Literature DB >> 34316068

DOME: recommendations for supervised machine learning validation in biology.

Ian Walsh1, Dmytro Fishman2, Dario Garcia-Gasulla3, Tiina Titma4, Gianluca Pollastri5, Jennifer Harrow6, Fotis E Psomopoulos7, Silvio C E Tosatto8.   

Abstract

Year:  2021        PMID： 34316068     DOI： 10.1038/s41592-021-01205-4

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


× No keyword cloud information.
  31 in total

Review 1.  Correct machine learning on protein sequences: a peer-reviewing perspective.

Authors:  Ian Walsh; Gianluca Pollastri; Silvio C E Tosatto
Journal:  Brief Bioinform       Date:  2015-09-26       Impact factor: 11.622

Review 2.  Machine Learning in Medicine.

Authors:  Alvin Rajkomar; Jeffrey Dean; Isaac Kohane
Journal:  N Engl J Med       Date:  2019-04-04       Impact factor: 91.245

Review 3.  Applications of machine learning in drug discovery and development.

Authors:  Jessica Vamathevan; Dominic Clark; Paul Czodrowski; Ian Dunham; Edgardo Ferran; George Lee; Bin Li; Anant Madabhushi; Parantu Shah; Michaela Spitzer; Shanrong Zhao
Journal:  Nat Rev Drug Discov       Date:  2019-06       Impact factor: 84.694

4.  Artificial intelligence faces reproducibility crisis.

Authors:  Matthew Hutson
Journal:  Science       Date:  2018-02-16       Impact factor: 47.728

5.  Deciphering the human phosphoproteome.

Authors:  Giulia Franciosa; Ana Martinez-Val; Jesper V Olsen
Journal:  Nat Biotechnol       Date:  2020-03       Impact factor: 54.908

Review 6.  Machine learning applications in genetics and genomics.

Authors:  Maxwell W Libbrecht; William Stafford Noble
Journal:  Nat Rev Genet       Date:  2015-05-07       Impact factor: 53.242

7.  A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Authors:  Jason H Yang; Sarah N Wright; Meagan Hamblin; Douglas McCloskey; Miguel A Alcantar; Lars Schrübbers; Allison J Lopatkin; Sangeeta Satish; Amir Nili; Bernhard O Palsson; Graham C Walker; James J Collins
Journal:  Cell       Date:  2019-05-09       Impact factor: 41.582

8.  Rein in the four horsemen of irreproducibility.

Authors:  Dorothy Bishop
Journal:  Nature       Date:  2019-04       Impact factor: 49.962

9.  A large-scale evaluation of computational protein function prediction.

Authors:  Predrag Radivojac; Wyatt T Clark; Tal Ronnen Oron; Alexandra M Schnoes; Tobias Wittkop; Artem Sokolov; Kiley Graim; Christopher Funk; Karin Verspoor; Asa Ben-Hur; Gaurav Pandey; Jeffrey M Yunes; Ameet S Talwalkar; Susanna Repo; Michael L Souza; Damiano Piovesan; Rita Casadio; Zheng Wang; Jianlin Cheng; Hai Fang; Julian Gough; Patrik Koskinen; Petri Törönen; Jussi Nokso-Koivisto; Liisa Holm; Domenico Cozzetto; Daniel W A Buchan; Kevin Bryson; David T Jones; Bhakti Limaye; Harshal Inamdar; Avik Datta; Sunitha K Manjari; Rajendra Joshi; Meghana Chitale; Daisuke Kihara; Andreas M Lisewski; Serkan Erdin; Eric Venner; Olivier Lichtarge; Robert Rentzsch; Haixuan Yang; Alfonso E Romero; Prajwal Bhat; Alberto Paccanaro; Tobias Hamp; Rebecca Kaßner; Stefan Seemayer; Esmeralda Vicedo; Christian Schaefer; Dominik Achten; Florian Auer; Ariane Boehm; Tatjana Braun; Maximilian Hecht; Mark Heron; Peter Hönigschmid; Thomas A Hopf; Stefanie Kaufmann; Michael Kiening; Denis Krompass; Cedric Landerer; Yannick Mahlich; Manfred Roos; Jari Björne; Tapio Salakoski; Andrew Wong; Hagit Shatkay; Fanny Gatzmann; Ingolf Sommer; Mark N Wass; Michael J E Sternberg; Nives Škunca; Fran Supek; Matko Bošnjak; Panče Panov; Sašo Džeroski; Tomislav Šmuc; Yiannis A I Kourmpetis; Aalt D J van Dijk; Cajo J F ter Braak; Yuanpeng Zhou; Qingtian Gong; Xinran Dong; Weidong Tian; Marco Falda; Paolo Fontana; Enrico Lavezzo; Barbara Di Camillo; Stefano Toppo; Liang Lan; Nemanja Djuric; Yuhong Guo; Slobodan Vucetic; Amos Bairoch; Michal Linial; Patricia C Babbitt; Steven E Brenner; Christine Orengo; Burkhard Rost; Sean D Mooney; Iddo Friedberg
Journal:  Nat Methods       Date:  2013-01-27       Impact factor: 28.547

