Publications by authors named "Jukka Corander"

100Publications

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

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

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

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

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.

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.

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

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

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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

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

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.

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

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

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.

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

Fast and flexible bacterial genomic epidemiology with PopPUNK.

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.

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

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

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December 2018

PANINI: Pangenome Neighbour Identification for Bacterial Populations.

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

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

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.

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

Identifying Bacterial Strains from Sequencing Data.

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

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

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

SuperDCA for genome-wide epistasis analysis.

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

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

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

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

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July 2018

Kpax3: Bayesian bi-clustering of large sequence datasets.

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.

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

Likelihood-free inference via classification.

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

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

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.

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

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

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

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

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May 2017

Bayesian identification of bacterial strains from sequencing data.

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 ).

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

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

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.

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

Helsinki Institute for Information Technology HIIT, Espoo, Finland.

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January 2017

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

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.

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

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

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.

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

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

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?

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.

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

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

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.

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.

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

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

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

Directional gene flow and ecological separation in .

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

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

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.

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.

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

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

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.

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