{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T03:40:14Z","timestamp":1768016414970,"version":"3.49.0"},"reference-count":20,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T00:00:00Z","timestamp":1668038400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"This study was supported by the Thomas Jefferson University Institutional Funds."}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The \u201creplication crisis\u201d is a methodological problem in which many scientific research findings have been difficult or impossible to replicate. Because the reproducibility of empirical results is an essential aspect of the scientific method, such failures endanger the credibility of theories based on them and possibly significant portions of scientific knowledge. An instance of the replication crisis, analytic replication, pertains to reproducing published results through computational reanalysis of the authors\u2019 original data. However, direct replications are costly, time-consuming, and unrewarded in today\u2019s publishing standards. We propose that bioinformatics and computational biology students replicate recent discoveries as part of their curriculum. Considering the above, we performed a pilot study in one of the graduate-level courses we developed and taught at our University. The course is entitled Intro to R Programming and is meant for students in our Master\u2019s and PhD programs who have little to no programming skills. As the course emphasized real-world data analysis, we thought it would be an appropriate setting to carry out this study. The primary objective was to expose the students to real biological data analysis problems. These include locating and downloading the needed datasets, understanding any underlying conventions and annotations, understanding the analytical methods, and regenerating multiple graphs from their assigned article. The secondary goal was to determine whether the assigned articles contained sufficient information for a graduate-level student to replicate its figures. Overall, the students successfully reproduced 39% of the figures. The main obstacles were the need for more advanced programming skills and the incomplete documentation of the applied methods. Students were engaged, enthusiastic, and focused throughout the semester. We believe that this teaching approach will allow students to make fundamental scientific contributions under appropriate supervision. It will teach them about the scientific process, the importance of reporting standards, and the importance of openness.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010615","type":"journal-article","created":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T18:24:17Z","timestamp":1668104657000},"page":"e1010615","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Reproducibility efforts as a teaching tool: A pilot study"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4119-0851","authenticated-orcid":true,"given":"Nestoras","family":"Karathanasis","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6071-8271","authenticated-orcid":true,"given":"Daniel","family":"Hwang","sequence":"additional","affiliation":[]},{"given":"Vibol","family":"Heng","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5973-8048","authenticated-orcid":true,"given":"Rimal","family":"Abhimannyu","sequence":"additional","affiliation":[]},{"given":"Phillip","family":"Slogoff-Sevilla","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5266-2477","authenticated-orcid":true,"given":"Gina","family":"Buchel","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7558-9006","authenticated-orcid":true,"given":"Victoria","family":"Frisbie","sequence":"additional","affiliation":[]},{"given":"Peiyao","family":"Li","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8541-4004","authenticated-orcid":true,"given":"Dafni","family":"Kryoneriti","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1529-8631","authenticated-orcid":true,"given":"Isidore","family":"Rigoutsos","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,11,10]]},"reference":[{"key":"pcbi.1010615.ref001","first-page":"5","article-title":"Bioconductor: open software development for computational biology and bioinformatics","author":"RC Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"pcbi.1010615.ref002","volume-title":"The book of R: a first course in programming and statistics by Tilman M. 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Kerr","year":"1998","journal-title":"Personal Soc Psychol Rev"},{"key":"pcbi.1010615.ref007","first-page":"1","article-title":"The Extent and Consequences of P-Hacking in Science","volume":"13","author":"ML Head","year":"2015","journal-title":"PLoS Biol"},{"key":"pcbi.1010615.ref008","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1037\/0033-2909.86.3.638","article-title":"The file drawer problem and tolerance for null results.","volume":"86","author":"R. Rosenthal","year":"1979","journal-title":"Psychol Bull."},{"key":"pcbi.1010615.ref009","first-page":"1","article-title":"No raw data, no science: another possible source of the reproducibility crisis","author":"T. Miyakawa","year":"2020","journal-title":"Mol Brain"},{"key":"pcbi.1010615.ref010","first-page":"96","article-title":"What does research reproducibility mean?","volume":"8","author":"SN Goodman","year":"2018","journal-title":"Get to Good Res Integr Biomed Sci"},{"key":"pcbi.1010615.ref011","author":"W Mark","year":"2014","journal-title":"How can scientists enhance rigor in conducting basic research and reporting research results?"},{"key":"pcbi.1010615.ref012","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1177\/1745691612459057","article-title":"Harnessing the Undiscovered Resource of Student Research Projects.","volume":"7","author":"JE Grahe","year":"2012","journal-title":"Perspect Psychol Sci."},{"key":"pcbi.1010615.ref013","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1177\/1745691612460686","article-title":"Teaching Replication.","volume":"7","author":"MC Frank","year":"2012","journal-title":"Perspect Psychol Sci."},{"key":"pcbi.1010615.ref014","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1017\/aap.2019.38","article-title":"How to Use Replication Assignments for Teaching Integrity in Empirical Archaeology.","volume":"8","author":"B Marwick","year":"2020","journal-title":"Adv Archaeol Pract."},{"key":"pcbi.1010615.ref015","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-11610-1","article-title":"Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis.","volume":"10","author":"J Vedanayagam","year":"2019","journal-title":"Nat Commun."},{"key":"pcbi.1010615.ref016","first-page":"1","article-title":"BMI1 regulates androgen receptor in prostate cancer independently of the polycomb repressive complex 1.","volume":"9","author":"S Zhu","year":"2018","journal-title":"Nat Commun."},{"key":"pcbi.1010615.ref017","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1016\/j.neuron.2018.05.014","article-title":"A Combination of Ontogeny and CNS Environment Establishes Microglial Identity.","volume":"98","author":"FC Bennett","year":"2018","journal-title":"Neuron"},{"key":"pcbi.1010615.ref018","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1016\/j.cell.2011.06.051","article-title":"The human mitochondrial transcriptome","volume":"146","author":"TR Mercer","year":"2011","journal-title":"Cell"},{"key":"pcbi.1010615.ref019","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"E Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010615.ref020","first-page":"3","article-title":"Is there a reproducibility crisis in science?","author":"M. 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