Skip to main content

Preparing and Structuring a Manuscript for Publication

  • Chapter
  • First Online:
The Quintessence of Basic and Clinical Research and Scientific Publishing

Abstract

The writing of scientific manuscripts is a common activity for researchers around the world. In this context, preparing and structuring a manuscript adequately takes time, training and practice. In this chapter, I highlight multiple recommendations from the recent scientific literature and from my expertise in the writing and review of a large number of articles. The common sections of original articles are briefly reviewed, in addition to key suggestions for structuring manuscripts. I also discuss interesting proposals from recent papers oriented to increase the quality of the manuscripts and improving research productivity, aiming to guarantee research integrity and study reproducibility. Novel authors would benefit from training activities, feedback from colleagues and the constant practice of writing.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bourne PE (2005) Ten simple rules for getting published. PLoS Comput Biol 1(5):e57

    Article  PubMed  PubMed Central  Google Scholar 

  2. Oshiro J, Caubet SL, Viola KE, Huber JM (2020) Going beyond “not enough time”: barriers to preparing manuscripts for academic medical journals. Teach Learn Med 32(1):71–81

    Article  PubMed  Google Scholar 

  3. Forero DA, Lopez-Leon S, Perry G (2020) A brief guide to the science and art of writing manuscripts in biomedicine. J Transl Med 18(1):425

    Article  PubMed  PubMed Central  Google Scholar 

  4. Barroga E, Matanguihan GJ (2021) Creating logical flow when writing scientific articles. J Korean Med Sci 36(40):e275

    Article  PubMed  PubMed Central  Google Scholar 

  5. Mensh B, Kording K (2017) Ten simple rules for structuring papers. PLoS Comput Biol 13(9):e1005619

    Article  PubMed  PubMed Central  Google Scholar 

  6. Bahadoran Z, Mirmiran P, Kashfi K, Ghasemi A (2019) The principles of biomedical scientific writing: title. Int J Endocrinol Metab 17(4):e98326

    Article  PubMed  PubMed Central  Google Scholar 

  7. Tullu MS (2019) Writing the title and abstract for a research paper: being concise, precise, and meticulous is the key. Saudi J Anaesth 13(Suppl 1):S12–SS7

    Article  PubMed  PubMed Central  Google Scholar 

  8. Annesley TM (2010) “It was a cold and rainy night”: set the scene with a good introduction. Clin Chem 56(5):708–713

    Article  CAS  PubMed  Google Scholar 

  9. Annesley TM (2010) Who, what, when, where, how, and why: the ingredients in the recipe for a successful Methods section. Clin Chem 56(6):897–901

    Article  CAS  PubMed  Google Scholar 

  10. Dwivedi AK (2022) How to write statistical analysis section in medical research. J Investig Med 70(8):1759–1770

    Article  PubMed  PubMed Central  Google Scholar 

  11. Rougier NP, Droettboom M, Bourne PE (2014) Ten simple rules for better figures. PLoS Comput Biol 10(9):e1003833

    Article  PubMed  PubMed Central  Google Scholar 

  12. Annesley TM (2010) Show your cards: the results section and the poker game. Clin Chem 56(7):1066–1070

    Article  CAS  PubMed  Google Scholar 

  13. Annesley TM (2010) The discussion section: your closing argument. Clin Chem 56(11):1671–1674

    Article  CAS  PubMed  Google Scholar 

  14. Meo SA (2018) Anatomy and physiology of a scientific paper. Saudi J Biol Sci 25(7):1278–1283

    Article  PubMed  PubMed Central  Google Scholar 

  15. Penders B (2018) Ten simple rules for responsible referencing. PLoS Comput Biol 14(4):e1006036

    Article  PubMed  PubMed Central  Google Scholar 

  16. Dunn AG, Coiera E, Mandl KD, Bourgeois FT (2016) Conflict of interest disclosure in biomedical research: a review of current practices, biases, and the role of public registries in improving transparency. Res Integr Peer Rev 1:1

