dots.mocr-mlx-evals / dots.mocr-5bit /long_tiny_text /12_pg71_pg1_pg1_repeat0.md
pcuenq's picture
pcuenq HF Staff
Upload folder using huggingface_hub
e2b9fae verified

Kelly, J.K., 1997. A test of neutrality based on interlocus associations. Genetics 146 (3), 1197–1206. Kim, S.Y., Pritchard, J.K., 2007. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genetics 3 (9), e147. Kim, Y., Stephan, W., 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160 (2), 765–777. Kim, Y., Stephan, W., 2003. Selective sweeps in the presence of interference among partially linked loci. Genetics 164 (1), 389–398. Kimura, M., 1985. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press. Knudsen, B., Miyamoto, M.M., 2001. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proceedings of the National Academy of Sciences of the United States of America 98 (25), 14512–14517. Knudsen, B., Miyamoto, M.M., Laipis, P.J., Silverman, D.N., 2003. Using evolutionary rates to investigate protein functional divergence and conservation: A case study of the carbonic anhydrases. Genetics 164 (4), 1261–1269. Le, S.Q., Gascuel, O., 2008. An improved general amino acid replacement matrix. Molecular Biology and Evolution 25 (7), 1307–1320. Li, H., Stephan, W., 2006. Inferring the demographic history and rate of adaptive substitution in drosophila. PLoS Genetics 2 (10), e166. Li, W., Liu, B., Yu, L., et al., 2009. Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants. BMC Evolutionary Biology 9 (1), 90. Lichtarge, O., Bourne, H.R., Cohen, F.E., 1996. An evolutionary trace method defines binding surfaces common to protein families. Journal of Molecular Biology 257 (2), 342–358. Lockless, S.W., Ranganathan, R., 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (5438), 295–299. Margulies, E.H., Cooper, G.M., Asimenos, G., et al., 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research 17 (6), 760–774. McDonald, J.H., Kreitman, M., 1991. Adaptive protein evolution at the adh locus in drosophila. Nature 351 (6328), 652–654. Mertz, B., Gu, X., Reilly, P.J., 2009. Analysis of functional divergence within two structurally related glycoside hydrolase families. Biopolymers 91 (6), 478495. Messier, W., Stewart, C.-B., 1997. Episodic adaptive evolution of primate lysozymes. Nature 385 (6612), 151–154. Miyata, T., Yasunaga, T., 1980. Molecular evolution of MRna: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. Journal of Molecular Evolution 16 (1), 23–36. Muse, S.V., Gaut, B.S., 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Molecular Biology and Evolution 11 (5), 715–724. Nei, M., Gojobori, T., 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3 (5), 418–426. Nielsen, R., 2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86 (6), 641–647. Nielsen, R., 2005. Molecular signatures of natural selection. Annual Review of Genetics 39, 197–218. Nielsen, R., Bustamante, C., Clark, A.G., et al., 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 3 (6), e170. Nielsen, R., Hubisz, M.J., Hellmann, I., et al., 2009. Darwinian and demographic forces affecting human protein coding genes. Genome Research 19 (5), 838–849. Nielsen, R., Yang, Z., 1998. Likelihood models for detecting positively selected amino acid sites and applications to the hiv-1 envelope gene. Genetics 148 (3), 929–936. Parsch, J., Novozhilov, S., Saminadin-Peter, S.S., Wong, K.M., Andolfatto, P., 2010. On the utility of short intron sequences as a reference for the detection of positive and negative selection in drosophila. Molecular Biology and Evolution 27 (6), 1226–1234. Penn, O., Stern, A., Rubinstein, N.D., et al., 2008. Evolutionary modeling of rate shifts reveals specificity determinants in hiv-1 subtypes. PLoS Computational Biology 4 (11), e1000214. Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R., Siepel, A., 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Research 20 (1), 110–121. Pollard, K.S., Salama, S.R., King, B., et al., 2006a. Forces shaping the fastest evolving regions in the human genome. PLoS Genetics 2 (10), e168. Pollard, K.S., Salama, S.R., Lambert, N., et al., 2006b. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443 (7108), 167–172.

