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

Author(s): 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
Published in: Vaccine, 2022, ISSN 0264-410X
Publisher: Elsevier BV
DOI: 10.1016/j.vaccine.2021.10.046

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

Author(s): 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
Published in: Frontiers in Microbiology, Issue 16, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.1101/703363

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

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

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

Author(s): 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
Published in: mBio, Issue 26, 2020, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03284-19

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

Author(s): Sergio Arredondo-Alonso, Anna K. Pöntinen, François Cléon, Rebecca A. Gladstone, Anita C. Schürch, Pål J. Johnsen, Ørjan Samuelsen, Jukka Corander
Published in: GigaScience, 2021, ISSN 2047-217X
Publisher: Oxford Academic
DOI: 10.1093/gigascience/giab079

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

Author(s): John A. Lees, T. Tien Mai, Marco Galardini, Nicole E. Wheeler, Samuel T. Horsfield, Julian Parkhill, Jukka Corander
Published in: mBio, 2020, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1101/852426

Genome evolution and emergence of pathogenicity in Avian Escherichia coli

Author(s): 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
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: 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

Author(s): 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
Published in: Lancet Microbe, Issue 17, 2021, ISSN 2666-5247
Publisher: Elsevier
DOI: 10.1016/s2666-5247(20)30224-x

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

Author(s): 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
Published in: mBio, Vol 11, Iss 1 (2020), Issue 8, 2020, ISSN 2150-7511
Publisher: 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

Author(s): Arredondo-Alonso, Sergio; Rogers, Malbert R. C.; Braat, Johanna C.; Verschuuren, T. D.; Top, Janetta; Corander, Jukka; Willems, Rob J.L.; Schürch, Anita C.
Published in: Microbial Genomics, Issue 15, 2018, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000224

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae

Author(s): 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
Published in: PLoS Biology, Vol 18, Iss 10, p e3000878 (2020), Issue 16, 2020, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3000878

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

Author(s): Jukka Corander, Ulpu Remes, Timo Koski
Published in: Kybernetika, 2021, ISSN 1805-949X
Publisher: 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

Author(s): John A. Lees, Gerry Tonkin-Hill, Zhirong Yang, Jukka Corander
Published in: Philosophical Transactions of the Royal Society B, 2022, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2021.0237

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

Author(s): 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
Published in: Genome Research, Issue 17, 2021, ISSN 1088-9051
Publisher: 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

Author(s): 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
Published in: Microbial Genomics, Issue 17, 2020, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1101/2020.10.20.346924

High-resolution sweep metagenomics using fast probabilistic inference

Author(s): 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
Published in: Wellcome Open Research, Issue 27, 2021, ISSN 2398-502X
Publisher: Wellcome
DOI: 10.17863/cam.78156

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

Author(s): Sudaraka Mallawaarachchi; Gerry Tonkin-Hill; Nicholas J Croucher; Paul Turner; Doug Speed; Jukka Corander; David Balding
Published in: NAR genomics and bioinformatics, 2022, ISSN 2631-9268
Publisher: Oxford University Press
DOI: 10.1093/nargab/lqac011

The global dissemination of hospital clones of Enterococcus faecium

Author(s): 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
Published in: Genome medicine, Issue 12, 2021, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-021-00868-0

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

Author(s): Mai The Tien, Turner Paul, Corander Jukka
Published in: BMC Bioinformatics, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.21203/rs.3.rs-200227/v1

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

Author(s): Kokko, Jan; Remes, Ulpu; Thomas, Owen; Pesonen, Henri; Corander, Jukka
Published in: Wellcome Open Research, Issue 31, 2019, ISSN 2398-502X
Publisher: 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

Author(s): 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
Published in: Lancet Microbe, 2021, ISSN 2666-5247
Publisher: Elsevier
DOI: 10.1016/s2666-5247(21)00031-8

Sequentially guided MCMC proposals for synthetic likelihoods and correlated synthetic likelihoods

Author(s): Umberto Picchini; Umberto Simola; Jukka Corander
Published in: Bayesian Analysis, 2022, ISSN 1931-6690
Publisher: Carnegie Mellon University
DOI: 10.1214/22-ba1305

