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De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria.

Redmond SN, MacInnis BM, Bopp S, Bei AK, Ndiaye D, Hartl DL, Wirth DF, Volkman SK, Neafsey DE.

Mol Biol Evol. 2018 Jul 1;35(7):1678-1689. doi: 10.1093/molbev/msy059.


Dramatic Changes in Malaria Population Genetic Complexity in Dielmo and Ndiop, Senegal, Revealed Using Genomic Surveillance.

Bei AK, Niang M, Deme AB, Daniels RF, Sarr FD, Sokhna C, Talla C, Faye J, Diagne N, Doucoure S, Mboup S, Wirth DF, Tall A, Ndiaye D, Hartl DL, Volkman SK, Toure-Balde A.

J Infect Dis. 2018 Jan 30;217(4):622-627. doi: 10.1093/infdis/jix580.


Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission.

Wong W, Wenger EA, Hartl DL, Wirth DF.

PLoS Comput Biol. 2018 Jan 9;14(1):e1005923. doi: 10.1371/journal.pcbi.1005923. eCollection 2018 Jan.


Cohort Profile: The Madagascar Health and Environmental Research (MAHERY) study in north-eastern Madagascar.

Golden CD, Anjaranirina EJG, Fernald LCH, Hartl DL, Kremen C, Milner DA Jr, Ralalason DH, Ramihantaniarivo H, Randriamady H, Rice BL, Vaitla B, Volkman SK, Vonona MA, Myers SS.

Int J Epidemiol. 2017 Dec 1;46(6):1747-1748d. doi: 10.1093/ije/dyx071. No abstract available.


Genome-Wide Association Studies of Drug-Resistance Determinants.

Volkman SK, Herman J, Lukens AK, Hartl DL.

Trends Parasitol. 2017 Mar;33(3):214-230. doi: 10.1016/ Epub 2016 Oct 27. Review.


Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal.

Wong W, Griggs AD, Daniels RF, Schaffner SF, Ndiaye D, Bei AK, Deme AB, MacInnis B, Volkman SK, Hartl DL, Neafsey DE, Wirth DF.

Genome Med. 2017 Jan 24;9(1):5. doi: 10.1186/s13073-017-0398-0.


Genetic evidence that the Makira region in northeastern Madagascar is a hotspot of malaria transmission.

Rice BL, Golden CD, Anjaranirina EJ, Botelho CM, Volkman SK, Hartl DL.

Malar J. 2016 Dec 20;15(1):596. doi: 10.1186/s12936-016-1644-4.


A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution.

Ogbunugafor CB, Hartl DL.

PLoS Comput Biol. 2016 Oct 13;12(10):e1005046. doi: 10.1371/journal.pcbi.1005046. eCollection 2016 Oct.


Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria.

Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C.

Annu Rev Genet. 2016 Nov 23;50:447-465. Epub 2016 Oct 3. Review.


Genotypic Context and Epistasis in Individuals and Populations.

Sackton TB, Hartl DL.

Cell. 2016 Jul 14;166(2):279-287. doi: 10.1016/j.cell.2016.06.047. Review.


Neighboring genes for DNA-binding proteins rescue male sterility in Drosophila hybrids.

Liénard MA, Araripe LO, Hartl DL.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4200-7. doi: 10.1073/pnas.1608337113. Epub 2016 Jun 29.


Biophysical principles predict fitness landscapes of drug resistance.

Rodrigues JV, Bershtein S, Li A, Lozovsky ER, Hartl DL, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1470-8. doi: 10.1073/pnas.1601441113. Epub 2016 Feb 29. Erratum in: Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):E1964.


Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance.

Ogbunugafor CB, Wylie CS, Diakite I, Weinreich DM, Hartl DL.

PLoS Comput Biol. 2016 Jan 25;12(1):e1004710. doi: 10.1371/journal.pcbi.1004710. eCollection 2016 Jan.


Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria.

Daniels R, Hamilton EJ, Durfee K, Ndiaye D, Wirth DF, Hartl DL, Volkman SK.

J Vis Exp. 2015 Nov 10;(105):e52839. doi: 10.3791/52839.


Behavioral idiosyncrasy reveals genetic control of phenotypic variability.

Ayroles JF, Buchanan SM, O'Leary C, Skutt-Kakaria K, Grenier JK, Clark AG, Hartl DL, de Bivort BL.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6706-11. doi: 10.1073/pnas.1503830112. Epub 2015 May 7.


Modeling malaria genomics reveals transmission decline and rebound in Senegal.

Daniels RF, Schaffner SF, Wenger EA, Proctor JL, Chang HH, Wong W, Baro N, Ndiaye D, Fall FB, Ndiop M, Ba M, Milner DA Jr, Taylor TE, Neafsey DE, Volkman SK, Eckhoff PA, Hartl DL, Wirth DF.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7067-72. doi: 10.1073/pnas.1505691112. Epub 2015 May 4.


