Publications

93. IK Kim, L Tian, R Chaffee, BC Haller, J Champer, PW Messer*, J Kim*. "Seed dormancy shapes gene drive dynamics in plants." Nature Plants. DOI →

92. P Xu, S Liang, A Hahn, V Zhao, W Lo, BC Haller, B Sobkowiak, MH Chitwood, C Colijn, T Cohen, KY Rhee, PW Messer, MT Wells, AG Clark, J Kim. "3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology." Methods in Ecology and Evolution. 17(4):1051. DOI →

91. IK Kim, PW Messer. "Predicting the invasiveness of threshold-dependent gene drives." bioRxiv. DOI →

90. AM Langmüller, KA Chandrasekher, BC Haller, SE Champer, CC Murdock, PW Messer. "Gaussian process emulation for modeling dengue outbreak dynamics." PLoS Computational Biology. 21(12):e1013849. DOI →

89. BC Haller, PL Ralph, PW Messer. "SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes." Molecular Biology and Evolution. 43(1):msaf313. DOI →

88. BC Haller, CW Nelson, MF Rodrigues, PW Messer. "SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution." Human Population Genetics and Genomics. 5(4):0006. DOI →

87. M Chotai, X Wei, PW Messer. "Signatures of selective sweeps in continuous-space populations." Genetics. 231:iyaf183. DOI →

86. AJ Lea, IV Caldas, KM Garske, J Echwa, M Gurven, C Handley, J Kahumbu, Kamau, P Kinyua, F Lotukoi, A Lopurudoi, S Lowasa, R Mallarino, D Martins, PW Messer, C Miano, B Muhoya, J Peng, T Phung, JD Rabinowitz, A Roichman, R Siford, A Stone, AM Taravella Oill, S Mathew, MA Wilson, JF Ayroles. "Adaptations to water stress and pastoralism in the Turkana of northwest Kenya." Science. 6766:1246. DOI →

85. Y Liu, SE Champer, J Champer. "Modeling control of invasive fire ants by gene drive." bioRxiv. DOI →

84. X Zhang, W Sun, IK Kim, PW Messer, J Champer. "Population dynamics in spatial suppression gene drive models and the effect of resistance, density dependence, and life history." bioRxiv. DOI →

83. ET Chevy, J Min, V Caudill, SE Champer, BC Haller, CT Rehmann, CCR Smith, S Tittes, PW Messer, AD Kern, S Ramachandran, PL Ralph. "Population genetics meets ecology: a guide to individual-based simulations in continuous landscapes." Ecology and Evolution. 15:e71098. DOI →

82. SE Champer, B Chae, BC Haller, J Champer, PW Messer. "Resource-explicit interactions in spatial population models." Methods in Ecology and Evolution. 15:2316. DOI →

81. BA Andersson, W Zhao, BC Haller, Å Brännström, XR Wang. "Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure." Molecular Ecology Resources. 23:1589. DOI →

80. J Du, W Chen, X Jia, X Xu, E Yang, R Zhou, Y Zhang, M Metzloff, PW Messer, J Champer. "Germline Cas9 promoters with improved performance for homing gene drive." Nature Communications. 15:4560. DOI →

79. AP Wilder, CC Steiner, S Hendricks, BC Haller, C Kim, ML Korody, OA Ryder. "Genetic load and viability of a future restored northern white rhino population." Evolutionary Applications. 17:e13683. DOI →

78. AM Langmüller, J Hermisson, CC Murdock, PW Messer. "Catching a wave: on the suitability of traveling-wave solutions in epidemiological modeling." Theoretical Population Biology. 162:1. Link →

77. AC Clark, A Alexander, R Edison, K Esvelt, S Kamau, L Dutoit, J Champer, SE Champer, PW Messer, NJ Gemmell. "A framework for identifying fertility gene targets for mammalian pest control." Molecular Ecology Resources. 24:e13901. DOI →

76. IV Caldas, AC Clark, PW Messer. "Inference of selective sweep parameters through supervised learning." bioRxiv. DOI →

75. R Shen, M Wenzel, PW Messer, CF Aquadro. "Evolution under a model of functionally buffered deleterious mutations can lead to positive selection in protein-coding genes." Evolution. 77:2200. DOI →

74. J Kim, KD Harris, IK Kim, S Shemesh, PW Messer*, G Greenbaum*. "Incorporating ecology into gene drive modeling." Ecology Letters. 26:S62. DOI →

