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	A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors [My Copy] Science, Vol. 315, No. 5809. (12 January 2007), pp. 233-237. by Sebastian J. Maerkl, Stephen R. Quake posted by 12 people absterga jjray dpollard emilyhare adepace aswin skoch3 EisenLab Koch_Lab blobbybirdman emptyhb brant
	Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. [My Copy] Nat Genet (17 September 2006) by Hilde Janssens, Shuling Hou, Johannes Jaeger, et al.Ah-Ram R. Kim, Ekaterina Myasnikova, David Sharp, John Reinitz posted by 9 people okarsligil brant dpollard adepace allPowerde Stew Bioinformatics EisenLab emptyhb
	Local DNA topography correlates with functional noncoding regions of the human genome. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. Parker, Loren Hansen, Hatice Ozel O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted by 45 people BergmanLab daveGerrard operon sujaikumar antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre Mycology stajich bpcusack jbhiatt djkt structural_bioinformatics dhlbh friendpine RockmanLab EisenLab cis-regulatory-evolution dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak
	Reliable prediction of regulator targets using 12 Drosophila genomes [My Copy] Genome Research, Vol. 17, No. 12. (7 December 2007), pp. 1919-1931. by Pouya Kheradpour, Alexander Stark, Sushmita Roy, Manolis Kellis posted by 12 people heliopais valeriehilgers dpollard lp2 nklee EisenLab maximilianh cis-regulatory-evolution roys caseybrown emptyhb barwil
	Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression [My Copy] Science, Vol. 317, No. 5844. (14 September 2007), pp. 1557-1560. by Christopher D. Brown, David S. Johnson, Arend Sidow posted by 13 people pradiptaray dpollard djkt joepickrell zwang Garamonfok Stew mimulus_99 EisenLab maximilianh cisevol cis-regulatory-evolution emptyhb
	Transcriptional Control in the Segmentation Gene Network of Drosophila [My Copy] PLoS Biol, Vol. 2, No. 9. (31 August 2004), e271. by Mark D. Schroeder, Michael Pearce, John Fak, et al.HongQing Fan, Ulrich Unnerstall, Eldon Emberly, Nikolaus Rajewsky, Eric D. Siggia, Ulrike Gaul posted by 14 people BergmanLab daveGerrard TranscriptionalRegulationWithThermodynamicModels indigoviolet dpollard adepace wrowell EisenLab Cline_lab UH - Computational Biology emptyhb dlmace pradiptaray balicea
	Two or Four Bristles: Functional Evolution of an Enhancer of scute in Drosophilidae [My Copy] PLoS Biology, Vol. 4, No. 12. (1 November 2006), e386. by Sylvain Marcellini, Pat Simpson posted by 5 people dpollard adepace emmahe EisenLab emptyhb
	The Evolution of Transcriptional Regulation in Eukaryotes [My Copy] Mol Biol Evol, Vol. 20, No. 9. (1 September 2003), pp. 1377-1419. by Gregory A. Wray, Matthew W. Hahn, Ehab Abouheif, et al.James P. Balhoff, Margaret Pizer, Matthew V. Rockman, Laura A. Romano posted by 17 people athma provero wrowell ana dpollard adepace nickluscombe anatiferous mimulus_99 structural_bioinformatics Bioinformatics EisenLab EBI-regulation cisevol cis-regulatory-evolution emptyhb emmahe
	Evolution of cis-regulatory sequence and function in Diptera [My Copy] Heredity, Vol. aop, No. current. by P. J. Wittkopp, posted by 9 people rouault indigoviolet dpollard adepace emmahe EisenLab cisevol cis-regulatory-evolution emptyhb
	Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races. [My Copy] Molecular biology and evolution, Vol. 23, No. 8. (5 August 2006), pp. 1585-1591. by Naoki Osada, Michael H. Kohn, Chung-I I. Wu posted by 7 people daveGerrard dpollard emilyhare adepace natstreet EisenLab emptyhb
	Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene [My Copy] Nature, Vol. 440, No. 7087., pp. 1050-1053. by Benjamin Prud'homme, Nicolas Gompel, Antonis Rokas, et al.Victoria A. Kassner, Thomas M. Williams, Shu-Dan Yeh, John R. True, Sean B. Carroll posted by 10 people RMGraze dpollard balicea tny adepace ranb Garamonfok EisenLab blobbybirdman emptyhb
	Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. [My Copy] Nature, Vol. 433, No. 7025. (3 February 2005), pp. 481-487. by N. Gompel, B. Prud'homme, P. J. Wittkopp, V. A. Kassner, S. B. Carroll posted by 10 people athma balabu dpollard emilyhare adepace EisenLab cisevol cis-regulatory-evolution emptyhb pradiptaray
