Scalable inference algorithms for Bayesian evolutionary epidemiology

Publications

International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

Auteurs: Gladstone, R.A.; Siira, L.; Brynildsrud, O.B.; Vestrheim, D.F.; Turner, P.; Clarke, S.C.; Srifuengfung, S.; Ford, R.; Lehmann, D.; Egorova, E.; Voropaeva, E.; Haraldsson, G.; Kristinsson, K.G.; McGee, L.; Breiman, R.F.; Bentley, S.D.; Sheppard, C.L.; Fry, N.K.; Corander, J.; Toropainen, M.; Steens, A.; Akpaka, P.E.; Ampofo, K.; Antonio, M.; Balaji, V.; Beall, B.W.; Belabbès, H.; Benisty, R.; Bigo
Publié dans: Vaccine, 2022, ISSN 0264-410X
Éditeur: Elsevier BV
DOI: 10.1016/j.vaccine.2021.10.046

Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov

Auteurs: Cristina Merla; Cristina Merla; Carla Rodrigues; Virginie Passet; Marta Corbella; Harry A. Thorpe; Teemu V. S. Kallonen; Teemu V. S. Kallonen; Zhiyong Zong; Piero Marone; Claudio Bandi; Claudio Bandi; Davide Sassera; Jukka Corander; Jukka Corander; Jukka Corander; Edward J. Feil; Sylvain Brisse
Publié dans: Frontiers in Microbiology, Numéro 16, 2019, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.1101/703363

Mode and dynamics of vanA -type vancomycin resistance dissemination in Dutch hospitals

Auteurs: Sergio Arredondo-Alonso; Sergio Arredondo-Alonso; Janetta Top; Jukka Corander; Jukka Corander; Jukka Corander; Rob J. L. Willems; Anita C. Schürch
Publié dans: Genome Medicine, Vol 13, Iss 1, Pp 1-18 (2021), Numéro 17, 2021, ISSN 1756-994X
Éditeur: BioMed Central
DOI: 10.1186/s13073-020-00825-3

Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium

Auteurs: Sergio Arredondo-Alonso; Janetta Top; Alan McNally; Santeri Puranen; Santeri Puranen; Maiju Pesonen; Maiju Pesonen; Johan Pensar; Pekka Marttinen; Johanna C. Braat; Malbert R. C. Rogers; W. van Schaik; Samuel Kaski; Rob J. L. Willems; Jukka Corander; Jukka Corander; Jukka Corander; Anita C. Schürch
Publié dans: mBio, Numéro 26, 2020, ISSN 2150-7511
Éditeur: American Society for Microbiology
DOI: 10.1128/mbio.03284-19

A high-throughput multiplexing and selection strategy to complete bacterial genomes

Auteurs: Sergio Arredondo-Alonso, Anna K. Pöntinen, François Cléon, Rebecca A. Gladstone, Anita C. Schürch, Pål J. Johnsen, Ørjan Samuelsen, Jukka Corander
Publié dans: GigaScience, 2021, ISSN 2047-217X
Éditeur: Oxford Academic
DOI: 10.1093/gigascience/giab079

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

Auteurs: John A. Lees, T. Tien Mai, Marco Galardini, Nicole E. Wheeler, Samuel T. Horsfield, Julian Parkhill, Jukka Corander
Publié dans: mBio, 2020, ISSN 2150-7511
Éditeur: American Society for Microbiology
DOI: 10.1101/852426

Genome evolution and emergence of pathogenicity in Avian Escherichia coli

Auteurs: Mageiros, Leonardos; Meric, Guillaume; Bayliss, Sion C.; Pensar, Johan; Ben Pascoe; Mourkas, Evangelos; Calland, Jessica K.; Yahara, Koji; Murray, Susan; Wilkinson, Thomas S.; Williams, Lisa K.; Hitchings, Matthew D.; Porter, Jonathan; Kemmett, Kirsty; Feil, Edward J.; Jolley, Keith A.; Williams, Nicola J.; Corander, Jukka; Sheppard, Samuel K
Publié dans: Nature Communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-20988-w

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions

Auteurs: Kantele, Anu; Kuenzli, Esther; Dunn, Steven J; Dance, David AB; Newton, Paul N; Davong, V; Mero, Sointu; Pakkanen, Sari H; Neumayr, Andreas; Hatz, Christoph; Snaith, Ann; Kallonen, Teemu; Corander, Jukka; McNally, Alan
Publié dans: Lancet Microbe, Numéro 17, 2021, ISSN 2666-5247
Éditeur: Elsevier
DOI: 10.1016/s2666-5247(20)30224-x

New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates.

