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

by Nicola De Maio, Chieh-Hsi Wu, Daniel J Wilson
Published 2016-09-01

Short-range template switching in great ape genomes explored using pair hidden Markov models.

by Conor R Walker, Aylwyn Scally, Nicola De Maio, Nick Goldman
Published 2021-03-01

Bayesian reconstruction of transmission within outbreaks using genomic variants.

by Nicola De Maio, Colin J Worby, Daniel J Wilson, Nicole Stoesser
Published 2018-04-01

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation.

by Nicola De Maio, Chieh-Hsi Wu, Kathleen M O'Reilly, Daniel Wilson
Published 2015-08-01

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

by Danny Ionescu, Mina Bizic-Ionescu, Nicola De Maio, Heribert Cypionka, Hans-Peter Grossart
Published 2017-09-01

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.

by Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stephane Guindon, Nicola De Maio
Published 2021-01-01

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.

by Robert Kofler, Pablo Orozco-terWengel, Nicola De Maio, Ram Vinay Pandey, Viola Nolte, Andreas Futschik, Carolin Kosiol, Christian Schlötterer
Published 2011-01-01

A phylogenetic approach for weighting genetic sequences

by Nicola De Maio, Alexander V. Alekseyenko, William J. Coleman-Smith, Fabio Pardi, Marc A. Suchard, Asif U. Tamuri, Jakub Truszkowski, Nick Goldman
Published 2021-05-01

Stability of SARS-CoV-2 phylogenies.

by 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 Corbett-Detig
Published 2020-11-01

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

by Joseph Crispell, Clare H Benton, Daniel Balaz, Nicola De Maio, Assel Ahkmetova, Adrian Allen, Roman Biek, Eleanor L Presho, James Dale, Glyn Hewinson, Samantha J Lycett, Javier Nunez-Garcia, Robin A Skuce, Hannah Trewby, Daniel J Wilson, Ruth N Zadoks, Richard J Delahay, Rowland Raymond Kao
Published 2019-12-01

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

by H. Soon Gweon, Liam P. Shaw, Jeremy Swann, Nicola De Maio, Manal AbuOun, Rene Niehus, Alasdair T. M. Hubbard, Mike J. Bowes, Mark J. Bailey, Tim E. A. Peto, Sarah J. Hoosdally, A. Sarah Walker, Robert P. Sebra, Derrick W. Crook, Muna F. Anjum, Daniel S. Read, Nicole Stoesser, on behalf of the REHAB consortium
Published 2019-10-01

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

by Andrew Stewardson, Tim Spelman, Sarah N Hilmer, Allen Cheng, Sarah Hilmer, Terry Haines, Trisha Peel, Anton Peleg, Natali Jokanovic, Rhonda L Stuart, Kathryn E Holt, Yun-Hee Jeon, Andrew J Stewardson, Trisha N Peel, Anton Y Peleg, Kathryn Holt, Rhonda Stuart, Sue Lee, Annette Schmiede, Marilyn Cruickshank, Nicola De Maio, Bupa Aged Care
Published 2021-03-01

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

by Remco 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
Published 2019-04-01

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

by Nicole Stoesser, Anna E. Sheppard, Louise Pankhurst, Nicola De Maio, Catrin E. Moore, Robert Sebra, Paul Turner, Luke W. Anson, Andrew Kasarskis, Elizabeth M. Batty, Veronica Kos, Daniel J. Wilson, Rattanaphone Phetsouvanh, David Wyllie, Evgeni Sokurenko, Amee R. Manges, Timothy J. Johnson, Lance B. Price, Timothy E. A. Peto, James R. Johnson, Xavier Didelot, A. Sarah Walker, Derrick W. Crook
Published 2016-03-01