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Items: 29

1.

Evidence of Early-Stage Selection on EPAS1 and GPR126 Genes in Andean High Altitude Populations.

Eichstaedt CA, Pagani L, Antao T, Inchley CE, Cardona A, Mörseburg A, Clemente FJ, Sluckin TJ, Metspalu E, Mitt M, Mägi R, Hudjashov G, Metspalu M, Mormina M, Jacobs GS, Kivisild T.

Sci Rep. 2017 Oct 12;7(1):13042. doi: 10.1038/s41598-017-13382-4.

2.

Local selection in the presence of high levels of gene flow: Evidence of heterogeneous insecticide selection pressure across Ugandan Culex quinquefasciatus populations.

Silva Martins WF, Wilding CS, Steen K, Mawejje H, Antão TR, Donnelly MJ.

PLoS Negl Trop Dis. 2017 Oct 3;11(10):e0005917. doi: 10.1371/journal.pntd.0005917. eCollection 2017 Oct.

3.

Massive introgression drives species radiation at the range limit of Anopheles gambiae.

Vicente JL, Clarkson CS, Caputo B, Gomes B, Pombi M, Sousa CA, Antao T, Dinis J, Bottà G, Mancini E, Petrarca V, Mead D, Drury E, Stalker J, Miles A, Kwiatkowski DP, Donnelly MJ, Rodrigues A, Torre AD, Weetman D, Pinto J.

Sci Rep. 2017 Apr 18;7:46451. doi: 10.1038/srep46451.

4.

Selective sweep on human amylase genes postdates the split with Neanderthals.

Inchley CE, Larbey CD, Shwan NA, Pagani L, Saag L, Antão T, Jacobs G, Hudjashov G, Metspalu E, Mitt M, Eichstaedt CA, Malyarchuk B, Derenko M, Wee J, Abdullah S, Ricaut FX, Mormina M, Mägi R, Villems R, Metspalu M, Jones MK, Armour JA, Kivisild T.

Sci Rep. 2016 Nov 17;6:37198. doi: 10.1038/srep37198.

5.

Genomic analyses inform on migration events during the peopling of Eurasia.

Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M.

Nature. 2016 Oct 13;538(7624):238-242. doi: 10.1038/nature19792. Epub 2016 Sep 21.

6.

Multi-layered population structure in Island Southeast Asians.

Mörseburg A, Pagani L, Ricaut FX, Yngvadottir B, Harney E, Castillo C, Hoogervorst T, Antao T, Kusuma P, Brucato N, Cardona A, Pierron D, Letellier T, Wee J, Abdullah S, Metspalu M, Kivisild T.

Eur J Hum Genet. 2016 Nov;24(11):1605-1611. doi: 10.1038/ejhg.2016.60. Epub 2016 Jun 15.

7.

Positive selection of AS3MT to arsenic water in Andean populations.

Eichstaedt CA, Antao T, Cardona A, Pagani L, Kivisild T, Mormina M.

Mutat Res. 2015 Oct;780:97-102. doi: 10.1016/j.mrfmmm.2015.07.007. Epub 2015 Jul 29.

8.

Plasmodium vivax Diversity and Population Structure across Four Continents.

Koepfli C, Rodrigues PT, Antao T, Orjuela-Sánchez P, Van den Eede P, Gamboa D, van Hong N, Bendezu J, Erhart A, Barnadas C, Ratsimbasoa A, Menard D, Severini C, Menegon M, Nour BY, Karunaweera N, Mueller I, Ferreira MU, Felger I.

PLoS Negl Trop Dis. 2015 Jun 30;9(6):e0003872. doi: 10.1371/journal.pntd.0003872. eCollection 2015.

9.

Genetic and phenotypic differentiation of an Andean intermediate altitude population.

Eichstaedt CA, Antão T, Cardona A, Pagani L, Kivisild T, Mormina M.

Physiol Rep. 2015 May;3(5). pii: e12376. doi: 10.14814/phy2.12376.

10.

A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.

Clemente FJ, Cardona A, Inchley CE, Peter BM, Jacobs G, Pagani L, Lawson DJ, Antão T, Vicente M, Mitt M, DeGiorgio M, Faltyskova Z, Xue Y, Ayub Q, Szpak M, Mägi R, Eriksson A, Manica A, Raghavan M, Rasmussen M, Rasmussen S, Willerslev E, Vidal-Puig A, Tyler-Smith C, Villems R, Nielsen R, Metspalu M, Malyarchuk B, Derenko M, Kivisild T.

Am J Hum Genet. 2014 Nov 6;95(5):584-589. doi: 10.1016/j.ajhg.2014.09.016. Epub 2014 Oct 23.

11.

Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation.

Clarkson CS, Weetman D, Essandoh J, Yawson AE, Maslen G, Manske M, Field SG, Webster M, Antão T, MacInnis B, Kwiatkowski D, Donnelly MJ.

Nat Commun. 2014 Jun 25;5:4248. doi: 10.1038/ncomms5248.

