Publications by authors named "Jukka Corander"

100Publications

A comprehensive and high-quality collection of genomes and their genes.

Authors:
Gal Horesh Grace A Blackwell Gerry Tonkin-Hill Jukka Corander Eva Heinz Nicholas R Thomson

Microb Genom 2021 Jan 8. Epub 2021 Jan 8.

Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.

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January 2021

A high prevalence of in () and related species in hospital wastewater in South West England.

Authors:
Marjorie J Gibbon Natacha Couto Sophia David Ruth Barden Richard Standerwick Kishore Jagadeesan Hollie Birkwood Punyawee Dulyayangkul Matthew B Avison Andrew Kannan Dan Kibbey Tim Craft Samia Habib Harry A Thorpe Jukka Corander Barbara Kasprzyk-Hordern Edward J Feil

Microb Genom 2021 Jan 8. Epub 2021 Jan 8.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.

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January 2021

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures.

Authors:
Gabrielle L Harrow John A Lees William P Hanage Marc Lipsitch Jukka Corander Caroline Colijn Nicholas J Croucher

ISME J 2021 Jan 6. Epub 2021 Jan 6.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK.

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January 2021

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, .

Authors:
Janetta Top Sergio Arredondo-Alonso Anita C Schürch Santeri Puranen Maiju Pesonen Johan Pensar Rob J L Willems Jukka Corander

Microb Genom 2020 Dec 30;6(12). Epub 2020 Nov 30.

Department of Biostatistics, University of Oslo, 0317 Oslo, Norway.

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December 2020

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.

Authors:
Taj Azarian Pamela P Martinez Brian J Arnold Xueting Qiu Lindsay R Grant Jukka Corander Christophe Fraser Nicholas J Croucher Laura L Hammitt Raymond Reid Mathuram Santosham Robert C Weatherholtz Stephen D Bentley Katherine L O'Brien Marc Lipsitch William P Hanage

PLoS Biol 2020 10 22;18(10):e3000878. Epub 2020 Oct 22.

Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America.

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October 2020

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies.

Authors:
Sara Lado Jean P Elbers Mark F Rogers José Melo-Ferreira Adiya Yadamsuren Jukka Corander Petr Horin Pamela A Burger

BMC Genomics 2020 Sep 3;21(1):606. Epub 2020 Sep 3.

Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.

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September 2020

The binding mechanism of the virulence factor adhesin P subtype to globotetraosylceramide is associated with systemic disease.

Authors:
Miralda Madar Johansson Eva Bélurier Anastassios C Papageorgiou Anders P Sundin Jani Rahkila Teemu Kallonen Ulf J Nilsson Santeri Maatsola Thomas K M Nyholm Jarmo Käpylä Jukka Corander Reko Leino Jukka Finne Susann Teneberg Sauli Haataja

J Biol Chem 2020 Oct 12;295(42):14305-14324. Epub 2020 Aug 12.

Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, Turku, Finland

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October 2020

Producing polished prokaryotic pangenomes with the Panaroo pipeline.

Authors:
Gerry Tonkin-Hill Neil MacAlasdair Christopher Ruis Aaron Weimann Gal Horesh John A Lees Rebecca A Gladstone Stephanie Lo Christopher Beaudoin R Andres Floto Simon D W Frost Jukka Corander Stephen D Bentley Julian Parkhill

Genome Biol 2020 07 22;21(1):180. Epub 2020 Jul 22.

Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.

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July 2020

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

Authors:
John A Lees T Tien Mai Marco Galardini Nicole E Wheeler Samuel T Horsfield Julian Parkhill Jukka Corander

mBio 2020 07 7;11(4). Epub 2020 Jul 7.

Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo, Oslo, Norway.

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July 2020

Genomic signatures of domestication in Old World camels.

Authors:
Robert Rodgers Fitak Elmira Mohandesan Jukka Corander Adiya Yadamsuren Battsetseg Chuluunbat Omer Abdelhadi Abdul Raziq Peter Nagy Chris Walzer Bernard Faye Pamela Anna Burger

Commun Biol 2020 Jun 19;3(1):316. Epub 2020 Jun 19.

Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.

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June 2020

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

Authors:
Sergio Arredondo-Alonso Martin Bootsma Yaïr Hein Malbert R C Rogers Jukka Corander Rob J L Willems Anita C Schürch

Bioinformatics 2020 06;36(12):3874-3876

Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.

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June 2020

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

Authors:
Jan Kokko Ulpu Remes Owen Thomas Henri Pesonen Jukka Corander

Wellcome Open Res 2019 10;4:197. Epub 2019 Dec 10.

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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December 2019

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

Authors:
Priyanka Kachroo Jesus M Eraso Randall J Olsen Luchang Zhu Samantha L Kubiak Layne Pruitt Prasanti Yerramilli Concepcion C Cantu Matthew Ojeda Saavedra Johan Pensar Jukka Corander Leslie Jenkins Lillian Kao Alejandro Granillo Adeline R Porter Frank R DeLeo James M Musser

mBio 2020 02 18;11(1). Epub 2020 Feb 18.

Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA

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February 2020

Designing ecologically optimized pneumococcal vaccines using population genomics.

Authors:
Caroline Colijn Jukka Corander Nicholas J Croucher

Nat Microbiol 2020 03 3;5(3):473-485. Epub 2020 Feb 3.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.

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March 2020

Strain Variability of under NaCl Stress Elucidated by a High-Throughput Microbial Growth Data Assembly and Analysis Protocol.

