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2019
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| 1. | Abudahab, Khalil; Prada, Joaquín; Yang, Zhirong; Bentley, Stephen; Croucher, Nicholas; Corander, Jukka; Anensen, David. PANINI: Pangenome Neighbour Identification for Bacterial Populations. Microbial Genomics 2019 ;Volume 5.(4) UiO |
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| 2. | Lu, Yao; Corander, Jukka; Yang, Zhirong. Doubly Stochastic Neighbor Embedding on Spheres. Pattern Recognition Letters 2019 ;Volume 128. p. 100-106 NTNU UiO |
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| 3. | Arredondo-Alonso, Sergio; Rogers, Malbert R.C.; Braat, Johanna C.; Verschuuren, Tess D.; Top, Janetta; Corander, Jukka; Willems, Rob J.L.; Schürch, Anita C.. 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 2019 ;Volume 5.(1) UiO |
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| 4. | Chiner-Oms, Álvaro; Sanchez-Buso, Leonor; Corander, Jukka; Gagneux, Sébastien; Harris, Simon R; Young, D; Gonzalez-Candelas, Fernando; Comas, Inaki. Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. Science Advances 2019 ;Volume 5.(6) UiO |
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| 5. | Colclough, Abigail; Corander, Jukka; Sheppard, Samuel K.; Bayliss, S. C.; Vos, Michiel. Patterns of cross-resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials. Evolutionary Applications 2019 ;Volume 12.(5) p. 878-887 UiO |
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| 6. | Corander, Jukka; Hyttinen, Antti; Kontinen, Juha; Pensar, Johan; Väänänen, Jouko. A logical approach to context-specific independence. Annals of Pure and Applied Logic 2019 ;Volume 170.(9) p. 975-992 UiO |
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| 7. | Cremers, Amelieke J. H.; Mobegi, Fredrick M.; Van Der Gaast-De Jongh, Christa; Van Weert, Michelle; Van Opzeeland, Fred J.; Vehkala, Minna; Knol, Mirjam J.; Bootsma, Hester J.; Välimäki, Niko; Croucher, Nicholas J.; Meis, Jacques F.; Bentley, Stephen; van Hijum, Sacha A.F.T.; Corander, Jukka; Zomer, Aldert L.; Ferwerda, Gerben; De Jonge, Marien I.. The contribution of genetic variation of streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease. Clinical Infectious Diseases 2019 ;Volume 68.(1) p. 61-69 UiO |
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| 8. | Elbers, Jean P; Rogers, Mark F; Perelman, Polina L; Proskuryakova, Anastasia A; Serdyukova, Natalia A; Johnson, Warren E.; Horin, Petr; Corander, Jukka; Murphy, David; Burger, Pamela A. Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary. Molecular Ecology Resources 2019 ;Volume 19.(4) p. 1015-1026 UiO |
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| 9. | Gladstone, Rebecca A; Lo, Stephanie W; Lees, John A; Croucher, Nicholas J.; van Tonder, Andries J.; Corander, Jukka; Page, Andrew J; Marttinen, Pekka; Bentley, Leon J.; Ochoa, Theresa J.; Ho, Pak Leung; du Plessis, Mignon; Cornick, Jennifer E.; Kwambana-Adams, Brenda; Benisty, Rachel; Nzenze, Susan A.; Madhi, Shabir A.; Hawkins, Paulina A.; Everett, Dean B.; Antonio, Martin; Dagan, Ron; Klugman, Keith; von Gottberg, Anne; McGee, Lesley; Breiman, Robert F.; Bentley, Stephen D.. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine 2019 ;Volume 43. p. 338-346 UiO |
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| 10. | Gouliouris, Theodore; Raven, Kathy E; Moradigaravand, Danesh; Ludden, Catherine; Coll, Francesc; Blane, Beth; Naydenova, Plamena; Horner, Carolyne; Brown, Nicholas M; Corander, Jukka; Limmathurotsakul, Direk; Parkhill, Julian; Peacock, Sharon J.. Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment. Genome Research 2019 ;Volume 29.(4) p. 626-634 UiO |
