Leonardo de Oliveira Martins

Publications

• Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of plasmodium vivax and related simian malaria parasites
• SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021
• Scalable neighbour search and alignment with uvaia
• Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management
• Antibiotics select for novel pathways of resistance in biofilms
• Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management
• Evolutionary Process of Deep-Sea Bathymodiolus Mussels
• Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees
• Distribution of distances between topologies and its effect on detection of phylogenetic recombination
• A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.
• Testing for universal common ancestry.
• Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count.
• Proving universal common ancestry with similar sequences.
• Unsorted homology within locus and species trees
• Taxonomic resolution of the ribosomal RNA operon in bacteria: Implications for its use with long read sequencing
• Tatajuba ― Exploring the distribution of homopolymer tracts
• Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine
• Evolutionary Dynamics of HIV-1 BF and CB Recombinants and Its Parental Counterparts in South America
• Species Tree Estimation from Genome-wide Data with Guenomu
• 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
• Species Tree Estimation from Genome-Wide Data with guenomu
• SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees
• 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
• Scalable neighbour search and alignment with uvaia
• A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
• SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021
• Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
• CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes
• Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern
• Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing
• Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages
• Evolutionary relationships of deep-sea mussels inferred by mitochondrial DNA sequences
• Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England
• Tatajuba: exploring the distribution of homopolymer tracts
• An integrated national scale SARS-CoV-2 genomic surveillance network
• Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing
• Infinitely long branches and an informal test of common ancestry
• The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
• 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
• Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
• Nanoneedle-Mediated Stimulation of Cell Mechanotransduction Machinery
• Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs
• The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England
• SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis
• SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees
• Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis
• Experimental evolution selects clinically relevant antibiotic resistance in biofilms but with collateral tradeoffs
• Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread
• Infinitely Long Branches and an Informal Test of Common Ancestry
• CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes
• Phylogeography of loaches of the genus lefua (balitoridae, cypriniformes) inferred from mitochondrial DNA sequences.
• Phylogenetic Likelihood
• Estimation of Species Trees
• SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021.
• Phylogenetic detection of recombination with a Bayesian prior on the distance between trees.
• Unsorted homology within locus and species trees.
• Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites.
• Evolutionary process of deep-sea bathymodiolus mussels.
• Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.
• Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
• The impact of viral mutations on recognition by SARS-CoV-2 specific T cells
• Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
• SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (vol 7, pg 1161, 2022)
• Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.
• Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
• 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
• Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021.
• Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
• The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.
• Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.
• Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.
• Recurrent SARS-CoV-2 mutations in immunodeficient patients.
• SARS-CoV-2 evolution during treatment of chronic infection
• Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
• Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic
• A likelihood-based index of protein protein binding affinities with application to influenza HA escape from antibodies.
• Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
• Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
• Genomic reconstruction of the SARS-CoV-2 epidemic in England