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

de Bernardi Schneider A, Su M, Hinrichs AS, Wang J, Amin H, Bell J, Wadford DA, O'Toole Á, Scher E, Perry MD, Turakhia Y, De Maio N, Hughes S, Corbett-Detig R.

Virus Evol, 2024

doi:10.1093/ve/vead085.

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

de Bernardi Schneider A, Su M, Hinrichs AS, Wang J, Amin H, Bell J, Wadford DA, O’Toole À, Scher E, Perry MD, Turakhia Y, De Maio N, Hughes S, Corbett-Detig R.

2023

doi:10.1101/2023.05.26.542489.

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.

Kramer AM, Thornlow B, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R.

Syst Biol, 2023

doi:10.1093/sysbio/syad031.

Maximum likelihood pandemic-scale phylogenetics.

De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N.

Nat Genet, 2023

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.

Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G.

Virus Evol, 2023

doi:10.1093/ve/vead010.

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.

Nat Biotechnol, 2023

doi:10.1038/s41587-022-01580-z.

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

Boulton W, Fidan FR, Denise H, Denise H, 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.

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape.

Turakhia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, Smith K, De Maio N, Haussler D, Lanfear R, Corbett-Detig R.

Nature, 2022

doi:10.1038/s41586-022-05189-9.

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

Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G.

2022

doi:10.1101/2022.07.07.498932.

Publisher Correction: 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, 2022

doi:10.1038/s41586-022-04887-8.

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.

Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches

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 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

Stoesser N, George R, Aiken Z, Phan H, Lipworth S, Wyllie D, Quan T, Mathers A, De Maio N, Seale A, Eyre D, Vaughan A, Swann J, Peto T, Crook D, Cawthorne J, Dodgson A, Walker A, TRACE Investigators’ Group.

2021

doi:10.1101/2021.11.26.21266267.

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.

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.

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.

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

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.

Multicentre stepped-wedge cluster randomised controlled trial of an antimicrobial stewardship programme in residential aged care: protocol for the START trial.

Jokanovic N, Haines T, Cheng AC, Holt KE, Hilmer SN, Jeon YH, Stewardson AJ, Stuart RL, Spelman T, Peel TN, Peleg AY, START Trial Group.

BMJ Open, 2021

doi:10.1136/bmjopen-2020-046142.

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.

Genomic network analysis of environmental and livestock F-type plasmid populations.

Matlock W, Chau KK, AbuOun M, Stubberfield E, Barker L, Kavanagh J, Pickford H, Gilson D, Smith RP, Gweon HS, Hoosdally SJ, Swann J, Sebra R, Bailey MJ, Peto TEA, Crook DW, Anjum MF, Read DS, Walker AS, Stoesser N, Shaw LP, REHAB consortium.

ISME J, 2021

doi:10.1038/s41396-021-00926-w.

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.

A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages.

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.

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.

Repeated global migrations on different plant hosts by the tropical pathogenPhytophthora palmivora

Wang J, Coffey MD, De Maio N, Goss EM.

2020

doi:10.1101/2020.05.13.093211.

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

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.

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

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.

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples.

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.

Large expert-curated database for benchmarking document similarity detection in biomedical literature search.

Brown P, Brown P, RELISH Consortium , Zhou Y.

Database (Oxford), 2019

doi:10.1093/database/baz085.

Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system.

Crispell J, Benton CH, Balaz D, De Maio N, Ahkmetova A, Allen A, Biek R, Presho EL, Dale J, Hewinson G, Lycett SJ, Nunez-Garcia J, Skuce RA, Trewby H, Wilson DJ, Zadoks RN, Delahay RJ, Kao RR.

Elife, 2019

doi:10.7554/elife.45833.

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.

De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N, On Behalf Of The Rehab Consortium.

Microb Genom, 2019

doi:10.1099/mgen.0.000294.

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N, Shaw LP, Stoesser N, Peto TEA, Crook DW, Walker AS.

2019

doi:10.1101/653774.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ.

PLoS Comput Biol, 2019

doi:10.1371/journal.pcbi.1006650.

