ENCODE

ENCODE
内容
相关信息
研究中心	斯坦福大学
实验室	圣塔克鲁兹加利福尼亚大学（2003-2012）; 斯坦福大学（2007年至今）;
创始人	Brian J Raney
发布日期	2010年
访问入口
网站	encodeproject.org
工具
其他

DNA元件百科全书（英语：Encyclopedia of DNA Elements，简称为ENCODE项目）是一个由美国国家人类基因组研究所(NHGRI)在2003年9月发起的一项公共联合研究项目^[2]，旨在找出人类基因组中所有功能组件^[1]^[3]^[4]^[5]。

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这是既完成人类基因组计划后国家人类基因组研究所开始的最重要的项目之一。

所有在该项目中产生的数据都会被迅速的在公共数据库中公开。

ENCODE分三个阶段实施：试验阶段，技术发展阶段，和生产阶段。

ENCODE一期项目：试验项目

试验项目测试和比较现有方法进行严格分析一个所定义的人类基因组序列的一部分。

ENCODE二期项目：生产阶段项目

Thumb — ENCODE数据的图像，在UCSC Genome Browser（英语：UCSC Genome Browser）。 This shows several tracks containing information on gene regulation. The gene on the left (ATP2B4) is transcribed in a wide variety of cells. The gene on the right is only transcribed in a few types of cells, including embryonic stem cells.

2007年9月，国家人类基因组研究所（NHGRI）开始了ENCODE项目生产阶段的拨款。在这个阶段，目标是分析整个基因组，并进行“额外中试规模研究”^[6]。

作为试点项目，生产工作被组织作为一个开放的联盟。 2007年10月，国家人类基因组研究所（NHGRI）在四年期间获拨款总额超过$8000万美元^[7]。生产阶段还包括一个数据协调中心，数据分析中心，和技术开发工作^[8]。当时该项目发展成为一个真正的全球性企业，涉及来自世界各地的32个实验室的440名科学家。

生产阶段结果

2012年9月5日，该项目的初步结果被整理为30篇论文并同时发表于多个刊物，包括6篇论文在《自然》、6篇论文在《基因组生物学》及18篇论文在《基因组研究》上^[9]^[10]。

最引人注目的发现是，人类DNA有生物活性的分数大于以前估计中即使是最乐观的估计还要高得多。这些发表的论文显示人类基因组内的非编码DNA至少80%是有生物活性的，而非像之前认为的仅仅是“垃圾”。这个结果非常重要，因为人类基因组中98%的DNA是非编码的，意味着它们并不直接编码任何蛋白质序列。