Auteurs: Priyanka Kachroo; Jesus M. Eraso; Randall J. Olsen; Randall J. Olsen; Luchang Zhu; Samantha L. Kubiak; Layne Pruitt; Prasanti Yerramilli; Concepcion C. Cantu; Matthew Ojeda Saavedra; Johan Pensar; Jukka Corander; Jukka Corander; Leslie Jenkins; Lillian S. Kao; Alejandro Granillo; Adeline R. Porter; Frank R. DeLeo; James M. Musser; James M. Musser
Publié dans: mBio, Vol 11, Iss 1 (2020), Numéro 8, 2020, ISSN 2150-7511
Éditeur: American Society for Microbiolgy
DOI: 10.1128/mbio.03363-19

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

Auteurs: Arredondo-Alonso, Sergio; Rogers, Malbert R. C.; Braat, Johanna C.; Verschuuren, T. D.; Top, Janetta; Corander, Jukka; Willems, Rob J.L.; Schürch, Anita C.
Publié dans: Microbial Genomics, Numéro 15, 2018, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1099/mgen.0.000224

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae

Auteurs: Taj Azarian; Taj Azarian; Pamela P. Martinez; Brian J. Arnold; Xueting Qiu; Lindsay R. Grant; Jukka Corander; Jukka Corander; Jukka Corander; Christophe Fraser; Nicholas J. Croucher; Laura L. Hammitt; Raymond Reid; Mathuram Santosham; Robert Weatherholtz; Stephen D. Bentley; Katherine L. O’Brien; Marc Lipsitch; William P. Hanage
Publié dans: PLoS Biology, Vol 18, Iss 10, p e3000878 (2020), Numéro 16, 2020, ISSN 1544-9173
Éditeur: Public Library of Science
DOI: 10.1371/journal.pbio.3000878

On the Jensen-Shannon divergence and the variation distance for categorical probability distributions

Auteurs: Jukka Corander, Ulpu Remes, Timo Koski
Publié dans: Kybernetika, 2021, ISSN 1805-949X
Éditeur: Academy of Sciences of the Czech Republic
DOI: 10.14736/kyb-2021-6-0879

Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation

Auteurs: John A. Lees, Gerry Tonkin-Hill, Zhirong Yang, Jukka Corander
Publié dans: Philosophical Transactions of the Royal Society B, 2022, ISSN 0962-8436
Éditeur: Royal Society of London
DOI: 10.1098/rstb.2021.0237

The effect of recombination on the evolution of a population of Neisseria meningitidis.

Auteurs: Neil MacAlasdair; Maiju Pesonen; Ola Brønstad Brynildsrud; Ola Brønstad Brynildsrud; Vegard Eldholm; Paul A. Kristiansen; Jukka Corander; Dominique A. Caugant; Dominique A. Caugant; Stephen D. Bentley
Publié dans: Genome Research, Numéro 17, 2021, ISSN 1088-9051
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.264465.120

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen Enterococcus faecium

Auteurs: Janetta Top; Sergio Arredondo-Alonso; Anita C. Schürch; Santeri Puranen; Santeri Puranen; Maiju Pesonen; Maiju Pesonen; Maiju Pesonen; Johan Pensar; Johan Pensar; Rob J. L. Willems; Jukka Corander; Jukka Corander; Jukka Corander
Publié dans: Microbial Genomics, Numéro 17, 2020, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1101/2020.10.20.346924

