Cymon John Cox. Completed the Doutoramento in PhD in 1998 by University of Reading and Bacharelato in Botany in 1994 by Bangor University. Is Principal Investigator in Centro de Ciências do Mar. Published 89 articles in journals. Works in the area(s) of Natural sciences with emphasis on Biological Sciences with emphasis on Evolutionary Biology and Exact Sciences with emphasis on Computer and Information Sciences with emphasis on Bioinformatics. In their professional activities interacted with 421 collaborator(s) co-authorship of scientific papers. In his curriculum Ciência Vitae the most frequent terms in the context of scientific, technological and artistic-cultural output are: Gene expression and regulation ; Phylogeny reconstruction; Green plant; Chloroplast; Empirical protein model; gcpREV; cpREV; Vertical transmission; Phylogenetic analyses; Bayesian inference; Sequence data; Mixed models; Microorganisms; Symbionts; Genomics; Reveals; Mrbayes; Microbiologia; Comunidades; Sistemas simbióticos; Biogeografia; biodiversity; marine biotechnology; model organisms; ecosystem functioning; CIÊNCIAS DO MAR & MUDANÇAS GLOBAIS; BIODIVERSIDADE; ECOLOGIA & SUSTENTABILIDADE; OCEANOGRAFIA & ENGENHARIA MARINHAS; BIOTECNOLOGIA; AQUACULTURA & PESCAS; .

Personal identification

Full name
Cymon John Cox

Citation names

  • Cox, Cymon J.

Author identifiers

Ciência ID
Google Scholar ID
Researcher Id
Scopus Author Id

Email addresses

  • cymon@ualg.pt (Professional)


  • 289800051 Ext.: 7380 (Professional)


  • Centro de Ciências do Mar (CCMAR). Centro de Ciências do Mar (CCMAR), Faculdade de Ciências do Mar e Ambient (FCMA), Universidade do Algarve, 8005-139, Faro, Montenegro, Portugal (Professional)


Knowledge fields

  • Natural sciences - Biological Sciences - Evolutionary Biology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics


Language Speaking Reading Writing Listening Peer-review
Portuguese Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Degree Classification
PhD (Doutoramento)
University of Reading, United Kingdom
"Phylogenetic relationships of the Eubryalean mosses (Bryineae, Musci)" (THESIS/DISSERTATION)
Botany (Bacharelato)
Bangor University, United Kingdom
BSc (2.1)


Host institution
2018/06/16 - Current Principal Investigator (Research) Centro de Ciências do Mar, Portugal
Centro de Ciências do Mar, Portugal
2013/06/16 - 2018/06/15 Coordinating Researcher (Research) Centro de Ciências do Mar, Portugal
2008/06/06 - 2013/06/12 Auxiliary Researcher (Research) Centro de Ciências do Mar, Portugal
2005/06/01 - 2008/05/31 Postdoc (Research) Natural History Museum, United Kingdom
2003/12/01 - 2005/05/31 Postdoc (Research) Duke University, United States
2001/12/01 - 2005/05/31 Postdoc (Research) Duke University, United States
1999/01/01 - 1999/10/31 Postdoc (Research) Natural History Museum, United Kingdom
1998/01/01 - 1998/12/31 Postdoc (Research) Natural History Museum, United Kingdom


Host institution
1999/11/01 - 2001/10/31 Mellon Research Fellow Duke University, United States


Designation Funders
Centro de Ciências do Mar, Portugal
Horizon Europe
2024/01 - 2026/12 European Research Infrastructure for Marine Bioprospecting European Commission
2021/01 - 2025/12 Centro de Investigação Marinha e Ambiental
Fundação para a Ciência e a Tecnologia
2022/08 - 2025/08 FAIR EArth Sciences & Environment services (FAIR-EASE) UK Research and Innovation
2021/09/01 - 2024/08/31 Bioaugmentation and conjugative plasmid transference using bacteria from extreme environments to enhance biodegradation of recalcitrant pollutants in WWTP granular sludge
Centro de Ciências do Mar, Portugal
Fundação para a Ciência e a Tecnologia
2019/03 - 2023/08 Providing an open collaborative space for digital biology in Europe European Commission
2019/01 - 2019/12 Centro de Ciências do Mar do Algarve
Fundação para a Ciência e a Tecnologia
2016/01 - 2018/12 Determining the causes of inter-genomic conflict in the land plant phylogeny Fundação para a Ciência e a Tecnologia
2014/03 - 2015/08 Illuminating the metabolism of foundational and elusive microbial symbionts in benthic ecosytems: a cultivation-independent quest for Hahellaceae (Gammaproteobacteria, Oceanospirillales) genomes Stichting Weten
2011/01 - 2014/01 The conquest of land: a phylogenetic study of charophyte and land plant chloroplast evolution using data- and time-heterogeneous substitution models. Fundação para a Ciência e a Tecnologia
2010/01 - 2013/06 Unlocking the bacterial diversity encrypted in the metagenomes of marine sponges Fundação para a Ciência e a Tecnologia
2010/01 - 2013/04 The origin and early diversification of plants: a phylogenomic approach employing novel composition-heterogeneous methods Fundação para a Ciência e a Tecnologia


