| Estimating the rate of evolution of the rate of molecular evolution. JL Thorne, H Kishino, IS Painter Molecular biology and evolution 15 (12), 1647-1657, 1998 | 1433 | 1998 |
| Divergence time and evolutionary rate estimation with multilocus data JL Thorne, H Kishino Systematic biology 51 (5), 689-702, 2002 | 1023 | 2002 |
| Performance of a divergence time estimation method under a probabilistic model of rate evolution H Kishino, JL Thorne, WJ Bruno Molecular biology and evolution 18 (3), 352-361, 2001 | 692 | 2001 |
| An evolutionary model for maximum likelihood alignment of DNA sequences JL Thorne, H Kishino, J Felsenstein Journal of Molecular Evolution 33, 114-124, 1991 | 545 | 1991 |
| Inching toward reality: an improved likelihood model of sequence evolution JL Thorne, H Kishino, J Felsenstein Journal of molecular evolution 34, 3-16, 1992 | 416 | 1992 |
| Molecular evidence on plant divergence times MJ Sanderson, JL Thorne, N Wikström, K Bremer American journal of botany 91 (10), 1656-1665, 2004 | 347 | 2004 |
| Assessing the impact of secondary structure and solvent accessibility on protein evolution N Goldman, JL Thorne, DT Jones Genetics 149 (1), 445-458, 1998 | 311 | 1998 |
| Protein evolution with dependence among codons due to tertiary structure DM Robinson, DT Jones, H Kishino, N Goldman, JL Thorne Molecular Biology and Evolution 20 (10), 1692-1704, 2003 | 241 | 2003 |
| The interface of protein structure, protein biophysics, and molecular evolution DA Liberles, SA Teichmann, I Bahar, U Bastolla, J Bloom, ... Protein Science 21 (6), 769-785, 2012 | 217 | 2012 |
| Combining protein evolution and secondary structure. JL Thorne, N Goldman, DT Jones Molecular biology and evolution 13 (5), 666-673, 1996 | 217 | 1996 |
| Time flies, a new molecular time-scale for brachyceran fly evolution without a clock BM Wiegmann, DK Yeates, JL Thorne, H Kishino Systematic biology 52 (6), 745-756, 2003 | 209 | 2003 |
| Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach EH Scholl, JL Thorne, JP McCarter, DM Bird Genome biology 4, 1-12, 2003 | 192 | 2003 |
| Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses N Goldman, JL Thorne, DT Jones Journal of molecular biology 263 (2), 196-208, 1996 | 161 | 1996 |
| Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution M Hasegawa, JL Thorne, H Kishino Genes & genetic systems 78 (4), 267-283, 2003 | 147 | 2003 |
| Freeing phylogenies from artifacts of alignment. JL Thorne, H Kishino Molecular biology and evolution 9 (6), 1148-1162, 1992 | 121 | 1992 |
| Models of protein sequence evolution and their applications JL Thorne Current opinion in genetics & development 10 (6), 602-605, 2000 | 106 | 2000 |
| Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach TK Seo, JL Thorne, M Hasegawa, H Kishino Genetics 160 (4), 1283-1293, 2002 | 83 | 2002 |
| Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences TK Seo, H Kishino, JL Thorne Molecular biology and evolution 21 (7), 1201-1213, 2004 | 74 | 2004 |
| Quantifying the impact of protein tertiary structure on molecular evolution SC Choi, A Hobolth, DM Robinson, H Kishino, JL Thorne Molecular biology and evolution 24 (8), 1769-1782, 2007 | 70 | 2007 |
| The topology-dependent permutation test for monophyly does not test for monophyly DL Swofford, JL Thorne, J Felsenstein, BM Wiegmann Systematic Biology 45 (4), 575-579, 1996 | 69 | 1996 |
