46. J Champer, J Zhao, S Champer, J Liu, PW Messer (2018). Population dynamics of underdominance gene drive systems in continuous space. bioRxiv.
45. J Champer, Z Wen, A Luthra, R Reeves, J Chung, Chen Liu, YL Lee, J Liu, E Yang, PW Messer, AG Clark (2018). Multiple loci of small effect confer wide variability in efficiency and resistance rate of CRISPR gene drive. bioRxiv.
44. BC Haller, PW Messer (2018). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution (in press).
43. J Champer, J Chung, YL Lee, C Liu, E Yang, Z Wen, AG Clark, PW Messer (2018). Molecular safeguarding of CRISPR gene drive experiments. bioRxiv.
42. J Liu, J Champer, J Liu, J Chung, R Reeves, A Luthra, YL Lee, AG Clark, PW Messer (2018). Maximum likelihood estimation of fitness components in experimental evolution. bioRxiv.
41. BC Haller, PW Messer (2018). SLiM 3: Forward genetic simulations beyond the Wright–Fisher model. Molecular Biology and Evolution (in press).
40. BC Haller, J Galloway, J Kelleher, PW Messer*, PL Ralph* (2018) (*co-senior authors). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources (in press).
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 (early online)
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 Stambler, L 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
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