Authors:
Mariella Aalto-Araneda Anna Pöntinen Maiju Pesonen Jukka Corander Annukka Markkula Taurai Tasara Roger Stephan Hannu Korkeala

Appl Environ Microbiol 2020 03 2;86(6). Epub 2020 Mar 2.

Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.

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March 2020

Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Authors:
Lucy A Weinert Roy R Chaudhuri Jinhong Wang Sarah E Peters Jukka Corander Thibaut Jombart Abiyad Baig Kate J Howell Minna Vehkala Niko Välimäki David Harris Tran Thi Bich Chieu Nguyen Van Vinh Chau James Campbell Constance Schultsz Julian Parkhill Stephen D Bentley Paul R Langford Andrew N Rycroft Brendan W Wren Jeremy Farrar Stephen Baker Ngo Thi Hoa Matthew T G Holden Alexander W Tucker Duncan J Maskell

Nat Commun 2019 Nov 22;10(1):5326. Epub 2019 Nov 22.

Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.

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November 2019

Description of sp. nov. and of sp. nov.

Authors:
Cristina Merla Carla Rodrigues Virginie Passet Marta Corbella Harry A Thorpe Teemu V S Kallonen Zhiyong Zong Piero Marone Claudio Bandi Davide Sassera Jukka Corander Edward J Feil Sylvain Brisse

Front Microbiol 2019 25;10:2360. Epub 2019 Oct 25.

Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France.

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October 2019

Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen.

Authors:
Brian Arnold Mashaal Sohail Crista Wadsworth Jukka Corander William P Hanage Shamil Sunyaev Yonatan H Grad

Mol Biol Evol 2020 02;37(2):417-428

Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA.

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February 2020

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

Authors:
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

Nucleic Acids Res 2019 10;47(18):e112

Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland.

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October 2019

The impact of antimicrobials on gonococcal evolution.

Authors:
Leonor Sánchez-Busó Daniel Golparian Jukka Corander Yonatan H Grad Makoto Ohnishi Rebecca Flemming Julian Parkhill Stephen D Bentley Magnus Unemo Simon R Harris

Nat Microbiol 2019 11 29;4(11):1941-1950. Epub 2019 Jul 29.

Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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November 2019

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species.

Authors:
Ricardo León-Sampedro Rosa Del Campo Mercedes Rodriguez-Baños Val F Lanza María José Pozuelo Carlos Francés-Cuesta Ana P Tedim Ana R Freitas Carla Novais Luísa Peixe Rob J L Willems Jukka Corander Fernando González Candelas Fernando Baquero Teresa M Coque

Environ Microbiol 2019 08 4;21(8):3046-3062. Epub 2019 Jul 4.

Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.

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August 2019

Patterns of cross-resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials.

Authors:
Abigail Colclough Jukka Corander Samuel K Sheppard Sion C Bayliss Michiel Vos

Evol Appl 2019 Jun 28;12(5):878-887. Epub 2019 Jan 28.

European Centre for Environment and Human Health University of Exeter Medical School Cornwall UK.

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June 2019

Fast hierarchical Bayesian analysis of population structure.

Authors:
Gerry Tonkin-Hill John A Lees Stephen D Bentley Simon D W Frost Jukka Corander

Nucleic Acids Res 2019 06;47(11):5539-5549

Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.

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June 2019

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

Authors:
Alan McNally Teemu Kallonen Christopher Connor Khalil Abudahab David M Aanensen Carolyne Horner Sharon J Peacock Julian Parkhill Nicholas J Croucher Jukka Corander

mBio 2019 04 23;10(2). Epub 2019 Apr 23.

Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom

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April 2019

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.

Authors:
Rebecca A Gladstone Stephanie W Lo John A Lees Nicholas J Croucher Andries J van Tonder Jukka Corander Andrew J Page Pekka Marttinen Leon J Bentley Theresa J Ochoa Pak Leung Ho Mignon du Plessis Jennifer E Cornick Brenda Kwambana-Adams Rachel Benisty Susan A Nzenze Shabir A Madhi Paulina A Hawkins Dean B Everett Martin Antonio Ron Dagan Keith P Klugman Anne von Gottberg Lesley McGee Robert F Breiman Stephen D Bentley

EBioMedicine 2019 May 16;43:338-346. Epub 2019 Apr 16.

Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK.

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May 2019

Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary.

Authors:
Jean P Elbers Mark F Rogers Polina L Perelman Anastasia A Proskuryakova Natalia A Serdyukova Warren E Johnson Petr Horin Jukka Corander David Murphy Pamela A Burger

Mol Ecol Resour 2019 Jul 17;19(4):1015-1026. Epub 2019 May 17.

Department of Integrative Biology and Evolution, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.

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July 2019

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

Authors:
Alexander M Wailan Francesc Coll Eva Heinz Gerry Tonkin-Hill Jukka Corander Nicholas A Feasey Nicholas R Thomson

Microb Genom 2019 04 28;5(4). Epub 2019 Mar 28.

1​Parasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.

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April 2019

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

Authors:
Theodore Gouliouris Kathy E Raven Danesh Moradigaravand Catherine Ludden Francesc Coll Beth Blane Plamena Naydenova Carolyne Horner Nicholas M Brown Jukka Corander Direk Limmathurotsakul Julian Parkhill Sharon J Peacock

Genome Res 2019 04 21;29(4):626-634. Epub 2019 Mar 21.

Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom.

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April 2019

Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Lineage Sequence Type 648.

