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  1. Article ; Online: A Bibliometric Analysis of Mexican Bioinformatics

    Dagoberto Armenta-Medina / Christian Díaz de León Castañeda / Alma Armenta-Medina / Ernesto Perez-Rueda

    Biology, Vol 11, Iss 131, p

    A Portrait of Actors, Structure, and Dynamics

    2022  Volume 131

    Abstract: Bioinformatics is a very important informatics tool for health and biological sciences, focusing on biological data management. The objective of this work was to perform a bibliometric analysis regarding the development of Mexican bioinformatics. An ... ...

    Abstract Bioinformatics is a very important informatics tool for health and biological sciences, focusing on biological data management. The objective of this work was to perform a bibliometric analysis regarding the development of Mexican bioinformatics. An exhaustive revision of the literature associated with Mexican bioinformatics in a period of 25-years was performed. Bibliometric tools, such as performance analysis and science mapping were included in the analysis. We identified the main actors as well as the structure and dynamics of Mexican bioinformatics. Some of the main findings were as follows: the thematic structure in the field is defined by the research lines of outstanding authors; the outstanding collaborations of Mexican institutions with foreign countries and institutions are influenced by the geographic proximity and binational agreements, as well as philanthropic and academic programs that promote collaborations, and there is an inclination for health issues promoted by public health financing and philanthropic organizations. It is identified that publications had an explosion since 2012, we consider that this growth may be influenced by the democratization of data, derived from the mass sequencing of biological molecules stored in public databases.
    Keywords bibliometrics ; bibliographic databases ; Informatics ; health ; Information science ; bioinformatics ; Biology (General) ; QH301-705.5
    Subject code 001
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: A Web Application for Biomedical Text Mining of Scientific Literature Associated with Coronavirus-Related Syndromes

    Dagoberto Armenta-Medina / Aniel Jessica Leticia Brambila-Tapia / Sabino Miranda-Jiménez / Edel Rafael Rodea-Montero

    Diagnostics, Vol 12, Iss 887, p

    Coronavirus Finder

    2022  Volume 887

    Abstract: In this study, a web application was developed that comprises scientific literature associated with the Coronaviridae family, specifically for those viruses that are members of the Genus Betacoronavirus, responsible for emerging diseases with a great ... ...

    Abstract In this study, a web application was developed that comprises scientific literature associated with the Coronaviridae family, specifically for those viruses that are members of the Genus Betacoronavirus, responsible for emerging diseases with a great impact on human health: Middle East Respiratory Syndrome-Related Coronavirus (MERS-CoV) and Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV, SARS-CoV-2). The information compiled on this webserver aims to understand the basics of these viruses’ infection, and the nature of their pathogenesis, enabling the identification of molecular and cellular components that may function as potential targets on the design and development of successful treatments for the diseases associated with the Coronaviridae family. Some of the web application’s primary functions are searching for keywords within the scientific literature, natural language processing for the extraction of genes and words, the generation and visualization of gene networks associated with viral diseases derived from the analysis of latent semantic space, and cosine similarity measures. Interestingly, our gene association analysis reveals drug targets in understudies, and new targets suggested in the scientific literature to treat coronavirus.
    Keywords coronavirus ; natural language processing ; latent semantic analysis ; SARS ; MERS ; Medicine (General) ; R5-920
    Subject code 572
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Trends on Advanced Information and Communication Technologies for Improving Agricultural Productivities

    Dagoberto Armenta-Medina / Tania A. Ramirez-delReal / Daniel Villanueva-Vásquez / Cristian Mejia-Aguirre

    Agronomy, Vol 10, Iss 1989, p

    A Bibliometric Analysis

    2020  Volume 1989

    Abstract: In this work, an exhaustive revision is given of the literature associated with advanced information and communication technologies in agriculture within a window of 25 years using bibliometric tools enabled to detect of the main actors, structure, and ... ...

    Abstract In this work, an exhaustive revision is given of the literature associated with advanced information and communication technologies in agriculture within a window of 25 years using bibliometric tools enabled to detect of the main actors, structure, and dynamics in the scientific papers. The main findings are a trend of growth in the dynamics of publications associated with advanced information and communication technologies in agriculture productivity. Another assertion is that countries, like the USA, China, and Brazil, stand out in many publications due to allocating more resources to research, development, and agricultural productivity. In addition, the collaboration networks between countries are frequently in regions with closer cultural and idiomatic ties; additionally, terms’ occurrence are obtained with Louvain algorithm predominating four clusters: precision agriculture, smart agriculture, remote sensing, and climate smart agriculture. Finally, the thematic-map characterization with Callon’s density and centrality is applied in three periods. The first period of thematic analysis shows a transition in detecting the variability of a nutrient, such as nitrogen, through the help of immature georeferenced techniques, towards greater remote sensing involvement. In the transition from the second to the third stage, the maturation of technologies, such as unmanned aerial vehicles, wireless sensor networks, and the machine learning area, is observed.
    Keywords bibliometrics ; precision agriculture ; science mapping ; smart farming ; IoT ; Agriculture ; S
    Subject code 001
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Bioinformatics in Mexico

    Dagoberto Armenta-Medina / Christian Díaz de León-Castañeda / Brenda Valderrama-Blanco

    PLoS ONE, Vol 15, Iss 12, p e

    A diagnostic from the academic perspective and recommendations for a public policy.

