Research outputs
Selected research outputs
- Scalable neighbour search and alignment with uvaia (Journal article - 2024)
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages (Journal article - 2022)
- Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing (Journal article - 2022)
- Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England (Journal article - 2022)
- Tatajuba: exploring the distribution of homopolymer tracts (Journal article - 2022)
- Exposure of <i>Salmonella</i> biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs (Journal article - 2021)
- Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing. (Journal article - 2020)
- A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction (Journal article - 2016)
- Infinitely long branches and an informal test of common ancestry (Journal article - 2016)
- <i>SimPhy</i>: Phylogenomic Simulation of Gene, Locus, and Species Trees (Journal article - 2016)
2026
Structural and evolutionary insights into the isoprene monooxygenases
Larke-Mejia, N. L., Martins, L. D. O., & Murrell, J. C. (2026). Structural and evolutionary insights into the isoprene monooxygenases. FEMS MICROBIOLOGY ECOLOGY, 102(3). doi:10.1093/femsec/fiag004
2025
<i>Staphylococcus haemolyticus</i> Population Genomics Provides Insights into Pathogenicity and Commensalism
Population structure and gene flux of Listeria monocytogenes ST121 reveal prophages as a candidate driver of adaptation and persistence in food production environments.
Gutiérrez, A. V., Matthews, M., Diaz, M., Le Viet, T., de Oliveira Martins, L., Jørgensen, F., . . . Gilmour, M. W. (2025). Population structure and gene flux of Listeria monocytogenes ST121 reveal prophages as a candidate driver of adaptation and persistence in food production environments.. Microb Genom, 11(4). doi:10.1099/mgen.0.001397
Temporal dynamics of SARS-CoV-2 shedding in feces and saliva: a longitudinal study in Norfolk, United Kingdom during the 2021-2022 COVID-19 waves.
Kellingray, L., Savva, G. M., Garcia-Gutierrez, E., Snell, J., Romano, S., Yara, D. A., . . . Sayavedra, L. (2025). Temporal dynamics of SARS-CoV-2 shedding in feces and saliva: a longitudinal study in Norfolk, United Kingdom during the 2021-2022 COVID-19 waves.. Microbiology spectrum, e0319524. doi:10.1128/spectrum.03195-24
A multi-isolate genomic approach identifies diverse<i> Escherichia</i><i> coli</i> contamination and antimicrobial resistance carriage on retail foods
Astorga, G., Bloomfield, S. J., Palau, R., Janecko, N., Martins, L. D. O., Singh, D., . . . Mather, A. E. (2025). A multi-isolate genomic approach identifies diverse<i> Escherichia</i><i> coli</i> contamination and antimicrobial resistance carriage on retail foods. MICROBIAL GENOMICS, 11(10). doi:10.1099/mgen.0.001549
2024
Capturing clinically relevant<i> Campylobacter</i> attributes through direct whole genome sequencing of stool
Djeghout, B., Le-Viet, T., Martins, L. D. O., Savva, G. M., Evans, R., Baker, D., . . . Janecko, N. (2024). Capturing clinically relevant<i> Campylobacter</i> attributes through direct whole genome sequencing of stool. MICROBIAL GENOMICS, 10(8). doi:10.1099/mgen.0.001284
Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine
Ereqat, S., Alikhan, N. -F., Al-Jawabreh, A., Matthews, M., Al-Jawabreh, A., Martins, L. D. O., . . . Nasereddin, A. (2024). Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine. PATHOGENS, 13(6). doi:10.3390/pathogens13060521
Scalable neighbour search and alignment with uvaia
Martins, L. D. O., Mather, A. E., & Page, A. J. (2024). Scalable neighbour search and alignment with uvaia. PEERJ, 12. doi:10.7717/peerj.16890
2023
Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis
Asante, I. A., Hsu, S. N., Boatemaa, L., Kwasah, L., Adusei-Poku, M., Odoom, J. K., . . . Ampofo, W. K. (2023). Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis. LANCET GLOBAL HEALTH, 11(7), E1075-E1085. doi:10.1016/S2214-109X(23)00189-4
The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.
Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., . . . COVID-19 Genomics UK (COG-UK) Consortium. (2023). The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.. PloS one, 18(4), e0284187. doi:10.1371/journal.pone.0284187
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.
