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Items: 1 to 50 of 166

1.

Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen.

Arnold B, Sohail M, Wadsworth C, Corander J, Hanage WP, Sunyaev S, Grad YH.

Mol Biol Evol. 2019 Oct 7. pii: msz225. doi: 10.1093/molbev/msz225. [Epub ahead of print]

PMID:
31589312
2.

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex.

Chiner-Oms Á, Sánchez-Busó L, Corander J, Gagneux S, Harris SR, Young D, González-Candelas F, Comas I.

Sci Adv. 2019 Jun 12;5(6):eaaw3307. doi: 10.1126/sciadv.aaw3307. eCollection 2019 Jun.

3.

Genome-wide epistasis and co-selection study using mutual information.

Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J, Tonkin-Hill G, Pesonen M, Xu Y, Sipola A, Sánchez-Busó L, Lees JA, Chewapreecha C, Bentley SD, Harris SR, Parkhill J, Croucher NJ, Corander J.

Nucleic Acids Res. 2019 Oct 10;47(18):e112. doi: 10.1093/nar/gkz656.

4.

The impact of antimicrobials on gonococcal evolution.

Sánchez-Busó L, Golparian D, Corander J, Grad YH, Ohnishi M, Flemming R, Parkhill J, Bentley SD, Unemo M, Harris SR.

Nat Microbiol. 2019 Jul 29. doi: 10.1038/s41564-019-0501-y. [Epub ahead of print]

PMID:
31358980
5.

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species.

León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM.

Environ Microbiol. 2019 Aug;21(8):3046-3062. doi: 10.1111/1462-2920.14702. Epub 2019 Jul 4.

PMID:
31162871
6.

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

Colclough A, Corander J, Sheppard SK, Bayliss SC, Vos M.

Evol Appl. 2019 Jan 28;12(5):878-887. doi: 10.1111/eva.12762. eCollection 2019 Jun.

7.

Fast hierarchical Bayesian analysis of population structure.

Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J.

Nucleic Acids Res. 2019 Jun 20;47(11):5539-5549. doi: 10.1093/nar/gkz361.

8.

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

McNally A, Kallonen T, Connor C, Abudahab K, Aanensen DM, Horner C, Peacock SJ, Parkhill J, Croucher NJ, Corander J.

MBio. 2019 Apr 23;10(2). pii: e00644-19. doi: 10.1128/mBio.00644-19.

9.

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.

Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD; Global Pneumococcal Sequencing Consortium.

EBioMedicine. 2019 May;43:338-346. doi: 10.1016/j.ebiom.2019.04.021. Epub 2019 Apr 16.

10.

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

Elbers JP, Rogers MF, Perelman PL, Proskuryakova AA, Serdyukova NA, Johnson WE, Horin P, Corander J, Murphy D, Burger PA.

Mol Ecol Resour. 2019 Jul;19(4):1015-1026. doi: 10.1111/1755-0998.13020. Epub 2019 May 17.

11.

rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.

Wailan AM, Coll F, Heinz E, Tonkin-Hill G, Corander J, Feasey NA, Thomson NR.

Microb Genom. 2019 Apr;5(4). doi: 10.1099/mgen.0.000264. Epub 2019 Mar 28.

12.

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment.

Gouliouris T, Raven KE, Moradigaravand D, Ludden C, Coll F, Blane B, Naydenova P, Horner C, Brown NM, Corander J, Limmathurotsakul D, Parkhill J, Peacock SJ.

Genome Res. 2019 Apr;29(4):626-634. doi: 10.1101/gr.232629.117. Epub 2019 Mar 21.

13.

Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648.

Schaufler K, Semmler T, Wieler LH, Trott DJ, Pitout J, Peirano G, Bonnedahl J, Dolejska M, Literak I, Fuchs S, Ahmed N, Grobbel M, Torres C, McNally A, Pickard D, Ewers C, Croucher NJ, Corander J, Guenther S.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e00243-19. doi: 10.1128/AAC.00243-19. Print 2019 Jun.

PMID:
30885899
14.

Correction: Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence.

