Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research DOI Creative Commons

Federico Vello,

Francesco Filippini, Irene Righetto

и другие.

Viruses, Год журнала: 2024, Номер 16(9), С. 1425 - 1425

Опубликована: Сен. 6, 2024

Computer-aided analysis of proteins or nucleic acids seems like a matter course nowadays; however, the history Bioinformatics and Computational Biology is quite recent. The advent high-throughput sequencing has led to production "big data", which also affected field virology. collaboration between communities bioinformaticians virologists already started few decades ago it was strongly enhanced by recent SARS-CoV-2 pandemics. In this article, first in series on how bioinformatics can enhance virus research, we show that highly useful information retrievable from selected general dedicated databases. Indeed, an enormous amount information-both terms nucleotide/protein sequences their annotation-is deposited databases international organisations participating International Nucleotide Sequence Database Collaboration (INSDC). However, more virus-specific have been established are progressively enriched with contents features reported article. Since viruses intracellular obligate parasites, special focus given host-pathogen protein-protein interaction Finally, illustrate several phylogenetic phylodynamic tools, combining algorithms practical use them case studies validate usefulness. Databases tools for functional inference will be covered next article series:

Язык: Английский

REST Is Restless in Neuronal and Non-Neuronal Virus Infections: An In Silico Analysis-Based Perspective DOI Creative Commons

Vinod Soman Pillai,

Shilpa Ravindran,

Gayathri Krishna

и другие.

Viruses, Год журнала: 2025, Номер 17(2), С. 234 - 234

Опубликована: Фев. 8, 2025

Repressor element-1 silencing transcription factor or neuron-restrictive silencer (REST/NRSF) is an extensively studied neuronal gene regulator both in cells and non-neuronal cells. Even though the role of REST host cellular regulation well established, its establishment viral infections capability to stabilize destabilize such are scarcely studied. Co-repressor DNA modifiers involved REST-mediated repressive action target genes. The co-repressors together individually as genes has been unraveled a few viruses HIV influenza two herpesvirus family members, namely herpes simplex virus type 1 (HSV-1) Kaposi’s sarcoma-associated (KSHV). Here, we summarize all studies with gain better insight into biology infections. We also focus on unraveling possible RE-1 binding sites Epstein–Barr (EBV) genome, well-known human oncogenic that associated infectious mononucleosis neoplasms B-cell lymphomas, nasopharyngeal carcinoma, gastric etc. An silico-based approach was employed towards prediction elements EBV genome. This review advances present knowledge infection which will aid future efforts understanding how acts herpesviruses other for their pathogenesis.

Язык: Английский

Процитировано

0
Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research DOI Creative Commons

Federico Vello,

Francesco Filippini, Irene Righetto

и другие.

Viruses, Год журнала: 2024, Номер 16(9), С. 1425 - 1425

Опубликована: Сен. 6, 2024

Computer-aided analysis of proteins or nucleic acids seems like a matter course nowadays; however, the history Bioinformatics and Computational Biology is quite recent. The advent high-throughput sequencing has led to production "big data", which also affected field virology. collaboration between communities bioinformaticians virologists already started few decades ago it was strongly enhanced by recent SARS-CoV-2 pandemics. In this article, first in series on how bioinformatics can enhance virus research, we show that highly useful information retrievable from selected general dedicated databases. Indeed, an enormous amount information-both terms nucleotide/protein sequences their annotation-is deposited databases international organisations participating International Nucleotide Sequence Database Collaboration (INSDC). However, more virus-specific have been established are progressively enriched with contents features reported article. Since viruses intracellular obligate parasites, special focus given host-pathogen protein-protein interaction Finally, illustrate several phylogenetic phylodynamic tools, combining algorithms practical use them case studies validate usefulness. Databases tools for functional inference will be covered next article series:

Язык: Английский

Процитировано

1