Nicola de Maio (Nicola De Maio)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 23

Top Topics

Dna Methylation

Respiratory Syndrome Coronavirus

Artificial Intelligence

Top Venues

PLoS computational biology

Virus evolution

bioRxiv : the preprint server for biology

Molecular biology and evolution

This page only lists publications with an associated author ORCID identifier.

Publications

Martin Hunt, Angie S Hinrichs, Daniel Paolo Anderson, Lily Karim, Bethany L Dearlove, Jeff Knaggs, Bede Constantinides, Philip W Fowler, Gillian Rodger, Teresa Street, Sheila F Lumley, Hermione Webster, Theo Sanderson, Christopher Ruis, Nicola de Maio, Lucas N Amenga-Etego, Dominic Selorm Yao Amuzu, Martin Avaro, Gordon Akanzuwine Awandare, Reuben Ayivor-Djanie, Matthew Bashton, Elizabeth M Batty, Yaw Bediako, Denise De Belder, Estefania Benedetti, Andreas Bergthaler, Stefan A Boers, Josefina Campos, Rosina Afua Ampomah Carr, Facundo Cuba, Maria Elena Dattero, Wanwisa Dejnirattisai, Alexander T Dilthey, Kwabena Obeng Duedu, Lukas Endler, Ilka Engelmann, Ngiambudulu M Francisco, Jonas Fuchs, Etienne Gnimpieba Z, Soraya Groc, Jones Gyamfi, Dennis Heemskerk, Torsten Houwaart, Nei-Yuan Hsiao, Matthew Huska, Martin Hölzer, Arash Iranzadeh, Hanna Jarva, Chandima Jeewandara, Bani Jolly, Rageema Joseph, Ravi Kant, Karrie Ko Kwan Ki, Satu Kurkela, Maija Lappalainen, Marie Lataretu, Chang Liu, Gathsaurie Neelika Malavige, Tapfumanei Mashe, Juthathip Mongkolsapaya, Brigitte Montes, José Arturo Molina-Mora, Collins Misita Morang'a, Bernard Mvula, Niranjan Nagarajan, Andrew Nelson, Joyce M Ngoi, Joana Paula da Paixão, Marcus Panning, Tomás Javier Poklepovich, Peter Kojo Quashie, Diyanath Ranasinghe, Mara Russo, James Emmanuel San, Nicholas D Sanderson, Vinod Scaria, Gavin Screaton, Tarja A Sironen, Abay Sisay, Darren L Smith, Teemu Smura, Piyada Supasa, Chayaporn Suphavilai, Jeremy Swann, Houriiyah Tegally, Bryan Tegomoh, Olli Vapalahti, Andreas Walker, Robert John Wilkinson, Carolyn Williamson, null null, Tulio de Oliveira, Timothy Ea Peto, Derrick Crook, Russell Corbett-Detig, Zamin Iqbal
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny. bioRxiv : the preprint server for biology (2024)
Adriano de Bernardi Schneider, Michelle Su, Angie S Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A Wadford, Áine Niamh O'Toole, Emily Scher, Marc D Perry, Yatish Turakhia, Nicola de Maio, Scott Hughes, Russ Corbett-Detig
SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method. Virus evolution 10 (1) (2024)
Nhan Ly-Trong, Chris Bielow, Nicola de Maio, Bui Quang Minh
CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era. Molecular biology and evolution 41 (7) (2024)
Nhan Ly-Trong, Chris Bielow, Nicola de Maio, Bui Quang Minh
CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era. Molecular biology and evolution 41 (7) (2024)
Martin Hunt, Angie S Hinrichs, Daniel Paolo Anderson, Lily Karim, Bethany L Dearlove, Jeff Knaggs, Bede Constantinides, Philip W Fowler, Gillian Rodger, Teresa Street, Sheila F Lumley, Hermione Webster, Theo Sanderson, Christopher Ruis, Nicola de Maio, Lucas N Amenga-Etego, Dominic Selorm Yao Amuzu, Martin Avaro, Gordon Akanzuwine Awandare, Reuben Ayivor-Djanie, Matthew Bashton, Elizabeth M Batty, Yaw Bediako, Denise De Belder, Estefania Benedetti, Andreas Bergthaler, Stefan A Boers, Josefina Campos, Rosina Afua Ampomah Carr, Facundo Cuba, Maria Elena Dattero, Wanwisa Dejnirattisai, Alexander T Dilthey, Kwabena Obeng Duedu, Lukas Endler, Ilka Engelmann, Ngiambudulu M Francisco, Jonas Fuchs, Etienne Gnimpieba Z, Soraya Groc, Jones Gyamfi, Dennis Heemskerk, Torsten Houwaart, Nei-Yuan Hsiao, Matthew Huska, Martin Hölzer, Arash Iranzadeh, Hanna Jarva, Chandima Jeewandara, Bani Jolly, Rageema Joseph, Ravi Kant, Karrie Ko Kwan Ki, Satu Kurkela, Maija Lappalainen, Marie Lataretu, Chang Liu, Gathsaurie Neelika Malavige, Tapfumanei Mashe, Juthathip Mongkolsapaya, Brigitte Montes, José Arturo Molina-Mora, Collins Misita Morang'a, Bernard Mvula, Niranjan Nagarajan, Andrew Nelson, Joyce M Ngoi, Joana Paula da Paixão, Marcus Panning, Tomás Javier Poklepovich, Peter Kojo Quashie, Diyanath Ranasinghe, Mara Russo, James Emmanuel San, Nicholas D Sanderson, Vinod Scaria, Gavin Screaton, Tarja A Sironen, Abay Sisay, Darren L Smith, Teemu Smura, Piyada Supasa, Chayaporn Suphavilai, Jeremy Swann, Houriiyah Tegally, Bryan Tegomoh, Olli Vapalahti, Andreas Walker, Robert John Wilkinson, Carolyn Williamson, null null, Tulio de Oliveira, Timothy Ea Peto, Derrick Crook, Russell Corbett-Detig, Zamin Iqbal