Designation Funders
2017/05/01 - 2021/09/30 European Marine Biological Resource Centre Portugal
Centro de Ciências do Mar, Portugal
Comissão de Coordenação e Desenvolvimento Regional do Algarve

Fundação para a Ciência e a Tecnologia
2011/01/01 - 2012/12/31 Projecto Estratégico - LA 15 - 2011-2012
Centro de Ciências do Mar, Portugal

Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Fundação para a Ciência e a Tecnologia


Conference abstract
  1. Lago-Lestón M.A.; Hardoim, Cristiane C.P.; Pires, Francisco R.; Gonçalves, Jorge M.S.; Cox, Cymon J.; Xavier, Joana R.; Costa, Rodrigo. "Unravelling the structure of the marine sponge microbiome across biogeographical gradients [poster]". Paper presented in 9th World Sponge Conference, Perth, 2013.
  2. Hardoim, Cristiane C.P.; Cardinale, Massimiliano; Cúcio, Ana C. B.; Xavier, Joana R.; Cox, Cymon J.; Costa, Rodrigo. "Degrees of host specificity, effects of sample handling, and extent of cultivation bias elucidated for bacterial communities in closely related marine sponges [oral presentation]". Paper presented in 9th World Sponge Conference, Perth, 2013.
  3. Costa, Rodrigo; Hardoim, Cristiane C.P.; Esteves, Ana I.S.; Lago-Lestón M.A.; Cox, Cymon J.; Xavier, Joana R.. "Challenging the specificity of the marine sponge microbiome - a biogeographical approach". Paper presented in 9th World Sponge Conference, Perth, 2013.
Conference paper
  1. Carlier, Jorge Daniel Dias; Lara-Moreno, Alba; Martins, António ; Cox, Cymon J.; Isabel Marín-Beltrán; Tânia Cristina Luz Palma; Maria Clara Semedo da Silva Costa. Corresponding author: Carlier, Jorge Daniel Dias. "Selection of bacterial strains to bioaugment granular sludge and improve the removal of recalcitrant pollutants". Paper presented in International Conference on Environmental Science & Technology (CEST), Athens, 2023.
Journal article
  1. João M. Brazão; Peter G. Foster; Cymon J. Cox. "Data-specific substitution models improve protein-based phylogenetics". PeerJ (2023): https://doi.org/10.7717/peerj.15716.
  2. Jinren Yu; Yanting Niu; Yichen You; Cymon J. Cox; Russell L. Barrett; Anna Trias-Blasi; Jing Guo; et al. "Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan–Hengduan Mountains". New Phytologist (2023): https://doi.org/10.1111/nph.18580.
  3. Regina L. Cunha; Katy R. Nicastro; Gerardo I. Zardi; Celine Madeira; Christopher D. McQuaid; Cymon J. Cox; Rita Castilho. "Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus". PeerJ (2022): https://doi.org/10.7717/peerj.13953.
  4. Susana C. Almeida; João Neiva; Filipe Sousa; Neusa Martins; Cymon J. Cox; José Melo-Ferreira; Michael D. Guiry; Ester A. Serrão; Gareth A. Pearson. "A low-latitude species pump: Peripheral isolation, parapatric speciation and mating-system evolution converge in a marine radiation". Molecular Ecology (2022): https://doi.org/10.1111/mec.16623.
  5. Katia Pes; Annika Friese; Cymon J. Cox; Vincent Laizé; Ignacio Fernández. "Biochemical and molecular responses of the Mediterranean mussel (Mytilus galloprovincialis) to short-term exposure to three commonly prescribed drugs". Marine Environmental Research 168 (2021): 105309-105309. https://doi.org/10.1016/j.marenvres.2021.105309.
  6. Williams, T.A.; Schrempf, D.; Szöllosi, G.J.; Cox, C.J.; Foster, P.G.; Embley, T.M.. "Inferring the Deep Past from Molecular Data". Genome Biology and Evolution 13 5 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85116952648&partnerID=MN8TOARS.
  7. Keller-Costa, T.; Lago-Lestón, A.; Saraiva, J.P.; Toscan, R.; Silva, S.G.; Gonçalves, J.; Cox, C.J.; et al. "Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals". Microbiome 9 1 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85101487987&partnerID=MN8TOARS.
  8. Tom A. Williams; Cymon J. Cox; Peter G. Foster; Gergely J. Szöllosi; T. Martin Embley. "Author Correction: Phylogenomics provides robust support for a two-domains tree of life". Nature Ecology & Evolution 4 11 (2020): 1568-1568. https://doi.org/10.1038/s41559-020-01347-2.
  9. Carlier, J.D.; Ettamimi, S.; Cox, C.J.; Hammani, K.; Ghazal, H.; Costa, M.C.. "Prokaryotic diversity in stream sediments affected by acid mine drainage". Extremophiles 24 6 (2020): 809-819. http://www.scopus.com/inward/record.url?eid=2-s2.0-85090314367&partnerID=MN8TOARS.
  10. Sousa, F.; Civán, P.; Foster, P.G.; Cox, C.J.. "The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models". Frontiers in Plant Science 11 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85088942017&partnerID=MN8TOARS.
