-
1
-
-
84870706630
-
Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites
-
Amambua-Ngwa, A., Tetteh, K. K., Manske, M., Gomez-Escobar, N., Stewart, L. B., Deerhake, M. E., Cheeseman, I. H., Newbold, C. I., Holder, A. A., Knuepfer, E., Janha, O., Jallow, M., Campino, S., Macinnis, B., Kwiatkowski, D. P. and Conway, D. J. (2012). Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites. PLoS Genetics 8, e1002992. doi: 10.1371/journal.pgen.1002992.
-
(2012)
PLoS Genetics
, vol.8
, pp. e1002992
-
-
Amambua-Ngwa, A.1
Tetteh, K.K.2
Manske, M.3
Gomez-Escobar, N.4
Stewart, L.B.5
Deerhake, M.E.6
Cheeseman, I.H.7
Newbold, C.I.8
Holder, A.A.9
Knuepfer, E.10
Janha, O.11
Jallow, M.12
Campino, S.13
MacInnis, B.14
Kwiatkowski, D.P.15
Conway, D.J.16
-
2
-
-
22144499620
-
An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood
-
Anderson, E. C. (2005). An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood. Genetics 170, 955-967. doi: 10.1534/genetics.104.038349.
-
(2005)
Genetics
, vol.170
, pp. 955-967
-
-
Anderson, E.C.1
-
3
-
-
0033795404
-
Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum
-
Anderson, T. J., Haubold, B., Williams, J. T., Estrada-Franco, J. G., Richardson, L., Mollinedo, R., Bockarie, M., Mokili, J., Mharakurwa, S., French, N., Whitworth, J., Velez, I. D., Brockman, A. H., Nosten, F., Ferreira, M. U. and Day, K. P. (2000). Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Molecular Biology and Evolution 17, 1467-1482.
-
(2000)
Molecular Biology and Evolution
, vol.17
, pp. 1467-1482
-
-
Anderson, T.J.1
Haubold, B.2
Williams, J.T.3
Estrada-Franco, J.G.4
Richardson, L.5
Mollinedo, R.6
Bockarie, M.7
Mokili, J.8
Mharakurwa, S.9
French, N.10
Whitworth, J.11
Velez, I.D.12
Brockman, A.H.13
Nosten, F.14
Ferreira, M.U.15
Day, K.P.16
-
4
-
-
55249099284
-
Life history determines genetic structure and evolutionary potential of host-parasite interactions
-
Barrett, L. G., Thrall, P. H., Burdon, J. J. and Linde, C. C. (2008). Life history determines genetic structure and evolutionary potential of host-parasite interactions. Trends in Ecology and Evolution 23, 678-685. doi: 10.1016/j.tree.2008.06.017.
-
(2008)
Trends in Ecology and Evolution
, vol.23
, pp. 678-685
-
-
Barrett, L.G.1
Thrall, P.H.2
Burdon, J.J.3
Linde, C.C.4
-
5
-
-
52049123852
-
Estimation of 2Nes from temporal allele frequency data
-
Bollback, J. P., York, T. L. and Nielsen, R. (2008). Estimation of 2Nes from temporal allele frequency data. Genetics 179, 497-502. doi: 10.1534/genetics.107.085019.
-
(2008)
Genetics
, vol.179
, pp. 497-502
-
-
Bollback, J.P.1
York, T.L.2
Nielsen, R.3
-
6
-
-
0035076088
-
Differences in population structure of the anther smut fungus Microbotryum violaceum on two closely related host species, Silene latifolia and S dioica
-
Bucheli, E., Gautschi, B. and Shykoff, J.A. (2001). Differences in population structure of the anther smut fungus Microbotryum violaceum on two closely related host species, Silene latifolia and S. dioica. Molecular Ecology 10, 285-294.
