Publications

2015

Eldholm V, Monteserin J, Rieux A, Lopez B, Sobkowiak B, Ritacco V, Balloux F. Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain. Nat Commun. 2015 May 11;6:7119. doi:10.1038/ncomms8119

Weinert LA, Depledge DP, Kundu S, Gershon AA, Nichols RA, Balloux F, Welch JJ, Breuer J. Rates of vaccine evolution show strong effects of latency: implications for varicella zoster virus epidemiology. Mol Biol Evol. 2015 Apr;32(4):1020-8. doi: 10.1093/molbev/msu406.

Ngando JE, Rieux A, Nguidjo O, Pignolet L, Dubois C, Mehl A, Zapater MF, Carlier J, de Lapeyre de Bellaire L. A novel bioassay to monitor fungicide sensitivity in Mycosphaerella fijiensis. Pest Manag Sci. 2015 Mar;71(3):441-51. doi: 10.1002/ps.3825.

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, BalaS, 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. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet. 2015 Mar;47(3):235-41. doi: 10.1038/ng.3215.

Lassalle F, Périan S, Bataillon T, Nesme X, Duret L, Daubin V. GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands. PLoS Genet. 2015 Feb 6;11(2):e1004941. Doi: 10.1371/journal.pgen.1004941.

Moltke I, Fumagalli M, Korneliussen TS, Crawford JE, Bjerregaard P, Jørgensen  ME, Grarup N, Gulløv HC, Linneberg A, Pedersen O, Hansen T, Nielsen R, Albrechtsen A. Uncovering the genetic history of the present-day Greenlandic population. Am J Hum Genet. 2015 Jan 8;96(1):54-69. doi: 10.1016/j.ajhg.2014.11.012.

2014

Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):E5661-9. doi: 10.1073/pnas.1416991111.

Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M,  Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J,  Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18655-60. doi: 10.1073/pnas.1412627111.

Price SJ, Garner TW, Nichols RA, Balloux F, Ayres C, Mora-Cabello de Alba A, Bosch J. Collapse of amphibian communities due to an introduced Ranavirus. Curr Biol. 2014 Nov 3;24(21):2586-91. doi: 10.1016/j.cub.2014.09.028.

Eldholm V, Norheim G, von der Lippe B, Kinander W, Dahle UR, Caugant DA, Mannsåker T, Mengshoel AT, Dyrhol-Riise AM, Balloux F. Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient. Genome Biol. 2014 Nov 7;15(11):490. doi: 10.1186/s13059-014-0490-3.

Rieux A, Eriksson A, Li M, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares A, Manica A, Balloux F. Improved calibration of the human mitochondrial clock using ancient genomes. Mol Biol Evol. 2014 Oct;31(10):2780-92. doi:10.1093/molbev/msu222.

Fumagalli M, Sironi M. Human genome variability, natural selection and infectious diseases. Curr Opin Immunol. 2014 Oct;30:9-16. doi: 10.1016/j.coi.2014.05.001.

Spagnoletti M, Ceccarelli D, Rieux A, Fondi M, Taviani E, Fani R, Colombo MM, Colwell RR, Balloux F. Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage. MBio 2014 Aug 19;5(4). pii: e01356-14. doi: 10.1128/mBio.01356-14.

Rieux A, Soubeyrand S, Bonnot F, Klein EK, Ngando JE, Mehl A, Ravigne V, Carlier J, de Lapeyre de Bellaire L. Long-distance wind-dispersal of spores in a  fungal plant pathogen: estimation of anisotropic dispersal kernels from an extensive field experiment. PLoS One. 2014 Aug 12;9(8):e103225. doi: 10.1371/journal.pone.0103225

Spagnoletti M, Ceccarelli D, Rieux A, Fondi M, Taviani E, Fani R, Colombo MM,  Colwell RR, Balloux F. Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage. MBio. 2014  Aug 19;5(4). pii: e01356-14. doi: 10.1128/mBio.01356-14.

Moltke I, Grarup N, Jørgensen ME, Bjerregaard P, Treebak JT, Fumagalli M, Korneliussen TS, Andersen MA, Nielsen TS, Krarup NT, Gjesing AP, Zierath JR, Linneberg A, Wu X, Sun G, Jin X, Al-Aama J, Wang J, Borch-Johnsen K, Pedersen O,  Nielsen R, Albrechtsen A, Hansen T. A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. Nature. 2014 Aug 14;512(7513):190-3. doi: 10.1038/nature13425.

Eldholm V, Haugen A, Zienolddiny S. CTCF mediates the TERT enhancer-promoter interactions in lung cancer cells: identification of a novel enhancer region involved in the regulation of TERT gene. Int J Cancer. 2014 May 15;134(10):2305-13. doi: 10.1002/ijc.28570.

Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O'Connell MJ, McInerney JO, Born EW, Dalén L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R, Willerslev E, Wang J. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell. 2014 May 8;157(4):785-94. doi: 10.1016/j.cell.2014.03.054.

Fumagalli M, Vieira FG, Linderoth T, Nielsen R. ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics. 2014 May 15;30(10):1486-7. doi: 10.1093/bioinformatics/btu041

Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D. Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Mol Phylogenet Evol. 2014 Apr;73:202-7. doi: 10.1016/j.ympev.2014.01.005.

Wang AD, Sharp NP, Agrawal AF. Sensitivity of the distribution of mutational fitness effects to environment, genetic background, and adaptedness: a case study with Drosophila. Evolution. 2014 Mar;68(3):840-53. doi: 10.1111/evo.12309.

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. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 2014 Feb  13;506(7487):225-9. doi: 10.1038/nature13025

Depledge DP, Kundu S, Jensen NJ, Gray ER, Jones M, Steinberg S, Gershon A, Kinchington PR, Schmid DS, Balloux F, Nichols RA, Breuer J. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol Biol Evol. 2014 Feb;31(2):397-409. doi: 10.1093/molbev/mst210.

2013

Valia R, Taviani E, Spagnoletti M, Ceccarelli D, Cappuccinelli P, Colombo MM. Vibrio cholerae O1 epidemic variants in Angola: a retrospective study between 1992 and 2006. Front Microbiol. 2013 Nov 28;4:354. doi: 10.3389/fmicb.2013.00354.

Ceccarelli D, Spagnoletti M, Hasan NA, Lansing S, Huq A, Colwell RR. A new integrative conjugative element detected in Haitian isolates of Vibrio cholera non-O1/non-O139. Res Microbiol. 2013 Nov;164(9):891-3. doi: 10.1016/j.resmic.2013.08.004

Bermond G, Blin A, Vercken E, Ravigné V, Rieux A, Mallez S, Morel-Journel T, Guillemaud T. Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks. Mol Ecol. 2013 Nov;22(21):5368-81. doi: 10.1111/mec.12489.

Fumagalli M. Assessing the effect of sequencing depth and sample size in population genetics inferences. PLoS One. 2013 Nov 18;8(11):e79667. doi: 10.1371/journal.pone.0079667.

Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sánchez E, Albrechtsen A, Nielsen R. Quantifying population genetic differentiation from next-generation sequencing data. Genetics. 2013 Nov;195(3):979-92. doi: 10.1534/genetics.113.154740.

Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R. Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res. 2013 Nov;23(11):1852-61. doi: 10.1101/gr.157388.113

Farrer RA, Henk DA, Garner TW, Balloux F, Woodhams DC, Fisher MC. Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity. PLoS Genet. 2013 Aug;9(8):e1003703. doi: 10.1371/journal.pgen.1003703. 

Somel M, Wilson Sayres MA, Jordan G, Huerta-Sanchez E, Fumagalli M, Ferrer-Admetlla A, Nielsen R. A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes. Mol Biol Evol. 2013 Aug;30(8):1808-15. doi: 10.1093/molbev/mst098.

Khouadja S, Suffredini E, Spagnoletti M, Croci L, Colombo MM, Amina B. Presence of pathogenic Vibrio parahaemolyticus in waters and seafood from the Tunisian Sea. World J Microbiol Biotechnol. 2013 Aug;29(8):1341-8. doi: 10.1007/s11274-013-1297-1.

Doherty-Bone TM, Ndifon RK, Nyingchia ON, Landrie FE, Yonghabi FT, Duffus ALJ, Price SJ, Perkins M, Bielby J, Kome NB, LeBreton M, Gonwouo LN & AA Cunningham. Morbidity and mortality of the critically endangered Lake Oku clawed frog (Xenopus longipes). Endangered Species Research. 2103 Aug;21: 115-128 doi: 10.3354/esr00514

Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert  M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT,  Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF,  Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 2013 Jul 4;499(7456):74-8. doi: 10.1038/nature12323. 

Rieux A., Lenormand T., Carlier J., De Lapeyre De Bellaire L. and Ravigne V: Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen. Ecology Letters, 2013 Jun;16(6):721-30. doi: 10.1111/ele.12090.

Cagliani R, Guerini FR, Rubio-Acero R, Baglio F, Forni D, Agliardi C, Griffanti L,Fumagalli M, Pozzoli U, Riva S, Calabrese E, Sikora M, Casals F, Comi GP, Bresolin N, Cáceres M, Clerici M, Sironi M. Long-standing balancing selection in the THBS4 gene: influence on sex-specific brain expression and gray  matter volumes in Alzheimer disease. Hum Mutat. 2013 May;34(5):743-53. doi: 10.1002/humu.22301.