[1]
Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent, WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. January 2011, 39 (Database issue): D871–5. PMC 3013645 . PMID 21037257. doi:10.1093/nar/gkq1017.
[2]
Maher B. ENCODE: The human encyclopaedia. Nature. 2012, 489 (7414): 46–48. doi:10.1038/489046a.
[3]
The ENCODE Project Consortium. A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLOS Biology. 2011-04-19, 9 (4): e1001046 [2018-04-02]. ISSN 1545-7885. doi:10.1371/journal.pbio.1001046. （原始内容存档于2018-03-28）（英语）.
[4]
ENCODE Project Consortium, Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R. Gingeras, Elliott H. Margulies, Zhiping Weng, Michael Snyder, Emmanouil T. Dermitzakis, Robert E. Thurman, Michael S. Kuehn, Christopher M. Taylor, Shane Neph, Christoph M. Koch, Saurabh Asthana, Ankit Malhotra, Ivan Adzhubei, Jason A. Greenbaum, Robert M. Andrews, Paul Flicek, Patrick J. Boyle, Hua Cao, Nigel P. Carter, Gayle K. Clelland, Sean Davis, Nathan Day, Pawandeep Dhami, Shane C. Dillon, Michael O. Dorschner, Heike Fiegler, Paul G. Giresi, Jeff Goldy, Michael Hawrylycz, Andrew Haydock, Richard Humbert, Keith D. James, Brett E. Johnson, Ericka M. Johnson, Tristan T. Frum, Elizabeth R. Rosenzweig, Neerja Karnani, Kirsten Lee, Gregory C. Lefebvre, Patrick A. Navas, Fidencio Neri, Stephen C. J. Parker, Peter J. Sabo, Richard Sandstrom, Anthony Shafer, David Vetrie, Molly Weaver, Sarah Wilcox, Man Yu, Francis S. Collins, Job Dekker, Jason D. Lieb, Thomas D. Tullius, Gregory E. Crawford, Shamil Sunyaev, William S. Noble, Ian Dunham, France Denoeud, Alexandre Reymond, Philipp Kapranov, Joel Rozowsky, Deyou Zheng, Robert Castelo, Adam Frankish, Jennifer Harrow, Srinka Ghosh, Albin Sandelin, Ivo L. Hofacker, Robert Baertsch, Damian Keefe, Sujit Dike, Jill Cheng, Heather A. Hirsch, Edward A. Sekinger, Julien Lagarde, Josep F. Abril, Atif Shahab, Christoph Flamm, Claudia Fried, Jörg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Missal, Andrea Tanzer, Stefan Washietl, Jan Korbel, Olof Emanuelsson, Jakob S. Pedersen, Nancy Holroyd, Ruth Taylor, David Swarbreck, Nicholas Matthews, Mark C. Dickson, Daryl J. Thomas, Matthew T. Weirauch, James Gilbert, Jorg Drenkow, Ian Bell, XiaoDong Zhao, K. G. Srinivasan, Wing-Kin Sung, Hong Sain Ooi, Kuo Ping Chiu, Sylvain Foissac, Tyler Alioto, Michael Brent, Lior Pachter, Michael L. Tress, Alfonso Valencia, Siew Woh Choo, Chiou Yu Choo, Catherine Ucla, Caroline Manzano, Carine Wyss, Evelyn Cheung, Taane G. Clark, James B. Brown, Madhavan Ganesh, Sandeep Patel, Hari Tammana, Jacqueline Chrast, Charlotte N. Henrichsen, Chikatoshi Kai, Jun Kawai, Ugrappa Nagalakshmi, Jiaqian Wu, Zheng Lian, Jin Lian, Peter Newburger, Xueqing Zhang, Peter Bickel, John S. Mattick, Piero Carninci, Yoshihide Hayashizaki, Sherman Weissman, Tim Hubbard, Richard M. Myers, Jane Rogers, Peter F. Stadler, Todd M. Lowe, Chia-Lin Wei, Yijun Ruan, Kevin Struhl, Mark Gerstein, Stylianos E. Antonarakis, Yutao Fu, Eric D. Green, Ulaş Karaöz, Adam Siepel, James Taylor, Laura A. Liefer, Kris A. Wetterstrand, Peter J. Good, Elise A. Feingold, Mark S. Guyer, Gregory M. Cooper, George Asimenos, Colin N. Dewey, Minmei Hou, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Löytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, Haiyan Huang, Nancy R. Zhang, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Michael Seringhaus, Deanna Church, Kate Rosenbloom, W. James Kent, Eric A. Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Serafim Batzoglou, Nick Goldman, Ross C. Hardison, David Haussler, Webb Miller, Arend Sidow, Nathan D. Trinklein, Zhengdong D. Zhang, Leah Barrera, Rhona Stuart, David C. King, Adam Ameur, Stefan Enroth, Mark C. Bieda, Jonghwan Kim, Akshay A. Bhinge, Nan Jiang, Jun Liu, Fei Yao, Vinsensius B. Vega, Charlie W. H. Lee, Patrick Ng, Atif Shahab, Annie Yang, Zarmik Moqtaderi, Zhou Zhu, Xiaoqin Xu, Sharon Squazzo, Matthew J. Oberley, David Inman, Michael A. Singer, Todd A. Richmond, Kyle J. Munn, Alvaro Rada-Iglesias, Ola Wallerman, Jan Komorowski, Joanna C. Fowler, Phillippe Couttet, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Cordelia F. Langford, David A. Nix, Ghia Euskirchen, Stephen Hartman, Alexander E. Urban, Peter Kraus, Sara Van Calcar, Nate Heintzman, Tae Hoon Kim, Kun Wang, Chunxu Qu, Gary Hon, Rosa Luna, Christopher K. Glass, M. Geoff Rosenfeld, Shelley Force Aldred, Sara J. Cooper, Anason Halees, Jane M. Lin, Hennady P. Shulha, Xiaoling Zhang, Mousheng Xu, Jaafar N. S. Haidar, Yong Yu, Yijun Ruan, Vishwanath R. Iyer, Roland D. Green, Claes Wadelius, Peggy J. Farnham, Bing Ren, Rachel A. Harte, Angie S. Hinrichs, Heather Trumbower, Hiram Clawson, Jennifer Hillman-Jackson, Ann S. Zweig, Kayla Smith, Archana Thakkapallayil, Galt Barber, Robert M. Kuhn, Donna Karolchik, Lluis Armengol, Christine P. Bird, Paul I. W. de Bakker, Andrew D. Kern, Nuria Lopez-Bigas, Joel D. Martin, Barbara E. Stranger, Abigail Woodroffe, Eugene Davydov, Antigone Dimas, Eduardo Eyras, Ingileif B. Hallgrímsdóttir, Julian Huppert, Michael C. Zody, Gonçalo R. Abecasis, Xavier Estivill, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. B. 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, Maxim Koriabine, Mikhail Nefedov, Kazutoyo Osoegawa, Yuko Yoshinaga, Baoli Zhu, Pieter J. de Jong. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007-06-14, 447 (7146): 799–816 [2019-02-12]. ISSN 1476-4687. PMC 2212820 . PMID 17571346. doi:10.1038/nature05874. （原始内容存档于2019-06-19）.
[5]
Roderic Guigó, Paul Flicek, Josep F. Abril, 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. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology. 2006,. 7 Suppl 1: S2.1–31 [2019-02-12]. ISSN 1474-760X. doi:10.1186/gb-2006-7-s1-s2. （原始内容存档于2016-04-01）.
[6]
Genome.gov | ENCODE and modENCODE Projects. The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01 [2011-08-05]. （原始内容存档于2011-08-07）.
[7]
National Human Genome Research Institute - Organization. The NIH Almanac. United States National Institutes of Health. [2011-08-05]. （原始内容存档于2015-10-04）.
[8]
Genome.gov | ENCODE Participants and Projects. The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01 [2011-08-05]. （原始内容存档于2011-08-07）.
[9]
ENCODE project at UCSC. ENCODE Consortium. [2012-09-05]. （原始内容存档于2012-09-10）.
[10]
Walsh, Fergus. Detailed map of genome function. BBC News. 2012-09-05 [2012-09-06]. （原始内容存档于2012-09-06）.

