Jukka Corander

• van Hal, Sebastiaan J; Willems, Rob J L; Gouliouris, Theodore; Ballard, Susan A; Coque, Teresa M & Hammerum, Anette M [Vis alle 16 forfattere av denne artikkelen] (2022). The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis. Lancet Microbe. ISSN 2666-5247. 3(2), s. e133–e141. doi: 10.1016/S2666-5247%2821%2900236-6.
• Mallawaarachchi, Sudaraka; Tonkin-Hill, Gerry; Croucher, Nicholas J.; Turner, Paul; Speed, Doug & Corander, Jukka [Vis alle 7 forfattere av denne artikkelen] (2022). Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae. NAR Genomics and Bioinformatics. ISSN 2631-9268. 4(1). doi: 10.1093/nargab/lqac011.
• Corander, Jukka; Remes, Ulpu Maria Vilhelmiina & Koski, Timo (2021). On the Jensen-Shannon divergence and the variation distance for categorical probability distributions. Kybernetika (Praha). ISSN 0023-5954. 57(6), s. 879–907. doi: 10.14736/kyb-2021-6-0879.
• Gladstone, Rebecca Ashley; Siira, Lotta; Brynildsrud, Ola Brønstad; Vestrheim, Didrik Frimann; Turner, Paul & Clarke, S.C. [Vis alle 21 forfattere av denne artikkelen] (2021). International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease. Vaccine. ISSN 0264-410X. 40(7), s. 1054–1060. doi: 10.1016/j.vaccine.2021.10.046. Fulltekst i vitenarkiv Vis sammendrag

  Background: Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them. Methods: Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating. Results: Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017. Conclusion: The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

• Mäklin, Tommi; Kallonen, Teemu; David, Sophia; Boinett, Christine J.; Pascoe, Ben & Meric, Guillaume [Vis alle 13 forfattere av denne artikkelen] (2021). High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review: 1 approved, 1 approved with reservations]. Wellcome Open Research. ISSN 2398-502X. 5(14). doi: 10.12688/WELLCOMEOPENRES.15639.2. Fulltekst i vitenarkiv
• Biffignandi, Gherard Batisti; Gibbon, Marjorie J.; Corbella, Marta; Thorpe, Harry Arthur Frank Wright; Merla, Cristina & Castelli, Michele [Vis alle 13 forfattere av denne artikkelen] (2021). Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae. G3: Genes, Genomes, Genetics. ISSN 2160-1836. 11(2). doi: 10.1093/g3journal/jkab019. Fulltekst i vitenarkiv
• Horesh, Gal; Blackwell, Grace A.; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva & Thomson, Nicholas R. (2021). A comprehensive and high-quality collection of escherichia coli genomes and their genes. Microbial Genomics. ISSN 2057-5858. 7(2), s. 1–15. doi: 10.1099/mgen.0.000499. Fulltekst i vitenarkiv
• Wee, Bryan A.; Alves, Joana; Lindsay, Diane S. J.; Klatt, Ann-Brit; Sargison, Fiona A. & Cameron, Ross L. [Vis alle 13 forfattere av denne artikkelen] (2021). Population analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing. Nature Communications. ISSN 2041-1723. 12(1). doi: 10.1038/s41467-021-27478-z. Fulltekst i vitenarkiv
• Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka & Heinz, Eva [Vis alle 7 forfattere av denne artikkelen] (2021). Different evolutionary trends form the twilight zone of the bacterial pan-genome. Microbial Genomics. ISSN 2057-5858. 7(9). doi: 10.1099/MGEN.0.000670. Fulltekst i vitenarkiv
• Gibbon, Marjorie J.; Couto, Natacha; David, Sophia; Barden, Ruth; Standerwick, Richard & Jagadeesan, Kishore Kumar [Vis alle 17 forfattere av denne artikkelen] (2021). A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England. Microbial Genomics. ISSN 2057-5858. 7(3). doi: 10.1099/mgen.0.000509. Fulltekst i vitenarkiv
• Kantele, Anu; Kuenzli, Esther; Dunn, Steven; Dance, David A.B.; Newton, Paul N. & Davong, Viengmon [Vis alle 14 forfattere av denne artikkelen] (2021). Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study. Lancet Microbe. ISSN 2666-5247. 2(4), s. e151–e158. doi: 10.1016/S2666-5247%2820%2930224-X. Fulltekst i vitenarkiv
• Alonso, Sergio Arredondo; Pöntinen, Anna Kaarina; Cleon, Francois Pierre Alexandre; Gladstone, Rebecca Ashley; Schürch, Anita C. & Johnsen, Pål Jarle [Vis alle 8 forfattere av denne artikkelen] (2021). A high-throughput multiplexing and selection strategy to complete bacterial genomes. GigaScience. ISSN 2047-217X. 10(12), s. 1–13. doi: 10.1093/gigascience/giab079. Fulltekst i vitenarkiv
• Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin & Mäkinen, Veli [Vis alle 9 forfattere av denne artikkelen] (2021). Bacterial genomic epidemiology with mixed samples. Microbial Genomics. ISSN 2057-5858. 7(11), s. 1–18. doi: 10.1099/MGEN.0.000691. Fulltekst i vitenarkiv
• Chewapreecha, Claire; Pensar, Johan; Chattagul, Supaksorn; Pesonen, Maiju; Sangphukieo, Apiwat & Boonklang, Phumrapee [Vis alle 18 forfattere av denne artikkelen] (2021). Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 39(1). doi: 10.1093/molbev/msab306. Fulltekst i vitenarkiv
• Suotsalo, Kimmo; Xu, Yingying; Corander, Jukka & Pensar, Johan (2021). High-dimensional structure learning of sparse vector autoregressive models using fractional marginal pseudo-likelihood. Statistics and computing. ISSN 0960-3174. 31(73). doi: 10.1007/s11222-021-10049-z. Fulltekst i vitenarkiv
• Pöntinen, Anna Kaarina; Top, Janetta; Alonso, Sergio Arredondo; Tonkin-Hill, Gerry; Freitas, Ana R. & Novais, Carla [Vis alle 21 forfattere av denne artikkelen] (2021). Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nature Communications. ISSN 2041-1723. 12. doi: 10.1038/s41467-021-21749-5. Fulltekst i vitenarkiv
• Calland, Jessica K.; Pascoe, Ben; Bayliss, Sion; Mourkas, Evangelos; Berthenet, Elvire & Thorpe, Harry Arthur Frank Wright [Vis alle 12 forfattere av denne artikkelen] (2021). Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genetics. ISSN 1553-7390. 17(9). doi: 10.1371/journal.pgen.1009829. Fulltekst i vitenarkiv
• MacAlasdair, Neil; Pesonen, Maiju; Brynildsrud, Ola Brønstad; Eldholm, Vegard; Kristiansen, Paul Arne & Corander, Jukka [Vis alle 8 forfattere av denne artikkelen] (2021). The effect of recombination on the evolution of a population of Neisseria meningitidis. Genome Research. ISSN 1088-9051. 31(7), s. 1258–1268. doi: 10.1101/gr.264465.120. Fulltekst i vitenarkiv
• Mageiros, Leonardos; Meric, Guillaume; Bayliss, Sion; Pensar, Johan; Pascoe, Ben & Mourkas, Evangelos [Vis alle 19 forfattere av denne artikkelen] (2021). Genome evolution and the emergence of pathogenicity in avian Escherichia coli. Nature Communications. ISSN 2041-1723. 12(1). doi: 10.1038/s41467-021-20988-w. Fulltekst i vitenarkiv
• van Hal, Sebastiaan J.; Willems, Rob J.L.; Gouliouris, Theodore; Ballard, Susan A.; Coque, Teresa M. & Hammerum, Anette M. [Vis alle 21 forfattere av denne artikkelen] (2021). The global dissemination of hospital clones of Enterococcus faecium. Genome Medicine. ISSN 1756-994X. 13(52). doi: 10.1186/s13073-021-00868-0. Fulltekst i vitenarkiv
• Gladstone, Rebecca Ashley; McNally, Alan; Pöntinen, Anna Kaarina; Tonkin-Hill, Gerry; Lees, John A. & Skytén, Kusti Onni [Vis alle 29 forfattere av denne artikkelen] (2021). Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study. Lancet Microbe. ISSN 2666-5247. 2(7), s. e331–e341. doi: 10.1016/S2666-5247%2821%2900031-8. Fulltekst i vitenarkiv
• Alonso, Sergio Arredondo; Top, Janetta; Corander, Jukka; Willems, Rob J. L. & Schürch, Anita C. (2021). Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals. Genome Medicine. ISSN 1756-994X. 13(1), s. 1–18. doi: 10.1186/s13073-020-00825-3. Fulltekst i vitenarkiv
• Mai, The Tien; Turner, Paul & Corander, Jukka (2021). Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting. BMC Bioinformatics. ISSN 1471-2105. 22(1). doi: 10.1186/s12859-021-04079-7. Fulltekst i vitenarkiv
• Harrow, Gabrielle L.; Lees, John A.; Hanage, William P.; Lipsitch, Marc; Corander, Jukka & Colijn, Caroline [Vis alle 7 forfattere av denne artikkelen] (2021). Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. The ISME Journal. ISSN 1751-7362. 15, s. 1523–1538. doi: 10.1038/s41396-020-00867-w. Fulltekst i vitenarkiv
• Aalto-Araneda, Mariella; Pöntinen, Anna; Pesonen, Maiju; Corander, Jukka; Markkula, Annukka & Tasara, Taurai [Vis alle 8 forfattere av denne artikkelen] (2020). Strain Variability of Listeria monocytogenes under NaCl Stress Elucidated by a High-Throughput Microbial Growth Data Assembly and Analysis Protocol. Applied and Environmental Microbiology. ISSN 0099-2240. 86(6). doi: 10.1128/AEM.02378-19.
