Tag encode [76 articles] Export

Recent papers classified by the tag encode.

	GENCODE: producing a reference annotation for ENCODE. [My Copy] Genome biology, Vol. 7 Suppl 1, No. Suppl 1. (2006) by Jennifer Harrow, France Denoeud, Adam Frankish, et al.Alexandre Reymond, Chao-Kung K. Chen, Jacqueline Chrast, Julien Lagarde, James G. Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos E. Antonarakis, Roderic Guigo posted to gencode encode coding by aprasad on 2009-11-12 16:29:44 as along with 4 people inesdesantiago timhubbard olympos wenhan
	Unlocking the secrets of the genome [My Copy] Nature, Vol. 459, No. 7249. (17 June 2009), pp. 927-930. by Susan E. Celniker, Laura A. L. Dillon, Mark B. Gerstein, et al.Kristin C. Gunsalus, Steven Henikoff, Gary H. Karpen, Manolis Kellis, Eric C. Lai, Jason D. Lieb, David M. MacAlpine, Gos Micklem, Fabio Piano, Michael Snyder, Lincoln Stein, Kevin P. White, Robert H. Waterston posted to modencode genomics encode by daveGerrard on 2009-10-26 15:13:48 as along with 4 people and 2 groups polivares roys isimpson TRHvidsten BergmanLab Jarman Lab
	What is a gene, post-ENCODE? History and updated definition [My Copy] Genome Research, Vol. 17, No. 6. (June 2007), pp. 669-681. by Mark B. Gerstein, Can Bruce, Joel S. Rozowsky, et al.Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, Sherman Weissman, Michael Snyder posted to gene encode by daveGerrard on 2009-10-26 14:16:36 as along with 35 people and 4 groups Yanno inesdesantiago kentz ddcttrl bertelsen tmarscha thegoose2 burak guhjy carolh12 eweaver dpollard balicea dchughes dullhunk madhadron cottrell grahamc egonw ghattem sujaikumar Garamonfok PunkRock jasonbobe PredictER cabbagezs Jporci kmdaily krokicki antonkratz Minty hpaces tharris altotor mjoach Bioinformatics EisenLab G4ID Genetics-of-Gambling
	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. [My Copy] Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816. by E. Encode posted to transcription genomics encode chromatin by daveGerrard on 2009-10-26 09:56:14 as along with 25 people and 2 groups bartjacobse daforerog isimpson sharpton jessopher timhubbard scjparker polivares coela ilyashl aprasad myrtilus daed waszak guhjy jfr chad_davis kengg olympos blobbybirdman shikin fpattyn yevishere elfar eskay Bioinformatics UH - Computational Biology
	Construction of a genome-scale structural map at single-nucleotide resolution [My Copy] Genome Research, Vol. 17, No. 6. (June 2007), pp. 947-953. by Jason A. Greenbaum, Bo Pang, Thomas D. Tullius posted to structure map encode by aprasad on 2009-10-24 20:01:56 as along with 5 people and 1 group antonkratz hagechouchin443 dnewburger akundaje ghattem Bioinformatics
	High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. [My Copy] Nucleic acids research, Vol. 37, No. 1. (1 January 2009), pp. 14-25. by Tom Whitington, Andrew C. Perkins, Timothy L. Bailey posted to tfbs integration encode chromatin by akundaje on 2009-09-22 22:18:17 as along with 7 people vingron inesdesantiago polivares lptolik WanderingAengus xili03 maximilianh
	The ENCODE Project at UC Santa Cruz. [My Copy] Nucleic acids research, Vol. 35, No. Database issue. (January 2007), pp. D663-D667. by Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, et al.Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, ENCODE Project Consortium, David Haussler, W. James Kent posted to encode by inesdesantiago on 2009-08-17 15:53:55 as along with 1 person hagechouchin443
	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [My Copy] Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816. by The ENCODE Project Consortium posted to encode functional-genomics survey by bertelsen on 2009-07-22 22:31:38 as along with 30 people and 4 groups balajis gderwin polivares Eroslavochka timflutre pengchy raistrick guhjy cmmorel dpollard ilh djkt plofje ramensky joepickrell massivemayhem fishtank Garamonfok jmuhlich bioyang cabbagezs xingxu antonkratz mimulus_99 julianjonker gjuggler drbal maralena ep161302 jasonflannick JLab Bioinformatics EisenLab SorgerLab
	Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. [My Copy] Nature, Vol. 457, No. 7232. (19 February 2009), pp. 1028-1032. by Affymetrix ENCODE Transcriptome Project, Cold Spring Harbor Laboratory ENCODE Transcriptome Project posted to cage encode ncrna by guhjy on 2009-07-22 08:36:37 as along with 11 people gdb jfr daforerog fenghezi jochenG rdowell mtagaya djkt jbhiatt megraw mhamada
	Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. [My Copy] Genome research, Vol. 17, No. 6. (1 June 2007), pp. 746-759. by F. Denoeud, P. Kapranov, C. Ucla, et al.A. Frankish, R. Castelo, J. Drenkow, J. Lagarde, T. Alioto, C. Manzano, J. Chrast, S. Dike, C. Wyss, C. N. Henrichsen, N. Holroyd, M. C. Dickson, R. Taylor, Z. Hance, S. Foissac, R. M. Myers, J. Rogers, T. Hubbard, J. Harrow, R. Guigó, T. R. Gingeras, S. E. Antonarakis, A. Reymond posted to encode genome_annotation tjph by timhubbard on 2009-07-13 21:25:19 as along with 7 people and 1 group aprasad myrtilus djkt olympos ghattem xingxu jasonflannick Bioinformatics
	EGASP: the human ENCODE Genome Annotation Assessment Project. [My Copy] Genome biology, Vol. 7 Suppl 1 (2006) by Roderic Guigó, Paul Flicek, Josep F. Abril, et al.Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B. Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R. Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E. Lewis, Martin G. Reese posted to encode gene_prediction genome_annotation tjph by timhubbard on 2009-07-13 21:17:16 as along with 4 people and 2 groups rshe jfr indigoviolet wenhan Bioinformatics EisenLab
	The ENCODE (ENCyclopedia Of DNA Elements) Project. [My Copy] Science (New York, N.Y.), Vol. 306, No. 5696. (22 October 2004), pp. 636-640. by posted to encode genome_annotation tjph by timhubbard on 2009-07-13 08:46:07 as along with 13 people and 1 group polivares ilyashl raistrick setar balajis skhadar qfwills djkt frohike JeffR100 olympos hpaces siebert Bioinformatics
	Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions [My Copy] Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 242-251. by Elfar Torarinsson, Zizhen Yao, Eric D. Wiklund, et al.Jesper B. Bramsen, Claus Hansen, Jorgen Kjems, Niels Tommerup, Walter L. Ruzzo, Jan Gorodkin posted to encode ncrna by galka8_diploma on 2009-06-29 13:24:55 as along with 3 people djkt cabbagezs xingxu
	Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 865-876. by N. Karnani, C. Taylor, A. Malhotra, A. Dutta posted to encode quakeatl replication tor by polivares to the group JLab on 2009-06-24 10:39:49 as along with 3 people and 1 group jackjackjjj ghattem elzodw Bioinformatics
	Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 760-774. by Elliott H. Margulies, Gregory M. Cooper, George Asimenos, et al.Daryl J. Thomas, Colin N. Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Ariel S. Schwartz, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Loytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B. Brown, Peter Bickel, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Eric A. Stone, Kate R. Rosenbloom, James W. Kent, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. Maduro, Baishali Maskeri, Jennifer C. Mcdowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Angie Hinrichs, Heather Trumbower, Hiram Clawson, Ann Zweig, Robert M. Kuhn, Galt Barber, Rachel Harte, Donna Karolchik, Matthew A. Field, Richard A. Moore, Carrie A. Matthewson, Jacqueline E. Schein, Marco A. Marra, Stylianos E. Antonarakis, Serafim Batzoglou, Nick Goldman, Ross Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D. Green, Arend Sidow posted to cis-elements encode evolution mammals quakeatl by polivares to the group BergmanLab on 2009-06-23 17:13:54 as along with 11 people and 4 groups daveGerrard timflutre aprasad dpollard dchughes AaronDarling djkt ghattem Garamonfok gjuggler elfar Bioinformatics EisenLab G4ID Genetics-of-Gambling
