References for module 3 - Good Academic Practices
References for module 3 - Good Academic Practices
Module 4 – Violations of Research Integrity [link!]
Design and conduct
ALLEA (2023). The European Code of Conduct for Research Integrity: Revised Edition 2023. Berlin. DOI 10.26356/ECOC
Allen, C., & Mehler, D. M. A. (2019). Open science challenges, benefits and tips in early career and beyond. PLOS Biology , 17 (5), Article e3000246. https://doi.org/10.1371/journal.pbio.3000246
Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533, 452–454. https://doi.org/10.1038/533452a
Camerer, C. F., Dreber, A., Holzmeister, F., Ho, T.-H., Huber, J., Johannesson, M., Kirchler, M., Nave, G., Nosek, B. A., Pfeiffer, T., Altmejd, A., Buttrick, N., Chan, T., Chen, Y., Forsell, E., Gampa, A., Heikensten, E., Hummer, L., Imai, T., … Wu, H. (2018). Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015. Nature Human Behaviour, 2(9), 637–644. https://doi.org/10.1038/s41562-018-0399-z
Center for Open Science. (n.d.). Registered Reports: Peer review before results are known to align scientific values and practices. Retrieved May 26, 2021, from https://www.cos.io/initiatives/registered-reports
Cochrane Methods Bias. (n.d.). Reporting Biases. Retrieved May 26, 2021, from https://methods.cochrane.org/bias/reporting-biases
Collaboration, O. S. (2015). Estimating the reproducibility of psychological science. Science, 349(6251). https://doi.org/10.1126/science.aac4716
Data dredging. (2021). In Wikipedia. https://en.wikipedia.org/w/index.php?title=Data_dredging&oldid=1023475448
Data driven hypotheses without disclosure (‘HARKing’). (2021, maart 26). The Embassy of Good Science. https://embassy.science/wiki/Theme:26631aa0-18f0-4635-b71b-80a6f4e58d33
Dutilh, G., Sarafoglou, A., & Wagenmakers, E.-J. (2019). Flexible yet fair: Blinding analyses in experimental psychology. Synthese, 198, 5745-5772. https://doi.org/10.1007/s11229-019-02456-7
Eckers, J. C., Swick, A. D., & Kimple, R. J. (2018). Identity Crisis – Rigor and Reproducibility in Human Cell Lines. Radiation Research, 189(6), 551–552. https://doi.org/10.1667/RR15086.1
Enago Academy. (2018, September 20). Alarming Reproducibility Crisis Invading Social Sciences Journals. https://www.enago.com/academy/alarming-reproducibility-crisis-invading-social-sciences-journals/
Enago Academy. (2020, April 3). Should You Pre-Register Your Research Study? A Quick Guide. https://www.enago.com/academy/pre-registration-of-your-research/
Garner, H. R., McIver, L. J., & Waitzkin, M. B. (2013). Same work, twice the money? Nature, 493(7434), 599–601. https://doi.org/10.1038/493599a
Head, M. L., Holman, L., Lanfear, R., Kahn, A. T., & Jennions, M. D. (2015). The Extent and Consequences of P-Hacking in Science. PLOS Biology , 13 (3), Article e1002106. https://doi.org/10.1371/journal.pbio.1002106
Ioannidis, J. P. A. (2005, August 30). Why Most Published Research Findings Are False. PLOS Medicine , 2 (8), e124. https://doi.org/10.1371/journal.pmed.0020124
Jp, S., Ld, N., & U, S. (2011, October 17). False-positive psychology: Undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychological Science, 22(11), 1359-1366. https://doi.org/10.1177/0956797611417632
Kafkafi, N., Agassi, J., Chesler, E. J., Crabbe, J. C., Crusio, W. E., Eilam, D., Gerlai, R., Golani, I., Gomez-Marin, A., Heller, R., Iraqi, F., Jaljuli, I., Karp, N. A., Morgan, H., Nicholson, G., Pfaff, D. W., Richter, S. H., Stark, P. B., Stiedl, O., … Benjamini, Y. (2018). Reproducibility and replicability of rodent phenotyping in preclinical studies. Neuroscience & Biobehavioral Reviews, 87, 218–232. https://doi.org/10.1016/j.neubiorev.2018.01.003
Kerr, N. L. (1998). HARKing: Hypothesizing After the Results are Known. Personality and Social Psychology Review, 2(3), 196–217. https://doi.org/10.1207/s15327957pspr0203_4
KNAW, NFU, NWO, TO2-Federatie, Vereniging Hogescholen, & VSNU. (2018). Nederlandse gedragscode wetenschappelijke integriteit. Data Archiving and Networked Services. https://doi.org/10.17026/DANS-2CJ-NVWU
