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Your search keyword '"James G. R. Gilbert"' showing total 2 results
Start Over Author "James G. R. Gilbert" Publisher nature publishing group
2 results on '"James G. R. Gilbert"'

1. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author

Nan Jiang, Alfonso Valencia, Rachel A. Harte, Abigail Woodroffe, Michael Seringhaus, Andrew Haydock, Eugene Davydov, Todd M. Lowe, Peggy J. Farnham, Robert E. Thurman, Tyler Alioto, Adam Ameur, Morgan Park, Roderic Guigó, Archana Thakkapallayil, Philipp Kapranov, Francis S. Collins, Donna Karolchik, Stefan Washietl, Kerstin Lindblad-Toh, Michael L. Tress, Barbara E. Stranger, Gregory M. Cooper, Kun Wang, Thomas R. Gingeras, Serafim Batzoglou, Peter D. Ellis, Annie Yang, Stylianos E. Antonarakis, Jonghwan Kim, Robert M. Andrews, W. James Kent, Kuo Ping Chiu, Madhavan Ganesh, Jason D. Lieb, Shane Neph, Albin Sandelin, Michael Hawrylycz, Eric S. Lander, Matthew T. Weirauch, Nick Goldman, Alexander E. Urban, Ian Bell, Anason S. Halees, Jan Komorowski, Webb Miller, Kandhadayar G. Srinivasan, Evelyn Cheung, David B. Jaffe, Peter J. Good, Gregory Lefebvre, Yuko Yoshinaga, Sylvain Foissac, Alexander W. Bruce, Mark Dickson, Christoph M. Koch, Antigone S. Dimas, Zhengdong D. Zhang, Matthew J. Oberley, Paul I.W. de Bakker, Arend Sidow, Xueqing Zhang, Molly Weaver, Jane Rogers, Jacquelyn R. Idol, Jeff Goldy, Haiyan Huang, William Stafford Noble, Angie S. Hinrichs, Sandeep Patel, David A. Nix, Lluís Armengol, Siew Woh Choo, Hong Sain Ooi, Sara Van Calcar, Ivan Adzhubei, Job Dekker, Sara J. Cooper, Hari Tammana, Valerie Maduro, Jason A. Greenbaum, Bing Ren, Sharon L. Squazzo, Jennifer C. McDowell, Chikatoshi Kai, Ivo L. Hofacker, Ian Dunham, Peter J. Bickel, Nancy Holroyd, Eduardo Eyras, Julien Lagarde, Fei Yao, Man Yu, Piero Carninci, Chia-Lin Wei, Alice C. Young, Yong Yu, Daryl J. Thomas, George Asimenos, Xiaoqin Xu, Galt P. Barber, Andrea Tanzer, Juan I. Montoya-Burgos, Sujit Dike, Nathan Day, Gregory E. Crawford, Michele Clamp, Todd Richmond, Nuria Lopez-Bigas, Vishwanath R. Iyer, Ewan Birney, Richard Humbert, Gary C. Hon, David Swarbreck, Xiaobin Guan, Sarah Wilcox, Nate Heintzman, Josep F. Abril, Elaine R. Mardis, Stefan Enroth, Charlie W.H. Lee, Nicholas Matthews, Benedict Paten, Robert Castelo, Michael A. Singer, Mousheng Xu, Chiou Yu Choo, Nancy F. Hansen, Elizabeth Rosenzweig, Patrick A. Navas, Jacqueline Chrast, Brett E. Johnson, Jan O. Korbel, Simon Whelan, Stephen Hartman, Ulas Karaoz, Ingileif B. Hallgrímsdóttir, David Haussler, Michael R. Brent, Jill Cheng, Gonçalo R. Abecasis, Ann S. Zweig, Sherman M. Weissman, Michael O. Dorschner, Jin Lian, Vinsensius B. Vega, Cordelia Langford, Alexandre