Almeida-Silva Fabricio

Almeida-Silva Fabricio - Postdoctoral fellow @ BIOINFORMATICS AND EVOLUTIONARY GENOMICS

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

Ren-Gang Zhang, Hong-Yun Shang, Richard Ian Milne, Fabricio Almeida-Silva, Hengchi Chen, Min-Jie Zhou, Heng Shu, Kai-Hua Jia, Yves Van de Peer, Yong-Peng Ma

(2025/04) - Nucleic Acids Research

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

Fabricio Almeida-Silva, Yves Van de Peer

(2025/05) -

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

Sergio Gabriel Olvera-Vazquez, Xilong Chen, Aurélie Mesnil, Camille Meslin, Fabricio Almeida-Silva, Johann Confais, Yann Bourgeois, Célia Lougmani, Karine Alix, Nicolas Francillonne, Nathalie Choisne, Stephane Cauet, Jean-Christophe Simon, Christelle Buchard, Nathalie Rodde, David Ogereau, Claire Mottet, Alexandre Degrave, Elorri Segura, Benoît Barrès, Emmanuelle Jacquin-Joly, William Marande, Dominique Lavenier, Fabrice Legeai, Amandine Cornille

(2025/04) -

DOI
31. Learning and teaching biological data science in the Bioconductor community

Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C. Culhane, Sean Davis, Maria A. Doyle, Ludwig Geistlinger, Andrew R. Ghazi, Susan Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson

(2025/04) - PLOS Computational Biology

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

Dayana K. Turquetti-Moraes, Cláudio Benício Cardoso-Silva, Fabricio Almeida-Silva, Thiago M. Venancio

(2025/01) - Plant Physiology and Biochemistry

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

Claudio Benicio Cardoso-Silva, Gabriel Quintanilha-Peixoto, Dayana Kelly Turquetti-Morares, Fabricio Almeida-Silva, Thiago Venancio

(2025/07) -

DOI
28. Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Lucas Prost‐Boxoen, Quinten Bafort, Antoine Van de Vloet, Fabricio Almeida‐Silva, Yunn Thet Paing, Griet Casteleyn, Sofie D'hondt, Olivier De Clerck, Yves Van de Peer

(2025/01) - New Phytologist

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

Fabricio Almeida-Silva, Yves Van de Peer, Janet Kelso

(2025/02) - Bioinformatics

DOI
26. Microsynteny Analysis Clarifies the Early Diversification of Cypriniform Fishes

Daniel J. MacGuigan, Hannah M. Waterman, Jessie A. Pelosi, Nathan J.C. Backenstose, Sarah L. Chang, Milton Tan, Fabrício Almeida-Silva, Trevor J. Krabbenhoft

(2025/09) -

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

Ayat Taheri, Fabricio Almeida-Silva, Yaojie Zhang, Xueqing Fu, Ling Li, Yuliang Wang, Kexuan Tang

(2025/05) -

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

Fabricio Almeida-Silva, Yves Van de Peer

(2025/10) - The Plant Cell

DOI
23. Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids

Sergio Gabriel Olvera-Vazquez, Xilong Chen, Aurélie Mesnil, Camille Meslin, Fabricio Almeida-Silva, Johann Confais, Yann Bourgeois, Gianluca Lombardi, Célia Lougmani, Karine Alix, Nicolas Francillonne, Nathalie Choisne, Stephane Cauet, Jean-Christophe Simon, Christelle Buchard, Nathalie Rodde, David Ogereau, Claire Mottet, Alexandre Degrave, Elorri Segura, Alessandra Carbone, Barrès Benoit, Emmanuelle Jacquin-Joly, William Marande, Dominique Lavenier, Fabrice Legeai, Amandine Cornille, John True

(2025/11) - Molecular Biology and Evolution

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

Kevelin Barbosa‐Xavier, Francisnei Pedrosa‐Silva, Fabricio Almeida‐Silva, Thiago M. Venancio

(2024/11) - Physiologia Plantarum

DOI
21. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Fabricio Almeida‐Silva, Lucas Prost‐Boxoen, Yves Van de Peer

(2024/07) - New Phytologist

DOI
20. The immediate metabolomic effects of whole‐genome duplication in the greater duckweed, Spirodela polyrhiza

Tian Wu, Quinten Bafort, Frederik Mortier, Fabricio Almeida‐Silva, Annelore Natran, Yves Van de Peer

(2024/08) - American Journal of Botany

DOI
19. The Rise of Polyploids During Environmental Upheaval

Hengchi Chen, Fabricio Almeida-Silva, Garben Logghe, Steven Maere, Dries Bonte, Yves Van de Peer

(2024/11) -

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

Fabricio Almeida‐Silva, Francisnei Pedrosa‐Silva, Thiago M. Venancio

(2023/11) - The Plant Journal

DOI
17. Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta)

Vitor Batista Pinto, Pedro Marcus Pereira Vidigal, Maximiller Dal-Bianco, Fabricio Almeida-Silva, Thiago Motta Venancio, José Marcelo Soriano Viana