	Multi-scale correlations in continuous genomic data. [My Copy] Pac Symp Biocomput (2008), pp. 201-215. by R. E. Thurman, W. S. Noble, J. A. Stamatoyannopoulos posted to chip-chip chip-seq chromatin encode genome-wide heterochromatin signature by sebastien_vigneau on 2009-05-18 01:19:03 as along with 5 people and 1 group timflutre Eroslavochka guhjy operon dpollard EisenLab
	Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome [My Copy] Genome Research, Vol. 16, No. 1. (January 2006), pp. 1-10. by Sara J. Cooper, Nathan D. Trinklein, Elizabeth D. Anton, Loan Nguyen, Richard M. Myers posted to core encode general_exam promoter transcriptional_regulation by rpatward on 2009-05-05 22:48:46 as along with 4 people absterga troels_marstrand xiaobeizhao olympos
	Replication-timing-correlated spatial chromatin arrangements in cancer and in primate interphase nuclei [My Copy] J Cell Sci, Vol. 121, No. 11. (1 June 2008), pp. 1876-1886. by Florian Grasser, Michaela Neusser, Heike Fiegler, et al.Tobias Thormeyer, Marion Cremer, Nigel P. Carter, Thomas Cremer, Stefan Muller posted to encode nuclear_architecture nuclear_sub-compartments rep_origins replication tor by polivares to the group JLab on 2009-04-24 16:53:51 as along with 1 person and 1 group inesdesantiago BergmanLab
	Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. [My Copy] Nature biotechnology, Vol. 27, No. 4. (April 2009), pp. 361-368. by Madeleine P. Ball, Jin Billy B. Li, Yuan Gao, et al.Je-Hyuk H. Lee, Emily M. LeProust, In-Hyun H. Park, Bin Xie, George Q. Daley, George M. Church posted to bisulphite encode epigenetics methylation sequencing by neils on 2009-04-08 00:55:23 as along with 5 people and 1 group saravana guhjy bpcusack absterga jbhiatt BenosLab
	Identification of higher-order functional domains in the human ENCODE regions [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 917-927. by Robert E. Thurman, Nathan Day, William S. Noble, John A. Stamatoyannopoulos posted to bioinformatics chromatin encode genomics wavelets by timflutre on 2009-03-21 20:23:11 as along with 3 people and 1 group ghattem epigenetics jasonflannick Bioinformatics
	The External RNA Controls Consortium: a progress report [My Copy] Nat Meth, Vol. 2, No. 10. (October 2005), pp. 731-734. posted to analysis arrays comparing computer database encode by myrtilus on 2009-03-03 17:28:29 as
	Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. [My Copy] Genome research, Vol. 17, No. 6. (1 June 2007), pp. 787-797. by Zhengdong D. Zhang, Alberto Paccanaro, Yutao Fu, et al.Sherman Weissman, Zhiping Weng, Joseph Chang, Michael Snyder, Mark B. Gerstein posted to chip encode motif regulatory tfbs by aprasad on 2009-01-12 13:58:23 as along with 9 people and 5 groups paccanarolab ana Borelli kengg ghattem epigenetics blobbybirdman inesdesantiago jasonflannick Paccanaro Lab structural_bioinformatics Bioinformatics Plantandetc UH - Computational Biology
	Raising the estimate of functional human sequences. [My Copy] Genome Res (9 August 2007) by Michael Pheasant, John S. S. Mattick posted to encode file-import-09-01-04 genomics human transcription by hdopazo on 2008-12-21 21:31:22 as along with 11 people and 1 group galka8_diploma guhjy jfr andersbj djkt grahamc lp2 cabbagezs nklee ljs mimulus_99 microRNA
	Genome-wide studies highlight indirect links between human replication origins and gene regulation. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (6 October 2008) by Jean-Charles C. Cadoret, Françoise Meisch, Vahideh Hassan-Zadeh, et al.Isabelle Luyten, Claire Guillet, Laurent Duret, Hadi Quesneville, Marie-Noëlle N. Prioleau posted to encode origin replication_transcription by polivares on 2008-10-30 11:13:50 as along with 5 people and 2 groups urgi cisevol Eroslavochka inesdesantiago bpcusack JLab BenosLab
	The landscape of histone modifications across 1% of the human genome in five human cell lines [My Copy] Genome Research, Vol. 17, No. 6. (1 June 2007), pp. 691-707. by Christoph M. Koch, Robert M. Andrews, Paul Flicek, et al.Shane C. Dillon, UlaÅ KaraÃ¶z, Gayle K. Clelland, Sarah Wilcox, David M. Beare, Joanna C. Fowler, Phillippe Couttet, Keith D. James, Gregory C. Lefebvre, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Pawandeep Dhami, Cordelia F. Langford, Zhiping Weng, Ewan Birney, Nigel P. Carter, David Vetrie, Ian Dunham posted to encode by jasonflannick on 2008-07-11 17:16:55 as along with 8 people and 1 group tonamswish guhjy djkt olympos ghattem epigenetics maximilianh xingxu Bioinformatics
	Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 798-806. by H. Xi, Y. Yu, Y. Fu, J. Foley, A. Halees, Z. Weng posted to encode by jasonflannick on 2008-07-11 17:16:41 as along with 4 people thegoose megraw idonaldson ghattem
	Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 720-731. by Nathan D. Trinklein, Ulas Karaoz, Jiaqian Wu, et al.Anason Halees, Force, Patrick J. Collins, Deyou Zheng, Zhengdong D. Zhang, Mark B. Gerstein, Michael Snyder, Richard M. Myers, Zhiping Weng posted to encode by jasonflannick on 2008-07-11 17:16:38 as along with 5 people guhjy djkt olympos cjeans Garamonfok
	The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 732-745. by Joel S. Rozowsky, Daniel Newburger, Fred Sayward, et al.Jiaqian Wu, Greg Jordan, Jan O. Korbel, Ugrappa Nagalakshmi, Jin Yang, Deyou Zheng, Roderic Guigo, Thomas R. Gingeras, Sherman Weissman, Perry Miller, Michael Snyder, Mark B. Gerstein posted to encode by jasonflannick on 2008-07-11 17:16:32 as along with 5 people and 1 group GeeSharpMinor djkt olympos ghattem gjuggler Bioinformatics
	Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). [My Copy] Genome research, Vol. 17, No. 6. (June 2007), pp. 828-838. by Yijun Ruan, Hong Sain S. Ooi, Siew Woh W. Choo, et al.Kuo Ping P. Chiu, Xiao Dong D. Zhao, K. G. Srinivasan, Fei Yao, Chiou Yu Y. Choo, Jun Liu, Pramila Ariyaratne, Wilson G. Bin, Vladimir A. Kuznetsov, Atif Shahab, Wing-Kin K. Sung, Guillaume Bourque, Nallasivam Palanisamy, Chia-Lin L. Wei posted to encode by jasonflannick on 2008-07-11 17:16:26 as along with 4 people and 3 groups guhjy dchughes ghattem caseybrown Bioinformatics G4ID Genetics-of-Gambling
	Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. [My Copy] Genome Res (21 November 2006) by Olof Emanuelsson, Ugrappa Nagalakshmi, Deyou Zheng, et al.Joel S S. Rozowsky, Alexander E E. Urban, Jiang Du, Zheng Lian, Viktor Stolc, Sherman Weissman, Michael Snyder, Mark Gerstein posted to encode by jasonflannick on 2008-07-11 17:16:15 as along with 2 people GeeSharpMinor eckart_bindewald
	Genome-wide analysis of mammalian promoter architecture and evolution. [My Copy] Nature genetics, Vol. 38, No. 6. (28 June 2006), pp. 626-635. by Piero Carninci, Albin Sandelin, Boris Lenhard, et al.Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin A. Semple, Martin S. Taylor, Pär G. Engström, Martin C. Frith, Alistair R. Forrest, Wynand B. Alkema, Sin Lam L. Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M. Grimmond, Christine A. Wells, Valerio Orlando, Claes Wahlestedt, Edison T. Liu, Matthias Harbers, Jun Kawai, Vladimir B. Bajic, David A. Hume, Yoshihide Hayashizaki posted to encode by jasonflannick on 2008-07-11 17:16:04 as along with 19 people and 4 groups rsaito guhjy antonkratz athma inesdesantiago rpatward hagechouchin443 nklee djkt jfr xwbcn dchughes tabu samal nickluscombe xiaobeizhao cisevol eviledv gjuggler G4ID EBI-regulation Genetics-of-Gambling cis-regulatory-evolution
	Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. [My Copy] Science (New York, N.Y.), Vol. 308, No. 5725. (20 May 2005), pp. 1149-1154. by Jill Cheng, Philipp Kapranov, Jorg Drenkow, et al.Sujit Dike, Shane Brubaker, Sandeep Patel, Jeffrey Long, David Stern, Hari Tammana, Gregg Helt, Victor Sementchenko, Antonio Piccolboni, Stefan Bekiranov, Dione K. Bailey, Madhavan Ganesh, Srinka Ghosh, Ian Bell, Daniela S. Gerhard, Thomas R. Gingeras posted to encode by jasonflannick on 2008-07-11 17:15:52 as along with 10 people bartjacobse haarcuba xingxu hagechouchin443 inesdesantiago GeeSharpMinor karbak tmmurali tuck bertelsen
