Fabricio Almeida‐Silva

GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.

The Arabidopsis PAL3 is a carboxy-tyrosine ammonia lyase

The paper identifies PAL3 in Arabidopsis as a novel enzyme converting 3-carboxy-tyrosine into carboxy-p-coumaric acid, reclassifying it as a 3-carboxy-tyrosine ammonia lyase.

Microsynteny Analysis Clarifies the Early Diversification of Cypriniform Fishes

This paper uses microsynteny analysis to resolve deep phylogenetic relationships in Cypriniform fishes, showing it outperforms sequence-based methods in resolving contentious nodes.

The Rise of Polyploids During Environmental Upheaval

This study identifies 132 ancient whole-genome duplication events in angiosperms, showing they cluster around periods of environmental upheaval and extinction.

Gene family expansions and nodule-specific expression patterns reveal the recruitment of Beta-Glucosidases and Cytochrome P450 genes to nodulation in soybean

Artemisia Database: A Comprehensive Resource for Gene Expression and Functional Insights in Artemisia annua

The paper introduces Artemisia-DB, a gene expression atlas for Artemisia annua, revealing a potential regulatory link between auxin signaling and artemisinin biosynthesis.

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes

In spatial transcriptomes from five plant species, segmental (including whole-genome) duplicates show higher, broader, spatially variable expression and redundancy, while small-scale duplicates diverge asymmetrically.

Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids

The paper analyzes olfactory and gustatory receptor genes and transposable elements in aphid genomes to understand their evolutionary dynamics and role in host adaptation.

SOI: Robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

This paper introduces the Orthology Index (OI) to robustly identify orthologous synteny, demonstrating its scalability and reliability across diverse polyploidization events and applications in plant evolutionary genomics.

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

doubletrouble identifies and classifies gene and genome duplications across 822 eukaryotic genomes, offering tools for analysis and visualization.

Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

This study investigates gene expression changes in Chlamydomonas triploids resulting from asymmetric genome merging, finding expression dominance, proteostasis restoration, and enhanced fitness.

Cannabis Expression Atlas: a comprehensive resource for integrative analysis of Cannabis sativa L. gene expression

The paper compiles and analyzes Cannabis RNA-Seq data to create a database for gene expression studies in Cannabis sativa L.

Multiomic analysis of genes related to oil traits in legumes provide insights into lipid metabolism and oil richness in soybean

This study analyzes oil-related gene families across legumes to understand lipid metabolism and oil richness in soybean, identifying gene expansions and expression patterns linked to seed oil content.

HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

HybridExpress is an R/Bioconductor package for analyzing gene expression in hybrid triplets, providing tools for normalization, clustering, classification, and functional analysis.

Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package

The paper introduces cogeqc, an R/Bioconductor package to assess genome assembly, annotation, orthogroup inference, and synteny detection quality in comparative genomics.

syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

syntenet infers and analyzes synteny networks from whole-genome protein sequences to identify taxon-specific gene clusters and resolve phylogenetic relationships.

cageminer: an R/Bioconductor package to prioritize candidate genes by integrating GWAS and gene coexpression networks

cageminer integrates GWAS and gene coexpression networks to prioritize candidate genes by filtering for physical proximity to SNPs, coexpression with known trait-associated genes, and expression changes in relevant conditions.

BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction

BioNERO provides an integrated R/Bioconductor package for streamlined biological network reconstruction, combining preprocessing, network inference, and functional analysis into a single workflow.