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Grant support

This work was supported by grant PID2019-111256RB-I00 funded by MCIN/AEI/10.13039/501100011033 to R.D.U.; P.H.N. supported by Comunidad deMadrid's [PEJ-2019-AI/BMD-13961 to R.D.U.].

Impact on the Sustainable Development Goals (SDGs)

Analysis of institutional authors

Diaz-Uriarte RCorresponding Author
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EvAM-Tools: tools for evolutionary accumulation and cancer progression models

Publicated to:BIOINFORMATICS. 38 (24): 5457-5459 - 2022-12-15 38(24), DOI: 10.1093/bioinformatics/btac710

Authors: Diaz-Uriarte R, Herrera-Nieto P

Affiliations

Department of Biochemistry, Universidad Autónoma de Madrid, Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain. - Author
Univ Autonoma Madrid, Inst Invest Biomed Alberto Sols UAM CSIC, Dept Biochem, Madrid, Spain - Author

Abstract

EvAM-Tools is an R package and web application that provides a unified interface to state-of-the-art cancer progression models (CPMs) and, more generally, evolutionary models of event accumulation. The output includes, in addition to the fitted models, the transition (and transition rate) matrices between genotypes and the probabilities of evolutionary paths. Generation of random cancer progression models is also available. Using the GUI in the web application, users can easily construct models (modifying Directed Acyclic Graphs -DAGs- of restrictions, matrices of mutual hazards, or specifying genotype composition), generate data from them (with user-specified observational/genotyping error), and analyze the data.Implemented in R and C; open source code available under the GNU Affero General Public License v3.0 at https://github.com/rdiaz02/EvAM-Tools. Docker images freely available from https://hub.docker.com/u/rdiaz02. Web app freely accessible at https://iib.uam.es/evamtools.Supplementary data are available at Bioinformatics online.© The Author(s) 2022. Published by Oxford University Press.

Keywords
Astronomia / físicaBiochemical research methodsBiochemistryBiodiversidadeBiology, miscellaneousBiotechnology & applied microbiologyBiotecnologíaCiência da computaçãoCiências agrárias iCiências biológicas iCiências biológicas iiCiências biológicas iiiComputational mathematicsComputational theory and mathematicsComputer science applicationsComputer science, interdisciplinary applicationsEconomiaEngenharias ivGeneral medicineInterdisciplinarMatemática / probabilidade e estatísticaMathematical & computational biologyMathematics, interdisciplinary applicationsMedicina iMedicina iiMedicina veterinariaMolecular biologyNutriçãoOdontologíaStatistics & probabilityStatistics and probability

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, 2022, it was in position 8/77, 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 the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 3.97, which 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: Dimensions May 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-05-06, the following number of citations:

  • Scopus: 5
  • Google Scholar: 5
  • Open Alex: 8
  • OpenCitations: 9
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 2025-05-06:

  • 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: 1 (PlumX).

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://repositorio.uam.es/handle/10486/711662
Continuing with the social impact of the work, it is important to emphasize that, due to its content, it can be assigned to the area of interest of ODS 17 - Strengthen the means of implementation and revitalize the Global Partnership for Sustainable Development, with a probability of 42% according to the mBERT algorithm developed by Aurora University.
Leadership analysis of institutional authors

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 (DIAZ URIARTE, RAMON) and Last Author (Herrera-Nieto P).

the author responsible for correspondence tasks has been DIAZ URIARTE, RAMON.