schejter, Ben-Zion Shilo, Naama Barkai posted by 5 people dpollard emilyhare adepace lusk EisenLab
	LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. [My Copy] Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731. by M. Brudno, C. B. Do, G. M. Cooper, et al.M. F. Kim, E. Davydov, E. D. Green, A. Sidow, S. Batzoglou, posted by 16 people treangen operon balajis dpollard xwbcn dquest adepace hdopazo lusk Garamonfok adijr natstreet nklee EisenLab Neeperando kcrawlik
	Turnover of binding sites for transcription factors involved in early Drosophila development. [My Copy] Gene, Vol. 310 (22 May 2003), pp. 215-220. by J. Costas, F. Casares, J. Vieira posted by 4 people dpollard EisenLab cisevol cis-regulatory-evolution
	Discovering and detecting transposable elements in genome sequences [My Copy] Brief Bioinform, Vol. 8, No. 6. (10 October 2007), pp. bbm048-392. by Casey M. Bergman, Hadi Quesneville posted by 17 people operon orzenil gwallau natstreet druvus gpappas dpollard timflutre GustavoLacerda cabbagezs EisenLab maximilianh cisevol BergmanLab urgi yoanjacquemin pradiptaray
	PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation [My Copy] Genome Biology, Vol. 8 (04 October 2007), R207. by Elodie Portales-Casamar, Stefan Kirov, Jonathan Lim, et al.Stuart Lithwick, Magdalena I. Swanson, Amy Ticoll, Jay Snoddy, Wyeth W. Wasserman posted by 6 people dpollard EisenLab cisevol cis-regulatory-evolution BergmanLab pradiptaray
	Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo [My Copy] PLoS Biology, Vol. 5, No. 5. (1 May 2007), e117. by Stefano De Renzis, Olivier Elemento, Saeed Tavazoie, Eric F. Wieschaus posted by 7 people daveGerrard BergmanLab cisevol dpollard wrowell EisenLab Cline_lab
	Innovation and robustness in complex regulatory gene networks [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 34. (21 August 2007), pp. 13591-13596. by S. Ciliberti, O. C. Martin, A. Wagner posted by 16 people abhishek_tiwari mjoach ocs benjaminsb balicea dakelley cmzmasek GEB dlobo jmenche dpollard sebastien_vigneau zwang EisenLab cisevol cis-regulatory-evolution
	A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms [My Copy] PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e106. by Stephen B. Montgomery, Obi L. Griffith, Johanna M. Schuetz, Angela Brooks-Wilson, Steven J. Jones posted by 5 people dpollard Bioinformatics EisenLab cisevol cis-regulatory-evolution
	Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction [My Copy] Genome Biology, Vol. 8 (08 June 2007), R106. by Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Straehle, Ferenc Mueller posted by 7 people jochenG maximilianh dpollard cjeans EisenLab cisevol cis-regulatory-evolution
	A stochastic model for the evolution of transcription factor binding site abundance. [My Copy] J Theor Biol (7 March 2007) by Günter P P. Wagner, Wolfgang Otto, Vincent Lynch, Peter F F. Stadler posted by 6 people thegoose bmajoros dpollard EisenLab cisevol cis-regulatory-evolution
	Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. [My Copy] Genetics, Vol. 175, No. 3. (1 March 2007), pp. 1071-1077. by Henry Chung, Michael R. Bogwitz, Caroline McCart, et al.Alex Andrianopoulos, Richard H. Ffrench-Constant, Philip Batterham, Phillip J. Daborn posted by 4 people dpollard EisenLab cisevol cis-regulatory-evolution
	Evidence for turnover of functional noncoding DNA in mammalian genome evolution. [My Copy] Genomics, Vol. 84, No. 5. (November 2004), pp. 806-813. by N. G. Smith, M. Brandström, H. Ellegren posted by 7 people galka8_diploma aprasad devin dpollard EisenLab cisevol cis-regulatory-evolution
	Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over [My Copy] Genome Biology, Vol. 8 (06 February 2007), R18. by Penelope R. Haddrill, Daniel L. Halligan, Dimitris Tomaras, Brian Charlesworth posted by 6 people dpollard djkt EisenLab cisevol cis-regulatory-evolution smbe2008
	A SNP in a half-binding site creates p53 and estrogen receptor control of VEGFR-1. [My Copy] Mol Cell Biol (22 January 2007) by Daniel Menendez, Alberto Inga, Joyce Snipe, Oliver Krysiak, Gilbert Schönfelder, Michael A A. Resnick posted by 4 people dpollard EisenLab cisevol cis-regulatory-evolution
	Heat-Shock Promoters: Targets for Evolution by <italic>P</italic> Transposable Elements in <italic>Drosophila</italic> [My Copy] PLoS Genet, Vol. 2, No. 10. (6 October 2006), e165. by Jean-Claude Walser, Bing Chen, Martin E. Feder posted by 5 people dpollard EisenLab cisevol cis-regulatory-evolution BergmanLab
	The regulatory content of intergenic DNA shapes genome architecture. [My Copy] Genome Biol, Vol. 5, No. 4. (2004) by C. E. Nelson, B. M. Hersh, S. B. Carroll posted by 13 people thegoose2 daveGerrard JustinCrocker C. elegans / WormBase tharris dpollard madhadron elzodw EisenLab blobbybirdman cisevol cis-regulatory-evolution BergmanLab
	Co-evolution of transcription factors and their targets depends on mode of regulation [My Copy] Genome Biology, Vol. 7 (19 July 2006), R62. by Ruth Hershberg, Hanah Margalit posted by 7 people indigoviolet dpollard cjeans EisenLab cisevol cis-regulatory-evolution PetrovLab
	Evolutionary turnover of mammalian transcription start sites. [My Copy] Genome Res (10 May 2006) by Martin C C. Frith, Jasmina Ponjavic, David Fredman, et al.Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayshizaki, Albin Sandelin posted by 9 people galka8_diploma dpollard cmm jsnoddy EisenLab FAB-lab cisevol cis-regulatory-evolution gjuggler
	Multiple sequence alignment accuracy and evolutionary distance estimation. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by M. S. Rosenberg posted by 6 people treangen aprasad dpollard EisenLab cisevol cis-regulatory-evolution
	Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome [My Copy] Genome Biology, Vol. 3, No. 12. (2002) by Casey Bergman, Barret Pfeiffer, Diego R. Limas, et al.Roger Hoskins, Andreas Gnirke, Chris Mungall, Adrienne Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed George, Pieter de Jong, Juan Botas, Gerald Rubin, Susan Celniker posted by 8 people hrogers indigoviolet dpollard nklee EisenLab cisevol cis-regulatory-evolution brant
	Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (16 March 2006) by Rahul Siddharthan posted by 6 people aprasad cis-regulatory-evolution cisevol dpollard lilou EisenLab
	Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts [My Copy] Nature, Vol. 440, No. 7082., pp. 341-345. by Devin R. Scannell, Kevin P. Byrne, Jonathan L. Gordon, Simon Wong, Kenneth H. Wolfe posted by 8 people RMGraze dpollard cmm echinotrix souravc EisenLab FAB-lab cisevol
	Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans. [My Copy] PLoS Biol, Vol. 3, No. 12. (15 November 2005) by Matthew V V. Rockman, Matthew W W. Hahn, Nicole Soranzo, Fritz Zimprich, David B B. Goldstein, Gregory A A. Wray posted by 15 people provero cube_and_beyond mbj imouthesmp indigoviolet dpollard Archaeogenetics happy_manatee djkt mgaldzic EisenLab CHIP cisevol cis-regulatory-evolution jphekman
