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Perspectives on ENCODE
Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal, Bronwen Aken, Rizi Ai, Jennifer A. Akiyama, Omar Al Jammal, Henry Amrhein, Stacie M. Anderson, Gregory R. Andrews, Igor Antoshechkin, Kristin Ardlie, Joel Armstrong, Matthew Astley, Budhaditya Banerjee, Amira Barkal, If H. A. Barnes, Iros Barozzi, Daniel Barrell, Gemma Barson, Daniel J. Bates, Ulugbek K. Baymuradov, Cassandra Bazile, M Beer, Samantha Beik, M. A. Bender, Ruth Bennett, Louis Philip Benoit Bouvrette, B Bernstein, Andrew Berry, Anand Bhaskar, Alexandra Bignell, Steven M. Blue, David M. Bodine, Carles A. Boix, Nathan Boley, Tyler Borrman, Beatrice Borsari, Alan P. Boyle, Laurel A. Brandsmeier, Alessandra Breschi, Emery H. Bresnick, Jason A. Brooks, Michael Buckley, Christopher B. Burge, Rachel Byron, Eileen Cahill, Lingling Cai, Lulu Cao, Mark Carty, Rosa Castanon, Andrés Castillo, Hassan Chaı̈b, Esther T. Chan, Daniel R. Chee, Sora Chee, Hao Chen, Huaming Chen, Jiayu Chen, Songjie Chen, J. Michael Cherry, Surya B. Chhetri, Jyoti S. Choudhary, Jacqueline Chrast, Dongjun Chung, Declan Clarke, Neal Cody, Candice J. Coppola, Julie Coursen, Anthony D’Ippolito, Stephen Dalton, Cassidy Danyko, Claire Davidson, José Dávila-Velderrain, Carrie Davis, Job Dekker, Alden Deran, Gilberto DeSalvo, Gloria Despacio-Reyes, Colin N. Dewey, Diane E. Dickel, Morgan Diegel, Mark Diekhans, Vishnu Dileep, Bo Ding, Sarah Djebali, Alexander Dobin, Daniel Domı́nguez, Sarah Donaldson, Jörg Drenkow, Timothy R. Dreszer, Yotam Drier, Michael O. Duff, Douglass Dunn, Catharine Eastman, Joseph R. Ecker, Matthew D. Edwards, Nicole El-Ali, Shaimae I. Elhajjajy, Keri Elkins, Andrew Emili, Charles B. Epstein, Rachel C. Evans, Iakes Ezkurdia, Kaili Fan, Peggy Farnham, Nina Farrell, Elise A. Feingold, Anne-Maud Ferreira, Katherine Fisher-Aylor, Stephen Fitzgerald, Paul Flicek, Chuan-Sheng Foo, Kevin Fortier, Adam Frankish, Peter Freese, Shaliu Fu, Xiang‐Dong Fu, Yu Fu, Y. Fukuda, Mariateresa Fulciniti, Alister P. W. Funnell, Idan Gabdank, Timur R. Galeev, Mingshi Gao, Carlos García Girón, Tyler H. Garvin, Chelsea Gelboin-Burkhart, Grigorios Georgolopoulos, Mark Gerstein, Belinda Giardine, David K. Gifford, David M. Gilbert, Daniel A. Gilchrist, Shawn Gillespie, T Gingeras, Peng Gong, Álvaro González, José M. González, Peter J. Good, Alon Goren, David U. Gorkin, Brenton R. Graveley, Michael Gray, Jack Greenblatt, Ed Griffiths, Mark Groudine, Fabian Grubert, Mengting Gu, Roderic Guigó, Hongbo Guo, Yuming Guo, Yuchun Guo, Gamze Gürsoy, María Gutiérrez‐Arcelus, Jessica Halow, Ross C. Hardison, Matthew P. Hardy, Manoj Hariharan, Arif Harmanci, Anne Harrington, Jennifer Harrow, Tatsunori Hashimoto, Richard Hasz, Meital Hatan, Eric Haugen, James E. Hayes, Peng He, Yupeng He, Nastaran Heidari, David G. Hendrickson, Elisabeth F. Heuston, Jason A. Hilton, Benjamin C. Hitz, Abigail Hochman, Cory Holgren, Lei Hou, Shuyu Hou, Yun-Hua Esther Hsiao, Shanna Hsu, Hui Huang, Tim Hubbard, Jack Huey, Timothy