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

Gweon HS, Shaw LP, Swann J, Maio ND, AbuOun M, Hubbard ATM, Bowes MJ, Bailey MJ, Peto TEA, Hoosdally SJ, Walker AS, Sebra RP, Crook DW, Anjum M, Read DS, Stoesser N, on behalf of the REHAB consortium.

2019

doi:10.1101/593301.

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

De Maio N, Shaw LP, Hubbard A, George S, Sanderson N, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N, on behalf of the REHAB consortium.

2019

doi:10.1101/530824.

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, Maio ND, Matschiner M, Mendes FK, Müller NF, Ogilvie H, Plessis Ld, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu C, Xie D, Zhang C, Stadler T, Drummond AJ.

2018

doi:10.1101/474296.

Bayesian reconstruction of transmission within outbreaks using genomic variants.

De Maio N, Worby CJ, Wilson DJ, Stoesser N.

PLoS Comput Biol, 2018

doi:10.1371/journal.pcbi.1006117.

Two Distinct Patterns of Clostridium difficile Diversity Across Europe Indicating Contrasting Routes of Spread.

Eyre DW, Davies KA, Davis G, Fawley WN, Dingle KE, De Maio N, Karas A, Crook DW, Peto TEA, Walker AS, Wilcox MH, EUCLID Study Group.

Clin Infect Dis, 2018

doi:10.1093/cid/ciy252.

Frequent recombination of pneumococcal capsule highlights future risks of emergence of novel serotypes

Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C.

2017

doi:10.1101/098335.

Bayesian Reconstruction of Transmission within Outbreaks using Genomic Variants

De Maio N, Worby CJ, Wilson DJ, Stoesser N.

2017

doi:10.1101/213819.

Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission.

Martin J, Phan HTT, Findlay J, Stoesser N, Pankhurst L, Navickaite I, De Maio N, Eyre DW, Toogood G, Orsi NM, Kirby A, Young N, Turton JF, Hill RLR, Hopkins KL, Woodford N, Peto TEA, Walker AS, Crook DW, Wilcox MH.

J Antimicrob Chemother, 2017

doi:10.1093/jac/dkx264.

Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum.

Ionescu D, Bizic-Ionescu M, De Maio N, Cypionka H, Grossart HP.

Nat Commun, 2017

doi:10.1038/s41467-017-00342-9.

Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.

Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C.

Mol Biol Evol, 2017

doi:10.1093/molbev/msx173.

The Bacterial Sequential Markov Coalescent.

De Maio N, Wilson DJ.

Genetics, 2017

doi:10.1534/genetics.116.198796.

Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference

Schrempf D, Minh BQ, De Maio N, von Haeseler A, Kosiol C.

2016

doi:10.1101/048496.

The Bacterial Sequential Markov Coalescent

De Maio N, Wilson DJ.

2016

doi:10.1101/090845.

SimBac: simulation of whole bacterial genomes with homologous recombination.

Brown T, Didelot X, Wilson DJ, Maio N.

Microb Genom, 2016

doi:10.1099/mgen.0.000044.

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent.

De Maio N, Wu CH, Wilson DJ.

PLoS Comput Biol, 2016

doi:10.1371/journal.pcbi.1005130.

Reversible polymorphism-aware phylogenetic models and their application to tree inference.

Schrempf D, Minh BQ, De Maio N, von Haeseler A, Kosiol C.

J Theor Biol, 2016

doi:10.1016/j.jtbi.2016.07.042.

PoMo: An Allele Frequency-based Approach for Species Tree Estimation

De Maio N, Schrempf D, Kosiol C.

2015

doi:10.1101/016360.

Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

Stoesser N, Sheppard A, Pankhurst L, de Maio N, Moore CE, Sebra R, Turner P, Anson LW, Kasarskis A, Batty EM, Kos V, Wilson DJ, Phetsouvanh R, Wyllie D, Sokurenko E, Manges AR, Johnson TJ, Price LB, Peto TEA, Johnson JR, Didelot X, Walker AS, Crook DW, Modernising Medical Microbiology Informatics Group.

2015

doi:10.1101/030668.