Koul, A., Becchio, C., & Cavallo, A. (2018). Cross-Validation Approaches for Replicability in Psychology. Frontiers in Psychology, 9(1117). https://doi.org/10.3389/fpsyg.2018.01117
Kupferschmidt, K. (2018, September 21). More and more scientists are preregistering their studies. Should you? Science. https://doi.org/10.1126/science.aav4786
MacCoun, R., & Perlmutter, S. (2015). Blind analysis: Hide results to seek the truth. Nature News, 526(7572), 187-189. https://doi.org/10.1038/526187a
Marshall, D. & Shanahan, D. (2016, February 12). It’s a kind of magic: how to improve adherence to reporting guidelines. BMC Series Blog. http://blogs.biomedcentral.com/bmcseriesblog/2016/02/12/kind-magic-improve-adherence-reporting-guidelines/
Minikel, E. (2016, March 17). John Ioannidis: The state of research on research. CureFFI.org, https://www.cureffi.org/2016/03/17/john-ioannidis-the-state-of-research-on-research/
Munafò, M. R., Nosek, B. A., Bishop, D. V. M., Button, K. S., Chambers, C. D., Percie du Sert, N., Simonsohn, U., Wagenmakers, E.-J., Ware, J. J., & Ioannidis, J. P. A. (2017). A manifesto for reproducible science. Nature Human Behaviour, 1(1), 1–9. https://doi.org/10.1038/s41562-016-0021
National Academies of Sciences, Engineering and Medicine (2019). Reproducibility and Replicability in Science. https://doi.org/10.17226/25303
Nissen, S. B., Magidson, T., Gross, K., & Bergstrom, C. T. (2016). Publication bias and the canonization of false facts. eLife, 5, Article e21451. https://doi.org/10.7554/eLife.21451
Nosek, B. A., Ebersole, C. R., DeHaven, A. C., & Mellor, D. T. (2018). The preregistration revolution. Proceedings of the National Academy of Sciences, 115(11), 2600–2606. https://doi.org/10.1073/pnas.1708274114
Nosek, B. A., & Lakens, D. (2014). Registered Reports. Social Psychology, 45(3), 137–141. https://doi.org/10.1027/1864-9335/a000192
Pusztai, L., Hatzis, C., & Andre, F. (2013). Reproducibility of research and preclinical validation: Problems and solutions. Nature Reviews. Clinical Oncology, 10(12), 720–724. https://doi.org/10.1038/nrclinonc.2013.171
Scheel, A. M., Schijen, M., & Lakens, D. (2020, February 5). An excess of positive results: Comparing the standard Psychology literature with Registered Reports . PsyArXiv . https://doi.org/10.31234/osf.io/p6e9c
Smith, J., & Noble, H. (2014). Bias in research. Evidence Based Nursing , 17 (4), 100. https://doi.org/10.1136/eb-2014-101946
Stanford University. (n.d.). Gendered Innovations. Retrieved May 26, 2021, from http://genderedinnovations.stanford.edu/index.html
Steegen, S., Tuerlinckx, F., Gelman, A., & Vanpaemel, W. (2016). Increasing Transparency Through a Multiverse Analysis. Perspectives on Psychological Science, 11(5), 702–712. https://doi.org/10.1177/1745691616658637
Union, P. O. of the E. (2014, September 5). Gender in EU-funded research: Toolkit. [Website]. Publications Office of the European Union. http://op.europa.eu/en/publication-detail/-/publication/c118ea10-58fa-4173-a2c4-65c746918c20
The Embassy of Good Science. (2021, March 26). Data driven hypotheses without disclosure (‘HARKing’). https://embassy.science/wiki/Theme:26631aa0-18f0-4635-b71b-80a6f4e58d33
The Embassy of Good Science. (2021, March 26) Inappropriate study design. https://embassy.science/wiki/Theme:E14104ce-3608-4069-b297-f93b2d77b095
U.S. National Library of Medicine. (n.d.). Research Reporting Guidelines and Initiatives: By Organization. Retrieved May 26, 2021, from https://www.nlm.nih.gov/services/research_report_guide.html
Research Data Management
Corti, L., Van den Eynden, V., Bishop, L., & Woollard, M. (2014). Managing and Sharing Research Data: A Guide to Good Practice. Sage Publishing. https://doi.org/10.25607/OBP-1540
GO FAIR (n.d.). FAIR Principles. Retreived May 27, 2021 from https://www.go-fair.org/fair-principles/
Lamprecht, A.-L., Garcia, L., Kuzak, M., Martinez, C., Arcila, R., Martin Del Pico, E., Dominguez Del Angel, V., van de Sandt, S., Ison, J., Martinez, P. A., McQuilton, P., Valencia, A., Harrow, J., Psomopoulos, F., Gelpi, J. L., Chue Hong, N., Goble, C., & Capella-Gutierrez, S. (2020). Towards FAIR principles for research software. Data Science, 3(1), 37–59. https://doi.org/10.3233/DS-190026