官方网站 - ENCODE Project at UCSC
ENCODE project（页面存档备份，存于互联网档案馆） at the National Human Genome Research Institute
ENCODE/GENCODE project（页面存档备份，存于互联网档案馆） at the Wellcome Trust Sanger Institute
ENCODE-sponsored introductory tutorial
FactorBook（页面存档备份，存于互联网档案馆）
ENCODE threads Explorer（页面存档备份，存于互联网档案馆） at the Nature (journal)

[Raney2011-1] [1]
Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent, WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. January 2011, 39 (Database issue): D871–5. PMC 3013645 . PMID 21037257. doi:10.1093/nar/gkq1017.

[2] [2]
Maher B. ENCODE: The human encyclopaedia. Nature. 2012, 489 (7414): 46–48. doi:10.1038/489046a.

[3] [3]
The ENCODE Project Consortium. A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLOS Biology. 2011-04-19, 9 (4): e1001046 [2018-04-02]. ISSN 1545-7885. doi:10.1371/journal.pbio.1001046. （原始内容存档于2018-03-28）（英语）.

[birney-4] [4]
ENCODE Project Consortium, Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R. Gingeras, Elliott H. Margulies, Zhiping Weng, Michael Snyder, Emmanouil T. Dermitzakis, Robert E. Thurman, Michael S. Kuehn, Christopher M. Taylor, Shane Neph, Christoph M. Koch, Saurabh Asthana, Ankit Malhotra, Ivan Adzhubei, Jason A. Greenbaum, Robert M. Andrews, Paul Flicek, Patrick J. Boyle, Hua Cao, Nigel P. Carter, Gayle K. Clelland, Sean Davis, Nathan Day, Pawandeep Dhami, Shane C. Dillon, Michael O. Dorschner, Heike Fiegler, Paul G. Giresi, Jeff Goldy, Michael Hawrylycz, Andrew Haydock, Richard Humbert, Keith D. James, Brett E. Johnson, Ericka M. Johnson, Tristan T. Frum, Elizabeth R. Rosenzweig, Neerja Karnani, Kirsten Lee, Gregory C. Lefebvre, Patrick A. Navas, Fidencio Neri, Stephen C. J. Parker, Peter J. Sabo, Richard Sandstrom, Anthony Shafer, David Vetrie, Molly Weaver, Sarah Wilcox, Man Yu, Francis S. Collins, Job Dekker, Jason D. Lieb, Thomas D. Tullius, Gregory E. Crawford, Shamil Sunyaev, William S. Noble, Ian Dunham, France Denoeud, Alexandre Reymond, Philipp Kapranov, Joel Rozowsky, Deyou Zheng, Robert Castelo, Adam Frankish, Jennifer Harrow, Srinka Ghosh, Albin Sandelin, Ivo L. Hofacker, Robert Baertsch, Damian Keefe, Sujit Dike, Jill Cheng, Heather A. Hirsch, Edward A. Sekinger, Julien Lagarde, Josep F. Abril, Atif Shahab, Christoph Flamm, Claudia Fried, Jörg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Missal, Andrea Tanzer, Stefan Washietl, Jan Korbel, Olof Emanuelsson, Jakob S. Pedersen, Nancy Holroyd, Ruth Taylor, David Swarbreck, Nicholas Matthews, Mark C. Dickson, Daryl J. Thomas, Matthew T. Weirauch, James Gilbert, Jorg Drenkow, Ian Bell, XiaoDong Zhao, K. G. Srinivasan, Wing-Kin Sung, Hong Sain Ooi, Kuo Ping Chiu, Sylvain Foissac, Tyler Alioto, Michael Brent, Lior Pachter, Michael L. Tress, Alfonso Valencia, Siew Woh Choo, Chiou Yu Choo, Catherine Ucla, Caroline Manzano, Carine Wyss, Evelyn Cheung, Taane G. Clark, James B. Brown, Madhavan Ganesh, Sandeep Patel, Hari Tammana, Jacqueline Chrast, Charlotte N. Henrichsen, Chikatoshi Kai, Jun Kawai, Ugrappa Nagalakshmi, Jiaqian Wu, Zheng Lian, Jin Lian, Peter Newburger, Xueqing Zhang, Peter Bickel, John S. Mattick, Piero Carninci, Yoshihide Hayashizaki, Sherman Weissman, Tim Hubbard, Richard M. Myers, Jane Rogers, Peter F. Stadler, Todd M. Lowe, Chia-Lin Wei, Yijun Ruan, Kevin Struhl, Mark Gerstein, Stylianos E. Antonarakis, Yutao Fu, Eric D. Green, Ulaş Karaöz, Adam Siepel, James Taylor, Laura A. Liefer, Kris A. Wetterstrand, Peter J. Good, Elise A. Feingold, Mark S. Guyer, Gregory M. Cooper, George Asimenos, Colin N. Dewey, Minmei Hou, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Löytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, Haiyan Huang, Nancy R. Zhang, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Michael Seringhaus, Deanna Church, Kate Rosenbloom, W. James Kent, Eric A. Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Serafim Batzoglou, Nick Goldman, Ross C. Hardison, David Haussler, Webb Miller, Arend Sidow, Nathan D. Trinklein, Zhengdong D. Zhang, Leah Barrera, Rhona Stuart, David C. King, Adam Ameur, Stefan Enroth, Mark C. Bieda, Jonghwan Kim, Akshay A. Bhinge, Nan Jiang, Jun Liu, Fei Yao, Vinsensius B. Vega, Charlie W. H. Lee, Patrick Ng, Atif Shahab, Annie Yang, Zarmik Moqtaderi, Zhou Zhu, Xiaoqin Xu, Sharon Squazzo, Matthew J. Oberley, David Inman, Michael A. Singer, Todd A. Richmond, Kyle J. Munn, Alvaro Rada-Iglesias, Ola Wallerman, Jan Komorowski, Joanna C. Fowler, Phillippe Couttet, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Cordelia F. Langford, David A. Nix, Ghia Euskirchen, Stephen Hartman, Alexander E. Urban, Peter Kraus, Sara Van Calcar, Nate Heintzman, Tae Hoon Kim, Kun Wang, Chunxu Qu, Gary Hon, Rosa Luna, Christopher K. Glass, M. Geoff Rosenfeld, Shelley Force Aldred, Sara J. Cooper, Anason Halees, Jane M. Lin, Hennady P. Shulha, Xiaoling Zhang, Mousheng Xu, Jaafar N. S. Haidar, Yong Yu, Yijun Ruan, Vishwanath R. Iyer, Roland D. Green, Claes Wadelius, Peggy J. Farnham, Bing Ren, Rachel A. Harte, Angie S. Hinrichs, Heather Trumbower, Hiram Clawson, Jennifer Hillman-Jackson, Ann S. Zweig, Kayla Smith, Archana Thakkapallayil, Galt Barber, Robert M. Kuhn, Donna Karolchik, Lluis Armengol, Christine P. Bird, Paul I. W. de Bakker, Andrew D. Kern, Nuria Lopez-Bigas, Joel D. Martin, Barbara E. Stranger, Abigail Woodroffe, Eugene Davydov, Antigone Dimas, Eduardo Eyras, Ingileif B. Hallgrímsdóttir, Julian Huppert, Michael C. Zody, Gonçalo R. Abecasis, Xavier Estivill, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. B. 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, Maxim Koriabine, Mikhail Nefedov, Kazutoyo Osoegawa, Yuko Yoshinaga, Baoli Zhu, Pieter J. de Jong. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007-06-14, 447 (7146): 799–816 [2019-02-12]. ISSN 1476-4687. PMC 2212820 . PMID 17571346. doi:10.1038/nature05874. （原始内容存档于2019-06-19）.

