Rossini B., Guyot R., Alcantara M., Batista A., Bourgeois Y., Silvestre M., Alves P., Moraes S., Moraes M., Marino C. 2025. High-quality DNA extraction method enabling long-read sequencing in challenging native plant species. Academia Molecular Biology and Genomics. 2.

Coba-Males MA., Orozco-Arias S., Guyot R., Vela D. 2025. Identification of transposable elements and satellite DNA in the Neotropical species Drosophila amaguana from the Ecuadorian Andean Forests. PLoS One. 20. e0337390.

Waschburger E., Filgueiras J., Antoniolli H., Deprá M., Guyot R., Turchetto-Zolet A. 2025. Transposable elements: a key piece in the genomic evolution and adaptation of Myrtaceae species. Mobile DNA. 16.

Bezandry R., Dupeyron M., Gonzalez-Garcia L., Anest A., Hamon P., Ranarijaona H. L. T., Vavitsara M., Sabatier S., Guyot R. 2024. The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes. PLOS ONE. 19(1). e0296362.

Correia de Lemos S. M. C., Paschoal A. R., Guyot R., Medema M., Domingues D. S. 2024. Genome mining of metabolic gene clusters in the Rubiaceae family. Computational and Structural Biotechnology Journal. 23. 22-33.

Salojaervi J., Rambani A., Yu Z., Guyot R., Strickler S., Lepelley M., Wang C., Rajaraman S., Rastas P., Zheng C. F., Munoz D. S., Meidanis J., Paschoal A. R., Bawin Y., Krabbenhoft T. J., Wang Z. Q., Fleck S. J., Aussel R., Bellanger L., Charpagne A., Fournier C., Kassam M., Lefebvre G., Metairon S., Moine D., Rigoreau M., Stolte J., Hamon P., Couturon E., Tranchant-Dubreuil C., Mukherjee M., Lan T. Y., Engelhardt J., Stadler P., De Lemos S. M. C., Suzuki S. I., Sumirat U., Wai C. M., Dauchot N., Orozco-Arias S., Garavito A., Kiwuka C., Musoli P., Nalukenge A., Guichoux E., Reinout H., Smit M., Carretero-Paulet L., Guerreiro O., Braghini M. T., Padilha L., Sera G. H., Ruttink T., Henry R., Marraccini P., Van de Peer Y., Andrade A., Domingues D., Giuliano G., Mueller L., Pereira L. F., Plaisance S., Poncet V., Rombauts S., Sankoff D., Albert V. A., Crouzillat D., De Kochko A., Descombes P. 2024. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature Genetics. 56. 721-731.

Orozco-Arias S., Humberto Lopez-Murillo L., Candamil-Cortés M. S., Arias M., Jaimes P. A., Rossi Paschoal A., Tabares-Soto R., Isaza G., Guyot R. 2023. Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes. Briefings in Bioinformatics. 24(1). bbac511.

Orozco-Arias S., Lopez-Murillo L. H., Piña J. S., Valencia-Castrillon E., Tabares-Soto R., Castillo-Ossa L., Isaza G., Guyot R. 2023. Genomic object detection: an improved approach for transposable elements detection and classification using convolutional neural networks. PLOS ONE. 18(9). e0291925.

Orozco-Arias S., Dupeyron M., Gutiérrez-Duque D., Tabares-Soto R., Guyot R. 2023. High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes. Genome. 66(3). 51-61.

Piña J. S., Orozco-Arias S., Tobón-Orozco N., Camargo-Forero L., Tabares-Soto R., Guyot R. 2023. G-SAIP: graphical sequence alignment through parallel programming in the post-genomic era. Evolutionary Bioinformatics. 19.

Verstraete B., Janssens S., Block P. D., Asselman P., Méndez G., Ly S. N., Hamon P., Guyot R. 2023. Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes. PeerJ. 11. e15778.

Camargo-Forero N., Orozco-Arias S., Perez Agudelo J. M., Guyot R. 2023. HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Archives of Virology. 168. 125.

Lozano-Arce D., García T., Gonzalez-Garcia L. N., Guyot R., Chacón-Sánchez M. I., Duitama J. 2023. Selection signatures and population dynamics of transposable elements in lima bean. Communications Biology. 6. 1-13.