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| 11. | Kachroo, Priyanka; Eraso, Jesus M.; Beres, Stephen B.; Olsen, Randall J.; Zhu, Luchang; Nasser, Waleed; Bernard, Paul E.; Cantu, Conception C.; Saavedra, Matthew Ojeda; Arredondo, María José; Strope, Benjamin; Do, Hackwon; Kumaraswami, Muthiah; Vuopio, Jaana; Gröndahl-Yli-Hannuksela, Kirsi; Kristinsson, Karl G.; Gottfredsson, Magnus; Pesonen, Maiju; Pensar, Johan; Davenport, Emily R.; Clark, Andrew G.; Corander, Jukka; Caugant, Dominique A; Gaini, Shahin; Magnussen, Marita Debess; Kubiak, Samantha L.; Nguyen, Hoang A. T.; Long, S. Wesley; Porter, Adeline R.; DeLeo, Frank R.; Musser, James M.. Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis. Nature Genetics 2019 ;Volume 51.(3) p. 548-559 FHI UiO |
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| 12. | Lees, John A; Harris, Simon R; Tonkin-Hill, Gerry; Gladstone, Rebecca A; Lo, Stephanie W; Weiser, Jeffrey N; Corander, Jukka; Bentley, Stephen D; Croucher, Nicholas J. Fast and flexible bacterial genomic epidemiology with PopPUNK.. Genome Research 2019 ;Volume 29.(2) p. 304-316 UiO |
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| 13. | Léon-Sampedro, Ricardo; del Campo, Rosa; Rodriguez-Baños, Mercedes; Lanza, Val F.; Pozuelo, María José; Francés-Cuesta, Carlos; Tedim, Ana P.; Freitas, Ana R.; Novais, Carla; Peixe, Luísa; Willems, Rob J.L.; Corander, Jukka; González Candelas, Fernando; Baquero, Fernando; Coque, Teresa M.. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environmental Microbiology 2019 ;Volume 21.(8) p. 3046-3062 UiO |
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| 14. | Lintusaari, Jarno; Blomstedt, Paul; Rose, Brittany; Sivula, Tuomas; Gutmann, Michael U.; Kaski, Samuel; Corander, Jukka. Resolving outbreak dynamics using approximate bayesian computation for stochastic birth-death models. Wellcome Open Research 2019 ;Volume 4.(14) FHI UiO |
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| 15. | McNally, Alan; Kallonen, Teemu; Connor, Christopher; Abudahab, Khalil; Aanensen, David M.; Horner, Carolyne S; Peacock, Sharon J.; Parkhill, Julian; Croucher, Nicholas J.; Corander, Jukka. Diversification of colonization factors in a multidrug-resistant escherichia coli lineage evolving under negative frequency- dependent selection. mBio 2019 ;Volume 10.(2) UiO |
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| 16. | Merla, Cristina; Rodrigues, Carla; Passet, Virginie; Corbella, Marta; Thorpe, Harry A; Kallonen, Teemu; Zong, Zhiyong; Marone, Piero; Bandi, Claudio; Sassera, Davide; Corander, Jukka; Feil, Edward J.; Brisse, Sylvain. Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.. Frontiers in Microbiology 2019 ;Volume 10.(2360) p. 1-9 UiO |
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| 17. | Pensar, Johan; Puranen, Santeri; Arnold, Brian; MacAlasdair, Neil; Kuronen, Juri; Tonkin-Hill, Gerry; Pesonen, Maiju; Xu, Yingying; Sipola, Aleksi; Sanchez-Buso, Leonor; Lees, John A; Chewapreecha, Claire; Bentley, Stephen D; Harris, Simon R; Parkhill, Julian; Croucher, Nicholas J; Corander, Jukka. Genome-wide epistasis and co-selection study using mutual information. Nucleic Acids Research 2019 ;Volume 47.(18) p. 1-14 UiO |
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| 18. | Sanchez-Buso, Leonor; Golparian, Daniel; Corander, Jukka; Grad, Yonatan H.; Ohnishi, Makoto; Flemming, Rebecca; Parkhill, Julian; Bentley, Stephen D; Unemo, Magnus; Harris, Simon R. The impact of antimicrobials on gonococcal evolution. Nature Microbiology 2019 UiO |
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| 19. | Schaufler, Katharina; Semmler, Torsten; Wieler, Lothar H.; Trott, Darren J.; Pitout, Johann; Peirano, Gisele; Bonnedahl, Jonas; Dolejska, Monika; Literak, Ivan; Fuchs, Stephan; Ahmed, Niyaz; Grobbel, Mirjam; Torres, Carmen; McNally, Alan; Pickard, Derek; Ewers, Christa; Croucher, Nicholas J.; Corander, Jukka; Guenther, Sebastian. Genomic and functional analysis of emerging virulent and multidrug-resistant Escherichia coli lineage sequence type 648. Antimicrobial Agents and Chemotherapy 2019 ;Volume 63:e00243-19.(6) p. 1-12 UiO |
