Scientist in Molecular Evolution at European Bioinformatics Institute
Publications
SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python
Boulton W, Fidan FR, De Maio N, Goldman N.
2022
doi:10.1101/2022.12.10.519890.
VGsim: Scalable viral genealogy simulator for global pandemic.
Shchur V, Spirin V, Sirotkin D, Burovski E, De Maio N, Corbett-Detig R.
PLoS Comput Biol, 2022
doi:10.1371/journal.pcbi.1010409.
Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G.
2022
doi:10.1101/2022.07.07.498932.
phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.
De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N.
PLoS Comput Biol, 2022
doi:10.1371/journal.pcbi.1010056.
Accounting for spatial sampling patterns in Bayesian phylogeography.
Guindon S, De Maio N.
Proc Natl Acad Sci U S A, 2021
doi:10.1073/pnas.2105273118.
Thornlow B, Kramer A, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R.
2021
doi:10.1101/2021.12.02.471004.
Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M.
Nature, 2021
doi:10.1038/s41586-021-04069-y.
Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a.
Lin SK, De Maio N, Pedergnana V, Wu CH, Thézé J, Wilson DJ, Barnes E, Ansari MA.
Virus Evol, 2021
doi:10.1093/ve/veab065.
A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees.
McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y.
Mol Biol Evol, 2021
doi:10.1093/molbev/msab264.
Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region
Turkahia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, De Maio N, Haussler D, Lanfear R, Corbett-Detig R.
2021
doi:10.1101/2021.08.04.455157.
Genetic Variability of the SARS-CoV-2 Pocketome.
Yazdani S, De Maio N, Ding Y, Shahani V, Goldman N, Schapira M.
J Proteome Res, 2021
doi:10.1021/acs.jproteome.1c00206.
A phylogenetic approach for weighting genetic sequences.
De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N.
BMC Bioinformatics, 2021
doi:10.1186/s12859-021-04183-8.
Genomic reconstruction of the SARS-CoV-2 epidemic in England
Vöhringer HS, Sanderson T, Sinnott M, Maio ND, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani C, Gonçalves S, Jackson D, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M, The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) Consortium.
2021
doi:10.1101/2021.05.22.21257633.
Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R.
Nat Genet, 2021
doi:10.1038/s41588-021-00862-7.
Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.
De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N.
Genome Biol Evol, 2021
doi:10.1093/gbe/evab087.
Yazdani S, De Maio N, Ding Y, Shahani V, Goldman N, Schapira M.
2021
doi:10.1101/2021.03.23.436637.
phastSim: efficient simulation of sequence evolution for pandemic-scale datasets
De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N.
2021
doi:10.1101/2021.03.15.435416.
Short-range template switching in great ape genomes explored using pair hidden Markov models.
Walker CR, Scally A, De Maio N, Goldman N.
PLoS Genet, 2021
doi:10.1371/journal.pgen.1009221.
Want to track pandemic variants faster? Fix the bioinformatics bottleneck.
Hodcroft EB, De Maio N, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C.
Nature, 2021
doi:10.1038/d41586-021-00525-x.
Global spread and evolutionary history of HCV subtype 3a
lin S, De Maio N, Pedergnana V, Wu C, Thézé J, Barnes E, Ansari MA.
2021
doi:10.1101/2021.02.03.429581.
Mutation rates and selection on synonymous mutations in SARS-CoV-2
De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N.
2021
doi:10.1101/2021.01.14.426705.
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.
Kalkauskas A, Perron U, Sun Y, Goldman N, Baele G, Guindon S, De Maio N.
PLoS Comput Biol, 2021
doi:10.1371/journal.pcbi.1008561.
Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, Meex C, Bontems S, André E, Gilbert M, Walker C, Maio N, Faria NR, Hadfield J, Hayette MP, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes P.
Mol Biol Evol, 2021
doi:10.1093/molbev/msaa284.
The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment.
De Maio N.
Syst Biol, 2021
doi:10.1093/sysbio/syaa050.
Masking strategies for SARS-CoV-2 alignments
De Maio N, Walker C, Borges R, Weilguny L, Slodkowicz G, Goldman N.
2020
doi:.
Issues with SARS-CoV-2 sequencing data
De Maio N, Walker C, Borges R, Weilguny L, Slodkowicz G, Goldman N.
2020
doi:.
Phylogenetic Novelty Scores: a New Approach for Weighting Genetic Sequences
De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N.
2020
doi:10.1101/2020.12.03.410100.
Stability of SARS-CoV-2 phylogenies.
Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R.
PLoS Genet, 2020
doi:10.1371/journal.pgen.1009175.
Short-range template switching in great ape genomes explored using a pair hidden Markov model
Walker CR, Scally A, De Maio N, Goldman N.
2020
doi:10.1101/2020.11.09.374694.
Wang J, Coffey MD, De Maio N, Goss EM.
2020
doi:10.1101/2020.05.13.093211.
Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, Meex C, Bontems S, André E, Gilbert M, Walker C, De Maio N, Faria NR, Hadfield J, Hayette M, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes P.
2020
doi:10.1101/2020.05.05.078758.
Sampling bias and model choice in continuous phylogeography: getting lost on a random walk
Kalkauskas A, Perron U, Sun Y, Goldman N, Baele G, Guindon S, De Maio N.
2020
doi:10.1101/2020.02.18.954057.
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design
Weilguny L, De Maio N, Munro R, Manser C, Birney E, Loose M, Goldman N.
2020
doi:10.1101/2020.02.07.938670.
Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N, Shaw LP, Stoesser N, Peto TEA, Crook DW, Walker AS.
Gigascience, 2020
doi:10.1093/gigascience/giaa007.
Gweon HS, Shaw LP, Swann J, De Maio N, AbuOun M, Niehus R, Hubbard ATM, Bowes MJ, Bailey MJ, Peto TEA, Hoosdally SJ, Walker AS, Sebra RP, Crook DW, Anjum MF, Read DS, Stoesser N, REHAB consortium.
Environ Microbiome, 2019
doi:10.1186/s40793-019-0347-1.
Teaching and Supervisions
2024/2025:
- Foundations of phylogenetic inference - Training Lead, Trainer
2023/2024:
- Introduction to Phylogenetics - Training Lead, Trainer
- Working with Bacterial Genomes - Trainer
2022/2023:
- Introduction to Phylogenetics - Training Lead, Trainer
2019/2020:
- Molecular Phylogenetics - Training Lead, Trainer
2018/2019:
- Molecular Phylogenetics - Training Lead, Trainer
2017/2018:
- Molecular Phylogenetics - Trainer