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny. bioRxiv : the preprint server for biology (2024)
Nhan Ly-Trong, Chris Bielow, Nicola de Maio, Bui Quang Minh
CMAPLE: efficient phylogenetic inference in the pandemic era. Molecular biology and evolution (2024)
Adriano de Bernardi Schneider, Michelle Su, Angie S Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A Wadford, Áine Niamh O'Toole, Emily Scher, Marc D Perry, Yatish Turakhia, Nicola de Maio, Scott Hughes, Russ Corbett-Detig
SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method. Virus evolution 10 (1) (2024)
Alexander M Kramer, Bryan Thornlow, Cheng Ye, Nicola de Maio, Jakob McBroome, Angie S Hinrichs, Robert Lanfear, Yatish Turakhia, Russell Corbett-Detig
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. Systematic biology (2023)
Nicola de Maio, Prabhav Kalaghatgi, Yatish Turakhia, Russell Corbett-Detig, Bui Quang Minh, Nick Goldman
Maximum likelihood pandemic-scale phylogenetics. Nature genetics (2023)
Maylis Layan, Nicola Felix Müller, Simon Dellicour, Nicola de Maio, Hervé Bourhy, Simon Cauchemez, Guy Baele
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus evolution 9 (1) (2023)
Maylis Layan, Nicola Felix Müller, Simon Dellicour, Nicola de Maio, Hervé Bourhy, Simon Cauchemez, Guy Baele
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus evolution 9 (1) (2023)
Bryan Thornlow, Alexander Kramer, Cheng Ye, Nicola de Maio, Jakob McBroome, Angie S Hinrichs, Robert Lanfear, Yatish Turakhia, Russell Corbett-Detig
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. bioRxiv : the preprint server for biology (2022)
Vladimir Shchur, Vadim Spirin, Dmitry Sirotkin, Evgeni Burovski, Nicola de Maio, Russell B Corbett-Detig
VGsim: Scalable viral genealogy simulator for global pandemic. PLoS computational biology 18 (8) (2022)
Nicola de Maio, William Boulton, Lukas Weilguny, Conor R Walker, Yatish Turakhia, Russell B Corbett-Detig, Nick Goldman
phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets. PLoS computational biology 18 (4) (2022)
Nicola de Maio, Prabhav Kalaghatgi, Yatish Turakhia, Russell Corbett-Detig, Bui Quang Minh, Nick Goldman
Maximum likelihood pandemic-scale phylogenetics. bioRxiv : the preprint server for biology (2022)
Stéphane Guindon, Nicola de Maio
Accounting for spatial sampling patterns in Bayesian phylogeography. Proceedings of the National Academy of Sciences of the United States of America 118 (52) (2022)
Conor R Walker, Aylwyn Scally, Nicola de Maio, Nick Goldman
Short-range template switching in great ape genomes explored using pair hidden Markov models. PLoS genetics 17 (3) (2021)
Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stephane Guindon, Nicola de Maio
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk. PLoS computational biology 17 (1) (2021)
Shang-Kuan Lin, Nicola de Maio, Vincent Pedergnana, Chieh-Hsi Wu, Julien Thézé, Daniel J Wilson, Eleanor Barnes, M Azim Ansari
Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a. Virus evolution 7 (2) (2021)
Yatish Turakhia, Nicola de Maio, Bryan Thornlow, Landen Gozashti, Robert Lanfear, Conor R Walker, Angie S Hinrichs, Jason D Fernandes, Rui Borges, Greg Slodkowicz, Lukas Weilguny, David Haussler, Nick Goldman, Russell B Corbett-Detig
Stability of SARS-CoV-2 phylogenies. PLoS genetics 16 (11) (2020)
Remco R Bouckaert, Timothy G Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola de Maio, Michael Matschiner, Fábio K Mendes, Nicola F Müller, Huw A Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J Drummond
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology 15 (4) (2019)
Nicola de Maio, Colin J Worby, Daniel J Wilson, Nicole E Stoesser
Bayesian reconstruction of transmission within outbreaks using genomic variants. PLoS computational biology 14 (4) (2018)
Nicola de Maio, Daniel J Wilson
The Bacterial Sequential Markov Coalescent. Genetics 206 (1) (2017)