Authors:
Katharina Schaufler Torsten Semmler Lothar H Wieler Darren J Trott Johann Pitout Gisele Peirano Jonas Bonnedahl Monika Dolejska Ivan Literak Stephan Fuchs Niyaz Ahmed Mirjam Grobbel Carmen Torres Alan McNally Derek Pickard Christa Ewers Nicholas J Croucher Jukka Corander Sebastian Guenther

Antimicrob Agents Chemother 2019 06 24;63(6). Epub 2019 May 24.

Institute of Microbiology and Epizootics, Free University Berlin, Berlin, Germany

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June 2019

Correction: Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence.

Authors:
Annemieke Smet Koji Yahara Mirko Rossi Alfred Tay Steffen Backert Armin Ensser James G Fox Bram Flahou Richard Ducatelle Freddy Haesebrouck Jukka Corander

ISME J 2019 Jul;13(7):1890

Department of Biostatistics, University of Oslo, Oslo, Norway.

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July 2019

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

Authors:
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 Corander Dominique A Caugant Shahin Gaini Marita Debess Magnussen Samantha L Kubiak Hoang A T Nguyen S Wesley Long Adeline R Porter Frank R DeLeo James M Musser

Nat Genet 2019 03 18;51(3):548-559. Epub 2019 Feb 18.

Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX, USA.

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March 2019

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

Authors:
Sergio Arredondo-Alonso Malbert R C Rogers Johanna C Braat Tess D Verschuuren Janetta Top Jukka Corander Rob J L Willems Anita C Schürch

Microb Genom 2019 01;5(1)

1​Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.

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January 2019

Fast and flexible bacterial genomic epidemiology with PopPUNK.

Authors:
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

Genome Res 2019 02 24;29(2):304-316. Epub 2019 Jan 24.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.

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February 2019

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

Authors:
John A Lees Marco Galardini Stephen D Bentley Jeffrey N Weiser Jukka Corander

Bioinformatics 2018 12;34(24):4310-4312

Department of Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.

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December 2018

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.

Authors:
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 K Sheppard

Nat Commun 2018 11 28;9(1):5034. Epub 2018 Nov 28.

The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK.

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November 2018

PANINI: Pangenome Neighbour Identification for Bacterial Populations.

Authors:
Khalil Abudahab Joaquín M Prada Zhirong Yang Stephen D Bentley Nicholas J Croucher Jukka Corander David M Aanensen

Microb Genom 2019 04 22;5(4). Epub 2018 Nov 22.

1​Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.

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April 2019

Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.

Authors:
Theodore Gouliouris Kathy E Raven Catherine Ludden Beth Blane Jukka Corander Carolyne S Horner Juan Hernandez-Garcia Paul Wood Nazreen F Hadjirin Milorad Radakovic Mark A Holmes Marcus de Goffau Nicholas M Brown Julian Parkhill Sharon J Peacock

mBio 2018 11 6;9(6). Epub 2018 Nov 6.

Department of Medicine, University of Cambridge, Cambridge, United Kingdom

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November 2018

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

Authors:
Sergio Arredondo-Alonso Malbert R C Rogers Johanna C Braat Tess D Verschuuren Janetta Top Jukka Corander Rob J L Willems Anita C Schürch

Microb Genom 2018 11 1;4(11). Epub 2018 Nov 1.

1​Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.

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November 2018

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

Authors:
Gerry Tonkin-Hill John A Lees Stephen D Bentley Simon D W Frost Jukka Corander

Wellcome Open Res 2018 30;3:93. Epub 2018 Jul 30.

Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.

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July 2018

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

Authors:
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

Nat Ecol Evol 2018 09 23;2(9):1468-1478. Epub 2018 Jul 23.

The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.

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September 2018

Identifying Bacterial Strains from Sequencing Data.

Authors:
Tommi Mäklin Jukka Corander Antti Honkela

Methods Mol Biol 2018 ;1807:1-7

Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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March 2019

The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract.

Authors:
Xiaoxi B Lin Tuo Wang Paul Stothard Jukka Corander Jun Wang John F Baines Sarah C L Knowles Laima Baltrūnaitė Guergana Tasseva Robert Schmaltz Stephanie Tollenaar Liz A Cody Theodore Grenier Wei Wu Amanda E Ramer-Tait Jens Walter

ISME J 2018 11 16;12(11):2770-2784. Epub 2018 Jul 16.

Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada.

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November 2018

Inverse finite-size scaling for high-dimensional significance analysis.

Authors:
Yingying Xu Santeri Puranen Jukka Corander Yoshiyuki Kabashima

Phys Rev E 2018 Jun;97(6-1):062112

Department of Mathematical and Computing Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8552, Japan.

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June 2018

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

Authors:
Annemieke Smet Koji Yahara Mirko Rossi Alfred Tay Steffen Backert Ensser Armin James G Fox Bram Flahou Richard Ducatelle Freddy Haesebrouck Jukka Corander

ISME J 2018 10 25;12(10):2518-2531. Epub 2018 Jun 25.

Department of Biostatistics, University of Oslo, Oslo, Norway.

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October 2018

SuperDCA for genome-wide epistasis analysis.

Authors:
Santeri Puranen Maiju Pesonen Johan Pensar Ying Ying Xu John A Lees Stephen D Bentley Nicholas J Croucher Jukka Corander

Microb Genom 2018 06 29;4(6). Epub 2018 May 29.

5​Department of Biostatistics, University of Oslo, 0317 Oslo, Norway.

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June 2018

The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease.

