(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 Metzloff, E Yang, S Dhole, AG Clark, PW Messer, J Champer (2022). Experimental demonstration of tethered gene drive systems for confined population modification or suppression. BMC Biology. 20:119
64. E Yang, M Metzloff, AM 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 alleles. G3: 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. , , , , (2020). Design and analysis of CRISPR-based underdominance toxin-antidote gene drives. Evolutionary Applications. 14:1052
55. 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 Clark, PW Messer (2020). A CRISPR homing gene drive targeting a haplolethal gene removes resistance alleles and successfully spreads through a cage population. PNAS. 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 Clark, PW 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. , , , , , , (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 Clark, PW 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 Haller, PW 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 Haller, PW 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 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 (*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
Theses:
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
Messer Lab 