Archer JP, Whiteley G, Casewell NR, Harrison RA, Wagstaff SC. (2014)
VTBuilder: a tool for the assembly of multi isoform transcriptomes.
BMC Bioinformatics. Dec 3;15(1):389. [Epub ahead of print] PMID: 25465054

Gibson RM, Meyer AM, Winner D, Archer J, Feyertag F, Ruiz-Mateos E, Leal M, Robertson DL, Schmotzer CL, Quiñones-Mateu ME. (2014)
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.
Antimicrob Agents Chemother. Jan;58(4):2167-85. doi: 10.1128/AAC.02710-13. Epub 2014 Jan 27. PMID: 24468782

Kim EY, Lorenzo-Redondo R, Little SJ, Chung YS, Phalora PK, Maljkovic Berry I, Archer J, Penugonda S, Fischer W, Richman DD, Bhattacharya T, Malim MH, Wolinsky SM. (2014)
Human APOBEC3 induced mutation of human immunodeficiency virus type-1 contributes to adaptation and evolution in natural infection.
PLoS Pathog. 2014 Jul 31;10(7):e1004281. doi: 10.1371/journal.ppat.1004281. eCollection 2014 Jul. PMID: 25080100

Weber J., Vazquez A.C., Winner D., Gibson R.M., Rhea A.M., Rose J.D., Wylie D., Henry K., Wright A., King K., Archer J., Poveda E., Soriano V., Robertson D.L., Olivo P.D., Arts E.J., Quiones-Mateu M.E. (2013)
Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism.
J Clin Microbiol., May;51(5):1517-27. doi: 10.1128/JCM.00092-13. Epub 2013 Mar 13. PMID: 23486708

Archer, J., Weber, J., Henry, K., Winner, D., Gibson, R., Lee., L, Paxinos, E., Arts, EJ., Robertson, DL., Mimms, L. & Quiñones-Mateu, ME (2012)
Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism.
PLoS ONE, Nov 14; 10.1371/journal.pone.0049602. PMID: 23166726

Archer, J., Baillie G., Watson SJ., Kellam P., Rambaut A. & Robertson DL. (2012)
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.
BMC Bioinformatics, Mar 23;13(1):47. [Epub ahead of print]. PMID: 22443413

Williams, SG., Madan, R., Norris, MG., Archer, J., Mizuguchi, K., Robertson, DL. & Lovell, SC. (2011).
Using knowledge of protein structural constraints to predict the evolution of HIV-1.
Journal of Molecular Biology, Jul 29;410(5):1023-34. PMID: 21763504

Archer, J., Rambaut, A., Taillon, B., Harrigan, P., Lewis, M. & Robertson, D (2010).
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time-An Ultra-Deep Approach.
PLoS computational biology, 6(12), e1001022. PMID: 21187908

Archer, J., Braverman, M., Taillon, B., Desany, B., James, I., Harrigan, P., Lewis, M. & Robertson, D (2009).
Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing.
AIDS (London, England), 23(10), 1209-18. PMID: 19424056

Huxley-Jones, J., Pinney, J., Archer, J., Robertson, D. & Boot-Handford, R (2009).
Back to basics--how the evolution of the extracellular matrix underpinned vertebrate evolution.
International journal of experimental pathology, 90(2), 95-100. PMID: 19335547

Simon-Loriere, E., Galetto, R., Hamoudi, M., Archer, J., Lefeuvre, P., Martin, D., Robertson, D. & Negroni, M (2009).
Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus.
PLoS pathogens, 5(5), e1000418. PMID: 19424420

Archer, J., Pinney, J., Fan, J., Simon-Loriere, E., Arts, E., Negroni, M. & Robertson, D (2008).
Identifying the important HIV-1 recombination breakpoints.
PLoS computational biology, 4(9), e1000178. PMID: 18787691

Archer, J. & Robertson, D (2007).
CTree: comparison of clusters between phylogenetic trees made easy.
Bioinformatics (Oxford, England), 23(21), 2952-3. PMID: 17717036

Archer, J. & Robertson, D (2007).
Understanding the diversification of HIV-1 groups M and O.
AIDS (London, England), 21(13), 1693-700. PMID: 17690566

Baird, H., Galetto, R., Gao, Y., Simon-Loriere, E., Abreha, M., Archer, J., Fan, J., Robertson, D., Arts, E. & Negroni, M (2006).
Sequence determinants of breakpoint location during HIV-1 intersubtype recombination.
Nucleic acids research, 34(18), 5203-16. PMID: 17003055

Taylor, M., Bilo, K., Cross, H., Archer, J. & Underwood, A (1999).
16S rDNA phylogeny and ultrastructural characterization of Wolbachia intracellular bacteria of the filarial nematodes Brugia malayi, B. pahangi, and Wuchereria bancrofti.
Experimental parasitology, 91(4), 356-61. PMID: 10092480