• Top, Janetta; Arredondo-Alonso, Sergio; Schürch, Anita C.; Puranen, Santeri; Pesonen, Maiju & Pensar, Johan [Vis alle 8 forfattere av denne artikkelen] (2020). Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium. Microbial Genomics. ISSN 2057-5858. 6(12), s. 1–8. doi: 10.1099/mgen.0.000488. Fulltekst i vitenarkiv
• Tonkin-Hill, Gerry; MacAlasdair, Neil; Ruis, Christopher; Weimann, Aaron; Horesh, Gal & Lees, John A. [Vis alle 14 forfattere av denne artikkelen] (2020). Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biology. ISSN 1465-6906. 21, s. 1–21. doi: 10.1186/s13059-020-02090-4. Fulltekst i vitenarkiv
• Azarian, Taj; Martinez, Pamela P.; Arnold, Brian; Qiu, Xueting; Grant, Lindsay R. & Corander, Jukka [Vis alle 16 forfattere av denne artikkelen] (2020). Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biology. ISSN 1544-9173. 18(10). doi: 10.1371/journal.pbio.3000878. Fulltekst i vitenarkiv
• Arredondo-Alonso, Sergio; Top, Janetta; McNally, Alan; Puranen, Santeri; Pesonen, Maiju & Pensar, Johan [Vis alle 14 forfattere av denne artikkelen] (2020). Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium. mBio. ISSN 2161-2129. 11(1). doi: 10.1128/mBio.03284-19. Fulltekst i vitenarkiv
• Colijn, Caroline; Corander, Jukka & Croucher, Nicholas J. (2020). Designing ecologically optimized pneumococcal vaccines using population genomics. Nature Microbiology. ISSN 2058-5276. 5(3), s. 473–485. doi: 10.1038/s41564-019-0651-y.
• Arnold, Brian; Sohail, Mashaal; Wadsworth, Crista; Corander, Jukka; Hanage, William P. & Sunyaev, Shamil R. [Vis alle 7 forfattere av denne artikkelen] (2020). Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 37(2), s. 417–428. doi: 10.1093/molbev/msz225.
• Pensar, Johan; Xu, Yingying; Puranen, Juha Santeri; Pesonen, Maiju; Kabashima, Yoshiyuki & Corander, Jukka (2020). High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study. Computational Statistics & Data Analysis. ISSN 0167-9473. 141, s. 62–76. doi: 10.1016/j.csda.2019.06.012. Fulltekst i vitenarkiv
• Schaufler, Katharina; Semmler, Torsten; Wieler, Lothar H.; Trott, Darren J.; Pitout, Johann & Peirano, Gisele [Vis alle 19 forfattere av denne artikkelen] (2019). Genomic and functional analysis of emerging virulent and multidrug-resistant Escherichia coli lineage sequence type 648. Antimicrobial Agents and Chemotherapy. ISSN 0066-4804. 63:e00243-19(6), s. 1–12. doi: 10.1128/AAC.00243-19.
• Elbers, Jean P; Rogers, Mark F; Perelman, Polina L; Proskuryakova, Anastasia A; Serdyukova, Natalia A & Johnson, Warren E. [Vis alle 10 forfattere av denne artikkelen] (2019). Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary. Molecular Ecology Resources. ISSN 1755-098X. 19(4), s. 1015–1026. doi: 10.1111/1755-0998.13020. Fulltekst i vitenarkiv
• Léon-Sampedro, Ricardo; del Campo, Rosa; Rodriguez-Baños, Mercedes; Lanza, Val F.; Pozuelo, María José & Francés-Cuesta, Carlos [Vis alle 15 forfattere av denne artikkelen] (2019). Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environmental Microbiology. ISSN 1462-2912. 21(8), s. 3046–3062. doi: 10.1111/1462-2920.14702.