Smet A, Yahara K, Rossi M, Tay A, Backert S, Ensser A, Fox JG, Flahou B, Ducatelle R, Haesebrouck F, Corander J.

ISME J. 2019 Jul;13(7):1890. doi: 10.1038/s41396-019-0380-5.

15.

Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis.

Kachroo P, Eraso JM, Beres SB, Olsen RJ, Zhu L, Nasser W, Bernard PE, Cantu CC, Saavedra MO, Arredondo MJ, Strope B, Do H, Kumaraswami M, Vuopio J, Gröndahl-Yli-Hannuksela K, Kristinsson KG, Gottfredsson M, Pesonen M, Pensar J, Davenport ER, Clark AG, Corander J, Caugant DA, Gaini S, Magnussen MD, Kubiak SL, Nguyen HAT, Long SW, Porter AR, DeLeo FR, Musser JM.

Nat Genet. 2019 Mar;51(3):548-559. doi: 10.1038/s41588-018-0343-1. Epub 2019 Feb 18.

PMID:
30778225
16.

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

Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC.

Microb Genom. 2019 Jan;5(1). doi: 10.1099/mgen.0.000249. No abstract available.

17.

Fast and flexible bacterial genomic epidemiology with PopPUNK.

Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ.

Genome Res. 2019 Feb;29(2):304-316. doi: 10.1101/gr.241455.118. Epub 2019 Jan 24.

18.

pyseer: a comprehensive tool for microbial pangenome-wide association studies.

Lees JA, Galardini M, Bentley SD, Weiser JN, Corander J.

Bioinformatics. 2018 Dec 15;34(24):4310-4312. doi: 10.1093/bioinformatics/bty539.

19.

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.

Méric G, Mageiros L, Pensar J, Laabei M, Yahara K, Pascoe B, Kittiwan N, Tadee P, Post V, Lamble S, Bowden R, Bray JE, Morgenstern M, Jolley KA, Maiden MCJ, Feil EJ, Didelot X, Miragaia M, de Lencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK.

Nat Commun. 2018 Nov 28;9(1):5034. doi: 10.1038/s41467-018-07368-7.

20.

PANINI: Pangenome Neighbour Identification for Bacterial Populations.

Abudahab K, Prada JM, Yang Z, Bentley SD, Croucher NJ, Corander J, Aanensen DM.

Microb Genom. 2019 Apr;5(4). doi: 10.1099/mgen.0.000220. Epub 2018 Nov 22.

21.

Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.

Gouliouris T, Raven KE, Ludden C, Blane B, Corander J, Horner CS, Hernandez-Garcia J, Wood P, Hadjirin NF, Radakovic M, Holmes MA, de Goffau M, Brown NM, Parkhill J, Peacock SJ.

MBio. 2018 Nov 6;9(6). pii: e01780-18. doi: 10.1128/mBio.01780-18.

22.

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

Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000224. Epub 2018 Nov 1. Erratum in: Microb Genom. 2019 Jan;5(1):.

23.

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J.

Wellcome Open Res. 2018 Jul 30;3:93. doi: 10.12688/wellcomeopenres.14694.1. eCollection 2018.

24.

Gene exchange drives the ecological success of a multi-host bacterial pathogen.

Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR.

Nat Ecol Evol. 2018 Sep;2(9):1468-1478. doi: 10.1038/s41559-018-0617-0. Epub 2018 Jul 23.

25.

Identifying Bacterial Strains from Sequencing Data.

Mäklin T, Corander J, Honkela A.

Methods Mol Biol. 2018;1807:1-7. doi: 10.1007/978-1-4939-8561-6_1.

PMID:
30030799
26.

The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract.

Lin XB, Wang T, Stothard P, Corander J, Wang J, Baines JF, Knowles SCL, Baltrūnaitė L, Tasseva G, Schmaltz R, Tollenaar S, Cody LA, Grenier T, Wu W, Ramer-Tait AE, Walter J.

ISME J. 2018 Nov;12(11):2770-2784. doi: 10.1038/s41396-018-0211-0. Epub 2018 Jul 16.

PMID:
30013162
27.

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

Xu Y, Puranen S, Corander J, Kabashima Y.