	A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression [My Copy] Nature, Vol. 438, No. 7065., pp. 220-223. by Scott A. Rifkin, David Houle, Junhyong Kim, Kevin P. White posted by 12 people BergmanLab daveGerrard dayjm indigoviolet dpollard adepace johncumbers djkt mimulus_99 EisenLab caseybrown emptyhb
	Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila. [My Copy] Mol Biol Evol (23 July 2007) by Sònia Casillas, Antonio Barbadilla, Casey M M. Bergman posted by 10 people operon dpollard emilyhare Garamonfok Stew EisenLab cisevol cis-regulatory-evolution emptyhb brant
	Conservation of RET Regulatory Function from Human to Zebrafish Without Sequence Similarity. [My Copy] Science (23 March 2006) by Shannon Fisher, Elizabeth A A. Grice, Ryan M M. Vinton, Seneca L L. Bessling, Andrew S S. McCallion posted by 9 people aprasad adepace nickluscombe EisenLab EBI-regulation maximilianh cisevol cis-regulatory-evolution emptyhb
	Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. [My Copy] Genome Biol, Vol. 5, No. 9. (2004) by B. P. Berman, B. D. Pfeiffer, T. R. Laverty, et al.S. L. Salzberg, G. M. Rubin, M. B. Eisen, S. E. Celniker posted by 13 people emptyhb cajunsushi mbeisen indigoviolet adepace Stew nklee EisenLab cisevol cis-regulatory-evolution maximilianh Auger Dead 60's
	Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence [My Copy] PLoS Genetics, Vol. 4, No. 2. (1 February 2008), e29. by Dirk A. Kleinjan, Ruth M. Bancewicz, Philippe Gautier, et al.Ralf Dahm, Helia B. Schonthaler, Giuseppe Damante, Anne Seawright, Ann M. Hever, Patricia L. Yeyati, Veronica van Heyningen, Pedro Coutinho posted by 6 people JustinCrocker brant gjuggler emptyhb maximilianh Stew
	Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. [My Copy] PLoS biology, Vol. 6, No. 2. (12 February 2008), e27. by X. Y. Li, S. MacArthur, R. Bourgon, et al.D. Nix, D. A. Pollard, V. N. Iyer, A. Hechmer, L. Simirenko, M. Stapleton, C. L. Luengo Hendriks, H. C. Chu, N. Ogawa, W. Inwood, V. Sementchenko, A. Beaton, R. Weiszmann, S. E. Celniker, D. W. Knowles, T. Gingeras, T. P. Speed, M. B. Eisen, M. D. Biggin posted by 10 people gdb BergmanLab daveGerrard kengg maximilianh caseybrown emptyhb brant isimpson Stew
	Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity [My Copy] Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59. by O. Hallikas, K. Palin, N. Sinjushina, et al.R. Rautiainen, J. Partanen, E. Ukkonen, J. Taipale posted by 22 people absterga xingxu cisstem Terkko kaarsinogen tuck brant xwbcn dchughes nickluscombe olympos cabbagezs karfunkel Bioinformatics EisenLab G4ID EBI-regulation Genetics-of-Gambling maximilianh heliopais oelemento emptyhb
	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
	Evolution of alternative transcriptional circuits with identical logic [My Copy] Nature, Vol. 443, No. 7110. (28 September 2006), pp. 415-420. by Annie E. Tsong, Brian B. Tuch, Hao Li, Alexander D. Johnson posted by 14 people biomcgary cmzmasek balabu marcius brant adepace aswin srfairclough EisenLab BioinfoCIPF SGU-CIPF cisevol cis-regulatory-evolution emptyhb
	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
	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
	Diversity and Complexity in DNA Recognition by Transcription Factors [My Copy] Science, Vol. 324, No. 5935. (26 June 2009), pp. 1720-1723. by Gwenael Badis, Michael F. Berger, Anthony A. Philippakis, et al.Shaheynoor Talukder, Andrew R. Gehrke, Savina A. Jaeger, Esther T. Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen, Hanna Kuznetsov, Chi-Fong Wang, David Coburn, Daniel E. Newburger, Quaid Morris, Timothy R. Hughes, Martha L. Bulyk posted by 24 people nklee sconlan isimpson jbhiatt daforerog absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts RockmanLab dpollard siebert JustinCrocker burak aalibes dipenps roys emptyhb tmmurali
