Jeffrey Thorne

Yang, Y., Xu, T., Conant, G., Kishino, H., Thorne, J. L., & Ji, X. (2023). Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization. MOLECULAR BIOLOGY AND EVOLUTION, 40(9). https://doi.org/10.1093/molbev/msad198

Ji, X., Fisher, A. A., Su, S., Thorne, J. L., Potter, B., Lemey, P., … Suchard, M. A. (2023, July 17). Scalable Bayesian Divergence Time Estimation With Ratio Transformations. SYSTEMATIC BIOLOGY. https://doi.org/10.1093/sysbio/syad039

Hao, Y., Fleming, J., Petterson, J., Lyons, E., Edger, P. P., Pires, J. C., … Conant, G. C. (2022, May 10). Convergent evolution of polyploid genomes from across the eukaryotic tree of life. G3-GENES GENOMES GENETICS, Vol. 5. https://doi.org/10.1093/g3journal/jkac094

Seo, T.-K., Redelings, B. D., & Thorne, J. L. (2022). 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(34). https://doi.org/10.1073/pnas.2204435119

Gunady, E. F., Ware, K. E., Plumlee, S. H., Devos, N., Corcoran, D., Prinz, J., … Somarelli, J. A. (2022). Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers A pilot study. EVOLUTION MEDICINE AND PUBLIC HEALTH, 10(1), 221–230. https://doi.org/10.1093/emph/eoac016

Seo, T.-K., Gascuel, O., & Thorne, J. L. (2021, September 1). Measuring Phylogenetic Information of Incomplete Sequence Data. SYSTEMATIC BIOLOGY. https://doi.org/10.1093/sysbio/syab073

Campbell, C. R., Tiley, G. P., Poelstra, J. W., Hunnicutt, K. E., Larsen, P. A., Lee, H.-J., … Yoder, A. D. (2021, July 16). Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. HEREDITY. https://doi.org/10.1038/s41437-021-00446-5

Somarelli, J. A., Boddy, A. M., Gardner, H. L., DeWitt, S. B., Tuohy, J., Megquier, K., … Eward, W. C. (2020). Improving Cancer Drug Discovery by Studying Cancer across the Tree of Life. MOLECULAR BIOLOGY AND EVOLUTION, 37(1), 11–17. https://doi.org/10.1093/molbev/msz254

Larson, G., Thorne, J. L., & Schmidler, S. (2020). Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models. JOURNAL OF COMPUTATIONAL BIOLOGY, 27(3), 361–375. https://doi.org/10.1089/cmb.2019.0500

Larson, G., Thorne, J. L., & Schmidler, S. (2018). Modeling Dependence in Evolutionary Inference for Proteins. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, RECOMB 2018, Vol. 10812, pp. 122–137. https://doi.org/10.1007/978-3-319-89929-9_8

Ji, X., Griffing, A., & Thorne, J. L. (2016). A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast. MOLECULAR BIOLOGY AND EVOLUTION, 33(9), 2469–2476. https://doi.org/10.1093/molbev/msw114

Lee, H. J., Kishino, H., Rodrigue, N., & Thorne, J. L. (2016). Grouping substitution types into different relaxed molecular clocks. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 371(1699).

Lassiter, E. S., Russ, C., Nusbaum, C., Zeng, Q., Saville, A. C., Olarte, R. A., … Ristaino, J. B. (2015). Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species. Current Genetics, 61(4), 567–577. https://doi.org/10.1007/s00294-015-0480-3

Lee, H.-J., Rodrigue, N., & Thorne, J. L. (2015). Relaxing the Molecular Clock to Different Degrees for Different Substitution Types. MOLECULAR BIOLOGY AND EVOLUTION, 32(8), 1948–1961. https://doi.org/10.1093/molbev/msv099

Wang, K., Yu, S., Ji, X., Lakner, C., Griffing, A., & Thorne, J. L. (2015). Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution. EVOLUTIONARY BIOINFORMATICS, 11. https://doi.org/10.4137/ebo.s22911

Hobolth, A., & Thorne, J. L. (2014). Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution. Bayesian Phylogenetics: Methods, Algorithms, and Applications, 247–275.

Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., … Whelan, S. (2012). The interface of protein structure, protein biophysics, and molecular evolution. Protein Science, 21(6), 769–785. https://doi.org/10.1002/pro.2071

Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., … Lakner, C. (2012). [Review of The interface of protein structure, protein biophysics, and molecular evolution]. Protein Science, 21(6), 769–785.

Yokoyama, K. D., Thorne, J. L., & Wray, G. A. (2011). Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution. GENOME BIOLOGY AND EVOLUTION, 3, 66–74. https://doi.org/10.1093/gbe/evq078

Cartwright, R. A., Lartillot, N., & Thorne, J. L. (2011). History Can Matter: Non-Markovian Behavior of Ancestral Lineages. SYSTEMATIC BIOLOGY, 60(3), 276–290. https://doi.org/10.1093/sysbio/syr012

Choi, S. C., Stone, E. A., Kishino, H., & Thorne, J. L. (2009). Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. Gene, 441(1-2), 45–52. https://doi.org/10.1016/j.gene.2008.07.020

Choi, S. C., Redelings, B. D., & Thorne, J. L. (2008). Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 363(1512), 3931–3939. https://doi.org/10.1098/rstb.2008.0167

