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2024
1 Paganini, Julian A.; Kerkvliet, Jesse J.; Vader, Lisa; Plantinga, Nienke L.; Meneses, Rodrigo; Corander, Jukka; Willems, Rob J. L.; Alonso, Sergio Arredondo; Schürch, Anita C..
PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Microbial Genomics 2024 ;Volum 10.(2) s. -
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2 pesonen, maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka; Johannessen, Mona; Hanssen, Anne-Merethe Christiansen.
Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Frontiers in Cellular and Infection Microbiology 2024 ;Volum 14.
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3 Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Pesonen, Henri; Pesonen, Maiju; Cleon, Francois Pierre Alexandre; Parcell, Benjamin J; Kallonen, Teemu; Simonsen, Gunnar Skov; Croucher, Nicholas J; McNally, Alan; Parkhill, Julian; Johnsen, Pål Jarle; Samuelsen, Ørjan; Corander, Jukka.
Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study. Lancet Microbe 2024 ;Volum 5.(2) s. e142-e150
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2023
4 Alonso, Sergio Arredondo; Blundell-Hunter, George; Fu, Zuyi; Gladstone, Rebecca Ashley; Fillol-Salom, Alfred; Loraine, Jessica; Cloutman-Green, Elaine; Johnsen, Pål Jarle; Samuelsen, Ørjan; Pöntinen, Anna Kaarina; Cleon, Francois Pierre Alexandre; Chavez-Bueno, Susana; De la Cruz, Miguel A.; Ares, Miguel A.; Vongsouvath, Manivanh; Chmielarczyk, Agnieszka; Horner, Carolyne; Klein, Nigel; McNally, Alan; Reis, Joice N.; Penadés, José R.; Thomson, Nicholas R.; Corander, Jukka; Taylor, Peter W.; McCarthy, Alex J..
Evolutionary and functional history of the Escherichia coli K1 capsule. Nature Communications 2023 ;Volum 14.(1) s. -
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5 Alonso, Sergio Arredondo; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina; Gama, João Alves; Schürch, Anita C.; Lanza, Val F.; Johnsen, Pål Jarle; Samuelsen, Ørjan; Tonkin-Hill, Gerry; Corander, Jukka.
Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR Genomics and Bioinformatics 2023 ;Volum 5.(3) s. -
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6 Angchagun, Kesorn; Boonklang, Phumrapee; Chomkatekaew, Chalita; Pakdeerat, Sukritpong; Wongsuwan, Gumphol; Amornchai, Premjit; Wuthiekanun, Vanaporn; Panapipat, Salwaluk; Ngernseng, Thatsanun; Waithira, Naomi; Walton, Steve; Limmathurotsakul, Direk; Surawong, Anoree; Siriboon, Suwatthiya; Chamnan, Parinya; Chantratita, Narisara; Dunachie, Susie; Corander, Jukka; Davenport, Emma E.; Knight, Julian; Parkhill, Julian; Peacock, Sharon J.; Thomson, Nicholas R.; Day, Nicholas P.J.; Chewapreecha, Claire.
BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection. Wellcome Open Research 2023 ;Volum 8. s. -
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7 Bastakoti, Srijana; Pesonen, Maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka; Johannessen, Mona Susan; Hanssen, Anne-Merethe Christiansen.
Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Centre for new antibacterial strategies (CANS) DAY; 2023-02-23 - 2023-02-23
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8 Bastakoti, Srijana; Pesonen, Maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka; Johannessen, Mona Susan; Hanssen, Anne-Merethe Christiansen.
Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Norwegian Consortium for Microbial Genomics (NCMG) Meeting; 2023-12-07 - 2024-01-07
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9 Calland, Jessica Kate; Haukka, Kaisa; Kpordze, Stephen W; Brusah, Atanyiwoen; Corbella, Marta; Merla, Cristina; Samuelsen, Ørjan; Feil, Edward J; Sassera, Davide; Karikari, Akosua B; Saba, Courage K S; Thorpe, Harry; Corander, Jukka.