Cotton, S., McHugh, M. P., Dewar, R., Haas, J. G., Templeton, K., & COVID-19 Genomics UK (COG-UK) Consortium. (2023). Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.. The Journal of hospital infection, 135, 28-36. doi:10.1016/j.jhin.2023.02.010
SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis
Nyagupe, C., Martins, L. D. O., Gumbo, H., Mashe, T., Takawira, T., Maeka, K. K., . . . Mavenyengwa, R. T. (2023). SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis. SAMJ SOUTH AFRICAN MEDICAL JOURNAL, 113(3), 141-147. doi:10.7196/SAMJ.2023.v113i3.16762
2022
COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study
Klaser, K., Molteni, E., Graham, M., Canas, L. S., Osterdahl, M. F., Antonelli, M., . . . Duncan, E. L. (2022). COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-14016-0
Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing
Raphenya, A. R., Robertson, J., Jamin, C., de Oliveira Martins, L., Maguire, F., McArthur, A. G., & Hays, J. P. (2022). Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing. SCIENTIFIC DATA, 9(1). doi:10.1038/s41597-022-01463-7
Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England
Eales, O., Martins, L. D. O., Page, A. J., Wang, H., Bodinier, B., Tang, D., . . . Chadeau-Hyam, M. (2022). Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-32096-4
Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., . . . Harrison, E. M. (2022). Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-28371-z
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
Nickbakhsh, S., Hughes, J., Christofidis, N., Griffiths, E., Shaaban, S., Enright, J., . . . Smith-Palmer, A. (2022). Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12(1). doi:10.1038/s41598-022-15661-1
SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2
Eales, O., Page, A. J., de Oliveira Martins, L., Wang, H., Bodinier, B., Haw, D., . . . Elliott, P. (2022). SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases, 22(1). doi:10.1186/s12879-022-07628-4
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Tegally, H., San, J. E., Cotten, M., Moir, M., Tegomoh, B., Mboowa, G., . . . Wilkinson, E. (2022). The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. SCIENCE, 378(6615), 42-+. doi:10.1126/science.abq5358
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (vol 7, pg 1161, 2022)
Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., . . . Thomson, E. C. (2022). SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (vol 7, pg 1161, 2022). NATURE MICROBIOLOGY, 7(10), 1709. doi:10.1038/s41564-022-01241-6
Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages
Ceron-Romero, M. A., Fonseca, M. M., de Oliveira Martins, L., Posada, D., & Katz, L. A. (2022). Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages. GENOME BIOLOGY AND EVOLUTION, 14(8). doi:10.1093/gbe/evac119
Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021
Smallman-Raynor, M. R., & Cliff, A. D. (2022). Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021. EPIDEMIOLOGY & INFECTION, 150. doi:10.1017/S0950268822001285
Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.
Wright, D. W., Harvey, W. T., Hughes, J., Cox, M., Peacock, T. P., Colquhoun, R., . . . Carabelli, A. M. (2022). Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.. Virus evolution, 8(1), veac023. doi:10.1093/ve/veac023
Tatajuba: exploring the distribution of homopolymer tracts
Martins, L. D. O., Bloomfield, S., Stoakes, E., Grant, A., Page, A. J., & Mather, A. E. (2022). Tatajuba: exploring the distribution of homopolymer tracts. NAR GENOMICS AND BIOINFORMATICS, 4(1). doi:10.1093/nargab/lqac003
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., . . . Consor, C. G. U. K. C. O. G. -U. K. (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-021-27942-w
Recurrent SARS-CoV-2 mutations in immunodeficient patients
Wilkinson, S. A. J., Richter, A., Casey, A., Osman, H., Mirza, J. D., Stockton, J., . . . Loman, N. J. (2022). Recurrent SARS-CoV-2 mutations in immunodeficient patients. VIRUS EVOLUTION, 8(2). doi:10.1093/ve/veac050
Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
Merhi, G., Trotter, A. J., Martins, L. D. O., Koweyes, J., Le-Viet, T., Abou Naja, H., . . . Tokajian, S. (2022). Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021. MICROBIAL GENOMICS, 8(7). doi:10.1099/mgen.0.000838
2021
SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2