Likelihood-free inference by ratio estimation

Author(s): Thomas Owen, Dutta Ritabrata, Corander Jukk, Kaski Samuel, Gutmann Michael
Published in: Bayesian Analysis, 2021, ISSN 1936-0975
Publisher: Carnegie Mellon University
DOI: 10.1214/20-ba1238

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

Author(s): 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
Published in: Molecular Biology and Evolution, Issue 21, 2020, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1101/634147

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

Author(s): 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
Published in: PLoS Genetics, 2021, ISSN 1553-7404
Publisher: Public Library of Science
DOI: 10.1371/journal.pgen.1009829

Bacterial Genomic Epidemiology with Mixed Samples

Author(s): Tommi Mäklin, Teemu Kallonen, Jarno Alanko, Ørjan Samuelsen, Kristin Hegstad, Veli Mäkinen, Jukka Corander, Eva Heinz, Antti Honkela
Published in: Microbial Genomics, 2021, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000691

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

Author(s): 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
Published in: Molecular Biology and Evolution, 2021, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab306

SuperDCA for genome-wide epistasis analysis

Author(s): Santeri Puranen, Maiju Pesonen, Johan Pensar, Ying Ying Xu, John A. Lees, Stephen D. Bentley, Nicholas J. Croucher, Jukka Corander
Published in: Microbial Genomics, Issue 4/6, 2018, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000184

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

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

Bacmeta: simulator for genomic evolution in bacterial metapopulations

Author(s): Aleksi Sipola, Pekka Marttinen, Jukka Corander
Published in: Bioinformatics, Issue 34/13, 2018, Page(s) 2308-2310, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty093

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

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

Inverse finite-size scaling for high-dimensional significance analysis

Author(s): Yingying Xu, Santeri Puranen, Jukka Corander, Yoshiyuki Kabashima
Published in: Physical Review E, Issue 97/6, 2018, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1103/physreve.97.062112

ELFI: Engine for Likelihood-Free Inference

Author(s): Jarno Lintusaari, Henri Vuollekoski, Antti Kangasrääsiö, Kusti Skytén, Marko Järvenpää, Pekka Marttinen, Michael U. Gutmann, Aki Vehtari, Jukka Corander, Samuel Kaski
Published in: Journal of Machine Learning Research, 2018, ISSN 1533-7928
Publisher: MIT Press

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

Author(s): John A Lees, Marco Galardini, Stephen D Bentley, Jeffrey N Weiser, Jukka Corander
Published in: Bioinformatics, Issue 34/24, 2018, Page(s) 4310-4312, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty539

PANINI: Pangenome Neighbour Identification for Bacterial Populations

Author(s): Khalil Abudahab, Joaquín M. Prada, Zhirong Yang, Stephen D. Bentley, Nicholas J. Croucher, Jukka Corander, David M. Aanensen
Published in: Microbial Genomics, 2018, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000220

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

Author(s): 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
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: 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

Author(s): 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
Published in: Nature Genetics, Issue 51/3, 2019, Page(s) 548-559, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-018-0343-1

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

Author(s): 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
Published in: Nature Ecology & Evolution, Issue 2/9, 2018, Page(s) 1468-1478, ISSN 2397-334X
Publisher: NPG
DOI: 10.1038/s41559-018-0617-0

Fast and flexible bacterial genomic epidemiology with PopPUNK

Author(s): 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
Published in: Genome Research, Issue 29/2, 2019, Page(s) 304-316, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.241455.118

Weak Epistasis May Drive Adaptation in Recombining Bacteria

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

Designing ecologically optimized pneumococcal vaccines using population genomics

Author(s): Caroline Colijn, Jukka Corander, Nicholas J. Croucher
Published in: Nature Microbiology, 2020, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-019-0651-y

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

Author(s): U. Simola, B. Pelssers, D. Barge, J. Conrad, J. Corander
Published in: Journal of Instrumentation, Issue 14/03, 2019, Page(s) P03004-P03004, ISSN 1748-0221
Publisher: Institute of Physics
DOI: 10.1088/1748-0221/14/03/P03004

