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Analysis of institutional authors

Garijo D.Author

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June 9, 2019
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Article

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

Publicated to: PLoS One. 8 (11): e80278- - 2013-11-27 8(11), DOI: 10.1371/journal.pone.0080278

Authors:

Garijo, Daniel; Kinnings, Sarah; Xie, Li; Xie, Lei; Zhang, Yinliang; Bourne, Philip E; Gil, Yolanda
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Affiliations

CUNY Hunter Coll, Dept Comp Sci, New York, NY 10021 USA - Author
Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA - Author
Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA - Author
Univ Politecn Madrid, Fac Informat, Ontol Engn Grp, Madrid, Spain - Author
Univ Sci & Technol China, Sch Life Sci, Hefei, Anhui, Peoples R China - Author
Univ So Calif, Dept Comp Sci, Los Angeles, CA 90089 USA - Author
Univ So Calif, Inst Informat Sci, Los Angeles, CA USA - Author
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Abstract

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to reproducibility maps that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one's own laboratory.
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Keywords

Computational biologyHumansInternetRepeatabilityReproducibility of resultsSoftware

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal PLoS One due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2013, it was in position 8/55, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 1.35. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 13, 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2026-04-24, the following number of citations:

  • WoS: 65
  • Scopus: 75
  • Europe PMC: 48
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-24:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 192.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 192 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 109.
  • The number of mentions on the social network Facebook: 1 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 110 (Altmetric).
  • The number of mentions in news outlets: 3 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://oa.upm.es/21853/

As a result of the publication of the work in the institutional repository, statistical usage data has been obtained that reflects its impact. In terms of dissemination, we can state that, as of

  • Views: 371
  • Downloads: 595
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: China; United States of America.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (GARIJO VERDEJO, DANIEL) .

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Awards linked to the item

This research is sponsored by Elsevier Labs, the National Science Foundation with award number IIS-0948429, the Air Force Office of Scientific Research with award number FA9550-11-1-0104, internal funds from the University of Southern California's Information Sciences Institute and from the University of California, San Diego, and by a Formacion de Profesorado Universitario grant from the Spanish Ministry of Science and Innovation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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