Gonzalez-García L. N., Lozano-Arce D., Londoño J. P., Guyot R., Duitama J. 2023. Efficient homology-based annotation of transposable elements using minimizers. Applications in Plant Sciences. 11(4). e11520.

De Assis R., Gonçalves L. S. A., Guyot R., Vanzela A. L. L. 2023. Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. Genome. 66(10). 269-280.

Orozco-Arias S., Candamil M. S., Jaimes P. A., Cristancho M., Tabares-Soto R., Guyot R. 2022. Composition and diversity of LTR retrotransposons in the coffee leaf rust genome (Hemileia vastatrix). Agronomy. 12(7). 1665.

Orozco-Arias S., Candamil-Cortes M. S., Jaimes P. A., Valencia-Castrillon E., Tabares-Soto R., Isaza G., Guyot R. 2022. Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning. Journal of Integrative Bioinformatics. 19(3). 20210036.

Cintra L. A., De Souza T. B., Parteka L. M., Barreto L. M., Pereira L. F. P., Gaeta M. L., Guyot R., Vanzela A. L. L. 2022. An 82 bp tandem repeat family typical of 3′ non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres. Genome. 65(3). 137-151.

Hu G. B., Feng J. T., Xiang X., Wang J. B., Salojarvi J., Liu C. M., Wu Z. X., Zhang J. S., Liang X. M., Jiang Z. D., Liu W., Ou L. X., Li J. W., Fan G. Y., Mai Y. X., Chen C. J., Zhang X. T., Zheng J. K., Zhang Y. Q., Peng H. X., Yao L. X., Wai C. M., Luo X. P., Fu J. X., Tang H. B., Lan T. Y., Lai B. A., Sun J. H., Wei Y. Z., Li H. L., Chen J. Z., Huang X. M., Yan Q., Liu X., Mchale L. K., Rolling L., Guyot R., Sankoff D., Zheng C. F., Albert V. A., Ming R. A., Chen H. B., Xia R., Li J. G. 2022. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nature Genetics. 54. 73-83.

Duitama J., Bartley L. E., Guyot R., Sharma R. 2022. Grass genome evolution and domestication [Editorial]. Frontiers in Plant Science. 13.

Budzinski I. G. F., Camargo P. O., Lemos S. M. C., Guyot R., Calzado N. F., Ivamoto-Suzuki S. T., Domingues D. S. 2022. Transcriptomic alterations in roots of two contrasting Coffea arabica cultivars after hexanoic acid priming. Frontiers in Genetics. 13.

Buitrago Acosta M. C., Montufar R., Guyot R., Mariac C., Tranbarger T. J., Restrepo S., Couvreur T. L. P. 2022. Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis. Mitochondrial DNA Part B: Resources. 7(8). 1540-1544.

Orozco-Arias S., Jaimes P. A., Candamil M. S., Jiménez-Varón C. F., Tabares-Soto R., Isaza G., Guyot R. 2021. InpactorDB: a classified lineage-level plant LTR retrotransposon reference library for free-alignment methods based on machine learning. Genes. 12(2). 190.

Raharimalala N., Rombauts S., McCarthy A., Garavito A., Orozco-Arias S., Bellanger L., Morales-Correa A. Y., Froger S., Michaux S., Berry V., Metairon S., Fournier C., Lepelley M., Mueller L., Couturon E., Hamon P., Rakotomalala J.-J., Descombes P., Guyot R., Crouzillat D. 2021. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago. Scientific Reports. 11. 8119.

Orozco-Arias S., Candamil-Cortés M. S., Jaimes P. A., Piña J. S., Tabares-Soto R., Guyot R., Isaza G. 2021. K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes. PeerJ. 9. e11456.

Ayala-Usma D. A., Cárdenas M., Guyot R., Mares M. C. D., Bernal A., Muñoz A. R., Restrepo S. 2021. A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans. BMC Genomics. 22. 795.

Orozco-Arias S., Tobon-Orozco N., Piña J. S., Jiménez-Varón C. F., Tabares-Soto R., Guyot R. 2020. TIP_finder: an HPC software to detect transposable element insertion polymorphisms in large genomic datasets. Biology. 9(9). 281.

