Leonardo De Oliveira Martins

Leonardo De Oliveira Martins
Quadram Institute

Ph.D.

About

74
Publications
14,174
Reads
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1,544
Citations
Introduction
I like to develop phylogenomic models of gene family evolution using hierarchical Bayesian framework. In the process, I am investigating the alignment problem, heterogeneity in phylogenetics, distance measures for trees... I am also interested in data sciences applied to Microscopy Image Analysis and Chemometrics.
Additional affiliations
April 2015 - February 2016
Imperial College London
Position
  • Research Associate
March 2009 - present
University of Vigo
Position
  • PostDoc Position
January 2008 - February 2009
The University of Tokyo
Education
April 2004 - July 2008
The University of Tokyo
Field of study
  • Agricultural and Environmental Biology
April 2003
The University of Tokyo
Field of study
  • Research student
August 1999 - September 2002
Independent Researcher
Field of study
  • Biotechnology

Publications

Publications (74)
Article
Full-text available
The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant (first detected in November 2021) exhibited a high degree of immune evas...
Article
Full-text available
Advances in phylogenomics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eu...
Article
The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of w...
Article
Full-text available
Background: Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detec...
Preprint
Full-text available
Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequ...
Preprint
The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants which have led to substantial changes in the epidemiology of the virus. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant w...
Article
Full-text available
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was as...
Article
Full-text available
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was as...
Article
Full-text available
Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding c...
Article
Full-text available
Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding c...
Article
Full-text available
Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialized bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivi...
Preprint
Full-text available
Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Here we present phylogenetic relationships and lineage dynamics within England (a...
Article
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authori...
Article
Full-text available
Most bacteria in nature exist in biofilms, which are inherently tolerant to antibiotics. There is currently very limited understanding of how biofilms evolve in response to sub-lethal concentrations of antimicrobials. In this study, we use a biofilm evolution model to study the effects of sub-inhibitory concentrations of three antibiotics on Salmon...
Article
Full-text available
The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the world’s largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 that began in March 2021. In Pakistan, during the th...
Article
p class="MsoNormal">SARS-CoV-2 infections were rising during early summer 2021 in many countries associated with the Delta variant. We assessed RT-PCR swab-positivity in the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. We observed sustained exponential growth with average doubling time (June July 2021) of 25 days dri...
Article
Full-text available
Background Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe...
Article
Full-text available
The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predomina...
Article
Full-text available
The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantl...
Preprint
Full-text available
Background: The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just twenty six SARS-CoV-2 genomes available for th...
Article
Full-text available
The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we...
Preprint
Full-text available
The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the worlds largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 beginning in March 2021. Currently very few SARS-CoV-...
Preprint
Full-text available
Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialised bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivi...
Article
Full-text available
Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the associatio...
Preprint
Full-text available
Advances in phylogenetics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eu...
Article
Full-text available
We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates cont...
Preprint
Full-text available
Zimbabwe reported its first case of SARS-Cov-2 infection in March 2020, and case numbers increased to more than 8,099 to 16th October 2020. An understanding of the SARS-Cov-2 outbreak in Zimbabwe will assist in the implementation of effective public health interventions to control transmission. Nasopharyngeal samples from 92,299 suspected and confi...
Preprint
Full-text available
The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3,200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) w...
Article
Full-text available
Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability o...
Preprint
Full-text available
The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a til...
Article
Full-text available
DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. However, bacterial cells usually have multiple copies of this ribosomal operon, and choosing the...
Preprint
Full-text available
Long-read sequencing technologies enable capture of the full-length of ribosomal RNA operons in a single read. Bacterial cells usually have multiple copies of this ribosomal operon; sequence variation within a species of bacterium can exceed variation between species. For uncultured organisms this may affect the overall taxonomic resolution, to gen...
Article
Full-text available
Biomaterial substrates can be engineered to present topographical signals to cells which, through interactions between the material and active components of the cell membrane, regulate key cellular processes and guide cell fate decisions. However, targeting mechanoresponsive elements that reside within the intracellular domain is a concept that has...
Chapter
The history of particular genes and that of the species that carry them can be different for a variety of reasons. In particular, gene trees and species trees can differ due to well-known evolutionary processes such as gene duplication and loss, lateral gene transfer, or incomplete lineage sorting. Species tree reconstruction methods have been deve...
Article
Full-text available
Background: The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequence alignment, which was howe...
Article
Full-text available
We present a fast and flexible software package -SimPhy- for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer -all three potentially leading to species-tree/gene-tree discordance- and gene conversion. SimPhy implements a hierarchical phylogenetic model in which t...
Preprint
Full-text available
The evidence for universal common ancestry (UCA) is vast and persuasive, and a phylogenetic test was proposed for quantifying its odds against independently originated sequences based on the comparison between one and several trees. This test was successfully applied to a well-supported homologous sequence alignment, being however criticized once s...
Preprint
The history of particular genes and that of the species that carry them can be different due to different reasons. In particular, gene trees and species trees can truly differ due to well-known evolutionary processes like gene duplication and loss, lateral gene transfer or incomplete lineage sorting. Different species tree reconstruction methods ha...
Chapter
During the last decades, gene trees have been often interpreted as species phylogenies. However, the extensive gene tree discordance found in multi-locus datasets has put into question this interpretation, and a variety of new methods that explicitly consider species trees have been proposed in recent years. Some of these explicitly consider evolut...
Article
Full-text available
Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage...
Conference Paper
Full-text available
Background / Purpose: We present SimPhy, a new fast and flexible simulation tool that simulates gene family evolution, taking into account incomplete lineage sorting (ILS), gene duplication and loss (GDL) and horizontal gene transfer (HGT). SimPhy also simulates realistic rate heterogeneities, applied at every simulation layer and can obtain the...
Article
The input data for any phylogenetic analysis is a set of characters belonging to different individuals or loci, and assumed to have a common ancestor. Given a set of aligned deoxyribonucleic acid (DNA) or protein sequences, the likelihood of a phylogenetic tree depicting their ancestry relationships will be proportional to the probability of the al...
Article
Full-text available
Background The human APOBEC3G (A3G) protein activity is associated with innate immunity against HIV-1 by inducing high rates of guanosines to adenosines (G-to-A) mutations (viz., hypermutation) in the viral DNA. If hypermutation is not enough to disrupt the reading frames of viral genes, it may likely increase the HIV-1 diversity. To counteract hos...
Article
Full-text available
Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizont...
Conference Paper
Background / Purpose: This poster describes the software biomc2, which detects phylogenetic recombination using a prior distribution of distances between topologies of consecutive alignment segments. Main conclusion: We present its usage on an HIV genomic dataset and on simulated alignments, where we show the importance of our chosen probabili...
Article
Full-text available
Background: Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different...
Data
Malaria parasite species and isolates used in the present study. Table showing malaria parasite species and isolates as well as accession numbers of sequences obtained in this study and retrieved from the GenBank database.
Data
Predicted molecular weight of MSP-1 of P. vivax and P. vivax-related simian malaria parasites. Table showing variation in molecular weights and amino acid lengths of MSP-1 among P. vivax and P. vivax-related simian malaria parasites and within several parasite species.
Data
Phylogenetic trees for estimating divergence times among P. vivax and P. vivax-related simian malaria parasite lineages. Figure S2 showing a method for phylogeny-based estimation of divergence times among P. vivax and P. vivax-related simian malaria parasite lineages.
Data
Positional overlap of positively selected amino acid regions of MSP-1 from P. vivax, P. inui and P. cynomolgi. Figure S3 showing five overlapping positively selected amino acid sequence regions of P. vivax, P. inui and P. cynomolgi that were inferred by the omegaMap.
Data
Amino acid sequence alignment of MSP-1 from P. vivax and P. vivax-related simian malaria parasite species. Figure S1 showing amino acid alignment of MSP-1 from P. gonderi, P. fragile, P. coatneyni, P. knowlesi, P. hylobati, P. inui, P. fieldi, P. vivax, and P. cynomolgi. This figure contains information of sequence regions of four inter-species var...
Data
Indels and repeats in a variable block (VB4) of msp1 from P. inui. Figure S4 showing a highly variable sequences due to indels and repetitive sequences in a variable block (VB4) of P. inui msp1.
Article
Full-text available
The 200 kDa merozoite surface protein 1 (MSP-1) of malaria parasites, a strong vaccine candidate, plays a key role during erythrocyte invasion and is a target of host protective immune response. Plasmodium vivax, the most widespread human malaria parasite, is closely related to parasites that infect Asian Old World monkeys, and has been considered...
Article
Full-text available
Inferences about the evolutionary history of biological sequence data are greatly influenced by the presence of recombination, that tends to disrupt the phylogenetic signal. Current recombination detection procedures focus on the phylogenetic disagreement of the data along the aligned sequences, but only recently the link between the quantification...
Data
Description of the 11 HIV-1 sequences used in the recombination detection analysis. (0.02 MB PDF)
Data
Full-text available
MAP topologies for the HIV-1 dataset, arbitrarily rooted at subtype C sequence. (0.05 MB PDF)
Data
Full-text available
Failure of distances in estimating the number of SPR operations. (0.09 MB PDF)