Messer Lab — Publications

(Messer lab members highlighted in bold)

73. 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 (2023). Adaptations to water stress and pastoralism in the Turkana of northwest Kenya. bioRxiv.

73. IV Caldas, AC Clark, PW Messer (2023). Inference of selective sweep parameters through supervised learning. bioRxiv.

72. R Shen, M Wenzel, PW Messer, CF Aquadro (2023). A model of functionally buffered deleterious mutations can lead to signatures of positive selection. bioRxiv.

71. J Kim, KD Harris, IK Kim, S Shemesh, PW Messer*, G Greenbaum* (*equal contribution) (2023). Incorporating ecology into gene drive modeling. Ecology Letters. (in press)

70. BC Haller, PW Messer (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist. 201:5

69. A Mazo-Vargas, AM Langmüller, A Wilder, KRL van der Burg, JJ Lewis, PW Messer, L Zhang, A Martin, RD Reed (2022). Deep cis-regulatory homology of the butterfly wing pattern ground plan. Science. 378:304

68. SE Champer, IK Kim, AC Clark, PW Messer, J Champer (2022). Anopheles homing suppression drive candidates exhibit unexpected performance differences in simulations with spatial structure. eLife. 11:e79121

67. BC Haller (2022). Ten simple rules for reporting a bug. PLoS Computational Biology. 18(10): e1010540.

66. AM Langmüller, J Champer, S Lapinska, L Xie, M Metzloff, J Liu, Y Xu, J Du, AG Clark, PW Messer (2022). Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations. eLife. 11:e71809.

65. M MetzloffE Yang, S Dhole, AG Clark, PW MesserJ Champer (2022). Experimental demonstration of tethered gene drive systems for confined population modification or suppressionBMC Biology. 20:119

64. E YangM MetzloffAM Langmüller, AG Clark, PW Messer, J Champer (2022). A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance allelesG3: Genes, Genomes, Genetics. jkac081

63. R Shen, PW Messer (2022). Predicting the genomic resolution of bulk segregant analysis. G3: Genes, Genomes, Genetics. 12:jkac012

62. SE Champer, N Oakes, R Sharma, P Garcia-Diaz, J Champer, PW Messer (2021). Modeling CRISPR gene drives for suppression of invasive rodents using a supervised machine learning framework. PLoS Computational Biology. 17:e1009660

61. N Garud, PW Messer, DA Petrov (2021). Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data. PLoS Genetics. 17:e1009373

60. M Munasinghe, BC Haller, AG Clark (2021). Migration Restores Hybrid Incompatibility Driven By Mitochondrial-Nuclear Sexual Conflict. Proc. Biol. Sci. 289:20212561.

58. J Champer, I Kim, SE Champer, AG Clark, PW Messer (2021). Suppression gene drive in continuous space can result in unstable persistence of both drive and wild-type alleles. Molecular Ecology. 30:1086

57. KC Long, … , J Champer, … , PW Messer, … , OS Akbari (44 authors) (2020). Core commitments for field trials of gene drive organisms. Science. 370:14179

56. J ChamperSE ChamperI Kim, AG ClarkPW Messer (2020). Design and analysis of CRISPR-based underdominance toxin-antidote gene drives. Evolutionary Applications. 14:1052

55. J Cury, BC Haller, G Achaz, F Jay (2020). Simulation of bacterial populations with SLiM. Peer Community Journal. 2:e7

54. J Champer, E Yang, E Lee, J Liu, AG ClarkPW Messer (2020). A CRISPR homing gene drive targeting a haplolethal gene removes resistance alleles and successfully spreads through a cage populationPNAS. 117:24377

53. RN Lou,  NO Therkildsen, PW Messer (2020). The effects of quantitative trait architecture on detection power in short-term artificial selection experiments. G3: Genes, Genomes, Genetics. 9:3213

52. JR Adrion, … , PW Messer, … , Kern AD (28 authors) (2020). A community-maintained standard library of population genetic models. eLife. 9:e54967

51. J Champer, I Kim, SE Champer, AG ClarkPW Messer (2020). Performance analysis of novel toxin-antidote CRISPR gene drive systems. BMC Biology. 18:27

50. MV Matz, EA Treml, BC Haller (2020). Estimating the potential for coral adaptation to global warming across the Indo‐West Pacific. Global Change Biology. 26:3473

49. J Champer, J Zhao, SE Champer, J Liu, PW Messer (2020). Population dynamics of underdominance gene drive systems in continuous space. ACS Synthetic Biology. 9:779

48. SE ChamperS OhC LiuZ WenAG ClarkPW MesserJ Champer (2020). Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs. Science Advances. 6:eaaz0525

47. J Champer, YL Lee, E Yang, C Liu, AG ClarkPW Messer (2020). A toxin-antidote CRISPR gene drive system for regional population modification. Nature Communications. 11:1082

46. Giese, JL Frieß, NH Barton, PW Messer, F Débarre, MF Schetelig, N Windbichler, H Meimberg, C Boëte (2019). Gene Drives: Dynamics and Regulatory Matters. Bioessays. 41:1900151

45. J Champer, Z Wen, A Luthra, R Reeves, J Chung, C Liu, YL Lee, J Liu, E Yang, PW Messer, AG Clark (2019). CRISPR Gene Drive Efficiency and Resistance Rate Is Highly Heritable with No Common Genetic Loci of Large Effect. Genetics. 212:333

44. BC HallerPW Messer (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution. 36:1101

43. J Liu, J Champer, AM Langmüller, J Liu, J Chung, R Reeves, A Luthra, YL Lee, AH Vaughn, AG Clark, PW Messer (2019). Maximum likelihood estimation of fitness components in experimental evolution. Genetics. 211:1005

42. J Champer, J Chung, YL Lee, C Liu, E Yang, Z Wen, AG Clark, PW Messer (2019). Molecular safeguarding of CRISPR gene drive experiments. eLife. 8:e41439

41. BC HallerPW Messer (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher model. Molecular Biology and Evolution. 36:632

40. BC Haller, J Galloway, J Kelleher, PW Messer*, PL Ralph* (*co-senior authors) (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources. 19:552

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 (2018). Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains. PNAS. 

