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Jeffrey L. Thorne, Ph.D. - Publications

Affiliations: 
Genetics North Carolina State University, Raleigh, NC 
Area:
molecular evolution
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49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Yang Y, Xu T, Conant G, Kishino H, Thorne JL, Ji X. Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization. Molecular Biology and Evolution. PMID 37675606 DOI: 10.1093/molbev/msad198  0.506
2023 Ji X, Fisher AA, Su S, Thorne JL, Potter B, Lemey P, Baele G, Suchard MA. Scalable Bayesian divergence time estimation with ratio transformations. Systematic Biology. PMID 37458991 DOI: 10.1093/sysbio/syad039  0.574
2022 Seo TK, Redelings BD, Thorne JL. Correlations between alignment gaps and nucleotide substitution or amino acid replacement. Proceedings of the National Academy of Sciences of the United States of America. 119: e2204435119. PMID 35972964 DOI: 10.1073/pnas.2204435119  0.764
2021 Seo TK, Gascuel O, Thorne JL. Measuring Phylogenetic Information of Incomplete Sequence Data. Systematic Biology. PMID 34469581 DOI: 10.1093/sysbio/syab073  0.627
2021 Campbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee HJ, Thorne JL, Dos Reis M, Yoder AD. Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Heredity. PMID 34272504 DOI: 10.1038/s41437-021-00446-5  0.545
2020 Larson G, Thorne JL, Schmidler S. Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 32053390 DOI: 10.1089/Cmb.2019.0500  0.367
2017 Seo TK, Thorne JL. Information Criteria for Comparing Partition Schemes. Systematic Biology. PMID 29309694 DOI: 10.1093/Sysbio/Syx097  0.566
2016 Lee HJ, Kishino H, Rodrigue N, Thorne JL. Grouping substitution types into different relaxed molecular clocks. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 371. PMID 27325837 DOI: 10.1098/Rstb.2015.0141  0.575
2016 Ji X, Griffing A, Thorne JL. A phylogenetic approach finds abundant interlocus gene conversion in yeast. Molecular Biology and Evolution. PMID 27297467 DOI: 10.1093/Molbev/Msw114  0.58
2015 Wang K, Yu S, Ji X, Lakner C, Griffing A, Thorne JL. Roles of solvent accessibility and gene expression in modeling protein sequence evolution. Evolutionary Bioinformatics Online. 11: 85-96. PMID 25987828 DOI: 10.4137/Ebo.S22911  0.78
2015 Lee HJ, Rodrigue N, Thorne JL. Relaxing the Molecular Clock to Different Degrees for Different Substitution Types. Molecular Biology and Evolution. 32: 1948-61. PMID 25931515 DOI: 10.1093/Molbev/Msv099  0.639
2012 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, ... ... Thorne JL, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  0.707
2012 Thorne JL, Lartillot N, Rodrigue N, Choi SC. Codon models as a vehicle for reconciling population genetics with interspecific sequence data Codon Evolution: Mechanisms and Models. DOI: 10.1093/acprof:osobl/9780199601165.003.0007  0.573
2011 Cartwright RA, Lartillot N, Thorne JL. History can matter: non-Markovian behavior of ancestral lineages. Systematic Biology. 60: 276-90. PMID 21398626 DOI: 10.1093/Sysbio/Syr012  0.622
2011 Yokoyama KD, Thorne JL, Wray GA. Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution. Genome Biology and Evolution. 3: 66-74. PMID 21118975 DOI: 10.1093/Gbe/Evq078  0.358
2009 Choi SC, Stone EA, Kishino H, Thorne JL. Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. Gene. 441: 45-52. PMID 18725272 DOI: 10.1016/J.Gene.2008.07.020  0.623
2008 Choi SC, Redelings BD, Thorne JL. Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3931-9. PMID 18852105 DOI: 10.1098/Rstb.2008.0167  0.786
2008 Kitazoe Y, Kishino H, Hasegawa M, Nakajima N, Thorne JL, Tanaka M. Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates. Plos One. 3: e3343. PMID 18836526 DOI: 10.1371/Journal.Pone.0003343  0.368
2008 Xiang QY, Thorne JL, Seo TK, Zhang W, Thomas DT, Ricklefs RE. Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors. Molecular Phylogenetics and Evolution. 49: 327-42. PMID 18682295 DOI: 10.1016/J.Ympev.2008.07.010  0.648
2007 Thorne JL. Protein evolution constraints and model-based techniques to study them. Current Opinion in Structural Biology. 17: 337-41. PMID 17572082 DOI: 10.1016/J.Sbi.2007.05.006  0.491
2007 Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL. Quantifying the impact of protein tertiary structure on molecular evolution. Molecular Biology and Evolution. 24: 1769-82. PMID 17522088 DOI: 10.1093/Molbev/Msm097  0.781
2007 Thorne JL, Choi SC, Yu J, Higgs PG, Kishino H. Population genetics without intraspecific data. Molecular Biology and Evolution. 24: 1667-77. PMID 17470435 DOI: 10.1093/Molbev/Msm085  0.786
2007 Lin YM, Fang SC, Thorne JL. A tabu search algorithm for maximum parsimony phylogeny inference European Journal of Operational Research. 176: 1908-1917. DOI: 10.1016/J.Ejor.2005.10.031  0.483