Cagliani R, Pozzoli U, Forni D, Cassinotti A, Fumagalli M, Giani M, Fichera M, Lombardini M, Ardizzone S, Asselta R, de Franchis R, Riva S, Biasin M, Comi GP, Bresolin N, Clerici M, Sironi M. Crohn's disease loci are common targets of protozoa-driven selection. Mol Biol Evol. 2013 May;30(5):1077-87. doi: 10.1093/molbev/mst020.

McInnes L, Jones FA, Orme CD, Sobkowiak B, Barraclough TG, Chase MW, Govaerts R, Soltis DE, Soltis PS, Savolainen V. Do global diversity patterns of vertebrates reflect those of monocots? PLoS One. 2013 May1;8(5):e56979. doi:10.1371/journal.pone.0056979.

Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz  C, Sismeiro O, Vallenet D, Santini JM, Bertin PN. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26. Genome Biol Evol. 2013 Apr ;5(5):934-53. doi: 10.1093/gbe/evt061.

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. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res. 2013 Apr;23(4):653-64. doi: 10.1101/gr.147710.112.

Bigot T, Daubin V, Lassalle F, Perrière G. TPMS: a set of utilities for querying collections of gene trees. BMC Bioinformatics. 2013 Mar 27;14:109. doi:10.1186/1471-2105-14-109.

Cui Y, Yu C, Yan Y, Li D, Li Y, Jombart T, Weinert LA, Wang Z, Guo Z, Xu L, Zhang Y, Zheng H, Qin N, Xiao X, Wu M, Wang X, Zhou D, Qi Z, Du Z, Wu H, Yang X, Cao H, Wang H, Wang J, Yao S, Rakin A, Li Y, Falush D, Balloux F, Achtman M, Song Y, Wang J, Yang R. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):577-82. doi: 10.1073/pnas.1205750110.

Rieux A, De Lapeyre De Bellaire L, Zapater MF, Ravigne V and Carlier J: Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis. Heredity 2013 Jan;110(1):29-38. doi: 10.1038/hdy.2012.55

Jones, FA, Sobkowiak B, C. D. L. Orme, R. Goeaverts, and V Savolainen. Mracoecological correlates of global monocot species richness. Early events in monocot evolution. Cambridge University Press. 2013.

2012

Perillo J, Ceccarelli D, Spagnoletti M, Lollai S, Cappuccinelli P, Colombo MM. Molecular characterization of enterotoxigenic and borderline oxacillin resistant  Staphylococcus strains from ovine milk. Food Microbiol. 2012 Dec;32(2):265-73. doi: 10.1016/j.fm.2012.06.009.

Farrer RA, Weinert LA, Bielby J, Garner TW, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, Anderson L, Pond SL, Shahar-Golan R, Henk DA, Fisher MC. Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18732-6. doi: 10.1073/pnas.1111915108.

Wang AD, Agrawal AF. DNA repair pathway choice is influenced by the health of  Drosophila melanogaster. Genetics. 2012 Oct;192(2):361-70. doi: 10.1534/genetics.112.143321.

Eriksson A, Betti L, Friend AD, Lycett SJ, Singarayer JS, von Cramon-Taubadel N, Valdes PJ, Balloux F, Manica A. Late Pleistocene climate change and the global expansion of anatomically modern humans. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16089-94. doi: 10.1073/pnas.1209494109.

Chymkowitch P, Eldholm V, Lorenz S, Zimmermann C, Lindvall JM, Bjørås M, Meza-Zepeda LA, Enserink JM. Cdc28 kinase activity regulates the basal transcription machinery at a subset of genes. Proc Natl Acad Sci U S A. 2012 Jun  26;109(26):10450-5. doi: 10.1073/pnas.1200067109.

Taviani E, Spagnoletti M, Ceccarelli D, Haley BJ, Hasan NA, Chen A, Colombo MM, Huq A, Colwell RR. Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae. FEBS Lett. 2012 Jun 4;586(11):1617-21. doi: 10.1016/j.febslet.2012.03.064.

Cagliani R, Riva S, Marino C, Fumagalli M, D'Angelo MG, Riva V, Comi GP, Pozzoli U, Forni D, Cáceres M, Bresolin N, Clerici M, Sironi M. Variants in SNAP25 are targets of natural selection and influence verbal performances in women. Cell Mol Life Sci. 2012 May;69(10):1705-15. doi: 10.1007/s00018-011-0896-y

Qutob N, Balloux F, Raj T, Liu H, Marion de Procé S, Trowsdale J, Manica A. Signatures of historical demography and pathogen richness on MHC class I genes.Immunogenetics. 2012 Mar;64(3):165-75. doi: 10.1007/s00251-011-0576-y.