	Systems genetics of complex traits in Drosophila melanogaster [My Copy] Nature Genetics, Vol. 41, No. 3. (22 February 2009), pp. 299-307. by Julien F. Ayroles, Mary A. Carbone, Eric A. Stone, et al.Katherine W. Jordan, Richard F. Lyman, Michael M. Magwire, Stephanie M. Rollmann, Laura H. Duncan, Faye Lawrence, Robert R. H. Anholt, Trudy F. C. Mackay posted by 19 people vingron BergmanLab daveGerrard ongenetics timflutre FuncGen thokall bernadettgaal RockmanLab dpollard semrich roys rdiaz fenghezi emptyhb bertrandservin daforerog provero djkt
	Population genomics of domestic and wild yeasts. [My Copy] Nature, Vol. 458, No. 7236. (19 March 2009), pp. 337-341. by G. Liti, D. M. Carter, A. M. Moses, et al.J. Warringer, L. Parts, S. A. James, R. P. Davey, I. N. Roberts, A. Burt, V. Koufopanou, I. J. Tsai, C. M. Bergman, D. Bensasson, M. J. O'Kelly, A. van Oudenaarden, D. B. Barton, E. Bailes, A. N. Nguyen, M. Jones, M. A. Quail, I. Goodhead, S. Sims, F. Smith, A. Blomberg, R. Durbin, E. J. Louis posted by 16 people michaelbarton aprasad emptyhb benjaminsb RockmanLab dpollard fungal absterga anphony druvus Mycology stajich jasontsai Koch_Lab skoch3 dullhunk
	Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae [My Copy] Nature (11 February 2009) by Joseph Schacherer, Joshua A. Shapiro, Douglas M. Ruderfer, Leonid Kruglyak posted by 8 people ilyashl fungal emptyhb Mycology stajich RockmanLab dpollard anphony
	Evolution of Regulatory Sequences in 12 Drosophila Species [My Copy] PLoS Genet, Vol. 5, No. 1. (January 2009), e1000330. by Jaebum Kim, Xin He, Saurabh Sinha posted by 16 people daveGerrard kevinemamy RockmanLab dpollard caseybrown druvus WanderingAengus BergmanLab JustinCrocker cis-regulatory-evolution cisevol cajunsushi djkt emptyhb cabbagesofdoom Stew
	Speciation through sensory drive in cichlid fish [My Copy] Nature, Vol. 455, No. 7213. (2 October 2008), pp. 620-626. by Ole Seehausen, Yohey Terai, Isabel S. Magalhaes, et al.Karen L. Carleton, Hillary D. Mrosso, Ryutaro Miyagi, Inke van der Sluijs, Maria V. Schneider, Martine E. Maan, Hidenori Tachida, Hiroo Imai, Norihiro Okada posted by 7 people haloin RockmanLab dpollard qwermish emptyhb jbsaltz stevanspringer
	Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 2. (22 January 2002), pp. 763-768. by M. Markstein, P. Markstein, V. Markstein, M. S. Levine posted by 4 people emptyhb indigoviolet dpollard EisenLab
	Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome [My Copy] Genome Research, Vol. 17, No. 12. (7 December 2007), pp. 1755-1762. by Peter Andolfatto posted by 7 people druvus dpollard djkt usagi-kirin mimulus_99 EisenLab emptyhb
	Global analysis of patterns of gene expression during Drosophila embryogenesis [My Copy] Genome Biology, Vol. 8 (23 July 2007), R145. by Pavel Tomancak, Benjamin P. Berman, Amy Beaton, et al.Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E. Celniker, Gerald M. Rubin posted by 6 people emptyhb benlansdel cajunsushi dpollard EisenLab caseybrown
	Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. [My Copy] Genome Res (5 July 2007) by Daryi Wang, Huang-Mo M. Sung, Tzi-Yuan Y. Wang, et al.Chih-Jen J. Huang, Peggy Yang, Tiffany Chang, Yang-Chao C. Wang, Da-Lun L. Tseng, Jen-Pey P. Wu, Tso-Ching C. Lee, Ming-Che C. Shih, Wen-Hsiung H. Li posted by 9 people azazello dpollard jwestbrook emarker EisenLab King_Lab cisevol cis-regulatory-evolution emptyhb
	Morphological evolution through multiple cis-regulatory mutations at a single gene [My Copy] Nature (15 July 2007) by Alistair P. Mcgregor, Virginie Orgogozo, Isabelle Delon, et al.Jennifer Zanet, Dayalan G. Srinivasan, François Payre, David L. Stern posted by 11 people pradiptaray athma dpollard djkt zwang Stew xingxu EisenLab cisevol cis-regulatory-evolution emptyhb
	Canalization of segmentation and its evolution in Drosophila. [My Copy] Proc Natl Acad Sci U S A (14 June 2007) by Susan E E. Lott, Martin Kreitman, Arnar Palsson, Elena Alekseeva, Michael Z Z. Ludwig posted by 3 people dpollard emptyhb EisenLab
	Colloquium Papers: Emerging principles of regulatory evolution. [My Copy] Proc Natl Acad Sci U S A, Vol. 104 Suppl 1 (15 May 2007), pp. 8605-8612. by B. Prud'homme, N. Gompel, S. B. Carroll posted by 8 people daveGerrard athma dpollard EisenLab blobbybirdman cisevol cis-regulatory-evolution emptyhb
