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Items: 1 to 20 of 84

1.

Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis.

Eldholm V, Pettersson JH, Brynildsrud OB, Kitchen A, Rasmussen EM, Lillebaek T, Rønning JO, Crudu V, Mengshoel AT, Debech N, Alfsnes K, Bohlin J, Pepperell CS, Balloux F.

Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13881-13886.

2.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JT, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D.

Nature. 2016 Sep 21;538(7624):201-206. doi: 10.1038/nature18964. [Epub ahead of print]

PMID:
27654912
3.

Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: a Cross-Sectional Cohort Study in Malawi.

Shaw L, Harjunmaa U, Doyle R, Mulewa S, Charlie D, Maleta K, Callard R, Walker AS, Balloux F, Ashorn P, Klein N.

Appl Environ Microbiol. 2016 Sep 16;82(19):6057-67. doi: 10.1128/AEM.01756-16.

4.

Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis.

Eldholm V, Rieux A, Monteserin J, Lopez JM, Palmero D, Lopez B, Ritacco V, Didelot X, Balloux F.

Elife. 2016 Aug 9;5. pii: e16644. doi: 10.7554/eLife.16644.

5.

Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out.

Eldholm V, Balloux F.

Trends Microbiol. 2016 Aug;24(8):637-48. doi: 10.1016/j.tim.2016.03.007. Review.

PMID:
27068531
6.

Inferences from tip-calibrated phylogenies: a review and a practical guide.

Rieux A, Balloux F.

Mol Ecol. 2016 May;25(9):1911-24. doi: 10.1111/mec.13586. Review.

7.

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, Damgaard Pde B, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E.

Science. 2015 Aug 21;349(6250):aab3884. doi: 10.1126/science.aab3884.

8.

A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis.

Price SJ, Garner TW, Balloux F, Ruis C, Paszkiewicz KH, Moore K, Griffiths AG.

PLoS One. 2015 Jun 25;10(6):e0130500. doi: 10.1371/journal.pone.0130500.

9.

Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain.

Eldholm V, Monteserin J, Rieux A, Lopez B, Sobkowiak B, Ritacco V, Balloux F.

Nat Commun. 2015 May 11;6:7119. doi: 10.1038/ncomms8119.

10.

The genomic and phenotypic diversity of Schizosaccharomyces pombe.

Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O'Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J.

Nat Genet. 2015 Mar;47(3):235-41. doi: 10.1038/ng.3215.

11.

Rates of vaccine evolution show strong effects of latency: implications for varicella zoster virus epidemiology.

Weinert LA, Depledge DP, Kundu S, Gershon AA, Nichols RA, Balloux F, Welch JJ, Breuer J.

Mol Biol Evol. 2015 Apr;32(4):1020-8. doi: 10.1093/molbev/msu406.

12.

Collapse of amphibian communities due to an introduced Ranavirus.

Price SJ, Garner TW, Nichols RA, Balloux F, Ayres C, Mora-Cabello de Alba A, Bosch J.

Curr Biol. 2014 Nov 3;24(21):2586-91. doi: 10.1016/j.cub.2014.09.028.

13.

Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient.

Eldholm V, Norheim G, von der Lippe B, Kinander W, Dahle UR, Caugant DA, Mannsåker T, Mengshoel AT, Dyrhol-Riise AM, Balloux F.

Genome Biol. 2014 Nov 7;15(11):490. doi: 10.1186/s13059-014-0490-3.

14.

Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage.

Spagnoletti M, Ceccarelli D, Rieux A, Fondi M, Taviani E, Fani R, Colombo MM, Colwell RR, Balloux F.

MBio. 2014 Aug 19;5(4). pii: e01356-14. doi: 10.1128/mBio.01356-14.

15.

Improved calibration of the human mitochondrial clock using ancient genomes.

Rieux A, Eriksson A, Li M, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares A, Manica A, Balloux F.

Mol Biol Evol. 2014 Oct;31(10):2780-92. doi: 10.1093/molbev/msu222.

16.

The genome of a Late Pleistocene human from a Clovis burial site in western Montana.

Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E.

Nature. 2014 Feb 13;506(7487):225-9. doi: 10.1038/nature13025.

17.

Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans.

Depledge DP, Kundu S, Jensen NJ, Gray ER, Jones M, Steinberg S, Gershon A, Kinchington PR, Schmid DS, Balloux F, Nichols RA, Breuer J.

Mol Biol Evol. 2014 Feb;31(2):397-409. doi: 10.1093/molbev/mst210.

18.

Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity.

Farrer RA, Henk DA, Garner TW, Balloux F, Woodhams DC, Fisher MC.

PLoS Genet. 2013;9(8):e1003703. doi: 10.1371/journal.pgen.1003703.

19.

Regular treatments of praziquantel do not impact on the genetic make-up of Schistosoma mansoni in Northern Senegal.

Huyse T, Van den Broeck F, Jombart T, Webster BL, Diaw O, Volckaert FA, Balloux F, Rollinson D, Polman K.

Infect Genet Evol. 2013 Aug;18:100-5. doi: 10.1016/j.meegid.2013.05.007.

PMID:
23684792
20.

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic.

Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlicková H, Coombs G, Kearns AM, Hill RL, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramírez S, Feil EJ, Hudson LO, Enright MC, Balloux F, Aanensen DM, Spratt BG, Fitzgerald JR, Parkhill J, Achtman M, Bentley SD, Nübel U.

Genome Res. 2013 Apr;23(4):653-64. doi: 10.1101/gr.147710.112.

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