	Genetic interactions between polymorphisms that affect gene expression in yeast [My Copy] Nature, Vol. 436, No. 7051., pp. 701-703. by Rachel B. Brem, John D. Storey, Jacqueline Whittle, Leonid Kruglyak posted by 8 people lp2 JAShapiro dpollard EisenLab cisevol cis-regulatory-evolution mrockman RockmanLab
	Comparative analysis indicates regulatory neofunctionalization of yeast duplicates [My Copy] Genome Biology, Vol. 8, No. 4. (05 April 2007), R50. by Itay Tirosh, Naama Barkai posted by 8 people azazello ptrobajo adepace stajich EisenLab cisevol cis-regulatory-evolution ajpowell
	Inference of Positive and Negative Selection on the 5' Regulatory Regions of Drosophila Genes [My Copy] Mol Biol Evol, Vol. 21, No. 2. (1 February 2004), pp. 374-383. by Michael H. Kohn, Shu Fang, Chung-I Wu posted by 5 people Garamonfok adepace EisenLab cisevol cis-regulatory-evolution
	Human-mouse genome comparisons to locate regulatory sites. [My Copy] Nat Genet, Vol. 26, No. 2. (October 2000), pp. 225-228. by W. W. Wasserman, M. Palumbo, W. Thompson, J. W. Fickett, C. E. Lawrence posted by 4 people adepace EisenLab cisevol cis-regulatory-evolution
	Rapid evolution of cis-regulatory sequences via local point mutations. [My Copy] Mol Biol Evol, Vol. 18, No. 9. (September 2001), pp. 1764-1770. by J. R. Stone, G. A. Wray posted by 4 people adepace EisenLab cisevol cis-regulatory-evolution
	Coevolution in bicoid-dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera. [My Copy] Evol Dev, Vol. 4, No. 4. (g 2002), pp. 265-277. by P. J. Shaw, N. S. Wratten, A. P. McGregor, G. A. Dover posted by 4 people adepace EisenLab cisevol cis-regulatory-evolution
	The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster [My Copy] PNAS, Vol. 98, No. 7. (27 March 2001), pp. 3920-3925. by Aya Takahashi, Shun-Chern Tsaur, Jerry A. Coyne, Chung-I Wu posted by 5 people RMGraze adepace EisenLab cisevol cis-regulatory-evolution
	Genome-wide associations of gene expression variation in humans. [My Copy] PLoS Genet, Vol. 1, No. 6. (December 2005) by B. E. Stranger, M. S. Forrest, A. G. Clark, et al.M. J. Minichiello, S. Deutsch, R. Lyle, S. Hunt, B. Kahl, S. E. Antonarakis, S. Tavaré, P. Deloukas, E. T. Dermitzakis posted by 14 people zufar pengchy psique adepace rdiaz qfwills noano ashandanj jo_davies Bioinformatics EisenLab cisevol cis-regulatory-evolution shikin
	A genetic signature of interspecies variations in gene expression. [My Copy] Nature genetics, Vol. 38, No. 7. (18 July 2006), pp. 830-834. by Itay Tirosh, Adina Weinberger, Miri Carmi, Naama Barkai posted by 13 people roys BergmanLab daveGerrard cabbagezs cis-regulatory-evolution cisevol adepace nickluscombe aswin cjeans EisenLab EBI-regulation caseybrown
	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 by 5 people lusk maximilianh brant cisevol cis-regulatory-evolution
	A probabilistic method to detect regulatory modules. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by S. Sinha, E. van Nimwegen, E. D. Siggia posted by 7 people maximilianh indigoviolet dquest lusk EisenLab cisevol cis-regulatory-evolution
	MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. [My Copy] Genome Biol, Vol. 5, No. 12. (2004) by A. M. Moses, D. Y. Chiang, D. A. Pollard, V. N. Iyer, M. B. Eisen posted by 7 people tuck indigoviolet lusk Garamonfok EisenLab cisevol cis-regulatory-evolution
	Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence. [My Copy] Genome Res, Vol. 15, No. 2. (February 2005), pp. 205-213. by C. S. Chin, J. H. Chuang, H. Li posted by 5 people briann lusk nklee cisevol cis-regulatory-evolution
	Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi [My Copy] PLoS Biol, Vol. 2, No. 12. (9 November 2004), e398. by Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen posted by 10 people roys matted mbeisen tsackton nickluscombe lusk EisenLab EBI-regulation cisevol cis-regulatory-evolution
	A Quick Guide to Teaching R Programming to Computational Biology Students [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000482. by Stephen J. Eglen posted by 67 people nuin kaliczp maren sobolevnrm ltitodem zchen75 artaban421 natstreet jasonn tomhebbron psique Bioinformatics - CRUK Stew eshirdel guhjy polivares ajw fishtank diamantis fastjoe23 kshameer daveGerrard hrogers JoeBanks BergmanLab cisevol srijit hwright Ayest VGreiff welliegirl asadrahman rdiaz ptrobajo heliopais coffeerv Vincent_Rouilly marekrud tnhh barry ansobol Zephyrus walshtp bertelsen fgibson pkonings Borelli klauso dlizcano dswan skembel djkt jclau lwaldron phoenixzxl timhubbard eLearning in Leicester AJCann thegoose dullhunk brianb neils silberbauer daforerog Journal picks ppgardne druvus
	A Quick Guide to Organizing Computational Biology Projects [My Copy] PLoS Comput Biol, Vol. 5, No. 7. (31 July 2009), e1000424. by William S. Noble posted by 68 people annakcroft brianb nuin skembel pekrau Sergey_gerbek mordiano remoteFuture Yanno Pedro Martinez EvoDevo lab Barcelona aaltenburger marekrud guhjy dolchan frohike operon Orengo Group Journal Picks CorinYeats artaban421 antonkratz tomhebbron maren bayesian daveGerrard JoeBanks jcaddy somak bertelsen ptrobajo nperoni daforerog mmwoodman charris5 GustavoLacerda pmendes fgibson rdiaz Zephyrus heliopais franklu310 lmichan silberbauer leemond31 jlangdon robfsouza Bioinformatics - CRUK Stew pmung reyez kshameer djkt pawelsobko jjray dswan apaydin renatomilani VGreiff cabbagesofdoom ccsbs wei_tang fenghezi BergmanLab cisevol structural_bioinformatics McCammon barry sdaehne druvus
	BioMart--biological queries made easy. [My Copy] BMC genomics, Vol. 10, No. 1. (2009), 22. by Damian Smedley, Syed Haider, Benoit Ballester, et al.Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk posted by 34 people aaltenburger artaban421 sjcockell lmichan jdbowes fgibson pekrau gangcai daforerog jfr fisherp allysonlister Bioinformatics - CRUK Stew grahamc Bioinformatics dswan Roswell Cancer Crosstalk Zephyrus renatomilani guhjy natstreet pablocarb Cortel dbk mitko brianb ajaymalik neils kshameer dullhunk druvus BergmanLab cisevol
	Fast Evolution of Core Promoters in Primate Genomes [My Copy] Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1239-1244. by Han Liang, Yeong-Shin Lin, Wen-Hsiung Li posted by 5 people nhp cisevol cis-regulatory-evolution Stew aprasad
	The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species. [My Copy] Cell, Vol. 132, No. 5. (7 March 2008), pp. 783-793. by S. Jeong, M. Rebeiz, P. Andolfatto, T. Werner, J. True, S. B. Carroll posted by 5 people athma maximilianh Stew cisevol cis-regulatory-evolution
	Conserved eukaryotic transposable elements and the evolution of gene regulation. [My Copy] Cell Mol Life Sci (20 November 2007) by J Jurka posted by 8 people gpappas dchughes Stew maximilianh cisevol cis-regulatory-evolution idonaldson BergmanLab
	Adaptive Evolution of Conserved Noncoding Elements in Mammals [My Copy] PLoS Genetics, Vol. 3, No. 9. (1 September 2007), e147. by Su Y. Kim, Jonathan K. Pritchard posted by 17 people sujaikumar sriesenfeld mattjb livingthingdan djkt stajich Garamonfok cabbagezs Stew EisenLab ComplexAdaptiveSystems DSTO-CAS livingthing cisevol cis-regulatory-evolution rrhudson bpcusack
