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

F Almeida-Silva, TM Venancio - Functional & Integrative Genomics, 2022 - Springer
Currently, standard network analysis workflows rely on many different packages, often
requiring users to have a solid statistics and programming background. Here, we present …

Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms

F Almeida-Silva, Y Van de Peer - Molecular biology and …, 2023 - academic.oup.com
Angiosperms have a complex history of whole-genome duplications (WGDs), with varying
numbers and ages of WGD events across clades. These WGDs have greatly affected the …

[HTML][HTML] Pathogenesis-related protein 1 (PR-1) genes in soybean: Genome-wide identification, structural analysis and expression profiling under multiple biotic and …

F Almeida-Silva, TM Venancio - Gene, 2022 - Elsevier
Plant pathogenesis-related (PR) proteins are a large group of proteins, classified in 17
families, that are induced by pathological conditions. Here, we characterized the soybean …

[HTML][HTML] Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal …

F Almeida-Silva, TM Venancio - Scientific Reports, 2021 - nature.com
Soybean is one of the most important legume crops worldwide. However, soybean yield is
dramatically affected by fungal diseases, leading to economic losses of billions of dollars …

[HTML][HTML] StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

VS Bonthala, B Stich - Plant Cell Reports, 2024 - Springer
Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks
third in food production after wheat and rice. Despite the availability of several potato …

The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA‐seq samples

F Almeida‐Silva, F Pedrosa‐Silva… - The Plant …, 2023 - Wiley Online Library
Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products
due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA …

[HTML][HTML] Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.)

AG Shahriari, Z Soltani, A Tahmasebi, P Poczai - Genes, 2022 - mdpi.com
Drought is a major abiotic stressor that causes yield losses and limits the growing area for
most crops. Soybeans are an important legume crop that is sensitive to water-deficit …

[HTML][HTML] Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

DK Turquetti-Moraes, KC Moharana, F Almeida-Silva… - Gene, 2022 - Elsevier
Soybean is a major source of edible protein and oil. Oil content is a quantitative trait that is
significantly determined by genetic and environmental factors. Over the past 30 years, a …

The state of the art in soybean transcriptomics resources and gene coexpression networks

F Almeida-Silva, KC Moharana, TM Venancio - in silico Plants, 2021 - academic.oup.com
In the past decade, over 3000 samples of soybean transcriptomic data have accumulated in
public repositories. Here, we review the state of the art in soybean transcriptomics …

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

F Almeida-Silva, Y Van de Peer - bioRxiv, 2024 - biorxiv.org
Gene and genome duplications are major evolutionary forces that shape the diversity and
complexity of life. However, different duplication modes have distinct impacts on gene …