Authors:
Amelieke J H Cremers Fredrick M Mobegi Christa van der Gaast-de Jongh Michelle van Weert Fred J van Opzeeland Minna Vehkala Mirjam J Knol Hester J Bootsma Niko Välimäki Nicholas J Croucher Jacques F Meis Stephen Bentley Sacha A F T van Hijum Jukka Corander Aldert L Zomer Gerben Ferwerda Marien I de Jonge

Clin Infect Dis 2019 01;68(1):61-69

Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.

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January 2019

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

Authors:
Aleksi Sipola Pekka Marttinen Jukka Corander

Bioinformatics 2018 07;34(13):2308-2310

Department of Mathematics and Statistics, University of Helsinki, Finland.

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July 2018

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

Authors:
Guillaume Méric Alan McNally Alberto Pessia Evangelos Mourkas Ben Pascoe Leonardos Mageiros Minna Vehkala Jukka Corander Samuel K Sheppard

Genome Biol Evol 2018 03;10(3):763-774

Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, United Kingdom.

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March 2018

Kpax3: Bayesian bi-clustering of large sequence datasets.

Authors:
Alberto Pessia Jukka Corander

Bioinformatics 2018 06;34(12):2132-2133

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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June 2018

Weak Epistasis May Drive Adaptation in Recombining Bacteria.

Authors:
Brian J Arnold Michael U Gutmann Yonatan H Grad Samuel K Sheppard Jukka Corander Marc Lipsitch William P Hanage

Genetics 2018 03 12;208(3):1247-1260. Epub 2018 Jan 12.

Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115.

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March 2018

Identification of a Novel Genomic Island Associated with -Type Vancomycin Resistance in Six Dutch Vancomycin-Resistant Enterococcus faecium Isolates.

Authors:
Janetta Top Jan C Sinnige Ellen C Brouwer Guido Werner Jukka Corander Juliëtte A Severin Rogier Jansen E Bathoorn Marc J M Bonten John W A Rossen Rob J L Willems

Antimicrob Agents Chemother 2018 03 23;62(3). Epub 2018 Feb 23.

Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.

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March 2018

Likelihood-free inference via classification.

Authors:
Michael U Gutmann Ritabrata Dutta Samuel Kaski Jukka Corander

Stat Comput 2018 13;28(2):411-425. Epub 2017 Mar 13.

4Department of Biostatistics, University of Oslo, Oslo, Norway.

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March 2017

Disease evolution in mixed connective tissue disease: results from a long-term nationwide prospective cohort study.

Authors:
Silje Reiseter Ragnar Gunnarsson Jukka Corander Joanna Haydon May Brit Lund Trond Mogens Aaløkken Eli Taraldsrud Siri Opsahl Hetlevik Øyvind Molberg

Arthritis Res Ther 2017 12 21;19(1):284. Epub 2017 Dec 21.

Institute of Clinical Medicine, University of Oslo, Postbox 1171, Blindern, 0318, Oslo, Norway.

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December 2017

Phylogeographic separation and formation of sexually discrete lineages in a global population of .

Authors:
Tristan Seecharran Laura Kalin-Manttari Katja Koskela Simo Nikkari Benjamin Dickins Jukka Corander Mikael Skurnik Alan McNally

Microb Genom 2017 10 18;3(10):e000133. Epub 2017 Sep 18.

5​Institute of Microbiology and Infection, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK.

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October 2017

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Authors:
Jukka Corander Christophe Fraser Michael U Gutmann Brian Arnold William P Hanage Stephen D Bentley Marc Lipsitch Nicholas J Croucher

Nat Ecol Evol 2017 Dec 16;1(12):1950-1960. Epub 2017 Oct 16.

MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.

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December 2017

A Bayesian Decision-Support Tool for Child Sexual Abuse Assessment and Investigation.

Authors:
Alessandro Tadei Johan Pensar Jukka Corander Katarina Finnilä Pekka Santtila Jan Antfolk

Sex Abuse 2019 Jun 21;31(4):374-396. Epub 2017 Sep 21.

1 Åbo Akademi University, Turku, Finland.

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June 2019

Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs.

Authors:
Bram Flahou Mirko Rossi Jaco Bakker Jan Am Langermans Edwin Heuvelman Jay V Solnick Miriam E Martin Jani O'Rourke Le Duc Ngoan Nguyen Xuan Hoa Masahiko Nakamura Anders Øverby Hidenori Matsui Hiroyoshi Ota Takehisa Matsumoto Dennis L Foss Laurice A Kopta Oladipo Omotosho Maria Pia Franciosini Patrizia Casagrande Proietti Aizhen Guo Han Liu Gabriela Borilova Ana Paula Bracarense Sara K Lindén Sofie De Bruyckere Guangzhi Zhang Chloë De Witte Annemieke Smet Frank Pasmans Richard Ducatelle Jukka Corander Freddy Haesebrouck

ISME J 2018 01 8;12(1):77-86. Epub 2017 Sep 8.

Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium.

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January 2018

Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels.

Authors:
Elmira Mohandesan Robert R Fitak Jukka Corander Adiya Yadamsuren Battsetseg Chuluunbat Omer Abdelhadi Abdul Raziq Peter Nagy Gabrielle Stalder Chris Walzer Bernard Faye Pamela A Burger

Sci Rep 2017 08 30;7(1):9970. Epub 2017 Aug 30.

Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.

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August 2017

Systematic longitudinal survey of invasive in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.

