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This work was supported by the European Commission (FP7-HEALTH: READNA project; FP7-INFRASTRUCTURES: ESGI project; BLUEPRINT project), the Spanish Ministry of Economy, Industry and Competitiveness (BIO2015 grant 71969 REDI, 'Centro de Excelencia Severo Ochoa' and EMBL Partnership), and the Generalitat de Catalunia (CERCA Programme).

Analysis of institutional authors

Heath, SimonAuthorGut, IvoAuthorMerkel ACorresponding AuthorFernandez-Callejo MAuthorCasals EAuthor
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Article

gemBS: high throughput processing for DNA methylation data from bisulfite sequencing

Publicated to:Bioinformatics. 35 (5): 737-742 - 2019-03-01 35(5), DOI: 10.1093/bioinformatics/bty690

Authors: Merkel, A; Fernández-Callejo, M; Casals, E; Marco-Sola, S; Schuyler, R; Gut, IG; Heath, SC

Affiliations

Barcelona Inst Sci & Technol, CNAG, CRG, Barcelona 08028, Spain - Author
Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.;Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.;Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.;Universitat Autònoma de Barcelona, Bellaterra, Spain.;Department of Immunology and Microbiology, University of Colorado, Aurora, CO, USA.;Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.;Universitat Pompeu Fabra (UPF), Barcelona, Spain.;Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.;Universitat Pompeu Fabra (UPF), Barcelona, Spain. - Author
Univ Autonoma Barcelona, Bellaterra 08193, Spain - Author
Univ Colorado, Dept Immunol & Microbiol, Aurora, CO 80045 USA - Author
UPF, Barcelona 08002, Spain - Author
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Abstract

DNA methylation is essential for normal embryogenesis and development in mammals and can be captured at single base pair resolution by whole genome bisulfite sequencing (WGBS). Current available analysis tools are becoming rapidly outdated as they lack sensible functionality and efficiency to handle large amounts of data now commonly created.We developed gemBS, a fast high-throughput bioinformatics pipeline specifically designed for large scale BS-Seq analysis that combines a high performance BS-mapper (GEM3) and a variant caller specifically for BS-Seq data (BScall). gemBS provides genotype information and methylation estimates for all genomic cytosines in different contexts (CpG and non-CpG) and a set of quality reports for comprehensive and reproducible analysis. gemBS is highly modular and can be easily automated, while producing robust and accurate results.gemBS is released under the GNU GPLv3+ license. Source code and documentation are freely available from www.statgen.cat/gemBS.Supplementary data are available at Bioinformatics online.© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Keywords
AnimalsDna methylationHigh-throughput nucleotide sequencingHydrogen sulfiteSequence analysis, dnaSoftwareSulfites

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Bioinformatics 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, 2019, it was in position 3/59, thus managing to position itself as a Q1 (Primer Cuartil), in the category Mathematical & Computational Biology. Notably, the journal is positioned above the 90th percentile.

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: 1.78. 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 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 1.29 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 10.71 (source consulted: Dimensions May 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-05-23, the following number of citations:

  • WoS: 37
  • Scopus: 36
  • Europe PMC: 23
  • OpenCitations: 51
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 2025-05-23:

  • 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: 113.
  • 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: 113 (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: 8.83.
  • The number of mentions on the social network X (formerly Twitter): 4 (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.
Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: 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 (MERKEL, ANGELIKA) and Last Author (Heath SC).

the author responsible for correspondence tasks has been MERKEL, ANGELIKA.