High-resolution sweep metagenomics using fast probabilistic inference

Auteurs: Tommi Mäklin; Teemu Kallonen; Teemu Kallonen; Sophia David; Christine J. Boinett; Ben Pascoe; Guillaume Méric; David M. Aanensen; David M. Aanensen; David M. Aanensen; Edward J. Feil; Stephen Baker; Julian Parkhill; Samuel K. Sheppard; Jukka Corander; Jukka Corander; Jukka Corander; Antti Honkela; Antti Honkela
Publié dans: Wellcome Open Research, Numéro 27, 2021, ISSN 2398-502X
Éditeur: Wellcome
DOI: 10.17863/cam.78156

Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae

Auteurs: Sudaraka Mallawaarachchi; Gerry Tonkin-Hill; Nicholas J Croucher; Paul Turner; Doug Speed; Jukka Corander; David Balding
Publié dans: NAR genomics and bioinformatics, 2022, ISSN 2631-9268
Éditeur: Oxford University Press
DOI: 10.1093/nargab/lqac011

The global dissemination of hospital clones of Enterococcus faecium

Auteurs: Sebastiaan J. van Hal; Sebastiaan J. van Hal; Rob J. L. Willems; Theodore Gouliouris; Susan A Ballard; Teresa M. Coque; Anette M. Hammerum; Kristin Hegstad; Hendrik T. Westh; Benjamin P Howden; Surbhi Malhotra-Kumar; Guido Werner; Katsunori Yanagihara; Ashlee M. Earl; Katherine E. Raven; Jukka Corander; Jukka Corander; Rory Bowden; Rory Bowden; Rory Bowden
Publié dans: Genome medicine, Numéro 12, 2021, ISSN 1756-994X
Éditeur: BioMed Central
DOI: 10.1186/s13073-021-00868-0

Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting

Auteurs: Mai The Tien, Turner Paul, Corander Jukka
Publié dans: BMC Bioinformatics, 2021, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.21203/rs.3.rs-200227/v1

PYLFIRE: Python implementation of likelihood-free inference by ratio estimation.

Auteurs: Kokko, Jan; Remes, Ulpu; Thomas, Owen; Pesonen, Henri; Corander, Jukka
Publié dans: Wellcome Open Research, Numéro 31, 2019, ISSN 2398-502X
Éditeur: Wellcome
DOI: 10.12688/wellcomeopenres.15583.1

Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections: a nationwide longitudinal microbial population genomic study in Norway between 2002-2017

Auteurs: Rebecca A Gladstone, Alan McNally, Anna K. Pöntinen, Gerry Tonkin-Hill, John A. Lees, Kusti O. Skytén, François Cléon, Martin O. K. Christensen, Bjørg C. Haldorsen, Kristina K. Bye, Karianne W. Gammelsrud, Reidar Hjetland, Angela Kümmel, Hege E. Larsen, Paul Christoffer Lindemann, Iren H. Löhr, Åshild Marvik, Einar Nilsen, Marie T. Noer, Gunnar S. Simonsen, Martin Steinbakk, Ståle Toftela
Publié dans: Lancet Microbe, 2021, ISSN 2666-5247
Éditeur: Elsevier
DOI: 10.1016/s2666-5247(21)00031-8

Sequentially guided MCMC proposals for synthetic likelihoods and correlated synthetic likelihoods

Auteurs: Umberto Picchini; Umberto Simola; Jukka Corander
Publié dans: Bayesian Analysis, 2022, ISSN 1931-6690
Éditeur: Carnegie Mellon University
DOI: 10.1214/22-ba1305

Likelihood-free inference by ratio estimation

Auteurs: Thomas Owen, Dutta Ritabrata, Corander Jukk, Kaski Samuel, Gutmann Michael
Publié dans: Bayesian Analysis, 2021, ISSN 1936-0975
Éditeur: Carnegie Mellon University
DOI: 10.1214/20-ba1238

Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen

Auteurs: Brian J. Arnold; Mashaal Sohail; Mashaal Sohail; Crista B. Wadsworth; Jukka Corander; Jukka Corander; William P. Hanage; Shamil R. Sunyaev; Shamil R. Sunyaev; Yonatan H. Grad; Yonatan H. Grad
Publié dans: Molecular Biology and Evolution, Numéro 21, 2020, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.1101/634147

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages.