Balloux F, Lehmann L. Substitution rates at neutral genes depend on population size under fluctuating demography and overlapping generations. Evolution. 2012 Feb;66(2):605-11. doi: 10.1111/j.1558-5646.2011.01458.x.

Yalcindag E, Elguero E, Arnathau C, Durand P, Akiana J, Anderson TJ, Aubouy A, Balloux F, Besnard P, Bogreau H, Carnevale P, D'Alessandro U, Fontenille D, Gamboa D, Jombart T, Le Mire J, Leroy E, Maestre A, Mayxay M, Ménard D, Musset L, Newton PN, Nkoghé D, Noya O, Ollomo B, Rogier C, Veron V, Wide A, Zakeri S, Carme B, Legrand E, Chevillon C, Ayala FJ, Renaud F, Prugnolle F. Multiple independent  introductions of Plasmodium falciparum in South America. Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):511-6. doi: 10.1073/pnas.1119058109.

Cagliani R, Fumagalli M, Guerini FR, Riva S, Galimberti D, Comi GP, Agliardi  C, Scarpini E, Pozzoli U, Forni D, Caputo D, Asselta R, Biasin M, Paraboschi EM,  Bresolin N, Clerici M, Sironi M. Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis. Hum Genet. 2012 Jan;131(1):87-97. doi: 10.1007/s00439-011-1053-2

Spagnoletti M, Ceccarelli D, Colombo MM. Rapid detection by multiplex PCR of Genomic Islands, prophages and Integrative Conjugative Elements in V. cholera 7th pandemic variants. J Microbiol Methods. 2012 Jan;88(1):98-102. doi: 10.1016/j.mimet.2011.10.017.

2011

Sironi M, Guerini FR, Agliardi C, Biasin M, Cagliani R, Fumagalli M, Caputo D, Cassinotti A, Ardizzone S, Zanzottera M, Bolognesi E, Riva S, Kanari Y, Miyazawa M, Clerici M. An evolutionary analysis of RAC2 identifies haplotypes associated with human autoimmune diseases. Mol Biol Evol. 2011 Dec;28(12):3319-29. doi: 10.1093/molbev/msr164.

Manry J, Laval G, Patin E, Fornarino S, Itan Y, Fumagalli M, Sironi M, Tichit M, Bouchier C, Casanova JL, Barreiro LB, Quintana-Murci L. Evolutionary genetic dissection of human interferons. J Exp Med. 2011 Dec 19;208(13):2747-59. doi: 10.1084/jem.20111680.

Zimmermann C, Chymkowitch P, Eldholm V, Putnam CD, Lindvall JM, Omerzu M, Bjørås M, Kolodner RD, Enserink JM. A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 to cell cycle progression. Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18748-53. doi: 10.1073/pnas.1115885108.

Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admetlla A, Pattini L, Nielsen R. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet. 2011 Nov;7(11):e1002355.  doi: 10.1371/journal.pgen.1002355..

Cagliani R, Riva S, Fumagalli M, Biasin M, Caputo SL, Mazzotta F, Piacentini  L, Pozzoli U, Bresolin N, Clerici M, Sironi M. A positively selected APOBEC3H haplotype is associated with natural resistance to HIV-1 infection. Evolution. 2011 Nov;65(11):3311-22. doi: 10.1111/j.1558-5646.2011.01368.x.

Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A,  Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M,  Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut  FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science. 2011 Oct 7;334(6052):94-8. doi: 10.1126/science.1211177.

Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams  M, Abrouk D, Lavire C, Oger-Desfeux C, Hommais F, Guéguen L, Daubin V, Muller D,  Nesme X. Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol. 2011 Jul;3:762-81. doi: 10.1093/gbe/evr070.

Cagliani R, Riva S, Pozzoli U, Fumagalli M, Comi GP, Bresolin N, Clerici M, Sironi M. Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving. BMC Evol Biol. 2011 Jun 17;11:171. doi: 10.1186/1471-2148-11-171.

Ceccarelli D, Spagnoletti M, Bacciu D, Cappuccinelli P, Colombo MM. New V. cholerae atypical El Tor variant emerged during the 2006 epidemic outbreak in Angola. BMC Microbiol. 2011 Jun 13;11:130. doi: 10.1186/1471-2180-11-130.

Ceccarelli D, Spagnoletti M, Cappuccinelli P, Burrus V, Colombo MM. Origin of  Vibrio cholerae in Haiti. Lancet Infect Dis. 2011 Apr;11(4):262. doi: 10.1016/S1473-3099(11)70078-0.

Ceccarelli D, Spagnoletti M, Bacciu D, Danin-Poleg Y, Mendiratta DK, Kashi Y, Cappuccinelli P, Burrus V, Colombo MM. ICEVchInd5 is prevalent in epidemic Vibrio cholerae O1 El Tor strains isolated in India. Int J Med Microbiol. 2011 Apr;301(4):318-24. doi: 10.1016/j.ijmm.2010.11.005.