Genomic reconstruction of the SARS-CoV-2 epidemic in England
Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), 506-511. doi:10.1038/s41586-021-04069-y
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes
Baker, D. J., Aydin, A., Le-Viet, T., Kay, G. L., Rudder, S., Martins, L. D. O., . . . O'Grady, J. (2021). CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes. GENOME MEDICINE, 13(1). doi:10.1186/s13073-021-00839-5
Exposure of <i>Salmonella</i> biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs
Trampari, E., Holden, E. R., Wickham, G. J., Ravi, A., Martins, L. D. O., Savva, G. M., & Webber, M. A. (2021). Exposure of <i>Salmonella</i> biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs. NPJ BIOFILMS AND MICROBIOMES, 7(1). doi:10.1038/s41522-020-00178-0
Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
Mashe, T., Takawira, F. T., Martins, L. D. O., Gudza-Mugabe, M., Chirenda, J., Munyanyi, M., . . . Mhlanga, G. (2021). Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. LANCET GLOBAL HEALTH, 9(12), E1658-E1666. doi:10.1016/S2214-109X(21)00434-4
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells
de, S. T. I., Liu, G., Lindsey, B. B., Dong, D., Moore, S. C., Hsu, N. S., . . . Dong, T. (2021). The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. ISCIENCE, 24(11). doi:10.1016/j.isci.2021.103353
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Wilkinson, E., Giovanetti, M., Tegally, H., San, J. E., Lessells, R., Cuadros, D., . . . de Oliveira, T. (2021). A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. SCIENCE, 374(6566), 423-+. doi:10.1126/science.abj4336
Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study.
Twohig, K. A., Nyberg, T., Zaidi, A., Thelwall, S., Sinnathamby, M. A., Aliabadi, S., . . . COVID-19 Genomics UK (COG-UK) consortium. (2021). Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study.. The Lancet. Infectious diseases, 22(1), 35-42. doi:10.1016/s1473-3099(21)00475-8
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic
Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R. M., Darby, A. C., . . . Rambaut, A. (2021). Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell. doi:10.1016/j.cell.2021.08.014
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., . . . Gupta, R. K. (2021). Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. CELL REPORTS, 35(13). doi:10.1016/j.celrep.2021.109292
SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021
Tatajuba ― Exploring the distribution of homopolymer tracts
The impact of SARS-CoV-2 infection in children with rheumatic/autoinflammatory diseases on immunosuppressive treatment: a single centre experience
Maritsi, D. N., Krepis, P., Vartzelis, G., Syggelou, A., & Tsolia, M. N. (2023). The impact of SARS-CoV-2 infection in children with rheumatic/autoinflammatory diseases on immunosuppressive treatment: a single centre experience. CLINICAL AND EXPERIMENTAL RHEUMATOLOGY, 41(9), S4-S5. doi:10.1038/s41586-021-03470-x
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., . . . Gupta, R. K. (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. NATURE, 593(7857), 136-+. doi:10.1038/s41586-021-03412-7
Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study
Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsaysky, T., . . . Ourselin, S. (2021). Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. LANCET PUBLIC HEALTH, 6(5), E335-E345. doi:10.1016/S2468-2667(21)00055-4
Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern
Mashe, T., Takawira, F. T., Gumbo, H., Juru, A., Nyagupe, C., Maeka, K. K., . . . Simbi, R. (2021). Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern. LANCET MICROBE, 2(5), E177. doi:10.1016/S2666-5247(21)00061-6
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., . . . Gupta, R. K. (2021). SARS-CoV-2 evolution during treatment of chronic infection. NATURE, 592(7853), 277-+. doi:10.1038/s41586-021-03291-y
Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., Filipe, A. D. S., Wojcechowskyj, J. A., . . . Snell, G. (2021). Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. CELL, 184(5), 1171-+. doi:10.1016/j.cell.2021.01.037
Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O'Toole, A., . . . Connor, T. R. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. CELL, 184(1), 64-+. doi:10.1016/j.cell.2020.11.020
Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.