The utility of genomic data for Plasmodium vivax population surveillance.

Daniels RF, Rice BL, Daniels NM, Volkman SK, Hartl DL.

Pathog Glob Health. 2015 May;109(3):153-61. doi: 10.1179/2047773215Y.0000000014. Epub 2015 Apr 18. Review.


Natural selection constrains neutral diversity across a wide range of species.

Corbett-Detig RB, Hartl DL, Sackton TB.

PLoS Biol. 2015 Apr 10;13(4):e1002112. doi: 10.1371/journal.pbio.1002112. eCollection 2015 Apr.


COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data.

Galinsky K, Valim C, Salmier A, de Thoisy B, Musset L, Legrand E, Faust A, Baniecki ML, Ndiaye D, Daniels RF, Hartl DL, Sabeti PC, Wirth DF, Volkman SK, Neafsey DE.

Malar J. 2015 Jan 19;14:4. doi: 10.1186/1475-2875-14-4.


What can we learn from fitness landscapes?

Hartl DL.

Curr Opin Microbiol. 2014 Oct;21:51-7. doi: 10.1016/j.mib.2014.08.001. Epub 2014 Oct 13. Review.


Clonal outbreak of Plasmodium falciparum infection in eastern Panama.

Obaldia N 3rd, Baro NK, Calzada JE, Santamaria AM, Daniels R, Wong W, Chang HH, Hamilton EJ, Arevalo-Herrera M, Herrera S, Wirth DF, Hartl DL, Marti M, Volkman SK.

J Infect Dis. 2015 Apr 1;211(7):1087-96. doi: 10.1093/infdis/jiu575. Epub 2014 Oct 21.


Positive selection drives faster-Z evolution in silkmoths.

Sackton TB, Corbett-Detig RB, Nagaraju J, Vaishna L, Arunkumar KP, Hartl DL.

Evolution. 2014 Aug;68(8):2331-42. doi: 10.1111/evo.12449. Epub 2014 Jun 6.


Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection.

Chang HH, Hartl DL.

Parasitology. 2015 Feb;142 Suppl 1:S98-S107. doi: 10.1017/S0031182014000067. Epub 2014 Feb 20.


Harnessing evolutionary fitness in Plasmodium falciparum for drug discovery and suppressing resistance.

Lukens AK, Ross LS, Heidebrecht R, Javier Gamo F, Lafuente-Monasterio MJ, Booker ML, Hartl DL, Wiegand RC, Wirth DF.

Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):799-804. doi: 10.1073/pnas.1320886110. Epub 2013 Dec 31.


Genome-wide gene expression effects of sex chromosome imprinting in Drosophila.

Lemos B, Branco AT, Jiang PP, Hartl DL, Meiklejohn CD.

G3 (Bethesda). 2014 Jan 10;4(1):1-10. doi: 10.1534/g3.113.008029.


Malaria life cycle intensifies both natural selection and random genetic drift.

Chang HH, Moss EL, Park DJ, Ndiaye D, Mboup S, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20129-34. doi: 10.1073/pnas.1319857110. Epub 2013 Nov 20.


Genetic incompatibilities are widespread within species.

Corbett-Detig RB, Zhou J, Clark AG, Hartl DL, Ayroles JF.

Nature. 2013 Dec 5;504(7478):135-7. doi: 10.1038/nature12678. Epub 2013 Nov 6.


Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease.

Yang S, Li J, Zhang X, Zhang Q, Huang J, Chen JQ, Hartl DL, Tian D.

Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18572-7. doi: 10.1073/pnas.1318211110. Epub 2013 Oct 21.


Accessible mutational trajectories for the evolution of pyrimethamine resistance in the malaria parasite Plasmodium vivax.

Jiang PP, Corbett-Detig RB, Hartl DL, Lozovsky ER.

J Mol Evol. 2013 Sep;77(3):81-91. doi: 10.1007/s00239-013-9582-z. Epub 2013 Sep 27.


The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression.

Meiklejohn CD, Coolon JD, Hartl DL, Wittkopp PJ.

Genome Res. 2014 Jan;24(1):84-95. doi: 10.1101/gr.156414.113. Epub 2013 Sep 16.


DNA-binding specificity changes in the evolution of forkhead transcription factors.

Nakagawa S, Gisselbrecht SS, Rogers JM, Hartl DL, Bulyk ML.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12349-54. doi: 10.1073/pnas.1310430110. Epub 2013 Jul 8.


Chromatin-associated proteins HP1 and Mod(mdg4) modify Y-linked regulatory variation in the drosophila testis.

Branco AT, Hartl DL, Lemos B.

Genetics. 2013 Jul;194(3):609-18. doi: 10.1534/genetics.113.150805. Epub 2013 May 1.


Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal.