	Evaluating the role of natural selection in the evolution of gene regulation [My Copy] Heredity, Vol. aop, No. current. by J. C. Fay, P. J. Wittkopp posted by 8 people jbsaltz dpollard djkt EisenLab cisevol cis-regulatory-evolution emptyhb gjuggler
	Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. [My Copy] Genes Dev, Vol. 21, No. 4. (15 February 2007), pp. 385-390. by J. Zeitlinger, R. P. Zinzen, A. Stark, et al.M. Kellis, H. Zhang, R. A. Young, M. Levine posted by 12 people BergmanLab daveGerrard emptyhb dpollard kengg johncumbers gsrats ghattem jtomasch Stew EisenLab Plantandetc
	Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes [My Copy] Science, Vol. 315, No. 5813. (9 February 2007), pp. 848-853. by Barbara E. Stranger, Matthew S. Forrest, Mark Dunning, et al.Catherine E. Ingle, Claude Beazley, Natalie Thorne, Richard Redon, Christine P. Bird, Anna de Grassi, Charles Lee, Chris Tyler-Smith, Nigel Carter, Stephen W. Scherer, Simon Tavare, Panagiotis Deloukas, Matthew E. Hurles, Emmanouil T. Dermitzakis posted by 38 people biovils lp2 daveGerrard sameersoi timhubbard Roswell Cancer Crosstalk Zephyrus ajbattle jonilaserson ilyashl emptyhb buyske zufar koller Visiting Position waszak daed psique jo_davies srp33 guhjy jfr dpollard balicea rdiaz qfwills djkt vplagnol shigepong jlangdon xingxu Bioinformatics EisenLab cisevol cis-regulatory-evolution caseybrown frohike jandot
	Biological function of unannotated transcription during the early development of Drosophila melanogaster [My Copy] Nature Genetics, Vol. 38, No. 10. (03 September 2006), pp. 1151-1158. by Robert J. Manak, Sujit Dike, Victor Sementchenko, et al.Philipp Kapranov, Frederic Biemar, Jeff Long, Jill Cheng, Ian Bell, Srinka Ghosh, Antonio Piccolboni, Thomas R. Gingeras posted by 19 people roys ThomasDOtto inesdesantiago BergmanLab daveGerrard GeeSharpMinor emptyhb dpollard neveaire djkt wrowell Stew xingxu Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience Cline_lab
	The cost of inbreeding in Arabidopsis. [My Copy] Nature, Vol. 416, No. 6880. (4 April 2002), pp. 531-534. by C. D. Bustamante, R. Nielsen, S. A. Sawyer, K. M. Olsen, M. D. Purugganan, D. L. Hartl posted by 4 people emptyhb dpollard djkt EisenLab
	Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution [My Copy] Cell, Vol. 125, No. 7. (30 June 2006), pp. 1387-1399. by Sangyun Jeong, Antonis Rokas, Sean B. Carroll posted by 5 people emptyhb dpollard emilyhare EisenLab cis-regulatory-evolution
	Close sequence comparisons are sufficient to identify human cis-regulatory elements. [My Copy] Genome Res (12 June 2006) by Shyam Prabhakar, Francis Poulin, Malak Shoukry, et al.Veena Afzal, Edward M M. Rubin, Olivier Couronne, Len A A. Pennacchio posted by 11 people indigoviolet dpollard samal nickluscombe olympos EisenLab EBI-regulation emptyhb bpcusack mariakmejia kcrawlik
	Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. [My Copy] Genome research, Vol. 16, No. 7. (2 July 2006), pp. 875-884. by Daniel L. Halligan, Peter D. Keightley posted by 12 people daveGerrard tkmaia caseybrown RMGraze dpollard penka jri EisenLab Nie cisevol cis-regulatory-evolution emptyhb
	Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3'UTR Evolution. [My Copy] Cell (7 December 2005) by Alexander Stark, Julius Brennecke, Natascha Bushati, Robert B B. Russell, Stephen M M. Cohen posted by 13 people daforerog natstreet jfr textoris dpollard mortenlindow mtagaya Garamonfok EisenLab microRNA Evangelia heliopais emptyhb
	NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. [My Copy] Nucleic acids research, Vol. 33, No. 5. (2005), pp. 1445-1453. by T. A. Down, T. J. Hubbard posted by 7 people timhubbard emptyhb lyongu dpollard dquest EisenLab waszak
	Conserved regulatory sequences in Atoh7 mediate non-conserved regulatory responses in retina ontogenesis. [My Copy] Development (Cambridge, England), Vol. 136, No. 22. (November 2009), pp. 3767-3777. by Dorota Skowronska-Krawczyk, Florence Chiodini, Martin Ebeling, et al.Christine Alliod, Adam Kundzewicz, Diogo Castro, Marc Ballivet, François Guillemot, Lidia Matter-Sadzinski, Jean-Marc M. Matter posted by 2 people emptyhb maximilianh
	Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance [My Copy] Nature, Vol. 461, No. 7262. (16 August 2009), pp. 399-401. by Dongliang Ge, Jacques Fellay, Alexander J. Thompson, et al.Jason S. Simon, Kevin V. Shianna, Thomas J. Urban, Erin L. Heinzen, Ping Qiu, Arthur H. Bertelsen, Andrew J. Muir, Mark Sulkowski, John G. McHutchison, David B. Goldstein posted by 4 people Journal picks maximilianh jbhiatt emptyhb
	Distinguishing direct versus indirect transcription factorâDNA interactions [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca GordÃ¢n, Alexander J. Hartemink, Martha L. Bulyk posted by 12 people oannes nklee djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	The Consequences of Base Pair Composition Biases for Regulatory Network Organization in Prokaryotes [My Copy] Mol Biol Evol, Vol. 26, No. 10. (1 October 2009), pp. 2171-2173. by Otto X. Cordero, Paulien Hogeweg posted by 4 people operon jjray emptyhb maximilianh
	A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation [My Copy] Science, Vol. 324, No. 5927. (1 May 2009), pp. 659-662. by Itay Tirosh, Sharon Reikhav, Avraham A. Levy, Naama Barkai posted by 9 people mjoach dbensasson dipenps absterga djkt jbhiatt maximilianh emptyhb TRHvidsten
	Chromatin structure analyses identify miRNA promoters. [My Copy] Genes & development, Vol. 22, No. 22. (15 November 2008), pp. 3172-3183. by Fatih Ozsolak, Laura L. Poling, Zhengxin Wang, et al.Hui Liu, X. Shirley Liu, Robert G. Roeder, Xinmin Zhang, Jun S. Song, David E. Fisher posted by 14 people danaiancu hrogers BergmanLab cisevol gdb maximilianh tonamswish heliopais microRNA jfr samgj emptyhb valeriehilgers pengchy
	Shadow Enhancers as a Source of Evolutionary Novelty [My Copy] Science, Vol. 321, No. 5894. (5 September 2008), 1314. by Joung-Woo Hong, David A. Hendrix, Michael S. Levine posted by 21 people mjoach daveGerrard BergmanLab cisevol TranscriptionalRegulationWithThermodynamicModels jfr rouault emptyhb GEB dlobo sebastien_vigneau Stew bpcusack Ema Roswell Cancer Crosstalk Zephyrus djkt natstreet isimpson maximilianh caseybrown
	Human-specific gain of function in a developmental enhancer. [My Copy] Science (New York, N.Y.), Vol. 321, No. 5894. (5 September 2008), pp. 1346-1350. by Shyam Prabhakar, Axel Visel, Jennifer A. Akiyama, et al.Malak Shoukry, Keith D. Lewis, Amy Holt, Ingrid Plajzer-Frick, Harris Morrison, David R. Fitzpatrick, Veena Afzal, Len A. Pennacchio, Edward M. Rubin, James P. Noonan posted by 16 people paulrigor Annab jfr Stew shoshin bpcusack emptyhb Roswell Cancer Crosstalk Zephyrus sebastien_vigneau djkt natstreet isimpson maximilianh caseybrown eskay
	A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity [My Copy] Genome Research, Vol. 18, No. 9. (7 September 2008), pp. 1422-1432. by Aileen M. Smith, Maria-Jose Sanchez, George A. Follows, et al.Sarah Kinston, Ian J. Donaldson, Anthony R. Green, Berthold GÃ¶ttgens posted by 7 people operon cisstem emptyhb maximilianh cisevol BergmanLab cis-regulatory-evolution
	Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i165-171. by Lucas D. Ward, Harmen J. Bussemaker posted by 7 people mox druvus kittipat emptyhb hplatero xili03 maximilianh
	Global Chromatin Domain Organization of the Drosophila Genome [My Copy] PLoS Genet, Vol. 4, No. 3. (28 March 2008), e1000045. by Elzo de Wit, Ulrich Braunschweig, Frauke Greil, Harmen J. Bussemaker, Bas van Steensel posted by 5 people caseybrown emptyhb Garamonfok maximilianh oelemento
	Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. [My Copy] PLoS genetics, Vol. 3, No. 11. (30 November 2007) by Pierre Fontanillas, Daniel L. Hartl, Max Reuter posted by 6 people timflutre inesdesantiago maximilianh emptyhb bpcusack shoshin
	Ultraconservation identifies a small subset of extremely constrained developmental enhancers. [My Copy] Nat Genet (6 January 2008) by Axel Visel, Shyam Prabhakar, Jennifer A A. Akiyama, et al.Malak Shoukry, Keith D D. Lewis, Amy Holt, Ingrid Plajzer-Frick, Veena Afzal, Edward M M. Rubin, Len A A. Pennacchio posted by 7 people cisstem Stew maximilianh gjuggler emptyhb bpcusack isimpson
	Functional tests of enhancer conservation between distantly related species [My Copy] Development, Vol. 130, No. 21. (1 November 2003), pp. 5133-5142. by Ilya Ruvinsky, Gary Ruvkun posted by 8 people thegoose2 C. elegans / WormBase tharris mikaelhuss maximilianh cisevol cis-regulatory-evolution emptyhb