Pond, S.L.K., Frost, S.D., 2005. Not so different after all: A comparison of methods for detecting amino acid sites under selection. Molecular Biology and Evolution 22 (5), 1208–1222. Pool, J.E., Hellmann, I., Jensen, J.D., Nielsen, R., 2010. Population genetic inference from genomic sequence variation. Genome Research 20 (3), 291–300. Prabhakar, S., Noonan, J.P., Paabo, S., Rubin, E.M., 2006. Accelerated evolution of conserved noncoding sequences in humans. Science 314 (5800), 786. Pupko, T., Galtier, N., 2002. A covarion-based method for detecting molecular adaptation: Application to the evolution of primate mitochondrial genomes. Proceedings of the Royal Society of London B: Biological Sciences 269 (1498), 1313–1316. Ratnakumar, A., Mousset, S., Glemin, S., et al., 2010. Detecting positive selection within genomes: The problem of biased gene conversion. Philosophical Transactions of the Royal Society B: Biological Sciences 365 (1552), 2571–2580. Rockman, M.V., Hahn, M.W., Soranzo, N., et al., 2005. Ancient and recent positive selection transformed opioid cis-regulation in humans. PLoS Biology 3 (12), e387. Sabeti, P.C., Reich, D.E., Higgins, J.M., et al., 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419 (6909), 832–837. Sawyer, S.A., Dykhuizen, D.E., Hartl, D.L., 1987. Confidence interval for the number of selectively neutral amino acid polymorphisms. Proceedings of the National Academy of Sciences of the United States of America 84 (17), 6225–6228. Sawyer, S.A., Hartl, D.L., 1992. Population genetics of polymorphism and divergence. Genetics 132 (4), 1161–1176. Siepel, A., Haussler, D., 2005. Phylogenetic hidden markov models. In: Nielsen, R. (Ed.), Statistical Methods in Molecular Evolution. New York: Springer, pp. 325–351. Suel, G.M., Lockless, S.W., Wall, M.A., Ranganathan, R., 2003. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nature Structural & Molecular Biology 10 (1), 59–69. Susko, E., Inagaki, Y., Field, C., Holder, M.E., Roger, A.J., 2002. Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Molecular Biology and Evolution 19 (9), 1514–1523. Swanson, W.J., Nielsen, R., Yang, Q., 2003. Pervasive adaptive evolution in mammalian fertilization proteins. Molecular Biology and Evolution 20 (1), 1820. Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (3), 585–595. Torgerson, D.G., Boyko, A.R., Hernandez, R.D., et al., 2009. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genetics 5 (8), e1000592. Wang, H.-C., Spencer, M., Susko, E., Roger, A.J., 2007. Testing for covarion-like evolution in protein sequences. Molecular Biology and Evolution 24 (1), 294–305. Weir, B.S., Cardon, L.R., Anderson, A.D., Nielsen, D.M., Hill, W.G., 2005. Measures of human population structure show heterogeneity among genomic regions. Genome Research 15 (11), 1468–1476. Whelan, S., Goldman, N., 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution 18 (5), 691–699. Williamson, S.H., Hernandez, R., Fledel-Alon, A., et al., 2005. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proceedings of the National Academy of Sciences of the United States of America 102 (22), 7882–7887. Wong, W.S., Nielsen, R., 2004. Detecting selection in noncoding regions of nucleotide sequences. Genetics 167 (2), 949–958. Wray, G.A., Hahn, M.W., Abouheif, E., et al., 2003. The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution 20 (9), 1377–1419. Yang, Z., 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution 15 (5), 568–573. Yang, Z., Bielawski, J.P., 2000. Statistical methods for detecting molecular adaptation. Trends in Ecology & Evolution 15 (12), 496–503. Yang, Z., Nielsen, R., 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution 17 (1), 32–43. Yang, Z., Nielsen, R., Goldman, N., 2009. In defense of statistical methods for detecting positive selection. Proceedings of the National Academy of Sciences of the United States of America 106 (36), E95. Yang, Z., Swanson, W.J., 2002. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Molecular Biology and Evolution 19 (1), 49–57. Zhai, W., Nielsen, R., Goldman, N., Yang, Z., 2012. Looking for Darwin in genomic sequences validity and success of statistical methods. Molecular Biology and Evolution 29 (10), 2889–2893.