    2020  Volume 0243531

    Abstract: In this work, we present a diagnostic analysis of strengths, weaknesses, opportunities and threats (SWOT) of the current state of Bioinformatics in Mexico. We conducted semi-structured interviews among researchers and academics with key expertise in this ...

    Abstract In this work, we present a diagnostic analysis of strengths, weaknesses, opportunities and threats (SWOT) of the current state of Bioinformatics in Mexico. We conducted semi-structured interviews among researchers and academics with key expertise in this field, identified by bibliometric analyses and qualitative sampling techniques. Additionally, an online survey was conducted reaching a higher number of respondents. Among the relevant findings of our study, the lack of specialized human resources and technological infrastructure stood out, along with deficiencies in the number and quality of academic programs, scarce public investment and a weak relationship between public and private institutions. However, there are great opportunities for developing a national Bioinformatics to support different economic sectors. In our opinion, this work could be useful to favor a comprehensive network among Mexican researchers, in order to lay the foundations of a national strategy towards a well designed public policy.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors.

    Ernesto Perez-Rueda / Rafael Hernandez-Guerrero / Mario Alberto Martinez-Nuñez / Dagoberto Armenta-Medina / Israel Sanchez / J Antonio Ibarra

    PLoS ONE, Vol 13, Iss 4, p e

    2018  Volume 0195332

    Abstract: Gene regulation at the transcriptional level is a central process in all organisms, and DNA-binding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing ... ...

    Abstract Gene regulation at the transcriptional level is a central process in all organisms, and DNA-binding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing gene expression. In general, TFs are composed of two domains: the DNA-binding domain (DBD) and an extra domain, which in this work we have named "companion domain" (CD). This latter could be involved in one or more functions such as ligand binding, protein-protein interactions or even with enzymatic activity. In contrast to DBDs, which have been widely characterized both experimentally and bioinformatically, information on the abundance, distribution, variability and possible role of the CDs is scarce. Here, we investigated these issues associated with the domain architectures of TFs in prokaryotic genomes. To this end, 19 families of TFs in 761 non-redundant bacterial and archaeal genomes were evaluated. In this regard we found four main groups based on the abundance and distribution in the analyzed genomes: i) LysR and TetR/AcrR; ii) AraC/XylS, SinR, and others; iii) Lrp, Fis, ArsR, and others; and iv) a group that included only two families, ArgR and BirA. Based on a classification of the organisms according to the life-styles, a major abundance of regulatory families in free-living organisms, in contrast with pathogenic, extremophilic or intracellular organisms, was identified. Finally, the protein architecture diversity associated to the 19 families considering a weight score for domain promiscuity evidenced which regulatory families were characterized by either a large diversity of CDs, here named as "promiscuous" families given the elevated number of variable domains found in those TFs, or a low diversity of CDs. Altogether this information helped us to understand the diversity and distribution of the 19 Prokaryotes TF families. Moreover, initial steps were taken to comprehend the variability of the extra domain in those TFs, which eventually might assist in ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M.

    Aniel Jessica Leticia Brambila-Tapia / Dagoberto Armenta-Medina / Nancy Rivera-Gomez / Ernesto Perez-Rueda

    PLoS ONE, Vol 9, Iss 6, p e

    2014  Volume 100349

    Abstract: Many virulence genes have been detected in attenuated mutants of Brucella melitensis 16 M; nevertheless, a complete report of these genes, including the main Cluster of Orthologous Groups (COG) represented as well as the taxonomical distribution among ... ...

    Abstract Many virulence genes have been detected in attenuated mutants of Brucella melitensis 16 M; nevertheless, a complete report of these genes, including the main Cluster of Orthologous Groups (COG) represented as well as the taxonomical distribution among all complete bacterial and archaeal genomes, has not been analyzed. In this work a total of 160 virulence genes that have been reported in attenuated mutants in B. melitensis were included and analyzed. Additionally, we obtained 250 B. melitensis randomly selected genes as a reference group for the taxonomical comparisons. The COGs and the taxonomical distribution profile for 789 nonredundant bacterial and archaeal genomes were obtained and compared with the whole-genome COG distribution and with the 250 randomly selected genes, respectively. The main COGs associated with virulence genes corresponded to the following: intracellular trafficking, secretion and vesicular transport (U); cell motility (N); nucleotide transport and metabolism (F); transcription (K); and cell wall/membrane/envelope biogenesis (M). In addition, we found that virulence genes presented a higher proportion of orthologs in the Euryarchaeota and Proteobacteria phyla, with a significant decrease in Chlamydiae, Bacteroidetes, Tenericutes, Firmicutes and Thermotogae. In conclusion, we found that genes related to specific functions are more relevant to B. melitensis virulence, with the COG U the most significant. Additionally, the taxonomical distribution of virulence genes highlights the importance of these genes in the related Proteobacteria, being less relevant in distant groups of organisms with the exception of Euryarchaeota.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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