J.L. Thorne homepage:  Research Overview    Publications    Research Group, Alumni, & Collaborators    Software (multidivtime)     Teaching     

Publications authored/co-authored by Jeffrey L. Thorne

Seo, T.-K., Redelings, B.D., and Thorne, J.L. (2022)   Correlations between alignment gaps and nucleotide substitution or amino acid replacement.   Proceedings of the National Academy of Sciences. 119(34): e2204435119.

Gunady, E.F., Ware, K.E., Hoskinson Plumlee, S., Devos, N., Corcoran, D., Prinz, J., Misetic, H., Ciccarelli, F.D., Harrison, T.M., Thorne, J.L., Schopler, R., Everitt, J.I., Eward, W.C., and Somarelli, J.A. (2022)   Exome sequencing of hepatocellular carcinoma in lemurs identifies cross-species similarities in cancer drivers: A pilot study.   Evolution, medicine, and public health. 10(1): 221-230.

Hao, Y., Fleming, J., Petterson, J., Lyons, E., Edger, P.P., Pires, J.C., Thorne, J.L., and Conant, G.C. (2022)   Convergent evolution of polyploid genomes from across the eukaryotic tree of life.   G3 12(6):jkac094.

Seo, T.-K., Gascuel, O., and Thorne, J.L. (2022)   Measuring Phylogenetic Information of Incomplete Sequence Data.   Systematic Biology 71(3): 630-648.

Campbell, C.R., Tiley, G.P., Poelstra, J.W., Hunnicutt, K.E., Larsen, P.A., Lee, H.-J., Thorne, J.L., dos Reis, M., and Yoder, A.D. (2021)   Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur.   Heredity 127:233-244.

Somarelli, J.A., Boddy, A.M., Gardner, H.L., DeWitt, S.B., Tuohy, J., Megquier, K., Sheth, M.U., Hsu, S.D., Thorne, J.L., London, C.A., and Eward, W.C. (2020)   Improving Cancer Drug Discovery by Studying Cancer across the Tree of Life.   Molecular Biology and Evolution. 37(1): 11-17.

Larson, G., Thorne, J.L., and Schmidler, S. (2020)   Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models.  J Comp. Biol. 27(3): 361-375.

Perron, U., Moal, I.H., Thorne, J.L., and Goldman, N. (2019)   Probabilistic Models for the Study of Protein Evolution.  Handbook of Statistical Genomics. Pp. 347-368.  Wiley Online Library.

Seo, T.-K., and Thorne, J.L. (2018)  Information criteria for comparing partition schemes.  Systematic Biology 67:616-632.

Larson, G., Thorne, J.L., and Schmidler, S. (2018)  Modeling Dependence in Evolutionary Inference for Proteins.   Research in Computational Molecular Biology, Proceedings of RECOMB 2018. Pp 122-137.

Xiang, J., Griffing, A., and Thorne, J.L. (2016)  A phylogenetic approach finds abundant interlocus gene conversion in yeast.   Molecular Biology and Evolution 33:2469--2476.

Lee, H.-J., Kishino, H., Rodrigue, N., and Thorne, J.L. (2016)   Grouping substitution types into different relaxed molecular clocks.   Phil. Trans. of Roy. Soc. B. 371: 20150141.

Lee, H.-J., Rodrigue, N., and Thorne, J.L. (2015)   Relaxing the Molecular Clock to Different Degrees for Different Substitution Types.   Molecular Biology and Evolution 32(8) 1948-1961.

Wang, K., Yu, S., Ji, X., Lakner, C., Griffing, A., and Thorne, J.L. (2015)   Roles of solvent accessibility and gene expression in modeling protein sequence evolution.   Evolutionary Bioinformatics 11:85-96.

Lassiter, E.S., Russ, C., Nusbaum, C., Zeng, Q., Saville, A., Olarte, R., Carbone, I., Hu, C.-H., Seguin-Orlando, A., Samaniego, J.A., Thorne, J.L., and Ristaino, J.B. (2015)   Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.   Current Genetics DOI: 10.1007/s00294-015-0480-3.

