Fabricio Almeida-Silva

Dec 7, 2024 | biorxiv.org | Ren-Gang Zhang |Hong-Yun Shang |Richard Milne |Fabricio Almeida-Silva

AbstractWith the explosive growth of whole-genome datasets, the accurate detection of orthologous synteny has become crucial for the reconstruction of evolutionary history. However, the currently available methods for the identification of orthologous synteny have great limitations: the methods are difficult to scale with varying polyploidy histories, and the accurate removal of out-paralogy is challenging.

Feb 29, 2024 | biorxiv.org | Fabricio Almeida-Silva

AbstractGene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data.

Nov 3, 2023 | besjournals.onlinelibrary.wiley.com | Fabricio Almeida-Silva

1 INTRODUCTION The availability of genomic data in public databases has increased exponentially due to advancements in sequencing technologies. However, a significant portion of this data is of poor quality, leading to incorrect or unreliable results in common analyses such as genome-wide synteny analysis and gene orthology detection (Feron & Waterhouse, 2022; Liu et al., 2018; Marks et al., 2021; Wang & Wang, 2022).

Apr 17, 2023 | biorxiv.org | Fabricio Almeida-Silva

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Mar 14, 2023 | biorxiv.org | Fabricio Almeida-Silva

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