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| 20. | Smet, Annemieke; Yahara, Koji; Rossi, Mirko; Tay, Alfred; Backert, Steffen; Ensser, Armin; Fox, James G.; Flahou, Bram; Ducatelle, Richard; Haesebrouck, Freddy; Corander, Jukka. 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 2019 UiO |
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| 21. | Tadei, Alessandro; Pensar, Johan; Corander, Jukka; Finnilä, Katarina; Santtila, Pekka; Antfolk, Jan. A Bayesian Decision-Support Tool for Child Sexual Abuse Assessment and Investigation. Sexual abuse. A Journal of Research and Treatment 2019 ;Volume 31.(4) p. 374-396 UiO |
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| 22. | Todorovic, Milica; Gutmann, Michael U.; Corander, Jukka; Rinke, Patrick. Bayesian inference of atomistic structure in functional materials. npj Computational Materials 2019 ;Volume 5.(1) UiO |
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| 23. | Tonkin-Hill, Gerry; Lees, John A; Bentley, Stephen D; Frost, Simon DW; Corander, Jukka. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Research 2019 ;Volume 47.(11) p. 5539-5549 UiO |
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| 24. | Wailan, Alexander M.; Coll, Francesc; Heinz, Eva; Tonkin-Hill, Gerry; Corander, Jukka; Feasey, Nicholas A.; Thomson, Nicholas R.. rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. Microbial Genomics 2019 ;Volume 5.(4) UiO |
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2018
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| 25. | Arnold, Brian; Gutmann, Michael U.; Grad, Yonatan H.; Sheppard, Samuel K.; Corander, Jukka; Lipsitch, Marc; Hanage, William P.. Weak epistasis may drive adaptation in recombining bacteria. Genetics 2018 ;Volume 208.(3) p. 1247-1260 UiO |
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| 26. | Arredondo-Alonso, Sergio; Rogers, Malbert R.C.; Braat, Johanna C.; Verschuuren, Tess D.; Top, Janetta; Corander, Jukka; Willems, Rob J.L.; Schürch, Anita C.. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microbial Genomics 2018 ;Volume 4.(11) p. 1-15 UiO |
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| 27. | Flahou, Bram; Rossi, Mirko; Bakker, Jaco; Langermans, Jan AM; Heuvelman, Edwin; Solnick, Jay V; Martin, Miriam E; O'Rourke, Jani; Ngoan, Le Duc; Hoa, Nguyen Xuan; Nakamura, Masahiko; Øverby, Anders; Matsui, Hidenori; Ota, Hiroyoshi; Matsumoto, Takehisa; Foss, Dennis L; Kopta, Laurice A; Omotosho, Oladipo; Franciosini, Maria Pia; Casagrande Proietti, Patrizia; Guo, Aizhen; Liu, Han; Borilova, Gabriela; Bracarense, Ana Paula; Linden, Sara K; De Bruyckere, Sofie; Zhang, Guangzhi; De Witte, Chloe; Smet, Annemieke; Pasmans, Frank; Ducatelle, Richard; Corander, Jukka; Haesebrouck, Freddy. Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs. The ISME Journal 2018 ;Volume 12.(1) p. 77-86 UiO |
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| 28. | Gouliouris, Theodore; Raven, Kathy E; Ludden, Catherine; Blane, Beth; Corander, Jukka; Horner, Carolyne S; Hernandez-Garcia, Juan; Wood, Paul; Hadjirin, Nazreen F; Radakovic, Milorad; Holmes, Mark; de Goffau, Marcus; Brown, Nicholas M; Parkhill, Julian; Peacock, Sharon J.. Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom. mBio 2018 ;Volume 9.(6) UiO |
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| 29. | Lees, John A; Galardini, Marco; Bentley, Stephen D; Weiser, Jeffrey N; Corander, Jukka. pyseer: a comprehensive tool for microbial pangenome-wide association studies. Bioinformatics 2018 ;Volume 34.(24) p. 4310-4312 UiO |