  11. Sousa, F.; Civán, P.; Brazão, J.; Foster, P.G.; Cox, C.J.. "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models". PeerJ 2020 4 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85085938070&partnerID=MN8TOARS.
  12. Egger, C.; Neusser, T.P.; Norenburg, J.; Leasi, F.; Buge, B.; Vannozzi, A.; Cunha, R.L.; Cox, C.J.; Jörger, K.M.. "Uncovering the shell game with barcodes: Diversity of meiofaunal caecidae snails (truncatelloidea, caenogastropoda) from Central America". ZooKeys 2020 968 (2020): 1-42. http://www.scopus.com/inward/record.url?eid=2-s2.0-85090967125&partnerID=MN8TOARS.
  13. Xue, J.-Y.; Dong, S.-S.; Wang, M.-Q.; Song, T.-Q.; Zhou, G.-C.; Li, Z.; Van de Peer, Y.; et al. "Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants". Journal of Systematics and Evolution (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85099760633&partnerID=MN8TOARS.
  14. Tom A. Williams; Cymon J. Cox; Peter G. Foster; Gergely J. Szöllosi; T. Martin Embley. "Phylogenomics provides robust support for a two-domains tree of life". Nature Ecology & Evolution (2019): https://doi.org/10.1038/s41559-019-1040-x.
  15. Elham Karimi; Tina Keller-Costa; Beate M. Slaby; Cymon J. Cox; Ulisses N. da Rocha; Ute Hentschel; Rodrigo Costa. "Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria". Scientific Reports (2019): https://doi.org/10.1038/s41598-019-38737-x.
  16. Fernández, I.; Fernandes, J.M.O.; Roberto, V.P.; Kopp, M.; Oliveira, C.; Riesco, M.F.; Dias, J.; et al. "Circulating small non-coding RNAs provide new insights into vitamin K nutrition and reproductive physiology in teleost fish". Biochimica et Biophysica Acta - General Subjects 1863 1 (2019): 39-51. http://www.scopus.com/inward/record.url?eid=2-s2.0-85054237185&partnerID=MN8TOARS.
  17. Liu, Y.; Johnson, M.G.; Cox, C.J.; Medina, R.; Devos, N.; Vanderpoorten, A.; Hedenäs, L.; et al. "Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes". Nature Communications 10 1 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85063749214&partnerID=MN8TOARS.
  18. de Sousa, C.B.; Cox, C.J.; Brito, L.; Pavão, M.M.; Pereira, H.; Ferreira, A.; Ginja, C.; et al. "Improved phylogeny of brown algae Cystoseira (Fucales) from the Atlantic-Mediterranean region based on mitochondrial sequences". PLoS ONE 14 1 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85060819574&partnerID=MN8TOARS.
  19. Ettamimi, S.; Carlier, J.D.; Cox, C.J.; Elamine, Y.; Hammani, K.; Ghazal, H.; Costa, M.C.. "A meta-taxonomic investigation of the prokaryotic diversity of water bodies impacted by acid mine drainage from the São Domingos mine in southern Portugal". Extremophiles 23 6 (2019): 821-834. http://www.scopus.com/inward/record.url?eid=2-s2.0-85073627708&partnerID=MN8TOARS.
  20. Filipe Sousa; Peter G. Foster; Philip C. J. Donoghue; Harald Schneider; Cymon J. Cox. "Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)". New Phytologist (2018): https://doi.org/10.1111/nph.15587.
  21. Cox, Cymon. "Identification of a fish short-chain dehydrogenase/reductase associated with bone metabolism". Gene 645 (2018): 137-145. https://www.sciencedirect.com/science/article/pii/S0378111917310740.
  22. Cox, C.J.. "Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies". Critical Reviews in Plant Sciences (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85054541689&partnerID=MN8TOARS.
  23. Puttick, M.N.; Morris, J.L.; Williams, T.A.; Cox, C.J.; Edwards, D.; Kenrick, P.; Pressel, S.; et al. "The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte". Current Biology 28 5 (2018): 733-745.e2. http://www.scopus.com/inward/record.url?eid=2-s2.0-85041996392&partnerID=MN8TOARS.
  24. Lu, L.; Cox, C.J.; Mathews, S.; Wang, W.; Wen, J.; Chen, Z.. "Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)". Cladistics (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85012111066&partnerID=MN8TOARS.
  25. Califano, G.; Castanho, S.; Soares, F.; Ribeiro, L.; Cox, C.J.; Mata, L.; Costa, R.. "Molecular taxonomic profiling of bacterial communities in a gilthead seabream (Sparus aurata) hatchery". Frontiers in Microbiology 8 FEB (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85014555519&partnerID=MN8TOARS.
  26. Jonathan Shaw, A.; Devos, N.; Liu, Y.; Cox, C.J.; Goffinet, B.; Flatberg, K.I.; Shaw, B.. "Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)". Annals of Botany 118 2 (2016): 185-196. http://www.scopus.com/inward/record.url?eid=2-s2.0-84982166211&partnerID=MN8TOARS.
  27. Rathore, O.S.; Faustino, A.; Prudêncio, P.; Van Damme, P.; Cox, C.J.; Martinho, R.G.. "Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms". Scientific Reports 6 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84958074128&partnerID=MN8TOARS.