Reymond, Mark Gerstein, Pawandeep Dhami, Ola Wallerman, Huaiyang Jiang, Lior Pachter, James Taylor, Eric A. Stone, David R. Inman, Yijun Ruan, Peter E. Newburger, Roland Green, Ari Löytynoja, Shelley Force Aldred, Alvaro Rada-Iglesias, Baishali Maskeri, Joel Rozowsky, Jorg Drenkow, Colin N. Dewey, Srinka Ghosh, Yutao Fu, Kayla E. Smith, Xavier Estivill, Donna M. Muzny, Christine P. Bird, Tim Hubbard, Jana Hertel, Kristin Missal, Neerja Karnani, Ericka M. Johnson, Nan Zhang, Zhou Zhu, Stephen C. J. Parker, Minmei Hou, Charlotte N. Henrichsen, Heather A. Hirsch, Caroline Manzano, Laura A. Liefer, Kim C. Worley, Robert Baertsch, Mark S. Guyer, Ross C. Hardison, Zheng Lian, Hiram Clawson, Leah O. Barrera, Manja Lindemeyer, James Cuff, Chunxu Qu, Jun Kawai, Jennifer Hillman-Jackson, Eric D. Green, Robert W. Blakesley, Abel Ureta-Vidal, Rhona K. Stuart, Fabio Pardi, Peter J. Sabo, Edward A. Sekinger, John S. Mattick, Ankit Malhotra, Taane G. Clark, James G. R. Gilbert, James C. Mullikin, Deyou Zheng, Robert M. Kuhn, Tae Hoon Kim, M. Geoff Rosenfeld, Kirsten Lee, Jörg Hackermüller, Oliver M. Dovey, Deanna M. Church, Kyle J. Munn, Peter F. Stadler, Phillippe Couttet, Claudia Fried, Jaafar N. Haidar, Kris A. Wetterstrand, Wing-Kin Sung, Paul G. Giresi, Jia Qian Wu, Ruth Taylor, David A. Wheeler, Zarmik Moqtaderi, Adam Siepel, Michael Snyder, Ian Holmes, Jun Liu, Olof Emanuelsson, Kevin Struhl, Saurabh Asthana, Akshay Bhinge, Adam Frankish, Yoshihide Hayashizaki, Ghia Euskirchen, Joel D. Martin, Robert S. Fulton, Ugrappa Nagalakshmi, Heike Fiegler, Gayle K. Clelland, Shane C. Dillon, Fidencio Neri, Elliott H. Margulies, Sean Davis, Mark Bieda, Tristan Frum, Michael S. Kuehn, Heather Trumbower, Pamela J. Thomas, Kazutoyo Osoegawa, Richard A. Gibbs, Emmanouil T. Dermitzakis, Julian L. Huppert, Richard K. Wilson, Tina Graves, Zhiping Weng, Anthony Shafer, Baoli Zhu, Christopher K. Glass, Patrick J. Boyle, Hennady P. Shulha, Maxim Koriabine, Christoph Flamm, David Vetrie, Nigel P. Carter, Patrick Ng, Peter Kraus, John A. Stamatoyannopoulos, George M. Weinstock, Tim Massingham, Jane M. Lin, Damian Keefe, Jean L. Chang, Shamil R. Sunyaev, Sergey Nikolaev, Kate R. Rosenbloom, Carine Wyss, Hua Cao, Keith D. James, Michael C. Zody, Gerard G. Bouffard, Atif Shahab, Nathan D. Trinklein, James B. Brown, Erica Sodergren, Xiaodong Zhao, Rosa Luna, Sante Gnerre, Paul Flicek, Joanna C. Fowler, Andrew D. Kern, Jakob Skou Pedersen, David C. King, Anindya Dutta, Elise A. Feingold, Richard M. Myers, Richard Sandstrom, Catherine Ucla, Thomas D. Tullius, Mikhail Nefedov, Claes Wadelius, Jennifer Harrow, Christopher M. Taylor, Xiaoling Zhang, Pieter J. de Jong, Dermitzakis, Emmanouil, and Reymond, Alexandre