• Lintusaari, Jarno; Blomstedt, Paul; Rose, Brittany; Sivula, Tuomas; Gutmann, Michael U. & Kaski, Samuel [Vis alle 7 forfattere av denne artikkelen] (2019). Resolving outbreak dynamics using approximate bayesian computation for stochastic birth-death models. Wellcome Open Research. ISSN 2398-502X. 4(14). doi: 10.12688/wellcomeopenres.15048.2. Fulltekst i vitenarkiv
• Pensar, Johan; Puranen, Santeri; Arnold, Brian; MacAlasdair, Neil; Kuronen, Juri & Tonkin-Hill, Gerry [Vis alle 17 forfattere av denne artikkelen] (2019). Genome-wide epistasis and co-selection study using mutual information. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(18), s. 1–14. doi: 10.1093/nar/gkz656. Fulltekst i vitenarkiv
• Merla, Cristina; Rodrigues, Carla; Passet, Virginie; Corbella, Marta; Thorpe, Harry A & Kallonen, Teemu [Vis alle 13 forfattere av denne artikkelen] (2019). Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov. Frontiers in Microbiology. ISSN 1664-302X. 10(2360), s. 1–9. doi: 10.3389/fmicb.2019.02360. Fulltekst i vitenarkiv
• Tonkin-Hill, Gerry; Lees, John A; Bentley, Stephen D; Frost, Simon DW & Corander, Jukka (2019). Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(11), s. 5539–5549. doi: 10.1093/nar/gkz361. Fulltekst i vitenarkiv
• Sanchez-Buso, Leonor; Golparian, Daniel; Corander, Jukka; Grad, Yonatan H.; Ohnishi, Makoto & Flemming, Rebecca [Vis alle 10 forfattere av denne artikkelen] (2019). The impact of antimicrobials on gonococcal evolution. Nature Microbiology. ISSN 2058-5276. doi: 10.1038/s41564-019-0501-y.
• Lu, Yao; Corander, Jukka & Yang, Zhirong (2019). Doubly Stochastic Neighbor Embedding on Spheres. Pattern Recognition Letters. ISSN 0167-8655. 128, s. 100–106. doi: 10.1016/j.patrec.2019.08.026. Fulltekst i vitenarkiv
• Chiner-Oms, Álvaro; Sanchez-Buso, Leonor; Corander, Jukka; Gagneux, Sébastien; Harris, Simon R & Young, D [Vis alle 8 forfattere av denne artikkelen] (2019). Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. Science Advances. ISSN 2375-2548. 5(6). doi: 10.1126/sciadv.aaw3307. Fulltekst i vitenarkiv
• Corander, Jukka; Hyttinen, Antti; Kontinen, Juha; Pensar, Johan & Väänänen, Jouko (2019). A logical approach to context-specific independence. Annals of Pure and Applied Logic. ISSN 0168-0072. 170(9), s. 975–992. doi: 10.1016/j.apal.2019.04.004.
• Gladstone, Rebecca A; Lo, Stephanie W; Lees, John A; Croucher, Nicholas J.; van Tonder, Andries J. & Corander, Jukka [Vis alle 26 forfattere av denne artikkelen] (2019). International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine. ISSN 2352-3964. 43, s. 338–346. doi: 10.1016/j.ebiom.2019.04.021. Fulltekst i vitenarkiv
• Gouliouris, Theodore; Raven, Kathy E; Moradigaravand, Danesh; Ludden, Catherine; Coll, Francesc & Blane, Beth [Vis alle 13 forfattere av denne artikkelen] (2019). Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment. Genome Research. ISSN 1088-9051. 29(4), s. 626–634. doi: 10.1101/gr.232629.117. Fulltekst i vitenarkiv
• Cremers, Amelieke J. H.; Mobegi, Fredrick M.; Van Der Gaast-De Jongh, Christa; Van Weert, Michelle; Van Opzeeland, Fred J. & Vehkala, Minna [Vis alle 17 forfattere av denne artikkelen] (2019). The contribution of genetic variation of streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease. Clinical Infectious Diseases. ISSN 1058-4838. 68(1), s. 61–69. doi: 10.1093/cid/ciy417.
