The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography
暂无分享,去创建一个
Robert B. Heckendorn | Jacob Jaffe | Yinghong Lan | D. Weinreich | Yinghong Lan | Daniel M Weinreich | Robert B Heckendorn | Jacob Jaffe
[1] J.A.G.M. de Visser,et al. Deleterious mutations and the evolution of sex , 1996 .
[2] L. Darrell Whitley,et al. Predicting Epistasis from Mathematical Models , 1999, Evolutionary Computation.
[3] Frank J. Poelwijk,et al. Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data , 2006, PLoS Comput. Biol..
[4] B. Charlesworth,et al. Why sex and recombination? , 1998, Science.
[5] R. Punnett,et al. The Genetical Theory of Natural Selection , 1930, Nature.
[6] David M. McCandlish,et al. VISUALIZING FITNESS LANDSCAPES , 2011, Evolution; international journal of organic evolution.
[7] E. D. Weinberger,et al. Fourier and Taylor series on fitness landscapes , 1991, Biological Cybernetics.
[8] R. Lenski,et al. Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population , 2011, Science.
[9] Frank J. Poelwijk,et al. The Context-Dependence of Mutations: A Linkage of Formalisms , 2015, PLoS Comput. Biol..
[10] P. Stadler. Landscapes and their correlation functions , 1996 .
[11] Nigel F. Delaney,et al. Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins , 2006, Science.
[12] S. Wright,et al. Evolution in Mendelian Populations. , 1931, Genetics.
[13] S. Holm. A Simple Sequentially Rejective Multiple Test Procedure , 1979 .
[14] Kate B. Cook,et al. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity , 2014, Cell.
[15] J. Krug,et al. Exploring the Effect of Sex on Empirical Fitness Landscapes , 2009, The American Naturalist.
[16] Daniel E. Newburger,et al. Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.
[17] P. Stadler. Spectral Landscape Theory , 1999 .
[18] A. Dean,et al. Mechanistic approaches to the study of evolution: the functional synthesis , 2007, Nature Reviews Genetics.
[19] Michael Baym,et al. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes , 2015, Nature Communications.
[20] L. Avery,et al. Ordering gene function: the interpretation of epistasis in regulatory hierarchies. , 1992, Trends in genetics : TIG.
[21] E. D. Weinberger,et al. The NK model of rugged fitness landscapes and its application to maturation of the immune response. , 1989, Journal of theoretical biology.
[22] L. Pachter,et al. EPISTASIS AND SHAPES OF FITNESS LANDSCAPES , 2006, q-bio/0603034.
[23] A. Kondrashov. Deleterious mutations and the evolution of sexual reproduction , 1988, Nature.
[24] M. Whitlock,et al. FACTORS AFFECTING THE GENETIC LOAD IN DROSOPHILA: SYNERGISTIC EPISTASIS AND CORRELATIONS AMONG FITNESS COMPONENTS , 2000, Evolution; international journal of organic evolution.
[25] Richard A. Watson,et al. PERSPECTIVE:SIGN EPISTASIS AND GENETIC CONSTRAINT ON EVOLUTIONARY TRAJECTORIES , 2005 .
[26] M. Feldman,et al. On the evolutionary effect of recombination. , 1970, Theoretical population biology.
[27] Joshua D. Knowles,et al. Analysis of a complete DNA–protein affinity landscape , 2010, Journal of The Royal Society Interface.
[28] Alden H. Wright,et al. Efficient Linkage Discovery by Limited Probing , 2003, Evolutionary Computation.
[29] P. Phillips. The language of gene interaction. , 1998, Genetics.
[30] Michael J Harms,et al. Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps , 2016, Genetics.
[31] Niko Beerenwinkel,et al. Inferring Genetic Interactions From Comparative Fitness Data , 2017 .
[32] D. Weinreich,et al. Quantitative Description of a Protein Fitness Landscape Based on Molecular Features. , 2015, Molecular biology and evolution.
[33] Timothy B Sackton,et al. Genotypic Context and Epistasis in Individuals and Populations , 2016, Cell.
[34] Organic and GM—Why Not? , 2008, Science.
[35] J. Gore,et al. Hidden randomness between fitness landscapes limits reverse evolution. , 2011, Physical review letters.
[36] M. Kendall. A NEW MEASURE OF RANK CORRELATION , 1938 .
[37] Robert B. Heckendorn,et al. Should evolutionary geneticists worry about higher-order , 2013 .