Page, A. J., Mather, A. E., Le-Viet, T., Meader, E. J., Alikhan, N. -F., Kay, G. L., . . . The Covid-Genomics Uk Cog-Uk Consortium. (2021). Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.. Microbial genomics, 7(6). doi:10.1099/mgen.0.000589
SARS- CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021
Sarwar, M. B., Yasir, M., Alikhan, N. -F., Afzal, N., Martins, L. D. O., Le Viet, T., . . . Jahan, S. (2021). SARS- CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021. MICROBIAL GENOMICS, 7(11). doi:10.1099/mgen.0.000693
2020
An integrated national scale SARS-CoV-2 genomic surveillance network
Darby, A. (2020). An integrated national scale SARS-CoV-2 genomic surveillance network. The Lancet Microbe. doi:10.1016/s2666-5247(20)30054-9
Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing.
de Oliveira Martins, L., Page, A. J., Mather, A. E., & Charles, I. G. (2020). Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing.. NAR genomics and bioinformatics, 2(1), lqz016. doi:10.1093/nargab/lqz016
Experimental evolution selects clinically relevant antibiotic resistance in biofilms but with collateral tradeoffs
Trampari, E., Holden, E., Wickham, G., Ravi, A., Prischi, F., Martins, L. D. O., . . . Webber, M. (2020). Experimental evolution selects clinically relevant antibiotic resistance in biofilms but with collateral tradeoffs. Access Microbiology, 2(1). doi:10.1099/acmi.mim2019.po0001
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
Alm, E., Broberg, E. K., Connor, T., Hodcroft, E. B., Komissarov, A. B., Maurer-Stroh, S., . . . Pereyaslov, D. (2020). Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. EUROSURVEILLANCE, 25(32), 7-14. doi:10.2807/1560-7917.ES.2020.25.32.2001410
2019
Taxonomic resolution of the ribosomal RNA operon in bacteria: Implications for its use with long read sequencing
Antibiotics select for novel pathways of resistance in biofilms
Nanoneedle-Mediated Stimulation of Cell Mechanotransduction Machinery
Hansel, C. S., Crowder, S. W., Cooper, S., Gopal, S., Pardelha da Cruz, M. J., Martins, L. D. O., . . . Stevens, M. M. (2019). Nanoneedle-Mediated Stimulation of Cell Mechanotransduction Machinery. ACS NANO, 13(3), 2913-2926. doi:10.1021/acsnano.8b06998
2017
Species Tree Estimation from Genome-Wide Data with guenomu
de Oliveira Martins, L., & Posada, D. (2017). Species Tree Estimation from Genome-Wide Data with guenomu. In BIOINFORMATICS, VOL I: DATA, SEQUENCE ANALYSIS, AND EVOLUTION, 2ND EDITION (Vol. 1525, pp. 461-478). doi:10.1007/978-1-4939-6622-6_18
2016
A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction
De Oliveira Martins, L., Mallo, D., & Posada, D. (2016). A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. SYSTEMATIC BIOLOGY, 65(3), 397-416. doi:10.1093/sysbio/syu082
Infinitely long branches and an informal test of common ancestry
de Oliveira Martins, L., & Posada, D. (2016). Infinitely long branches and an informal test of common ancestry. BIOLOGY DIRECT, 11. doi:10.1186/s13062-016-0120-y
<i>SimPhy</i>: Phylogenomic Simulation of Gene, Locus, and Species Trees
Mallo, D., De Oliveira Martins, L., & Posada, D. (2016). <i>SimPhy</i>: Phylogenomic Simulation of Gene, Locus, and Species Trees. SYSTEMATIC BIOLOGY, 65(2), 334-344. doi:10.1093/sysbio/syv082
2015
Infinitely Long Branches and an Informal Test of Common Ancestry
Species Tree Estimation from Genome-wide Data with Guenomu
<i>SimPhy</i>: Phylogenomic Simulation of Gene, Locus and Species Trees
Phylogenetic Likelihood
de Oliveira Martins, L., Mallo, D., & Posada, D. (n.d.). Phylogenetic Likelihood. Wiley. doi:10.1002/9780470015902.a0005141
2014
Estimation of Species Trees
Mallo, D., de Oliveira Martins, L., & Posada, D. (n.d.). Estimation of Species Trees. Wiley. doi:10.1002/9780470015902.a0025781
Unsorted Homology within Locus and Species Trees
Mallo, D., De Oliveira Martins, L., & Posada, D. (2014). Unsorted Homology within Locus and Species Trees. SYSTEMATIC BIOLOGY, 63(6), 988-992. doi:10.1093/sysbio/syu050
Testing for Universal Common Ancestry
de Oliveira Martins, L., & Posada, D. (2014). Testing for Universal Common Ancestry. SYSTEMATIC BIOLOGY, 63(5), 838-842. doi:10.1093/sysbio/syu041
2013
Codon pairs of the HIV-1 <i>vif</i> gene correlate with CD4+T cell count
Bizinoto, M. C., Yabe, S., Leal, E., Kishino, H., de Oliveira Martins, L., de Lima, M. L., . . . Janini, L. M. (2013). Codon pairs of the HIV-1 <i>vif</i> gene correlate with CD4+T cell count. BMC INFECTIOUS DISEASES, 13. doi:10.1186/1471-2334-13-173
2012
Proving universal common ancestry with similar sequences.