  28. Marques, C.L.; Fernández, I.; Viegas, M.N.; Cox, C.J.; Martel, P.; Rosa, J.; Cancela, M.L.; Laizé, V.. "Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: Molecular and evolutionary perspectives". Cellular and Molecular Life Sciences 73 4 (2016): 841-857. http://www.scopus.com/inward/record.url?eid=2-s2.0-84957432211&partnerID=MN8TOARS.
  29. Martínez-Garrido, J.; Serrão, E.A.; Engelen, A.H.; Cox, C.J.; García-Murillo, P.; González-Wangüemert, M.. "Multilocus genetic analyses provide insight into speciation and hybridization in aquatic grasses, genus Ruppia". Biological Journal of the Linnean Society 117 2 (2016): 177-191. http://www.scopus.com/inward/record.url?eid=2-s2.0-84954366476&partnerID=MN8TOARS.
  30. Laenen, B.; Machac, A.; Gradstein, S.R.; Shaw, B.; Patiño, J.; Désamoré, A.; Goffinet, B.; et al. "Increased diversification rates follow shifts to bisexuality in liverworts". New Phytologist 210 3 (2016): 1121-1129. http://www.scopus.com/inward/record.url?eid=2-s2.0-84957538086&partnerID=MN8TOARS.
  31. Civán, P.; Craig, H.; Cox, C.J.; Brown, T.A.. "Multiple domestications of Asian rice". Nature Plants 2 4 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84979284294&partnerID=MN8TOARS.
  32. Laenen, B.; Machac, A.; Gradstein, S.R.; Shaw, B.; Patiño, J.; Désamoré, A.; Goffinet, B.; et al. "Geographical range in liverworts: Does sex really matter?". Journal of Biogeography 43 3 (2016): 627-635. http://www.scopus.com/inward/record.url?eid=2-s2.0-84958172114&partnerID=MN8TOARS.
  33. Ramos, A.A.; Weydmann, A.; Cox, C.J.; Canário, A.V.M.; Serrão, E.A.; Pearson, G.A.. "A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures". Marine Genomics 23 (2015): 27-29. http://www.scopus.com/inward/record.url?eid=2-s2.0-84941741524&partnerID=MN8TOARS.
  34. Pearson, G.A.; Lago-Leston, A.; Cánovas, F.; Cox, C.J.; Verret, F.; Lasternas, S.; Duarte, C.M.; Agusti, S.; Serrão, E.A.. "Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula". ISME Journal 9 10 (2015): 2275-2289. http://www.scopus.com/inward/record.url?eid=2-s2.0-84942198453&partnerID=MN8TOARS.
  35. Civan, P.; Foster, P.G.; Embley, M.T.; Séneca, A.; Cox, C.J.. "Analyses of charophyte chloroplast genomes help characterize theancestral chloroplastgenomeof land plants". Genome Biology and Evolution 6 4 (2014): 897-911. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902994618&partnerID=MN8TOARS.
  36. Silva, I.A.L.; Cox, C.J.; Leite, R.B.; Cancela, M.L.; Conceição, N.. "Evolutionary conservation of TFIIH subunits: Implications for the use of zebrafish as a model to study TFIIH function and regulation". Comparative Biochemistry and Physiology Part - B: Biochemistry and Molecular Biology 172-173 1 (2014): 9-20. http://www.scopus.com/inward/record.url?eid=2-s2.0-84899696368&partnerID=MN8TOARS.
  37. Li, B.; Lopes, J.S.; Foster, P.G.; Embley, T.M.; Cox, C.J.. "Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins". Molecular Biology and Evolution 31 7 (2014): 1697-1709. http://www.scopus.com/inward/record.url?eid=2-s2.0-84903714806&partnerID=MN8TOARS.
  38. Cox, C.J.; Li, B.; Foster, P.G.; Embley, T.M.; Civán, P.. "Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions". Systematic Biology 63 2 (2014): 272-279. http://www.scopus.com/inward/record.url?eid=2-s2.0-84894600564&partnerID=MN8TOARS.
  39. Laenen, B.; Shaw, B.; Schneider, H.; Goffinet, B.; Paradis, E.; Désamoré, A.; Heinrichs, J.; et al. "Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts". Nature Communications 5 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84923364745&partnerID=MN8TOARS.
  40. Liu, Y.; Cox, C.J.; Wang, W.; Goffinet, B.. "Mitochondrial phylogenomics of early land plants: Mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias". Systematic Biology 63 6 (2014): 862-878. http://www.scopus.com/inward/record.url?eid=2-s2.0-84909618628&partnerID=MN8TOARS.
  41. Hardoim, C.C.P.; Cardinale, M.; Cúcio, A.C.B.; Esteves, A.I.S.; Berg, G.; Xavier, J.R.; Cox, C.J.; Costa, R.. "Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges". Frontiers in Microbiology 5 NOV (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84987811126&partnerID=MN8TOARS.
  42. Williams, T.A.; Foster, P.G.; Cox, C.J.; Embley, T.M.. "An archaeal origin of eukaryotes supports only two primary domains of life". Nature 504 7479 (2013): 231-236. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890355580&partnerID=MN8TOARS.
  43. Hardoim, C.C.P.; Esteves, A.I.S.; Pires, F.R.; Gonçalves, J.M.S.; Cox, C.J.; Xavier, J.R.; Costa, R.. "Phylogenetically and Spatially Close Marine Sponges Harbour Divergent Bacterial Communities". PLoS ONE 7 12 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84871657844&partnerID=MN8TOARS.