	Differential analysis for high density tiling microarray data [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (24 September 2007), 359. by Srinka Ghosh, Heather A. Hirsch, Edward A. Sekinger, Philipp Kapranov, Kevin Struhl, Thomas R. Gingeras posted to analysis differential encode microarray statistics tiling by bertelsen on 2008-06-13 21:04:57 as along with 4 people ashishanand humburg jfr GeeSharpMinor
	Large-Scale Transcriptional Activity in Chromosomes 21 and 22 [My Copy] Science, Vol. 296, No. 5569. (3 May 2002), pp. 916-919. by Philipp Kapranov, Simon E. Cawley, Jorg Drenkow, et al.Stefan Bekiranov, Robert L. Strausberg, Stephen P. A. Fodor, Thomas R. Gingeras posted to affymetrix encode microarray by bertelsen on 2008-06-04 23:08:30 as along with 6 people haarcuba inesdesantiago coela GeeSharpMinor evaf reyez
	Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. [My Copy] Cell, Vol. 116, No. 4. (20 February 2004), pp. 499-509. by S. Cawley, S. Bekiranov, H. H. Ng, et al.P. Kapranov, E. A. Sekinger, D. Kampa, A. Piccolboni, V. Sementchenko, J. Cheng, A. J. Williams, R. Wheeler, B. Wong, J. Drenkow, M. Yamanaka, S. Patel, S. Brubaker, H. Tammana, G. Helt, K. Struhl, T. R. Gingeras posted to non-protein-coding affymetrix encode microarray rna by bertelsen on 2008-06-04 23:08:03 as along with 5 people and 1 group evaf mtagaya kengg olympos brant Plantandetc
	Functional constraint and small insertions and deletions in the ENCODE regions of the human genome [My Copy] Genome Biology, Vol. 8 (04 September 2007), R180. by Taane G. Clark, Toby Andrew, Gregory M. Cooper, Elliot H. Marguiles, James C. Mullikin, David J. Balding posted to encode indel molevol by caseybrown on 2008-06-01 13:45:57 as along with 3 people and 1 group cisevol ryanraaum aprasad cis-regulatory-evolution
	Mapping of Small RNAs in the Human ENCODE Regions [My Copy] The American Journal of Human Genetics, Vol. 82, No. 4. (11 April 2008), pp. 971-981. by Christelle Borel, Maryline Gagnebin, Corinne Gehrig, Evgenia V. Kriventseva, Evgeny M. Zdobnov, Stylianos E. Antonarakis posted to encode ncrna by eskay on 2008-05-26 15:14:57 as along with 1 person inesdesantiago
	Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency. [My Copy] BMC Genomics, Vol. 9 (09 April 2008), 155. by Galih Kunarso, Kee-Yew Wong, Lawrence W. Stanton, Leonard Lipovich posted to encode ncrna ncrna-long by maximilianh on 2008-04-13 12:21:49 as
	ENCODE: More genomic empowerment. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 667-668. by G. M. Weinstock posted to encode by maximilianh on 2008-04-07 16:07:25 as along with 4 people and 4 groups dchughes ghattem wenhan blobbybirdman Bioinformatics G4ID Genetics-of-Gambling UH - Computational Biology
	Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data [My Copy] PLoS Genetics, Vol. 3, No. 1. (1 January 2007), e2. by Sergey Nikolaev, Juan I. Montoya-Burgos, Elliott H. Margulies, et al.Nisc C. Program, Jacques Rougemont, Bruno Nyffeler, Stylianos E. Antonarakis posted to printed phylogeny mammals evolution encode by Garamonfok on 2008-03-11 10:40:10 as along with 2 people aprasad maximilianh
	ENCODE and our very busy genome [My Copy] Nature Genetics, Vol. 39, No. 7., pp. 817-818. by Steven Henikoff posted to encode genome by yezq on 2007-12-20 12:27:31 as along with 2 people and 2 groups grahamc blobbybirdman Bioinformatics UH - Computational Biology
	The ENCODE Project at UC Santa Cruz. [My Copy] Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007) by D. J. Thomas, K. R. Rosenbloom, H. Clawson, et al.A. S. Hinrichs, H. Trumbower, B. J. Raney, D. Karolchik, G. P. Barber, R. A. Harte, J. Hillman-Jackson, R. M. Kuhn, B. L. Rhead, K. E. Smith, A. Thakkapallayil, A. S. Zweig, , D. Haussler, W. J. Kent posted to encode functional-annotation genomics h_sapiens by blobbybirdman to the group UH - Computational Biology on 2007-10-11 14:35:57 as along with 1 group Bioinformatics
	Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 775-786. by D. C. King, J. Taylor, Y. Zhang, et al.Y. Cheng, H. A. Lawson, J. Martin, , F. Chiaromonte, W. Miller, R. C. Hardison posted to cis-regulatory comparative encode by Stew on 2007-10-02 16:57:50 as along with 2 people and 2 groups ghattem Garamonfok Bioinformatics UH - Computational Biology
	Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 839-851. by D. Zheng, A. Frankish, R. Baertsch, et al.P. Kapranov, A. Reymond, S. W. Choo, Y. Lu, F. Denoeud, S. E. Antonarakis, M. Snyder, Y. Ruan, C. L. Wei, T. R. Gingeras, R. Guigó, J. Harrow, M. B. Gerstein posted to pseudogene encode by dchughes to the group Genetics-of-Gambling on 2007-09-17 13:09:22 as along with 2 people and 2 groups olympos ghattem Bioinformatics G4ID
	A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly [My Copy] Genome Research, Vol. 17, No. 6. (June 2007), pp. 960-964. by Daniel Blankenberg, James Taylor, Ian Schenck, et al.Jianbin He, Yi Zhang, Matthew Ghent, Narayanan Veeraraghavan, Istvan Albert, Webb Miller, Kateryna D. Makova, Ross C. Hardison, Anton Nekrutenko posted to encode by guhjy on 2007-09-07 17:08:19 as along with 2 people and 1 group antonkratz ghattem Bioinformatics
	Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 910-916. by A. A. Bhinge, J. Kim, G. M. Euskirchen, M. Snyder, V. R. Iyer posted to encode by ghattem on 2007-07-13 15:41:58 as along with 2 people and 1 group icases levydavid01 TNT
	Independent and complementary methods for large-scale structural analysis of mammalian chromatin. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 928-939. by J. H. Dennis, H. Y. Fan, S. M. Reynolds, et al.G. Yuan, J. C. Meldrim, D. J. Richter, D. G. Peterson, O. J. Rando, W. S. Noble, R. E. Kingston posted to encode by ghattem on 2007-07-13 15:41:41 as
	Detection of DNA structural motifs in functional genomic elements. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 940-946. by J. A. Greenbaum, S. C. Parker, T. D. Tullius posted to encode by ghattem on 2007-07-13 15:41:33 as along with 4 people and 1 group scjparker akundaje wowalz athma Bioinformatics
	The ENCODEdb portal: simplified access to ENCODE Consortium data. [My Copy] Genome research, Vol. 17, No. 6. (June 2007), pp. 954-959. by L. L. Elnitski, P. Shah, R. T. Moreland, L. Umayam, T. G. Wolfsberg, A. D. Baxevanis posted to encode by ghattem on 2007-07-13 15:41:02 as along with 1 person and 1 group guhjy Bioinformatics
	Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 898-909. by Ghia M. Euskirchen, Joel S. Rozowsky, Chia-Lin Wei, et al.Wah H. Lee, Zhengdong D. Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B. Gerstein, Yijun Ruan, Michael Snyder posted to encode by ghattem on 2007-07-13 15:40:26 as along with 6 people and 4 groups kengg jtaylor epigenetics blobbybirdman idonaldson isimpson Bioinformatics Plantandetc UH - Computational Biology BergmanLab

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genomics	61
genome	17
gene	15
human	15
comparative-analysis	9
evolution	9
chromatin	8
transcription	7
mammal	6
ncrna	6
h_sapiens	5
mammals	5
printed	5
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tor	5
bioinformatics	4
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methylation	4
microarray	4
project	4
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chip-chip	3
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functional	3
h3k4me1	3
h3k4me3	3
indel	3
neurons	3
nuclear_architecture	3
nuclear_sub-compartments	3
nucleosome	3
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pseudogene	3
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rep_origins	3
tfbs	3
action	2
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coding	2
constraint	2
dopamine	2
epigenetics	2
genome-wide	2
genomic	2
mattick	2
midbrain	2
model	2
motif	2
nonconserved_functional_dna	2
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promotors	2
quakeatl	2
race	2
rna	2
rna_structure	2
sequences	2
summary	2
tss	2
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modencode	1
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mutation_rate	1
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origin	1
phylogenetics	1
phylogenomics	1
phylogeny	1
primate	1
replication_transcription	1
sequencing	1
signature	1
tez	1
tree	1

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