Subjects
DNA Replication, RNA, Messenger/genetics, Chromatin Immunoprecipitation, Heterozygote, RNA, Untranslated, Transcription, Genetic, Systems biology, Histones/metabolism, RNA, Untranslated/genetics, Pilot Projects, Genomics, Computational biology, Regulatory Sequences, Nucleic Acid, Biology, ENCODE, Genome, Article, DNase-Seq, Histones, Evolution, Molecular, Exons/genetics, Humans, ddc:576.5, Transcription Factors/metabolism, RNA, Messenger, Conserved Sequence, Chromatin/genetics/metabolism, Genetics, Transcription, Genetic/ genetics, Multidisciplinary, Genome, Human, GENCODE, Genetic Variation, Exons, Chromatin, Genetic Variation/genetics, Regulatory Sequences, Nucleic Acid/ genetics, Human genome, Conserved Sequence/genetics, Transcription Initiation Site, Functional genomics, Genome, Human/ genetics, Transcription Factors, Protein Binding
Abstract

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view about chromatin structure has emerged, including its interrelationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded novel mechanistic and evolutionary insights about the functional landscape of the human genome. Together, these studies are defining a path forward to pursue a more-comprehensive characterisation of human genome function.

Published
2007

2. The DNA sequence of human chromosome 22

Author

L. Song, D. M. Lloyd, R. M. Swann, Ian F Korf, Lucinda Fulton, Carol Soderlund, I. D. Martyn, A. King, W Burrill, H. Wu, Y. Ramsey, Tracy Rohlfing, Mark T. Ross, Robert S. Fulton, L. Spragon, Darek Kedra, Laurens G. Wilming, Lisa Edelmann, James G. R. Gilbert, L. Williams, L. Chu, K. Fleming, J. Burgess, S. Shaull, M. N. Whiteley, Phil Latreille, Y. Qian, Ian Dunham, Dan Layman, Jennifer Lewis, A. C.C. Wong, Nobuyoshi Shimizu, Noriaki Aoki, Melanie M. Wall, Margaret A. Leversha, Ingegerd Fransson, M. Vaudin, Takashi Sasaki, Bernice E. Morrow, Graeme T Clark, S. Lewis, S. M. Clegg, H. Ramsay, A M Kimberley, S. J. Dodsworth, Melvin I. Simon, Stephan Beck, D. Conroy, Joseph A. Murray, Michele Clamp, Jan P. Dumanski, Christine Lloyd, Joseph L. McClay, P. Hu, Genwei Zhang, Adrienne Hunt, Steve Kenton, Antony V. Cox, Tina Graves, T. Nguyen, Lesley J. Rogers, Kazuhiko Kawasaki, Luc J. Smink, C. Dockree, J. M. Fey, J. C. Davis, U. J. Kim, Nigel P. Carter, Philip Ozersky, R. W. Heathcott, Richard Durbin, Ai Shintani, J Bailey, S. Bourne, Feng Chen, Harminder Sehra, Sulagna C. Saitta, G. Hall-Tamlyn, Charmain L. Wright, A. A. Garner, T. Do, Jane Rogers, Rebekah Hall, Joseph A. Bedell, Shuichi Asakawa, K Bates, J P Almeida, C. Hall, R. Pavitt, Charlotte G. Cole, K. Hinds, N Corby, V. Cobley, D. Pearson, Beverly S. Emanuel, C. Odell, Carl E.G. Bruder, Darren Grafham, Hiroki Kurahashi, Cordelia Langford, Dave Willey, T. E. Wilmer, David R. Bentley, I. Tapia, Hiroaki Shizuya, Myriam Peyrard, Tamim H. Shaikh, J K Kershaw, F. Fang, LaDeana W. Hillier, P. Loh, C L Bagguley, Tim Hubbard, John Sulston, Z. Wang, Kazunori Shibuya, R. E. Collier, Melanie E. Goward, K F Barlow, Richard Bruskiewich, M. L. Budarf, Yuan Chen, Kathryn L. Evans, Sarah E. Hunt, Judy S. Crabtree, Benjamin Phillimore, Stuart McLaren, M Mashreghi-Mohammadi, S. Chissoe, D. Willingham, J. Hawkins, Huaqin Pan, Q. Wang, Michelle Smith, H. Bradshaw, C. Walker, C. D. Skuce, Jim White, Amanda McMurray, Lucy Matthews, John Burton, Patricia Wohldmann, G. Bemis, O. Beasley, Robert H. Waterston, David W. Johnson, Elaine R. Mardis, H. Williamson, D. Buck, Yuhang Wang, Andrew D. Ellington, Zijin Du, Eyal Seroussi, Susumu Mitsuyama, A. Wamsley, Joanne O. Nelson, Y. Yoshizaki, K. P. O'Brien, H. I. Lao, R. Connor, S. Smalley, Anne Bridgeman, R Ainscough, Matthew Jones, Elisabeth Dawson, Joanna Collins, Pawandeep Dhami, S. Holmes, S. Phan, L. Ray, Angela Dorman, O. T. McCann, Christine P. Bird, Sarah Milne, Q. Ren, B. J. Mortimore, Carol Scott, Lisa French, Shuk-Mei Ho, G. J. Coville, Richard K. Wilson, Patrick Minx, Ziyun Yao, Jun Kudoh, David Beare, Charles A. Steward, Hongshing Lai, Alexander Johnson, Scott M. Williams, Robert W. Plumb, M. Zhan, Y. Fu, A. V. Pearce, S. Blakey, D. Goela, Gavin K. Laird, N. Miller, Matt Cordes, Kymberlie H. Pepin, Sam Phillips, David Bentley, Stéphane Deschamps, A. Do, Shaoping Lin, Shinsei Minoshima, Bruce A. Roe, Axin Hua, S. Qi, C Carder, Paul Scheet, Mark Griffiths, A K Babbage, J. M. Wallis, Heather E. McDermid, Eda Malaj, D. Sloan, and K. Kemp

Subjects
Multidisciplinary, Sequence analysis, Chromosomes, Human, Pair 22, Molecular Sequence Data, Nucleic acid sequence, Gene Dosage, Chromosome Mapping, Computational biology, DNA, Sequence Analysis, DNA, Biology, ENCODE, Genome, Complete sequence, Mice, Species Specificity, Human Genome Project, Animals, Humans, Human genome, Sequence (medicine), Genomic organization, Repetitive Sequences, Nucleic Acid
Abstract

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.

Published
1999

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