  44. Williams, T.A.; Foster, P.G.; Nye, T.M.W.; Cox, C.J.; Martin Embley, T.. "A congruent phylogenomic signal places eukaryotes within the Archaea". Proceedings of the Royal Society B: Biological Sciences 279 1749 (2012): 4870-4879. http://www.scopus.com/inward/record.url?eid=2-s2.0-84869133972&partnerID=MN8TOARS.
  45. Huttunen, S.; Bell, N.; Bobrova, V.K.; Buchbender, V.; Buck, W.R.; Cox, C.J.; Goffinet, B.; et al. "Disentangling knots of rapid evolution: Origin and diversification of the moss order Hypnales". Journal of Bryology 34 3 (2012): 187-211. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866519671&partnerID=MN8TOARS.
  46. Forrest, L.L.; Wickett, N.J.; Cox, C.J.; Goffinet, B.. "Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure". Plant Ecology and Evolution 144 1 (2011): 29-43. http://www.scopus.com/inward/record.url?eid=2-s2.0-79955744844&partnerID=MN8TOARS.
  47. Shaw, A.J.; Devos, N.; Cox, C.J.; Boles, S.B.; Shaw, B.; Buchanan, A.M.; Cave, L.; Seppelt, R.. "Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?". Molecular Phylogenetics and Evolution 55 3 (2010): 1139-1145. http://www.scopus.com/inward/record.url?eid=2-s2.0-77953129459&partnerID=MN8TOARS.
  48. Conceição, N.; Cox, C.J.; Simões, B.; Viegas, M.; Cancela, M.L.. "Comparative promoter analysis and its application to the identification of candidate regulatory factors of cartilage-expressed genes". Journal of Applied Ichthyology 26 2 (2010): 245-250. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954196316&partnerID=MN8TOARS.
  49. Shaw, A.J.; Cox, C.J.; Buck, W.R.; Devos, N.; Buchanan, A.M.; Cave, L.; Seppelt, R.; et al. "Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses)". American Journal of Botany 97 9 (2010): 1511-1531. http://www.scopus.com/inward/record.url?eid=2-s2.0-78049311808&partnerID=MN8TOARS.
  50. Waeschenbach, A.; Cox, C.J.; Littlewood, D.T.J.; Porter, J.S.; Taylor, P.D.. "First molecular estimate of cyclostome bryozoan phylogeny confirms extensive homoplasy among skeletal characters used in traditional taxonomy". Molecular Phylogenetics and Evolution 52 1 (2009): 241-251. http://www.scopus.com/inward/record.url?eid=2-s2.0-64549124256&partnerID=MN8TOARS.
  51. Foster, P.G.; Cox, C.J.; Martin Embley, T.. "The primary divisions of life: A phylogenomic approach employing composition-heterogeneous methods". Philosophical Transactions of the Royal Society B: Biological Sciences 364 1527 (2009): 2197-2207. http://www.scopus.com/inward/record.url?eid=2-s2.0-67651039738&partnerID=MN8TOARS.
  52. Cock, P.J.A.; Antao, T.; Chang, J.T.; Chapman, B.A.; Cox, C.J.; Dalke, A.; Friedberg, I.; et al. "Biopython: Freely available Python tools for computational molecular biology and bioinformatics". Bioinformatics 25 11 (2009): 1422-1423. http://www.scopus.com/inward/record.url?eid=2-s2.0-65649092976&partnerID=MN8TOARS.
  53. Shaw, A.J.; Holz, I.; Cox, C.J.; Goffinet, B.. "Phylogeny, character evolution, and biogeography of the gondwanic moss family Hypopterygiaceae (Bryophyta)". Systematic Botany 33 1 (2008): 21-30. http://www.scopus.com/inward/record.url?eid=2-s2.0-41849115634&partnerID=MN8TOARS.
  54. Cox, C.J.; Foster, P.G.; Hirt, R.P.; Harris, S.R.; Embley, T.M.. "The archaebacterial origin of eukaryotes". Proceedings of the National Academy of Sciences of the United States of America 105 51 (2008): 20356-20361. http://www.scopus.com/inward/record.url?eid=2-s2.0-58149512792&partnerID=MN8TOARS.
  55. Goffinet, B.; Wickett, N.J.; Werner, O.; Ros, R.M.; Shaw, A.J.; Cox, C.J.. "Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta)". Annals of Botany 99 4 (2007): 747-753. http://www.scopus.com/inward/record.url?eid=2-s2.0-34249935531&partnerID=MN8TOARS.
  56. Kauff, F.; Cox, C.J.; Lutzoni, F.. "WASABI: An automated sequence processing system for multigene phylogenies". Systematic Biology 56 3 (2007): 523-531. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548590647&partnerID=MN8TOARS.
  57. James, T.Y.; Kauff, F.; Schoch, C.L.; Matheny, P.B.; Hofstetter, V.; Cox, C.J.; Celio, G.; et al. "Reconstructing the early evolution of Fungi using a six-gene phylogeny". Nature 443 7113 (2006): 818-822. http://www.scopus.com/inward/record.url?eid=2-s2.0-33750329972&partnerID=MN8TOARS.
  58. Shaw, A.J.; Cox, C.J.; Goffinet, B.. "Global patterns of moss diversity: Taxonomic and molecular inferences". Taxon 54 2 (2005): 337-352. http://www.scopus.com/inward/record.url?eid=2-s2.0-21244487846&partnerID=MN8TOARS.