Rieux A, Halkett F, de Lapeyre de Bellaire L, Zapater MF, Rousset F, Ravigne V, Carlier J: Inferences on pathogenic fungus population structures from microsatellite data: new insights from spatial genetics approaches. Molecular ecology 2011 Apr;20(8):1661-74. doi: 10.1111/j.1365-294X.2011.05053.x

Abbot P, Abe J, Alcock J, Alizon S, Alpedrinha JA, Andersson M, Andre JB, van Baalen M, Balloux F, Balshine S, Barton N, Beukeboom LW, Biernaskie JM, Bilde T,  Borgia G, Breed M, Brown S, Bshary R, Buckling A, Burley NT, Burton-Chellew MN, Cant MA, Chapuisat M, Charnov EL, Clutton-Brock T, Cockburn A, Cole BJ, Colegrave N, Cosmides L, Couzin ID, Coyne JA, Creel S, Crespi B, Curry RL, Dall SR, Day T,  Dickinson JL, Dugatkin LA, El Mouden C, Emlen ST, Evans J, Ferriere R, Field J, Foitzik S, Foster K, Foster WA, Fox CW, Gadau J, Gandon S, Gardner A, Gardner MG, Getty T, Goodisman MA, Grafen A, Grosberg R, Grozinger CM, Gouyon PH, Gwynne D, Harvey PH, Hatchwell BJ, Heinze J, Helantera H, Helms KR, Hill K, Jiricny N, Johnstone RA, Kacelnik A, Kiers ET, Kokko H, Komdeur J, Korb J, Kronauer D, Kümmerli R, Lehmann L, Linksvayer TA, Lion S, Lyon B, Marshall JA, McElreath R, Michalakis Y, Michod RE, Mock D, Monnin T, Montgomerie R, Moore AJ, Mueller UG, Noë R, Okasha S, Pamilo P, Parker GA, Pedersen JS, Pen I, Pfennig D, Queller DC,  Rankin DJ, Reece SE, Reeve HK, Reuter M, Roberts G, Robson SK, Roze D, Rousset F, Rueppell O, Sachs JL, Santorelli L, Schmid-Hempel P, Schwarz MP, Scott-Phillips T, Shellmann-Sherman J, Sherman PW, Shuker DM, Smith J, Spagna JC, Strassmann B,  Suarez AV, Sundström L, Taborsky M, Taylor P, Thompson G, Tooby J, Tsutsui ND, Tsuji K, Turillazzi S, Ubeda F, Vargo EL, Voelkl B, Wenseleers T, West SA, West-Eberhard MJ, Westneat DF, Wiernasz DC, Wild G, Wrangham R, Young AJ, Zeh DW, Zeh JA, Zink A. Inclusive fitness theory and eusociality. Nature. 2011 Mar 24;471(7339):E1-4; author reply E9-10. doi: 10.1038/nature09831.

2010

Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner  P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet. 2010 Dec;42(12):1140-3. doi: 10.1038/ng.705.

Robert S, Rieux A, Argout X, Carlier J, Zapater MF. Optimized genotyping with  microsatellite markers in the fungal banana pathogen Mycosphaerella fijiensis (Mycosphaerellaceae). Am J Bot. 2010 Dec;97(12):e130-2. doi: 10.3732/ajb.1000295.

Cagliani R, Riva S, Biasin M, Fumagalli M, Pozzoli U, Lo Caputo S, Mazzotta F, Piacentini L, Bresolin N, Clerici M, Sironi M. Genetic diversity at endoplasmic reticulum aminopeptidases is maintained by balancing selection and is associated with natural resistance to HIV-1 infection. Hum Mol Genet. 2010 Dec 1;19(23):4705-14. doi: 10.1093/hmg/ddq401.

Fumagalli M, Cagliani R, Riva S, Pozzoli U, Biasin M, Piacentini L, Comi GP,  Bresolin N, Clerici M, Sironi M. Population genetics of IFIH1: ancient population structure, local selection, and implications for susceptibility to type 1 diabetes. Mol Biol Evol. 2010 Nov;27(11):2555-66. doi: 10.1093/molbev/msq141.

Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010 Oct 15;11:94. doi: 10.1186/1471-2156-11-94.

Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M. The landscape of human genes involved in the immune response to parasitic worms.  BMC Evol Biol. 2010 Aug 31;10:264. doi: 10.1186/1471-2148-10-264

Torri F, Akelai A, Lupoli S, Sironi M, Amann-Zalcenstein D, Fumagalli M, Dal  Fiume C, Ben-Asher E, Kanyas K, Cagliani R, Cozzi P, Trombetti G, Strik Lievers L, Salvi E, Orro A, Beckmann JS, Lancet D, Kohn Y, Milanesi L, Ebstein RB, Lerer  B, Macciardi F. Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence. FASEB J. 2010 Aug;24(8):3066-82. doi: 10.1096/fj.09-152611

Cagliani R, Fumagalli M, Riva S, Pozzoli U, Fracassetti M, Bresolin N, Comi GP, Sironi M. Polymorphisms in the CPB2 gene are maintained by balancing selection and result in haplotype-preferential splicing of exon 7. Mol Biol Evol.2010 Aug;27(8):1945-54. doi: 10.1093/molbev/msq082.

Jombart T, Balloux F, Dray S. adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics. 2010 Aug 1;26(15):1907-9. doi: 10.1093/bioinformatics/btq292.

Tanabe K, Mita T, Jombart T, Eriksson A, Horibe S, Palacpac N, Ranford-Cartwright L, Sawai H, Sakihama N, Ohmae H, Nakamura M, Ferreira MU, Escalante AA, Prugnolle F, Björkman A, Färnert A, Kaneko A, Horii T, Manica A, Kishino H, Balloux F. Plasmodium falciparum accompanied the human expansion out of Africa. Curr Biol. 2010 Jul 27;20(14):1283-9. doi: 10.1016/j.cub.2010.05.053.

Eldholm V, Johnsborg O, Straume D, Ohnstad HS, Berg KH, Hermoso JA, Håvarstein LS. Pneumococcal CbpD is a murein hydrolase that requires a dual cell envelope binding specificity to kill target cells during fratricide. Mol Microbiol. 2010 May;76(4):905-17. doi: 10.1111/j.1365-2958.2010.07143.x.

Eldholm V, Gutt B, Johnsborg O, Brückner R, Maurer P, Hakenbeck R, Mascher T,  Håvarstein LS. The pneumococcal cell envelope stress-sensing system LiaFSR is activated by murein hydrolases and lipid II-interacting antibiotics. J Bacteriol. 2010 Apr;192(7):1761-73. doi: 10.1128/JB.01489-09.

Nübel U, Dordel J, Kurt K, Strommenger B, Westh H, Shukla SK, Zemlicková H, Leblois R, Wirth T, Jombart T, Balloux F, Witte W. A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathog. 2010 Apr 8;6(4):e1000855. doi: 10.1371/journal.ppat.1000855

Pozzoli U, Fumagalli M, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M. The role of protozoa-driven selection in shaping human genetic variability. Trends Genet. 2010 Mar;26(3):95-9. doi: 10.1016/j.tig.2009.12.010.

Hiby SE, Ashrafian-Bonab M, Farrell L, Single RM, Balloux F, Carrington M, Moffett A, Ebrahimi Z. Distribution of killer cell immunoglobulin-like receptors  (KIR) and their HLA-C ligands in two Iranian populations. Immunogenetics. 2010 Feb;62(2):65-73. doi: 10.1007/s00251-009-0408-5.

Cagliani R, Fumagalli M, Riva S, Pozzoli U, Comi GP, Bresolin N, Sironi M. Genetic variability in the ACE gene region surrounding the Alu I/D polymorphism is maintained by balancing selection in human populations. Pharmacogenet Genomics. 2010 Feb;20(2):131-4. doi: 10.1097/FPC.0b013e3283333532.

Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M. Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach. PLoS Genet. 2010 Feb 19;6(2):e1000849. doi: 10.1371/journal.pgen.1000849.

Del Rio P, Dell'Abate P, Gomes B, Fumagalli M, Papadia C, Coruzzi A, Leonardi F, Pucci F, Sianesi M. Analysis of risk factors for complications in 262 cases of laparoscopic colectomy. Ann Ital Chir. 2010 Jan-Feb;81(1):21-30.

Betti L, Balloux F, Hanihara T, Manica A. The relative role of drift and selection in shaping the human skull. Am J Phys Anthropol. 2010 Jan;141(1):76-82. doi: 10.1002/ajpa.21115.

2009

Wang AD, Sharp NP, Spencer CC, Tedman-Aucoin K, Agrawal AF. Selection, epistasis, and parent-of-origin effects on deleterious mutations across environments in Drosophila melanogaster. Am Nat. 2009 Dec;174(6):863-74. doi: 10.1086/645088.

Wozniak RA, Fouts DE, Spagnoletti M, Colombo MM, Ceccarelli D, Garriss G, Déry C, Burrus V, Waldor MK. Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 2009 Dec;5(12):e1000786. doi: 10.1371/journal.pgen.1000786.