Phys Rev E. 2018 Jun;97(6-1):062112. doi: 10.1103/PhysRevE.97.062112.

PMID:
30011500
28.

Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence.

Smet A, Yahara K, Rossi M, Tay A, Backert S, Armin E, Fox JG, Flahou B, Ducatelle R, Haesebrouck F, Corander J.

ISME J. 2018 Oct;12(10):2518-2531. doi: 10.1038/s41396-018-0199-5. Epub 2018 Jun 25. Erratum in: ISME J. 2019 Feb 28;:.

29.

SuperDCA for genome-wide epistasis analysis.

Puranen S, Pesonen M, Pensar J, Xu YY, Lees JA, Bentley SD, Croucher NJ, Corander J.

Microb Genom. 2018 Jun;4(6). doi: 10.1099/mgen.0.000184. Epub 2018 May 29.

30.

The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease.

Cremers AJH, Mobegi FM, van der Gaast-de Jongh C, van Weert M, van Opzeeland FJ, Vehkala M, Knol MJ, Bootsma HJ, Välimäki N, Croucher NJ, Meis JF, Bentley S, van Hijum SAFT, Corander J, Zomer AL, Ferwerda G, de Jonge MI.

Clin Infect Dis. 2019 Jan 1;68(1):61-69. doi: 10.1093/cid/ciy417.

PMID:
29788414
31.

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

Sipola A, Marttinen P, Corander J.

Bioinformatics. 2018 Jul 1;34(13):2308-2310. doi: 10.1093/bioinformatics/bty093.

PMID:
29474733
32.

Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism.

Méric G, McNally A, Pessia A, Mourkas E, Pascoe B, Mageiros L, Vehkala M, Corander J, Sheppard SK.

Genome Biol Evol. 2018 Mar 1;10(3):763-774. doi: 10.1093/gbe/evy026.

33.

Kpax3: Bayesian bi-clustering of large sequence datasets.

Pessia A, Corander J.

Bioinformatics. 2018 Jun 15;34(12):2132-2133. doi: 10.1093/bioinformatics/bty056.

PMID:
29425273
34.

Weak Epistasis May Drive Adaptation in Recombining Bacteria.

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP.

Genetics. 2018 Mar;208(3):1247-1260. doi: 10.1534/genetics.117.300662. Epub 2018 Jan 12.

35.

Identification of a Novel Genomic Island Associated with vanD-Type Vancomycin Resistance in Six Dutch Vancomycin-Resistant Enterococcus faecium Isolates.

Top J, Sinnige JC, Brouwer EC, Werner G, Corander J, Severin JA, Jansen R, Bathoorn E, Bonten MJM, Rossen JWA, Willems RJL.

Antimicrob Agents Chemother. 2018 Feb 23;62(3). pii: e01793-17. doi: 10.1128/AAC.01793-17. Print 2018 Mar.

36.

Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands.

van den Bunt G, Top J, Hordijk J, de Greeff SC, Mughini-Gras L, Corander J, van Pelt W, Bonten MJM, Fluit AC, Willems RJL.

J Antimicrob Chemother. 2018 Mar 1;73(3):607-614. doi: 10.1093/jac/dkx455.

PMID:
29294027
37.

Disease evolution in mixed connective tissue disease: results from a long-term nationwide prospective cohort study.

Reiseter S, Gunnarsson R, Corander J, Haydon J, Lund MB, Aaløkken TM, Taraldsrud E, Hetlevik SO, Molberg Ø.

Arthritis Res Ther. 2017 Dec 21;19(1):284. doi: 10.1186/s13075-017-1494-7.

38.

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

Seecharran T, Kalin-Manttari L, Koskela K, Nikkari S, Dickins B, Corander J, Skurnik M, McNally A.

Microb Genom. 2017 Sep 18;3(10):e000133. doi: 10.1099/mgen.0.000133. eCollection 2017 Oct.

39.

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJ.

Nat Ecol Evol. 2017 Dec;1(12):1950-1960. doi: 10.1038/s41559-017-0337-x. Epub 2017 Oct 16.

40.

A Bayesian Decision-Support Tool for Child Sexual Abuse Assessment and Investigation.