Martins, L. D. O., & Posada, D. (2012). Proving universal common ancestry with similar sequences.. Trends in evolutionary biology, 4(1), e5. doi:10.4081/eb.2012.e5
2010
Evolutionary Process of Deep-Sea <i>Bathymodiolus</i> Mussels
Miyazaki, J. -I., de Oliveira Martins, L., Fujita, Y., Matsumoto, H., & Fujiwara, Y. (2010). Evolutionary Process of Deep-Sea <i>Bathymodiolus</i> Mussels. PLOS ONE, 5(4). doi:10.1371/journal.pone.0010363
Lineage-specific positive selection at the merozoite surface protein 1 (<i>msp1</i>) locus of <i>Plasmodium vivax</i> and related simian malaria parasites
Sawai, H., Otani, H., Arisue, N., Palacpac, N., de Oliveira Martins, L., Pathirana, S., . . . Tanabe, K. (2010). Lineage-specific positive selection at the merozoite surface protein 1 (<i>msp1</i>) locus of <i>Plasmodium vivax</i> and related simian malaria parasites. BMC EVOLUTIONARY BIOLOGY, 10. doi:10.1186/1471-2148-10-52
Distribution of distances between topologies and its effect on detection of phylogenetic recombination
de Oliveira Martins, L., & Kishino, H. (2010). Distribution of distances between topologies and its effect on detection of phylogenetic recombination. ANNALS OF THE INSTITUTE OF STATISTICAL MATHEMATICS, 62(1), 145-159. doi:10.1007/s10463-009-0259-8
2008
Evolutionary Dynamics of HIV-1 BF and CB Recombinants and Its Parental Counterparts in South America
Evolutionary Dynamics of HIV-1 BF and CB Recombinants and Its Parental Counterparts in South America (2008). Retrovirology: Research and Treatment, 1, 1-14. doi:10.4137/rrt.s1045
Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees
Martins, L. D. O., Leal, E., & Kishino, H. (2008). Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees. PLOS ONE, 3(7). doi:10.1371/journal.pone.0002651
2007
A likelihood-based index of protein-protein binding affinities with application to influenza HA escape from antibodies
Watabe, T., Kishino, H., Martins, L. D. O., & Kitazoe, Y. (2007). A likelihood-based index of protein-protein binding affinities with application to influenza HA escape from antibodies. MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1627-1638. doi:10.1093/molbev/msm079
2006
Evolutionary relationships of deep-sea mussels inferred by mitochondrial DNA sequences
Iwasaki, H., Kyuno, A., Shintaku, M., Fujita, Y., Fujiwara, Y., Fujikura, K., . . . Miyazaki, J. -I. (2006). Evolutionary relationships of deep-sea mussels inferred by mitochondrial DNA sequences. MARINE BIOLOGY, 149(5), 1111-1122. doi:10.1007/s00227-006-0268-6
2005
Phylogeography of loaches of the <i>Genus lefua</i> (Balitoridae, Cypriniformes) inferred from mitochondrial DNA sequences
Mihara, M., Sakai, T., Nakao, K., de Oliveira Martins, L., Hosoya, K., & Miyazaki, J. -I. (2005). Phylogeography of loaches of the <i>Genus lefua</i> (Balitoridae, Cypriniformes) inferred from mitochondrial DNA sequences. ZOOLOGICAL SCIENCE, 22(2), 157-168. doi:10.2108/zsj.22.157