My publications


20. Almeida-Silva F, Van de Peer Y (2024). “doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.” bioRxiv.

19. Almeida-Silva F, Prost-Boxoen L, Van de Peer Y (2024). “HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors.” bioRxiv.


18. Almeida-Silva F, Zhao T, Ullrich KK, Schranz ME, Van de Peer Y (2023). “syntenet: an R/Bioconductor package for the inference and analysis of synteny networks.” Bioinformatics, 39(1), btac806.

17. Almeida-Silva F, Van de Peer Y (2023). “Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.” Molecular Biology and Evolution, 40(7), msad141.

16. Almeida-Silva F, Van de Peer Y (2023). “Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package.” Methods in Ecology and Evolution.

15. Almeida-Silva F, Pedrosa-Silva F, Venancio TM (2023). “The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples.” The Plant Journal.

14. Almeida-Silva F, Venancio TM (2023). “Discovering and prioritizing candidate resistance genes against soybean pests by integrating GWAS and gene coexpression networks.” Gene, 860, 147231.

13. Cao Y, Almeida-Silva F, Zhang W, Ding Y, Bai D, Bai W, Zhang B, Van de Peer Y, Zhang D (2023). “Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp.(Juglandaceae).” Molecular Biology and Evolution, 40(6), msad121.

12. Cherene MB, Taveira GB, Almeida-Silva F, da Silva MS, Cavaco MC, da Silva-Ferreira AT, Perales JEA, de Oliveira Carvalho A, Venâncio TM, da Motta OV, others (2023). “Structural and Biochemical Characterization of Three Antimicrobial Peptides from Capsicum annuum L. var. annuum Leaves for Anti-Candida Use.” Probiotics and Antimicrobial Proteins, 1-18.

11. Pinto VB, Vidigal PMP, Dal-Bianco M, Almeida-Silva F, Venancio TM, Viana JMS (2023). “Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta).” Scientific Reports, 13(1), 19400.


10. Almeida-Silva F, Venancio TM (2022). “cageminer: an R/Bioconductor package to prioritize candidate genes by integrating genome-wide association studies and gene coexpression networks.” in silico Plants, 4(2), diac018.

9. Turquetti-Moraes DK, Moharana KC, Almeida-Silva F, Pedrosa-Silva F, Venancio TM (2022). “Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean.” Gene, 808, 145976.

8. Almeida-Silva F, Venancio TM (2022). “Pathogenesis-related protein 1 (PR-1) genes in soybean: Genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses.” Gene, 809, 146013.

7. Almeida-Silva F, Venancio TM (2022). “BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction.” Functional & Integrative Genomics, 22(1), 131-136.

6. Irineu LESdS, Soares CdP, Soares TS, Almeida FAd, Almeida-Silva F, Gazara RK, Meneses CHSG, Canellas LP, Silveira V, Venancio TM, others (2022). “Multiomic approaches reveal hormonal modulation and nitrogen uptake and assimilation in the initial growth of maize inoculated with Herbaspirillum seropedicae.” Plants, 12(1), 48.


5. Almeida-Silva F, Moharana KC, Venancio TM (2021). “The state of the art in soybean transcriptomics resources and gene coexpression networks.” in silico Plants, 3(1), diab005.

4. Sangi S, Araújo PM, Coelho FS, Gazara RK, Almeida-Silva F, Venancio TM, Grativol C (2021). “Genome-wide analysis of the COBRA-Like gene family supports gene expansion through Whole-Genome Duplication in soybean (Glycine max).” Plants, 10(1), 167.

3. Almeida-Silva F, Venancio TM (2021). “Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens.” Scientific Reports, 11(1), 24453.


2. Machado FB, Moharana KC, Almeida-Silva F, Gazara RK, Pedrosa-Silva F, Coelho FS, Grativol C, Venancio TM (2020). “Systematic analysis of 1298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas.” The Plant Journal, 103(5), 1894-1909.

1. Almeida-Silva F, Moharana KC, Machado FB, Venancio TM (2020). “Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks.” Planta, 252, 1-12.