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, D De Belder, E Benedetti, A Bergthaler, SA Boers, J Campos, RAA Carr, YYC Chen, F Cuba, ME Dattero, W Dejnirattisai, A Dilthey, KO Duedu, L Endler, I Engelmann, NM Francisco, J Fuchs, EZ Gnimpieba, S Groc, J Gyamfi, D Heemskerk, T Houwaart, N-Y Hsiao, M Huska, M Hölzer, A Iranzadeh, H Jarva, C Jeewandara, B Jolly, R Joseph, R Kant, KKK Ki, S Kurkela, M Lappalainen, M Lataretu, J Lemieux, C Liu, GN Malavige, T Mashe, J Mongkolsapaya, B Montes, JAM Mora, CM Morang'a, B Mvula, N Nagarajan, A Nelson, JM Ngoi, JP da Paixão, M Panning, T Poklepovich, PK Quashie, D Ranasinghe, M Russo, JE San, ND Sanderson, V Scaria, G Screaton, OM Sessions, T Sironen, A Sisay, D Smith, T Smura, P Supasa, C Suphavilai, J Swann, H Tegally, B Tegomoh, O Vapalahti, A Walker, RJ Wilkinson, C Williamson, X Zair, IMSSC Laboratory Network Consortium, T de Oliveira, TE Peto, D Crook, R Corbett-Detig, Z Iqbal

– 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

– Nature 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

– Molecular Biology and Evolution

(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

– Molecular biology and evolution

(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 Antimicrob Resist

(2024)

dlae140

(doi: 10.1093/jacamr/dlae140)

CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era

N Ly-Trong, C Bielow, N De Maio, BQ Minh

– Mol Biol Evol

(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, D De Belder, E Benedetti, A Bergthaler, SA Boers, J Campos, RAA Carr, YYC Chen, F Cuba, ME Dattero, W Dejnirattisai, A Dilthey, KO Duedu, L Endler, I Engelmann, NM Francisco, J Fuchs, EZ Gnimpieba, S Groc, J Gyamfi, D Heemskerk, T Houwaart, N-Y Hsiao, M Huska, M Hölzer, A Iranzadeh, H Jarva, C Jeewandara, B Jolly, R Joseph, R Kant, KKK Ki, S Kurkela, M Lappalainen, M Lataretu, J Lemieux, C Liu, GN Malavige, T Mashe, J Mongkolsapaya, B Montes, JAM Mora, CM Morang'a, B Mvula, N Nagarajan, A Nelson, JM Ngoi, JP da Paixão, M Panning, T Poklepovich, PK Quashie, D Ranasinghe, M Russo, JE San, ND Sanderson, V Scaria, G Screaton, OM Sessions, T Sironen, A Sisay, D Smith, T Smura, P Supasa, C Suphavilai, J Swann, H Tegally, B Tegomoh, O Vapalahti, A Walker, RJ Wilkinson, C Williamson, X Zair, IMSSC2 Laboratory Network Consortium, T de Oliveira, TE Peto, D Crook, R Corbett-Detig, Z Iqbal

– bioRxiv

(2024)

2024.04.29.591666

(doi: 10.1101/2024.04.29.591666)

Department of Applied Mathematics and Theoretical Physics

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