Preprinting microbiology

mBio

Volumn 8, Issue 3, 2017, Pages

  Schloss, Patrick D ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Microbiology; Open science; Peer review; Publishing

Indexed keywords

ARTICLE; BIOCHEMISTRY; INFORMATION DISSEMINATION; INTERNET; MEDICAL LITERATURE; MEDICAL RESEARCH; MICROBIOLOGY; MICROORGANISM; PEER REVIEW; PREPRINT; PRINTING; PRIORITY JOURNAL; PUBLICATION; PUBLISHING; SCIENTIST; TECHNOLOGY; PROCEDURES; TRENDS;

INFORMATION DISSEMINATION; MICROBIOLOGY; PUBLISHING;

EID: 85022345858     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00438-17     Document Type: Article

References (49)

1. Vale RD. 2015. Accelerating scientific publication in biology. Proc Natl Acad Sci USA 112:13439–13446. https://doi.org/10.1073/pnas.1511912112.
2. Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, Gravel D. 2013. The case for open preprints in biology. PLoS Biol 11:e1001563. https://doi.org/10.1371/journal.pbio.1001563.
3. Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wol-berger C. 2016. Preprints for the life sciences. Science 352:899–901. https://doi.org/10.1126/science.aaf9133.
4. Bhalla N. 2016. Has the time come for preprints in biology? Mol Biol Cell 27:1185–1187. https://doi.org/10.1091/mbc.E16-02-0123.
5. National Institutes of Health. 2017. Reporting preprints and other interim research products. Notice no. NOT-OD-17-050. National Institutes of Health, Bethesda, MD. https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html.
6. Nature Publishing Group. 1966. Preprints galore. Nature 211:897–898. https://doi.org/10.1038/211897a0.
7. Till JE. 2001. Predecessors of preprint servers. Learn Publ 14:7–13. https://doi.org/10.1087/09531510125100214.
8. Ginsparg P. 2011. ArXiv at 20. Nature 476:145–147. https://doi.org/10.1038/476145a.
9. Shuai X, Pepe A, Bollen J. 2012. How the scientific community reacts to newly submitted preprints: article downloads, twitter mentions, and citations. PLoS One 7:e47523. https://doi.org/10.1371/journal.pone.0047523.
10. Callaway E. 2013. Biomedical journal and publisher hope to bring preprints to life. Nat Med 19:512. https://doi.org/10.1038/nm0513-512.
11. American Society for Microbiology. 2016. mBio instructions to authors. American Society for Microbiology, Washington, DC. http://mbio.asm.org/site/misc/journal-ita_edi.xhtml.
12. ASAPbio. 23 February 2017. ASAPbio awarded $1 million from Helmsley Charitable Trust for next-generation life sciences preprint infrastructure. ASAPbio, San Francisco, CA. http://asapbio.org/feb23.
13. Angell M, Kassirer JP. 1991. The Ingelfinger Rule revisited. N Engl J Med 325:1371–1373. https://doi.org/10.1056/NEJM199111073251910.
14. International Committee of Medical Journal Editors. 2017. Recommendations for the conduct, reporting, editing, and publication of scholarly work in medical journals. International Committee of Medical Journal Editors. http://www.icmje.org/news-and-editorials/icmje-recommendations _annotated_dec16.pdf.
15. Wikipedia contributors. 21 April 2017. List of academic journals by preprint policy, on Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy. Accessed 21 April 2017.
16. SHERPA/RoMEO. 21 April 2017. Publisher copyright policies and self-archiving. SHERPA/RoMEO, London, United Kingdom. http://www.sherpa.ac.uk/romeo/index.php.
17. Drubin DG. 2016. The mismeasure of scientific research articles and why MBoC quickly embraced preprints. Mol Biol Cell 27:3181–3182. https://doi.org/10.1091/mbc.E16-09-0651.
18. Spier R. 2002. The history of the peer-review process. Trends Biotechnol 20:357–358. https://doi.org/10.1016/s0167-7799(02)01985-6.
19. Burnham JC. 1990. The evolution of editorial peer review. JAMA 263: 1323–1329. https://doi.org/10.1001/jama.1990.03440100023003.
20. Pulverer B. 2016. Preparing for preprints. EMBO J 35:2617–2619. https://doi.org/10.15252/embj.201670030.
21. Loew LM. 2016. Peer review and bioRxiv. Biophys J 111:E01–E02. https://doi.org/10.1016/j.bpj.2016.06.035.
22. Vale RD, Hyman AA. 2016. Priority of discovery in the life sciences. eLife 5:e16931. https://doi.org/10.7554/eLife.16931.
23. Federation of American Societies for Experimental Biology. 6 December 2016. Interim research product RFI response from FASEB. Federation of American Societies for Experimental Biology, Bethesda, MD. http://www.faseb.org/Portals/2/PDFs/opa/2016/Interim%20Research%20Product %20RFI.pdf.
24. Chawla DS. 20 January 2017. When a preprint becomes the final paper. Nature http://www.nature.com/news/when-a-preprint-becomes-the -final-paper-1.21333.
25. Black A, Potter B, Dudas G, Feldstein L, Grubaugh ND, Andersen KG, Ellis BR, Ellis EM, Bedford T. 2017. Genetic characterization of the Zika virus epidemic in the US Virgin Islands. bioRxiv https://doi.org/10.1101/113100.
26. Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis S-O, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. 2015. Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Syst 1:72–87. https://doi.org/10.1016/j.cels.2015.01.001.
27. Petit RA, III, Ezewudo M, Joseph SJ, Read TD. 2015. Searching for anthrax in the New York City Subway metagenome. Zenodo https://doi.org/10.5281/zenodo.17158.
28. Ackelsberg J, Rakeman J, Hughes S, Petersen J, Mead P, Schriefer M, Kingry L, Hoffmaster A, Gee JE. 2015. Lack of evidence for plague or anthrax on the New York city subway. Cell Syst 1:4–5. https://doi.org/10.1016/j.cels.2015.07.008.
29. Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis S-O, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. 2015. Modern methods for delineating metagenomic complexity. Cell Syst 1:6–7. https://doi.org/10.1016/j.cels.2015.07.007.
30. Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B. 2015. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci USA 112:15976–15981. https://doi.org/10.1073/pnas.1510461112.
31. Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M. 2016. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. bioRxiv https://doi.org/10.1101/033464.
32. Boothby TC, Goldstein B. 2016. Reply to Bemm et al. and Arakawa: identifying foreign genes in independent Hypsibius dujardini genome assemblies. Proc Natl Acad Sci USA 113:E3058–E3061. https://doi.org/10.1073/pnas.1601149113.
33. Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M. 2016. No evidence for extensive horizontal gene transfer in the genome of the tardigrada Hypsibius dujardini. Proc Natl Acad Sci USA 113:5053–5058. https://doi.org/10.1073/pnas.1600338113.
34. Bemm F, Weiss CL, Schultz J, Förster F. 2016. Genome of a tardigrade: horizontal gene transfer or bacterial contamination? Proc Natl Acad Sci 113:E3054–E3056. https://doi.org/10.1073/pnas.1525116113.
35. Arakawa K. 2016. No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci USA 113: E3057. https://doi.org/10.1073/pnas.1602711113.
36. Delmont TO, Eren AM. 2016. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies. PeerJ 4:e1839. https://doi.org/10.7717/peerj.1839.
37. Bik EM, Casadevall A, Fang FC. 2016. The prevalence of inappropriate image duplication in biomedical research publications. bioRxiv https://doi.org/10.1101/049452.
38. Bik EM, Casadevall A, Fang FC. 2016. The prevalence of inappropriate image duplication in biomedical research publications. mBio 7:e00809-16. https://doi.org/10.1128/mBio.00809-16.
39. Wolfe-Simon F, Switzer Blum J, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, Oremland RS. 2011. A bacterium that can grow by using arsenic instead of phosphorus. Science 332:1163–1166. https://doi.org/10.1126/science.1197258
40. Altmetric, Inc. 24 November 2016. How is the Altmetric Attention Score calculated? Almetric, Inc, London, United Kingdom. https://help.altmetric.com/support/solutions/articles/6000060969-how-is-the-altmetric-attention -score-calculated-.
41. Schloss PD, Westcott SL, Jenior ML, Highlander SK. 2015. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ PrePrints 3:e778v1. https://doi.org/10.7287/peerj.preprints.778v1.
42. Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK. 2016. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ PrePrints 4:e778v2. https://doi.org/10.7287/peerj.preprints.778v2.
43. Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK. 2016. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ 4:e1869. https://doi.org/10.7717/peerj.1869.
44. Baxter NT, Koumpouras CC, Rogers MA, Ruffin MT, Schloss P. 2016. DNA from fecal immunochemical test can replace stool for microbiota-based colorectal cancer screening. bioRxiv https://doi.org/10.1101/048389.
45. Baxter NT, Koumpouras CC, Rogers MAM, Ruffin MT, Schloss PD. 2016. DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model. Microbiome 4:59. https://doi.org/10.1186/s40168-016-0205-y.
46. Imperiale MJ, Shenk T, Bertuzzi S. 2016. mSphereDirect: author-initiated peer review of manuscripts. mSphere 1:e00307-16. https://doi.org/10.1128/msphere.00307-16.
47. Vence T. 18 January 2017. Journals seek out preprints. TheScientist http://www.the-scientist.com/?articles.view/articleNo/48068/title/Journals-Seek -Out-Preprints/.
48. Barsh GS, Bergman CM, Brown CD, Singh ND, Copenhaver GP. 2016. Bringing PLOS Genetics editors to preprint servers. PLoS Genet 12: e1006448. https://doi.org/10.1371/journal.pgen.1006448.
49. Hockett KL, Nishimura MT, Karlsrud E, Dougherty K, Baltrus DA. 2013. Interactions between genome architecture and virulence genes in Pseudomonas syringae, strain CC1557 as a model. bioRxiv https://doi.org/10.1101/000869.