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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; .
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Identificação

Identificação pessoal

Nome completo
Cymon John Cox

Nomes de citação

  • Cox, Cymon J.

Identificadores de autor

Ciência ID
6B15-9771-1D04
ORCID iD
0000-0002-4927-979X
Google Scholar ID
f5M7DhkAAAAJ
Researcher Id
D-1303-2012
Scopus Author Id
7402112716

Endereços de correio eletrónico

  • cymon@ualg.pt (Profissional)

Telefones

Telefone
  • 289800051 Ext.: 7380 (Profissional)

Moradas

  • 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 (Profissional)

Websites

Domínios de atuação

  • Ciências Naturais - Ciências Biológicas - Biologia da Evolução das Espécies
  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1)
Formação
Grau Classificação
1998
Concluído
 PhD (Doutoramento)
University of Reading, Reino Unido
"Phylogenetic relationships of the Eubryalean mosses (Bryineae, Musci)" (TESE/DISSERTAÇÃO)
 PhD
1994
Concluído
 Botany (Bacharelato)
Bangor University, Reino Unido
 BSc (2.1)
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2018/06/16 - Atual Investigador principal (carreira) (Investigação) Centro de Ciências do Mar, Portugal
Centro de Ciências do Mar, Portugal
2013/06/16 - 2018/06/15 Investigador Coordenador (carreira) (Investigação) Centro de Ciências do Mar, Portugal
2008/06/06 - 2013/06/12 Investigador Auxiliar (carreira) (Investigação) Centro de Ciências do Mar, Portugal
2005/06/01 - 2008/05/31 Pós-doutorado (Investigação) Natural History Museum, Reino Unido
2003/12/01 - 2005/05/31 Pós-doutorado (Investigação) Duke University, Estados Unidos
2001/12/01 - 2005/05/31 Pós-doutorado (Investigação) Duke University, Estados Unidos
1999/01/01 - 1999/10/31 Pós-doutorado (Investigação) Natural History Museum, Reino Unido
1998/01/01 - 1998/12/31 Pós-doutorado (Investigação) Natural History Museum, Reino Unido

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
1999/11/01 - 2001/10/31 Mellon Research Fellow Duke University, Estados Unidos
Projetos

Bolsa

Designação Financiadores
2024/04/01 - 2029/03/31 AQUASERV - RESEARCH INFRASTRUCTURE SERVICES FOR SUSTAINABLE AQUACULTURE, FISHERIES AND THE BLUE ECONOMY
101131121
Centro de Ciências do Mar, Portugal
 Horizon Europe
Em curso
2024/01 - 2026/12 European Research Infrastructure for Marine Bioprospecting
101131663
 European Commission
2021/01 - 2025/12 Centro de Investigação Marinha e Ambiental
168238UID
 Fundação para a Ciência e a Tecnologia
2022/08 - 2025/08 FAIR EArth Sciences & Environment services (FAIR-EASE)
10039779
 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
PTDC/CTA-AMB/7782/2020
DOI: 10.54499/PTDC/CTA-AMB/7782/2020
Centro de Ciências do Mar, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2019/03 - 2023/08 Providing an open collaborative space for digital biology in Europe
824087
 European Commission
2019/01 - 2019/12 Centro de Ciências do Mar do Algarve
154715UID
 Fundação para a Ciência e a Tecnologia
2016/01 - 2018/12 Determining the causes of inter-genomic conflict in the land plant phylogeny
grant.Provided by PTCRIS: 140124
 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
grant.Provided by PTCRIS: 134689
 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.
grant.Provided by PTCRIS: 113129
 Fundação para a Ciência e a Tecnologia
2010/01 - 2013/06 Unlocking the bacterial diversity encrypted in the metagenomes of marine sponges
grant.Provided by PTCRIS: 101431
 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
grant.Provided by PTCRIS: 99565
 Fundação para a Ciência e a Tecnologia

Projeto

Designação Financiadores
2017/05/01 - 2021/09/30 European Marine Biological Resource Centre Portugal
PINFRA/22121/2016
ALG-01-0145-FEDER-022121
Centro de Ciências do Mar, Portugal
 Comissão de Coordenação e Desenvolvimento Regional do Algarve