Authors:
Teemu Kallonen Hayley J Brodrick Simon R Harris Jukka Corander Nicholas M Brown Veronique Martin Sharon J Peacock Julian Parkhill

Genome Res 2017 Jul 18. Epub 2017 Jul 18.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.

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July 2017

Genetic effects on life-history traits in the Glanville fritillary butterfly.

Authors:
Anne Duplouy Swee C Wong Jukka Corander Rainer Lehtonen Ilkka Hanski

PeerJ 2017 25;5:e3371. Epub 2017 May 25.

Department of Biosciences, University of Helsinki, Helsinki, Finland.

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May 2017

Progression and mortality of interstitial lung disease in mixed connective tissue disease: a long-term observational nationwide cohort study.

Authors:
Silje Reiseter Ragnar Gunnarsson Trond Mogens Aaløkken May Brit Lund Georg Mynarek Jukka Corander Joanna Haydon Øyvind Molberg

Rheumatology (Oxford) 2018 02;57(2):255-262

Institute of Clinical Medicine, University of Oslo, Norway.

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February 2018

Bayesian identification of bacterial strains from sequencing data.

Authors:
Aravind Sankar Brandon Malone Sion C Bayliss Ben Pascoe Guillaume Méric Matthew D Hitchings Samuel K Sheppard Edward J Feil Jukka Corander Antti Honkela

Microb Genom 2016 08 25;2(8):e000075. Epub 2016 Aug 25.

1​Helsinki Institute for Information Technology, Department of Computer Science, University of Helsinki, Helsinki, Finland.

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August 2016

Response to 'Refined analyses suggest that recombination is a minor source of genomic diversity in chronic cystic fibrosis infections' by ).

Authors:
Sophie E Darch Alan McNally Jukka Corander Stephen P Diggle

Microb Genom 2016 03 2;2(3):e000054. Epub 2016 Mar 2.

1​School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.

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March 2016

Monomorphic genotypes within a generalist lineage of show signs of global dispersion.

Authors:
Ann-Katrin Llarena Ji Zhang Minna Vehkala Niko Välimäki Marjaana Hakkinen Marja-Liisa Hänninen Mati Roasto Mihkel Mäesaar Eduardo Taboada Dillon Barker Giuliano Garofolo Cesare Cammà Elisabetta Di Giannatale Jukka Corander Mirko Rossi

Microb Genom 2016 10 21;2(10):e000088. Epub 2016 Oct 21.

1​Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.

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October 2016

Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus.

Authors:
Susan Murray Ben Pascoe Guillaume Méric Leonardos Mageiros Koji Yahara Matthew D Hitchings Yasmin Friedmann Thomas S Wilkinson Fraser J Gormley Dietrich Mack James E Bray Sarah Lamble Rory Bowden Keith A Jolley Martin C J Maiden Sarah Wendlandt Stefan Schwarz Jukka Corander J Ross Fitzgerald Samuel K Sheppard

Genome Biol Evol 2017 04;9(4):830-842

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom.

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April 2017

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.

Authors:
Marcin J Skwark Nicholas J Croucher Santeri Puranen Claire Chewapreecha Maiju Pesonen Ying Ying Xu Paul Turner Simon R Harris Stephen B Beres James M Musser Julian Parkhill Stephen D Bentley Erik Aurell Jukka Corander

PLoS Genet 2017 02 16;13(2):e1006508. Epub 2017 Feb 16.

Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.

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February 2017

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

Authors:
Rafal Mostowy Nicholas J Croucher Cheryl P Andam Jukka Corander William P Hanage Pekka Marttinen

Mol Biol Evol 2017 05;34(5):1167-1182

Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland.

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May 2017

Fundamentals and Recent Developments in Approximate Bayesian Computation.

Authors:
Jarno Lintusaari Michael U Gutmann Ritabrata Dutta Samuel Kaski Jukka Corander

Syst Biol 2017 01;66(1):e66-e82

Helsinki Institute for Information Technology HIIT, Espoo, Finland.

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January 2017

Global and regional dissemination and evolution of Burkholderia pseudomallei.

Authors:
Claire Chewapreecha Matthew T G Holden Minna Vehkala Niko Välimäki Zhirong Yang Simon R Harris Alison E Mather Apichai Tuanyok Birgit De Smet Simon Le Hello Chantal Bizet Mark Mayo Vanaporn Wuthiekanun Direk Limmathurotsakul Rattanaphone Phetsouvanh Brian G Spratt Jukka Corander Paul Keim Gordon Dougan David A B Dance Bart J Currie Julian Parkhill Sharon J Peacock

Nat Microbiol 2017 Jan 23;2:16263. Epub 2017 Jan 23.

Department of Medicine, University of Cambridge, CB2 0QQ, UK.

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January 2017

On the inconsistency of ℓ -penalised sparse precision matrix estimation.

Authors:
Otte Heinävaara Janne Leppä-Aho Jukka Corander Antti Honkela

BMC Bioinformatics 2016 Dec 13;17(Suppl 16):448. Epub 2016 Dec 13.

Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland.

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December 2016

Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.

Authors:
Cheryl P Andam Patrick K Mitchell Alanna Callendrello Qiuzhi Chang Jukka Corander Chrispin Chaguza Lesley McGee Bernard W Beall William P Hanage

J Clin Microbiol 2017 04 18;55(4):1104-1115. Epub 2017 Jan 18.

Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA

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April 2017

Understanding pneumococcal serotype 1 biology through population genomic analysis.

