Messer Lab — Publications


37. PW Messer, IH Cheeseman, NR Garud, PS Pennings, S Nair, M Manske, DP Kwiatkowski, AP Phyo, FH Nosten, DA Petrov, TJ Anderson
Empirical evaluation of the power of selection scans to identify hard and soft selective sweeps in malaria parasites. (in revision)

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. (in press)

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. (early online)

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


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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