    Article  PubMed  PubMed Central  Google Scholar 

  17. Forero DA, Lopez-Leon S, Gonzalez-Giraldo Y, Bagos PG (2019) Ten simple rules for carrying out and writing meta-analyses. PLoS Comput Biol 15(5):e1006922

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Gregory AT, Denniss AR (2018) An introduction to writing narrative and systematic reviews—tasks, tips and traps for aspiring authors. Heart Lung Circ 27(7):893–898

    Article  PubMed  Google Scholar 

  19. Zhang W (2014) Ten simple rules for writing research papers. PLoS Comput Biol 10(1):e1003453

    Article  PubMed  PubMed Central  Google Scholar 

  20. Lengauer T, Nussinov R (2015) How to write a presubmission inquiry. PLoS Comput Biol 11(2):e1004098

    Article  PubMed  PubMed Central  Google Scholar 

  21. Vitse CL, Poland GA (2017) Writing a scientific paper—a brief guide for new investigators. Vaccine 35(5):722–728

    Article  PubMed  Google Scholar 

  22. Zeng A, Fan Y, Di Z, Wang Y, Havlin S (2021) Fresh teams are associated with original and multidisciplinary research. Nat Hum Behav 5(10):1314–1322

    Article  PubMed  Google Scholar 

  23. Kornhaber RA, McLean LM, Baber RJ (2015) Ongoing ethical issues concerning authorship in biomedical journals: an integrative review. Int J Nanomedicine 10:4837–4846

    Article  PubMed  PubMed Central  Google Scholar 

  24. Patience GS, Galli F, Patience PA, Boffito DC (2019) Intellectual contributions meriting authorship: survey results from the top cited authors across all science categories. PLoS One 14(1):e0198117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Zimba O, Gasparyan AY (2020) Scientific authorship: a primer for researchers. Reumatologia 58(6):345–349

    Article  PubMed  PubMed Central  Google Scholar 

  26. Moshontz H, Ebersole CR, Weston SJ, Klein RAJS, Compass PP (2021) A guide for many authors: writing manuscripts in large collaborations. Soc Personal Psychol Compass 15(4):e12590

    Article  Google Scholar 

  27. Shaffril HAM, Samsuddin SF, Samah AA (2021) The ABC of systematic literature review: the basic methodological guidance for beginners. Qual Quant 55(4):1319–1346

    Article  Google Scholar 

  28. Gusenbauer M, Haddaway NR (2020) Which academic search systems are suitable for systematic reviews or meta-analyses? Evaluating retrieval qualities of Google Scholar, PubMed, and 26 other resources. Res Synth Methods 11(2):181–217

    Article  PubMed  PubMed Central  Google Scholar 

  29. Gusenbauer MJS (2019) Google Scholar to overshadow them all? Comparing the sizes of 12 academic search engines and bibliographic databases. Scientometrics 118(1):177–214

    Article  Google Scholar 

  30. Smalheiser NR, Fragnito DP, Tirk EE (2021) Anne O’Tate: value-added PubMed search engine for analysis and text mining. PLoS One 16(3):e0248335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Fusar-Poli P, Radua J (2018) Ten simple rules for conducting umbrella reviews. Evid Based Ment Health 21(3):95–100

    Article  PubMed  PubMed Central  Google Scholar 

  32. Ioannidis JP, Greenland S, Hlatky MA, Khoury MJ, Macleod MR, Moher D et al (2014) Increasing value and reducing waste in research design, conduct, and analysis. Lancet 383(9912):166–175

    Article  PubMed  PubMed Central  Google Scholar 

  33. Page MJ, Moher D, Bossuyt PM, Boutron I, Hoffmann TC, Mulrow CD et al (2021) PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. BMJ 372:n160

    Article  PubMed  PubMed Central  Google Scholar 

  34. Schulz KF, Altman DG, Moher D, Group C (2010) CONSORT 2010 statement: updated guidelines for reporting parallel group randomised trials. BMC Med 8:18