12.

Genome-wide analysis of cold adaptation in indigenous Siberian populations.

Cardona A, Pagani L, Antao T, Lawson DJ, Eichstaedt CA, Yngvadottir B, Shwe MT, Wee J, Romero IG, Raj S, Metspalu M, Villems R, Willerslev E, Tyler-Smith C, Malyarchuk BA, Derenko MV, Kivisild T.

PLoS One. 2014 May 21;9(5):e98076. doi: 10.1371/journal.pone.0098076. eCollection 2014.

13.

Effects of overlapping generations on linkage disequilibrium estimates of effective population size.

Waples RS, Antao T, Luikart G.

Genetics. 2014 Jun;197(2):769-80. doi: 10.1534/genetics.114.164822. Epub 2014 Apr 8.

14.

The Andean adaptive toolkit to counteract high altitude maladaptation: genome-wide and phenotypic analysis of the Collas.

Eichstaedt CA, Antão T, Pagani L, Cardona A, Kivisild T, Mormina M.

PLoS One. 2014 Mar 31;9(3):e93314. doi: 10.1371/journal.pone.0093314. eCollection 2014.

15.
16.

Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar.

Pierron D, Razafindrazaka H, Pagani L, Ricaut FX, Antao T, Capredon M, Sambo C, Radimilahy C, Rakotoarisoa JA, Blench RM, Letellier T, Kivisild T.

Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):936-41. doi: 10.1073/pnas.1321860111. Epub 2014 Jan 6.

17.

Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies.

Migliano AB, Romero IG, Metspalu M, Leavesley M, Pagani L, Antao T, Huang DW, Sherman BT, Siddle K, Scholes C, Hudjashov G, Kaitokai E, Babalu A, Belatti M, Cagan A, Hopkinshaw B, Shaw C, Nelis M, Metspalu E, Mägi R, Lempicki RA, Villems R, Lahr MM, Kivisild T.

Hum Biol. 2013 Feb-Jun;85(1-3):251-84.

PMID:
24297229
18.

A Large Plasmodium vivax Reservoir and Little Population Structure in the South Pacific.

Koepfli C, Timinao L, Antao T, Barry AE, Siba P, Mueller I, Felger I.

PLoS One. 2013 Jun 18;8(6):e66041. doi: 10.1371/journal.pone.0066041. Print 2013.

19.

Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations.

Huerta-Sánchez E, Degiorgio M, Pagani L, Tarekegn A, Ekong R, Antao T, Cardona A, Montgomery HE, Cavalleri GL, Robbins PA, Weale ME, Bradman N, Bekele E, Kivisild T, Tyler-Smith C, Nielsen R.

Mol Biol Evol. 2013 Aug;30(8):1877-88. doi: 10.1093/molbev/mst089. Epub 2013 May 10.

20.

Policy options for deploying anti-malarial drugs in endemic countries: a population genetics approach.

Antao T, Hastings I.

Malar J. 2012 Dec 17;11:422. doi: 10.1186/1475-2875-11-422.

21.

Mcheza: a workbench to detect selection using dominant markers.

Antao T, Beaumont MA.

Bioinformatics. 2011 Jun 15;27(12):1717-8. doi: 10.1093/bioinformatics/btr253. Epub 2011 Apr 19.

PMID:
21505032
22.

Evolutionary parasitology applied to control and elimination policies.

Antao T.

Trends Parasitol. 2011 Jun;27(6):233-4. doi: 10.1016/j.pt.2011.03.004. Epub 2011 Apr 14. No abstract available.

PMID:
21497137
23.

ogaraK: a population genetics simulator for malaria.

Antao T, Hastings IM.

Bioinformatics. 2011 May 1;27(9):1335-6. doi: 10.1093/bioinformatics/btr139. Epub 2011 Mar 16.

PMID:
21414984
24.

interPopula: a Python API to access the HapMap Project dataset.

Antao T.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S10. doi: 10.1186/1471-2105-11-S12-S10.

25.

Early detection of population declines: high power of genetic monitoring using effective population size estimators.

Antao T, Pérez-Figueroa A, Luikart G.

Evol Appl. 2011 Jan;4(1):144-54. doi: 10.1111/j.1752-4571.2010.00150.x. Epub 2010 Aug 3.

26.

Environmental, pharmacological and genetic influences on the spread of drug-resistant malaria.

Antao T, Hastings IM.

Proc Biol Sci. 2011 Jun 7;278(1712):1705-12. doi: 10.1098/rspb.2010.1907. Epub 2010 Nov 17.

27.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

28.

LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method.

Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G.

BMC Bioinformatics. 2008 Jul 28;9:323. doi: 10.1186/1471-2105-9-323.

29.

MODELER4SIMCOAL2: a user-friendly, extensible modeler of demography and linked loci for coalescent simulations.

Antao T, Beja-Pereira A, Luikart G.

Bioinformatics. 2007 Jul 15;23(14):1848-50. Epub 2007 May 8.

PMID:
17488756

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