73. BC Haller, PW Messer. "SLiM 4: Multispecies eco-evolutionary modeling." The American Naturalist. 201:5. DOI →

72. A Mazo-Vargas, AM Langmüller, A Wilder, KRL van der Burg, JJ Lewis, PW Messer, L Zhang, A Martin, RD Reed. "Deep cis-regulatory homology of the butterfly wing pattern ground plan." Science. 378:304. DOI →

71. SE Champer, IK Kim, AC Clark, PW Messer, J Champer. "Anopheles homing suppression drive candidates exhibit unexpected performance differences in simulations with spatial structure." eLife. 11:e79121. DOI →

70. BC Haller. "Ten simple rules for reporting a bug." PLoS Computational Biology. 18(10):e1010540. DOI →

69. AM Langmüller, J Champer, S Lapinska, L Xie, M Metzloff, J Liu, Y Xu, J Du, AG Clark, PW Messer. "Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations." eLife. 11:e71809. DOI →

68. SM Schaal, BC Haller, KE Lotterhos. "Inversion invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow." Philosophical Transactions of the Royal Society B. 377:20210200. DOI →

67. M Metzloff, E Yang, S Dhole, AG Clark, PW Messer, J Champer. "Experimental demonstration of tethered gene drive systems for confined population modification or suppression." BMC Biology. 20:119. DOI →

66. ES Sorojsrisom, BC Haller, BA Ambrose, DAR Eaton. "Selection on the gametophyte: Modeling alternation of generations in plants." Applications in Plant Sciences. 10:e11472. DOI →

65. ÁJ Láruson, MC Fitzpatrick, SR Keller, BC Haller, KE Lotterhos. "Seeing the forest for the trees: Assessing genetic offset predictions from gradient forest." Evolutionary Applications. 15:403. DOI →

64. E Yang, M Metzloff, AM Langmüller, AG Clark, PW Messer, J Champer. "A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles." G3: Genes, Genomes, Genetics. jkac081. DOI →

63. R Shen, PW Messer. "Predicting the genomic resolution of bulk segregant analysis." G3: Genes, Genomes, Genetics. 12:jkac012. DOI →

62. SE Champer, N Oakes, R Sharma, P Garcia-Diaz, J Champer, PW Messer. "Modeling CRISPR gene drives for suppression of invasive rodents using a supervised machine learning framework." PLoS Computational Biology. 17:e1009660. DOI →

61. N Garud, PW Messer, DA Petrov. "Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data." PLoS Genetics. 17:e1009373. DOI →

60. M Munasinghe, BC Haller, AG Clark. "Migration Restores Hybrid Incompatibility Driven By Mitochondrial-Nuclear Sexual Conflict." Proceedings of the Royal Society B. 289:20212561. DOI →

58. J Champer, I Kim, SE Champer, AG Clark, PW Messer. "Suppression gene drive in continuous space can result in unstable persistence of both drive and wild-type alleles." Molecular Ecology. 30:1086. DOI →

57. KC Long, et al. (44 authors including J Champer, PW Messer). "Core commitments for field trials of gene drive organisms." Science. 370:14179. DOI →

56. J Champer, SE Champer, I Kim, AG Clark, PW Messer. "Design and analysis of CRISPR-based underdominance toxin-antidote gene drives." Evolutionary Applications. 14:1052. DOI →

55. J Cury, BC Haller, G Achaz, F Jay. "Simulation of bacterial populations with SLiM." Peer Community Journal. 2:e7. DOI →

54. J Champer, E Yang, E Lee, J Liu, AG Clark, PW Messer. "A CRISPR homing gene drive targeting a haplolethal gene removes resistance alleles and successfully spreads through a cage population." PNAS. 117:24377. DOI →

53. RN Lou, NO Therkildsen, PW Messer. "The effects of quantitative trait architecture on detection power in short-term artificial selection experiments." G3. 9:3213. DOI →

52. JR Adrion, et al. (28 authors including PW Messer). "A community-maintained standard library of population genetic models." eLife. 9:e54967. DOI →

51. J Champer, I Kim, SE Champer, AG Clark, PW Messer. "Performance analysis of novel toxin-antidote CRISPR gene drive systems." BMC Biology. 18:27. DOI →

50. MV Matz, EA Treml, BC Haller. "Estimating the potential for coral adaptation to global warming across the Indo-West Pacific." Global Change Biology. 26:3473. DOI →

