Publications 
Preprints
Wellbank C. and Aris-Brosou S. Viral evolutionary dynamics predict Influenza-Like-Illnesses in patients. bioRxiv. (bioRxiv preprint).
Ibeh N. and Aris-Brosou S. Estimation of sub-epidemic dynamics by means of Sequential Monte Carlo Approximate Bayesian Computation: an application to the Swiss HIV Cohort Study. bioRxiv. (bioRxiv preprint).
2021
58. Shoji A., Elliott K.H., Watanuki Y., Basu N., Whelan S., Cunningham J., Hatch S., Mizukawa H., Nakayama S.M.M., Ikenaka Y., Ishizuka M. and Aris-Brosou S. In press. Geolocators link marine mercury with levels in wild seabirds throughout their annual cycle: consequences for trans-ecosystem biotransport. Environmental Pollution. NN:NNN-NNN. (reprint).
2020
57. Colby G., Ruuskanen M.O., St.Pierre K.A., St.Louis V.L., Poulain A.J., Aris-Brosou S. 2020. Warming climate is reducing the diversity of dominant microbes in the largest High Arctic lake. Frontiers in Microbiology. 11:2316. (bioRxiv preprint; reprint).
56. Dench J., Hinz A., Aris-Brosou S. and Kassen R. 2020. Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection. Evolutionary Applications. 13:782-794. (bioRxiv preprint; reprint).
55. Ruuskanen M.O., Aris-Brosou S. and Poulain A.J. 2020. Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere. The ISME Journal. 14:788-800. (reprint; Nature Microbiology Community blog post).
54. Ruuskanen M.O., Colby G., St.Pierre K.A., St.Louis V.L., Aris-Brosou S. and Poulain A.J. 2020. Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments. Limnology and Oceanography. 65:S233-S247. (bioRxiv preprint; reprint).
2019
53. Aris-Brosou S. 2019. Direct evidence of an increasing mutational load in humans. Molecular Biology and Evolution. 36:2823–2829. (bioRxiv preprint; reprint). Featured on the cover of New Scientist (Issue 3247, Sep 14, 2019).
52. Aris-Brosou S., Parent L. and Ibeh N. 2019. Episodic diversifying selection and intragenomic interactions shape the evolution of DNA and RNA viruses. Viruses. 11:677. (bioRxiv preprint; reprint).
51. Guigueno M.F., Shoji A., Elliott K.H. and Aris-Brosou S. 2019. Flight costs in volant vertebrates: a phylogenetically-controlled meta-analysis of birds and bats. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. 235:193-201. (reprint).
50. Long G.S., Hussen M., Dench J. and Aris-Brosou S. 2019. Identifying genetic determinants of complex phenotypes from whole genome sequence data. BMC Genomics. 20:470. (bioRxiv preprint; reprint).
49. Aris-Brosou S. and Rodrigue N. 2019. A not-so-long introduction to computational molecular evolution. Methods in Molecular Biology. 1910:71-117. (reprint).
48. Shoji A., Elliott K.H., Aris-Brosou S., Mizukawa H., Nakayama S.M.M., Ikenaka Y., Ishizuka M. , Kuwae T., Watanabe K., Gonzalez J.E. and Watanuki Y. 2019. Biotransport of metallic trace elements from marine to terrestrial ecosystems by seabirds. Environmental Toxicology and Chemistry. 38:106-114.(reprint).
2018
47. Ruuskanen M.O., St.Pierre K.A., St.Louis V.L., Aris-Brosou S. and Poulain A.J. 2018. Physicochemical drivers of microbial community structures in sediments of Lake Hazen, Nunavut, Canada. Frontiers in Microbiology. 9:1138. (reprint).
46. Byrne L., Chapleau F. and Aris-Brosou S. 2018. How the Central American Seaway and an ancient northern passage affected Flatfish diversification. Molecular Biology and Evolution. 35:1982-1989. (bioRxiv preprint; reprint).
45. Aris-Brosou S., Kim J., Li L. and Liu H. 2018. Predicting the reasons of customer complaints: a first step towards anticipating quality issues of in vitro diagnostics assays with machine learning. JMIR Medical Informatics. 6:e34. (reprint).
2017
44. Aris-Brosou S., Ibeh N. and Noel J. 2017. Viral outbreaks involve destabilised viruses: evidence from Ebola, Influenza and Zika. Scientific Reports. 7:11881.(bioRxiv preprint; reprint).
43. Nshogozabahizi J.C., Dench J. and Aris-Brosou S. 2017. Widespread historical contingency in Influenza viruses. Genetics. 205:409-420. (bioRxiv preprint; reprint). Issue highlights. Our cover image submission was displayed on the journal's carousel.
2016
42. Ibeh N., Nshogozabahizi J.C. and Aris-Brosou S. 2016. Both epistasis and diversifying selection drive the structural evolution of the EBOV Glycoprotein mucin-like domain. Journal of Virology. 90:5475-5484. (reprint).