-
(2001)
Molecular Ecology
, vol.10
, pp. 285-294
-
-
Bucheli, E.1
Gautschi, B.2
Shykoff, J.A.3
-
7
-
-
84867826577
-
Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population
-
Chang, H. H., Park, D. J., Galinsky, K. J., Schaffner, S. F., Ndiaye, D., Ndir, O., Mboup, S., Wiegand, R. C., Volkman, S. K., Sabeti, P. C., Wirth, D. F., Neafsey, D. E. and Hartl, D. L. (2012). Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population. Molecular Biology and Evolution 29, 3427-3439. doi: 10.1093/molbev/mss161.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 3427-3439
-
-
Chang, H.H.1
Park, D.J.2
Galinsky, K.J.3
Schaffner, S.F.4
Ndiaye, D.5
Ndir, O.6
Mboup, S.7
Wiegand, R.C.8
Volkman, S.K.9
Sabeti, P.C.10
Wirth, D.F.11
Neafsey, D.E.12
Hartl, D.L.13
-
8
-
-
84890280930
-
The malaria life cycle intensifies both natural selection and random genetic drift
-
Chang, H. H., Moss, E. L., Park, D. J., Ndiaye, D., Mboup, S., Volkman, S. K., Sabeti, P. C., Wirth, D. F., Neafsey, D. E. and Hartl, D. L. (2013). The malaria life cycle intensifies both natural selection and random genetic drift. Proceedings of the National Academy of Sciences USA 110, 20129-20134. doi: 10.1073/pnas.1319857110.
-
(2013)
Proceedings of the National Academy of Sciences USA
, vol.110
, pp. 20129-20134
-
-
Chang, H.H.1
Moss, E.L.2
Park, D.J.3
Ndiaye, D.4
Mboup, S.5
Volkman, S.K.6
Sabeti, P.C.7
Wirth, D.F.8
Neafsey, D.E.9
Hartl, D.L.10
-
9
-
-
84875952747
-
Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal
-
Daniels, R., Chang, H. H., Sene, P. D., Park, D. C., Neafsey, D. E., Schaffner, S. F., Hamilton, E. J., Lukens, A. K., Van Tyne, D., Mboup, S., Sabeti, P. C., Ndiaye, D., Wirth, D. F., Hartl, D. L. and Volkman, S. K. (2013). Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal. PLoS ONE 8, e60780. doi: 10.1371/journal.pone.0060780.
-
(2013)
PLoS ONE
, vol.8
, pp. e60780
-
-
Daniels, R.1
Chang, H.H.2
Sene, P.D.3
Park, D.C.4
Neafsey, D.E.5
Schaffner, S.F.6
Hamilton, E.J.7
Lukens, A.K.8
Van Tyne, D.9
Mboup, S.10
Sabeti, P.C.11
Ndiaye, D.12
Wirth, D.F.13
Hartl, D.L.14
Volkman, S.K.15
-
10
-
-
0033911640
-
Hitchhiking under positive Darwinian selection
-
Fay, J. C. and Wu, C. I. (2000). Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413.
-
(2000)
Genetics
, vol.155
, pp. 1405-1413
-
-
Fay, J.C.1
Wu, C.I.2
-
11
-
-
0027453041
-
Statistical tests of neutrality of mutations
-
Fu, Y. X. and Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics 133, 693-709.
-
(1993)
Genetics
, vol.133
, pp. 693-709
-
-
Fu, Y.X.1
Li, W.H.2
-
12
-
-
73449149044
-
Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
-
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H. and Bustamante, C. D. (2009). Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genetics 5, e1000695. doi: 10.1371/journal.pgen.1000695.
-
(2009)
PLoS Genetics
, vol.5
, pp. e1000695
-
-
Gutenkunst, R.N.1
Hernandez, R.D.2
Williamson, S.H.3
Bustamante, C.D.4
-
13
-
-
0037432740
-
Early origin and recent expansion of Plasmodium falciparum
-
Joy, D. A., Feng, X., Mu, J., Furuya, T., Chotivanich, K., Krettli, A. U., Ho, M., Wang, A., White, N. J., Suh, E., Beerli, P. and Su, X. Z. (2003). Early origin and recent expansion of Plasmodium falciparum. Science 300, 318-321. doi: 10.1126/science.1081449.
-
(2003)
Science
, vol.300
, pp. 318-321
-
-
Joy, D.A.1
Feng, X.2
Mu, J.3
Furuya, T.4
Chotivanich, K.5
Krettli, A.U.6
Ho, M.7
Wang, A.8
White, N.J.9
Suh, E.10
Beerli, P.11
Su, X.Z.12
-
14
-
-
84867176367
-
Estimating allele age and selection coefficient from time-serial data
-
Malaspinas, A. S.,Malaspinas, O., Evans, S. N. and Slatkin, M. (2012). Estimating allele age and selection coefficient from time-serial data. Genetics 192, 599-607. doi: 10.1534/genetics.112.140939.