Hobolth, A., and Thorne, J.L. (2014)   Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution.   Chapter 12 (pages 247-276) in "Bayesian Phylogenetics: Methods, Algorithms, and Applications", edited by M.-H. Chen, L. Kuo, and P.O. Lewis. Chapman and Hall / CRC Mathematical and Computational Biology.

Liberles, D.A., Teichmann, S.A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L.J., de Koning, A.P.J., Dokholyan, N.V., Echave, J., Elofsson, A., Gerloff, D.L., Goldstein, R.A., Grahnen, J.A., Holder, M.T., Lakner, C., Lartillot, N., Lovell, S.C., Naylor, G., Perica, T., Pollock, D.D., Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjolander, K., Sunyaev, S., Teufel, A.I., Thorne, J.L., Thornton, J.W., Weinreich, D.M. and Whelan, S. (2012)   The interface of protein structure, protein biophysics, and molecular evolution.   Protein Science 21(6):769-785.

Thorne, J.L., Lartillot, L., Rodrigue, N., and Choi, S.C. (2012)   Codon models as a vehicle for reconciling population genetics with inter-specific sequence data.   Chapter 7 (pages 97-1100 In "Codon Evolution"), edited by G.M. Cannarozzi and A. Schneider. Oxford University Press.

Yokoyama, K.D., Thorne, J.L., and Wray, G.A. (2011)   Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution.   Genome Biology and Evolution 3:66-74.

Cartwright, R.A., Lartillot, L., and Thorne, J.L. (2011)   History can matter: Non-Markovian behavior of ancestral lineages.   Systematic Biology 60:276-290.

Choi, S.C., Stone, E.A., Kishino, H., and Thorne, J.L. (2009)  Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci.  Gene 441:45-52.

Choi, S.C., Redelings, B.D., and Thorne, J.L.  (2008) Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences.  Phil. Trans. R. Soc. B. 363:3931-3939.

Xiang, Q.-Y., Thorne, J.L., Seo, T.-K., Zhang, W., Thomas, D.T., and Ricklefs, R.E.  (2008) Rates of nucleotide substitution in Cornaceae (Cornales) - pattern of variation and underlying causal factors.  Mol. Phylo. Evol. 49:327-342.

Kitazoe, Y., Kishino, H., Hasegawa, M., Nakajima, N., Thorne, J.L., and Tanaka, M.  (2008) Adaptive Threonine Increase in Transmembrane Regions of Mitochondrial Proteins in Higher Primates. PLoS ONE 3(10): e3343.

Seo, T.-K., Kishino, H., and Thorne, J.L. (2008)  Bayesian divergence time estimation using codon model.  Proceedings of the Institute of Statistical Mathematics.  56(1): 37-54.  (PDF file, In Japanese)

Thorne, J.L.  (2008)  Models and their evolution.  Wissenschaftskolleg zu Berlin 2006/2007 Yearbook.  (PDF file of proofs)

Lin, Y.-M., Fang, S.-C., Thorne, J.L. (2007) A TABU search algorithm for maximum parsimony phylogeny inference. Eur. J. Operational Research 176:1908-1917. (PDF file)

Thorne J.L., Goldman N. (2007) Probabilistic models for the study of protein evolution. Balding, Bishop, and Cannings, eds. Handbook of Statistical Genetics, Third Edition. Wiley and Sons. Volume I : 439-459.

Thorne, J.L., Choi, S. C., Yu, J., Higgs, P.G., Kishino, H. (2007) Population genetics without intraspecific data. Mol. Biol. Evol. 24:1667-1677. (PDF file)

Choi, S. C., Hobolth, A., Robinson, D. M., Kishino, H., Thorne, J.L. (2007) Quantifying the impact of protein tertiary structure on molecular evolution. Mol. Biol. Evol. 24:1769-1782. (PDF file)

Thorne, J.L. (2007) Protein evolution constraints and model-based techniques to study them. Current Opinion in Structural Biology 17:337-341. (PDF file)

Yu, J., Thorne, J.L. (2006) Testing for spatial clustering of amino acid replacements within protein tertiary structure. J. Mol. Evol. 62(6):682-692. (PDF file)

Yu, J., Thorne J.L. (2006) Dependence among sites in RNA evolution. Mol. Biol. Evol. 23(8): 1525-1537. (PDF file)

