The bioinformatics wealth of nations

Bibliometric analysis of hypospadias from 1998-2023

Introduction

To analyze the development trends and research hotspots in the field of hypospadias through bibliometric analysis.

Methods

Utilizing three bibliometric mapping tools-bibliometrix R package, VOSviewer, and CiteSpace, we summarized the overview information of the retrieved literature. We conducted analyses on the co-occurrence and development trends of authors, institutions, countries, and keywords.

Results

A total of 3,647 hypospadias-related publications were included, with contributions from 14,633 authors. The keyword co-occurrence network identified seven clusters related to the diagnosis, pathophysiology, and treatment of hypospadias. Researchers have primarily focused on the genetic mechanisms of hypospadias, the role of environmental factors, surgical outcomes, anesthesia techniques, and patient satisfaction post-surgery. Emerging research hotspots include the precise selection of surgical flap sources, genomic alterations, and the correlation with syndromes related to disorders of sex development, all of which show strong potential for future breakthroughs.

Discussion

Bibliometric analysis provides a comprehensive understanding of the research hotspots and development trends in hypospadias, thereby enriching the field of hypospadias research.

Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq

BACKGROUND

Bioinformatics is fundamental to biomedical sciences, but its mastery presents a steep learning curve for bench biologists and clinicians. Learning to code while analyzing data is difficult. The curve may be flattened by separating these two aspects and providing intermediate steps for budding bioinformaticians. Single-cell analysis is in great demand from biologists and biomedical scientists, as evidenced by the proliferation of training events, materials, and collaborative global efforts like the Human Cell Atlas. However, iterative analyses lacking reinstantiation, coupled with unstandardized pipelines, have made effective single-cell training a moving target.

FINDINGS

To address these challenges, we present a Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for single-cell RNA sequencing (scRNA-seq) analysis, which offers parallel analytical methods using a graphical interface (buttons) or code. With clear, interoperable materials, MIGHTS facilitates smooth transitions between environments. Bridging the biologist-programmer gap, MIGHTS emphasizes interdisciplinary communication for effective learning at all levels. Real-world data analysis in MIGHTS promotes critical thinking and best practices, while FAIR data principles ensure validation of results. MIGHTS is freely available, hosted on the Galaxy Training Network, and leverages Galaxy interfaces for analyses in both settings. Given the ongoing popularity of Python-based (Scanpy) and R-based (Seurat & Monocle) scRNA-seq analyses, MIGHTS enables analyses using both.

CONCLUSIONS

MIGHTS consists of 11 tutorials, including recordings, slide decks, and interactive visualizations, and a demonstrated track record of sustainability via regular updates and community collaborations. Parallel pathways in MIGHTS enable concurrent training of scientists at any programming level, addressing the heterogeneous needs of novice bioinformaticians.

Assessing the publication output in the field of forensic science and legal medicine using Web of Science database from 2011 to 2020

The aim of this study was threefold. First, it analyzed the characteristics of the publication outputs for the Legal Medicine (LM) category using the Web of Science (WoS) database during 2011-2020. Second, it discussed the distribution of the papers for the 25 most productive countries/regions in terms of quality and quantity, such as the h-index and GDP per capita. Finally, it investigated the trend and temporal stability of the journal impact factor (JIF) and determined the percentage of the journal self-citations. The findings suggested that the number of papers, the average number of pages of the papers, the average number of cited references in the papers, the average number of authors per paper, the percentage of open access papers, as well as international and domestic collaboration tended to increase regularly. However, the productivity was limited when compared to the whole WoS database, since there was no significant change in the number of the journals. The countries/regions with the highest number of publications were not those that made the most impact in terms of the widespread impact of the publications. The level of international cooperation and the funding for the research had dramatic impact on the visibility of papers. The average JIF has increased significantly while the journal self-citation rates have decreased in a similar way. The journals have had very stable (have not fluctuated) impact factors over time. During the period studied, the journals with the higher impact factors (Q1, Q2) published many more papers than journals with the lower impact factors (Q3, Q4).

Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology

Aims

Resource‐strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings.

Methods

We used simple information theory calculations on a brain cancer simulation model and real‐world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&E and Olig2 stained images obtained from digital slides. An auto‐adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH‐mutant tumors.

Results

Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH‐mutant tumors. The predictive models may facilitate the reduction of false‐positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing.

Conclusions

We posit that this approach provides an improvement on the cIMPACT‐NOW workflow recommendations for IDH‐mutant tumors and a framework for future resource and testing allocation.

The past, present and future of genomics and bioinformatics: A survey of Brazilian scientists

Brazil has one of the highest rates of scientific production, occupying the ninth position among countries with genome-sequencing projects. Considering the rapid development of this research area and the diversity of professionals involved, the present study aims to understand the expectations, past experiences and the current scenario of Brazilian research in bioinformatics and genomics. The present research was carried out by analyzing the perceptions of 576 researchers in genomics and bioinformatics in Brazil through content and sentiment analysis techniques. This group of participants is equivalent to 48% of the members of the research community. The results suggest that most researchers have a positive perception of the potential of this research area. However, there is concern about the lack of funding for investing in equipment and professional training. As part of a wish list for the future, researchers highlighted the need for higher funding, formal education, and collaboration among research networks. When asked about genomics and bioinformatics in other countries, the participants recognize that sequencing technologies and infrastructure are more accessible, allowing better data volume expansion.

African Global Representation in Biomedical Sciences

African populations are diverse in their ethnicity, language, culture, and genetics. Although plagued by high disease burdens, until recently the continent has largely been excluded from biomedical studies. Along with limitations in research and clinical infrastructure, human capacity, and funding, this omission has resulted in an underrepresentation of African data and disadvantaged African scientists. This review interrogates the relative abundance of biomedical data from Africa, primarily in genomics and other omics. The visibility of African science through publications is also discussed. A challenge encountered in this review is the relative lack of annotation of data on their geographical or population origin, with African countries represented as a single group. In addition to the abovementioned limitations,the global representation of African data may also be attributed to the hesitation to deposit data in public repositories. Whatever the reason, the disparity should be addressed, as African data have enormous value for scientists in Africa and globally.

Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review

BACKGROUND

The successful sequencing of SARS-CoV-2 cleared the way for the use of omics technologies and integrative biology research for combating the COVID-19 pandemic. Currently, many research groups have slowed down their respective projects to concentrate efforts in the study of the biology of SARS-CoV-2. In this bibliometric analysis and mini-review, we aimed to describe how computational methods or omics approaches were used during the first months of the COVID-19 pandemic.

METHODS

We analyzed bibliometric data from Scopus, BioRxiv, and MedRxiv (dated June 19th, 2020) using quantitative and knowledge mapping approaches. We complemented our analysis with a manual process of carefully reading the selected articles to identify either the omics or bioinformatic tools used and their purpose.

RESULTS

From a total of 184 articles, we found that metagenomics and transcriptomics were the main sources of data to perform phylogenetic analysis aimed at corroborating zoonotic transmission, identifying the animal origin and taxonomic allocation of SARS-CoV-2. Protein sequence analysis, immunoinformatics and molecular docking were used to give insights about SARS-CoV-2 targets for drug and vaccine development. Most of the publications were from China and USA. However, China, Italy and India covered the top 10 most cited papers on this topic.

CONCLUSION

We found an abundance of publications using omics and bioinformatics approaches to establish the taxonomy and animal origin of SARS-CoV-2. We encourage the growing community of researchers to explore other lesser-known aspects of COVID-19 such as virus-host interactions and host response.