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Record W4376118380 · doi:10.1038/s41587-023-01793-w

Pangenome graph construction from genome alignments with Minigraph-Cactus

2023· article· en· W4376118380 on OpenAlexaff
Glenn Hickey, Jean Monlong, Jana Ebler, Adam M. Novak, Jordan M. Eizenga, Yan Gao, Haley Abel, Lucinda Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark Chaisson, Pi-Chuan Chang, Xian Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert Cook‐Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Evan E. Eichler, Susan Fairley, Olivier Fédrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos García Girón, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira M. Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Wen‐Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian Lucas, Hugo Magalhães, Santiago Marco‐Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann M. Mc Cartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubskỳ, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valérie Schneider, Baergen I. Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad Abou Tayoun, Françoise Thibaud‐Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian P. Walenz, Ting Wang, Jonathan Wood, Aleksey V. Zimin, Justin M. Zook, Heng Li, Benedict Paten

Bibliographic record

VenueNature Biotechnology · 2023
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenomics and Phylogenetic Studies
Canadian institutionsMcGill University
FundersNational Human Genome Research InstituteNational Heart, Lung, and Blood InstituteHigh Performance Research Computing, Texas A and M UniversityNational Institutes of HealthHeinrich-Heine-Universität Düsseldorf
KeywordsCactusGenomeBiologyGeneticsComputational biologyEvolutionary biologyGeneBotany

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)0.001
metaresearch head score (Gemma)0.002
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Simulation or modeling · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.018
Threshold uncertainty score0.061

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0010.002
Meta-epidemiology (narrow)0.0020.001
Meta-epidemiology (broad)0.0010.001
Bibliometrics0.0030.003
Science and technology studies0.0010.000
Scholarly communication0.0010.001
Open science0.0010.001
Research integrity0.0010.002
Insufficient payload (model declined to judge)0.0180.004

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 head0.207
Teacher spread0.202 · 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.

The models applied no category: nothing in the taxonomy fit this work.
Study designSimulation or modeling
Domainnot available
GenreMethods

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

Citations306
Published2023
Admission routes1
Has abstractno

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