Wilkinson, M. D., Dumontier, M., Aalbersberg, Ij. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3(1), 160018. https://doi.org/10.1038/sdata.2016.18
Reporting results
All European Academies. (n.d.). The European Code of Conduct for Research Integrity. Retrieved May 27, 2021, from https://allea.org/code-of-conduct/
Bik, E. (2019, juni 4). False affiliations and fake authors. Science Integrity Digest. https://scienceintegritydigest.com/2019/06/04/false-affiliations-and-fake-authors/
Bik, E. M., Casadevall, A., & Fang, F. C. (2016, May 17). The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications. BioRxiv, 049452. https://doi.org/10.1101/049452
Bourne, P. E., Polka, J. K., Vale, R. D., & Kiley, R. (2017). Ten simple rules to consider regarding preprint submission. PLOS Computational Biology, 13(5), Article e1005473. https://doi.org/10.1371/journal.pcbi.1005473
Callaway, E. (n.d.). Faked peer reviews prompt 64 retractions: Nature News & Comment. Nature. Retrieved May 27, 2021, from https://www.nature.com/news/faked-peer-reviews-prompt-64-retractions-1.18202
Committee on Publication Ethics. (n.d.). Authorship and contributorship. Retrieved May 27, 2021, from https://publicationethics.org/authorship
COPE Council. (2018, March). COPE Discussion Document: Preprints. https://publicationethics.org/files/u7140/COPE_Preprints_Mar18.pdf
Cornell University. (n.d.). ArXiv.org e-Print archive. Retrieved May 27, 2021, from https://arxiv.org/
Cromey, D. W. (2013). Digital images are data: And should be treated as such. In: D.J. Taatjes & J. Roth (Eds.), Methods in Molecular Biology: Vol.931. Cell Imaging Techniques. Methods and Protocols (pp. 1-27). Humana Press. https://doi.org/10.1007/978-1-62703-056-4_1
Directory of Open Access Journals (n.d.). Find Open Access journals or articles. Retrieved May 27, 2021, from https://doaj.org/ Ghent University. (n.d.). ORCID: what is it? (re)search tips. Retrieved May 27, 2021, from https://onderzoektips.ugent.be/en/tips/00001581/
HARKing. (2021). In Wikipedia. https://en.wikipedia.org/w/index.php?title=HARKing&oldid=1020774842
Heidari, S., Babor, T. F., De Castro, P., Tort, S., & Curno, M. (2016). Sex and Gender Equity in Research: Rationale for the SAGER guidelines and recommended use. Research Integrity and Peer Review, 1(1), 2. https://doi.org/10.1186/s41073-016-0007-6
Het uitgavecontract, Wetboek van economisch recht. Art. XI 196 § 2/1 (2018). http://www.ejustice.just.fgov.be/cgi_loi/loi_a1.pl?language=nl&la=N&cn=2013022819&table_name=wet&&caller=list&N&fromtab=wet&tri=dd+AS+RANK&rech=1&numero=1&sql=(text+contains+(%27%27))#Art.XI.196
Het uitgavecontract, Wetboek van economisch recht. Art. XI. 197. (2014). http://www.ejustice.just.fgov.be/cgi_loi/loi_a1.pl?language=nl&la=N&cn=2013022819&table_name=wet&&caller=list&N&fromtab=wet&tri=dd+AS+RANK&rech=1&numero=1&sql=(text+contains+(%27%27))#Art.XI.197
International Committee of Medical Journal Editors. (n.d.). Defining the Role of Authors and Contributors. Retrieved May 27, 2021, from http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html
Jisc Digital resources. (n.d.). Sherpa Romeo. Retrieved May 27, 2021, from https://v2.sherpa.ac.uk/romeo/
Kerr, N. L. (1998). HARKing: Hypothesizing After the Results are Known. Personality and Social Psychology Review, 2(3), 196–217. https://doi.org/10.1207/s15327957pspr0203_4
Matosin, N., Frank, E., Engel, M., Lum, J. S., & Newell, K. A. (2014). Negativity towards negative results: A discussion of the disconnect between scientific worth and scientific culture. Disease Models & Mechanisms , 7(2), 171–173. https://doi.org/10.1242/dmm.015123
Mudrak, B. (n.d.). What Are Preprints, and How Do They Benefit Authors? AJE Scholar. Retrieved May 27, 2021, from https://www.aje.com/arc/benefits-of-preprints-for-researchers/
Open Access Belgium (n.d.). Open science in Belgium. Retrieved May 27, 2021, from https://openaccess.be/ SPARC Europe (n.d.).
