Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species

Autor: Jennifer R. Wortman, Claire M. Fraser, Steven L. Salzberg, Aihui Wang, Theresa Zutavern, Jessica Simmons, Mihaela Pertea, Kelly Moffat, Weiwei Jin, Wei Zhu, Larry Overton, Aymeric R. De Vazeille, Lance E. Palmer, Stacey E. Iobst, Emily P. Huang, Joseph Hsiao, Jos Luis Goicoechea, Rod A. Wing, Hye-Ran Lee, Jennifer Currie, Luke J. Tallon, Shelly Kernodle-Thompson, Victoria Zismann, David Kudrna, Fusheng Wei, Tamara Feldblyum, Matt Reardon, Sujit Dike, Melissa De La Bastide, Teresa Utterback, R. Preston, Richard K. Wilson, C. Robin Buell, Owen White, Patrick Minx, Rama Maiti, Kristi Collura, Jia Liu, Jetty S.S. Ammiraju, Kristine Jones, Susan Van Aken, Meizhong Luo, Mary Kim, W. Richard McCombie, Hey Ran Kim, Ryan Oates, William Nelson, Scott A. Jackson, Jayati Bera, Teri Rambo, Jessica Hill, Andrew O'haughnessy, Jayati Weaver, Holly Cordum, Matthew R. Lewis, Lori Spiegel, Shaohua Jin, David C Henry, Shivani Johri, Carol Soderlund, Kristen Webb, Christopher A. Saski, Douglas Fadrosh, Jiming Jiang, Michael Palmer, Shu Ouyang, Brian J. Haas, Tamara Tsitrin, Yeisoo Yu, Gina L Pries, Qiaoping Yuan, Lidia Nascimento

Publikováno v: Genome Research. 15:1284-1291

Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5a99d951dbfa7f781ee9708013f1c9b1
https://doi.org/10.1101/gr.3869505

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

Autor: Jeffrey C. Long, Philipp Kapranov, Thomas R. Gingeras, Gregg Helt, Sujit Dike, Jill Cheng, Jorg Drenkow

Publikováno v: Genome Research. 15:987-997

Recently, we mapped the sites of transcription across ∼30% of the human genome and elucidated the structures of several hundred novel transcripts. In this report, we describe a novel combination of techniques including the rapid amplification of cD

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::47a6c8fa6e3a4ef80feaed00415b8df7
https://doi.org/10.1101/gr.3455305

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

Autor: 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

Publikováno v: Nature, Vol. 447, No 7146 (2007) pp. 799-816
Birney, E, Stamatoyannopoulos, J A, Dutta, A, Guigó, R, Gingeras, T R, Margulies, E H, Weng, Z, Snyder, M, Dermitzakis, E T, Thurman, R E, Kuehn, M S, Taylor, C M, Neph, S, Koch, C M, Asthana, S, Malhotra, A, Adzhubei, I, Greenbaum, J A, Andrews, R M, Flicek, P, Boyle, P J, Cao, H, Carter, N P, Clelland, G K, Davis, S, Day, N, Dhami, P, Dillon, S C, Dorschner, M O, Fiegler, H, Giresi, P G, Goldy, J, Hawrylycz, M, Haydock, A, Humbert, R, James, K D, Johnson, B E, Johnson, E M, Frum, T T, Rosenzweig, E R, Karnani, N, Lee, K, Lefebvre, G C, Navas, P A, Neri, F, Parker, S C J, Sabo, P J, Sandstrom, R, Shafer, A, Pedersen, J S & ENCODE Project Consortium 2007, ' Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project ', Nature, vol. 447, no. 7146, pp. 799-816 . https://doi.org/10.1038/nature05874

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 nu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cad7d3cc6b84a6569cb6ed707e357d08
https://resolver.caltech.edu/CaltechAUTHORS:20170307-121815071

Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

Autor: France Denoeud, Philipp Kapranov, Catherine Ucla, Adam Frankish, Robert Castelo, Jorg Drenkow, Julien Lagarde, Tyler Alioto, Caroline Manzano, Jacqueline Chrast, Sujit Dike, Carine Wyss, Charlotte N. Henrichsen, Nancy Holroyd, Mark C. Dickson, Ruth Taylor, Zahra Hance, Sylvain Foissac, Richard M. Myers, Jane Rogers, Tim Hubbard, Jennifer Harrow, Roderic Guigó, Thomas R. Gingeras, Stylianos E. Antonarakis, Alexandre Reymond

Publikováno v: Genome Research, Vol. 17, No 6 (2007) pp. 746-759
Genome Research
Genome Research, Cold Spring Harbor Laboratory Press, 2007, 17 (6), pp.746-759. ⟨10.1101/gr.5660607⟩
Recercat. Dipósit de la Recerca de Catalunya
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Notice à Reprendre Sur les Auteurs; This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot proj

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::51107e83e0683a5a26791d1d51b9acb8
http://hdl.handle.net/10230/16477

Biological function of unannotated transcription during the early development of Drosophila melanogaster

Autor: Philipp Kapranov, Frédéric Biemar, Ian Bell, J. Robert Manak, Victor Sementchenko, Jill Cheng, Sujit Dike, Antonio Piccolboni, Jeffrey Long, Srinka Ghosh, Thomas R. Gingeras

Publikováno v: Nature genetics. 38(10)

Many animal and plant genomes are transcribed much more extensively than current annotations predict. However, the biological function of these unannotated transcribed regions is largely unknown. Approximately 7% and 23% of the detected transcribed n

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::697a5104b6d6c91142a22ef40bee088e
https://pubmed.ncbi.nlm.nih.gov/17006461