• Lees, John A; Harris, Simon R; Tonkin-Hill, Gerry; Gladstone, Rebecca A; Lo, Stephanie W & Weiser, Jeffrey N [Vis alle 9 forfattere av denne artikkelen] (2019). Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Research. ISSN 1088-9051. 29(2), s. 304–316. doi: 10.1101/gr.241455.118. Fulltekst i vitenarkiv
• McNally, Alan; Kallonen, Teemu; Connor, Christopher; Abudahab, Khalil; Aanensen, David M. & Horner, Carolyne S [Vis alle 10 forfattere av denne artikkelen] (2019). Diversification of colonization factors in a multidrug-resistant escherichia coli lineage evolving under negative frequency- dependent selection. mBio. ISSN 2161-2129. 10(2). doi: 10.1128/mBio.00644-19. Fulltekst i vitenarkiv
• Wailan, Alexander M.; Coll, Francesc; Heinz, Eva; Tonkin-Hill, Gerry; Corander, Jukka & Feasey, Nicholas A. [Vis alle 7 forfattere av denne artikkelen] (2019). rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. Microbial Genomics. ISSN 2057-5858. 5(4). doi: 10.1099/mgen.0.000264. Fulltekst i vitenarkiv
• Colclough, Abigail; Corander, Jukka; Sheppard, Samuel K.; Bayliss, S. C. & Vos, Michiel (2019). Patterns of cross-resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials. Evolutionary Applications. ISSN 1752-4571. 12(5), s. 878–887. doi: 10.1111/eva.12762. Fulltekst i vitenarkiv
• Tadei, Alessandro; Pensar, Johan; Corander, Jukka; Finnilä, Katarina; Santtila, Pekka & Antfolk, Jan (2019). A Bayesian Decision-Support Tool for Child Sexual Abuse Assessment and Investigation. Sexual abuse. A Journal of Research and Treatment. ISSN 1079-0632. 31(4), s. 374–396. doi: 10.1177/1079063217732791.
• Todorovic, Milica; Gutmann, Michael U.; Corander, Jukka & Rinke, Patrick (2019). Bayesian inference of atomistic structure in functional materials. npj Computational Materials. ISSN 2057-3960. 5(1). doi: 10.1038/s41524-019-0175-2. Fulltekst i vitenarkiv
• Kachroo, Priyanka; Eraso, Jesus M.; Beres, Stephen B.; Olsen, Randall J.; Zhu, Luchang & Nasser, Waleed [Vis alle 31 forfattere av denne artikkelen] (2019). Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis. Nature Genetics. ISSN 1061-4036. 51(3), s. 548–559. doi: 10.1038/s41588-018-0343-1.
• Abudahab, Khalil; Prada, Joaquín; Yang, Zhirong; Bentley, Stephen; Croucher, Nicholas & Corander, Jukka [Vis alle 7 forfattere av denne artikkelen] (2019). PANINI: Pangenome Neighbour Identification for Bacterial Populations. Microbial Genomics. ISSN 2057-5858. 5(4). doi: 10.1099/mgen.0.000220. Fulltekst i vitenarkiv
• Tonkin-Hill, Gerry; Lees, John A.; Bentley, Stephen D.; Frost, Simon D. W. & Corander, Jukka (2018). RhierBAPs: An R implementation of the population clustering algorithm hierbaps [version 1; referees: 2 approved]. Wellcome Open Research. ISSN 2398-502X. 3, s. 1–10. doi: 10.12688/wellcomeopenres.14694.1.
• Puranen, Santeri; Pesonen, Maiju; Pensar, Johan; Xu, Ying Ying; Lees, John A. & Bentley, Stephen D. [Vis alle 8 forfattere av denne artikkelen] (2018). SuperDCA for genome-wide epistasis analysis. Microbial Genomics. ISSN 2057-5858. 4(6), s. 1–12. doi: 10.1099/mgen.0.000184.
• Meric, Guillaume; Mageiros, Leonardos; Pensar, Johan; Laabei, Maisem; Yahara, Koji & Pascoe, Ben [Vis alle 25 forfattere av denne artikkelen] (2018). Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nature Communications. ISSN 2041-1723. 9(1). doi: 10.1038/s41467-018-07368-7. Fulltekst i vitenarkiv
• Arredondo-Alonso, Sergio; Rogers, Malbert R.C.; Braat, Johanna C.; Verschuuren, Tess D.; Top, Janetta & Corander, Jukka [Vis alle 8 forfattere av denne artikkelen] (2018). mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microbial Genomics. ISSN 2057-5858. 4(11), s. 1–15. doi: 10.1099/mgen.0.000224. Fulltekst i vitenarkiv
• Lees, John A; Galardini, Marco; Bentley, Stephen D; Weiser, Jeffrey N & Corander, Jukka (2018). pyseer: a comprehensive tool for microbial pangenome-wide association studies. Bioinformatics. ISSN 1367-4803. 34(24), s. 4310–4312. doi: 10.1093/bioinformatics/bty539. Fulltekst i vitenarkiv
• Top, Janetta; Sinnige, Jan C.; Brouwer, Ellen C.; Werner, Guido; Corander, Jukka & Severin, Juliëtte A. [Vis alle 11 forfattere av denne artikkelen] (2018). Identification of a novel genomic island associated with vand-type vancomycin resistance in six Dutch vancomycin-resistant enterococcus faecium isolates. Antimicrobial Agents and Chemotherapy. ISSN 0066-4804. 62:e01793(3), s. 1–7. doi: 10.1128/AAC.01793-17.