41. Labonté K. and Aris-Brosou S. 2016. Automatic detection of rate change in large data sets with an unsupervised approach: the case of influenza viruses. Genome. 59:253-262. (reprint).
40. Shoji A., Aris-Brosou S., Owen E., Bolton M., Boyle D., Fayet A., Dean B., Kirk H., Freeman R., Perrins C.M. and Guilford T. 2016. Foraging flexibility and search patterns are unlinked during breeding in a free-ranging seabird. Marine Biology. 163:72. (reprint).
39. Shoji A., Aris-Brosou S. and Elliott K.H. 2016. Physiological constraints and dive behavior scale in tandem with body mass in auks: A comparative analysis. Comparative Biochemistry and Physiology - Part A. 196:54-60. (reprint).
2015
38. Pelin A., Selman M., Aris-Brosou S.,Farinelli L. and Corradi N. 2015. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environmental Microbiology. 17:4443-4458. (reprint).
37. Poulain A., Aris-Brosou S., Blais J., Brazeau M., Paterson A. and Keller B. 2015. Microbial DNA records historical delivery of anthropogenic mercury. The ISME Journal. 9:2541-2550. (reprint). Editors' Choice in Science (Volume 349, Number 6244, Issue of 10 July 2015).
36. Shoji A., Aris-Brosou S., Culina A., Fayet A., Kirk H., Padget O., Juarez-Martinez I., Boyle D., Nakata T., Perrins C.M. and Guilford T. 2015. Breeding phenology and winter activity predict subsequent breeding success in a trans-global migratory seabird. Biology Letters 11:20150671. (reprint).
35. Shoji A., Aris-Brosou S., Fayet A., Padget O., Perrins C.M. and Guilford T. 2015. Dual foraging and pair-coordination during chick provisioning by Manx shearwaters: empirical evidence supported by a simple model. Journal of Experimental Biology. 218:2116-2123. (reprint).
34. Shoji A., Elliott K.H., Aris-Brosou S., Wilson R.P. and Gaston A.J. 2015. Predictors of incubation costs in seabirds: an evolutionary perspective. Ibis. 157:44-53. (reprint).
2014
33. Young J.R, Liu H., Probert I., Aris-Brosou S. and de Vargas C. 2014. Morphospecies versus phylospecies concepts for evaluating phytoplankton diversity: the case of the Coccolithophores. Cryptogamie, Algologie. 35:353-377. (reprint).
32. Shoji A.,Owen E., Bolton M., Dean B., Kirk H., Fayet A., Boyle D., Freeman R., Perrins C., Aris-Brosou S. and Guilford T. 2014. Flexible foraging strategies in a diving seabird with high flight cost. Marine Biology. 161:2121-2129. (reprint).
31. Aris-Brosou S. 2014. Inferring influenza global transmission networks without complete phylogenetic information. Evolutionary Applications. 7:403-412. (reprint; SI file).
30. Stoeva M.K., Aris-Brosou S., Chetélat J., Hintelmann H., Pelletier P. and Poulain A.J. 2014. Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics. PLoS ONE. 9(3):e89531. (reprint).
29. Garcia V. and Aris-Brosou S. 2014. Comparative dynamics and distribution of influenza drug resistance acquisition to protein M2 and neuraminidase inhibitors. Molecular Biology and Evolution. 31(2):355-363. (reprint). Press release: in MBE.
28. Sandie R. and Aris-Brosou S. 2014. Predicting the emergence of H3N2 influenza viruses reveals contrasted modes of evolution of HA and NA antigens. Journal of Molecular Evolution. 78:1-12. (reprint; SI file; original cover figure).
27. Hill P., Piel J., Aris-Brosou S., Krištůfek V., van Elsas J.D., Boddy C.N. and Dijkhuizen L. 2014. Habitat specific type I polyketide synthases in soils and street sediments. Journal of Industrial Microbiology & Biotechnology. 41:75-85. (reprint).
2013
26. Zheng Y. and Aris-Brosou S. 2013. Approximate Bayesian Computation algorithms for estimating network model parameters. Joint Statistical Meeting Proceedings - Biometrics Section. 2013:2239-2253. (preprint).
25. Rahnama L. and Aris-Brosou S. 2013. Phylodynamics of the emergence of influenza viruses after cross-species transmission. PLoS ONE.8(12):e82486. (reprint).
2012
24. Ragonnet-Cronin M., Aris-Brosou S., Joanisse I., Merks H., Vallée D., Caminiti K., Rekart M., Gilbert M., Krajden M., Cook D., Kim J., Malloch L., Sandstrom P. and Brooks J. 2012. Genetic diversity as a marker for timing infection in HIV patients: evaluation of a 6-month window and comparison with BED. Journal of Infectious Diseases. 206:756-764. (reprint).
23. Ragonnet-Cronin M., Aris-Brosou S., Joanisse I., Merks H., Vallée D., Caminiti K., Sandstrom P. and Brooks J. 2012. Adaptive evolution of HIV at HLA epitopes is associated with ethnicity in Canada. PLoS ONE 7(5):e36933. (reprint).