49. J Champer, J Zhao, SE Champer, J Liu, PW Messer. "Population dynamics of underdominance gene drive systems in continuous space." ACS Synthetic Biology. 9:779. DOI →

48. SE Champer, S Oh, C Liu, Z Wen, AG Clark, PW Messer, J Champer. "Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs." Science Advances. 6:eaaz0525. DOI →

47. J Champer, YL Lee, E Yang, C Liu, AG Clark, PW Messer. "A toxin-antidote CRISPR gene drive system for regional population modification." Nature Communications. 11:1082. DOI →

46. Giese, JL Frieß, NH Barton, PW Messer, F Débarre, MF Schetelig, N Windbichler, H Meimberg, C Boëte. "Gene Drives: Dynamics and Regulatory Matters." Bioessays. 41:1900151. DOI →

45. J Champer, Z Wen, A Luthra, R Reeves, J Chung, C Liu, YL Lee, J Liu, E Yang, PW Messer, AG Clark. "CRISPR Gene Drive Efficiency and Resistance Rate Is Highly Heritable with No Common Genetic Loci of Large Effect." Genetics. 212:333. DOI →

44. BC Haller, PW Messer. "Evolutionary modeling in SLiM 3 for beginners." Molecular Biology and Evolution. 36:1101. DOI →

43. J Liu, J Champer, AM Langmüller, J Liu, J Chung, R Reeves, A Luthra, YL Lee, AH Vaughn, AG Clark, PW Messer. "Maximum likelihood estimation of fitness components in experimental evolution." Genetics. 211:1005. DOI →

42. J Champer, J Chung, YL Lee, C Liu, E Yang, Z Wen, AG Clark, PW Messer. "Molecular safeguarding of CRISPR gene drive experiments." eLife. 8:e41439. Link →

41. BC Haller, PW Messer. "SLiM 3: Forward genetic simulations beyond the Wright–Fisher model." Molecular Biology and Evolution. 36:632. DOI →

40. BC Haller, J Galloway, J Kelleher, PW Messer*, PL Ralph*. "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes." Molecular Ecology Resources. 19:552. DOI →

39. NR Polato, BA Gill, AA Shah, MM Gray, KL Casner, A Barthelet, PW Messer, MP Simmons, JM Guayasamin, AC Encalada, BC Kondratieff, AS Flecker, SA Thomas, CK Ghalambor, NL Poff, WC Funk, KR Zamudio. "Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains." PNAS. 115:12471.

38. D Duneau, H Sun, J Revah, K San Miguel, HD Kunerth, IV Caldas, PW Messer, J Scott, N Buchon. "Signatures of insecticide selection in the genome of Drosophila melanogaster." G3. 8:3469.

37. J Champer, J Liu, S Oh, R Reeves, A Luthra, N Oakes, AG Clark, PW Messer. "Reducing resistance allele formation in CRISPR gene drive." PNAS. 115:5522.

36. J Champer, R Reeves, S Oh, C Liu, J Liu, AG Clark, PW Messer. "Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations." PLoS Genetics. 13:e1006796.

35. BC Haller, PW Messer. "asymptoticMK: A web-based tool for the asymptotic McDonald–Kreitman test." G3. 7:1569.

34. M Champer, AM Wong, J Champer, IL Brito, PW Messer, JY Hou, JD Wright. "The role of the vaginal microbiome in gynecological cancer: a review." BJOG. 125:309.

33. RL Unckless, AG Clark, PW Messer. "Evolution of resistance against CRISPR/Cas9 gene drive." Genetics. 205:827.

32. BC Haller, PW Messer. "SLiM 2: Flexible, interactive forward genetic simulations." Molecular Biology and Evolution. 34:230.

31. AJ Sams, A Dumaine, Y Nédélec, V Yotova, C Alfieri, JE Tanner, PW Messer*, LB Barreiro*. "Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans." Genome Biology. 17:246.

30. Y Nédélec, J Sanz, G Baharian, ZA Szpiech, A Pacis, A Dumaine, JC Grenier, A Freiman, AJ Sams, S Hebert, A Pagé Sabourin, F Luca, R Blekhman, RD Hernandez, R Pique-Regi, J Tung, V Yotova, LB Barreiro. "Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens." Cell. 167:657.

