Nicola De Maio

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models.

Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics

Assessing phylogenetic confidence at pandemic scales.

Detecting Interspecific Positive Selection Using Convolutional Neural Networks.

Highly Recurrent Multinucleotide Mutations in SARS-CoV-2.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.

SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics

Detecting interspecific positive selection using convolutional neural networks

Highly recurrent multi-nucleotide mutations in SARS-CoV-2

Maximum likelihood pandemic-scale phylogenetics.

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

Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations.

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method

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

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

SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python

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

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

Genomic reconstruction of the SARS-CoV-2 epidemic in England

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

Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a.

The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs

Stability of SARS-CoV-2 phylogenies.

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

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

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