Brown AR, Hosken DJ, Balloux F, Bickley LK, LePage G, Owen SF, Hetheridge MJ, Tyler CR. Genetic variation, inbreeding and chemical exposure--combined effects in wildlife and critical considerations for ecotoxicology. Philos Trans R Soc Lond B Biol Sci. 2009 Nov 27;364(1534):3377-90. doi: 10.1098/rstb.2009.0126.

Balloux F, Handley LJ, Jombart T, Liu H, Manica A. Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. Proc Biol Sci. 2009 Oct 7;276(1672):3447-55. doi: 10.1098/rspb.2009.0752

Jombart T, Eggo RM, Dodd P, Balloux F. Spatiotemporal dynamics in the early stages of the 2009 A/H1N1 influenza pandemic. PLoS Curr. 2009 Aug 31;1:RRN1026.

Eldholm V, Johnsborg O, Haugen K, Ohnstad HS, Håvarstein LS. Fratricide in Streptococcus pneumoniae: contributions and role of the cell wall hydrolases CbpD, LytA and LytC. Microbiology. 2009 Jul;155(Pt 7):2223-34. doi: 10.1099/mic.0.026328-0.

Cagliani R, Fumagalli M, Pozzoli U, Riva S, Comi GP, Torri F, Macciardi F, Bresolin N, Sironi M. Diverse evolutionary histories for beta-adrenoreceptor genes in humans. Am J Hum Genet. 2009 Jul;85(1):64-75. doi: 10.1016/j.ajhg.2009.06.005.

Cagliani R, Fumagalli M, Pozzoli U, Riva S, Cereda M, Comi GP, Pattini L, Bresolin N, Sironi M. A complex selection signature at the human AVPR1B gene. BMC Evol Biol. 2009 Jun 1;9:123. doi: 10.1186/1471-2148-9-123.

Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Riva S, Clerici M, Bresolin N, Sironi M. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. J Exp Med. 2009 Jun 8;206(6):1395-408. doi: 10.1084/jem.20082779.

Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly  NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Alpuche-Aranda CM, Chapela IB, Zavala EP, Guevara DM, Checchi F, Garcia E, Hugonnet S, Roth C; WHO Rapid Pandemic Assessment Collaboration. Pandemic potential of a strain of influenza A (H1N1): early findings. Science. 2009 Jun 19;324(5934):1557-61. doi: 10.1126/science.1176062.

Betti L, Balloux F, Amos W, Hanihara T, Manica A. Distance from Africa, not climate, explains within-population phenotypic diversity in humans. Proc Biol Sci. 2009 Mar 7;276(1658):809-14. doi: 10.1098/rspb.2008.1563.

Fumagalli M, Cagliani R, Pozzoli U, Riva S, Comi GP, Menozzi G, Bresolin N, Sironi M. Widespread balancing selection and pathogen-driven selection at blood group antigen genes. Genome Res. 2009 Feb;19(2):199-212. doi: 10.1101/gr.082768.108.

Del Rio P, Dell'Abate P, Soliani P, Arcuri MF, Gomes B, Fumagalli M, Sianesi M. Defunctioning stoma in high-risk rectal anastomosis. Acta Biomed. 2009;80(3):234-7.

2008

Schwarz S, Morelli G, Kusecek B, Manica A, Balloux F, Owen RJ, Graham DY, van der Merwe S, Achtman M, Suerbaum S. Horizontal versus familial transmission of Helicobacter pylori. PLoS Pathog. 2008 Oct;4(10):e1000180. doi: 10.1371/journal.ppat.1000180.

Cagliani R, Fumagalli M, Riva S, Pozzoli U, Comi GP, Menozzi G, Bresolin N, Sironi M. The signature of long-standing balancing selection at the human defensin beta-1 promoter. Genome Biol. 2008;9(9):R143. doi: 10.1186/gb-2008-9-9-r143.

Johnsborg O, Eldholm V, Bjørnstad ML, Håvarstein LS. A predatory mechanism dramatically increases the efficiency of lateral gene transfer in Streptococcus pneumoniae and related commensal species. Mol Microbiol. 2008 Jul;69(1):245-53.doi: 10.1111/j.1365-2958.2008.06288.x.

Pozzoli U, Menozzi G, Fumagalli M, Cereda M, Comi GP, Cagliani R, Bresolin N, Sironi M. Both selective and neutral processes drive GC content evolution in the  human genome. BMC Evol Biol. 2008 Mar 27;8:99. doi: 10.1186/1471-2148-8-99.

Agrawal AF, Wang AD. Increased transmission of mutations by low-condition females: evidence for condition-dependent DNA repair. PLoS Biol. 2008 Feb;6(2):e30. doi: 10.1371/journal.pbio.0060030

2007

Johnsborg O, Eldholm V, Håvarstein LS. Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol. 2007 Dec;158(10):767-78

Dahle UR, Eldholm V, Winje BA, Mannsåker T, Heldal E. Impact of immigration on the molecular epidemiology of Mycobacterium tuberculosis in a low-incidence country. Am J Respir Crit Care Med. 2007 Nov 1;176(9):930-5.