    Article  PubMed  PubMed Central  Google Scholar 

  35. von Elm E, Altman DG, Egger M, Pocock SJ, Gotzsche PC, Vandenbroucke JP et al (2007) The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. PLoS Med 4(10):e296

    Article  Google Scholar 

  36. Collins GS, Reitsma JB, Altman DG, Moons KG (2015) Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD): the TRIPOD statement. BMC Med 13:1

    Article  PubMed  PubMed Central  Google Scholar 

  37. Percie du Sert N, Ahluwalia A, Alam S, Avey MT, Baker M, Browne WJ et al (2020) Reporting animal research: explanation and elaboration for the ARRIVE guidelines 2.0. PLoS Biol 18(7):e3000411

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Abdill RJ, Blekhman R (2019) Tracking the popularity and outcomes of all bioRxiv preprints. Elife 8:e45133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ettinger CL, Sadanandappa MK, Gorgulu K, Coghlan KL, Hallenbeck KK, Puebla I (2022) A guide to preprinting for early-career researchers. Biol Open 11(7):bio059310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Henderson EL, Chambers CD (2022) Ten simple rules for writing a Registered Report. PLoS Comput Biol 18(10):e1010571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Carroll MW (2013) Creative Commons and the openness of open access. N Engl J Med 368(9):789–791

    Article  CAS  PubMed  Google Scholar 

  42. Langham-Putrow A, Bakker C, Riegelman A (2021) Is the open access citation advantage real? A systematic review of the citation of open access and subscription-based articles. PLoS One 16(6):e0253129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Colavizza G, Hrynaszkiewicz I, Staden I, Whitaker K, McGillivray B (2020) The citation advantage of linking publications to research data. PLoS One 15(4):e0230416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM (2021) Sharing biological data: why, when, and how. FEBS Lett 595(7):847–863

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A et al (2016) The FAIR guiding principles for scientific data management and stewardship. Sci Data 3:160018

    Article  PubMed  PubMed Central  Google Scholar 

  46. Forero DA, Curioso WH, Patrinos GP (2021) The importance of adherence to international standards for depositing open data in public repositories. BMC Res Notes 14(1):405

    Article  PubMed  PubMed Central  Google Scholar 

  47. Shaw DM, Erren TC (2015) Ten simple rules for protecting research integrity. PLoS Comput Biol 11(10):e1004388

    Article  PubMed  PubMed Central  Google Scholar 

  48. Bradshaw MS, Payne SH (2021) Detecting fabrication in large-scale molecular omics data. PLoS One 16(11):e0260395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Fang FC, Steen RG, Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42):17028–17033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Perez-Neri I, Pineda C, Sandoval H (2022) Threats to scholarly research integrity arising from paper mills: a rapid scoping review. Clin Rheumatol 41(7):2241–2248

    Article  PubMed  Google Scholar 

  51. Gaudino M, Robinson NB, Audisio K, Rahouma M, Benedetto U, Kurlansky P et al (2021) Trends and characteristics of retracted articles in the biomedical literature, 1971 to 2020. JAMA Intern Med 181(8):1118–1121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Morreim EH, Winer JC (2023) Guest authorship as research misconduct: definitions and possible solutions. BMJ Evid Based Med 28(1):1–4

    Article  CAS  PubMed  Google Scholar 

  53. Chiu K, Grundy Q, Bero L (2017) ‘Spin’ in published biomedical literature: a methodological systematic review. PLoS Biol 15(9):e2002173

    Article  PubMed  PubMed Central  Google Scholar 

  54. Huang GC, Truglio J, Potter J, White A, Hunt S (2022) Anti-bias and inclusive language in scholarly writing: a primer for authors. Acad Med 97(12):1870

    Article  PubMed  Google Scholar 

  55. Flanagin A, Frey T, Christiansen SL, Committee AMAMoS (2021) Updated guidance on the reporting of race and ethnicity in medical and science journals. JAMA 326(7):621–627