Authors:
Chrispin Chaguza Jennifer E Cornick Simon R Harris Cheryl P Andam Laura Bricio-Moreno Marie Yang Feyruz Yalcin Sani Ousmane Shanil Govindpersad Madikay Senghore Chinelo Ebruke Mignon Du Plessis Anmol M Kiran Gerd Pluschke Betuel Sigauque Lesley McGee Keith P Klugman Paul Turner Jukka Corander Julian Parkhill Jean-Marc Collard Martin Antonio Anne von Gottberg Robert S Heyderman Neil French Aras Kadioglu William P Hanage Dean B Everett Stephen D Bentley

BMC Infect Dis 2016 11 8;16(1):649. Epub 2016 Nov 8.

Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK.

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November 2016

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Authors:
Solveig K Sieberts Fan Zhu Javier García-García Eli Stahl Abhishek Pratap Gaurav Pandey Dimitrios Pappas Daniel Aguilar Bernat Anton Jaume Bonet Ridvan Eksi Oriol Fornés Emre Guney Hongdong Li Manuel Alejandro Marín Bharat Panwar Joan Planas-Iglesias Daniel Poglayen Jing Cui Andre O Falcao Christine Suver Bruce Hoff Venkat S K Balagurusamy Donna Dillenberger Elias Chaibub Neto Thea Norman Tero Aittokallio Muhammad Ammad-Ud-Din Chloe-Agathe Azencott Víctor Bellón Valentina Boeva Kerstin Bunte Himanshu Chheda Lu Cheng Jukka Corander Michel Dumontier Anna Goldenberg Peddinti Gopalacharyulu Mohsen Hajiloo Daniel Hidru Alok Jaiswal Samuel Kaski Beyrem Khalfaoui Suleiman Ali Khan Eric R Kramer Pekka Marttinen Aziz M Mezlini Bhuvan Molparia Matti Pirinen Janna Saarela Matthias Samwald Véronique Stoven Hao Tang Jing Tang Ali Torkamani Jean-Phillipe Vert Bo Wang Tao Wang Krister Wennerberg Nathan E Wineinger Guanghua Xiao Yang Xie Rae Yeung Xiaowei Zhan Cheng Zhao Jeff Greenberg Joel Kremer Kaleb Michaud Anne Barton Marieke Coenen Xavier Mariette Corinne Miceli Nancy Shadick Michael Weinblatt Niek de Vries Paul P Tak Danielle Gerlag Tom W J Huizinga Fina Kurreeman Cornelia F Allaart S Louis Bridges Lindsey Criswell Larry Moreland Lars Klareskog Saedis Saevarsdottir Leonid Padyukov Peter K Gregersen Stephen Friend Robert Plenge Gustavo Stolovitzky Baldo Oliva Yuanfang Guan Lara M Mangravite

Nat Commun 2016 10 10;7:13205. Epub 2016 Oct 10.

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October 2016

Identifying Multiple Potential Metabolic Cycles in Time-Series from Biolog Experiments.

Authors:
Mikhail Shubin Katharina Schaufler Karsten Tedin Minna Vehkala Jukka Corander

PLoS One 2016;11(9):e0162276. Epub 2016 Sep 27.

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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September 2016

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.

Authors:
John A Lees Minna Vehkala Niko Välimäki Simon R Harris Claire Chewapreecha Nicholas J Croucher Pekka Marttinen Mark R Davies Andrew C Steer Steven Y C Tong Antti Honkela Julian Parkhill Stephen D Bentley Jukka Corander

Nat Commun 2016 09 16;7:12797. Epub 2016 Sep 16.

Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.

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September 2016

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.

Authors:
Alan McNally Yaara Oren Darren Kelly Ben Pascoe Steven Dunn Tristan Sreecharan Minna Vehkala Niko Välimäki Michael B Prentice Amgad Ashour Oren Avram Tal Pupko Ulrich Dobrindt Ivan Literak Sebastian Guenther Katharina Schaufler Lothar H Wieler Zong Zhiyong Samuel K Sheppard James O McInerney Jukka Corander

PLoS Genet 2016 09 12;12(9):e1006280. Epub 2016 Sep 12.

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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September 2016

What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.

Authors:
Thomas R Connor Sian V Owen Gemma Langridge Steve Connell Satheesh Nair Sandra Reuter Timothy J Dallman Jukka Corander Kristine C Tabing Simon Le Hello Maria Fookes Benoît Doublet Zhemin Zhou Theresa Feltwell Matthew J Ellington Silvia Herrera Matthew Gilmour Axel Cloeckaert Mark Achtman Julian Parkhill John Wain Elizabeth De Pinna François-Xavier Weill Tansy Peters Nick Thomson

mBio 2016 08 23;7(4). Epub 2016 Aug 23.

Wellcome Trust Sanger Institute, Hinxton, United Kingdom London School of Hygiene and Tropical Medicine, London, United Kingdom.

