Messer Lab — Publications

(Messer lab members highlighted in bold)

72. IV Caldas, AC Clark, PW Messer (2022). Inference of selective sweep parameters through supervised learning. bioRxiv.

71. R Shen, M Wenzel, PW Messer, CF Aquadro (2022). A model of functionally buffered deleterious mutations can lead to signatures of positive selection. bioRxiv.

70. BC Haller, PW Messer (2022). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist. (early online)

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* (2019) (*co-senior authors). 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 (2010) (*equal contribution). 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 (2009) (*equal contribution). 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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