2006 Yu J, Thorne JL. Testing for spatial clustering of amino acid replacements within protein tertiary structure. Journal of Molecular Evolution. 62: 682-92. PMID 16752209 DOI: 10.1007/S00239-005-0107-2  0.746
2006 Yu J, Thorne JL. Dependence among sites in RNA evolution. Molecular Biology and Evolution. 23: 1525-37. PMID 16720696 DOI: 10.1093/Molbev/Msl015  0.78
2005 Seo TK, Kishino H, Thorne JL. Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America. 102: 4436-41. PMID 15764703 DOI: 10.1073/Pnas.0408313102  0.624
2004 Sanderson MJ, Thorne JL, Wikström N, Bremer K. Molecular evidence on plant divergence times. American Journal of Botany. 91: 1656-65. PMID 21652315 DOI: 10.3732/Ajb.91.10.1656  0.336
2004 Seo TK, Kishino H, Thorne JL. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Molecular Biology and Evolution. 21: 1201-13. PMID 15014159 DOI: 10.1093/Molbev/Msh088  0.628
2004 Thorne JL. Discussions on “A Bayesian Approach to DNA Sequence Segmentation” Biometrics. 60: 584-585. DOI: 10.1111/J.0006-341X.2004.206_5.X  0.344
2003 Wiegmann BM, Yeates DK, Thorne JL, Kishino H. Time flies, a new molecular time-scale for brachyceran fly evolution without a clock. Systematic Biology. 52: 745-56. PMID 14668115 DOI: 10.1093/Sysbio/52.6.745  0.451
2003 Hasegawa M, Thorne JL, Kishino H. Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. Genes & Genetic Systems. 78: 267-83. PMID 14532706 DOI: 10.1266/Ggs.78.267  0.469
2003 Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL. Protein evolution with dependence among codons due to tertiary structure. Molecular Biology and Evolution. 20: 1692-704. PMID 12885968 DOI: 10.1093/Molbev/Msg184  0.656
2003 Scholl EH, Thorne JL, McCarter JP, Bird DM. Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biology. 4: R39. PMID 12801413 DOI: 10.1186/Gb-2003-4-6-R39  0.675
2002 Thorne JL, Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology. 51: 689-702. PMID 12396584 DOI: 10.1080/10635150290102456  0.425
2002 Seo TK, Thorne JL, Hasegawa M, Kishino H. Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genetics. 160: 1283-93. PMID 11973287  0.569
2002 Seo TK, Thorne JL, Hasegawa M, Kishino H. A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics (Oxford, England). 18: 115-23. PMID 11836219 DOI: 10.1093/Bioinformatics/18.1.115  0.654
2001 Kishino H, Thorne JL, Bruno WJ. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution. 18: 352-61. PMID 11230536 DOI: 10.1093/Oxfordjournals.Molbev.A003811  0.434
2000 Thorne JL. Models of protein sequence evolution and their applications. Current Opinion in Genetics & Development. 10: 602-5. PMID 11088008 DOI: 10.1016/S0959-437X(00)00142-8  0.523
1998 Thorne JL, Kishino H, Painter IS. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution. 15: 1647-57. PMID 9866200 DOI: 10.1093/Oxfordjournals.Molbev.A025892  0.504
1998 Liò P, Goldman N, Thorne JL, Jones3 DT. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics (Oxford, England). 14: 726-33. PMID 9789098 DOI: 10.1093/Bioinformatics/14.8.726  0.476
1998 Goldman N, Thorne JL, Jones DT. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics. 149: 445-58. PMID 9584116  0.337
1996 Goldman N, Thorne JL, Jones DT. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. Journal of Molecular Biology. 263: 196-208. PMID 8913301 DOI: 10.1006/Jmbi.1996.0569  0.448
1996 Thorne JL, Goldman N, Jones DT. Combining protein evolution and secondary structure. Molecular Biology and Evolution. 13: 666-73. PMID 8676741 DOI: 10.1093/Oxfordjournals.Molbev.A025627  0.5
1996 Swofford DL, Thorne JL, Felsenstein J, Wiegmann BM. The topology-dependent permutation test for monophyly does not test for monophyly Systematic Biology. 45: 575-579. DOI: 10.1093/Sysbio/45.4.575  0.519
1996 Swofford DL, Thorne JL, Felsenstein J, Wiegmann BM. The topology-dependent permutation test for monophyly does not test for monophyly Systematic Biology. 45: 575-579. DOI: 10.1093/Sysbio/45.4.575  0.519
1995 Thorne JL, Churchill GA. Estimation and reliability of molecular sequence alignments. Biometrics. 51: 100-13. PMID 7766767 DOI: 10.2307/2533318  0.622
1992 Thorne JL, Kishino H, Felsenstein J. Inching toward reality: an improved likelihood model of sequence evolution. Journal of Molecular Evolution. 34: 3-16. PMID 1556741 DOI: 10.1007/Bf00163848  0.652
1992 Thorne JL, Kishino H. Freeing phylogenies from artifacts of alignment. Molecular Biology and Evolution. 9: 1148-62. PMID 1435239 DOI: 10.1093/Oxfordjournals.Molbev.A040783  0.445
1991 Thorne JL, Kishino H, Felsenstein J. An evolutionary model for maximum likelihood alignment of DNA sequences. Journal of Molecular Evolution. 33: 114-24. PMID 1920447 DOI: 10.1007/Bf02193625  0.666
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