-
(2012)
Genetics
, vol.192
, pp. 599-607
-
-
Malaspinas, A.S.1
Malaspinas, O.2
Evans, S.N.3
Slatkin, M.4
-
15
-
-
84863982076
-
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
-
Manske, M., Miotto, O., Campino, S., Auburn, S., Almagro-Garcia, J., Maslen, G., O'Brien, J., Djimde, A., Doumbo, O., Zongo, I., Ouedraogo, J. B., Michon, P., Mueller, I., Siba, P., Nzila, A., Borrmann, S., Kiara, S. M., Marsh, K., Jiang, H., Su, X. Z., Amaratunga, C., Fairhurst, R., Socheat, D., Nosten, F., Imwong, M., White, N. J., Sanders, M., Anastasi, E., Alcock, D., Drury, E., Oyola, S., Quail, M. A., Turner, D. J., Ruano-Rubio, V., Jyothi, D., Amenga-Etego, L., Hubbart, C., Jeffreys, A., Rowlands, K., Sutherland, C., Roper, C., Mangano, V., Modiano, D., Tan, J. C., Ferdig, M. T., Amambua-Ngwa, A., Conway, D. J., Takala-Harrison, S., Plowe, C. V., Rayner, J. C., Rockett, K. A., Clark, T. G., Newbold, C. I., Berriman, M., MacInnis, B. and Kwiatkowski, D. P. (2012). Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 487, 375-379. doi: 10.1038/nature11174.
-
(2012)
Nature
, vol.487
, pp. 375-379
-
-
Manske, M.1
Miotto, O.2
Campino, S.3
Auburn, S.4
Almagro-Garcia, J.5
Maslen, G.6
O'Brien, J.7
Djimde, A.8
Doumbo, O.9
Zongo, I.10
Ouedraogo, J.B.11
Michon, P.12
Mueller, I.13
Siba, P.14
Nzila, A.15
Borrmann, S.16
Kiara, S.M.17
Marsh, K.18
Jiang, H.19
Su, X.Z.20
Amaratunga, C.21
Fairhurst, R.22
Socheat, D.23
Nosten, F.24
Imwong, M.25
White, N.J.26
Sanders, M.27
Anastasi, E.28
Alcock, D.29
Drury, E.30
Oyola, S.31
Quail, M.A.32
Turner, D.J.33
Ruano-Rubio, V.34
Jyothi, D.35
Amenga-Etego, L.36
Hubbart, C.37
Jeffreys, A.38
Rowlands, K.39
Sutherland, C.40
Roper, C.41
Mangano, V.42
Modiano, D.43
Tan, J.C.44
Ferdig, M.T.45
Amambua-Ngwa, A.46
Conway, D.J.47
Takala-Harrison, S.48
Plowe, C.V.49
Rayner, J.C.50
Rockett, K.A.51
Clark, T.G.52
Newbold, C.I.53
Berriman, M.54
MacInnis, B.55
Kwiatkowski, D.P.56
more..
-
16
-
-
0026428610
-
Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald, J. H. and Kreitman, M. (1991). Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652-654. doi: 10.1038/351652a0.
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
17
-
-
26444574740
-
Recombination hotspots and population structure in Plasmodium falciparum
-
Mu, J., Awadalla, P., Duan, J., McGee, K. M., Joy, D. A., McVean, G. A. and Su, X. Z. (2005). Recombination hotspots and population structure in Plasmodium falciparum. PLoS Biology 3, e335. doi: 10.1371/journal.pbio.0030335.
-
(2005)
PLoS Biology
, vol.3
, pp. e335
-
-
Mu, J.1
Awadalla, P.2
Duan, J.3
McGee, K.M.4
Joy, D.A.5
McVean, G.A.6
Su, X.Z.7
-
18
-
-
77649188974
-
Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs
-
Mu, J., Myers, R. A., Jiang, H., Liu, S., Ricklefs, S., Waisberg, M., Chotivanich, K., Wilairatana, P., Krudsood, S., White, N. J., Udomsangpetch, R., Cui, L., Ho, M., Ou, F., Li, H., Song, J., Li, G., Wang, X., Seila, S., Sokunthea, S., Socheat, D., Sturdevant, D. E., Porcella, S. F., Fairhurst, R. M., Wellems, T. E., Awadalla, P. and Su, X. Z. (2010). Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nature Genetics 42, 268-271. doi: 10.1038/ng.528.
