Literature DB >> 34462593

Reproducibility standards for machine learning in the life sciences.

Benjamin J Heil1, Michael M Hoffman2,3,4,5, Florian Markowetz6, Su-In Lee7, Casey S Greene8,9, Stephanie C Hicks10.   

Abstract

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Year:  2021        PMID： 34462593      PMCID： PMC9131851          DOI： 10.1038/s41592-021-01256-7

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   47.990


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  12 in total

1.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

Authors:  Ron Edgar; Michael Domrachev; Alex E Lash
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  Sharing biological data: why, when, and how.

Authors:  Samantha L Wilson; Gregory P Way; Wout Bittremieux; Jean-Paul Armache; Melissa A Haendel; Michael M Hoffman
Journal:  FEBS Lett       Date:  2021-04       Impact factor: 4.124

3.  Nextflow enables reproducible computational workflows.

Authors:  Paolo Di Tommaso; Maria Chatzou; Evan W Floden; Pablo Prieto Barja; Emilio Palumbo; Cedric Notredame
Journal:  Nat Biotechnol       Date:  2017-04-11       Impact factor: 54.908

4.  Snakemake--a scalable bioinformatics workflow engine.

Authors:  Johannes Köster; Sven Rahmann
Journal:  Bioinformatics       Date:  2012-08-20       Impact factor: 6.937

5.  Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist.

Authors:  Beau Norgeot; Giorgio Quer; Brett K Beaulieu-Jones; Ali Torkamani; Raquel Dias; Milena Gianfrancesco; Rima Arnaout; Isaac S Kohane; Suchi Saria; Eric Topol; Ziad Obermeyer; Bin Yu; Atul J Butte
Journal:  Nat Med       Date:  2020-09       Impact factor: 53.440

6.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

7.  The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.

Authors:  Žiga Avsec; Roman Kreuzhuber; Johnny Israeli; Nancy Xu; Jun Cheng; Avanti Shrikumar; Abhimanyu Banerjee; Daniel S Kim; Thorsten Beier; Lara Urban; Anshul Kundaje; Oliver Stegle; Julien Gagneur
Journal:  Nat Biotechnol       Date:  2019-06       Impact factor: 54.908

8.  MINIMAR (MINimum Information for Medical AI Reporting): Developing reporting standards for artificial intelligence in health care.

Authors:  Tina Hernandez-Boussard; Selen Bozkurt; John P A Ioannidis; Nigam H Shah
Journal:  J Am Med Inform Assoc       Date:  2020-12-09       Impact factor: 4.497

Review 9.  Responsible, practical genomic data sharing that accelerates research.

Authors:  James Brian Byrd; Anna C Greene; Deepashree Venkatesh Prasad; Xiaoqian Jiang; Casey S Greene
Journal:  Nat Rev Genet       Date:  2020-07-21       Impact factor: 53.242

10.  A call for public archives for biological image data.

Authors:  Jan Ellenberg; Jason R Swedlow; Mary Barlow; Charles E Cook; Ugis Sarkans; Ardan Patwardhan; Alvis Brazma; Ewan Birney
Journal:  Nat Methods       Date:  2018-11       Impact factor: 28.547
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  14 in total

1.  Open microscopy in the life sciences: quo vadis?

Authors:  Johannes Hohlbein; Benedict Diederich; Barbora Marsikova; Emmanuel G Reynaud; Séamus Holden; Wiebke Jahr; Robert Haase; Kirti Prakash
Journal:  Nat Methods       Date:  2022-09       Impact factor: 47.990

Review 2.  Obtaining genetics insights from deep learning via explainable artificial intelligence.

Authors:  Gherman Novakovsky; Nick Dexter; Maxwell W Libbrecht; Wyeth W Wasserman; Sara Mostafavi
Journal:  Nat Rev Genet       Date:  2022-10-03       Impact factor: 59.581

3.  An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.

Authors:  Marouen Ben Guebila; Deborah Weighill; Camila M Lopes-Ramos; Rebekka Burkholz; Romana T Pop; Kalyan Palepu; Mia Shapoval; Maud Fagny; Daniel Schlauch; Kimberly Glass; Michael Altenbuchinger; Marieke L Kuijjer; John Platig; John Quackenbush
Journal:  Nat Methods       Date:  2022-05       Impact factor: 47.990

4.  Reproducibility of prediction models in health services research.

Authors:  Lazaros Belbasis; Orestis A Panagiotou
Journal:  BMC Res Notes       Date:  2022-06-11

5.  Using a ResNet-18 Network to Detect Features of Alzheimer's Disease on Functional Magnetic Resonance Imaging: A Failed Replication. Comment on Odusami et al. Analysis of Features of Alzheimer's Disease: Detection of Early Stage from Functional Brain Changes in Magnetic Resonance Images Using a Finetuned ResNet18 Network. Diagnostics 2021, 11, 1071.

Authors:  Peter J Nicholas; Alex To; Onur Tanglay; Isabella M Young; Michael E Sughrue; Stéphane Doyen
Journal:  Diagnostics (Basel)       Date:  2022-04-27

Review 6.  Challenges in translational machine learning.

Authors:  Artuur Couckuyt; Ruth Seurinck; Annelies Emmaneel; Katrien Quintelier; David Novak; Sofie Van Gassen; Yvan Saeys
Journal:  Hum Genet       Date:  2022-03-04       Impact factor: 5.881

Review 7.  Prospects of Surface-Enhanced Raman Spectroscopy for Biomarker Monitoring toward Precision Medicine.

Authors:  Javier Plou; Pablo S Valera; Isabel García; Carlos D L de Albuquerque; Arkaitz Carracedo; Luis M Liz-Marzán
Journal:  ACS Photonics       Date:  2022-02-02       Impact factor: 7.529

Review 8.  A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.

Authors:  Xinsong Du; Juan J Aristizabal-Henao; Timothy J Garrett; Mathias Brochhausen; William R Hogan; Dominick J Lemas
Journal:  Metabolites       Date:  2022-01-17

9.  Ten quick tips for deep learning in biology.

Authors:  Benjamin D Lee; Anthony Gitter; Casey S Greene; Sebastian Raschka; Finlay Maguire; Alexander J Titus; Michael D Kessler; Alexandra J Lee; Marc G Chevrette; Paul Allen Stewart; Thiago Britto-Borges; Evan M Cofer; Kun-Hsing Yu; Juan Jose Carmona; Elana J Fertig; Alexandr A Kalinin; Brandon Signal; Benjamin J Lengerich; Timothy J Triche; Simina M Boca
Journal:  PLoS Comput Biol       Date:  2022-03-24       Impact factor: 4.475

10.  Multivariable prediction models for health care spending using machine learning: a protocol of a systematic review.

Authors:  Andrew W Huang; Martin Haslberger; Neto Coulibaly; Omar Galárraga; Arman Oganisian; Lazaros Belbasis; Orestis A Panagiotou
Journal:  Diagn Progn Res       Date:  2022-03-24
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