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Conceição N, Cox CJ, Simões B, Viegas M, M. Cancela L. Comparative promoter analysis and its application to the identification of candidate regulatory factors of cartilage-expressed genes. Journal of Applied Ichthyology. 2010;26(2):245 - 250. doi:10.1111/jai.2010.26.issue-210.1111/j.1439-0426.2010.01415.x
Cunha RL, Nicastro KR, Zardi GI, et al. Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus. PeerJ. 2022;10:e13953. doi:10:e13953 https://doi.org/10.7717/peerj.13953
Marques CL, Fernández I, Viegas MN, et al. Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives. Cellular and Molecular Life Sciences. 2016;73(4):841-857. doi:10.1007/s00018-015-2024-x
Vanderpoorten A, Hedenäs L, Cox CJ, A. Shaw J, Hedenäs L. Circumscription, Classification, and Taxonomy of Amblystegiaceae (Bryopsida) Inferred from Nuclear and Chloroplast DNA Sequence Data and Morphology. Taxon. 2002;51(1):115. doi:10.2307/1554968
Fernández I, Fernandes JMO, Roberto VP, et al. Circulating small non-coding RNAs provide new insights into vitamin K nutrition and reproductive physiology in teleost fish. Biochimica et Biophysica Acta (BBA) - General Subjects. 2019;1863(1):39-51. doi:10.1016/j.bbagen.2018.09.017
Schneider H, Russell SJ, Cox CJ, et al. Chloroplast Phylogeny of Asplenioid Ferns based on rbcL and trnL-F Spacer Sequences (Polypodiidae, Aspleniaceae) and its Implications for Biogeography. Systematic Botany. 2004;29(2):260 - 274. doi:10.1600/036364404774195476
Sousa F, Civán P, Foster PG, Cox CJ. The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition ModelsDataSheet_1.pdfDataSheet_2.pdf. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.0106210.3389/fpls.2020.01062.s00110.3389/fpls.2020.01062.s002
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Goffinet B, Cox CJ, A. Shaw J, Hedderson TA. The Bryophyta (Mosses): Systematic and Evolutionary Inferences from an rps4 Gene (cpDNA) Phylogeny. Annals of Botany. 2001;87(2):191 - 208. doi:10.1006/anbo.2000.1318
Cock PJA, Antao T, Chang JT, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25(11):1422 - 1423. doi:10.1093/bioinformatics/btp163
Pes K, Friese A, Cox CJ, Laizé V, Fernández I. Biochemical and molecular responses of the Mediterranean mussel (Mytilus galloprovincialis) to short-term exposure to three commonly prescribed drugs. Marine Environmental Research. 2021;168:105309. doi:10.1016/j.marenvres.2021.105309
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Lutzoni F, Kauff F, Cox CJ, et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany. 2004;91(10):1446 - 1480. doi:10.3732/ajb.91.10.1446
Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proceedings of the National Academy of Sciences. 2008;105(51):20356 - 20361. doi:10.1073/pnas.0810647105
Williams TA, Foster PG, Cox CJ, T. Embley M. An archaeal origin of eukaryotes supports only two primary domains of life. Nature. 2013;504(7479):231 - 236. doi:10.1038/nature12779
Civa  P, Foster PG, Embley MT, Seneca A, Cox CJ. Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants. Genome Biology and Evolution. 2014;6(4):897 - 911. doi:10.1093/gbe/evu061
Rathore OSingh, Faustino A, Prudêncio P, Van Damme P, Cox CJ, Martinho RGonçalo. Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms. Scientific Reports. 2016;6:21304. doi:10.1038/srep21304
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Cox CJ, Foster PG. A 20-state empirical amino-acid substitution model for green plant chloroplasts. Molecular Phylogenetics and Evolution. 2013;68(2):218 - 220. doi:10.1016/j.ympev.2013.03.030