R. Hughes, Toby Hunt, Sean Ibarrientos, Robbyn Issner, Mineo Iwata, Osagie Izuogu, Tommi Jaakkola, Nader Jameel, Camden Jansen, Lixia Jiang, Peng Jiang, Audra Johnson, Rory Johnson, Irwin Jungreis, Madhura Kadaba, Maya Kasowski, Mary Kasparian, Momoe Kato, Rajinder Kaul, Trupti Kawli, Mike Kay, Judith C. Keen, Sündüz Keleş, Cheryl A. Keller, David R. Kelley, Manolis Kellis, Pouya Kheradpour, Daniel Sunwook Kim, Anthony Kirilusha, Robert J. Klein, Birgit Knoechel, Samantha Kuan, Michael Kulik, Sushant Kumar, Anshul Kundaje, Tanya Kutyavin, Julien Lagarde, Bryan R. Lajoie, Nicole Lambert, John Lazar, Ah Young Lee, Donghoon Lee, Elizabeth Lee, Jin Wook Lee, Kristen Lee, Christina S. Leslie, Shawn Levy, Bin Li, Hairi Li, Nan Li, Shantao Li, Xiangrui Li, Yang Li, Ying Li, Yining Li, Yue Li, Maxwell W. Libbrecht, Shin Lin, Yiing Lin, Dianbo Liu, Jason Liu, Peng Liu, Tingting Liu, X. Shirley Liu, Yan Liu, Yaping Liu, Maria Long, Shaoke Lou, Jane Loveland, Aiping Lü, Yuheng Lu, Éric Lécuyer, Lijia Ma, Mark Mackiewicz, Brandon J. Mannion, Michael Mannstadt, Deepa Manthravadi, Georgi K. Marinov, Fergal J. Martin, Eugenio Mattei, Kenneth McCue, Megan McEown, Graham McVicker, Sarah K. Meadows, Alex Meissner, Eric M. Mendenhall, C. Luke Messer, Wouter Meuleman, Clifford A. Meyer, Steve Miller, Matthew G. Milton, Tejaswini Mishra, Dianna E. Moore, Helen M. Moore, Jill E. Moore, Samuel H. Moore, Jennifer Moran, A Mortazavi, Jonathan M. Mudge, Nikhil Munshi, Rabi Murad, R Myers, Vivek Nandakumar, Preetha Nandi, Anil Narasimha, Aditi K. Narayanan, Hannah Naughton, Fábio C. P. Navarro, Patrick A. Navas, Jurijs Nazarovs, Jemma Nelson, Shane Neph, Fidencio Neri, Joseph R. Nery, Amy R. Nesmith, J. Scott Newberry, Kimberly M. Newberry, Vu N. Ngo, Rosy Nguyen, Thai B. Nguyen, Tung Nguyen, Andrew Nishida, William Stafford Noble, Catherine S. Novak, Eva Maria Novoa, Briana Nuñez, Sara Olson, Ericka Otterman, Hakan Özadam, Michael Pagan, Tsultrim Palden, Xinghua Pan, Yongjin Park, E. Christopher Partridge, Benedict Paten, Florencia Pauli, Michael J. Pazin, Baikang Pei, L Pennacchio, Emily Perry, Dmitri D. Pervouchine, Nishigandha Phalke, Quan Pham, Doug Phanstiel, Ingrid Plajzer-Frick, Henry Pratt, Sebastian Preißl, Jonathan K. Pritchard, Yuri Pritykin, Michael Purcaro, Qian Qin, Giovanni Quinones-Valdez, Ines Rabano, Ernest Radovani, Anil Raj, Nisha Rajagopal, Oren Ram, Lucı́a Ramı́rez, Ricardo N. Ramírez, Dylan M. Rausch, Soumya Raychaudhuri, Joseph J. Raymond, Rozita Razavi, Timothy E. Reddy, Thomas Reimonn, Bing Ren, Alexandre Reymond, Alex Reynolds, Suhn K. Rhie, John L. Rinn, Miguel N. Rivera, Juan Carlos Rivera‐Mulia, Brian S. Roberts, José Manuel Rodrı́guez, Joel Rozowsky, Russell J.H. Ryan, Eric Rynes, Denis Salins, Richard Sandstrom, Takayo Sasaki, Shashank Sathe, Daniel Savic, Alexandra Scavelli, Jonathan Scheiman, Christoph N. Schlaffner, Jeffery A. Schloss, Frank W. Schmitges, Lei Hoon See, Anurag Sethi, Manu Setty, Anthony Shafer, Shuo Shan, Eilon Sharon, Quan Shen, Yin Shen, Richard I. Sherwood, Minyi Shi, Sunyoung