• Richardson, Emily J; Bacigalupe, Rodrigo; Harrison, Ewan M; Weinert, Lucy A.; Lycett, Samantha & Vrieling, Manouk [Vis alle 20 forfattere av denne artikkelen] (2018). Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nature Ecology and Evolution. ISSN 2397-334X. 2(9), s. 1468–1478. doi: 10.1038/s41559-018-0617-0. Fulltekst i vitenarkiv
• Flahou, Bram; Rossi, Mirko; Bakker, Jaco; Langermans, Jan AM; Heuvelman, Edwin & Solnick, Jay V [Vis alle 33 forfattere av denne artikkelen] (2018). Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs. The ISME Journal. ISSN 1751-7362. 12(1), s. 77–86. doi: 10.1038/ismej.2017.145.
• Gouliouris, Theodore; Raven, Kathy E; Ludden, Catherine; Blane, Beth; Corander, Jukka & Horner, Carolyne S [Vis alle 15 forfattere av denne artikkelen] (2018). Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom. mBio. ISSN 2161-2129. 9(6). doi: 10.1128/mBio.01780-18. Fulltekst i vitenarkiv
• Lin, Xiaoxi B.; Wang, Tuo; Stothard, Paul; Corander, Jukka; Wang, Jun & Baines, John F. [Vis alle 16 forfattere av denne artikkelen] (2018). The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract. The ISME Journal. ISSN 1751-7362. 12(11), s. 2770–2784. doi: 10.1038/s41396-018-0211-0.
• Arnold, Brian; Gutmann, Michael U.; Grad, Yonatan H.; Sheppard, Samuel K.; Corander, Jukka & Lipsitch, Marc [Vis alle 7 forfattere av denne artikkelen] (2018). Weak epistasis may drive adaptation in recombining bacteria. Genetics. ISSN 0016-6731. 208(3), s. 1247–1260. doi: 10.1534/genetics.117.300662. Fulltekst i vitenarkiv
• Lintusaari, Jarno; Vuollekoski, Henri; Kangasraasio, Antti; Skyten, Kusti; Jarvenpaa, Marko & Marttinen, Pekka [Vis alle 10 forfattere av denne artikkelen] (2018). ELFI: Engine for Likelihood-Free Inference . Journal of machine learning research. ISSN 1532-4435. 19(16), s. 1–7. Fulltekst i vitenarkiv
• Pessia, Alberto & Corander, Jukka (2018). Kpax3: Bayesian bi-clustering of large sequence datasets. Bioinformatics. ISSN 1367-4803. 34(12), s. 2132–2133. doi: 10.1093/bioinformatics/bty056. Fulltekst i vitenarkiv
• Meric, Guillaume; McNally, Alan; Pessia, Alberto; Mourkas, Evangelos; Pascoe, Ben & Mageiros, Leonardos [Vis alle 9 forfattere av denne artikkelen] (2018). Convergent amino acid signatures in polyphyletic campylobacter jejuni subpopulations suggest human niche tropism. Genome Biology and Evolution (GBE). ISSN 1759-6653. 10(3), s. 763–774. doi: 10.1093/gbe/evy026. Fulltekst i vitenarkiv
• Pensar, Johan; Kohonen, J & Corander, Jukka (2018). Exact Bayesian learning of Partition Directed Acyclic Graphs. Journal of Physics: Conference Series (JPCS). ISSN 1742-6588. 1036(1), s. 1–12. doi: 10.1088/1742-6596/1036/1/012017. Fulltekst i vitenarkiv
• Sipola, Aleksi; Marttinen, Pekka & Corander, Jukka (2018). Bacmeta: simulator for genomic evolution in bacterial metapopulations . Bioinformatics. ISSN 1367-4803. 34(13), s. 2308–2310. doi: 10.1093/bioinformatics/bty093. Fulltekst i vitenarkiv
• Xu, Yingying; Puranen, Santeri; Corander, Jukka & Kabashima, Yoshiyuki (2018). Inverse finite-size scaling for high-dimensional significance analysis. Physical review. E. ISSN 2470-0045. 97(6). doi: 10.1103/PhysRevE.97.062112. Fulltekst i vitenarkiv
• Van den Bunt, G.; Top, J.; Hordijk, J.; De Greeff, S.C.; Mughini-Gras, L. & Corander, Jukka [Vis alle 10 forfattere av denne artikkelen] (2018). Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands. Journal of Antimicrobial Chemotherapy. ISSN 0305-7453. 73(3), s. 607–614. doi: 10.1093/jac/dkx455.