Population structure and antimicrobial resistance among Klebsiella isolates sampled from human, animal, and environmental sources in Ghana: a cross-sectional genomic One Health study. Lancet Microbe 2023 ;Volum 4.(11) s. e943-e952
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10 Chaguza, Chrispin; Pöntinen, Anna Kaarina; Top, Janetta; Alonso, Sergio Arredondo; Freitas, Ana R.; Novais, Carla; Torres, Carmen; Bentley, Stephen D.; Peixe, Luisa; Coque, Teresa M.; Willems, Rob J L; Corander, Jukka.
The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection. Microbiology spectrum 2023 ;Volum 11.(6) s. e0020123-
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11 Connor, Christopher H.; Zucoloto, Amanda Z.; Munnoch, John T.; Yu, Ian-Ling; Corander, Jukka; Hoskisson, Paul A.; McDonald, Braedon; McNally, Alan.
Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLoS Biology 2023 ;Volum 21.(10) s. -
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12 Bastakoti, Srijana; Pesonen, maiju; Ajayi, Clément; Julin, Kjersti; Johannessen, Mona Susan; Corander, Jukka; Hanssen, Anne-Merethe Christiansen.
Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Nordic Society of Clinical Microbiology and Infectious Diseases (NSCMID) conference; 2023-09-19 - 2023-09-24
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13 Hanssen, Anne-Merethe Christiansen; Ajayi, Clément; Johannessen, Mona Susan; Julin, Kjersti; Pesonen, Maiju; Corander, Jukka; Corander, Jukka.
Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Norwegian Consortium for Microbial Genomics Meeting; 2023-12-07 - 2024-01-07
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14 Mai, The Tien; Lees, John A; Gladstone, Rebecca Ashley; Corander, Jukka.
Inferring the heritability of bacterial traits in the era of machine learning. Bioinformatics Advances 2023 ;Volum 3.(1) s. -
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15 Pereira, Ana P.; Antunes, Patrícia; Bierge, Paula; Willems, Rob J.L.; Corander, Jukka; Coque, Teresa M.; Pich, Oscar Q.; Peixe, Luisa; Freitas, Ana R.; Novais, Carla.
Unraveling Enterococcus susceptibility to quaternary ammonium compounds: genes, phenotypes, and the impact of environmental conditions. Microbiology spectrum 2023 ;Volum 11.(5) s. -
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16 Petazzoni, Greta; Bellinzona, Greta; Merla, Cristina; Corbella, Marta; Monzillo, Vincenzina; Samuelsen, Ørjan; Corander, Jukka; Sassera, Davide; Gaiarsa, Stefano; Cambieri, Patrizia.
The COVID-19 Pandemic Sparked off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital. Microbiology spectrum 2023 ;Volum 11.(2) s. -
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17 Picchini, Umberto; Simola, Umberto; Corander, Jukka.
Sequentially Guided MCMC Proposals for Synthetic Likelihoods and Correlated Synthetic Likelihoods. Bayesian Analysis 2023 ;Volum 18.(4) s. 1099-1129
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18 Rebelo, Andreia; Duarte, Bárbara; Ferreira, Carolina; Mourão, Joana; Ribeiro, Sofia; Freitas, Ana R.; Coque, Teresa M.; Willems, Rob; Corander, Jukka; Peixe, Luísa; Antunes, Patrícia; Novais, Carla.
Enterococcus spp. from chicken meat collected 20 years apart overcome multiple stresses occurring in the poultry production chain: Antibiotics, copper and acids. International journal of food microbiology 2023 ;Volum 384. s. -
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19 Snaith, Ann E.; Dunn, Steven J.; Moran, Robert A.; Newton, Paul N.; Dance, David A. B.; Davong, Viengmon; Kuenzli, Esther; Kantele, Anu; Corander, Jukka; McNally, Alan.
