A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics

Armenta-Medina, Dagoberto; Castañeda, Christian Díaz de León; Armenta-Medina, Alma; Pérez‐Rueda, Ernesto

doi:10.3390/biology11010131

Cited by 5 publications

(8 citation statements)

References 41 publications

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“…The following search strategy was used with limiting organizational affiliation to Iran in the keywords, abstract, and title fields. It should be noted that the same search strategy has been used in a study conducted by Armenta et al [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

Analysis of Persian Bioinformatics Research with Topic Modeling

Ebrahimi

Dehghani

Makkizadeh

2023

BioMed Research International

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Purpose. As a scientific field, bioinformatics has drawn remarkable attention from various fields, such as information technology, mathematics, and modern biological sciences, in recent years. The topic models originating from the field of natural language processing have become the focus of attention with the rapid accumulation of biological datasets. Thus, this research is aimed at modeling the topic content of the bioinformatics literature presented by Iranian researchers in the Scopus Citation Database. Methodology. This research was a descriptive-exploratory study, and the studied population included 3899 papers indexed in the Scopus database, which had been indexed in this database until March 9, 2022. The topic modeling was then performed on the abstracts and titles of the papers. A combination of LDA and TF-IDF was utilized for topic modeling. Findings. The data analysis with topic modeling resulted in identifying seven main topics “Molecular Modeling,” “Gene Expression,” “Biomarker,” “Coronavirus,” “Immunoinformatics,” “Cancer Bioinformatics,” and “Systems Biology.” Moreover, “Systems Biology” and “Coronavirus” had the largest and smallest clusters, respectively. Conclusion. The present investigation demonstrated an acceptable performance for the LDA algorithm in classifying the topics included in this field. The extracted topic clusters indicated excellent consistency and topic connection with each other.

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Section: Methodsmentioning

confidence: 99%

Analysis of Persian Bioinformatics Research with Topic Modeling

Ebrahimi

Dehghani

Makkizadeh

2023

BioMed Research International

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“…Documents were uploading in BibTeX format and analyzed using Bibliometrix, R package. We analyzed the data frame using the Biblioshiny web app (version 3.1.4; https://www.bibliometrix.org/home/, accessed on 21 February 2024) [9,22].…”

Section: Bibliographic Data Recoverymentioning

confidence: 99%

“…For each article, the address provided by the rst author's research institution, including the geographical eld of the countries included in the approach, was collected. When the rst author's address was not identi ed, the second author's institute was used [9,24].…”

Section: Country Of the Rst Authorsmentioning

confidence: 99%

“…The thematic evolution is organized in bibliometric maps and constructed by linking themes from one subperiod with those from the next subperiod through conceptual links. A communication path between themes is generated when there is a link between them, i.e., if they have common connective elements, such as keywords [9].…”

Section: Thematic Evolutionmentioning

confidence: 99%

“…Advances in whole-genome sequencing technologies and the use of high-density SNP arrays in scanning the genome for ROH has been proposed as an effective method for identifying IBD haplotypes are already available for humans and species of agricultural interest [5][6][7][8]. The scienti c knowledge acquired has contributed to revealing unknown aspects of the genome and biological systems, resulting in a signi cant increase in research and publications in the eld of molecular genetics [9] In this context, signi cant advances in whole-genome scale approaches, when applied to genomic scans, can reveal genomic patterns of runs of homozygosity (ROH), highlighting the genetic variation that exists between individuals and enabling the detection of associations between genomic regions and adaptive phenotypes.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and runs of homozygosity (ROH): A portrait of the quantitative academic publication dynamic and scientific metadata

Sobrinho,

Coelho,

Moura

et al. 2024

Preprint

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Background Autozygosity is the homozygous state of identical-by-descent (IBD) alleles, which can result from several phenomena. The increase in inbreeding (F) leads to different negative effects such as a reduction in genetic variance, with a reduction in individual performance (inbreeding depression) and lower population viability. Nowadays, among several alternative methods to estimate inbreeding, F estimated from Run of Homozygosity (FROH) is considered the most powerful. This study aimed to provide a systematic review to comprehensive understanding of the structure and dynamics of genomic diversity and the impact of ROH studies over the last decade, highlighting directions and opportunities for future research. Results 406 publications were identified on WoS core collection and applied to bibliometric analysis available in the R environment. The analysis revealed an increased number of publications per year. China, Italy, and the United States are the countries that published the most on the topic, with the main contributions published in journals such as Animals and Frontiers in Genetics. This study highlights the growing interest in the functional analysis of ROHs driven by computational tools capable of characterizing these genomic regions. Noteworthy are the PLINK software and the detectRUNS package, utilizing a sliding window methodology for SNP analysis in the genome. Beyond a global crisis of genetic diversity loss, challenges encompass ecological issues, habitat fragmentation, and isolated populations, as well as the availability of genetic variation in species domesticated by humans, which forms the foundation of our food supply. Conclusion A bibliometric analysis highlights the growing interest and progress of research in breeds of homozygosity (ROH) and genetic diversity, driven by the advancement of genomic technology and international collaboration. Asia, America and Europe lead in knowledge production. Advances like PLINK and detectRUNS in R mean a quest for more accurate analysis. Emerging topics such as migration and correlation indicate an increasing focus on the impact of ROH standards. Challenges include refining analytical techniques and exploring regions of high heterozygosity, promising future research directions.

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