10.  Cell Type Purification by Single-Cell Transcriptome-Trained Sorting.

Authors:  Chloé S Baron; Aditya Barve; Mauro J Muraro; Reinier van der Linden; Gitanjali Dharmadhikari; Anna Lyubimova; Eelco J P de Koning; Alexander van Oudenaarden
Journal:  Cell       Date:  2019-10-03       Impact factor: 41.582
View more
  21 in total

1.  Classification models and SAR analysis on HDAC1 inhibitors using machine learning methods.

Authors:  Rourou Li; Yujia Tian; Zhenwu Yang; Yueshan Ji; Jiaqi Ding; Aixia Yan
Journal:  Mol Divers       Date:  2022-06-23       Impact factor: 2.943

Review 2.  Current status of PTMs structural databases: applications, limitations and prospects.

Authors:  Alexandre G de Brevern; Joseph Rebehmed
Journal:  Amino Acids       Date:  2022-01-12       Impact factor: 3.520

3.  Constructing benchmark test sets for biological sequence analysis using independent set algorithms.

Authors:  Samantha Petti; Sean R Eddy
Journal:  PLoS Comput Biol       Date:  2022-03-07       Impact factor: 4.475

4.  Statistical quantification of confounding bias in machine learning models.

Authors:  Tamas Spisak
Journal:  Gigascience       Date:  2022-08-26       Impact factor: 7.658

5.  An approachable, flexible and practical machine learning workshop for biologists.

Authors:  Chris S Magnano; Fangzhou Mu; Rosemary S Russ; Milica Cvetkovic; Debora Treu; Anthony Gitter
Journal:  Bioinformatics       Date:  2022-06-24       Impact factor: 6.931

6.  DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data.

Authors:  Maria J Olmo-Uceda; Juan C Muñoz-Sánchez; Wilberth Lasso-Giraldo; Vicente Arnau; Wladimiro Díaz-Villanueva; Santiago F Elena
Journal:  Viruses       Date:  2022-05-23       Impact factor: 5.818

7.  Antibacterial Activity Prediction of Plant Secondary Metabolites Based on a Combined Approach of Graph Clustering and Deep Neural Network.

Authors:  Mohammad Bozlul Karim; Shigehiko Kanaya; Md Altaf-Ul-Amin
Journal:  Mol Inform       Date:  2022-01-28       Impact factor: 4.050

Review 8.  Harnessing the potential of machine learning for advancing "Quality by Design" in biomanufacturing.

Authors:  Ian Walsh; Matthew Myint; Terry Nguyen-Khuong; Ying Swan Ho; Say Kong Ng; Meiyappan Lakshmanan
Journal:  MAbs       Date:  2022 Jan-Dec       Impact factor: 5.857

9.  A Clinical Prognostic Model Based on Machine Learning from the Fondazione Italiana Linfomi (FIL) MCL0208 Phase III Trial.

Authors:  Gian Maria Zaccaria; Simone Ferrero; Eva Hoster; Roberto Passera; Andrea Evangelista; Elisa Genuardi; Daniela Drandi; Marco Ghislieri; Daniela Barbero; Ilaria Del Giudice; Monica Tani; Riccardo Moia; Stefano Volpetti; Maria Giuseppina Cabras; Nicola Di Renzo; Francesco Merli; Daniele Vallisa; Michele Spina; Anna Pascarella; Giancarlo Latte; Caterina Patti; Alberto Fabbri; Attilio Guarini; Umberto Vitolo; Olivier Hermine; Hanneke C Kluin-Nelemans; Sergio Cortelazzo; Martin Dreyling; Marco Ladetto
Journal:  Cancers (Basel)       Date:  2021-12-31       Impact factor: 6.639

Review 10.  Modeling approaches for probing cross-feeding interactions in the human gut microbiome.

Authors:  Pedro Saa; Arles Urrutia; Claudia Silva-Andrade; Alberto J Martín; Daniel Garrido
Journal:  Comput Struct Biotechnol J       Date:  2021-12-08       Impact factor: 7.271
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.