Tadei A, Pensar J, Corander J, Finnilä K, Santtila P, Antfolk J.

Sex Abuse. 2019 Jun;31(4):374-396. doi: 10.1177/1079063217732791. Epub 2017 Sep 21.

PMID:
28933247
41.

Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs.

Flahou B, Rossi M, Bakker J, Langermans JA, Heuvelman E, Solnick JV, Martin ME, O'Rourke J, Ngoan LD, Hoa NX, Nakamura M, Øverby A, Matsui H, Ota H, Matsumoto T, Foss DL, Kopta LA, Omotosho O, Franciosini MP, Casagrande Proietti P, Guo A, Liu H, Borilova G, Bracarense AP, Lindén SK, De Bruyckere S, Zhang G, De Witte C, Smet A, Pasmans F, Ducatelle R, Corander J, Haesebrouck F.

ISME J. 2018 Jan;12(1):77-86. doi: 10.1038/ismej.2017.145. Epub 2017 Sep 8.

42.

Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels.

Mohandesan E, Fitak RR, Corander J, Yadamsuren A, Chuluunbat B, Abdelhadi O, Raziq A, Nagy P, Stalder G, Walzer C, Faye B, Burger PA.

Sci Rep. 2017 Aug 30;7(1):9970. doi: 10.1038/s41598-017-08995-8.

43.

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.

Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, Peacock SJ, Parkhill J.

Genome Res. 2017 Jul 18. doi: 10.1101/gr.216606.116. [Epub ahead of print]

44.

Bayesian inference of physiologically meaningful parameters from body sway measurements.

Tietäväinen A, Gutmann MU, Keski-Vakkuri E, Corander J, Hæggström E.

Sci Rep. 2017 Jun 19;7(1):3771. doi: 10.1038/s41598-017-02372-1.

45.

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

Duplouy A, Wong SC, Corander J, Lehtonen R, Hanski I.

PeerJ. 2017 May 25;5:e3371. doi: 10.7717/peerj.3371. eCollection 2017.

46.

Progression and mortality of interstitial lung disease in mixed connective tissue disease: a long-term observational nationwide cohort study.

Reiseter S, Gunnarsson R, Mogens Aaløkken T, Lund MB, Mynarek G, Corander J, Haydon J, Molberg Ø.

Rheumatology (Oxford). 2018 Feb 1;57(2):255-262. doi: 10.1093/rheumatology/kex077.

PMID:
28379478
47.

Bayesian identification of bacterial strains from sequencing data.

Sankar A, Malone B, Bayliss SC, Pascoe B, Méric G, Hitchings MD, Sheppard SK, Feil EJ, Corander J, Honkela A.

Microb Genom. 2016 Aug 25;2(8):e000075. doi: 10.1099/mgen.0.000075. eCollection 2016 Aug.

48.

Response to 'Refined analyses suggest that recombination is a minor source of genomic diversity in Pseudomonas aeruginosa chronic cystic fibrosis infections' by ).

Darch SE, McNally A, Corander J, Diggle SP.

Microb Genom. 2016 Mar 2;2(3):e000054. doi: 10.1099/mgen.0.000054. eCollection 2016 Mar. No abstract available.

49.

Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion.

Llarena AK, Zhang J, Vehkala M, Välimäki N, Hakkinen M, Hänninen ML, Roasto M, Mäesaar M, Taboada E, Barker D, Garofolo G, Cammà C, Di Giannatale E, Corander J, Rossi M.

Microb Genom. 2016 Oct 21;2(10):e000088. doi: 10.1099/mgen.0.000088. eCollection 2016 Oct.

50.

Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus.

Murray S, Pascoe B, Méric G, Mageiros L, Yahara K, Hitchings MD, Friedmann Y, Wilkinson TS, Gormley FJ, Mack D, Bray JE, Lamble S, Bowden R, Jolley KA, Maiden MCJ, Wendlandt S, Schwarz S, Corander J, Fitzgerald JR, Sheppard SK.

Genome Biol Evol. 2017 Apr 1;9(4):830-842. doi: 10.1093/gbe/evx037.

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