OACA list. Retrieved May 27 Mei, 2021, from https://sparceurope.org/what-we-do/open-access/sparc-europe-open-access-resources/open-access-citation-advantage-service-oaca/oaca-list/
The Office of Research Integrity (n.d.) . Authorship practices to avoid conflicts. [Infographic]. Retrieved May 27, 2021, from https://ori.hhs.gov/infographics
The Open Knowledge Foundation. (n.d.). The Open Definition. (z.d.). Retrieved May 27, 2021, from http://opendefinition.org/
The Writing Center. (n.d.). When to Summarize, Paraphrase, and Quote. Retrieved May 27, 2021, from https://writingcenter.gmu.edu/guides/when-to-summarize-paraphrase-and-quote
VWCI (2020) Authorship contribution statements. General advice (published 14 December 2020). https://vcwi.be/sites/default/files/VCWI_Advice_AuthorshipContributions-provisional.pdf
Weissgerber, T. L., Milic, N. M., Winham, S. J., & Garovic, V. D. (2015). Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLOS Biology, 13(4), Article e1002128. https://doi.org/10.1371/journal.pbio.1002128
Weissgerber, T. L., Winham, S. J., Heinzen, E. P., Milin-Lazovic, J. S., Garcia-Valencia, O., Bukumiric, Z., Savic, M. D., Garovic, V. D., & Milic, N. M. (2019). Reveal, Don’t Conceal. Circulation, 140(18), 1506–1518. https://doi.org/10.1161/CIRCULATIONAHA.118.037777
Declaration of Conflict of Interest
All European Academies (ALLEA). (n.d.). The European Code of Conduct for Research Integrity. Retrieved May 27, 2021, from https://allea.org/code-of-conduct/
European Network of Research Ethics and Research Integrity. (2009). Codes of ethics for scientific research in Belgium. https://eneri.eu/wp-content/uploads/2018/10/Codes-of-Ethics-for-scientific-research-in-Belgium.pdf
European Network of Research Integrity Offices. (2019) Recommendations for the investigation of research misconduct. http://www.enrio.eu/wp-content/uploads/2019/03/INV-Handbook_ENRIO_web_final.pdf
Van der Burght, S., Vandevelde, K., & Van Cauwenberge, P. (2013). Potentiële belangenconflicten in wetenschappelijk onderzoek: Een bespreking in vogelvlucht. Deontologie en Tuchtrecht , 1 , 63–82.
Science Communication
Lewandowsky, S., Cook, J., Ecker, U. K. H., Albarracín, D., Amazeen, M. A., Kendeou, P., Lombardi, D., Newman, E. J., Pennycook, G., Porter, E. Rand, D. G., Rapp, D. N., Reifler, J., Roozenbeek, J., Schmid, P., Seifert, C. M., Sinatra, G. M., Swire-Thompson, B., van der Linden, S., Vraga, E. K., Wood, T. J., Zaragoza, M. S. (2020). The debunking handbook. Center for climate change communication. https://sks.to/db2020
Mersch, R. (2016). Waarom iedereen altijd gelijk heeft. Bezige Bij.
Van Dyck, M. (2020, October 3). Science communication with Maarten Van Dyck [Video]. YouTube. https://www.youtube.com/watch?v=vnCPNhupW4U
Research(er) assessment and evaluation
Curry, S., de Rijcke, S., Hatch, A., Pillay, D. (Gansen), van der Weijden, I., & Wilsdon, J. (2020). The changing role of funders in responsible research assessment: Progress, obstacles and the way ahead. Research on Research Institute. https://doi.org/10.6084/m9.figshare.13227914.v1
Moher, D., Bouter, L., Kleinert, S., Glasziou, P., Sham, M. H., Barbour, V., Coriat, A.-M., Foeger, N., & Dirnagl, U. (2019). The Hong Kong Principles for Assessing Researchers: Fostering Research Integrity. OSF Preprints. https://doi.org/10.31219/osf.io/m9abx