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Publisher Correction: A genomic catalog of Earth’s microbiomes
Stephen Nayfach, Simon Roux, R. Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Páez-Espino, I-Min A. Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, José P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood‐Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Helena Abreu, Silvia G. Acinas, Eric Allen, Michelle A. Allen, Gary L. Andersen, Alexandre M. B. Anesio, Graeme T. Attwood, Viridiana Avila‐Magaña, Yacine Badis, Jake V. Bailey, Brett J. Baker, Petr Baldrián, Hazel A. Barton, David A. C. Beck, Eric D. Becraft, Harry R. Beller, J. Michael Beman, Rizlan Bernier‐Latmani, Timothy D. Berry, Anthony D. Bertagnolli, Stefan Bertilsson, Jennifer Bhatnagar, Jordan T. Bird, Sara E. Blumer‐Schuette, Brendan J. M. Bohannan, Mikayla A. Borton, Allyson Brady, Susan H. Brawley, Juliet Brodie, Steven D. Brown, Jennifer R. Brum, Andreas Brune, Donald A. Bryant, Alison Buchan, Daniel H. Buckley, Joy Buongiorno, Hinsby Cadillo‐Quiroz, Sean M. Caffrey, Ashley Campbell, Barbara J. Campbell, Stephanie Carr, JoLynn Carroll, S. Craig Cary, Anna M. Cates, Rose Ann Cattolico, Ricardo Cavicchioli, Ludmila Chistoserdova, Maureen L. Coleman, Philippe Constant, Jonathan M. Conway, Walter P. Mac Cormack, Sean A. Crowe, Byron C. Crump, Cameron R. Currie, Rebecca Daly, Vincent J. Denef, Stuart E. Denman, Adey Feleke Desta, Hebe M. Dionisi, Jeremy A. Dodsworth, Nina Dombrowski, Timothy J. Donohue, Mark Dopson, Timothy Driscoll, Peter F. Dunfield, Christopher L. Dupont, Katherine A. Dynarski, Virginia P. Edgcomb, Elizabeth A. Edwards, Mostafa S. Elshahed, Israel Figueroa, Beverly E. Flood, Nathaniel W. Fortney, Caroline S. Fortunato, Christopher Francis, Claire M. M. Gachon, Sarahi L. Garcia, María Consuelo Gazitúa, Terry J. Gentry, Lena Gerwick, Javad Gharechahi, Peter Girguis, John M. Gladden, Mary R. Gradoville, Stephen E. Grasby, Kelly Gravuer, Christen L. Grettenberger, Robert J. Gruninger, Jiarong Guo, Mussie Y. Habteselassie, Steven Hallam, Roland Hatzenpichler, Bela Hausmann, Terry C. Hazen, Brian P. Hedlund, Cynthia Henny, Lydie Herfort, Maria Hernandez, Olivia S. Hershey, Matthias Hess, Emily B. Hollister, Laura Hug, Dana E. Hunt, Janet Jansson, Jessica Jarett, Vitaly V. Kadnikov, Charlene N. Kelly, Robert M. Kelly, William J. Kelly, Cheryl A. Kerfeld, Jeffrey A. Kimbrel, Jonathan L. Klassen, Konstantinos T. Konstantinidis, Laura L. Lee, Wen‐Jun Li, Andrew J. Loder, Alexander Loy, Mariana Lozada, Barbara J. MacGregor, Cara Magnabosco, Aline Maria da Silva, R. Michael L. McKay, Katherine D. McMahon, Christopher S. McSweeney, Mónica Medina, Laura Meredith, Jessica E. Mizzi, Thomas Möck, Lily Momper, Mary Ann Moran, Connor Morgan‐Lang, Duane P. Moser, Gerard Muyzer, David D. Myrold, Maisie Nash, Camilla Nesbø, Anthony P. Neumann, Rebecca B. Neumann, Daniel R. Noguera, Trent R. Northen, Jeanette M. Norton, Brent Nowinski, Klaus Nüsslein, Michelle O’Malley, Rafael S. Oliveira, Valéria Maia de Oliveira, T. C. Onstott, Jay Osvatic, Yang Ouyang, Maria Pachiadaki, Jacob Parnell, Laila P. Partida‐Martínez, Kabir Peay, Dale A. Pelletier, Xuefeng Peng, Michael Pester, Jennifer Pett‐Ridge, Sari Peura, Petra Pjevac, Alvaro M. Plominsky, Anja Poehlein, Phillip B. Pope, Nikolai V. Ravin, Molly C. Redmond, Rebecca A. Reiss, Virginia I. Rich, Christian Rinke, Jorge L. Mazza Rodrigues, Karen Rossmassler, Joshua Sackett, Ghasem Hosseini Salekdeh, S. R. Saleska, Matthew Scarborough, Daniel P. Schachtman, Christopher W. Schadt, Matthew Schrenk, Alexander Sczyrba, Aditi Sengupta, João Carlos Setúbal, Ashley Shade, Christine Sharp, David H. Sherman, О. V. Shubenkova, Isabel Natalia Sierra-Garcia, Rachel L. Simister, Holly