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Author Correction: Perspectives on ENCODE
Federi Bronwen co 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 Andrews, Igor Antoshechkin, Kristin Ardlie, Joel Armstrong, Matthew Astley, Budhaditya Banerjee, Amira Barkal, If H. A. Barnes, Iros Barozzi, Daniel Barrell, Gemma Barson, Daniel 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 del 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 Domínguez, 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, Y. 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 N. 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, Dong-Hoon Lee, Elizabeth Lee, Jin Wook Lee, Kristen Lee, Christina S. Leslie, Shawn Levy, Bin Li, Hairi Li, Nan Li, Shantao Li, Xiang-Rui 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 Lu, 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 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, Lucia Ramirez, 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 M Calama Rodríguez, 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 Slifer, Cricket A. Sloan, Anna L. 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, 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, Zheng Ye, Guoqing Zhong, Xiaoqiao Zhou, Yun Zhu, Jared Zimmerman
Bibliographic record
VenueNature · 2022
Typeerratum
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenetics, Bioinformatics, and Biomedical Research
Canadian institutionsUniversity of TorontoMcGill UniversitySimon Fraser UniversityUniversité de MontréalMontreal Clinical Research Institute
FundersNational Cancer InstituteNational Human Genome Research Institute
KeywordsENCODEComputational biologyComputer scienceBiologyGeneticsGene
Abstract
In the original article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
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)0.001
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow), Research integrity, Insufficient payload (model declined to judge)
Consensus categoriesResearch integrity
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Other · Consensus signal: Other
Teacher disagreement score0.258
Threshold uncertainty score1.000
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| 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 | 0.001 | 0.000 |
| Research integrity | 0.005 | 0.008 |
| Insufficient payload (model declined to judge) | 0.001 | 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 head0.011
GPT teacher head0.304
Teacher spread0.293 · 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 itClassification
machine, unvalidatedMachine predicted; both teacher heads agree on what is shown here.
Study designNot applicable
Domainnot available
GenreOther
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".
Quick stats
Citations0
Published2022
Admission routes1
Has abstractyes