Auteurs: Jessica K. Calland, Ben Pascoe, Sion C. Bayliss, Evangelos Mourkas, Elvire Berthenet, Harry A. Thorpe, Matthew D. Hitchings, Edward J. Feil, Jukka Corander, Martin J. Blaser, Daniel Falush, Samuel K. Sheppard
Publié dans: PLoS Genetics, 2021, ISSN 1553-7404
Éditeur: Public Library of Science
DOI: 10.1371/journal.pgen.1009829

Bacterial Genomic Epidemiology with Mixed Samples

Auteurs: Tommi Mäklin, Teemu Kallonen, Jarno Alanko, Ørjan Samuelsen, Kristin Hegstad, Veli Mäkinen, Jukka Corander, Eva Heinz, Antti Honkela
Publié dans: Microbial Genomics, 2021, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1099/mgen.0.000691

Co-evolutionary signals identify Burkholderia pseudomallei survival strategies in a hostile environment

Auteurs: Claire Chewapreecha, Johan Pensar, Supaksorn Chattagul, Maiju Pesonen, Apiwat Sangphukieo, Phumrapee Boonklang, Chotima Potisap, Sirikamon Koosakulnirand, Edward J Feil, Susanna Dunachie, Narisara Chantratita, Direk Limmathurotsakul, Sharon J Peacock, Nick PJ Day, Julian Parkhill, Nicholas R Thomson, Rasana W Sermswan, Jukka Corander
Publié dans: Molecular Biology and Evolution, 2021, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msab306

SuperDCA for genome-wide epistasis analysis

Auteurs: Santeri Puranen, Maiju Pesonen, Johan Pensar, Ying Ying Xu, John A. Lees, Stephen D. Bentley, Nicholas J. Croucher, Jukka Corander
Publié dans: Microbial Genomics, Numéro 4/6, 2018, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1099/mgen.0.000184

Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism

Auteurs: Guillaume Méric, Alan McNally, Alberto Pessia, Evangelos Mourkas, Ben Pascoe, Leonardos Mageiros, Minna Vehkala, Jukka Corander, Samuel K Sheppard
Publié dans: Genome Biology and Evolution, Numéro 10/3, 2018, Page(s) 763-774, ISSN 1759-6653
Éditeur: Oxford University Press
DOI: 10.1093/gbe/evy026

Bacmeta: simulator for genomic evolution in bacterial metapopulations

Auteurs: Aleksi Sipola, Pekka Marttinen, Jukka Corander
Publié dans: Bioinformatics, Numéro 34/13, 2018, Page(s) 2308-2310, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty093

Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence

Auteurs: Annemieke Smet, Koji Yahara, Mirko Rossi, Alfred Tay, Steffen Backert, Ensser Armin, James G. Fox, Bram Flahou, Richard Ducatelle, Freddy Haesebrouck, Jukka Corander
Publié dans: The ISME Journal, Numéro 12/10, 2018, Page(s) 2518-2531, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-018-0199-5

Inverse finite-size scaling for high-dimensional significance analysis

Auteurs: Yingying Xu, Santeri Puranen, Jukka Corander, Yoshiyuki Kabashima
Publié dans: Physical Review E, Numéro 97/6, 2018, ISSN 2470-0045
Éditeur: American Physical Society
DOI: 10.1103/physreve.97.062112

ELFI: Engine for Likelihood-Free Inference

Auteurs: Jarno Lintusaari, Henri Vuollekoski, Antti Kangasrääsiö, Kusti Skytén, Marko Järvenpää, Pekka Marttinen, Michael U. Gutmann, Aki Vehtari, Jukka Corander, Samuel Kaski
Publié dans: Journal of Machine Learning Research, 2018, ISSN 1533-7928
Éditeur: MIT Press

pyseer: a comprehensive tool for microbial pangenome-wide association studies

Auteurs: John A Lees, Marco Galardini, Stephen D Bentley, Jeffrey N Weiser, Jukka Corander
Publié dans: Bioinformatics, Numéro 34/24, 2018, Page(s) 4310-4312, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty539

