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Complete publication page from Pubmed

42. Daniel M. Weinreich (2020) Herding a biological population with quantum control tools. Nature Physics https://doi.org/10.1038/s41567-020-01050-w

41. Jordan Yang, Nandita Naik, Jagdish Suresh Patel, Christopher S. Wylie, Wenze Gu, Jessie Huang, F. Marty Ytreberg, Mandar T. Naik, Daniel M. Weinreich, and Brenda M. Rubenstein (2020) Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness. PLoS One 15(5): e0233509. https://doi.org/10.1371/journal.pone.0233509  Raynes, Yevgeniy and Daniel M. Weinreich (2019) Selection on mutators is not frequency-dependent. eLife 8:e51177.40.
40. Raynes Y, Sniegowski PD, Weinreich DM. Migration promotes mutator alleles in subdivided populations. Evolution. 2019 Mar;73(3):600-608. doi: 10.1111/evo.13681. Epub 2019 Jan 16. PubMed PMID: 30632605.
 
39. Raynes Y, Weinreich DM. Genomic clustering of fitness-affecting mutations favors the evolution of chromosomal instability. Evol Appl. 2019 Feb;12(2):301-313. doi: 10.1111/eva.12717. eCollection 2019 Feb. PubMed PMID: 30697341; PubMed Central PMCID: PMC6346662.
 
38. Ferretti L, Weinreich D, Tajima F, Achaz G. Evolutionary constraints in fitness landscapes. Heredity (Edinb). 2018 Nov;121(5):466-481. doi: 10.1038/s41437-018-0110-1. Epub 2018 Jul 11. PubMed PMID: 29993041; PubMed Central PMCID: PMC6180097.
 
37. Raynes Y, Wylie CS, Sniegowski PD, Weinreich DM. Sign of selection on mutation rate modifiers depends on population size. Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):3422-3427. doi: 10.1073/pnas.1715996115. Epub 2018 Mar 12. PubMed PMID: 29531067; PubMed Central PMCID: PMC5879664.
 
36. Stover KK, Weinreich DM, Roberts TJ, Brainerd EL. Patterns of musculoskeletal growth and dimensional changes associated with selection and developmental plasticity in domestic and wild strain turkeys. Ecol Evol. 2018 Mar;8(6):3229-3239. doi: 10.1002/ece3.3881. eCollection 2018 Mar. PubMed PMID: 29607020; PubMed Central PMCID: PMC5869219.
 
35. Weinreich DM, Lan Y, Jaffe J, Heckendorn RB. The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography. J Stat Phys. 2018;172(1):208-225. doi: 10.1007/s10955-018-1975-3. Epub 2018 Feb 7. PubMed PMID: 29904213; PubMed Central PMCID: PMC5986866.
 
34. Knies JL, Cai F, Weinreich DM. Enzyme Efficiency but Not Thermostability Drives Cefotaxime Resistance Evolution in TEM-1 β-Lactamase. Mol Biol Evol. 2017 May 1;34(5):1040-1054. doi: 10.1093/molbev/msx053. PubMed PMID: 28087769; PubMed Central PMCID: PMC5400381.
 
33. Graves CJ, Weinreich DM. Variability in Fitness Effects Can Preclude Selection of the Fittest. Annual review of ecology, evolution, and systematics. 2017; 48:399-417. doi: 10.1146/annurev-ecolsys-110316-022722.
 
32. Ferretti L, Schmiegelt B, Weinreich D, Yamauchi A, Kobayashi Y, Tajima F, Achaz G. Measuring epistasis in fitness landscapes: The correlation of fitness effects of mutations. J Theor Biol. 2016 May 7;396:132-43. doi: 10.1016/j.jtbi.2016.01.037. Epub 2016 Feb 20. PubMed PMID: 26854875.
 
31. Baker CW, Miller CR, Thaweethai T, Yuan J, Baker MH, Joyce P, Weinreich DM. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174. G3 (Bethesda). 2016 Apr 7;6(4):939-55. doi: 10.1534/g3.115.024075. PubMed PMID: 26921293; PubMed Central PMCID: PMC4825663.
 