[5] [5]
Roderic Guigó, Paul Flicek, Josep F. Abril, 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. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology. 2006,. 7 Suppl 1: S2.1–31 [2019-02-12]. ISSN 1474-760X. doi:10.1186/gb-2006-7-s1-s2. （原始内容存档于2016-04-01）.

[urlGenome.gov_|_ENCODE_and_modENCODE_Projects-6] [6]
Genome.gov | ENCODE and modENCODE Projects. The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01 [2011-08-05]. （原始内容存档于2011-08-07）.

[NIHalmanac-7] [7]
National Human Genome Research Institute - Organization. The NIH Almanac. United States National Institutes of Health. [2011-08-05]. （原始内容存档于2015-10-04）.

[urlGenome.gov_|_ENCODE_Participants_and_Projects-8] [8]
Genome.gov | ENCODE Participants and Projects. The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01 [2011-08-05]. （原始内容存档于2011-08-07）.

[9] [9]
ENCODE project at UCSC. ENCODE Consortium. [2012-09-05]. （原始内容存档于2012-09-10）.

[10] [10]
Walsh, Fergus. Detailed map of genome function. BBC News. 2012-09-05 [2012-09-06]. （原始内容存档于2012-09-06）.

[2]

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[3]

[4]

[5]

[6]

[7]

[8]

[9]

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ENCODE

ENCODE一期项目：试验项目

ENCODE二期项目：生产阶段项目

生产阶段结果

Wikiwand in your browser!

ENCODE

ENCODE一期项目：试验项目

ENCODE二期项目：生产阶段项目

生产阶段结果

Wikiwand in your browser!

ENCOD项目

参见

参考文献

外部链接