PANINI: Pangenome Neighbour Identification for Bacterial Populations

Auteurs: Khalil Abudahab, Joaquín M. Prada, Zhirong Yang, Stephen D. Bentley, Nicholas J. Croucher, Jukka Corander, David M. Aanensen
Publié dans: Microbial Genomics, 2018, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1099/mgen.0.000220

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

Auteurs: Guillaume Méric, Leonardos Mageiros, Johan Pensar, Maisem Laabei, Koji Yahara, Ben Pascoe, Nattinee Kittiwan, Phacharaporn Tadee, Virginia Post, Sarah Lamble, Rory Bowden, James E. Bray, Mario Morgenstern, Keith A. Jolley, Martin C. J. Maiden, Edward J. Feil, Xavier Didelot, Maria Miragaia, Herminia de Lencastre, T. Fintan Moriarty, Holger Rohde, Ruth Massey, Dietrich Mack, Jukka Corander, Samuel
Publié dans: Nature Communications, Numéro 9/1, 2018, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-018-07368-7

Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis

Auteurs: Priyanka Kachroo, Jesus M. Eraso, Stephen B. Beres, Randall J. Olsen, Luchang Zhu, Waleed Nasser, Paul E. Bernard, Concepcion C. Cantu, Matthew Ojeda Saavedra, María José Arredondo, Benjamin Strope, Hackwon Do, Muthiah Kumaraswami, Jaana Vuopio, Kirsi Gröndahl-Yli-Hannuksela, Karl G. Kristinsson, Magnus Gottfredsson, Maiju Pesonen, Johan Pensar, Emily R. Davenport, Andrew G. Clark, Jukka Corand
Publié dans: Nature Genetics, Numéro 51/3, 2019, Page(s) 548-559, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-018-0343-1

Gene exchange drives the ecological success of a multi-host bacterial pathogen

Auteurs: Emily J. Richardson, Rodrigo Bacigalupe, Ewan M. Harrison, Lucy A. Weinert, Samantha Lycett, Manouk Vrieling, Kirsty Robb, Paul A. Hoskisson, Matthew T. G. Holden, Edward J. Feil, Gavin K. Paterson, Steven Y. C. Tong, Adebayo Shittu, Willem van Wamel, David M. Aanensen, Julian Parkhill, Sharon J. Peacock, Jukka Corander, Mark Holmes, J. Ross Fitzgerald
Publié dans: Nature Ecology & Evolution, Numéro 2/9, 2018, Page(s) 1468-1478, ISSN 2397-334X
Éditeur: NPG
DOI: 10.1038/s41559-018-0617-0

Fast and flexible bacterial genomic epidemiology with PopPUNK

Auteurs: John A. Lees, Simon R. Harris, Gerry Tonkin-Hill, Rebecca A. Gladstone, Stephanie W. Lo, Jeffrey N. Weiser, Jukka Corander, Stephen D. Bentley, Nicholas J. Croucher
Publié dans: Genome Research, Numéro 29/2, 2019, Page(s) 304-316, ISSN 1088-9051
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.241455.118

Weak Epistasis May Drive Adaptation in Recombining Bacteria

Auteurs: Brian J. Arnold, Michael U. Gutmann, Yonatan H. Grad, Samuel K. Sheppard, Jukka Corander, Marc Lipsitch, William P. Hanage
Publié dans: Genetics, Numéro 208/3, 2018, Page(s) 1247-1260, ISSN 0016-6731
Éditeur: Genetics Society of America
DOI: 10.1534/genetics.117.300662

Designing ecologically optimized pneumococcal vaccines using population genomics

Auteurs: Caroline Colijn, Jukka Corander, Nicholas J. Croucher
Publié dans: Nature Microbiology, 2020, ISSN 2058-5276
Éditeur: Nature Publishing Group
DOI: 10.1038/s41564-019-0651-y

Machine learning accelerated likelihood-free event reconstruction in dark matter direct detection

Auteurs: U. Simola, B. Pelssers, D. Barge, J. Conrad, J. Corander
Publié dans: Journal of Instrumentation, Numéro 14/03, 2019, Page(s) P03004-P03004, ISSN 1748-0221
Éditeur: Institute of Physics
DOI: 10.1088/1748-0221/14/03/P03004