Fundação para a Ciência e a Tecnologia
Concluído
2011/01/01 - 2012/12/31 Projecto Estratégico - LA 15 - 2011-2012
PEst-C/MAR/LA0015/2011
Centro de Ciências do Mar, Portugal

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

Publicações

Artigo em conferência
  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. Autor correspondente: Carlier, Jorge Daniel Dias. "Selection of bacterial strains to bioaugment granular sludge and improve the removal of recalcitrant pollutants". Trabalho apresentado em International Conference on Environmental Science & Technology (CEST), Athens, 2023.
    Submetido
Artigo em revista
  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.
    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.
    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.
    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.
    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.
    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.
    10.1093/gbe/evab067
  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.
    10.1186/s40168-021-01031-y
  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.
    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.
    10.1007/s00792-020-01196-8
  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.
    10.3389/fpls.2020.01062
  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.
    10.7717/peerj.8995
  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.
    10.3897/zookeys.968.52986
  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.
    10.1111/jse.12708
  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.
    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.
    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.
    10.1016/j.bbagen.2018.09.017
  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.
    10.1038/s41467-019-09454-w
  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.
    10.1371/journal.pone.0210143
  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.
    10.1007/s00792-019-01136-1
  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.
    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.
    10.1016/j.gene.2017.12.021
  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.
    10.1080/07352689.2018.1482443
  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.
    10.1016/j.cub.2018.01.063
  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.
    10.1111/cla.12191
  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.
    10.3389/fmicb.2017.00204
  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.
    10.1093/aob/mcw086
  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.
    10.1038/srep21304
  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.
    10.1007/s00018-015-2024-x
  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.
    10.1111/bij.12666
  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.
    10.1111/nph.13835
  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.
    10.1038/NPLANTS.2016.37
  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.
    10.1111/jbi.12661
  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.
    10.1016/j.margen.2015.03.014
  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.
    10.1038/ismej.2015.40
  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.
    10.1093/gbe/evu061
  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.
    10.1016/j.cbpb.2014.03.007
  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.
    10.1093/molbev/msu105
  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.
    10.1093/sysbio/syt109
  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.
    10.1038/ncomms6134
  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.
    10.1093/sysbio/syu049
  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.
    10.3389/fmicb.2014.00611
  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.
    10.1038/nature12779
  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.
    10.1371/journal.pone.0053029
  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.
    10.1098/rspb.2012.1795
  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.
    10.1179/1743282012Y.0000000013
  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.
    10.5091/plecevo.2011.535
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  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.
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  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.
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  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.
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  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.
    10.3732/ajb.91.5.748
  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.
    10.3732/ajb.91.10.1446
  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.
    10.1600/036364404774195476
  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.
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  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.
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    10.1046/j.1365-294X.2003.01929.x
  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.
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  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.
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Resumo em conferência
  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]". Trabalho apresentado em 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]". Trabalho apresentado em 9th World Sponge Conference, Perth, 2013.
    Publicado
  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". Trabalho apresentado em 9th World Sponge Conference, Perth, 2013.
    Publicado
Tese / Dissertação
  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". Doutoramento, 2013. http://hdl.handle.net/10400.1/6738.

Outros

Conjunto de dados
  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".
    10.5281/zenodo.3554148
  2. Williams, Tom; Schrempf, Dominik; Sz¿¿ll¿¿si, Gergely J.; Cymon Cox; Foster, Peter G.; T. Martin Embley. Thermus-Deinococcus alignment.
    10.6084/m9.figshare.13708702.v1
  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".
    10.5281/zenodo.3886964
  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.
    10.5281/zenodo.20740
Outra produção
  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.
    10.1101/441774
  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.
    10.1590/S1517-83822013000100048
Atividades

Membro de associação

Nome da associação Tipo de participação
2019/01/01 - Atual 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

Membro de comissão

Descrição da atividade
Tipo de participação 		Instituição / Organização
2019/04/01 - Atual European Marine Biological Resource Center (EMBRC-ERIC) - Member of Working Group for e-Infrastructure
Consultor
 European Marine Biological Resource Centre, França