	The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster. [My Copy] Dev Biol (12 June 2007) by Gregory K K. Davis, Dayalan G G. Srinivasan, Patricia J J. Wittkopp, David L L. Stern posted by 4 people Stew EisenLab cisevol cis-regulatory-evolution
	Fast-evolving non-coding sequences in the human genome [My Copy] Genome Biology, Vol. 8 (19 June 2007), R118. by Christine P. Bird, Barbara E. Stranger, Maureen Liu, et al.Daryl J. Thomas, Catherine E. Ingle, Claude Beazley, Webb Miller, Matthew E. Hurles, Emmanouil T. Dermitzakis posted by 11 people balicea sriesenfeld xianjun djkt Stew jlangdon EisenLab cisevol cis-regulatory-evolution iris42 bpcusack
	Genome-wide identification of human functional DNA using a neutral indel model. [My Copy] PLoS computational biology, Vol. 2, No. 1. (13 January 2006) by Gerton Lunter, Chris P. Ponting, Jotun Hein posted by 15 people timflutre gjuggler nklee aprasad eckart_bindewald eweaver lhonigberg acidwizard juliettecolinas bpcusack Stew EisenLab cisevol cis-regulatory-evolution mailund
	Conserved noncoding sequences are selectively constrained and not mutation cold spots [My Copy] Nature Genetics, Vol. 38, No. 2. (25 December 2005), pp. 223-227. by Jared A. Drake, Christine Bird, James Nemesh, et al.Daryl J. Thomas, Christopher Newton-Cheh, Alexandre Reymond, Laurent Excoffier, Homa Attar, Stylianos E. Antonarakis, Emmanouil T. Dermitzakis, Joel N. Hirschhorn posted by 11 people daforerog provero xianjun aprasad ccots ashandanj Stew EisenLab cisevol cis-regulatory-evolution bpcusack
	Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences. [My Copy] Trends Genet, Vol. 21, No. 8. (August 2005), pp. 436-440. by K. Walter, I. Abnizova, G. Elgar, W. R. Gilks posted by 5 people aprasad Stew EisenLab cisevol cis-regulatory-evolution
	Highly conserved non-coding sequences are associated with vertebrate development. [My Copy] PLoS Biol, Vol. 3, No. 1. (January 2005) by A. Woolfe, M. Goodson, D. K. Goode, et al.P. Snell, G. K. McEwen, T. Vavouri, S. F. Smith, P. North, H. Callaway, K. Kelly, K. Walter, I. Abnizova, W. Gilks, Y. J. Edwards, J. E. Cooke, G. Elgar posted by 16 people BergmanLab daveGerrard aprasad diamantis nklee bryankr awoolfe djkt sujaikumar Stew EisenLab maximilianh cisevol cis-regulatory-evolution rrhudson gelgar
	Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites [My Copy] PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e90. by Timothy E. Reddy, Charles Delisi, Boris E. Shakhnovich posted by 4 people dpollard adepace ajgentles EisenLab
	Enhancer Responses to Similarly Distributed Antagonistic Gradients in Development [My Copy] PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e84. by Robert P. Zinzen, Dmitri Papatsenko posted by 3 people dpollard adepace EisenLab
	Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis [My Copy] Mol Syst Biol, Vol. 3 (16 January 2007) by Sean D. Hooper, Stephanie Boue, Roland Krause, et al.Lars J. Jensen, Christopher E. Mason, Murad Ghanim, Kevin P. White, Eileen E. M. Furlong, Peer Bork posted by 6 people indigoviolet dpollard adepace uz_labu_laimi EisenLab larsjuhljensen
	Two medfly promoters that have originated by recent gene duplication drive distinct sex, tissue and temporal expression patterns. [My Copy] Genetics, Vol. 156, No. 1. (September 2000), pp. 173-182. by G. K. Christophides, I. Livadaras, C. Savakis, K. Komitopoulou posted by 4 people brant dpollard adepace EisenLab