The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microbial Genomics 2023 ;Volum 9.(5) s. -
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20 Tonkin-Hill, Gerry; Corander, Jukka; Parkhill, Julian.
Challenges in prokaryote pangenomics. Microbial Genomics 2023 ;Volum 9.(5) s. -
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21 Tonkin-Hill, Gerry; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina; Alonso, Sergio Arredondo; Bentley, Stephen D.; Corander, Jukka.
Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. Genome Research 2023 ;Volum 33.(1) s. 129-140
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22 Yang, Zhirong; Chen, Yuwei; Sedov, Denis; Kaski, Samuel; Corander, Jukka.
Stochastic Cluster Embedding. Statistics and computing 2023 ;Volum 33.(12) s. -
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2022
23 Aushev, Alexander; Pesonen, Henri Eerikki; Heinonen, Markus; Corander, Jukka; Kaski, Samuel.
Likelihood-free inference with deep Gaussian processes. Computational Statistics & Data Analysis 2022 ;Volum 174. s. -
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24 Mäklin, Tommi; Thorpe, Harry Arthur Frank Wright; Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Shao, Yan; Pesonen, Maiju; McNally, Alan; Johnsen, Pål Jarle; Samuelsen, Ørjan; Lawley, Trevor D.; Honkela, Antti; Corander, Jukka.
Strong pathogen competition in neonatal gut colonisation. Nature Communications 2022 ;Volum 13.(1) s. -
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25 Thorpe, Harry Arthur Frank Wright; Booton, Ross; Kallonen, Teemu; Gibbon, Marjorie J.; Couto, Natacha; Passet, Virginie; López-Fernández, Sebastián; Rodrigues, Carla; Matthews, Louise; Mitchell, Sonia; Reeve, Richard; David, Sophia; Merla, Cristina; Corbella, Marta; Ferrari, Carolina; Comandatore, Francesco; Marone, Piero; Brisse, Sylvain; Sassera, Davide; Corander, Jukka; Feil, Edward J..
A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nature Microbiology 2022 ;Volum 7. s. 2054-2067
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26 Congo-Ouedraogo, M.; Poncin, T.; Sangaré, L.; Mérimèche, M.; Braille, A.; Jacquier, H.; Ouedraogo, A.-S.; Dah, E.; Traore, I.; Corander, Jukka; Haukka, K.; Berçot, B.; Godreuil, S..
Genomic and antimicrobial resistance analyses of Neisseria gonorrhoeae isolates, Burkina Faso, 2018–2019. Journal of the European Academy of Dermatology and Venereology 2022 s. -
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27 Corander, Jukka.
A conversation with Elja Arjas (Helsinki, November 2021 and March 2022). Scandinavian Journal of Statistics 2022 s. -
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28 Corander, Jukka; Hanage, William P; Pensar, Johan.
Causal discovery for the microbiome. Lancet Microbe 2022 ;Volum 3.(11) s. e881-e887
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29 Järvenpää, Marko Juhani; Corander, Jukka.
On predictive inference for intractable models via approximate Bayesian computation. Statistics and computing 2022 ;Volum 33.(2)
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30 Kičiatovas, Dovydas; Guo, Qingli; Kailas, Miika; Pesonen, Henri; Corander, Jukka; Kaski, Samuel; Pitkänen, Esa; Mustonen, Ville.
Identification of multiplicatively acting modulatory mutational signatures in cancer. BMC Bioinformatics 2022 ;Volum 23. s. -
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31 Kloos, Julia Maria; Jänisch, Lea; Pöntinen, Anna Kaarina; Samuelsen, Ørjan; Johnsen, Pål Jarle; Corander, Jukka; Gama, João Alves.
Different metabolic proficiency among dominant ExPEC lineages. ECCMID 2022; 2022-04-23 - 2022-04-26
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32 Lees, John A.; Tonkin-Hill, Gerry; Yang, Zhirong; Corander, Jukka.
Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation. Philosophical Transactions of the Royal Society of London. Biological Sciences 2022 ;Volum 377.(1861) s. -
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33 Li, Nien-Kung; Corander, Jukka; Grad, Yonatan H.; Chang, Hsiao-Han.
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales. Virus Evolution 2022 ;Volum 8.(2) s. -
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34 Mallawaarachchi, Sudaraka; Tonkin-Hill, Gerry; Croucher, Nicholas J.; Turner, Paul; Speed, Doug; Corander, Jukka; Balding, David J..
Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae. NAR Genomics and Bioinformatics 2022 ;Volum 4.(1) s. -
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35 Pereira, Ana P.; Antunes, Patrícia; Willems, Rob; Corander, Jukka; Coque, Teresa M.; Peixe, Luísa; Freitas, Ana R.; Novais, Carla.
Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans. Microbiology spectrum 2022 ;Volum 10.(4) s. -
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36 Pesonen, Henri; Simola, Umberto; Kohn Luque, Alvaro; Vuollekoski, Henri; Lai, Xiaoran; Frigessi, Arnoldo; Kaski, Samuel; Frazier, David T.; Maneesoonthorn, Worapree; Martin, Gael M.; Corander, Jukka.
ABC of the future. International Statistical Review 2022 s. -
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37 Ross, Theodor Anton; Pöntinen, Anna Kaarina; Janice, Jessin; Holsbø, Einar; Corander, Jukka; Hegstad, Kristin; Kampffmeyer, Michael.
Leveraging machine learning for finding novel putative virulence factors in Enterococcus faecium. 6th Annual meeting National Graduate School in Infection Biology and Antimicrobials; 2022-10-27 - 2022-10-28
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38 Simola, U.; Bonfanti, A.; Dumusque, X.; Cisewski-Kehe, J.; Kaski, S.; Corander, Jukka.
Accounting for stellar activity signals in radial-velocity data by using change point detection techniques. Astronomy and Astrophysics (A & A) 2022 ;Volum 664. s. -
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39 Tonkin-Hill, Gerry; Ling, Clare; Chaguza, Chrispin; Salter, Susannah J.; Hinfonthong, Pattaraporn; Nikolaou, Elissavet; Tate, Natalie; Pastusiak, Andrzej; Turner, Claudia; Chewapreecha, Claire; Frost, Simon D. W.; Corander, Jukka; Croucher, Nicholas J.; Turner, Paul; Bentley, Stephen D..
Pneumococcal within-host diversity during colonization, transmission and treatment. Nature Microbiology 2022 ;Volum 7.(11) s. 1791-1804
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40 van Hal, Sebastiaan J; Willems, Rob J L; Gouliouris, Theodore; Ballard, Susan A; Coque, Teresa M; Hammerum, Anette M; Hegstad, Kristin; Pinholt, Mette; Howden, Benjamin P; Malhotra-Kumar, Surbhi; Werner, Guido; Yanagihara, Katsunori; Earl, Ashlee M; Raven, Katherine E; Corander, Jukka; Bowden, Rory.
The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis. Lancet Microbe 2022 ;Volum 3.(2) s. e133-e141
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2021
41 Biffignandi, Gherard Batisti; Gibbon, Marjorie J.; Corbella, Marta; Thorpe, Harry Arthur Frank Wright; Merla, Cristina; Castelli, Michele; Kallonen, Teemu; Pegrum, Katie; Brisse, Sylvain; Corander, Jukka; Marone, Piero; Feil, Edward J.; Sassera, Davide.
Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae. G3: Genes, Genomes, Genetics 2021 ;Volum 11.(2) s. -
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42 Calland, Jessica K.; Pascoe, Ben; Bayliss, Sion; Mourkas, Evangelos; Berthenet, Elvire; Thorpe, Harry Arthur Frank Wright; Hitchings, Matthew D.; Feil, Edward J.; Corander, Jukka; Blaser, Martin J.; Falush, Daniel; Sheppard, Samuel K..
Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genetics 2021 ;Volum 17.(9) s. -
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43 Gibbon, Marjorie J.; Couto, Natacha; David, Sophia; Barden, Ruth; Standerwick, Richard; Jagadeesan, Kishore Kumar; Birkwood, Hollie; Dulyayangkul, Punyawee; Avison, Matthew B.; Kannan, Andrew; Kibbey, Dan; Craft, Tim; Habib, Samia; Thorpe, Harry Arthur Frank Wright; Corander, Jukka; Kasprzyk-Hordern, Barbara; Feil, Edward J..
A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England. Microbial Genomics 2021 ;Volum 7.(3) s. -
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44 Alonso, Sergio Arredondo; Pöntinen, Anna Kaarina; Cleon, Francois Pierre Alexandre; Gladstone, Rebecca Ashley; Schürch, Anita C.; Johnsen, Pål Jarle; Samuelsen, Ørjan; Corander, Jukka.
A high-throughput multiplexing and selection strategy to complete bacterial genomes. GigaScience 2021 ;Volum 10.(12) s. 1-13
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45 Alonso, Sergio Arredondo; Top, Janetta; Corander, Jukka; Willems, Rob J. L.; Schürch, Anita C..
Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals. Genome Medicine 2021 ;Volum 13.(1) s. 1-18
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46 MacAlasdair, Neil; Pesonen, Maiju; Brynildsrud, Ola Brønstad; Eldholm, Vegard; Kristiansen, Paul Arne; Corander, Jukka; Caugant, Dominique Andree Yvette; Bentley, Stephen D..
The effect of recombination on the evolution of a population of Neisseria meningitidis. Genome Research 2021 ;Volum 31.(7) s. 1258-1268
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47 Chewapreecha, Claire; Pensar, Johan; Chattagul, Supaksorn; Pesonen, Maiju; Sangphukieo, Apiwat; Boonklang, Phumrapee; Potisap, Chotima; Koosakulnirand, Sirikamon; Feil, Edward J.; Dunachie, Susanna; Chantratita, Narisara; Limmathurotsaku, Direk; Peacock, Sharon J.; Day, Nick P.J.; Parkhill, Julian; Thomson, Nicholas R.; Sermswan, Rasana W.; Corander, Jukka.
Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. Molecular Biology and Evolution (MBE) 2021 ;Volum 39.(1) s. -
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48 Corander, Jukka; Remes, Ulpu Maria Vilhelmiina; Koski, Timo.
On the Jensen-Shannon divergence and the variation distance for categorical probability distributions. Kybernetika (Praha) 2021 ;Volum 57.(6) s. 879-907
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49 Gladstone, Rebecca Ashley; McNally, Alan; Johnsen, Pål Jarle; Samuelsen, Ørjan; Corander, Jukka.
Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection – Authors’ reply. Lancet Microbe 2021 ;Volum 2.(10) s. e493-
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50 Gladstone, Rebecca Ashley; McNally, Alan; Pöntinen, Anna Kaarina; Tonkin-Hill, Gerry; Lees, John A.; Skytén, Kusti Onni; Cléon, Francois Pierre Alexandre; Christensen, Martin Owczarek Korsner; Haldorsen, Bjørg; Bye, Kristina Knudsen; Gammelsrud, Karianne Wiger; Hjetland, Reidar; Kümmel, Angela; Larsen, Hege; Lindemann, Paul Christoffer; Löhr, Iren Høyland; Marvik, Åshild; Nilsen, Einar; Noer, Marie Therese; Simonsen, Gunnar Skov; Steinbakk, Martin; Tofteland, Ståle; Vattøy, Marit; Bentley, Stephen D.; Croucher, Nicholas J.; Parkhill, Julian; Johnsen, Pål Jarle; Samuelsen, Ørjan; Corander, Jukka.
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 2021 ;Volum 2.(7) s. e331-e341
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