Daniels R, Chang HH, Séne PD, Park DC, Neafsey DE, Schaffner SF, Hamilton EJ, Lukens AK, Van Tyne D, Mboup S, Sabeti PC, Ndiaye D, Wirth DF, Hartl DL, Volkman SK.

PLoS One. 2013 Apr 4;8(4):e60780. doi: 10.1371/journal.pone.0060780. Print 2013.


Natural variation of the Y chromosome suppresses sex ratio distortion and modulates testis-specific gene expression in Drosophila simulans.

Branco AT, Tao Y, Hartl DL, Lemos B.

Heredity (Edinb). 2013 Jul;111(1):8-15. doi: 10.1038/hdy.2013.5. Epub 2013 Apr 17.


Population genomics of inversion polymorphisms in Drosophila melanogaster.

Corbett-Detig RB, Hartl DL.

PLoS Genet. 2012;8(12):e1003056. doi: 10.1371/journal.pgen.1003056. Epub 2012 Dec 20. Erratum in: PLoS Genet. 2013 Aug;9(8). doi:10.1371/annotation/b1cace11-17ed-456e-b8a9-006c09125bd0.


Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite.

Park DJ, Lukens AK, Neafsey DE, Schaffner SF, Chang HH, Valim C, Ribacke U, Van Tyne D, Galinsky K, Galligan M, Becker JS, Ndiaye D, Mboup S, Wiegand RC, Hartl DL, Sabeti PC, Wirth DF, Volkman SK.

Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):13052-7. doi: 10.1073/pnas.1210585109. Epub 2012 Jul 23.


Novel genes from formation to function.

Ponce R, Martinsen L, Vicente LM, Hartl DL.

Int J Evol Biol. 2012;2012:821645. doi: 10.1155/2012/821645. Epub 2012 Jul 3.


Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population.

Chang HH, Park DJ, Galinsky KJ, Schaffner SF, Ndiaye D, Ndir O, Mboup S, Wiegand RC, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL.

Mol Biol Evol. 2012 Nov;29(11):3427-39. doi: 10.1093/molbev/mss161. Epub 2012 Jun 24.


Y chromosome mediates ribosomal DNA silencing and modulates the chromatin state in Drosophila.

Zhou J, Sackton TB, Martinsen L, Lemos B, Eickbush TH, Hartl DL.

Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):9941-6. doi: 10.1073/pnas.1207367109. Epub 2012 Jun 4.


Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition.

Yeh SD, Do T, Chan C, Cordova A, Carranza F, Yamamoto EA, Abbassi M, Gandasetiawan KA, Librado P, Damia E, Dimitri P, Rozas J, Hartl DL, Roote J, Ranz JM.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2043-8. doi: 10.1073/pnas.1121327109. Epub 2012 Jan 23.


Application of genomics to field investigations of malaria by the international centers of excellence for malaria research.

Volkman SK, Ndiaye D, Diakite M, Koita OA, Nwakanma D, Daniels RF, Park DJ, Neafsey DE, Muskavitch MA, Krogstad DJ, Sabeti PC, Hartl DL, Wirth DF.

Acta Trop. 2012 Mar;121(3):324-32. doi: 10.1016/j.actatropica.2011.12.002. Epub 2011 Dec 13. Review.


Model transcriptional networks with continuously varying expression levels.

Carneiro MO, Taubes CH, Hartl DL.

BMC Evol Biol. 2011 Dec 19;11:363. doi: 10.1186/1471-2148-11-363.


Evolutionary paths to antibiotic resistance under dynamically sustained drug selection.

Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R.

Nat Genet. 2011 Dec 18;44(1):101-5. doi: 10.1038/ng.1034.


James F. Crow and the art of teaching and mentoring.

Hartl DL.

Genetics. 2011 Dec;189(4):1129-33. doi: 10.1534/genetics.111.135160.


Copy-number variation: the balance between gene dosage and expression in Drosophila melanogaster.

Zhou J, Lemos B, Dopman EB, Hartl DL.

Genome Biol Evol. 2011;3:1014-24. doi: 10.1093/gbe/evr023.


Interspecific Y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in Drosophila.

Sackton TB, Montenegro H, Hartl DL, Lemos B.

Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):17046-51. doi: 10.1073/pnas.1114690108. Epub 2011 Oct 3.


The evolutionary landscape of antifolate resistance in Plasmodium falciparum.

Costanzo MS, Hartl DL.

J Genet. 2011 Aug;90(2):187-90. Review.


Chimeric genes as a source of rapid evolution in Drosophila melanogaster.

Rogers RL, Hartl DL.

Mol Biol Evol. 2012 Feb;29(2):517-29. doi: 10.1093/molbev/msr184. Epub 2011 Jul 18.


Fitness trade-offs in the evolution of dihydrofolate reductase and drug resistance in Plasmodium falciparum.

Costanzo MS, Brown KM, Hartl DL.

PLoS One. 2011;6(5):e19636. doi: 10.1371/journal.pone.0019636. Epub 2011 May 23.

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