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Faculty of Mathematics

 

Dr Nicola De Maio

Publications

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.
A de Bernardi Schneider, M Su, AS Hinrichs, J Wang, H Amin, J Bell, DA Wadford, Á O'Toole, E Scher, MD Perry, Y Turakhia, N De Maio, S Hughes, R Corbett-Detig
– Virus Evolution
(2024)
10,
vead085
(doi: 10.1093/ve/vead085)
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.
AM Kramer, B Thornlow, C Ye, N De Maio, J McBroome, AS Hinrichs, R Lanfear, Y Turakhia, R Corbett-Detig
– Syst Biol
(2023)
72,
1039
(doi: 10.1093/sysbio/syad031)
Maximum likelihood pandemic-scale phylogenetics
N De Maio, P Kalaghatgi, Y Turakhia, R Corbett-Detig, BQ Minh, N Goldman
– Nat Genet
(2023)
55,
746
(doi: 10.1038/s41588-023-01368-0)
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations
M Layan, NF Müller, S Dellicour, N De Maio, H Bourhy, S Cauchemez, G Baele
– Virus Evol
(2023)
9,
vead010
(doi: 10.1093/ve/vead010)
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.
L Weilguny, N De Maio, R Munro, C Manser, E Birney, M Loose, N Goldman
– Nature Biotechnology
(2023)
41,
1018
(doi: 10.1038/s41587-022-01580-z)
VGsim: Scalable viral genealogy simulator for global pandemic
V Shchur, V Spirin, D Sirotkin, E Burovski, N De Maio, R Corbett-Detig
– PLOS Computational Biology
(2022)
18,
e1010409
(doi: 10.1371/journal.pcbi.1010409)
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape
Y Turakhia, B Thornlow, A Hinrichs, J McBroome, N Ayala, C Ye, K Smith, N De Maio, D Haussler, R Lanfear, R Corbett-Detig
– Nature
(2022)
609,
994
(doi: 10.1038/s41586-022-05189-9)
Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England
HS Vöhringer, T Sanderson, M Sinnott, N De Maio, T Nguyen, R Goater, F Schwach, I Harrison, J Hellewell, CV Ariani, S Gonçalves, DK Jackson, I Johnston, AW Jung, C Saint, J Sillitoe, M Suciu, N Goldman, J Panovska-Griffiths, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, E Birney, E Volz, S Funk, D Kwiatkowski et al.
– Nature
(2022)
606,
E18
(doi: 10.1038/s41586-022-04887-8)
phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.
N De Maio, W Boulton, L Weilguny, CR Walker, Y Turakhia, R Corbett-Detig, N Goldman
– Plos Computational Biology
(2022)
18,
e1010056
(doi: 10.1371/journal.pcbi.1010056)
Accounting for spatial sampling patterns in Bayesian phylogeography.
S Guindon, N De Maio
– Proc Natl Acad Sci U S A
(2021)
118,
e2105273118
(doi: 10.1073/pnas.2105273118)
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Email

nd597@cam.ac.uk

Room

G1.17

Study at Cambridge

About the University

Research at Cambridge