29. DP Toews, SA Taylor, R Vallender, A Brelsford, BG Butcher, PW Messer, IJ Lovette. "Plumage genes and little else distinguish the genomes of hybridizing warblers." Current Biology. 26:1.

28. PW Messer, SP Ellner, NG Hairston Jr. "Can population genetics adapt to rapid evolution?" Trends in Genetics. 32:408.

27. PW Messer. "Neutral models of genetic drift and mutation." In RM Kliman (ed.), Encyclopedia of Evolutionary Biology. 3:119.

26. F Schlamp, J van der Made, R Stambler, L Chesebrough, AR Boyko, PW Messer. "Evaluating the performance of selection scans to detect selective sweeps in domestic dogs." Molecular Ecology. 25:342.

25. RL Unckless, PW Messer, T Connallon, AG Clark. "Modeling the manipulation of natural populations by the Mutagenic Chain Reaction." Genetics. 201:425.

24. S Glemin, PF Arndt, PW Messer, DA Petrov, N Galtier, L Duret. "Quantification of GC-biased gene conversion in the human genome." Genome Research. 25:1215.

23. NR Garud, PW Messer, EO Buzbas, DA Petrov. "Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps." PLoS Genetics. 11:e1005004.

22. AG Clark, PW Messer. "Conundrum of jumbled mosquito genomes." Science. 347:27.

21. BA Wilson, DA Petrov, PW Messer. "Soft selective sweeps in complex demographic scenarios." Genetics. 198:669.

20. D Enard, PW Messer, DA Petrov. "Genome wide signals of positive selection in human evolution." Genome Research. 24:885.

19. PW Messer, DA Petrov. "Population genomics of rapid adaptation by soft selective sweeps." Trends in Ecology and Evolution. 28:659.

18. PW Messer. "SLiM: Simulating evolution with selection and linkage." Genetics. 194:1037.

17. PW Messer, DA Petrov. "Frequent adaptation and the McDonald-Kreitman test." PNAS. 110:8615.

16. DS Lawrie, PW Messer, R Hershberg, DA Petrov. "Strong purifying selection at synonymous sites in D. melanogaster." PLoS Genetics. 9:e1003527.

15. F Staubach, A Lorenc, PW Messer, K Tang, DA Petrov, D Tautz. "Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse." PLoS Genetics. 8:e1002891.

14. PW Messer, RA Neher. "Estimating the strength of selective sweeps from deep population diversity data." Genetics. 191:593.

13. D Sellis, BJ Callahan, DA Petrov, PW Messer. "Heterozygote advantage as a natural consequence of adaptation in diploids." PNAS. 108:20666.

12. DS Lawrie, DA Petrov, PW Messer. "Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection." Genome Biology and Evolution. 3:383.

11. TL Karasov*, PW Messer*, DA Petrov. "Evidence that adaptation in Drosophila is not limited by mutation at single sites." PLoS Genetics. 6:e1000924.

10. J Gonzalez, TL Karasov, PW Messer, DA Petrov. "Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila." PLoS Genetics. 6:e1000905.

9. PW Messer. "Measuring the rates of spontaneous mutation from deep and large-scale polymorphism data." Genetics. 182:1219.

8. J Gonzalez, JM Macpherson, PW Messer, DA Petrov. "Inferring the strength of selection in Drosophila under complex demographic models." Molecular Biology and Evolution. 26:513.

7. N de la Chaux, PW Messer, PF Arndt. "DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage." BMC Evolutionary Biology. 7:191.

6. PW Messer, PF Arndt. "The majority of recent short DNA insertions in the human genome are tandem duplications." Molecular Biology and Evolution. 24:1190.

5. PW Messer, R Bundschuh, M Vingron, PF Arndt. "Effects of long-range correlations in DNA on sequence alignment score statistics." Journal of Computational Biology. 14:655.

4. PW Messer, R Bundschuh, M Vingron, PF Arndt. "Alignment statistics for long-range correlated genomic sequences." RECOMB 2006. 426.

3. PW Messer, PF Arndt. "CorGen — measuring and generating long-range correlations for DNA sequence analysis." Nucleic Acids Research. 34:W692.

2. PW Messer, M Lässig, PF Arndt. "Universality of long-range correlations in expansion-randomization systems." Journal of Statistical Mechanics. P10004.

1. PW Messer, PF Arndt, M Lässig. "Solvable sequence evolution models and genomic correlations." Physical Review Letters. 94:138103.