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Record W3141635963 · doi:10.1186/s13059-021-02320-3

Response to correspondence on “Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation”

2021· letter· en· W3141635963 on OpenAlexaff
Channabasavaiah B. Gurumurthy, Aidan R. O’Brien, Rolen M. Quadros, John H. Adams, Pilar Alcaide, Shinya Ayabe, Johnathan Ballard, Surinder K. Batra, Marie‐Claude Beauchamp, Kathleen A. Becker, Guillaume Bernas, David Brough, Francisco J. Carrillo‐Salinas, Wesley Chan, Hanying Chen, Ruby Dawson, Victoria DeMambro, Jinke D’Hont, Katharine M. Dibb, James D. Eudy, Lin Gan, Jing Gao, Amy Gonzales, Anyonya R. Guntur, Huiping Guo, Donald W. Harms, Anne Harrington, Kathryn E. Hentges, Neil Humphreys, Shiho Imai, Hideshi Ishii, Mizuho Iwama, Eric Jonasch, Michelle Karolak, Bernard Keavney, Nay-Chi Khin, Masamitsu Konno, Yuko Kotani, Yayoi Kunihiro, Imayavaramban Lakshmanan, Catherine Larochelle, Catherine B. Lawrence, Lin Li, Volkhard Lindner, Xian-De Liu, Gloria López‐Castejón, Andrew Loudon, Jenna Lowe, Loydie Jerome-Majeweska, Taiji Matsusaka, Hiromi Miura, Yoshiki Miyasaka, Benjamin Morpurgo, Katherine J. Motyl, Yo-ichi Nabeshima, Koji Nakade, Toshiaki Nakashiba, Ken‐ichi Nakashima, Yuichi Obata, Sanae Ogiwara, Mariette Ouellet, Leif Oxburgh, Sandra Piltz, Ilka Pinz, Moorthy P. Ponnusamy, David Ray, Ronald Redder, Clifford J. Rosen, Nikki Ross, Mark Ruhe, Larisa Ryzhova, Ane Salvador, Sabrina Alam, Radislav Sedláček, Karan Sharma, Chad Smith, Katrien Staes, Lora Starrs, Fumihiro Sugiyama, Satoru Takahashi, Tomohiro Tanaka, Andrew W. Trafford, Yoshihiro Uno, Leen Vanhoutte, Frederique Vanrockeghem, Brandon Willis, Christian S. Wright, Yuko Yamauchi, Xin Yi, Kazuto Yoshimi, Xuesong Zhang, Yingxin Zhang, Masato Ohtsuka, Satyabrata Das, Daniel J. Garry, Tino Hochepied, Paul Q. Thomas, Jan Parker‐Thornburg, Antony Adamson, Atsushi Yoshiki, Jean-Francois Schmouth, Andrei Golovko, William R. Thompson, K. C. Kent Lloyd, Joshua A. Wood, Mitra Cowan, Tomoji Mashimo, Seiya Mizuno, Hao Zhu, Petr Kašpárek, Lucy Liaw, Joseph M. Miano, Gaétan Burgio

Bibliographic record

VenueGenome biology · 2021
Typeletter
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicCRISPR and Genetic Engineering
Canadian institutionsMcGill UniversityCentre Hospitalier de l’Université de MontréalMcGill University Health Centre
FundersSchool of Medicine, Tokai UniversitySchool of Medicine, Indiana UniversityUniversity of Texas MD Anderson Cancer CenterWellcome TrustManchester Collaborative Centre for Inflammation ResearchUniversiteit GentUniversity of ManchesterBritish Heart FoundationUniversity of RochesterDirectorate for Biological SciencesMedical Research CouncilChildren’s Hospital of Wisconsin Research InstituteMedical Center, University of RochesterUniversity of Nebraska Medical Center
KeywordsBiologyCRISPRHuman geneticsGeneticsAlleleComputational biologyCas9ReproducibilityGeneStatistics

Abstract

fetched live from OpenAlex
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.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.009
metaresearch head score (Gemma)0.029
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesMetaresearch
Consensus categoriesnone
DomainCandidate signal: Reproducibility · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Commentary · Consensus signal: Commentary
Teacher disagreement score0.991
Threshold uncertainty score0.058

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0090.029
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0020.002
Bibliometrics0.0010.001
Science and technology studies0.0060.003
Scholarly communication0.0050.002
Open science0.0020.002
Research integrity0.0450.042
Insufficient payload (model declined to judge)0.0060.007

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 head0.090
GPT teacher head0.452
Teacher spread0.361 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designNot applicable
DomainReproducibility
GenreCommentary

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

Citations15
Published2021
Admission routes1
Has abstractno

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