38. D Duneau, H Sun, J Revah, K San Miguel, HD Kunerth, IV Caldas, PW Messer, J Scott, N Buchon (2018). Signatures of insecticide selection in the genome of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 8:3469

37. J Champer, J Liu, S Oh, R Reeves, A Luthra, N Oakes, AG Clark, PW Messer (2018). 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 (2017). 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 (2017). asymptoticMK: A web-based tool for the asymptotic McDonald–Kreitman test. G3: Genes, Genomes, Genetics. 7:1569

34. M Champer, AM Wong, J Champer, IL Brito, PW Messer, JY Hou, JD Wright (2017). The role of the vaginal microbiome in gynecological cancer: a review. BJOG: An International Journal of Obstetrics & Gynaecology. 125:309

33. RL Unckless, AG Clark, PW Messer (2017). Evolution of resistance against CRISPR/Cas9 gene drive. Genetics. 205:827

32. BC Haller, PW Messer (2017). 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* (2016) (*co-senior authors). 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. (2016). 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 (2016). Plumage genes and little else distinguish the genomes of hybridizing warblers. Current Biology. 26:1

28. PW Messer, SP Ellner, NG Hairston, Jr. (2016). Can population genetics adapt to rapid evolution? Trends in Genetics. 32:408

27. PW Messer (2016). Neutral models of genetic drift and mutation. In: RM Kliman (ed.), The Encyclopedia of Evolutionary Biology. 3:119

26. F Schlamp, J van der Made, R StamblerL Chesebrough, AR Boyko, PW Messer (2016). 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 (2015). 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 (2015). Quantification of GC-biased gene conversion in the human genome. Genome Research. 25:1215

23. NR Garud, PW Messer, EO Buzbas, DA Petrov (2015). Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genetics. 11:e1005004

22. AG Clark, PW Messer (2015). Conundrum of jumbled mosquito genomes. Science. 347:27 

21. BA Wilson, DA Petrov, PW Messer (2014). Soft selective sweeps in complex demographic scenarios. Genetics. 198:669

20. D Enard, PW Messer, DA Petrov (2014). Genome wide signals of positive selection in human evolution. Genome Research. 24:885

19. PW Messer, DA Petrov (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends in Ecology and Evolution. 28:659

18. PW Messer (2013). SLiM: Simulating evolution with selection and linkage. Genetics. 194:1037

17. PW Messer, DA Petrov (2013). Frequent adaptation and the McDonald-Kreitman test. PNAS. 110:8615

16. DS Lawrie, PW Messer, R Hershberg, DA Petrov (2013). 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 (2012). Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (mus musculus). PLoS Genetics 8:e100289

14. PW Messer, RA Neher (2012). Estimating the strength of selective sweeps from deep population diversity data. Genetics.191:593

13. D Sellis, BJ Callahan, DA Petrov, PW Messer (2011). Heterozygote advantage as a natural consequence of adaptation in diploids. PNAS. 108:20666

12. DS Lawrie, DA Petrov, PW Messer (2011). Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection. Genome Biol Evol. 3:383

11. TL Karasov*, PW Messer*, DA Petrov (*equal contribution) (2010). 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 (2010). Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genetics. 6:e1000905

9. PW Messer (2009). 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 (*equal contribution) (2009). 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 (2007). 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 (2007). 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 (2007). 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 (2006). Alignment statistics for long-range correlated genomic sequences. RECOMB 2006. 426

3. PW Messer, PF Arndt (2006). CorGen — measuring and generating long-range correlations for DNA sequence analysis. Nucleic Acids Research. 34:W692

2. PW Messer, M Lassig, PF Arndt (2005). Universality of long-range correlations in expansion-randomization systems. Journal of Statistical Mechanics. P10004

1. PW Messer, PF Arndt, M Lassig (2005). Solvable sequence evolution models and genomic correlations. Physical Review Letters. 94:138103


IV Caldas (2022) The Inference of Selective Sweep Parameters from their Genomic Footprint. PhD Thesis. Field of Computational Biology, Cornell University. Supervisors: Philipp Messer and Andy Clark

R Shen (2022) Simulation-driven Analyses in Population Genetics: From Genetic Mapping to the Evolution of Genes and Populations. PhD Thesis. Field of Computational Biology, Cornell University. Supervisor: Philipp Messer

A Vaughn (2019) Source-sink Populations: The Coalescence Process in Heterogeneous Environments. Honors Thesis. Applied Mathematics, Cornell University. Supervisor: Philipp Messer

J Liu (2019) Maximum Likelihood Estimation of Fitness Components in Experimental Evolution. Honors Thesis. Biological Sciences, Cornell University. Supervisor: Philipp Messer

A Marderstein (2017) Approximate Bayesian Computation for Studying Selective Sweep Signatures in Local Coalescence Trees. Honors Thesis. College of Agriculture and Life Sciences, Cornell University. Supervisor: Philipp Messer

PW Messer (2008) Tandem Duplications in the Human Genome. PhD Thesis. Department of Mathematics, Free University Berlin. Supervisors: Martin Vingron and Peter Arndt

PW Messer (2005) Solvable Sequence Evolution Models and Genomic Correlations, Diploma Thesis, Institute for Theoretical Physics, University of Cologne. Supervisor: Michael Lassig

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