(2023/11) - Scientific Reports

DOI
16. Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms

Fabricio Almeida-Silva, Yves Van de Peer, Michael Purugganan

(2023/07) - Molecular Biology and Evolution

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

Fabricio Almeida‐Silva, Yves Van de Peer

(2023/12) - Methods in Ecology and Evolution

DOI
14. Structural and Biochemical Characterization of Three Antimicrobial Peptides from Capsicum annuum L. var. annuum Leaves for Anti-Candida Use

Milena Bellei Cherene, Gabriel Bonan Taveira, Fabricio Almeida-Silva, Marciele Souza da Silva, Marco Calvinho Cavaco, André Teixeira da Silva-Ferreira, Jonas Enrique Aguilar Perales, André de Oliveira Carvalho, Thiago Motta Venâncio, Olney Vieira da Motta, Rosana Rodrigues, Miguel Augusto Rico Botas Castanho, Valdirene Moreira Gomes

(2023/06) - Probiotics and Antimicrobial Proteins

DOI
13. Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae)

Yu Cao, Fabricio Almeida-Silva, Wei-Ping Zhang, Ya-Mei Ding, Dan Bai, Wei-Ning Bai, Bo-Wen Zhang, Yves Van de Peer, Da-Yong Zhang

(2023/06) - Molecular Biology and Evolution

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

Fabricio Almeida-Silva, Thiago M. Venancio

(2022/02) - Functional & Integrative Genomics

DOI
11. Multiomic Approaches Reveal Hormonal Modulation and Nitrogen Uptake and Assimilation in the Initial Growth of Maize Inoculated with Herbaspirillum seropedicae

Luiz Eduardo Souza da Silva Irineu, Cleiton de Paula Soares, Tatiane Sanches Soares, Felipe Astolpho de Almeida, Fabrício Almeida-Silva, Rajesh Kumar Gazara, Carlos Henrique Salvino Gadelha Meneses, Luciano Pasqualoto Canellas, Vanildo Silveira, Thiago Motta Venancio, Fabio Lopes Olivares

(2022/12) - Plants

DOI
10. Discovering and prioritizing candidate resistance genes against soybean pests by integrating GWAS and gene coexpression networks

Fabricio Almeida-Silva, Thiago M. Venancio

(2022/05) -

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

Fabricio Almeida-Silva, Tao Zhao, Kristian K Ullrich, M Eric Schranz, Yves Van de Peer, Pier Luigi Martelli

(2022/12) - Bioinformatics

DOI
8. Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens

Fabricio Almeida-Silva, Thiago M. Venancio

(2021/09) -

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

No contributors listed

(2021/01) - in silico Plants

DOI
6. Genome-Wide Analysis of the COBRA-Like Gene Family Supports Gene Expansion through Whole-Genome Duplication in Soybean (Glycine max).

No contributors listed

(2021/01) - Plants (Basel, Switzerland)

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

Fabricio Almeida-Silva, Thiago M. Venancio

(2021/08) -

DOI
4. Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

Dayana K. Turquetti-Moraes, Kanhu C. Moharana, Fabricio Almeida-Silva, Francisnei Pedrosa-Silva, Thiago M. Venancio

(2021/08) -

DOI
3. Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses

Fabricio Almeida-Silva, Thiago M. Venancio

(2021/03) -

DOI
2. Systematic analysis of 1,298 RNA‐Seq samples and construction of a comprehensive soybean ( Glycine max ) expression atlas

No contributors listed

(2020/05) - The Plant Journal

DOI
1. Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks

No contributors listed

(2020/12) - Planta

DOI

Almeida-Silva Fabricio

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

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

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

31. Learning and teaching biological data science in the Bioconductor community

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

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

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

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

26. Microsynteny Analysis Clarifies the Early Diversification of Cypriniform Fishes

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

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

23. Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids

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

21. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

20. The immediate metabolomic effects of whole‐genome duplication in the greater duckweed, Spirodela polyrhiza

19. The Rise of Polyploids During Environmental Upheaval

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

17. Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta)

16. Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms

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

14. Structural and Biochemical Characterization of Three Antimicrobial Peptides from Capsicum annuum L. var. annuum Leaves for Anti-Candida Use

13. Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae)

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

11. Multiomic Approaches Reveal Hormonal Modulation and Nitrogen Uptake and Assimilation in the Initial Growth of Maize Inoculated with Herbaspirillum seropedicae

10. Discovering and prioritizing candidate resistance genes against soybean pests by integrating GWAS and gene coexpression networks

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

8. Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens

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

6. Genome-Wide Analysis of the COBRA-Like Gene Family Supports Gene Expansion through Whole-Genome Duplication in Soybean (Glycine max).

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

4. Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

3. Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses

2. Systematic analysis of 1,298 RNA‐Seq samples and construction of a comprehensive soybean ( Glycine max ) expression atlas

1. Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks