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I completed my PhD at the University of Manchester, UK, in 2008 (supervised by Prof. David Robertson). My thesis focused on the evolutionary dynamics of HIV-1 and largely involved: analysis of next generation sequence data, software development, varying associated statistics, algorithm development, recombination detection and phylogeny. All chapters have been published. My postdoctoral research was driven by national and international collaborations. In 2008 I received funding from Pfizer, UK, to investigate the emergence of drug resistance mutations within HIV-1 populations. In 2009 I received funding from Case Western Reserve University Hospital, Cleveland, to develop a viral genotyping tool. Also in 2009 I wrote a successful Biotechnology and Biological Sciences Research Council (BBSRC) three year postdoc project with my PhD supervisor. The project involved the development of an environment for the handling of NGS data derived from viral populations. Since December 2014 I have been employed at the Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-INBIO), University of Porto. This position has allowed me to collaborate on a range of FCT projects as well as to write my own involving chimerism within de novo assembly software and its effects (title: De Novo based sequence assembly of next generation sequence data without chimeras: improved annotation, gene expression profiles and haplotype reconstruction.). My Latest Software include: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/
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Identification

Personal identification

Full name
John Archer

Citation names

  • Archer, John

Author identifiers

Ciência ID
8B1B-B02C-7621
ORCID iD
0000-0001-6212-0962

Languages

Language Speaking Reading Writing Listening Peer-review
English (Mother tongue)
Portuguese Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2)
Education
Degree Classification
2005/01/01 - 2008/06/01
Concluded
 PhD in Bioinformatics (Doctor of Philosophy)
Major in Bioinformatics
The University of Manchester, United Kingdom
"The Diversity of HIV-1" (THESIS/DISSERTATION)
2000/09/01 - 2001/09/01
Concluded
 Software Engineering (Mestrado)
Major in Software Engineering
University of Liverpool, United Kingdom
 Distinction
1995/09/01 - 1998/09/01
Concluded
 Microbiology (Bacharelato)
Major in Microbiology
University of Liverpool, United Kingdom
 2:1 (honours)
Affiliation

Science

Category
Host institution 		Employer
2014/12/01 - Current Principal Investigator (Research) Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
2013/12/01 - 2014/12/01 Postdoc (Research) Liverpool School of Tropical Medicine, United Kingdom
2008/01/01 - 2013/12/01 Postdoc (Research) The University of Manchester, United Kingdom
Projects

Grant

Designation Funders
2018/01/01 - Current How and why species multiply? Disentangling the evolution of the mantellid frogs of Madagascar to unveil the determinants of species diversification
PTDC/BIA-EVL/31254/2017
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2016/01/01 - Current MICROBIOMA - To be or not to be diseased: the effects of microbiome on parasitic infections in farmed seabream and sea bass
PTDC/MAR-BIO/0902/2014
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2016/01/01 - Current Is hybridization between wolves and dogs shaping the evolutionary trajectory of wolf populations in human-dominated landscapes?
PTDC/BIA-EVF/2460/2014
Research Fellow
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2011/01 - 2013/01 Understanding the evolution and diversity of viral pathogens using next generation sequencing technologies
BB/H012419/1
Post-doc Fellow
Biotechnology and Biological Sciences Research Council

Contract

Designation Funders
2018/01/01 - Current Climate Change and Local Adaptation: Challenges of a lizard whose sex is determined by environmental temperature
AAC/02/SAICT/2017/27958
Researcher
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2022/04/01 - 2024/12/01 Research Network in Biodiversity and Evolutionary Biology
UIDB/50027/2020
10.54499/UIDB/50027/2020
Researcher
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2022/04/01 - 2024/12/01 Research Network in Biodiversity and Evolutionary Biology
UIDP/50027/2020
10.54499/UIDP/50027/2020
Researcher
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2022/04/01 - 2024/12/01 Research Network in Biodiversity and Evolutionary Biology (InBIO)
LA/P/0048/2020
10.54499/LA/P/0048/2020
Researcher
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/01 - 2021/06/01 De Novo based sequence assembly of next generation sequence data without chimeras: improved annotation, gene expression profiles and haplotype reconstruction.
PTDC/BIA-EVL/29115/2017
Principal investigator
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing

Other

Designation Funders
2015/01/01 - Current ENVMETAGEN - Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics
H2020-WIDESPREAD-2014-2
Principal investigator
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
 EU Framework Programme for Research and Innovation Euratom
Ongoing
Outputs

Publications

Journal article
  1. Joana G Guedes; Rogério Ribeiro; Inês Carqueijeiro; Ana Luísa Guimarães; Cláudia Bispo; John Archer; Herlander Azevedo; et al. "The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism". Journal of Experimental Botany (2024): https://doi.org/10.1093/jxb/erad374.
    10.1093/jxb/erad374
  2. Diana Lobo; Katherine James; Raquel Linheiro; Raquel Godinho; John Patrick Archer. "On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves". PLOS ONE (2022): https://doi.org/10.1371/journal.pone.0274591.
    10.1371/journal.pone.0274591
  3. Raquel Linheiro; Eduardo Andrés-León; Stephen Sabatino; Diana Lobo; John Archer. "CView: A network based tool for enhanced alignment visualization". PLOS ONE (2022): https://doi.org/10.1371/journal.pone.0259726.
    10.1371/journal.pone.0259726
  4. Stephen J. Sabatino; Paulo Pereira; Miguel Carneiro; Jolita Dilyte; John Patrick Archer; Antonio Munoz; Francesco Nonnis-Marzano; Antonio Murias. "The genetics of adaptation in freshwater Eurasian shad ( Alosa )". Ecology and Evolution (2022): https://doi.org/10.1002/ece3.8908.
    10.1002/ece3.8908
  5. Raquel Linheiro; John Archer; Archer John; Linheiro Raquel. "Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly [version 1; peer review: awaiting peer review]". (2022): https://f1000research.com/articles/11-120/v1.
    10.12688/f1000research.108489.1
  6. Raquel Linheiro; Mihaela Pertea; John Archer. "CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure". PLOS Computational Biology 17 11 (2021): e1009631-e1009631. https://doi.org/10.1371/journal.pcbi.1009631.
    10.1371/journal.pcbi.1009631
  7. Freek J. Vonk; Israel Silman; Mátyás A. Bittenbinder; Harald M. I. Kerkkamp; Dwin G. B. Grashof; John P. Archer; Sandra Afonso; et al. "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 (2021): https://doi.org/10.1371/journal.pone.0258712.
    10.1371/journal.pone.0258712
  8. Gonçalo C. Cardoso; João M. Abreu; John Archer; Angelica Crottini; Paulo G. Mota. "Independent evolution of song diversity and song motor performance in canaries, goldfinches and allies indicates clade-specific trade-offs in birdsong". Evolution 74 6 (2020): 1170-1185. https://doi.org/10.1111/evo.13987.
    10.1111/evo.13987
  9. Grashof, Dwin G. B.; Kerkkamp, Harald M. I.; Afonso, Sandra; Archer, John; Harris, D. James; Richardson, Michael K.; Vonk, Freek J.; van der Meijden, Arie. "Transcriptome annotation and characterization of novel toxins in six scorpion species". BMC Genomics 20 1 (2019): http://dx.doi.org/10.1186/s12864-019-6013-6.
    10.1186/s12864-019-6013-6
  10. Gazda, Malgorzata A; Andrade, Pedro; Afonso, Sandra; Dilyte, Jolita; Archer, John P; Lopes, Ricardo J; Faria, Rui; Carneiro, Miguel. "Signatures of Selection on Standing Genetic Variation Underlie Athletic and Navigational Performance in Racing Pigeons". Molecular Biology and Evolution 35 5 (2018): 1176-1189. http://dx.doi.org/10.1093/molbev/msy030.
    10.1093/molbev/msy030
  11. Archer, John. "Lorenzo-Redondo et al. reply". (2017):
  12. Lorenzo-Redondo, R.; Fryer, H.R.; Bedford, T.; Kim, E.-Y.; Archer, J.; Pond, S.L.K.; Chung, Y.-S.; et al. "Lorenzo-Redondo et al. reply". Nature 551 7681 (2017): E10-E10. http://www.scopus.com/inward/record.url?eid=2-s2.0-85034807232&partnerID=MN8TOARS.
    10.1038/nature24635
  13. Carneiro, M.; Hu, D.; Archer, J.; Feng, C.; Afonso, S.; Chen, C.; Blanco-Aguiar, J.A.; et al. "Dwarfism and altered craniofacial development in rabbits is caused by a 12.1 kb deletion at the HMGA2 locus". Genetics 205 2 (2017): 955-965. http://www.scopus.com/inward/record.url?eid=2-s2.0-85021849586&partnerID=MN8TOARS.
    10.1534/genetics.116.196667
  14. Archer, John. "Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus.". Genetics (2016):
  15. Archer, John. "Persistent HIV-1 replication maintains the tissue reservoir during antiretroviral therapy". Nature (2016):
  16. Lorenzo-Redondo, R.; Fryer, H.R.; Bedford, T.; Kim, E.-Y.; Archer, J.; Kosakovsky Pond, S.L.; Chung, Y.-S.; et al. "Persistent HIV-1 replication maintains the tissue reservoir during therapy". Nature 530 7588 (2016): 51-56. http://www.scopus.com/inward/record.url?eid=2-s2.0-84957558724&partnerID=MN8TOARS.
    10.1038/nature16933
  17. Archer JP; Whiteley G; Casewell NR; Harrison RA; Wagstaff SC. "VTBuilder: a tool for the assembly of multi isoform transcriptomes.". (2014): http://europepmc.org/abstract/med/25465054.
    10.1186/s12859-014-0389-8
  18. Kim, E.-Y.; Lorenzo-Redondo, R.; Little, S.J.; Chung, Y.-S.; Phalora, P.K.; Maljkovic Berry, I.; Archer, J.; et al. "Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection". PLoS Pathogens 10 7 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84905399319&partnerID=MN8TOARS.
    10.1371/journal.ppat.1004281
  19. Gibson, R.M.; Meyer, A.M.; Winner, D.; Archer, J.; Feyertag, F.; Ruiz-Mateos, E.; Leal, M.; et al. "Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism". Antimicrobial Agents and Chemotherapy 58 4 (2014): 2167-2185. http://www.scopus.com/inward/record.url?eid=2-s2.0-84896944940&partnerID=MN8TOARS.
    10.1128/AAC.02710-13
  20. Weber, J.; Vazquez, A.C.; Winner, D.; Gibson, R.M.; Rhea, A.M.; Rose, J.D.; Wylie, D.; et al. "Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism". Journal of Clinical Microbiology 51 5 (2013): 1517-1527. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876750679&partnerID=MN8TOARS.
    10.1128/JCM.00092-13
  21. Archer, J.; Baillie, G.; Watson, S.J.; Kellam, P.; Rambaut, A.; Robertson, D.L.. "Analysis of high-depth sequence data for studying viral diversity: A comparison of next generation sequencing platforms using Segminator II". BMC Bioinformatics 13 1 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84858739096&partnerID=MN8TOARS.
    10.1186/1471-2105-13-47
  22. Archer, J.; Weber, J.; Henry, K.; Winner, D.; Gibson, R.; Lee, L.; Paxinos, E.; et al. "Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism". PLoS ONE 7 11 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84869122814&partnerID=MN8TOARS.
    10.1371/journal.pone.0049602
  23. Williams SG; Madan R; Norris MG; Archer J; Mizuguchi K; Robertson DL; Lovell SC. "Using knowledge of protein structural constraints to predict the evolution of HIV-1.". (2011): http://europepmc.org/abstract/med/21763504.
    10.1016/j.jmb.2011.04.037
  24. Archer, J.; Rambaut, A.; Taillon, B.E.; Richard Harrigan, P.; Lewis, M.; Robertson, D.L.. "The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach". PLoS Computational Biology 6 12 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78651228163&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1001022
  25. Simon-Loriere, E.; Galetto, R.; Hamoudi, M.; Archer, J.; Lefeuvre, P.; Martin, D.P.; Robertson, D.L.; Negroni, M.. "Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus". PLoS Pathogens 5 5 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-67249086022&partnerID=MN8TOARS.
    10.1371/journal.ppat.1000418
  26. Archer, J.; Braverman, M.S.; Taillon, B.E.; Desany, B.; James, I.; Harrigan, P.R.; Lewis, M.; Robertson, D.L.. "Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing". AIDS 23 10 (2009): 1209-1218. http://www.scopus.com/inward/record.url?eid=2-s2.0-67651055421&partnerID=MN8TOARS.
    10.1097/QAD.0b013e32832b4399
  27. Huxley-Jones, J.; Pinney, J.W.; Archer, J.; Robertson, D.L.; Boot-Handford, R.P.. "Back to basics - How the evolution of the extracellular matrix underpinned vertebrate evolution". International Journal of Experimental Pathology 90 2 (2009): 95-100. http://www.scopus.com/inward/record.url?eid=2-s2.0-62749135959&partnerID=MN8TOARS.
    10.1111/j.1365-2613.2008.00637.x
  28. Archer, J.; Pinney, J.W.; Fan, J.; Simon-Loriere, E.; Arts, E.J.; Negroni, M.; Robertson, D.L.. "Identifying the important HIV-1 recombination breakpoints". PLoS Computational Biology 4 9 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-52949114578&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1000178
  29. Archer, J.; Robertson, D.L.. "Understanding the diversification of HIV-1 groups M and O". AIDS 21 13 (2007): 1693-1700. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547750546&partnerID=MN8TOARS.
    10.1097/QAD.0b013e32825eabd0
  30. Archer, J.; Robertson, D.L.. "CTree: Comparison of clusters between phylogenetic trees made easy". Bioinformatics 23 21 (2007): 2952-2953. http://www.scopus.com/inward/record.url?eid=2-s2.0-36448980225&partnerID=MN8TOARS.
    10.1093/bioinformatics/btm410
  31. Baird, H.A.; Galetto, R.; Gao, Y.; Simon-Loriere, E.; Abreha, M.; Archer, J.; Fan, J.; et al. "Sequence determinants of breakpoint location during HIV-1 intersubtype recombination". Nucleic Acids Research 34 18 (2006): 5203-5216. http://www.scopus.com/inward/record.url?eid=2-s2.0-33750969087&partnerID=MN8TOARS.
    10.1093/nar/gkl669
  32. Taylor MJ; Bilo K; Cross HF; Archer JP; Underwood AP. "16S rDNA phylogeny and ultrastructural characterization of Wolbachia intracellular bacteria of the filarial nematodes Brugia malayi, B. pahangi, and Wuchereria bancrofti.". (1999): http://europepmc.org/abstract/med/10092480.
    10.1006/expr.1998.4383
Preprint
  1. Joana G. Guedes; Rogério Ribeiro; Inês Carqueijeiro; Ana Luísa Guimarães; Cláudia Bispo; John Archer; Herlander Azevedo; Nuno A. Fonseca; Mariana Sottomayor. "Idioblasts accumulating anticancer alkaloids inCatharanthus roseusleaves are a unique cell type". 2023. https://doi.org/10.1101/2023.02.24.529939.
    10.1101/2023.02.24.529939
  2. Diana Lobo; Raquel Godinho; John Patrick Archer. "On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves". 2022. https://doi.org/10.1101/2022.01.24.477470.
    10.1101/2022.01.24.477470
  3. Raquel Linheiro; Diana Lobo; Stephen Sabatino; John Archer. "CView: A network based tool for enhanced alignment visualization". 2022. https://doi.org/10.1101/2022.01.17.476623.
    10.1101/2022.01.17.476623

Other

Other output
  1. TVScript: A Tool for Exploring the Effects of Intra-Condition Variation on the Detection of Differentially Expressed Genes. 2021. Lobo, D.; Godinho, R.; Archer, J.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85133343113&partnerID=MN8TOARS.
    10.21203/rs.3.rs-468506
  2. Taming of the wild a new method for cross study RNA-seq analysis. 2020. Lobo, D.; Godinho, R.; Archer, J.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85133834516&partnerID=MN8TOARS.
    10.21203/rs.3.rs-27674
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2017/06/01 - 2021/06/01 A genome-wide perspective on the evolutionary trajectory of wolves in human-dominated landscapes.
Co-supervisor
 Bioinformatics ad evolution (PhD)
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal
2020/01/01 - 2021/01/01 Unlocking the gene/protein network involved in the metabolism of the anticancer alkaloids from Catharanthus roseus
Co-supervisor
 Bioinformatics (Master)
Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2017/09/01 - Current Bioinformatics course using next generation sequencing data covering the following topics: 1. Read mapping. 2. variant detection. 3. Haplotype reconstruction.                 4. Phylogenies. 5. De novo assembly. 6. Differential expression. 7. Quality filters applied to raw data and adaptor removal. 8. Gene prediction in prokaryotes and eukaryotes. 9. Functional annotation. Bioinformatics (Mestrado) Universidade do Porto, Portugal
2016/03/25 - Current This course will introduce students to the fundamentals of programming for bioinformatics using the Java programming language. Many of the concepts covered will be readily transferable to other languages. The course will largely focus on the Java language basics including: data types; program control structures; and object-oriented programming features of the language, with an emphasis on usage within areas of bioinformatics, for example file manipulation, package use and calling external software. By the end of the course students will have had a p Programming (Curso de doutoramento (conclusão de unidades curriculares)) Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal