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SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

PLoS computational biology, 2016-09, Vol.12 (9), p.e1005130-e1005130

2016

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New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

PLoS genetics, 2015-08, Vol.11 (8), p.e1005421-e1005421

2015

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Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Nature genetics, 2021-06, Vol.53 (6), p.809-816

2021

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phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets

PLoS computational biology, 2022-04, Vol.18 (4), p.e1010056-e1010056

2022

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A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages

Molecular biology and evolution, 2021-04, Vol.38 (4), p.1608-1613

2021

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Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

Gigascience, 2020-02, Vol.9 (2)

2020

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VGsim: Scalable viral genealogy simulator for global pandemic

PLoS computational biology, 2022-08, Vol.18 (8), p.e1010409-e1010409

2022

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VARIATION IN THERMAL PERFORMANCE AND REACTION NORMS AMONG POPULATIONS OF DROSOPHILA MELANOGASTER

Evolution, 2013-12, Vol.67 (12), p.3573-3587

2013

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The Satellite DNA PcH-Sat, Isolated and Characterized in the Limpet Patella caerulea (Mollusca, Gastropoda), Suggests the Origin from a Nin-SINE Transposable Element

Genes, 2024-04, Vol.15 (5), p.541

2024

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Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

PLoS computational biology, 2021-01, Vol.17 (1), p.e1008561-e1008561

2021

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Stability of SARS-CoV-2 phylogenies

PLoS genetics, 2020-11, Vol.16 (11), p.e1009175-e1009175

2020

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Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations

Virus evolution, 2023, Vol.9 (1), p.vead010-vead010

2023

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PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals

PloS one, 2011-01, Vol.6 (1), p.e15925-e15925

2011

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The Bacterial Sequential Markov Coalescent

Genetics (Austin), 2017-05, Vol.206 (1), p.333-343

2017

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Genomic network analysis of environmental and livestock F-type plasmid populations

The ISME Journal, 2021-08, Vol.15 (8), p.2322-2335

2021

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Disease and Disorders of Freshwater Unionid Mussels: A Brief Overview of Recent Studies

Frontiers in physiology, 2016-11, Vol.7, p.489-489

2016

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Fin Whale ( Balaenoptera physalus ) Mortality along the Italian Coast between 1624 and 2021

Animals (Basel), 2022-11, Vol.12 (22), p.3111

2022

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Short-range template switching in great ape genomes explored using pair hidden Markov models

PLoS genetics, 2021-03, Vol.17 (3), p.e1009221-e1009221

2021

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Bayesian reconstruction of transmission within outbreaks using genomic variants

PLoS computational biology, 2018-04, Vol.14 (4), p.e1006117-e1006117

2018

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Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

mBio, 2016-03, Vol.7 (2), p.e02162-e02162

2016

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Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission

Journal of antimicrobial chemotherapy, 2017-11, Vol.72 (11), p.3025-3034

2017

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The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment

Systematic biology, 2021-02, Vol.70 (2), p.236

De Maio, Nicola

2021

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A Mediterranean Monk Seal Pup on the Apulian Coast (Southern Italy): Sign of an Ongoing Recolonisation?

Diversity (Basel), 2020-06, Vol.12 (6), p.258

2020

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Life History Traits of Sperm Whales Physeter macrocephalus Linnaeus, 1758 Stranded along Italian Coasts (Cetartiodactyla: Physeteridae)

Animals (Basel), 2022-12, Vol.13 (1), p.79

2022

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SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets

A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system

VGsim: Scalable viral genealogy simulator for global pandemic

VARIATION IN THERMAL PERFORMANCE AND REACTION NORMS AMONG POPULATIONS OF DROSOPHILA MELANOGASTER

The Satellite DNA PcH-Sat, Isolated and Characterized in the Limpet Patella caerulea (Mollusca, Gastropoda), Suggests the Origin from a Nin-SINE Transposable Element

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

Stability of SARS-CoV-2 phylogenies

Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals

The Bacterial Sequential Markov Coalescent

Genomic network analysis of environmental and livestock F-type plasmid populations

Disease and Disorders of Freshwater Unionid Mussels: A Brief Overview of Recent Studies

Fin Whale ( Balaenoptera physalus ) Mortality along the Italian Coast between 1624 and 2021

Short-range template switching in great ape genomes explored using pair hidden Markov models

Bayesian reconstruction of transmission within outbreaks using genomic variants

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission

The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment

A Mediterranean Monk Seal Pup on the Apulian Coast (Southern Italy): Sign of an Ongoing Recolonisation?

Life History Traits of Sperm Whales Physeter macrocephalus Linnaeus, 1758 Stranded along Italian Coasts (Cetartiodactyla: Physeteridae)

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