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August 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Authors:
Solveig K Sieberts Fan Zhu Javier García-García Eli Stahl Abhishek Pratap Gaurav Pandey Dimitrios Pappas Daniel Aguilar Bernat Anton Jaume Bonet Ridvan Eksi Oriol Fornés Emre Guney Hongdong Li Manuel Alejandro Marín Bharat Panwar Joan Planas-Iglesias Daniel Poglayen Jing Cui Andre O Falcao Christine Suver Bruce Hoff Venkat S K Balagurusamy Donna Dillenberger Elias Chaibub Neto Thea Norman Tero Aittokallio Muhammad Ammad-Ud-Din Chloe-Agathe Azencott Víctor Bellón Valentina Boeva Kerstin Bunte Himanshu Chheda Lu Cheng Jukka Corander Michel Dumontier Anna Goldenberg Peddinti Gopalacharyulu Mohsen Hajiloo Daniel Hidru Alok Jaiswal Samuel Kaski Beyrem Khalfaoui Suleiman Ali Khan Eric R Kramer Pekka Marttinen Aziz M Mezlini Bhuvan Molparia Matti Pirinen Janna Saarela Matthias Samwald Véronique Stoven Hao Tang Jing Tang Ali Torkamani Jean-Phillipe Vert Bo Wang Tao Wang Krister Wennerberg Nathan E Wineinger Guanghua Xiao Yang Xie Rae Yeung Xiaowei Zhan Cheng Zhao Jeff Greenberg Joel Kremer Kaleb Michaud Anne Barton Marieke Coenen Xavier Mariette Corinne Miceli Nancy Shadick Michael Weinblatt Niek de Vries Paul P Tak Danielle Gerlag Tom W J Huizinga Fina Kurreeman Cornelia F Allaart S Louis Bridges Lindsey Criswell Larry Moreland Lars Klareskog Saedis Saevarsdottir Leonid Padyukov Peter K Gregersen Stephen Friend Robert Plenge Gustavo Stolovitzky Baldo Oliva Yuanfang Guan Lara M Mangravite

Nat Commun 2016 08 23;7:12460. Epub 2016 Aug 23.

Sage Bionetworks, Seattle, Washington 98115, USA.

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August 2016

Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?

Authors:
Ana M Guzman Prieto Willem van Schaik Malbert R C Rogers Teresa M Coque Fernando Baquero Jukka Corander Rob J L Willems

Front Microbiol 2016 26;7:788. Epub 2016 May 26.

Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands.

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June 2016

Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes.

Authors:
Stephen B Beres Priyanka Kachroo Waleed Nasser Randall J Olsen Luchang Zhu Anthony R Flores Ivan de la Riva Jesus Paez-Mayorga Francisco E Jimenez Concepcion Cantu Jaana Vuopio Jari Jalava Karl G Kristinsson Magnus Gottfredsson Jukka Corander Nahuel Fittipaldi Maria Chiara Di Luca Dezemona Petrelli Luca A Vitali Annessa Raiford Leslie Jenkins James M Musser

mBio 2016 05 31;7(3). Epub 2016 May 31.

Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, USA Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA

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May 2016

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

Authors:
David M Aanensen Edward J Feil Matthew T G Holden Janina Dordel Corin A Yeats Artemij Fedosejev Richard Goater Santiago Castillo-Ramírez Jukka Corander Caroline Colijn Monika A Chlebowicz Leo Schouls Max Heck Gerlinde Pluister Raymond Ruimy Gunnar Kahlmeter Jenny Åhman Erika Matuschek Alexander W Friedrich Julian Parkhill Stephen D Bentley Brian G Spratt Hajo Grundmann

mBio 2016 05 5;7(3). Epub 2016 May 5.

Department of Medical Microbiology, University Medical Center Groningen, Rijksuniversteit Groningen, Groningen, The Netherlands Department of Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany

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May 2016

Corrigendum: Climate induces seasonality in pneumococcal transmission.

Authors:
Elina Numminen Claire Chewapreecha Claudia Turner David Goldblatt Francois Nosten Stephen D Bentley Paul Turner Jukka Corander

Sci Rep 2016 Mar 29;6:23307. Epub 2016 Mar 29.

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March 2016

The impact of host metapopulation structure on the population genetics of colonizing bacteria.

Authors:
Elina Numminen Michael Gutmann Mikhail Shubin Pekka Marttinen Guillaume Méric Willem van Schaik Teresa M Coque Fernando Baquero Rob J L Willems Samuel K Sheppard Edward J Feil William P Hanage Jukka Corander

J Theor Biol 2016 May 23;396:53-62. Epub 2016 Feb 23.

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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May 2016

A tribute to Mats Gyllenberg, on the occasion of his 60th birthday.

Authors:
Jukka Corander Odo Diekmann Timo Koski

J Math Biol 2016 Mar;72(4):793-795

Department of Mathematics, KTH Royal Institute of Technology, Stockholm, Sweden.

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March 2016

On the Identifiability of Transmission Dynamic Models for Infectious Diseases.

Authors:
Jarno Lintusaari Michael U Gutmann Samuel Kaski Jukka Corander

Genetics 2016 Mar 6;202(3):911-8. Epub 2016 Jan 6.

Helsinki Institute for Information Technology (HIIT) and Department of Mathematics and Statistics, University of Helsinki, FI-00014 Helsinki, Finland.

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March 2016

Recombination produces coherent bacterial species clusters in both core and accessory genomes.

Authors:
Pekka Marttinen Nicholas J Croucher Michael U Gutmann Jukka Corander William P Hanage

Microb Genom 2015 Nov 5;1(5):e000038. Epub 2015 Nov 5.

Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA.

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November 2015

Recombination-mediated remodelling of host-pathogen interactions during niche adaptation.

Authors:
Laura E Spoor Emily Richardson Amy C Richards Gillian J Wilson Chriselle Mendonca Ravi Kr Gupta Paul R McAdam Stephen Nutbeam-Tuffs Nikki S Black James P O'Gara Chia Y Lee Jukka Corander J Ross Fitzgerald

Microb Genom 2015 Oct 30;1(4):e000036. Epub 2015 Oct 30.