	Genome-wide transcription and the implications for genomic organization [My Copy] Nature Reviews Genetics, Vol. 8, No. 6. (08 May 2007), pp. 413-423. by Philipp Kapranov, Aarron T. Willingham, Thomas R. Gingeras posted by 29 people Jporci bartjacobse bertelsen daforerog coela hagechouchin443 emptyhb pengchy guhjy balicea xico dchughes kengg sebastien_vigneau zwang ajgentles Ema asddd hanansh antonkratz Bioinformatics WetBiology G4ID Plantandetc Genetics-of-Gambling vietanh0 maximilianh GeeSharpMinor inesdesantiago
	A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. [My Copy] Nucleic Acids Res, Vol. 34, No. 8. (2006), pp. 2238-2246. by C. Zhang, Z. Xuan, S. Otto, et al.J. R. Hover, S. R. McCorkle, G. Mandel, M. Q. Zhang posted by 7 people BergmanLab polivares gpalidwor maximilianh emptyhb Auger Dead 60's
	MATCH: A tool for searching transcription factor binding sites in DNA sequences. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3576-3579. by A. E. Kel, E. Gössling, I. Reuter, E. Cheremushkin, O. V. Kel-Margoulis, E. Wingender posted by 8 people farhat setar aprasad reidy nklee danish_punter maximilianh emptyhb
	Experimental determination of the evolvability of a transcription factor. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 44. (3 November 2009), pp. 18650-18655. by Sebastian J. Maerkl, Stephen R. Quake posted by 6 people maximilianh kintoki emptyhb sameersoi aalibes bpcusack
	The Genetic Signatures of Noncoding RNAs [My Copy] PLoS Genet, Vol. 5, No. 4. (24 April 2009), e1000459. by John S. Mattick posted by 25 people hzoltan Zephyrus antonkratz bertelsen frohike natstreet guhjy gdb giovenko galka8_diploma aditi9783 daforerog ealloza RockmanLab dpollard hrogers coela ilyashl fenghezi reyez maximilianh giovanni djkt Mycology stajich
	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
	MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216. by Saurabh Sinha, Xin He posted by 10 people ana dpollard cjeans zwang EisenLab maximilianh cis-regulatory-evolution hpaces Ema uwe
	Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study [My Copy] Genome Biology, Vol. 8, No. 11. (08 November 2007), R236. by Arjun Bhutkar, William Gelbart, Temple Smith posted by 9 people daveGerrard operon indigoviolet dpollard balicea EisenLab maximilianh hpaces isimpson
	Enhanceosomes. [My Copy] Current opinion in genetics & development, Vol. 11, No. 2. (April 2001), pp. 205-208. by M. Merika, D. Thanos posted by 3 people maximilianh dpollard EisenLab
	We gather together: insulators and genome organization. [My Copy] Curr Opin Genet Dev (1 October 2007) by Julie A A. Wallace, Gary Felsenfeld posted by 6 people caseybrown dpollard dchughes EisenLab maximilianh sebastien_vigneau
	Modeling DNA-binding of Escherichia coli sigma70 exhibits a characteristic energy landscape around strong promoters [My Copy] Nucl. Acids Res. (16 October 2007), gkm720. by Johanna Weindl, Pavol Hanus, Zaher Dawy, Juergen Zech, Joachim Hagenauer, Jakob C. Mueller posted by 5 people jjray operon dpollard EisenLab maximilianh
	Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. [My Copy] BMC bioinformatics, Vol. 8, No. 1. (2007) by E. Redhead, T. L. Bailey posted by 9 people wowalz tmarscha dpollard cjeans nklee niallhaslam EisenLab maximilianh idonaldson
	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
	Incorporating evolution of transcription factor binding sites into annotated alignments. [My Copy] J Biosci, Vol. 32, No. 5. (August 2007), pp. 841-850. by A. S. Bais, S. Grossmann, M. Vingron posted by 4 people dpollard EisenLab maximilianh cis-regulatory-evolution
	Natural history and evolutionary principles of gene duplication in fungi [My Copy] Nature, Vol. 449, No. 7158. (06 September 2007), pp. 54-61. by Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev posted by 25 people Jporci bcondon GustavoLacerda biomcgary gdb schwartzjmc keb45 gjuggler aheilbut dpollard tny dchughes djkt stajich zwang lp2 tzhughes EisenLab G4ID Genetics-of-Gambling maximilianh Mycology pkm bpcusack dandaman