	Global variation in copy number in the human genome [My Copy] Nature, Vol. 444, No. 7118. (23 November 2006), pp. 444-454. by Richard Redon, Shumpei Ishikawa, Karen R. Fitch, et al.Lars Feuk, George H. Perry, T. Daniel Andrews, Heike Fiegler, Michael H. Shapero, Andrew R. Carson, Wenwei Chen, Eun K. Cho, Stephanie Dallaire, Jennifer L. Freeman, Juan R. Gonzalez, Monica Gratacos, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R. MacDonald, Christian R. Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J. Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F. Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P. Carter, Hiroyuki Aburatani, Charles Lee, Keith W. Jones, Stephen W. Scherer, Matthew E. Hurles posted by 49 people sameersoi lp2 ilyashl ajbattle darian jonilaserson jrvalcourt turnersd guhjy daforerog noushin Glires ivanek waszak jo_davies parkinson's disease references psique bpb jfr balajis pradiptaray dpollard mtagaya adepace aswin rdiaz qfwills ealloza vplagnol giovanni jeremymiller frohike vpschulz raiyar ramensky ccr azazello dbgrant colinveal xingxu Bioinformatics EisenLab BioinfoCIPF GeschwindLab steinmetzlab MBLAB srp33 Ema daed
	Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations [My Copy] BMC Genomics, Vol. 7 (15 September 2006), 235. by Debraj Guhathakurta, Tao Xie, Manish Anand, et al.Stephen W. Edwards, Guoya Li, Susana Wang, Eric E. Schadt posted by 6 people caseybrown maximilianh dpollard adepace natstreet EisenLab
	Genetic Dissection of Transcriptional Regulation in Budding Yeast [My Copy] Science, Vol. 296, No. 5568. (26 April 2002), pp. 752-755. by Rachel B. Brem, Gael Yvert, Rebecca Clinton, Leonid Kruglyak posted by 14 people balabu RMGraze JAShapiro brant dpollard adepace oannes raiyar lp2 jo_davies mimulus_99 EisenLab Regulomics_UCHSC steinmetzlab
	Diffusion and scaling during early embryonic pattern formation. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 51. (20 December 2005), pp. 18403-18407. by T. Gregor, W. Bialek, R. R. de Ruyter van Steveninck, D. W. Tank, E. F. Wieschaus posted by 3 people dpollard adepace EisenLab
	The design of transcription-factor binding sites is affected by combinatorial regulation. [My Copy] Genome Biol, Vol. 6, No. 12. (2005) by Y. Bilu, N. Barkai posted by 9 people chrn dpollard tabu samal adepace lewbin nklee EisenLab xili03
	A logical analysis of the Drosophila gap-gene system. [My Copy] J Theor Biol, Vol. 211, No. 2. (21 July 2001), pp. 115-141. by L. Sánchez, D. Thieffry posted by 7 people Antoine_Decrulle bshkspr bayesian dpollard adepace EisenLab UH - Computational Biology
	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 by 11 people natstreet lusk RockmanLab dpollard JustinCrocker BergmanLab daveGerrard emmahe maximilianh trfield idoerg
	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 by 6 people lusk dpollard EisenLab maximilianh cis-regulatory-evolution caseybrown
	Transcriptional regulation of a pair-rule stripe in Drosophila. [My Copy] Genes Dev, Vol. 5, No. 5. (May 1991), pp. 827-839. by S. Small, R. Kraut, T. Hoey, R. Warrior, M. Levine posted by 3 people lusk dpollard EisenLab
	Programming gene expression with combinatorial promoters. [My Copy] Molecular systems biology, Vol. 3 (13 November 2007) by Robert Sidney S. Cox, Michael G. Surette, Michael B. Elowitz posted by 20 people balabu TranscriptionalRegulationWithThermodynamicModels Synthetic_Biology_Literature Retchless tmmurali austin dpollard balicea kengg dbikard margaritis lusk cjeans zwang discreteonyxorb cabbagezs EisenLab Ema SynBioSys tresch