The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK.

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October 2015

Genetic import and phenotype specific alleles associated with hyper-invasion in Campylobacter jejuni.

Authors:
Abiyad Baig Alan McNally Steven Dunn Konrad H Paszkiewicz Jukka Corander Georgina Manning

BMC Genomics 2015 Oct 24;16:852. Epub 2015 Oct 24.

School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.

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October 2015

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Authors:
David Koslicki Saikat Chatterjee Damon Shahrivar Alan W Walker Suzanna C Francis Louise J Fraser Mikko Vehkaperä Yueheng Lan Jukka Corander

PLoS One 2015 23;10(10):e0140644. Epub 2015 Oct 23.

Dept of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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June 2016

Directional gene flow and ecological separation in .

Authors:
Sandra Reuter Jukka Corander Mark de Been Simon Harris Lu Cheng Miquette Hall Nicholas R Thomson Alan McNally

Microb Genom 2015 Sep 29;1(3):e000030. Epub 2015 Sep 29.

Pathogen Research Group, Nottingham Trent University, Nottingham NG11 8NS, UK.

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September 2015

Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.

Authors:
Mark de Been Mette Pinholt Janetta Top Stefan Bletz Alexander Mellmann Willem van Schaik Ellen Brouwer Malbert Rogers Yvette Kraat Marc Bonten Jukka Corander Henrik Westh Dag Harmsen Rob J L Willems

J Clin Microbiol 2015 Dec;53(12):3788-97

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December 2015

A Bayesian Predictive Model for Clustering Data of Mixed Discrete and Continuous Type.

Authors:
Paul Blomstedt Jing Tang Jie Xiong Christian Granlund Jukka Corander

IEEE Trans Pattern Anal Mach Intell 2015 Mar;37(3):489-98

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March 2015

The de novo genome assembly and annotation of a female domestic dromedary of North African origin.

Authors:
Robert R Fitak Elmira Mohandesan Jukka Corander Pamela A Burger

Mol Ecol Resour 2016 Jan 24;16(1):314-24. Epub 2015 Jul 24.

Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna, 1210, Austria.

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January 2016

K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets.

Authors:
Alberto Pessia Yonatan Grad Sarah Cobey Juha Santeri Puranen Jukka Corander

Microb Genom 2015 Jul 15;1(1):e000025. Epub 2015 Jul 15.

Department of Mathematics and Statistics, University of Helsinki, Finland.

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July 2015

Climate induces seasonality in pneumococcal transmission.

Authors:
Elina Numminen Claire Chewapreecha Claudia Turner David Goldblatt Francois Nosten Stephen D Bentley Paul Turner Jukka Corander

Sci Rep 2015 Jun 12;5:11344. Epub 2015 Jun 12.

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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June 2015

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Authors:
Lucy A Weinert Roy R Chaudhuri Jinhong Wang Sarah E Peters Jukka Corander Thibaut Jombart Abiyad Baig Kate J Howell Minna Vehkala Niko Välimäki David Harris Tran Thi Bich Chieu Nguyen Van Vinh Chau James Campbell Constance Schultsz Julian Parkhill Stephen D Bentley Paul R Langford Andrew N Rycroft Brendan W Wren Jeremy Farrar Stephen Baker Ngo Thi Hoa Matthew T G Holden Alexander W Tucker Duncan J Maskell

Nat Commun 2015 May 12;6:7272. Epub 2015 May 12.

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May 2015

Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.

Authors:
Guillaume Méric Maria Miragaia Mark de Been Koji Yahara Ben Pascoe Leonardos Mageiros Jane Mikhail Llinos G Harris Thomas S Wilkinson Joana Rolo Sarah Lamble James E Bray Keith A Jolley William P Hanage Rory Bowden Martin C J Maiden Dietrich Mack Hermínia de Lencastre Edward J Feil Jukka Corander Samuel K Sheppard

Genome Biol Evol 2015 Apr 16;7(5):1313-28. Epub 2015 Apr 16.

College of Medicine, Institute of Life Science, Swansea University, United Kingdom MRC CLIMB Consortium, Institute of Life Science, Swansea University, United Kingdom

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April 2015

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Authors:
Lucy A Weinert Roy R Chaudhuri Jinhong Wang Sarah E Peters Jukka Corander Thibaut Jombart Abiyad Baig Kate J Howell Minna Vehkala Niko Välimäki David Harris Tran Thi Bich Chieu Nguyen Van Vinh Chau James Campbell Constance Schultsz Julian Parkhill Stephen D Bentley Paul R Langford Andrew N Rycroft Brendan W Wren Jeremy Farrar Stephen Baker Ngo Thi Hoa Matthew T G Holden Alexander W Tucker Duncan J Maskell

Nat Commun 2015 Mar 31;6:6740. Epub 2015 Mar 31.

Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.

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March 2015

Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex.

Authors:
Laura Morley Alan McNally Konrad Paszkiewicz Jukka Corander Guillaume Méric Samuel K Sheppard Jochen Blom Georgina Manning

Appl Environ Microbiol 2015 Jun 20;81(11):3641-7. Epub 2015 Mar 20.

Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom

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June 2015

Novel R pipeline for analyzing Biolog Phenotypic MicroArray data.

Authors:
Minna Vehkala Mikhail Shubin Thomas R Connor Nicholas R Thomson Jukka Corander

PLoS One 2015 18;10(3):e0118392. Epub 2015 Mar 18.

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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February 2016