22. Aris-Brosou S. and Rodrigue N. 2012. The essentials of computational molecular evolution. in Evolutionary Genomics: statistical and computational methods. Anisimova M. (Ed.) Methods in Molecular Biology series. Humana-Springer. 855:111-52, (reprint; see also vol. 856).
2011
21. Rodrigue N. and Aris-Brosou S. 2011. Fast Bayesian choice of phylogenetic models: prospecting data-augmentation-based thermodynamic integration. Systematic Biology. 60:881-887. (reprint).
20. Polakof S., Panserat S., Craig P.M., Martyres D.J., Plagnes-Juan E., Savari S., Aris-Brosou S. and Moon T.W. 2011. The metabolic consequences of hepatic AMP-kinase phosphorylation in rainbow trout. PLoS ONE 6(5):e20228. (reprint).
19. Shoji A., Elliott K.H., Aris-Brosou S., Crump D. and Gaston A.J. 2011. Incubation patterns in a central-place forager affect lifetime reproductive success: scaling of patterns from a foraging bout to a lifetime. PLoS ONE 6(3):e17760. (reprint).
18. Abdussamad J. and Aris-Brosou S. 2011. The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host. BMC Evolutionary Biology. 11:6. (reprint).
2010
17. Aris-Brosou S. 2010. A simple measure of the dynamics of segmented genomes: an application to influenza. RECOMB-CG 2010, Lecture Notes in Bioinformatics. 6398:149-160. (reprint).
16. Nadin-Davis S.A., Feng Y., Mousse D., Wandeler A.I. and Aris-Brosou S. 2010. Spatial and temporal dynamics of rabies virus variants in big brown bat populations across Canada: footprints of an emerging zoonosis. Molecular Ecology. 19:2120–2136. (reprint; supplementary information).
15. Liu H., Aris-Brosou S., Probert I. and de Vargas C. 2010. A timeline of the environmental genetics of the haptophytes. Molecular Biology and Evolution. 27:161-176. (reprint; supplementary information).
2009
14. Liu H., Probert I., Uitz J., Claustre H., Aris-Brosou S., Frada M., Not F. and de Vargas C. 2009. Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans. Proceedings of the National Academy of Sciences USA. 106:12803-12808. (reprint and SI. Press releases: CNRS, Le Monde).
13. Aris-Brosou S., Chen X., Perry S.F. and Moon, T.W. 2009. Timing of the functional diversification of α- and β-adrenoceptors in fish and other vertebrates. Annals of the New York Academy of Sciences. 1163:343-347. (reprint).
2008
12. Aris-Brosou S. and X. Xia. 2008. Phylogenetic analyses: a toolbox expanding towards Bayesian methods. International Journal of Plant Genomics. 2008:683509. (reprint).
2007
11. Chen X., Perry S.F., Aris-Brosou S., Selva C. and Moon, T.W. 2007. Characterization and functional divergence of the alpha1-adrenoceptor gene family: insights from rainbow trout (Oncorhynchus mykiss). Physiological Genomics. 32:142-153. (reprint).
10. Martyniuk C.J., Aris-Brosou S., Drouin G., Cahn J. and Trudeau V.L. 2007. Early evolution of ionotropic GABA receptors and selective regimes acting on the mammalian-specific theta and epsilon subunits. PLoS ONE. 2(9):e894. (reprint).
9. Aris-Brosou S. 2007. Dating phylogenies with hybrid local molecular clocks. PLoS ONE. 2(9):e879. (reprint).
2006
8. Aris-Brosou S. and J.P. Bielawski. 2006. Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation. Gene. 378:58-64. (reprint; supplementary figures S1 and S2).
7. Aris-Brosou S. 2006. Identifying sites under positive selection with uncertain parameter estimates. Genome. 49:767-776. (reprint).
2005
6. Aris-Brosou S. 2005. Determinants of adaptive evolution at the molecular level: The extended complexity hypothesis. Molecular Biology and Evolution. 22:200-209. (reprint).
2003
5. Aris-Brosou S. 2003. Least and most powerful phylogenetic tests to elucidate the origin of the seed plants in presence of conflicting signals under misspecified models. Systematic Biology. 52:781-793. (reprint) -- 2004 Publisher's Award.
4. Aris-Brosou S. and Z. Yang. 2003. Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa. Molecular Biology and Evolution. 20:1947-1954. (pre-print, inc. supplementary information, and reprint).
3. Aris-Brosou S. 2003. How Bayes tests of molecular phylogenies compare with frequentist approaches. Bioinformatics. 19:618-624. (reprint; supplementary information here; see 'downloads' for scripts & datasets).
2002
2. Aris-Brosou S. and Z. Yang. 2002. The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny. Systematic Biology. 51:703-714. (reprint).
1996
1. Aris-Brosou S. and L. Excoffier. 1996. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Molecular Biology and Evolution. 13:494-504. (reprint).