Xiang, Q.-Y. (J., Thorne, J. L., Seo, T.-K., Zhang, W., Thomas, D. T., & Ricklefs, R. E. (2008). Rates of nucleotide substitution in Cornaceae (Cornales)—Pattern of variation and underlying causal factors. Molecular Phylogenetics and Evolution, 49(1), 327–342. https://doi.org/10.1016/j.ympev.2008.07.010

Lin, Y.-M., Fang, S.-C., & Thorne, J. L. (2007). A tabu search algorithm for maximum parsimony phylogeny inference. EUROPEAN JOURNAL OF OPERATIONAL RESEARCH, 176(3), 1908–1917. https://doi.org/10.1016/j.ejor.2005.10.031

Thorne, J. L., Choi, S. C., Yu, J., Higgs, P. G., & Kishino, H. (2007). Population genetics without intraspecific data. MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1667–1677. https://doi.org/10.1093/molbev/msm085

Thorne, J. L. (2007). Protein evolution constraints and model-based techniques to study them. CURRENT OPINION IN STRUCTURAL BIOLOGY, 17(3), 337–341. https://doi.org/10.1016/j.sbi.2007.05.006

Choi, S. C., Hobolth, A., Robinson, D. M., Kishino, H., & Thorne, J. L. (2007). Quantifying the impact of protein tertiary structure on molecular evolution. MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1769–1782. https://doi.org/10.1093/molbev/msm097

Yu, J., & Thorne, J. L. (2006). Dependence among sites in RNA evolution. MOLECULAR BIOLOGY AND EVOLUTION, 23(8), 1525–1537. https://doi.org/10.1093/molbev/msl015

Yu, J., & Thorne, J. L. (2006). Testing for spatial clustering of amino acid replacements within protein tertiary structure. JOURNAL OF MOLECULAR EVOLUTION, 62(6), 682–692. https://doi.org/10.1007/s00239-005-0107-2

Seo, T. K., Kishino, H., & Thorne, J. L. (2005). 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(12), 4436–4441. https://doi.org/10.1073/pnas.0408313102

Thorne, J. L. (2004, September). A Bayesian approach to DNA sequence segmentation - Discussion. BIOMETRICS, Vol. 60, pp. 584–585. https://doi.org/10.1111/j.0006-341X.2004.206_5.x

Seo, T. K., Kishino, H., & Thorne, J. L. (2004). Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. MOLECULAR BIOLOGY AND EVOLUTION, 21(7), 1201–1213. https://doi.org/10.1093/molbev/msh088

Sanderson, M. J., Thorne, J. L., Wikstrom, N., & Bremer, K. (2004). [Review of Molecular evidence on plant divergence times]. AMERICAN JOURNAL OF BOTANY, 91(10), 1656–1665. https://doi.org/10.3732/ajb.91.10.1656

Scholl, E. H., Thorne, J. L., McCarter, J. P., & Bird, D. M. (2003). Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biology, 4(6), R39–1.

Robinson, D. M., Jones, D. T., Kishino, H., Goldman, N., & Thorne, J. L. (2003). Protein evolution with dependence among codons due to tertiary structure. MOLECULAR BIOLOGY AND EVOLUTION, 20(10), 1692–1704. https://doi.org/10.1093/molbev/msg184

Wiegmann, B. M., Yeates, D. K., Thorne, J. L., & Kishino, H. (2003). Time flies, a new molecular time-scale for brachyceran fly evolution without a clock. Systematic Biology, 52(6), 745–756.

Hasegawa, M., Thorne, J. L., & Kishino, H. (2003). [Review of Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution]. GENES & GENETIC SYSTEMS, 78(4), 267–283. https://doi.org/10.1266/ggs.78.267

Seo, T. K., Thorne, J. L., Hasegawa, M., & Kishino, H. (2002). A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. BIOINFORMATICS, 18(1), 115–123. https://doi.org/10.1093/bioinformatics/18.1.115

Thorne, J. L., & Kishino, H. (2002). Divergence time and evolutionary rate estimation with multilocus data. SYSTEMATIC BIOLOGY, 51(5), 689–702. https://doi.org/10.1080/10635150290102456

Seo, T. K., Thorne, J. L., Hasegawa, M., & Kishino, H. (2002). Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach. Genetics, 160(4), 1283–1293.

Kishino, H., Thorne, J. L., & Bruno, W. J. (2001). Performance of a divergence time estimation method under a probabilistic model of rate evolution. MOLECULAR BIOLOGY AND EVOLUTION, 18(3), 352–361. https://doi.org/10.1093/oxfordjournals.molbev.a003811

Thorne, J. L. (2000). Models of protein sequence evolution and their applications. CURRENT OPINION IN GENETICS & DEVELOPMENT, 10(6), 602–605. https://doi.org/10.1016/S0959-437X(00)00142-8

Goldman, N., Thorne, J. L., & Jones, D. T. (1998). Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics, 149(1), 445–458.

Thorne, J. L., Kishino, H., & Painter, I. S. (1998). Estimating the rate of evolution of the rate of molecular evolution. MOLECULAR BIOLOGY AND EVOLUTION, 15(12), 1647–1657. https://doi.org/10.1093/oxfordjournals.molbev.a025892

Lio, P., Goldman, N., Thorne, J. L., & Jones, D. T. (1998). PASSML: combining evolutionary inference and protein secondary structure prediction. BIOINFORMATICS, 14(8), 726–733. https://doi.org/10.1093/bioinformatics/14.8.726