-
(2010)
Nature Genetics
, vol.42
, pp. 268-271
-
-
Mu, J.1
Myers, R.A.2
Jiang, H.3
Liu, S.4
Ricklefs, S.5
Waisberg, M.6
Chotivanich, K.7
Wilairatana, P.8
Krudsood, S.9
White, N.J.10
Udomsangpetch, R.11
Cui, L.12
Ho, M.13
Ou, F.14
Li, H.15
Song, J.16
Li, G.17
Wang, X.18
Seila, S.19
Sokunthea, S.20
Socheat, D.21
Sturdevant, D.E.22
Porcella, S.F.23
Fairhurst, R.M.24
Wellems, T.E.25
Awadalla, P.26
Su, X.Z.27
more..
-
19
-
-
0034809334
-
Statistical tests of selective neutrality in the age of genomics
-
Nielsen, R. (2001). Statistical tests of selective neutrality in the age of genomics. Heredity 86, 641-647.
-
(2001)
Heredity
, vol.86
, pp. 641-647
-
-
Nielsen, R.1
-
20
-
-
84872029995
-
Population genetic correlates of declining transmission in a human pathogen
-
Nkhoma, S. C., Nair, S., Al-Saai, S., Ashley, E., McGready, R., Phyo, A. P., Nosten, F. and Anderson, T. J. (2012). Population genetic correlates of declining transmission in a human pathogen. Molecular Ecology 22, 273-285. doi: 10.1111/mec.12099.
-
(2012)
Molecular Ecology
, vol.22
, pp. 273-285
-
-
Nkhoma, S.C.1
Nair, S.2
Al-Saai, S.3
Ashley, E.4
McGready, R.5
Phyo, A.P.6
Nosten, F.7
Anderson, T.J.8
-
21
-
-
84864655057
-
Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite
-
Park, D. J., Lukens, A. K., Neafsey, D. E., Schaffner, S. F., Chang, H. H., Valim, C., Ribacke, U., Van Tyne, D., Galinsky, K., Galligan, M., Becker, J. S., Ndiaye, D., Mboup, S., Wiegand, R. C., Hartl, D. L., Sabeti, P. C., Wirth, D. F. and Volkman, S. K. (2012). Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite. Proceedings of the National Academy of Sciences USA 109, 13052-13057. doi: 10.1073/pnas.1210585109.
-
(2012)
Proceedings of the National Academy of Sciences USA
, vol.109
, pp. 13052-13057
-
-
Park, D.J.1
Lukens, A.K.2
Neafsey, D.E.3
Schaffner, S.F.4
Chang, H.H.5
Valim, C.6
Ribacke, U.7
Van Tyne, D.8
Galinsky, K.9
Galligan, M.10
Becker, J.S.11
Ndiaye, D.12
Mboup, S.13
Wiegand, R.C.14
Hartl, D.L.15
Sabeti, P.C.16
Wirth, D.F.17
Volkman, S.K.18
-
22
-
-
0037167852
-
Detecting recent positive selection in the human genome from haplotype structure
-
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., Ackerman, H. C., Campbell, S. J., Altshuler, D., Cooper, R., Kwiatkowski, D., Ward, R. and Lander, E. S. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837. doi: 10.1038/nature01140.
-
(2002)
Nature
, vol.419
, pp. 832-837
-
-
Sabeti, P.C.1
Reich, D.E.2
Higgins, J.M.3
Levine, H.Z.4
Richter, D.J.5
Schaffner, S.F.6
Gabriel, S.B.7
Platko, J.V.8
Patterson, N.J.9
McDonald, G.J.10
Ackerman, H.C.11
Campbell, S.J.12
Altshuler, D.13
Cooper, R.14
Kwiatkowski, D.15
Ward, R.16
Lander, E.S.17
-
23
-
-
84872043188
-
Microsatellite loci over a thirtythree year period for a malaria parasite (Plasmodium mexicanum): Bottleneck in effective population size and effect on allele frequencies
-
Schall, J. J. and St Denis, K. M. (2013). Microsatellite loci over a thirtythree year period for a malaria parasite (Plasmodium mexicanum): bottleneck in effective population size and effect on allele frequencies. Parasitology 140, 21-28. doi: 10.1017/S0031182012001217.