  59. Goffinet, B.; Wickett, N.J.; Shaw, A.J.; Cox, C.J.. "Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses". Taxon 54 2 (2005): 353-360. http://www.scopus.com/inward/record.url?eid=2-s2.0-21344443911&partnerID=MN8TOARS.
  60. Shaw, A.J.; Melosik, I.; Cox, C.J.; Boles, S.B.. "Divergent and reticulate evolution in closely related species of Sphagnum section Subsecunda". Bryologist 108 3 (2005): 363-376. http://www.scopus.com/inward/record.url?eid=2-s2.0-23844456925&partnerID=MN8TOARS.
  61. Shaw, A.J.; Cox, C.J.; Boles, S.B.. "Phylogeny, species delimitation, and recombination in Sphagnum section Acutifolia". Systematic Botany 30 1 (2005): 16-33. http://www.scopus.com/inward/record.url?eid=2-s2.0-14244261083&partnerID=MN8TOARS.
  62. Shaw, A.J.; Cox, C.J.. "Variation in "biodiversity value" of peatmoss species in Sphagnum section Acutifolia (Sphagnaceae)". American Journal of Botany 92 11 (2005): 1774-1783. http://www.scopus.com/inward/record.url?eid=2-s2.0-27544446908&partnerID=MN8TOARS.
  63. Buck, W.R.; Cox, C.J.; Shaw, A.J.; Goffinet, B.. "Ordinal relationships of pleurocarpous mosses, with special emphasis on the hookeriales". Systematics and Biodiversity 2 2 (2004): 121-145. http://www.scopus.com/inward/record.url?eid=2-s2.0-85008857239&partnerID=MN8TOARS.
  64. Shaw, J.; Cox, C.J.; Boles, S.B.. "Phylogenetic relationships among Sphagnum sections: Hemitheca, Isocladus, and Subsecunda". Bryologist 107 2 (2004): 189-196. http://www.scopus.com/inward/record.url?eid=2-s2.0-2942621974&partnerID=MN8TOARS.
  65. Cox, C.J.; Goffinet, B.; Jonathan Shaw, A.; Boles, S.B.. "Phylogenetic relationships among the mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomic compartments". Systematic Botany 29 2 (2004): 234-250. http://www.scopus.com/inward/record.url?eid=2-s2.0-2542446337&partnerID=MN8TOARS.
  66. Vanderpoorten, A.; Shaw, A.J.; Cox, C.J.. "Evolution of multiple paralogous adenosine kinase genes in the moss genus Hygroamblystegium: Phylogenetic implications". Molecular Phylogenetics and Evolution 31 2 (2004): 505-516. http://www.scopus.com/inward/record.url?eid=2-s2.0-1542371109&partnerID=MN8TOARS.
  67. Goffinet, B.; Shaw, A.J.; Cox, C.J.. "Phylogenetic inferences in the dung-moss family splachnaceae from analyses of CPDNA sequence data and implications for the evolution of entomophily". American Journal of Botany 91 5 (2004): 748-759. http://www.scopus.com/inward/record.url?eid=2-s2.0-21244500530&partnerID=MN8TOARS.
  68. Lutzoni, F.; Kauff, F.; Cox, C.J.; McLaughlin, D.; Celio, G.; Dentinger, C.; Padamsee, M.; et al. "Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits". American Journal of Botany 91 10 (2004): 1446-1480. http://www.scopus.com/inward/record.url?eid=2-s2.0-32044471897&partnerID=MN8TOARS.
  69. Schneider, H.; Russell, S.J.; Cox, C.J.; Barker, F.; Henderson, S.; Rumsey, F.; Barrett, J.; Gibby, M.; Vogel, J.C.. "Chloroplast phylogeny of asplenioid ferns based on rbcL and trnL-F spacer sequences (Polypodiidae, Aspleniaceae) and its implications for biogeography". Systematic Botany 29 2 (2004): 260-274. http://www.scopus.com/inward/record.url?eid=2-s2.0-2542418254&partnerID=MN8TOARS.
  70. Hedderson, T.A.; Murray, D.J.; Cox, C.J.; Nowell, T.L.. "Phylogenetic Relationships of Haplolepideous Mosses (Dicranidae) Inferred from rps4 Gene Sequences". Systematic Botany 29 1 (2004): 29-41. http://www.scopus.com/inward/record.url?eid=2-s2.0-1442291203&partnerID=MN8TOARS.
  71. Diezmann, S.; Cox, C.J.; Schönian, G.; Vilgalys, R.J.; Mitchell, T.G.. "Phylogeny and evolution of medical species of candida and related taxa: A multigenic analysis". Journal of Clinical Microbiology 42 12 (2004): 5624-5635. http://www.scopus.com/inward/record.url?eid=2-s2.0-10844277854&partnerID=MN8TOARS.
  72. Pedersen, N.; Cox, C.J.; Hedenäs, L.. "Phylogeny of the moss family Bryaceae inferred from chloroplast DNA sequences and morphology". Systematic Botany 28 3 (2003): 471-482. http://www.scopus.com/inward/record.url?eid=2-s2.0-0041508608&partnerID=MN8TOARS.
  73. Shaw, A.J.; Cox, C.J.; Boles, S.B.. "Polarity of peatmoss (Sphagnum) evolution: Who says bryophytes have no roots?". American Journal of Botany 90 12 (2003): 1777-1787. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347723874&partnerID=MN8TOARS.
  74. Shaw, A.J.; Cox, C.J.; Goffinet, B.; Buck, W.R.; Boles, S.B.. "Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta)". Evolution 57 10 (2003): 2226-2241. http://www.scopus.com/inward/record.url?eid=2-s2.0-0242487487&partnerID=MN8TOARS.
  75. Cox, C.J.; Hedderson, T.A.J.. "Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence". Journal of Bryology 25 1 (2003): 31-40. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037242926&partnerID=MN8TOARS.