• Smet, Annemieke; Yahara, Koji; Rossi, Mirko; Tay, Alfred; Backert, Steffen & Armin, Ensser [Vis alle 11 forfattere av denne artikkelen] (2018). Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence. The ISME Journal. ISSN 1751-7362. s. 1–14. doi: 10.1038/s41396-018-0199-5.
• Reiseter, Silje; Gunnarsson, Ragnar; Corander, Jukka; Haydon, Joanna; Samersaw-Lund, May Brit & Aaløkken, Trond Mogens [Vis alle 9 forfattere av denne artikkelen] (2017). Disease evolution in mixed connective tissue disease: Results from a long-term nationwide prospective cohort study. Arthritis Research & Therapy. ISSN 1478-6354. 19(1). doi: 10.1186/s13075-017-1494-7. Fulltekst i vitenarkiv
• Kallonen, Teemu Ville Sakari; Brodrick, Hayley J; Harris, Simon R.; Corander, Jukka; Brown, Nicholas M & Martin, Veronique [Vis alle 8 forfattere av denne artikkelen] (2017). Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. Genome Research. ISSN 1088-9051. 27(8), s. 1437–1449. doi: 10.1101/gr.216606.116.
• Mohandesan, Elmira; Fitak, Robert R; Corander, Jukka; Yadamsuren, Adiya; Chuluunbat, Battsetseg & Abdelhadi, Omer [Vis alle 12 forfattere av denne artikkelen] (2017). Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels. Scientific Reports. ISSN 2045-2322. 7(1). doi: 10.1038/s41598-017-08995-8.
• Wei, Lu; Pitaval, Renaud-Alexandre; Corander, Jukka & Tirkkonen, Olav (2017). From random matrix theory to coding theory: Volume of a metric ball in unitary group. IEEE Transactions on Information Theory. ISSN 0018-9448. 63(5), s. 2814–2821. doi: 10.1109/TIT.2017.2681900.
• Corander, Jukka; Fraser, Christophe; Gutmann, Michael U.; Arnold, Brian; Hanage, William P & Bentley, Stephen D [Vis alle 8 forfattere av denne artikkelen] (2017). Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nature Ecology and Evolution. ISSN 2397-334X. 1(12), s. 1950–1960. doi: 10.1038/s41559-017-0337-x.
• Mostowy, Rafal; Croucher, Nicholas J.; Andam, Cheryl P; Corander, Jukka; Hanage, William P & Marttinen, Pekka (2017). Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 34(5), s. 1167–1182. doi: 10.1093/molbev/msx066.
• Murray, Susan; Pascoe, Ben; Meric, Guillaume; Mageiros, Leonardos; Yahara, Koji & Hitchings, Matthew D [Vis alle 20 forfattere av denne artikkelen] (2017). Recombination-mediated host adaptation by avian staphylococcus aureus. Genome Biology and Evolution (GBE). ISSN 1759-6653. 9(4), s. 830–842. doi: 10.1093/gbe/evx037.
• Pensar, Johan; Nyman, Henrik; Niiranen, Juha & Corander, Jukka (2017). Marginal pseudo-likelihood learning of discrete Markov network structures. Bayesian Analysis. ISSN 1936-0975. 12(4), s. 1195–1215. doi: 10.1214/16-BA1032.
• Tietavainen, A; Gutmann, Michael U.; Keski-Vakkuri, Esko; Corander, Jukka & Hæggstrom, Edward (2017). Bayesian inference of physiologically meaningful parameters from body sway measurements. Scientific Reports. ISSN 2045-2322. 7(1). doi: 10.1038/s41598-017-02372-1.
• Pensar, Johan; Nyman, Henrik & Corander, Jukka (2017). Structure Learning of Contextual Markov Networks using Marginal Pseudo-likelihood. Scandinavian Journal of Statistics. ISSN 0303-6898. 44(2), s. 455–479. doi: 10.1111/sjos.12260.
• Duplouy, Anne; Wong, Swee C; Corander, Jukka; Lehtonen, Rainer & Hanski, Ilkka (2017). Genetic effects on life-history traits in the Glanville fritillary butterfly. PeerJ. ISSN 2167-8359. 2017(5). doi: 10.7717/peerj.3371.