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS

Auteurs: Gerry Tonkin-Hill, John A. Lees, Stephen D. Bentley, Simon D.W. Frost, Jukka Corander
Publié dans: Wellcome Open Research, Numéro 3, 2018, Page(s) 93, ISSN 2398-502X
Éditeur: F1000
DOI: 10.12688/wellcomeopenres.14694.1

The impact of antimicrobials on gonococcal evolution

Auteurs: Leonor Sánchez-Busó, Daniel Golparian, Jukka Corander, Yonatan H. Grad, Makoto Ohnishi, Rebecca Flemming, Julian Parkhill, Stephen D. Bentley, Magnus Unemo, Simon R. Harris
Publié dans: Nature Microbiology, Numéro 4/11, 2019, Page(s) 1941-1950, ISSN 2058-5276
Éditeur: Nature Publishing Group
DOI: 10.1038/s41564-019-0501-y

Genome-wide epistasis and co-selection study using mutual information

Auteurs: Johan Pensar, Santeri Puranen, Brian Arnold, Neil MacAlasdair, Juri Kuronen, Gerry Tonkin-Hill, Maiju Pesonen, Yingying Xu, Aleksi Sipola, Leonor Sánchez-Busó, John A Lees, Claire Chewapreecha, Stephen D Bentley, Simon R Harris, Julian Parkhill, Nicholas J Croucher, Jukka Corander
Publié dans: Nucleic Acids Research, Numéro 47/18, 2019, Page(s) e112-e112, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz656

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

Auteurs: Alan McNally, Teemu Kallonen, Christopher Connor, Khalil Abudahab, David M. Aanensen, Carolyne Horner, Sharon J. Peacock, Julian Parkhill, Nicholas J. Croucher, Jukka Corander
Publié dans: mBio, Numéro 10/2, 2019, ISSN 2150-7511
Éditeur: American Society for Microbiology
DOI: 10.1128/mbio.00644-19

Resolving outbreak dynamics using approximate Bayesian computation for stochastic birth–death models

Auteurs: Jarno Lintusaari, Paul Blomstedt, Brittany Rose, Tuomas Sivula, Michael U. Gutmann, Samuel Kaski, Jukka Corander
Publié dans: Wellcome Open Research, Numéro 4, 2019, Page(s) 14, ISSN 2398-502X
Éditeur: F1000
DOI: 10.12688/wellcomeopenres.15048.2

Fast hierarchical Bayesian analysis of population structure

Auteurs: Gerry Tonkin-Hill, John A Lees, Stephen D Bentley, Simon D W Frost, Jukka Corander
Publié dans: Nucleic Acids Research, Numéro 47/11, 2019, Page(s) 5539-5549, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz361

Bayesian inference of atomistic structure in functional materials

Auteurs: Milica Todorović, Michael U. Gutmann, Jukka Corander, Patrick Rinke
Publié dans: npj Computational Materials, Numéro 5/1, 2019, ISSN 2057-3960
Éditeur: Nature Publishing Group
DOI: 10.1038/s41524-019-0175-2

High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study

Auteurs: Pensar, Johan; Xu, Yingying; Puranen, Santeri; Pesonen, Maiju; Kabashima, Yoshiyuki; Corander, Jukka
Publié dans: Computational Statistics and Data Analysis, Numéro 18, 2020, ISSN 0167-9473
Éditeur: Elsevier BV
DOI: 10.1016/j.csda.2019.06.012

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Auteurs: Gerry Tonkin-Hill; Gerry Tonkin-Hill; Neil MacAlasdair; Neil MacAlasdair; Christopher Ruis; Christopher Ruis; Aaron Weimann; Gal Horesh; John A. Lees; Rebecca A. Gladstone; Stephanie W. Lo; Christopher A. Beaudoin; R. Andres Floto; R. Andres Floto; Simon D. W. Frost; Simon D. W. Frost; Jukka Corander; Jukka Corander; Jukka Corander; Stephen D. Bentley; Julian Parkhill
Publié dans: Genome Biology, Vol 21, Iss 1, Pp 1-21 (2020), Numéro 34, 2020, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.17863/cam.55804