30. Ogbunugafor CB, Wylie CS, Diakite I, Weinreich DM, Hartl DL. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance. PLoS Comput Biol. 2016 Jan;12(1):e1004710. doi: 10.1371/journal.pcbi.1004710. eCollection 2016 Jan. PubMed PMID: 26808374; PubMed Central PMCID: PMC4726534.
 
29. Cruzan M, Weinreich D. Adaptive Landscapes . In: Elsevier’s Reference Modules in Life Sciences.  Amsterdam: Elsevier Publisher; 2016. 
 
28. Meini MR, Tomatis PE, Weinreich DM, Vila AJ. Quantitative Description of a Protein Fitness Landscape Based on Molecular Features. Mol Biol Evol. 2015 Jul;32(7):1774-87. doi: 10.1093/molbev/msv059. Epub 2015 Mar 12. PubMed PMID: 25767204; PubMed Central PMCID: PMC4476158.
 
27. Watson RA, Wagner GP, Pavlicev M, Weinreich DM, Mills R. The evolution of phenotypic correlations and "developmental memory". Evolution. 2014 Apr;68(4):1124-38. doi: 10.1111/evo.12337. Epub 2014 Feb 1. PubMed PMID: 24351058; PubMed Central PMCID: PMC4131988.
 
26. Weinreich DM, Lan Y, Wylie CS, Heckendorn RB. Should evolutionary geneticists worry about higher-order epistasis?.Curr Opin Genet Dev. 2013 Dec;23(6):700-7. doi: 10.1016/j.gde.2013.10.007. Epub 2013 Nov 27. Review. PubMed PMID: 24290990; PubMed Central PMCID: PMC4313208.
 
25. Weinreich DM, Knies JL. Fisher's geometric model of adaptation meets the functional synthesis: data on pairwise epistasis for fitness yields insights into the shape and size of phenotype space. Evolution. 2013 Oct;67(10):2957-72. doi: 10.1111/evo.12156. Epub 2013 Jun 5. PubMed PMID: 24094346; PubMed Central PMCID: PMC4282100.
 
24. Weinreich DM, Sindi S, Watson RA. Finding the boundary between evolutionary basins of attraction, and implications for Wright's fitness landscape analogy. Journal of statistical mechanics (Online). 2013 January; P01001. doi: doi:10.1088/1742-5468/2013/01/P01001.
 
23. Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution.Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review. PubMed PMID: 22528593; PubMed Central PMCID: PMC3403413.
 
22. Weinreich DM. High-throughput identification of genetic interactions in HIV-1. Nat Genet. 2011 May;43(5):398-400. doi: 10.1038/ng.820. PubMed PMID: 21522176.
 
21. Watson RA, Weinreich DM, Wakeley J. Genome structure and the benefit of sex. Evolution. 2011 Feb;65(2):523-36. doi: 10.1111/j.1558-5646.2010.01144.x. Epub 2010 Nov 5. PubMed PMID: 21029076.
 
20. Rand DM, Weinreich DM, Lerman D, Folk D, Gilchrist GW. Three selections are better than one: clinal variation of thermal QTL from independent selection experiments in Drosophila. Evolution. 2010 Oct;64(10):2921-34. doi: 10.1111/j.1558-5646.2010.01039.x. Epub 2010 Aug 19. PubMed PMID: 20497214; PubMed Central PMCID: PMC3148135.
 
19. O'Keefe KJ, Silander OK, McCreery H, Weinreich DM, Wright KM, Chao L, Edwards SV, Remold SK, Turner PE. Geographic differences in sexual reassortment in RNA phage. Evolution. 2010 Oct;64(10):3010-23. doi: 10.1111/j.1558-5646.2010.01040.x. Epub 2010 Aug 19. PubMed PMID: 20500219.
 
18. Christin PA, Weinreich DM, Besnard G. Causes and evolutionary significance of genetic convergence. Trends Genet. 2010 Sep;26(9):400-5. doi: 10.1016/j.tig.2010.06.005. Epub 2010 Aug 3. PubMed PMID: 20685006.
 
17. Weinreich D. Predicting molecular evolutionary trajectories in principle and in practice . In: Encyclopedia of Life Sciences.  Chichester: John Wiley and Sons, Ltd; 2010. 
 