  76. Vanderpoorten, A.; Goffinet, B.; Hedenäs, L.; Cox, C.J.; Shaw, A.J.. "A taxonomic reassessment of the Vittiaceae (Hypnales, Bryopsida): Evidence from phylogenetic analyses of combined chloroplast and nuclear sequence data". Plant Systematics and Evolution 241 1-2 (2003): 1-12. http://www.scopus.com/inward/record.url?eid=2-s2.0-0242424192&partnerID=MN8TOARS.
  77. Shaw, A.J.; Cox, C.J.; Boles, S.B.. "Global patterns in peatmoss biodiversity". Molecular Ecology 12 10 (2003): 2553-2570. http://www.scopus.com/inward/record.url?eid=2-s2.0-0141613151&partnerID=MN8TOARS.
  78. Vanderpoorten, A.; Hedenäs, L.; Cox, C.J.; Shaw, A.J.. "Phylogeny and morphological evolution of the Amblystegiaceae (Bryopsida)". Molecular Phylogenetics and Evolution 23 1 (2002): 1-21. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036402405&partnerID=MN8TOARS.
  79. Vanderpoorten, A.; Hedenäs, L.; Cox, C.J.; Shaw, A.J.. "Erratum: Circumscription, classification, and taxonomy of the Amblystegiaceae (Bryopsida) inferred from nuclear and chloroplast DNA sequence data and morphology (Taxon (2002) 51:1 (115-122))". Taxon 51 3 (2002): http://www.scopus.com/inward/record.url?eid=2-s2.0-36248965686&partnerID=MN8TOARS.
  80. Pinter, I.; Bakker, F.; Barrett, J.; Cox, C.; Gibby, M.; Henderson, S.; Morgan-Richards, M.; et al. "Phylogenetic and biosystematic relationships in four highly disjunct polyploid complexes in the subgenera Ceterach and Phyllitis in Asplenium (Aspleniaceae)". Organisms Diversity and Evolution 2 4 (2002): 299-311. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036459011&partnerID=MN8TOARS.
  81. Buck, W.R.; Shaw, A.J.; Cox, C.J.. "A new species of Leskeodon (Daltoniaceae) from Ecuador". Brittonia 54 3 (2002): 178-180. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036663366&partnerID=MN8TOARS.
  82. Vanderpoorten, A.; Hedenäs, L.; Cox, C.J.; Shaw, A.J.. "Circumscription, classification, and taxonomy of Amblystegiaceae (Bryopsida) inferred from nuclear and chloroplast DNA sequence data and morphology". Taxon 51 1 (2002): 115-122. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036264853&partnerID=MN8TOARS.
  83. Goffinet, B.; Cox, C.J.; Shaw, A.Jonathan; Hedderson, T.A.J.. "The bryophyta (mosses): Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny". Annals of Botany 87 2 (2001): 191-208. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034963628&partnerID=MN8TOARS.
  84. Newton, A.E.; Cox, C.J.; Duckett, J.G.; Wheeler, J.A.; Goffinet, B.; Hedderson, T.A.J.; Mishler, B.D.. "Evolution of the major moss lineages: Phylogenetic analyses based on multiple gene sequences and morphology". Bryologist 103 2 (2000): 187-211. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034119944&partnerID=MN8TOARS.
  85. Goffinet, B.; Cox, C.J.. "Phylogenetic relationships among basal-most arthrodontous mosses with special emphasis on the evolutionary significance of the Funariineae". Bryologist 103 2 (2000): 212-223. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034097905&partnerID=MN8TOARS.
  86. Cox, C.J.; Goffinet, B.; Newton, A.E.; Shaw, A.J.; Hedderson, T.A.J.. "Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclear and chloroplast DNA sequences". Bryologist 103 2 (2000): 224-241. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034086438&partnerID=MN8TOARS.
  87. Cox, C.J.; Hedderson, T.A.J.. "Phylogenetic relationships among the ciliate arthrodontous mosses: Evidence from chloroplast and nuclear DNA sequences". Plant Systematics and Evolution 215 1-4 (1999): 119-139. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032945369&partnerID=MN8TOARS.
  88. Hedderson, T.A.; Cox, C.J.; Gibbings, J.G.. "Phylogenetic relationships of the Wardiaceae (Musei); evidence from 18s rRNA and rps4 gene sequences". Bryologist 102 1 (1999): 26-31. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032896296&partnerID=MN8TOARS.
  89. Vogel, J.C.; Rumsey, F.J.; Russell, S.J.; Cox, C.J.; Holmes, J.S.; Bujnoch, W.; Stark, C.; Barrett, J.A.; Gibby, M.. "Genetic structure, reproductive biology and ecology of isolated populations of Asplenium csikii (Aspleniaceae, Pteridophyta)". Heredity 83 5 (1999): 604-612. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032763439&partnerID=MN8TOARS.
Thesis / Dissertation
  1. Hardoim, Cristiane Cassiolato Pires; Costa, Rodrigo; Cox, Cymon J.; Canario, Adelino V. M.. "Microbiome diversity and composition in the phylogenetically related marine sponges S. spinosulus and I. variabilis". PhD, 2013. http://hdl.handle.net/10400.1/6738.


