skip to content
Home

Faculty of Mathematics

 

Dr Nicola De Maio

Publications

IQ-TREE 3: phylogenomic inference software using complex evolutionary models
TKF Wong, N Ly-Trong, H Ren, P Demotte, H Baños, AJ Roger, E Susko, C Bielow, N De Maio, N Goldman, MW Hahn, M Dos Reis, LS Vinh, G Huttley, R Lanfear, BQ Minh
– Mol Biol Evol
(2026)
43,
msag117
(doi: 10.1093/molbev/msag117)
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
M Hunt, AS Hinrichs, D Anderson, L Karim, BL Dearlove, J Knaggs, B Constantinides, PW Fowler, G Rodger, T Street, S Lumley, H Webster, T Sanderson, C Ruis, B Kotzen, N de Maio, LN Amenga-Etego, DSY Amuzu, M Avaro, GA Awandare, R Ayivor-Djanie, T Barkham, M Bashton, EM Batty, Y Bediako et al.
– Nat Methods
(2026)
23,
653
(doi: 10.1038/s41592-025-02947-1)
Rate variation and recurrent sequence errors in pandemic-scale phylogenetics
N De Maio, M Willemsen, S Martin, Z Guo, A Saha, M Hunt, N Ly-Trong, BQ Minh, Z Iqbal, N Goldman
– Nat Methods
(2026)
23,
565
(doi: 10.1038/s41592-025-02932-8)
Assessing phylogenetic confidence at pandemic scales.
N De Maio, N Ly-Trong, S Martin, BQ Minh, N Goldman
– Nature
(2025)
647,
472
(doi: 10.1038/s41586-025-09567-x)
Highly Recurrent Multinucleotide Mutations in SARS-CoV-2
N De Maio, O Anoufa, K Smith, Y Turakhia, N Goldman
– Mol Biol Evol
(2025)
42,
msaf272
(doi: 10.1093/molbev/msaf272)
Detecting Interspecific Positive Selection Using Convolutional Neural Networks.
C West, CR Walker, S Arasti, V Vasilev, X Xu, N De Maio, N Goldman
– Mol Biol Evol
(2025)
42,
msaf154
(doi: 10.1093/molbev/msaf154)
SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.
W Boulton, FR Fidan, H Denise, N De Maio, N Goldman
– Bioinformatics
(2024)
40,
btae532
(doi: 10.1093/bioinformatics/btae532)
Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting
N Stoesser, R George, Z Aiken, HTT Phan, S Lipworth, TP Quan, AJ Mathers, N De Maio, AC Seale, DW Eyre, A Vaughan, J Swann, TEA Peto, DW Crook, J Cawthorne, A Dodgson, AS Walker, TRACE Investigators Group
– JAC-Antimicrobial Resistance
(2024)
6,
dlae140
(doi: 10.1093/jacamr/dlae140)
CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era
N Ly-Trong, C Bielow, N De Maio, BQ Minh
– Molecular Biology and Evolution
(2024)
41,
msae134
(doi: 10.1093/molbev/msae134)
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
M Hunt, AS Hinrichs, D Anderson, L Karim, BL Dearlove, J Knaggs, B Constantinides, PW Fowler, G Rodger, T Street, S Lumley, H Webster, T Sanderson, C Ruis, B Kotzen, N de Maio, LN Amenga-Etego, DSY Amuzu, M Avaro, GA Awandare, R Ayivor-Djanie, T Barkham, M Bashton, EM Batty, Y Bediako et al.
– bioRxiv
(2024)
2024.04.29.591666
(doi: 10.1101/2024.04.29.591666)
  • 1 of 7
  • >

Email

nd597@cam.ac.uk

Room

G1.17

Study at Cambridge

About the University

Research at Cambridge