	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 by 8 people lusk dpollard djkt stajich Garamonfok EisenLab maximilianh cis-regulatory-evolution
	Evolution of chromosome organization driven by selection for reduced gene expression noise [My Copy] Nature Genetics, Vol. 39, No. 8. (27 July 2007), pp. 945-949. by Nizar N. Batada, Laurence D. Hurst posted by 8 people jjray dpollard ealloza djkt lusk zwang EisenLab BioinfoCIPF
	Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses [My Copy] Genome Biology, Vol. 8 (05 June 2007), R101. by Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S. Halfon posted by 7 people JustinCrocker dpollard lusk cjeans EisenLab maximilianh isimpson
	Permissive and instructive anterior patterning rely on mRNA localization in the wasp embryo. [My Copy] Science, Vol. 315, No. 5820. (30 March 2007), pp. 1841-1843. by A. E. Brent, G. Yucel, S. Small, C. Desplan posted by 3 people dpollard lusk EisenLab
	Adaptations to fluctuating selection in Drosophila. [My Copy] Proc Natl Acad Sci U S A (7 February 2007) by Ville Mustonen, Michael Lässig posted by 3 people dpollard lusk EisenLab
	Thymine Dimerization in DNA Is an Ultrafast Photoreaction [My Copy] Science, Vol. 315, No. 5812. (2 February 2007), pp. 625-629. by Wolfgang J. Schreier, Tobias E. Schrader, Florian O. Koller, et al.Peter Gilch, Carlos E. Crespo-Hernandez, Vijay N. Swaminathan, Thomas Carell, Wolfgang Zinth, Bern Kohler posted by 4 people dna dpollard lusk EisenLab
	PhyloScan: Identification of transcription factor binding sites using cross-species evidence [My Copy] Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1. by Steven C. Carmack, Lee A. Mccue, Lee A. Newberg, Charles E. Lawrence posted by 5 people dpollard dquest lusk nklee EisenLab
	Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. [My Copy] Nature, Vol. 445, No. 7123. (4 January 2007), pp. 82-85. by Cathy Haag-Liautard, Mark Dorris, Xulio Maside, et al.Steven Macaskill, Daniel L. Halligan, David Houle, Brian Charlesworth, Peter D. Keightley posted by 9 people daveGerrard operon dpollard jri stajich ramensky lusk EisenLab gjuggler
	A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis [My Copy] BMC Evolutionary Biology, Vol. 6 (22 November 2006), 99. by David A. Fitzpatrick, Mary E. Logue, Jason E. Stajich, Geraldine Butler posted by 8 people tomt21 dpollard stajich lusk EisenLab cmzmasek kiekyon druvus
	Conserved sequences and the evolution of gene regulatory signals. [My Copy] Curr Opin Genet Dev, Vol. 15, No. 6. (December 2005), pp. 628-633. by M. D. Adams posted by 4 people dpollard cconboy lusk EisenLab
	Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. [My Copy] Nucleic Acids Res, Vol. 31, No. 20. (15 October 2003), pp. 6016-6026. by V. J. Makeev, A. P. Lifanov, A. G. Nazina, D. A. Papatsenko posted by 5 people lusk dpollard oannes EisenLab Regulomics_UCHSC
	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 by 3 people lusk adepace 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 by 4 people adepace olympos lusk EisenLab
	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 by 3 people lusk adepace EisenLab
	A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning [My Copy] Genome Research, Vol. 18, No. 7. (13 July 2008), pp. 1051-1063. by Anton Valouev, Jeffrey Ichikawa, Thaisan Tonthat, et al.Jeremy Stuart, Swati Ranade, Heather Peckham, Kathy Zeng, Joel A. Malek, Gina Costa, Kevin Mckernan, Arend Sidow, Andrew Fire, Steven M. Johnson posted by 11 people hagechouchin443 thegoose2 C. elegans / WormBase tharris maximilianh caseybrown vega dpollard RockmanLab Stew aalibes
	Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network. [My Copy] Genes Dev, Vol. 21, No. 19. (1 October 2007), pp. 2448-2460. by J. S. Jakobsen, M. Braun, J. Astorga, et al.E. H. Gustafson, T. Sandmann, M. Karzynski, P. Carlsson, E. E. Furlong posted by 4 people lp2 dpollard Stew EisenLab
	Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia. [My Copy] Proc Natl Acad Sci U S A (9 March 2007) by Carolyn S S. McBride posted by 6 people jbsaltz dpollard stajich zwang Stew EisenLab
	Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 14. (5 April 2005), pp. 4966-4971. by D. Papatsenko, M. Levine posted by 3 people adepace Stew EisenLab
	Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. [My Copy] BMC Bioinformatics, Vol. 3 (24 October 2002) by N. Rajewsky, M. Vergassola, U. Gaul, E. D. Siggia posted by 11 people BergmanLab daveGerrard maximilianh isimpson ansobol indigoviolet adepace koller Stew EisenLab csdhwang
	The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription [My Copy] Development, Vol. 133, No. 10. (15 May 2006), pp. 1967-1977. by John R. Bosch, Joseph A. Benavides, Thomas W. Cline posted by 8 people daveGerrard BergmanLab emilyhare adepace wrowell Stew EisenLab Cline_lab
	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 by 6 people lusk Bioinformatics - CRUK Stew jkim63 fpattyn nuin
	RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. [My Copy] Genome research, Vol. 18, No. 9. (11 September 2008), pp. 1509-1517. by John C. Marioni, Christopher E. Mason, Shrikant M. Mane, Matthew Stephens, Yoav Gilad posted by 49 people cthachuk hzoltan jwfoley heliopais debasis maren mtagaya mkiyer stubrown woodson8 jonilaserson burak Ayest ThomasDOtto SIMR bioinformatics huali n00c natstreet bandrewfox daed dandaman slevy03 pengchy felsani coela shikin fhalbrit inesdesantiago jmcq lp2 caseybrown jfr dakelley Ema balicea vega lusk semrich vmarshal fpattyn stajich Mycology giovanni ela503 Stew guhjy kengg shurjo GustavoLacerda
	The evolution of genetic networks by non-adaptive processes. [My Copy] Nature reviews. Genetics, Vol. 8, No. 10. (October 2007), pp. 803-813. by Michael Lynch posted by 17 people operon colmryan cambray dswan brant balicea dchughes aswin stajich margaritis zwang nosada17 Stew G4ID Genetics-of-Gambling lilith lusk
	The Origin of Subfunctions and Modular Gene Regulation [My Copy] Genetics, Vol. 170, No. 1. (1 May 2005), pp. 433-446. by Allan Force, William A. Cresko, F. Bryan Pickett, Steven R. Proulx, Chris Amemiya, Michael Lynch posted by 5 people leemond31 brant bluto Stew lusk
	Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques [My Copy] Genome Research, Vol. 16, No. 12. (19 December 2006), pp. 1455-1464. by Laura Elnitski, Victor X. Jin, Peggy J. Farnham, Steven J. M. Jones posted by 14 people matted gdb wowalz Bioinformatics - CRUK Stew heliopais dquest bryankr giovanni lusk SeungjoonOh cabbagezs GeschwindLab maximilianh
	Computational prediction of transcription-factor binding site locations [My Copy] Genome Biology, Vol. 5, No. 1. (2003), 201. by Martha Bulyk posted by 11 people Baschl marti tkmaia kaarsinogen lusk Stew nklee EisenLab yevishere xili03 aalibes
	DASMiner: discovering and integrating data from DAS sources [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 109. by Diogo Veiga, Helena Deus, Caner Akdemir, Ana T. Vasconcelos, Jonas Almeida posted by 4 people druvus kshameer BergmanLab cisevol