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Analysis of institutional authors

Blevins WrAuthorEspinar, LAuthor

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February 17, 2021
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Article

Uncovering de novo gene birth in yeast using deep transcriptomics

Publicated to:Nature Communications. 12 (1): 604- - 2021-12-01 12(1), DOI: 10.1038/s41467-021-20911-3

Authors: Blevins, WR; Ruiz-Orera, J; Messeguer, X; Blasco-Moreno, B; Villanueva-Cañas, JL; Espinar, L; Díez, J; Carey, LB; Albà, MM

Affiliations

Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany - Author
Catalan Inst Res & Adv Studies ICREA, Barcelona, Spain - Author
Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain - Author
Center for Quantitative Biology and Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China - Author
Computer Sciences Department, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain - Author
Ctr Nacl Anal Genom CNAG, Single Cell Genom Grp, Barcelona, Spain - Author
Ctr Regulatory Genom CRG, Dept Gene Regulat Stem Cells & Canc, Barcelona, Spain - Author
Department of Gene Regulation, Stem Cells and Cancer, Centre for Regulatory Genomics (CRG), Barcelona, Spain - Author
Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain - Author
Hosp del Mar Res Inst IMIM, Evolutionary Genom Grp, Res Programme Biomed Informat, Barcelona, Spain - Author
Max Delbruck Ctr Mol Med Helmholtz Assoc MDC, Cardiovasc & Metab Sci, Berlin, Germany - Author
Molecular Biology CORE, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain - Author
Molecular Virology group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain - Author
Peking Univ, Acad Adv Interdisciplinary Studies, Ctr Quantitat Biol & Peking Tsinghua Joint Ctr Li, Beijing, Peoples R China - Author
Single Cell Behavior Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain - Author
Single Cell Genomics Group, Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain - Author
Univ Barcelona, Hosp Clin, Mol Biol CORE, Barcelona, Spain - Author
Univ Politecn Catalunya UPC, Comp Sci Dept, Barcelona, Spain - Author
Univ Pompeu Fabra UPF, Barcelona, Spain - Author
Univ Pompeu Fabra UPF, Dept Expt & Hlth Sci, Mol Virol Grp, Barcelona, Spain - Author
Univ Pompeu Fabra UPF, Dept Expt & Hlth Sci, Single Cell Behav Grp, Barcelona, Spain - Author
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Abstract

De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts originate in more densely-packed genomes. Here, we identify 213 de novo originated transcripts in Saccharomyces cerevisiae using deep transcriptomics and genomic synteny information from multiple yeast species grown in two different conditions. We find that about half of the de novo transcripts are expressed from regions which already harbor other genes in the opposite orientation; these transcripts show similar expression changes in response to stress as their overlapping counterparts, and some appear to translate small proteins. Thus, a large fraction of de novo genes in yeast are likely to co-evolve with already existing genes. © 2021, The Author(s).

Keywords

ArticleConserved sequenceGene expressionGene expression regulation, fungalGene regulatory networksGenes, fungalGenomeGrowth responseNonhumanOpen reading framesPhysiological stressProteinRna, messengerSaccharomyces cerevisiaeSaccharomyces cerevisiae proteinsSyntenyTranscriptomeTranscriptomicsYeast

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nature Communications 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, 2021, it was in position 6/74, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences. 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: 2.69. 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: 3.03 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 18.54 (source consulted: Dimensions Aug 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-08-02, the following number of citations:

  • WoS: 52
  • Scopus: 53
  • Europe PMC: 32

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 2025-08-02:

  • 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: 94.
  • 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: 93 (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: 33.7.
  • The number of mentions on the social network X (formerly Twitter): 55 (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: China; Germany.

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 (Blevins, William) .