Orozco-Arias S., Pina J. S., Tabares-Soto R., Castillo-Ossa L. F., Guyot R., Isaza G. 2020. Measuring performance metrics of machine learning algorithms for detecting and classifying transposable elements. Processes. 8(6). 638.

Rimlinger A., Raharimalala N., Letort V., Rakotomalala J.-J., Crouzillat D., Guyot R., Hamon P., Sabatier S. 2020. Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar. Annals of Botany. 126(5). 849-863.

Wu S., Guyot R., Bocs S., Droc G., Oktavia F., Hu S., Tang C., Montoro P., Leclercq J. 2020. Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis. International Journal of Molecular Sciences. 21(12). 4220.

Charr J.-C., Garavito A., Guyeux C., Crouzillat D., Descombes P., Fournier C., Ly S. N., Raharimalala E. N., Rakotomalala J.-J., Stoffelen P., Janssens S., Hamon P., Guyot R. 2020. Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee). Molecular Phylogenetics and Evolution. 151. 106906.

Ly S. N., Garavito A., De Block P., Asselman P., Guyeux C., Charr J. C., Janssens S., Mouly A., Hamon P., Guyot R. 2020. Chloroplast genomes of Rubiaceae: comparative genomics and molecular phylogeny in subfamily Ixoroideae. PLOS ONE. 15(4). e0232295.

Lemos S. M. C., Fonçatti L. F. C., Guyot R., Paschoal A. R., Domingues D. S. 2020. Genome-wide screening and characterization of non-coding RNAs in Coffea canephora. Non-Coding RNA. 6(3). 39.

Konan J. A., Guyot R., Koffi K. K., Vroh-Bi I., Zoro A. I. B. 2020. Molecular confirmation of varietal status in bottle gourd (Lagenaria siceraria) using genotyping-by-sequencing. Genome. 63(11). 535-545.

Hufnagel B., Marques A., Soriano A., Marques L., Divol F., Doumas P., Sallet E., Mancinotti D., Carrere S., Marande W., Arribat S., Keller J., Huneau C., Blein T., Aime D., Laguerre M., Taylor J., Schubert V., Nelson M., Geu-Flores F., Crespi M., Gallardo K., Delaux P. M., Salse J., Berges H., Guyot R., Gouzy J., Peret B. 2020. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Nature Communications. 11. 492.

Guyot R., Hamon P., Couturon E., Raharimalala N., Rakotomalala J.-J., Lakkanna S., Sabatier S.-A., Affouard A., Bonnet P. 2020. WCSdb: a database of wild Coffea species. Database - The journal of Biological Databases and Curation. 2020. baaa069.

Rimlinger A., Raharimalala N., Letort V., Rakotomalala J.-J., Crouzillat D., Guyot R., Hamon P., Sabatier S. 2020. Phenotypic diversity assessment wihin a major ex situ collection of coffees in Madagascar. Annals of Botany. 126(5). 849-863.

Orozco-Arias S., Isaza G., Guyot R., Tabares-Soto R. 2019. A systematic review of the application of machine learning in the detection and classification of transposable elements. PeerJ. 7. e8311.

Orozco-Arias S., Isaza G., Guyot R. 2019. Retrotransposons in plant genomes: structure, identification, and classification through bioinformatics and machine learning. International Journal of Molecular Sciences. 20(15). 3837.

Guyeux C., Charr J.-C., Tran H. T. M., Furtado A., Henry R. J., Crouzillat D., Guyot R., Hamon P. 2019. Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species. PLOS ONE. 14(6). e0216347.

Dos Santos T. B., Soares J. D. M., Lima J. E., Silva J. C., Ivamoto S. T., Baba V. Y., Souza S. G. H., Lorenzetti A. P. R., Paschoal A. R., Meda A. R., Nishiyama M. Y., De Oliveira Ú. C., Mokochinski J. B., Guyot R., Junqueira-de-Azevedo I. L. M., Figueira A. V. O., Mazzafera P., Júnior O. R. Vieira, L. G. E., Pereira L. F. P., Domingues D. S. 2019. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses. Functional and Integrative Genomics. 19. 151-169.