• Skwark, Marcin J.; Croucher, Nicholas J.; Puranen, Santeri; Chewapreecha, Claire; Pesonen, Maiju & Xu, Ying Ying [Vis alle 14 forfattere av denne artikkelen] (2017). Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PLoS Genetics. ISSN 1553-7390. 13:e1006508(2), s. 1–24. doi: 10.1371/journal.pgen.1006508.
• Lintusaari, Jarno; Gutmann, Michael U.; Dutta, Ritabrata; Kaski, Samuel & Corander, Jukka (2017). Fundamentals and recent developments in approximate Bayesian computation. Systematic Biology. ISSN 1063-5157. 66(1), s. e66–e82. doi: 10.1093/sysbio/syw077.

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• Congo-Ouedraogo, M.; Poncin, T.; Sangaré, L.; Mérimèche, M.; Braille, A. & Jacquier, H. [Vis alle 13 forfattere av denne artikkelen] (2022). Genomic and antimicrobial resistance analyses of Neisseria gonorrhoeae isolates, Burkina Faso, 2018–2019. Journal of the European Academy of Dermatology and Venereology. ISSN 0926-9959. doi: 10.1111/jdv.18037.
• Kloos, Julia Maria; Jänisch, Lea; Pöntinen, Anna Kaarina; Samuelsen, Ørjan; Johnsen, Pål Jarle & Corander, Jukka [Vis alle 7 forfattere av denne artikkelen] (2022). Different metabolic proficiency among dominant ExPEC lineages.
• Mageiros, Leonardos; Meric, Guillaume; Bayliss, Sion; Pensar, Johan; Pascoe, Ben & Mourkas, Evangelos [Vis alle 19 forfattere av denne artikkelen] (2021). Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli (Nature Communications, (2021), 12, 1, (765), 10.1038/s41467-021-20988-w). Nature Communications. ISSN 2041-1723. 12(1). doi: 10.1038/s41467-021-22238-5.
• Corander, Jukka (2020). New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates. mBio. ISSN 2161-2129. doi: 10.1128/mBio.03363-19.
• Corander, Jukka (2020). PYLFIRE: Python implementation of likelihood-free inference by ratio estimation. Wellcome Open Research. ISSN 2398-502X. doi: 10.12688/wellcomeopenres.15583.1.
• Corander, Jukka (2020). gplas: a comprehensive tool for plasmid analysis using short-read graphs. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btaa233.
• Corander, Jukka (2020). Genomic signatures of domestication in Old World camels. Communications Biology. ISSN 2399-3642. doi: 10.1038/s42003-020-1039-5.
• Corander, Jukka (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. ISSN 1471-2164. doi: 10.1186/s12864-020-06990-4.
• Corander, Jukka (2020). The binding mechanism of the virulence factor Streptococcus suis adhesin P subtype to globotetraosylceramide is associated with systemic disease. Journal of Biological Chemistry. ISSN 0021-9258. doi: 10.1074/jbc.RA120.014818.
• Corander, Jukka (2020). Likelihood-free inference by ratio estimation. Bayesian Analysis. ISSN 1936-0975. doi: 10.1214/20-BA1238.
• Corander, Jukka (2020). Adaptive Approximate Bayesian Computation tolerance selection. Bayesian Analysis. ISSN 1936-0975. doi: 10.1214/20-BA1211.
• Corander, Jukka (2020). Improved prediction of bacterial genotype-phenotype associations using interpretable pangenome-spanning regressions. mBio. ISSN 2161-2129. doi: 10.1128/mBio.01344-20.
• Arredondo-Alonso, Sergio; Rogers, Malbert R.C.; Braat, Johanna C.; Verschuuren, Tess D.; Top, Janetta & Corander, Jukka [Vis alle 8 forfattere av denne artikkelen] (2019). Corrigendum: Mlplasmids: A user-friendly tool to predict plasmid-and chromosome-derived sequences for single species, (Microbial Genomics), (2018), 4, 10.1099/mgen.0.000224. Microbial Genomics. ISSN 2057-5858. 5(1). doi: 10.1099/mgen.0.000249.
• Smet, Annemieke; Yahara, Koji; Rossi, Mirko; Tay, Alfred; Backert, Steffen & Ensser, Armin [Vis alle 11 forfattere av denne artikkelen] (2019). Correction: Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence (The ISME Journal, (2018), 12, 10, (2518-2531), 10.1038/s41396-018-0199-5). The ISME Journal. ISSN 1751-7362. doi: 10.1038/s41396-019-0380-5.

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