	Cis- and Trans-Acting Elements Regulate the Mouse Psmb9 Meiotic Recombination Hotspot. [My Copy] PLoS Genet, Vol. 3, No. 6. (22 June 2007) by Frédéric Baudat, Bernard de Massy posted by 3 people dpollard EisenLab maximilianh
	Principles of Genome Evolution in the Drosophila melanogaster Species Group [My Copy] PLoS Biology, Vol. 5, No. 6. (1 June 2007), e152. by José M. Ranz, Damien Maurin, Yuk S. Chan, et al.Marcin von Grotthuss, Ladeana W. Hillier, John Roote, Michael Ashburner, Casey M. Bergman posted by 7 people braneyboo operon dpollard zwang nosada17 EisenLab maximilianh
	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
	Tissue-specific transcriptional regulation has diverged significantly between human and mouse. [My Copy] Nature genetics, Vol. 39, No. 6. (21 June 2007), pp. 730-732. by Duncan T. Odom, Robin D. Dowell, Elizabeth S. Jacobsen, et al.William Gordon, Timothy W. Danford, Kenzie D. MacIsaac, P. Alexander Rolfe, Caitlin M. Conboy, David K. Gifford, Ernest Fraenkel posted by 18 people vingron ajaymalik fenghezi dpollard gpalidwor dchughes cwbrown djkt cjeans EisenLab G4ID Genetics-of-Gambling maximilianh cis-regulatory-evolution fpattyn caseybrown yevishere gdb
	RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription [My Copy] Science, Vol. 316, No. 5830. (8 June 2007), pp. 1484-1488. by Philipp Kapranov, Jill Cheng, Sujit Dike, et al.David A. Nix, Radharani Duttagupta, Aarron T. Willingham, Peter F. Stadler, Jana Hertel, Jorg Hackermuller, Ivo L. Hofacker, Ian Bell, Evelyn Cheung, Jorg Drenkow, Erica Dumais, Sandeep Patel, Gregg Helt, Madhavan Ganesh, Srinka Ghosh, Antonio Piccolboni, Victor Sementchenko, Hari Tammana, Thomas R. Gingeras posted by 19 people gdb maximilianh GustavoLacerda marcius alexg dpollard xico mtagaya rdiaz djkt stajich mathijsv asddd EisenLab WetBiology BioinfoCIPF SGU-CIPF elfar xingxu
	Computation and Analysis of Genomic Multi-Sequence Alignments [My Copy] Annual Review of Genomics and Human Genetics, Vol. 8, No. 1. (9 May 2007), pp. 193-213. by Mathieu Blanchette posted by 9 people natstreet druvus treangen dpollard lilou nklee EisenLab maximilianh aprasad
	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
	A survey of motif discovery methods in an integrated framework [My Copy] Biology Direct, Vol. 1, No. 1. (06 April 2006), 11. by Geir K. Sandve, Finn Drabløs posted by 13 people tomhebbron Scis0000002 maximilianh wowalz AbnerCYH aprasad dpollard samal EisenLab yevishere csdhwang idonaldson yoonk
	Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis. [My Copy] Genome Res (13 March 2006) by Gayle K K. McEwen, Adam Woolfe, Debbie Goode, Tanya Vavouri, Heather Callaway, Greg Elgar posted by 8 people dpollard dchughes tabu sujaikumar EisenLab G4ID Genetics-of-Gambling maximilianh
	Toward Automatic Reconstruction of a Highly Resolved Tree of Life [My Copy] Science, Vol. 311, No. 5765. (3 March 2006), pp. 1283-1287. by Francesca D. Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J. Creevey, Berend Snel, Peer Bork posted by 27 people pablocarb cmura adampah druvus fhsantanna microbiology_nijmegen kinestetika dparks Retchless knaseanka dpollard tny dchughes nirfriedman cmm azazello wenhan EisenLab FAB-lab G4ID Genetics-of-Gambling MBLAB maximilianh cmzmasek lonshy diamantis Ema
	Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover [My Copy] Mol Biol Evol, Vol. 19, No. 7. (1 July 2002), pp. 1114-1121. by Emmanouil T. Dermitzakis, Andrew G. Clark posted by 9 people fenghezi pradiptaray provero adepace EisenLab cisevol cis-regulatory-evolution emptyhb xili03
	Detecting natural selection on cis-regulatory DNA [My Copy] Genetica, Vol. 129, No. 1. (January 2007), pp. 7-18. by Hahn, Matthew posted by 7 people provero Zephyrus adepace EisenLab cisevol cis-regulatory-evolution emptyhb
	The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 14. (5 April 2005), pp. 4960-4965. by A. Ochoa-Espinosa, G. Yucel, L. Kaplan, et al.A. Pare, N. Pura, A. Oberstein, D. Papatsenko, S. Small posted by 3 people adepace EisenLab emptyhb
	Evolution of development in closely related species of flies and worms. [My Copy] Nat Rev Genet, Vol. 3, No. 12. (December 2002), pp. 907-917. by P. Simpson posted by 6 people thegoose2 C. elegans / WormBase tharris adepace EisenLab emptyhb
	Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 24. (14 June 2005), pp. 8591-8596. by J. P. Balhoff, G. A. Wray posted by 6 people gderwin adepace EisenLab cisevol cis-regulatory-evolution emptyhb
	Evolution of gene expression in the Drosophila melanogaster subgroup. [My Copy] Nat Genet, Vol. 33, No. 2. (February 2003), pp. 138-144. by S. A. Rifkin, J. Kim, K. P. White posted by 8 people BergmanLab daveGerrard adepace eukfn emarker EisenLab caseybrown emptyhb
	Adaptive evolution of non-coding DNA in Drosophila [My Copy] Nature, Vol. 437, No. 7062. (20 October 2005), pp. 1149-1152. by Peter Andolfatto posted by 23 people gregoryross emptyhb timflutre provero tkmaia rouault stevanspringer bpb aprasad jmeppley balicea jimmithy emilyhare cdawson adepace pradiptaray Stew mimulus_99 EisenLab FAB-lab GIG cisevol cis-regulatory-evolution
	Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage [My Copy] Science, Vol. 309, No. 5736. (5 August 2005), pp. 938-940. by Jan Ihmels, Sven Bergmann, Maryam Gerami-Nejad, et al.Itai Yanai, Mark McClellan, Judith Berman, Naama Barkai posted by 15 people hge balabu roys Ema aalibes monod arve marcius adepace entropy EisenLab BioinfoCIPF SGU-CIPF janek04 emptyhb
	Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals [My Copy] Nature, Vol. aop, No. current. (27 February 2005) by Xiaohui Xie, Jun Lu, E. J. Kulbokas, et al.Todd R. Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S. Lander, Manolis Kellis posted by 33 people Dulce wowalz maximilianh_otx hagechouchin443 sterovetta kieran101 snuppepuppan BioGeek briann jtextori tmmurali okarsligil jfr balajis lyongu eckart_bindewald mtagaya adepace fisherp nickluscombe panetebrother smiddha franklin oscarluoinau Bioinformatics EisenLab microRNA EBI-regulation heliopais ale emptyhb maralena mariakmejia
	Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. [My Copy] Genome Res, Vol. 15, No. 1. (January 2005), pp. 1-18. by S. Richards, Y. Liu, B. R. Bettencourt, et al.P. Hradecky, S. Letovsky, R. Nielsen, K. Thornton, M. J. Hubisz, R. Chen, R. P. Meisel, O. Couronne, S. Hua, M. A. Smith, P. Zhang, J. Liu, H. J. Bussemaker, M. F. van Batenburg, S. L. Howells, S. E. Scherer, E. Sodergren, B. B. Matthews, M. A. Crosby, A. J. Schroeder, D. Ortiz-Barrientos, C. M. Rives, M. L. Metzker, D. M. Muzny, G. Scott, D. Steffen, D. A. Wheeler, K. C. Worley, P. Havlak, K. J. Durbin, A. Egan, R. Gill, J. Hume, M. B. Morgan, G. Miner, C. Hamilton, Y. Huang, L. Waldron, D. Verduzco, K. P. Clerc-Blankenburg, I. Dubchak, M. A. Noor, W. Anderson, K. P. White, A. G. Clark, S. W. Schaeffer, W. Gelbart, G. M. Weinstock, R. A. Gibbs posted by 14 people alhufton briann tsackton jshapiro operon indigoviolet penka adepace emptyhb EisenLab Nie cisevol cis-regulatory-evolution skumagai
	The Regulation and Evolution of a Genetic Switch Controlling Sexually Dimorphic Traits in Drosophila [My Copy] Cell, Vol. 134, No. 4. (22 August 2008), pp. 610-623. by Thomas M. Williams, Jane E. Selegue, Thomas Werner, Nicolas Gompel, Artyom Kopp, Sean B. Carroll posted by 3 people emptyhb brant caseybrown
	A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system [My Copy] Nucl. Acids Res. (10 March 2008), gkn048. by Marcus B. Noyes, Xiangdong Meng, Atsuya Wakabayashi, Saurabh Sinha, Michael H. Brodsky, Scot A. Wolfe posted by 2 people emptyhb brant
	Regulation of even-skipped stripe 2 in the Drosophila embryo. [My Copy] The EMBO journal, Vol. 11, No. 11. (November 1992), pp. 4047-4057. by S. Small, A. Blair, M. Levine posted by 2 people emptyhb brant
	Qualifying the relationship between sequence conservation and molecular function [My Copy] Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 201-205. by Gregory M. Cooper, Christopher D. Brown posted by 8 people farhat emptyhb aprasad brant djkt xingxu bpcusack nklee
	Adaptive gene expression divergence inferred from population genomics. [My Copy] PLoS genetics, Vol. 3, No. 10. (1 October 2007), pp. 2007-2013. by Alisha K. Holloway, Mara K. Lawniczak, Jason G. Mezey, David J. Begun, Corbin D. Jones posted by 7 people daveGerrard brant Garamonfok xingxu caseybrown sb_journal_club emptyhb