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 …
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 …
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 …
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 …
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 …
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 …
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 …
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 …
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
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 …
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 …
complexity of life. However, different duplication modes have distinct impacts on gene …