[38] D. Weinreich,et al. RAPID EVOLUTIONARY ESCAPE BY LARGE POPULATIONS FROM LOCAL FITNESS PEAKS IS LIKELY IN NATURE , 2005, Evolution; international journal of organic evolution.
[39] M. Nowak,et al. Stochastic Tunnels in Evolutionary Dynamics , 2004, Genetics.
[40] Tim F. Cooper,et al. The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape , 2013, PLoS genetics.
[41] J. W. Thornton,et al. Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites , 2015, eLife.
[42] Tyler N. Starr,et al. Epistasis in protein evolution , 2016, Protein science : a publication of the Protein Society.
[43] J. Meza,et al. Adaptive Landscapes of Resistance Genes Change as Antibiotic Concentrations Change. , 2015, Molecular biology and evolution.
[44] J. Krug,et al. Quantitative analyses of empirical fitness landscapes , 2012, 1202.4378.
[45] Sayan Mukherjee,et al. Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits , 2016, bioRxiv.
[46] Michael J. Harms,et al. High-order epistasis shapes evolutionary trajectories , 2017, PLoS Comput. Biol..
[47] M. Wade,et al. Epistasis and the Evolutionary Process , 2000 .
[48] J. Noel,et al. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases , 2008, Nature chemical biology.
[49] N. Barton,et al. Why sex and recombination? , 2009, Cold Spring Harbor symposia on quantitative biology.
[50] David W Hall,et al. Fitness epistasis among 6 biosynthetic loci in the budding yeast Saccharomyces cerevisiae. , 2010, The Journal of heredity.
[51] Thanat Chookajorn,et al. Stepwise acquisition of pyrimethamine resistance in the malaria parasite , 2009, Proceedings of the National Academy of Sciences.
[52] P. Phillips. Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems , 2008, Nature Reviews Genetics.
[53] D. J. Kiviet,et al. Empirical fitness landscapes reveal accessible evolutionary paths , 2007, Nature.
[54] D. Hartl,et al. Fitness Trade-Offs in the Evolution of Dihydrofolate Reductase and Drug Resistance in Plasmodium falciparum , 2011, PloS one.
[55] P. Stadler,et al. Random field models for fitness landscapes , 1999 .
[56] Elena R. Lozovsky,et al. Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. , 2010, Molecular biology and evolution.
[57] D. Mosier,et al. Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region , 2010, Genetics.
[58] W. Provine. Sewall Wright and evolutionary biology , 1987 .
[59] J. Krug,et al. Empirical fitness landscapes and the predictability of evolution , 2014, Nature Reviews Genetics.
[60] J. Krug,et al. Exact results for amplitude spectra of fitness landscapes. , 2013, Journal of theoretical biology.
[61] Ronald M. Nelson,et al. Higher order interactions: detection of epistasis using machine learning and evolutionary computation. , 2013, Methods in molecular biology.
[62] E. Ortlund,et al. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution , 2009, Nature.
[63] Elena R. Lozovsky,et al. Accessible Mutational Trajectories for the Evolution of Pyrimethamine Resistance in the Malaria Parasite Plasmodium vivax , 2013, Journal of Molecular Evolution.
[64] Robert B. Heckendorn,et al. Should evolutionary geneticists worry about higher-order epistasis? , 2013, Current opinion in genetics & development.
[65] J. Jensen,et al. On the (un-)predictability of a large intragenic fitness landscape , 2016, bioRxiv.
[66] R. Greenberg. Biometry , 1969, The Yale Journal of Biology and Medicine.
[67] Nigel F. Delaney,et al. Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation , 2011, Science.
[68] Kyung-Ah Sohn,et al. Fast detection of high-order epistatic interactions in genome-wide association studies using information theoretic measure , 2014, Comput. Biol. Chem..
[69] Brian W. Matthews,et al. Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing , 1990, Nature.
[70] B. Shraiman,et al. Competition between recombination and epistasis can cause a transition from allele to genotype selection , 2009, Proceedings of the National Academy of Sciences.
[71] H. A. Orr,et al. Fitness and its role in evolutionary genetics , 2009, Nature Reviews Genetics.
[72] Yuanying Chen,et al. Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary , 2023, bioRxiv.
[73] Stephen P. Miller,et al. The Biochemical Architecture of an Ancient Adaptive Landscape , 2005, Science.
[74] Jennifer L. Knies,et al. Enzyme Efficiency but Not Thermostability Drives Cefotaxime Resistance Evolution in TEM-1 β-Lactamase , 2017, Molecular biology and evolution.
[75] John Maynard Smith,et al. Natural Selection and the Concept of a Protein Space , 1970, Nature.