Shin, Noam Shoresh, Kyle Siebenthall, Cristina Sisu, Teri R. Slifer, Cricket A. Sloan, Anna M. Smith, Valentina Snetkova, M Snyder, Damek V. Spacek, Sharanya Srinivasan, Rohith Srivas, George Stamatoyannopoulos, J Stamatoyannopoulos, Rebecca Stanton, Dave Steffan, Sandra Stehling-Sun, J. Seth Strattan, Amanda Su, Balaji Sundararaman, Marie‐Marthe Suner, Tahin Syed, Matt Szynkarek, Forrest Y. Tanaka, Danielle Tenen, Mingxiang Teng, Jeffrey A. Thomas, Dave Toffey, Michael L. Tress, Diane Trout, Gosia Trynka, Junko Tsuji, Sean A. Upchurch, Oana Ursu, Barbara Uszczyńska-Ratajczak, Mia C. Uziel, Alfonso Valencia, Benjamin Van Biber, Arjan G. van der Velde, Eric L. Van Nostrand, Yekaterina Vaydylevich, Jesús Vázquez, Alec Victorsen, Jost Vielmetter, Jeff Vierstra, Axel Visel, Anna Vlasova, Christopher M. Vockley, Simona Volpi, Shinny Vong, Hao Wang, Mengchi Wang, Qin Wang, Ruth Wang, Tao Wang, Wei Wang, Xiaofeng Wang, Yanli Wang, Nathaniel Watson, Xintao Wei, Zhijie Wei, Hendrik Weisser, Sherman M. Weissman, Rene Welch, Robert E. Welikson, Zhiping Weng, Harm-Jan Westra, John W. Whitaker, Collin C. White, Kevin P. White, André Wildberg, Brian A. Williams, David Wine, Heather Witt, B Wold, Maxim Y. Wolf, James C. Wright, Rui Xiao, Xinshu Xiao, Jie Xu, Jinrui Xu, Koon‐Kiu Yan, Yongqi Yan, Hongbo Yang, Xinqiong Yang, Yiwen Yang, Galip Gürkan Yardımcı, Brian A. Yee, G Yeo, Taylor Young, Tianxiong Yu, Feng Yue, Chris Zaleski, Chongzhi Zang, Haoyang Zeng, Weihua Zeng, Daniel R. Zerbino, Jie Zhai, Lijun Zhan, Ye Zhan, Bo Zhang, Jialing Zhang, Jing Zhang, Kai Zhang, Lijun Zhang, Peng Zhang, Qi Zhang, Xiao‐Ou Zhang, Zhizhuo Zhang, Yuan Zhao, Ye Zheng, Guoqing Zhong, Xiaoqiao Zhou, Yun Zhu, Jared Zimmerman
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.
Bibliographic record
VenueNature · 2020
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenomics and Chromatin Dynamics
Canadian institutionsUniversity of TorontoMcGill UniversitySimon Fraser UniversityUniversité de MontréalMontreal Clinical Research Institute
FundersNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institute of General Medical SciencesNational Institutes of HealthNational Cancer InstituteNational Human Genome Research InstituteBiotechnology and Biological Sciences Research Council
KeywordsENCODEHuman genomeGeneBiologyGenomeChromatinComputational biologyGeneticsTranscription factorHistoneEvolutionary biology
Abstract
No abstract in any covered source. Its absence is recorded, not treated as a negative.
No abstract. This is not a gap in this database; OpenAlex has none either. 23.3% of the frame is in this state, and the screen finds HALF as much metaresearch here, so the absence is a measured bias rather than a missing field.
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.677
Threshold uncertainty score0.326
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.004
GPT teacher head0.224
Teacher spread0.220 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itQuick stats
Citations227
Published2020
Admission routes1
Has abstractno