16. Brown KM, Depristo MA, Weinreich DM, Hartl DL. Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways. Mol Biol Evol. 2009 Nov;26(11):2455-62. doi: 10.1093/molbev/msp151. Epub 2009 Jul 14. PubMed PMID: 19602543; PubMed Central PMCID: PMC2912465.
Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM,
15. Hartl DL. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12025-30. doi: 10.1073/pnas.0905922106. Epub 2009 Jul 8. PubMed PMID: 19587242; PubMed Central PMCID: PMC2715478.
 
14. DePristo MA, Hartl DL, Weinreich DM. Mutational reversions during adaptive protein evolution. Mol Biol Evol. 2007 Aug;24(8):1608-10. doi: 10.1093/molbev/msm118. Epub 2007 Jun 7. PubMed PMID: 17556755.
Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ. Empirical fitness landscapes reveal accessible evolutionary paths. Nature.2007 Jan 25;445(7126):383-6. doi: 10.1038/nature05451. PubMed PMID: 17251971.
 
13. Polz MF, Hunt DE, Preheim SP, Weinreich DM. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):2009-21. doi: 10.1098/rstb.2006.1928. Review. PubMed PMID: 17062417; PubMed Central PMCID: PMC1764928.
 
12. Watson RA, Weinreich DM, Wakeley J. Effects of intra-gene fitness interactions on the benefit of sexual recombination.Biochem Soc Trans. 2006 Aug;34(Pt 4):560-1. doi: 10.1042/BST0340560. PubMed PMID: 16856860.
 
11. Weinreich DM, Delaney NF, Depristo MA, Hartl DL. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science. 2006 Apr 7;312(5770):111-4. doi: 10.1126/science.1123539. PubMed PMID: 16601193.
 
10. Silander OK, Weinreich DM, Wright KM, O'Keefe KJ, Rang CU, Turner PE, Chao L. Widespread genetic exchange among terrestrial bacteriophages. Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19009-14. doi: 10.1073/pnas.0503074102. Epub 2005 Dec 19. PubMed PMID: 16365305; PubMed Central PMCID: PMC1323146.
 
9. Weinreich DM. The rank ordering of genotypic fitness values predicts genetic constraint on natural selection on landscapes lacking sign epistasis. Genetics. 2005 Nov;171(3):1397-405. doi: 10.1534/genetics.104.036830. Epub 2005 Aug 3. PubMed PMID: 16079241; PubMed Central PMCID: PMC1456840.
 
8. DePristo MA, Weinreich DM, Hartl DL. Missense meanderings in sequence space: a biophysical view of protein evolution.Nat Rev Genet. 2005 Sep;6(9):678-87. doi: 10.1038/nrg1672. Review. PubMed PMID: 16074985.
 
7. Weinreich DM, Chao L. Rapid evolutionary escape by large populations from local fitness peaks is likely in nature.Evolution. 2005 Jun;59(6):1175-82. PubMed PMID: 16050095.
 
6. Weinreich DM, Watson RA, Chao L. Perspective: Sign epistasis and genetic constraint on evolutionary trajectories.Evolution. 2005 Jun;59(6):1165-74. Review. PubMed PMID: 16050094.
 
5. Sheldahl LA, Weinreich DM, Rand DM. Recombination, dominance and selection on amino acid polymorphism in the Drosophila genome: contrasting patterns on the X and fourth chromosomes. Genetics. 2003 Nov;165(3):1195-208. PubMed PMID: 14668375; PubMed Central PMCID: PMC1462837.
 
4. Weinreich DM. The rates of molecular evolution in rodent and primate mitochondrial DNA. J Mol Evol. 2001 Jan;52(1):40-50. PubMed PMID: 11139293.
 
3. Rand DM, Weinreich DM, Cezairliyan BO. Neutrality tests of conservative-radical amino acid changes in nuclear- and mitochondrially-encoded proteins. Gene. 2000 Dec 30;261(1):115-25. doi: 10.1016/s0378-1119(00)00483-2. PubMed PMID: 11164043.
 
2. Weinreich DM, Rand DM. Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics. 2000 Sep;156(1):385-99. PubMed PMID: 10978302; PubMed Central PMCID: PMC1461243.
 
1. Nielsen R, Weinreich DM. The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory. Genetics. 1999 Sep;153(1):497-506. PubMed PMID: 10471729; PubMed Central PMCID: PMC1460725.