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS

Author(s): Gerry Tonkin-Hill, John A. Lees, Stephen D. Bentley, Simon D.W. Frost, Jukka Corander
Published in: Wellcome Open Research, Issue 3, 2018, Page(s) 93, ISSN 2398-502X
Publisher: F1000
DOI: 10.12688/wellcomeopenres.14694.1

The impact of antimicrobials on gonococcal evolution

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

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

Author(s): 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
Published in: Nucleic Acids Research, Issue 47/18, 2019, Page(s) e112-e112, ISSN 0305-1048
Publisher: 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

Author(s): Alan McNally, Teemu Kallonen, Christopher Connor, Khalil Abudahab, David M. Aanensen, Carolyne Horner, Sharon J. Peacock, Julian Parkhill, Nicholas J. Croucher, Jukka Corander
Published in: mBio, Issue 10/2, 2019, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.00644-19

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

Author(s): Jarno Lintusaari, Paul Blomstedt, Brittany Rose, Tuomas Sivula, Michael U. Gutmann, Samuel Kaski, Jukka Corander
Published in: Wellcome Open Research, Issue 4, 2019, Page(s) 14, ISSN 2398-502X
Publisher: F1000
DOI: 10.12688/wellcomeopenres.15048.2

Fast hierarchical Bayesian analysis of population structure

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

Bayesian inference of atomistic structure in functional materials

Author(s): Milica Todorović, Michael U. Gutmann, Jukka Corander, Patrick Rinke
Published in: npj Computational Materials, Issue 5/1, 2019, ISSN 2057-3960
Publisher: Nature Publishing Group
DOI: 10.1038/s41524-019-0175-2

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

Author(s): Pensar, Johan; Xu, Yingying; Puranen, Santeri; Pesonen, Maiju; Kabashima, Yoshiyuki; Corander, Jukka
Published in: Computational Statistics and Data Analysis, Issue 18, 2020, ISSN 0167-9473
Publisher: Elsevier BV
DOI: 10.1016/j.csda.2019.06.012

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Author(s): 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
Published in: Genome Biology, Vol 21, Iss 1, Pp 1-21 (2020), Issue 34, 2020, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.17863/cam.55804

Likelihood-Free Inference with Deep Gaussian Processes

Author(s): Alexander Aushev; Henri Pesonen; Markus Heinonen; Jukka Corander; Samuel Kaski
Published in: Computational Statistics and Data Analysis, 2022, ISSN 0167-9473
Publisher: Elsevier BV
DOI: 10.1016/j.csda.2022.107529

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

Author(s): 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
Published in: Microbial Genomics, Issue 20, 2019, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1101/404624

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

Author(s): Gal Horesh, Alyce Taylor-Brown; Stephanie McGimpsey, Florent Lassalle, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Published in: Microbial Genomics, 2021, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000670

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

Author(s): 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
Published in: Lancet Microbe, 2022, ISSN 2666-5247
Publisher: Elsevier
DOI: 10.1016/s2666-5247(21)00236-6

Adaptive Approximate Bayesian Computation Tolerance Selection

Author(s): Umberto Simola; Jessica Cisewski-Kehe; Michael U. Gutmann; Jukka Corander
Published in: Bayesian Analysis, 2021, ISSN 1931-6690
Publisher: Carnegie Mellon University
DOI: 10.1214/20-ba1211

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

Author(s): Arredondo-Alonso, Sergio; Bootsma, Martin; Hein, Yair; Rogers, Malbert R. C.; Corander, Jukka; Willems, Rob J. L.; Schurch, Anita C.
Published in: Bioinformatics, 2020, ISSN 1460-2059
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa233

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Author(s): 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
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: 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.

Author(s): 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
Published in: Genome Research, Issue 27, 2019, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.232629.117

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

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Published in: Microbial Genomics, 2021, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000499

Probabilistic elicitation of expert knowledge through assessment of computer simulations

Author(s): Thomas, Owen; Pesonen, Henri; Corander, Jukka
Published in: 2021
Publisher: arXiv.org
DOI: 10.48550/arxiv.2002.10902

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