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Bioinformatics - BIOINFORMATICS

Publications

11 Publications

Linheiro, R., Archer, J. (2022). Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly. F1000Research, 11: 120. doi: 10.12688/f1000research.108489.1 Open publication

Linheiro, R., Sabatino, S., Lobo, D., & Archer, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. doi: 10.1371/journal.pone.0259726 Open publication

Lobo, D., Linheiro, R., Godinho, R., Archer, J.P. (2022). On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves. PLOS ONE 17(9): e0274591. doi: 10.1371/journal.pone.0274591 Open publication

Sabatino, S. J., Pereira, P., Carneiro, M., Dilytė, J., Archer, J. P., Munoz, A., Nonnis-Marzano, F., & Murias, A. (2022). The genetics of adaptation in freshwater Eurasian shad (Alosa). Ecology and Evolution, 12(5), e8908. doi: 10.1002/ece3.8908 Open publication

Linheiro, R., Archer, J. (2021). CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure. PLOS Comput Biol., 17: e1009631. doi: 10.1371/journal.pcbi.1009631 Open publication

Vonk, F. J., Bittenbinder, M. A., Kerkkamp, H. M. I., Grashof, D. G. B., Archer, J. P., Afonso, S., Richardson, M. K., Kool, J., & van der Meijden, A. (2021). A non-lethal method for studying scorpion venom gland transcriptomes, with a review of potentially suitable taxa to which it can be applied. PLOS ONE, 16(11), e0258712. doi: 10.1371/journal.pone.0258712 Open publication

Cardoso, G. C., Abreu, J. M., Archer, J., Crottini, A., & Mota, P. G. (2020). Independent evolution of song diversity and song motor performance in canaries, goldfinches and allies indicates clade-specific trade-offs in birdsong. Evolution, 74(6), 1170–1185 doi: 10.1111/EVO.13987 Open publication

Grashof, DGB.; Kerkkamp, HMI.; Afonso, S.; Archer, J.; Harris, DJ.; Richardson, MK.; Vonk, FJ.; van der Meijden, A. (2019). Transcriptome annotation and characterization of novel toxins in six scorpion species. BMC Genomics 20, 645. doi: 10.1186/s12864-019-6013-6 Open publication

Gazda MA, Andrade P, Afonso S, Dilytė J, Archer J, Lopes RJ, Faria R, Carneiro M (2018) Signatures of Selection on Standing Genetic Variation Underlie Athletic and Navigational Performance in Racing Pigeons. Molecular Biology and Evolution, 35(5):1176–1189 doi: 10.1093/molbev/msy030 Open publication

Castro PH, Lilay GH, Muñoz-Mérida A, Schjoerring JK, Azevedo H, Assunção AGL (2017) Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants. Scientific Reports; 7: 3806. doi: 10.1038/s41598-017-03903-6 Open publication

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