Likelihood-Free Inference with Deep Gaussian Processes

Auteurs: Alexander Aushev; Henri Pesonen; Markus Heinonen; Jukka Corander; Samuel Kaski
Publié dans: Computational Statistics and Data Analysis, 2022, ISSN 0167-9473
Éditeur: Elsevier BV
DOI: 10.1016/j.csda.2022.107529

rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree

Auteurs: Alexander M. Wailan; Francesc Coll; Eva Heinz; Gerry Tonkin-Hill; Jukka Corander; Jukka Corander; Jukka Corander; Nicholas A. Feasey; Nicholas A. Feasey; Nicholas R. Thomson; Nicholas R. Thomson
Publié dans: Microbial Genomics, Numéro 20, 2019, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1101/404624

Different evolutionary trends form the twilight zone of the bacterial pan-genome

Auteurs: Gal Horesh, Alyce Taylor-Brown; Stephanie McGimpsey, Florent Lassalle, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Publié dans: Microbial Genomics, 2021, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1099/mgen.0.000670

The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis

Auteurs: Sebastiaan J. van Hal, Rob J. L. Willems, Theodore Gouliouris, Susan A. Ballard, Teresa M. Coque, Anette M. Hammerum, Kristin Hegstad, Mette Pinholt, Benjamin P. Howden, Surbhi Malhotra-Kumar, Guido Werner, Katsunori Yanagihara, Ashlee M. Earl, Katherine E. Raven, Jukka Corander, Rory Bowden
Publié dans: Lancet Microbe, 2022, ISSN 2666-5247
Éditeur: Elsevier
DOI: 10.1016/s2666-5247(21)00236-6

Adaptive Approximate Bayesian Computation Tolerance Selection

Auteurs: Umberto Simola; Jessica Cisewski-Kehe; Michael U. Gutmann; Jukka Corander
Publié dans: Bayesian Analysis, 2021, ISSN 1931-6690
Éditeur: Carnegie Mellon University
DOI: 10.1214/20-ba1211

gplas : a comprehensive tool for plasmid analysis using short-read graphs

Auteurs: Arredondo-Alonso, Sergio; Bootsma, Martin; Hein, Yair; Rogers, Malbert R. C.; Corander, Jukka; Willems, Rob J. L.; Schurch, Anita C.
Publié dans: Bioinformatics, 2020, ISSN 1460-2059
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btaa233

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Auteurs: Anna K. Pöntinen, Janetta Top, Sergio Arredondo-Alonso, Gerry Tonkin-Hill, Ana R. Freitas, Carla Novais, Rebecca A. Gladstone, Maiju Pesonen, Rodrigo Meneses, Henri Pesonen, John A. Lees, Dorota Jamrozy, Stephen D. Bentley, Val Fernandez Lanza, Carmen Torres, Luisa Peixe, Teresa M. Coque, Julian Parkhill, Anita C. Schürch, Rob J. L. Willems, Jukka Corander
Publié dans: Nature Communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-21749-5

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment.

Auteurs: Gouliouris, Theodore; Raven, Kathy E; Moradigaravand, Danesh; Ludden, Catherine; Coll, Francesc; Blane, Beth; Naydenova, Plamena; Horner, Carolyne; Brown, Nicholas M; Corander, Jukka; Limmathurotsakul, Direk; Parkhill, Julian; Peacock, Sharon
Publié dans: Genome Research, Numéro 27, 2019, ISSN 1088-9051
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.232629.117

A comprehensive and high-quality collection of Escherichia coli genomes and their genes

Auteurs: Gal Horesh, Grace A. Blackwell, Gerry Tonkin-Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Publié dans: Microbial Genomics, 2021, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1099/mgen.0.000499

Probabilistic elicitation of expert knowledge through assessment of computer simulations

Auteurs: Thomas, Owen; Pesonen, Henri; Corander, Jukka
Publié dans: 2021
Éditeur: arXiv.org
DOI: 10.48550/arxiv.2002.10902

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