M. Simon, Sara Sjöling, Joan L. Slonczewski, Rafael Soares Correa de Souza, John R. Spear, James Stegen, Ramūnas Stepanauskas, Frank J. Stewart, Garret Suen, Matthew B. Sullivan, D. Y. Sumner, Brandon K. Swan, Wesley D. Swingley, Jonathan Tarn, Gordon T. Taylor, Hanno Teeling, Memory Tekere, Andreas Teske, Torsten Thomas, Cameron Thrash, James M. Tiedje, Claire S. Ting, Benjamin Tully, Gene W. Tyson, David L. Valentine, Marc W. Van Goethem, Jean S. VanderGheynst, Tobin J. Verbeke, John Vollmers, Aurèle Vuillemin, Nicholas B. Waldo, David A. Walsh, Bart C. Weimer, Thea Whitman, Paul W. J. J. van der Wielen, Michael J. Wilkins, Timothy J. Williams, Ben J. Woodcroft, Jamie Woolet, Kelly Wrighton, Jun Ye, Erica B. Young, Noha H. Youssef, Feiqiao Brian Yu, Т. I. Zemskaya, Ryan Ziels, Tanja Woyke, Nigel J. Mouncey, Natalia Ivanova, Nikos C. Kyrpides, Emiley A. Eloe‐Fadrosh
Bibliographic record
VenueNature Biotechnology · 2020
Typearticle
Languageen
FieldEnvironmental Science
TopicMicrobial Community Ecology and Physiology
Canadian institutionsConcordia UniversityUniversity of WindsorUniversity of WaterlooGeological Survey of CanadaNatural Resources CanadaUniversity of CalgaryAgriculture and Agri-Food CanadaUniversity of British ColumbiaInstitut National de la Recherche ScientifiqueUniversity of TorontoMcMaster University
FundersLawrence Livermore National LaboratoryMikrobiologický Ústav, Akademie Věd České RepublikyAgriculture and Agri-Food CanadaSandia National LaboratoriesGreat Lakes Bioenergy Research CenterNatural Resources CanadaSchool of Life Sciences, Arizona State UniversityStockholms UniversitetCollege of Engineering, Michigan State UniversityAddis Ababa UniversityNorth Carolina State UniversityUniversity of WashingtonLinnéuniversitetetUniversidad de Buenos AiresOffice of ScienceMax-Planck-Institut für Terrestrische MikrobiologieAkademie Věd České RepublikyUniversität WienGeorgia Institute of TechnologyConsejo Nacional de Investigaciones Científicas y TécnicasBaqiyatallah University of Medical SciencesUniversity of TorontoUniversity of New South WalesDirectorate for Biological SciencesJoint Genome InstituteUniversity of OregonUniversity of WaikatoOregon State UniversityMontana State UniversityKoninklijk Nederlands Instituut voor Onderzoek der ZeeWest Virginia UniversityUniversity of California, San DiegoUniversity of MontanaUniversity of Arkansas for Medical SciencesPennsylvania State UniversityMichigan State UniversityMcMaster UniversityUniversity of California, DavisUniversity of AkronHarvard UniversityScience for Life LaboratoryUniversiteit UtrechtUniversity of MinnesotaOklahoma State UniversityAgResearchArizona State UniversityDivision of Ocean SciencesUniversity of Wisconsin-MadisonU.S. Department of EnergySveriges LantbruksuniversitetLembaga Ilmu Pengetahuan IndonesiaAarhus UniversitetOhio State UniversityClemson UniversityLouisiana State UniversityColorado State University
KeywordsMicrobiomeComputational biologyEarth (classical element)BiologyWorld Wide WebData scienceComputer scienceGeneticsAstronomy
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesInsufficient payload (model declined to judge)
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.640
Threshold uncertainty score0.998
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 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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 head0.006
GPT teacher head0.198
Teacher spread0.193 · 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; a candidate call from one teacher head, not a consensus.
Study designNot applicable
Domainnot available
GenreEmpirical
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
Citations26
Published2020
Admission routes2
Has abstractyes