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| 30. | Lin, Xiaoxi B.; Wang, Tuo; Stothard, Paul; Corander, Jukka; Wang, Jun; Baines, John F.; Knowles, Sarah C.L.; Baltrūnaitė, Laima; Tasseva, Guergana; Schmaltz, Robert; Tollenaar, Stephanie; Cody, Liz A.; Grenier, Theodore; Wu, Wei; Ramer-Tait, Amanda E.; Walter, Jens. The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract. The ISME Journal 2018 ;Volume 12.(11) p. 2770-2784 UiO |
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| 31. | Lintusaari, Jarno; Vuollekoski, Henri; Kangasraasio, Antti; Skyten, Kusti; Jarvenpaa, Marko; Marttinen, Pekka; Gutmann, Michael U.; Vehtari, Aki; Corander, Jukka; Kaski, Samuel. ELFI: Engine for Likelihood-Free Inference. Journal of machine learning research 2018 ;Volume 19.(16) p. 1-7 UiO |
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| 32. | Meric, Guillaume; Mageiros, Leonardos; Pensar, Johan; Laabei, Maisem; Yahara, Koji; Pascoe, Ben; Kittiwan, Nattinee; Tadee, Phacharaporn; Post, Virginia; Lamble, Sarah; Bowden, Rory; Bray, James E.; Morgenstern, Mario; Jolley, Keith A.; Maiden, Martin CJ; Feil, Edward J.; Didelot, Xavier; Miragaia, Maria; de Lencastre, Herminia; Moriarty, T Fintan; Rohde, Holger; Massey, Ruth; Mack, Dietrich; Corander, Jukka; Sheppard, Samuel K. Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nature Communications 2018 ;Volume 9.(1) UiO |
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| 33. | Meric, Guillaume; McNally, Alan; Pessia, Alberto; Mourkas, Evangelos; Pascoe, Ben; Mageiros, Leonardos; Vehkala, Minna; Corander, Jukka; Sheppard, Samuel K. Convergent amino acid signatures in polyphyletic campylobacter jejuni subpopulations suggest human niche tropism. Genome Biology and Evolution 2018 ;Volume 10.(3) p. 763-774 UiO |
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| 34. | Pensar, Johan; Kohonen, J; Corander, Jukka. Exact Bayesian learning of Partition Directed Acyclic Graphs. Journal of Physics: Conference Series 2018 ;Volume 1036.(1) p. 1-12 UiO |
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| 35. | Pessia, Alberto; Corander, Jukka. Kpax3: Bayesian bi-clustering of large sequence datasets. Bioinformatics 2018 ;Volume 34.(12) p. 2132-2133 UiO |
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| 36. | Puranen, Santeri; Pesonen, Maiju; Pensar, Johan; Xu, Ying Ying; Lees, John A.; Bentley, Stephen D.; Croucher, Nicholas J.; Corander, Jukka. SuperDCA for genome-wide epistasis analysis. Microbial Genomics 2018 ;Volume 4.(6) p. 1-12 UiO |
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| 37. | Richardson, Emily J; Bacigalupe, Rodrigo; Harrison, Ewan M; Weinert, Lucy A.; Lycett, Samantha; Vrieling, Manouk; Robb, Kirsty; Hoskisson, Paul A; Holden, Matthew T.G.; Feil, Edward J.; Paterson, Gavin K; Tong, Steven Y C; Shittu, Adebayo; van Wamel, Willem; Aanensen, David M.; Parkhill, Julian; Peacock, Sharon J.; Corander, Jukka; Holmes, Mark; Fitzgerald, J. Ross. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nature Ecology and Evolution 2018 ;Volume 2.(9) p. 1468-1478 UiO |
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| 38. | Sipola, Aleksi; Marttinen, Pekka; Corander, Jukka. Bacmeta: simulator for genomic evolution in bacterial metapopulations. Bioinformatics 2018 ;Volume 34.(13) p. 2308-2310 UiO |
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| 39. | Smet, Annemieke; Yahara, Koji; Rossi, Mirko; Tay, Alfred; Backert, Steffen; Armin, Ensser; Fox, James G.; Flahou, Bram; Ducatelle, R.; Haesebrouck, Freddy; Corander, Jukka. Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence. The ISME Journal 2018 p. 1-14 UiO |
