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Showing results 1-50 of 71 << Previous 1 2    Next >>

2019
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)
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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
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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)
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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)
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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)
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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)
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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
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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
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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
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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
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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
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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
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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)
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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
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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)
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2018
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
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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
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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
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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)
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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
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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
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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
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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)
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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)
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2017
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
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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
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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)
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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
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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
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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
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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
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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)
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