Literature DB >> 29079656

Don't just dump your data and run: Authors should submit as much experimental information as possible when uploading sequence data.

Matheus Sanitá Lima1, David Roy Smith1.   

Abstract

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Year:  2017        PMID: 29079656      PMCID: PMC5709767          DOI: 10.15252/embr.201745118

Source DB:  PubMed          Journal:  EMBO Rep        ISSN: 1469-221X            Impact factor:   8.807


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  10 in total

1.  Reminder to deposit DNA sequences.

Authors:  Mark Blaxter; Antoine Danchin; Babis Savakis; Kaoru Fukami-Kobayashi; Ken Kurokawa; Sumio Sugano; Richard J Roberts; Steven L Salzberg; Chung-I Wu
Journal:  Science       Date:  2016-05-11       Impact factor: 47.728

2.  1,500 scientists lift the lid on reproducibility.

Authors:  Monya Baker
Journal:  Nature       Date:  2016-05-26       Impact factor: 49.962

3.  A long journey to reproducible results.

Authors:  Gordon J Lithgow; Monica Driscoll; Patrick Phillips
Journal:  Nature       Date:  2017-08-22       Impact factor: 49.962

4.  Death of the genome paper.

Authors:  David Roy Smith
Journal:  Front Genet       Date:  2013-05-06       Impact factor: 4.599

5.  Closure of the NCBI SRA and implications for the long-term future of genomics data storage.

Authors:  David Lipman; Paul Flicek; Steven Salzberg; Mark Gerstein; Rob Knight
Journal:  Genome Biol       Date:  2011-03-22       Impact factor: 13.583

6.  The European Nucleotide Archive.

Authors:  Rasko Leinonen; Ruth Akhtar; Ewan Birney; Lawrence Bower; Ana Cerdeno-Tárraga; Ying Cheng; Iain Cleland; Nadeem Faruque; Neil Goodgame; Richard Gibson; Gemma Hoad; Mikyung Jang; Nima Pakseresht; Sheila Plaister; Rajesh Radhakrishnan; Kethi Reddy; Siamak Sobhany; Petra Ten Hoopen; Robert Vaughan; Vadim Zalunin; Guy Cochrane
Journal:  Nucleic Acids Res       Date:  2010-10-23       Impact factor: 16.971

7.  The Sequence Read Archive: explosive growth of sequencing data.

Authors:  Yuichi Kodama; Martin Shumway; Rasko Leinonen
Journal:  Nucleic Acids Res       Date:  2011-10-18       Impact factor: 16.971

Review 8.  Data access for the 1,000 Plants (1KP) project.

Authors:  Naim Matasci; Ling-Hong Hung; Zhixiang Yan; Eric J Carpenter; Norman J Wickett; Siavash Mirarab; Nam Nguyen; Tandy Warnow; Saravanaraj Ayyampalayam; Michael Barker; J Gordon Burleigh; Matthew A Gitzendanner; Eric Wafula; Joshua P Der; Claude W dePamphilis; Béatrice Roure; Hervé Philippe; Brad R Ruhfel; Nicholas W Miles; Sean W Graham; Sarah Mathews; Barbara Surek; Michael Melkonian; Douglas E Soltis; Pamela S Soltis; Carl Rothfels; Lisa Pokorny; Jonathan A Shaw; Lisa DeGironimo; Dennis W Stevenson; Juan Carlos Villarreal; Tao Chen; Toni M Kutchan; Megan Rolf; Regina S Baucom; Michael K Deyholos; Ram Samudrala; Zhijian Tian; Xiaolei Wu; Xiao Sun; Yong Zhang; Jun Wang; Jim Leebens-Mack; Gane Ka-Shu Wong
Journal:  Gigascience       Date:  2014-10-27       Impact factor: 6.524

9.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Authors:  Patrick J Keeling; Fabien Burki; Heather M Wilcox; Bassem Allam; Eric E Allen; Linda A Amaral-Zettler; E Virginia Armbrust; John M Archibald; Arvind K Bharti; Callum J Bell; Bank Beszteri; Kay D Bidle; Connor T Cameron; Lisa Campbell; David A Caron; Rose Ann Cattolico; Jackie L Collier; Kathryn Coyne; Simon K Davy; Phillipe Deschamps; Sonya T Dyhrman; Bente Edvardsen; Ruth D Gates; Christopher J Gobler; Spencer J Greenwood; Stephanie M Guida; Jennifer L Jacobi; Kjetill S Jakobsen; Erick R James; Bethany Jenkins; Uwe John; Matthew D Johnson; Andrew R Juhl; Anja Kamp; Laura A Katz; Ronald Kiene; Alexander Kudryavtsev; Brian S Leander; Senjie Lin; Connie Lovejoy; Denis Lynn; Adrian Marchetti; George McManus; Aurora M Nedelcu; Susanne Menden-Deuer; Cristina Miceli; Thomas Mock; Marina Montresor; Mary Ann Moran; Shauna Murray; Govind Nadathur; Satoshi Nagai; Peter B Ngam; Brian Palenik; Jan Pawlowski; Giulio Petroni; Gwenael Piganeau; Matthew C Posewitz; Karin Rengefors; Giovanna Romano; Mary E Rumpho; Tatiana Rynearson; Kelly B Schilling; Declan C Schroeder; Alastair G B Simpson; Claudio H Slamovits; David R Smith; G Jason Smith; Sarah R Smith; Heidi M Sosik; Peter Stief; Edward Theriot; Scott N Twary; Pooja E Umale; Daniel Vaulot; Boris Wawrik; Glen L Wheeler; William H Wilson; Yan Xu; Adriana Zingone; Alexandra Z Worden
Journal:  PLoS Biol       Date:  2014-06-24       Impact factor: 8.029

10.  Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists.

Authors:  Matheus Sanitá Lima; David Roy Smith
Journal:  G3 (Bethesda)       Date:  2017-11-06       Impact factor: 3.154

  10 in total
  4 in total

1.  Improving Reproducibility and Candidate Selection in Transcriptomics Using Meta-analysis.

Authors:  Laurence A Brown; Stuart N Peirson
Journal:  J Exp Neurosci       Date:  2018-02-27

2.  The archives are half-empty: an assessment of the availability of microbial community sequencing data.

Authors:  Stephanie D Jurburg; Maximilian Konzack; Nico Eisenhauer; Anna Heintz-Buschart
Journal:  Commun Biol       Date:  2020-08-28

3.  Co-cultivation, Co-culture, Mixed Culture, and Microbial Consortium of Fungi: An Understudied Strategy for Biomass Conversion.

Authors:  Matheus Sanitá Lima; Rosymar Coutinho de Lucas
Journal:  Front Microbiol       Date:  2022-01-20       Impact factor: 5.640

4.  Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries.

Authors:  Samuel Hunter; Rutendo F Sigauke; Jacob T Stanley; Mary A Allen; Robin D Dowell
Journal:  BMC Genomics       Date:  2022-03-07       Impact factor: 3.969

  4 in total

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