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| 40. | Top, Janetta; Sinnige, Jan C.; Brouwer, Ellen C.; Werner, Guido; Corander, Jukka; Severin, Juliëtte A.; Jansen, Rogier; Bathoorn, Erik; Bonten, Marc J.M.; Rossen, John W.A.; Willems, Rob J.L.. Identification of a novel genomic island associated with vand-type vancomycin resistance in six Dutch vancomycin-resistant enterococcus faecium isolates. Antimicrobial Agents and Chemotherapy 2018 ;Volume 62:e01793.(3) p. 1-7 UiO |
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| 41. | Van den Bunt, G.; Top, J.; Hordijk, J.; De Greeff, S.C.; Mughini-Gras, L.; Corander, Jukka; van Pelt, W.; Bonten, M.J.M.; Fluit, A.C.; Willems, Rob J.L.. Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands. Journal of Antimicrobial Chemotherapy 2018 ;Volume 73.(3) p. 607-614 UiO |
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| 42. | Xu, Yingying; Puranen, Santeri; Corander, Jukka; Kabashima, Yoshiyuki. Inverse finite-size scaling for high-dimensional significance analysis. Physical review. E 2018 ;Volume 97.(6) UiO |
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2017
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| 43. | Chewapreecha, Claire; Holden, Matthew T.G.; Vehkala, Minna; Välimäki, Niko; Yang, Zhirong; Harris, Simon R.; Mather, Alison E.; Tuanyok, Apichai; De Smet, Birgit; Le Hello, Simon; Bizet, Chantal; Mayo, Mark; Wuthiekanun, Vanaporn; Limmathurotsakul, Direk; Phetsouvanh, Rattanaphone; Spratt, Brian G.; Corander, Jukka; Keim, Paul; Dougan, Gordon; Dance, David A.B.; Currie, Bart J.; Parkhill, Julian; Peacock, Sharon J.. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nature Microbiology 2017 ;Volume 2:16263. p. 1-8 UiO |
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| 44. | Corander, Jukka; Fraser, Christophe; Gutmann, Michael U.; Arnold, Brian; Hanage, William P; Bentley, Stephen D; Lipsitch, Marc; Croucher, Nicholas J. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nature Ecology and Evolution 2017 ;Volume 1.(12) p. 1950-1960 UiO |
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| 45. | Duplouy, Anne; Wong, Swee C; Corander, Jukka; Lehtonen, Rainer; Hanski, Ilkka. Genetic effects on life-history traits in the Glanville fritillary butterfly. PeerJ 2017 ;Volume 2017.(5) UiO |
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| 46. | Gutmann, Michael; Dutta, Ritabrata; Kaski, Samuel; Corander, Jukka. Likelihood-free inference via classification. Statistics and computing 2017 ;Volume 28.(2) p. 411-425 UiO |
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| 47. | Kallonen, Teemu Ville Sakari; Brodrick, Hayley J; Harris, Simon R.; Corander, Jukka; Brown, Nicholas M; Martin, Veronique; Peacock, Sharon J.; Parkhill, Julian. Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. Genome Research 2017 ;Volume 27.(8) p. 1437-1449 UiO |
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| 48. | Leppä-aho, Janne; Pensar, Johan; Roos, Teemu; Corander, Jukka. Learning Gaussian graphical models with fractional marginal pseudo-likelihood. International Journal of Approximate Reasoning 2017 ;Volume 83. p. 21-42 UiO |
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| 49. | Lintusaari, Jarno; Gutmann, Michael U.; Dutta, Ritabrata; Kaski, Samuel; Corander, Jukka. Fundamentals and recent developments in approximate Bayesian computation. Systematic Biology 2017 ;Volume 66.(1) p. e66-e82 UiO |
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| 50. | Mohandesan, Elmira; Fitak, Robert R; Corander, Jukka; Yadamsuren, Adiya; Chuluunbat, Battsetseg; Abdelhadi, Omer; Raziq, Abdul; Nagy, Peter; Stalder, Gabrielle; Walzer, Chris; Faye, Bernard; Burger, Pamela A. Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels. Scientific Reports 2017 ;Volume 7.(1) UiO |
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