User profiles for Nicola De Maio
 | Nicola De MaioScientist in Molecular Evolution, European Bioinformatic Institute (EMBL-EBI), Cambridge Verified email at ebi.ac.uk Cited by 6955 |
[HTML][HTML] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary data. …
years with major new advances in nearly all aspects of the joint modelling of evolutionary data. …
[HTML][HTML] PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals
Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective
approach to determine genome-wide population genetic parameters. Here we introduce …
approach to determine genome-wide population genetic parameters. Here we introduce …
[HTML][HTML] Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic
As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation
of viral genome sequences is ushering in a new era of ‘genomic contact tracing’—that …
of viral genome sequences is ushering in a new era of ‘genomic contact tracing’—that …
Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131
Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant
extraintestinal pathogenic lineage within this clinically important species, and its …
extraintestinal pathogenic lineage within this clinically important species, and its …
[HTML][HTML] Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape
Accurate and timely detection of recombinant lineages is crucial for interpreting genetic
variation, reconstructing epidemic spread, identifying selection and variants of interest, and …
variation, reconstructing epidemic spread, identifying selection and variants of interest, and …
[HTML][HTML] New routes to phylogeography: a Bayesian structured coalescent approximation
Phylogeographic methods aim to infer migration trends and the history of sampled lineages
from genetic data. Applications of phylogeography are broad, and in the context of …
from genetic data. Applications of phylogeography are broad, and in the context of …
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses,
but short reads (<300 bp) do not usually enable complete genome assembly. Long-read …
but short reads (<300 bp) do not usually enable complete genome assembly. Long-read …
Want to track pandemic variants faster? Fix the bioinformatics bottleneck
… Nicola De Maio … Nicola De Maio … Nicola De Maio is a scientist in molecular evolution
at EMBL–European Bioinformatics Institute, Cambridge, UK. …
at EMBL–European Bioinformatics Institute, Cambridge, UK. …
[PDF][PDF] Mutation rates and selection on synonymous mutations in SARS-CoV-2
The COVID-19 pandemic has seen an unprecedented response from the sequencing
community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we …
community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we …
[HTML][HTML] Issues with SARS-CoV-2 sequencing data
We investigate oddities in the SARS-CoV-2 genome sequences from GISAID. Many putative
sequencing issues seem specific to genomic ends and to certain samples, and are easily …
sequencing issues seem specific to genomic ends and to certain samples, and are easily …