-
(2013)
Parasitology
, vol.140
, pp. 21-28
-
-
Schall, J.J.1
St Denis, K.M.2
-
24
-
-
0024313579
-
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
-
Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
25
-
-
79955632728
-
Identification and functional validation of the novel antimalarial resistance locus PF10-0355 in Plasmodium falciparum
-
Van Tyne, D., Park, D. J., Schaffner, S. F., Neafsey,D. E., Angelino, E., Cortese, J. F., Barnes, K. G., Rosen, D. M., Lukens, A. K., Daniels, R. F., Milner, D. A., Jr., Johnson, C. A., Shlyakhter, I., Grossman, S. R., Becker, J. S., Yamins, D., Karlsson, E. K., Ndiaye, D., Sarr, O., Mboup, S., Happi, C., Furlotte, N. A., Eskin, E., Kang, H. M., Hartl, D. L., Birren, B.W., Wiegand, R. C., Lander, E. S., Wirth, D. F., Volkman, S. K. and Sabeti, P. C. (2011). Identification and functional validation of the novel antimalarial resistance locus PF10-0355 in Plasmodium falciparum. PLoS Genetics 7, e1001383. doi: 10.1371/journal. pgen.1001383.
-
(2011)
PLoS Genetics
, vol.7
, pp. e1001383
-
-
Van Tyne, D.1
Park, D.J.2
Schaffner, S.F.3
Neafsey, D.E.4
Angelino, E.5
Cortese, J.F.6
Barnes, K.G.7
Rosen, D.M.8
Lukens, A.K.9
Daniels, R.F.10
Milner, D.A.11
Johnson, C.A.12
Shlyakhter, I.13
Grossman, S.R.14
Becker, J.S.15
Yamins, D.16
Karlsson, E.K.17
Ndiaye, D.18
Sarr, O.19
Mboup, S.20
Happi, C.21
Furlotte, N.A.22
Eskin, E.23
Kang, H.M.24
Hartl, D.L.25
Birren, B.W.26
Wiegand, R.C.27
Lander, E.S.28
Wirth, D.F.29
Volkman, S.K.30
Sabeti, P.C.31
more..
-
26
-
-
33644981509
-
A map of recent positive selection in the human genome
-
Voight, B. F., Kudaravalli, S., Wen, X. and Pritchard, J. K. (2006). A map of recent positive selection in the human genome. PLoS Biology 4, e72. doi: 10.1371/journal.pbio.0040072.
-
(2006)
PLoS Biology
, vol.4
, pp. e72
-
-
Voight, B.F.1
Kudaravalli, S.2
Wen, X.3
Pritchard, J.K.4
-
27
-
-
33845875437
-
A genome-wide map of diversity in Plasmodium falciparum
-
Volkman, S. K., Sabeti, P. C., DeCaprio, D., Neafsey, D. E., Schaffner, S. F., Milner, D. A., Jr., Daily, J. P., Sarr, O., Ndiaye, D., Ndir, O., Mboup, S., Duraisingh, M. T., Lukens, A., Derr, A., Stange-Thomann, N., Waggoner, S., Onofrio, R., Ziaugra, L., Mauceli, E., Gnerre, S., Jaffe, D. B., Zainoun, J., Wiegand, R. C., Birren, B.W., Hartl, D. L., Galagan, J. E., Lander, E. S. and Wirth, D. F. (2007). A genome-wide map of diversity in Plasmodium falciparum. Nature Genetics 39, 113-119. doi: 10.1038/ng1930.
-
(2007)
Nature Genetics
, vol.39
, pp. 113-119
-
-
Volkman, S.K.1
Sabeti, P.C.2
Decaprio, D.3
Neafsey, D.E.4
Schaffner, S.F.5
Milner, D.A.6
Daily, J.P.7
Sarr, O.8
Ndiaye, D.9
Ndir, O.10
Mboup, S.11
Duraisingh, M.T.12
Lukens, A.13
Derr, A.14
Stange-Thomann, N.15
Waggoner, S.16
Onofrio, R.17
Ziaugra, L.18
Mauceli, E.19
Gnerre, S.20
Jaffe, D.B.21
Zainoun, J.22
Wiegand, R.C.23
Birren, B.W.24
Hartl, D.L.25
Galagan, J.E.26
Lander, E.S.27
Wirth, D.F.28
more..
-
28
-
-
0024498122
-
A generalized approach for estimating effective population size from temporal changes in allele frequency
-
Waples, R. S. (1989). A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121, 379-391.
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(1989)
Genetics
, vol.121
, pp. 379-391
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Waples, R.S.1
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