Literature DB >> 24104757

The anatomy of successful computational biology software.

Stephen Altschul1, Barry Demchak, Richard Durbin, Robert Gentleman, Martin Krzywinski, Heng Li, Anton Nekrutenko, James Robinson, Wayne Rasband, James Taylor, Cole Trapnell.   

Abstract

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Year:  2013        PMID： 24104757      PMCID： PMC4166496          DOI： 10.1038/nbt.2721

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  8 in total

Review 1.  Orchestrating high-throughput genomic analysis with Bioconductor.

Authors:  Wolfgang Huber; Vincent J Carey; Robert Gentleman; Simon Anders; Marc Carlson; Benilton S Carvalho; Hector Corrada Bravo; Sean Davis; Laurent Gatto; Thomas Girke; Raphael Gottardo; Florian Hahne; Kasper D Hansen; Rafael A Irizarry; Michael Lawrence; Michael I Love; James MacDonald; Valerie Obenchain; Andrzej K Oleś; Hervé Pagès; Alejandro Reyes; Paul Shannon; Gordon K Smyth; Dan Tenenbaum; Levi Waldron; Martin Morgan
Journal:  Nat Methods       Date:  2015-02       Impact factor: 28.547

2.  Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie.

Authors:  Eleni Giannoulatou; Shin-Ho Park; David T Humphreys; Joshua W K Ho
Journal:  BMC Bioinformatics       Date:  2014-12-08       Impact factor: 3.169

Review 3.  CGAT: a model for immersive personalized training in computational genomics.

Authors:  David Sims; Chris P Ponting; Andreas Heger
Journal:  Brief Funct Genomics       Date:  2015-05-16       Impact factor: 4.241

4.  The Process of Analyzing Data is the Emergent Feature of Data Science.

Authors:  Frank Emmert-Streib; Salissou Moutari; Matthias Dehmer
Journal:  Front Genet       Date:  2016-02-09       Impact factor: 4.599

5.  SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

Authors:  Tomáš Vetrovský; Petr Baldrian; Daniel Morais
Journal:  Bioinformatics       Date:  2018-07-01       Impact factor: 6.937

6.  Challenges and recommendations to improve the installability and archival stability of omics computational tools.

Authors:  Serghei Mangul; Thiago Mosqueiro; Richard J Abdill; Dat Duong; Keith Mitchell; Varuni Sarwal; Brian Hill; Jaqueline Brito; Russell Jared Littman; Benjamin Statz; Angela Ka-Mei Lam; Gargi Dayama; Laura Grieneisen; Lana S Martin; Jonathan Flint; Eleazar Eskin; Ran Blekhman
Journal:  PLoS Biol       Date:  2019-06-20       Impact factor: 8.029

7.  Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.

Authors:  Paul P Gardner; James M Paterson; Stephanie McGimpsey; Fatemeh Ashari-Ghomi; Sinan U Umu; Aleksandra Pawlik; Alex Gavryushkin; Michael A Black
Journal:  Genome Biol       Date:  2022-02-16       Impact factor: 13.583

8.  On best practices in the development of bioinformatics software.

Authors:  Felipe da Veiga Leprevost; Valmir C Barbosa; Eduardo L Francisco; Yasset Perez-Riverol; Paulo C Carvalho
Journal:  Front Genet       Date:  2014-07-02       Impact factor: 4.599
  8 in total

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