    Article  PubMed  Google Scholar 

  56. Cook DA (2016) Twelve tips for getting your manuscript published. Med Teach 38(1):41–50

    Article  PubMed  Google Scholar 

  57. Busse C, August E (2021) How to write and publish a research paper for a peer-reviewed journal. J Cancer Educ 36(5):909–913

    Article  PubMed  Google Scholar 

  58. Aga SS, Nissar S (2022) Essential guide to manuscript writing for academic dummies: an editor’s perspective. Biochem Res Int 2022:1492058

    Article  PubMed  PubMed Central  Google Scholar 

  59. Huston P, Choi B (2017) A guide to publishing scientific research in the health sciences. Can Commun Dis Rep 43(9):169–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Ecarnot F, Seronde M-F, Chopard R, Schiele F, Meneveau NJEGM (2015) Writing a scientific article: a step-by-step guide for beginners. Eur Geriatr Med 6(6):573–579

    Article  Google Scholar 

  61. Iskander JK, Wolicki SB, Leeb RT, Siegel PZ (2018) Successful scientific writing and publishing: a step-by-step approach. Prev Chronic Dis 15:E79

    Article  PubMed  PubMed Central  Google Scholar 

  62. Peterson TC, Kleppner SR, Botham CM (2018) Ten simple rules for scientists: improving your writing productivity. PLoS Comput Biol 14(10):e1006379

    Article  PubMed  PubMed Central  Google Scholar 

  63. Forero DA, Moore JH (2016) Considerations for higher efficiency and productivity in research activities. BioData Min 9:35

    Article  PubMed  PubMed Central  Google Scholar 

  64. Yakhontova T (2021) What nonnative authors should know when writing research articles in English. J Korean Med Sci 36(35):e237

    Article  PubMed  PubMed Central  Google Scholar 

  65. Yakhontova T (2020) Conventions of English research discourse and the writing of non-Anglophone authors. J Korean Med Sci 35(40):e331

    Article  PubMed  PubMed Central  Google Scholar 

  66. Yakhontova T (2020) Punctuation mistakes in the english writing of non-Anglophone researchers. J Korean Med Sci 35(37):e299

    Article  PubMed  PubMed Central  Google Scholar 

  67. Yakhontova T (2020) English writing of non-Anglophone researchers. J Korean Med Sci 35(26):e216

    Article  PubMed  PubMed Central  Google Scholar 

  68. Sharma RK, Ogle HL (2022) Twelve tips for students who wish to write and publish. Med Teach 44(4):360–365

    Article  PubMed  Google Scholar 

  69. Annesley TM (2011) Top 10 tips for responding to reviewer and editor comments. Clin Chem 57(4):551–554

    Article  CAS  PubMed  Google Scholar 

  70. Guyatt GH, Brian Haynes R (2006) Preparing reports for publication and responding to reviewers’ comments. J Clin Epidemiol 59(9):900–906

    Article  PubMed  Google Scholar 

  71. Kotz D, Cals JW (2014) Effective writing and publishing scientific papers, part XII: responding to reviewers. J Clin Epidemiol 67(3):243

    Article  PubMed  Google Scholar 

  72. Busse CE, Anderson EW, Endale T, Smith YR, Kaniecki M, Shannon C et al (2022) Strengthening research capacity: a systematic review of manuscript writing and publishing interventions for researchers in low-income and middle-income countries. BMJ Glob Health 7(2):e008059

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

DAF has been previously supported by research grants from MinCiencias and DNI-Areandina.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Diego A. Forero .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Forero, D.A. (2023). Preparing and Structuring a Manuscript for Publication. In: Jagadeesh, G., Balakumar, P., Senatore, F. (eds) The Quintessence of Basic and Clinical Research and Scientific Publishing. Springer, Singapore. https://doi.org/10.1007/978-981-99-1284-1_42

Download citation

Publish with us

Policies and ethics