  1. Sousa, Filipe; Civán, Peter; Brazão, João; Foster, Peter G.; Cox, Cymon J.. Data from the article "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models".
  2. Williams, Tom; Schrempf, Dominik; Sz¿¿ll¿¿si, Gergely J.; Cymon Cox; Foster, Peter G.; T. Martin Embley. Thermus-Deinococcus alignment.
  3. Filipe de Sousa; Peter Civán; Peter G. Foster; Cymon J. Cox. data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models".
  4. Civan, Peter; Craig, Hayley; Cox, Cymon J.; Brown, Terence A; Civán, P.; Craig, H.; Cox, C.J.; Brown, T.A.. Three geographically separate domestications of Asian rice. 2015.
Other output
  1. A haplotype-resolved draft genome of the European sardine (Sardina pilchardus). GigaScience. 2018. Louro, B.; De Moro, G.; Garcia, C.; Cox, C.J.; Veríssimo, A.; Sabatino, S.J.; Santos, A.M.; Canário, A.V.M.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095641019&partnerID=MN8TOARS.
  2. A 20-state empirical amino-acid substitution model for green plant chloroplasts. We introduce a new empirical amino-acid substitution model intended for use with for green plant (Viridiplantae) chloroplast protein data, which we call gcpREV (green chloroplast reversible model). Relative exchange rates and base composition frequencies among amino-acids were calculated using a Markov-chain Monte Carlo analysis on a combined data set of 34 proteins sampled among 27 taxa of green. 2013. Cox, Cymon; Foster, P. G.; Cox, C.J.; Foster, P.G.. http://hdl.handle.net/10400.1/5527.
    http://dx.doi.org/ 10.1016/j.ympev.2013.03.030
  3. Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva. Poribacterial clone libraries constructed for Aplysina fulva sponge specimens were analysed with respect to diversity and phylogeny. Results imply the coexistence of several, prevalently "intra-specific" poribacterial genotypes in a single sponge host, and suggest quantitative analysis as a desirable approach in studies of the diversity and distribution of poribacterial cohorts in marine sponges.. 2013. Cox, Cymon; Hardoim, Cristiane; Peixoto, R. S.; Rosado, A. S.; da Silva Costa, Rodrigo; van Elsas, J. D.. http://hdl.handle.net/10400.1/12052.

Association member

Society Organization name Role
2019/01/01 - Current BioData.pt | ELIXIR-PT BioData.pt is a non-for-profit private association of 15 R&I organizations. BioData.pt is the Portuguese distributed infrastructure for biological data and the Portuguese ELIXIR node. BioData.pt supports the national scientific system through best practices in data management and state of the art data analysis. It interfaces with both academia and industry, making research available for innovation, namely in sectors such as agro-food and forestry, sea, and health. BioData.pt services include ELIXIR services such as Member (Vogal) of the Administrative Council

Committee member

Activity description
Institution / Organization
2019/04/01 - Current European Marine Biological Resource Center (EMBRC-ERIC) - Member of Working Group for e-Infrastructure
Advisor / Consultant
European Marine Biological Resource Centre, France