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Scalable inference algorithms for Bayesian evolutionary epidemiology

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Publications

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
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
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
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
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
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

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
DOI: 10.1038/s41524-019-0175-2