Szmaragd C, Balloux F. The population genomics of hepatitis B virus. Mol Ecol. 2007 Nov;16(22):4747-58.

Balloux F. [Helicobacter pylori, our faithful gastric companion]. Med Sci (Paris). 2007 Aug-Sep;23(8-9):705-6. French.

Handley LJ, Manica A, Goudet J, Balloux F. Going the distance: human population genetics in a clinal world. Trends Genet. 2007 Sep;23(9):432-9.

Manica A, Amos W, Balloux F, Hanihara T. The effect of ancient population bottlenecks on human phenotypic variation. Nature. 2007 Jul 19;448(7151):346-8.

Lehmann L, Balloux F. Natural selection on fecundity variance in subdivided populations: kin selection meets bet hedging. Genetics. 2007 May;176(1):361-77.

Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, Falush D, Stamer  C, Prugnolle F, van der Merwe SW, Yamaoka Y, Graham DY, Perez-Trallero E, Wadstrom T, Suerbaum S, Achtman M. An African origin for the intimate association between humans and Helicobacter pylori. Nature. 2007 Feb 22;445(7130):915-8

2006

Eldholm V, Matee M, Mfinanga SG, Heun M, Dahle UR. A first insight into the genetic diversity of Mycobacterium tuberculosis in Dar es Salaam, Tanzania, assessed by spoligotyping. BMC Microbiol. 2006 Sep 13;6:76.

Liu H, Prugnolle F, Manica A, Balloux F. A geographically explicit genetic model of worldwide human-settlement history. Am J Hum Genet. 2006 Aug;79(2):230-7.

de Meeûs T, Lehmann L, Balloux F. Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice. Infect Genet Evol. 2006 Mar;6(2):163-70.

Szmaragd C, Nichols RA, Balloux F. A novel approach to characterise pathogen  candidate genetic polymorphisms involved in clinical outcome. Infect Genet Evol. 2006 Jan;6(1):38-45.

2005

Manica A, Prugnolle F, Balloux F. Geography is a better determinant of human  genetic differentiation than ethnicity. Hum Genet. 2005 Dec;118(3-4):366-71.

De Meeûs T, Balloux F. F-statistics of clonal diploids structured in numerous demes. Mol Ecol. 2005 Aug;14(9):2695-702.

Prugnolle F, Manica A, Charpentier M, Guégan JF, Guernier V, Balloux F. Pathogen-driven selection and worldwide HLA class I diversity. Curr Biol. 2005 Jun 7;15(11):1022-7.

Halkett F, Simon JC, Balloux F. Tackling the population genetics of clonal and partially clonal organisms. Trends Ecol Evol. 2005 Apr;20(4):194-201.

Gantenbein B, Fet V, Gantenbein-Ritter IA, Balloux F. Evidence for recombination in scorpion mitochondrial DNA (Scorpiones: Buthidae). Proc Biol Sci. 2005 Apr 7;272(1564):697-704.

Prugnolle F, Manica A, Balloux F. Geography predicts neutral genetic diversity of human populations. Curr Biol. 2005 Mar 8;15(5):R159-60.

Prugnolle F, Liu H, de Meeûs T, Balloux F. Population genetics of complex life-cycle parasites: an illustration with trematodes. Int J Parasitol. 2005 Mar;35(3):255-63.

2004

de Meeûs T, Balloux F. Clonal reproduction and linkage disequilibrium in diploids: a simulation study. Infect Genet Evol. 2004 Dec;4(4):345-51

Balloux F. Heterozygote excess in small populations and the heterozygote-excess effective population size. Evolution. 2004 Sep;58(9):1891-900.

2003

Balloux F, Lehmann L. Random mating with a finite number of matings. Genetics. 2003 Dec;165(4):2313-5.

Balloux F, Lehmann L, de Meeûs T. The population genetics of clonal and partially clonal diploids. Genetics. 2003 Aug;164(4):1635-44.

Rivero A, Balloux F, West SA. Testing for epistasis between deleterious mutations in a parasitoid wasp. Evolution. 2003 Jul;57(7):1698-703

Roulin A, Ducrest AL, Balloux F, Dijkstra C, Riols C. A female melanin ornament signals offspring fluctuating asymmetry in the barn owl. Proc Biol Sci.  2003 Jan 22;270(1511):167-71.

2002

Balloux F, Lugon-Moulin N. The estimation of population differentiation with  microsatellite markers. Mol Ecol. 2002 Feb;11(2):155-65. Review.