Thorne, J.L. and Kishino, H. (2005) Estimation of divergence times from molecular sequence data. In Statistical methods in molecular evolution. R. Nielsen, ed. Springer Verlag, pp.235-256 (PDF format preprint)

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.  Proc. Natl. Acad. Sci. U.S.A. 102(12): 4436-4441. (PDF file)

Thorne, J.L.  (2004) Discussant (pages 584-585) on ``A Bayesian approach to DNA sequence segmentation'', a paper by Richard J. Boys and Daniel A. Henderson. Biometrics 60:573-588.   (PDF file)

Sanderson, M.J., Thorne, J.L., Wikstrom, N., and Bremer, K. (2004) Molecular evidence on plant divergence times. Am. J.Bot., 91:1656-1665.  (PDF file)

Seo, T.-K., Kishino, H., and Thorne, J.L. (2004) Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol. Biol. Evol. 21: 1201-1213. (PDF file)

Scholl EH, Thorne JL, McCarter JP, Bird DM.  (2003) Horizontally transferred genes in plant-parasitic nematodes: A high-throughput genomic approach. Genome Biology  4(6):R39 (PDF file)

Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL (2003) Protein evolution with dependence among codons due to tertiary structure. Mol.Biol. Evol. 20(10):1692-1704 (PDF file)

Hasegawa M, Thorne JL, Kishino H (2003)  Time scale of eutherian evolution estimated without assuming constant rate of molecular evolution. Genes and Genetic Systems 78(4): 267-283. (review) (PDF file)

Wiegmann BM, Yeates DK, Thorne JL, Kishino H.  (2003) Time Flies: A new molecular time-scale for fly evolution without a clock.  Systematic Biology 52(6):745-756. (PDF file)

Thorne, J.L. and Goldman, N. (2003) Probabilistic models for the study of protein evolution. (revised for second edition) In Handbook of Statistical Genetics, Second Edition. D.J. Balding, M. Bishop, and C. Cannings, eds.John Wiley and Sons, Inc.

Seo T-K, Thorne JL, 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. (PDF file)

Thorne JL, Kishino H (2002) Divergence time estimation and rate evolution with multilocus data sets.  Systematic Biology 51:689-702. (PDF file)

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

Bird, D. McK., Clifton, S. W., Kepler, T., Kieber, J.J., Thorne, J. and C. H. Opperman (2002) Genomic dissection of a nematode-plant interaction:A tool to study plant biology. Plant Physiology 129:394-395.

Kishino H, Thorne JL (2002) Bayesian hierarchical model of rate of molecular evolution.  Proceedings of the Institute of Statistical Mathematics.50(1): 17-31 (in Japanese).

Thorne JL, Goldman N (2001)  Probabilistic Models for the Study of Protein Evolution.  Balding, Bishop, and Cannings, eds. Handbook of Statistical Genetics.  Wiley and Sons.

Kishino H, Thorne JL, Bruno WJ (2001)  Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Bio Evol, 18:352-361. (PDF file)

Thorne JL (2000)  Models of Protein Sequence Evolution and their Applications.  Curr Opin Genet Dev, 10:602-605. (PDF file)

Goldman N, Thorne JL, Jones DT (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458.(PDF file)

Lio P, Goldman N, Thorne JL, Jones DT (1998)  PASSML: combining Protein Secondary Structure Prediction and Evolutionary Inference. Bioinformatics 14:726-733 (PDF file)

Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol Bio Evol  15:1647-1657. (PDF file)

Swofford D, Thorne JL, Felsenstein J, Wiegmann B (1996) The topology-dependent permutation test for monophyly does not test for monophyly. Sys Bio 45:575-579

Goldman N, Thorne JL, Jones DT (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Bio 263(2): 196-208 (PDF file)

Thorne JL, Goldman N, Jones DT (1996) Combining protein evolution and secondary structure. Mol Bio Evol 13:666-673 (PDF file)

Thorne JL, Churchill GA (1995) Estimation and reliability of molecular sequence alignments. Biometrics 51:100-113 (PDF file)

Thorne JL, Kishino H, Felsenstein J (1992) Inching toward reality: An improved likelihood model of sequence evolution. J Mol Evol 34:3-16 (PDF file)

Thorne JL, Kishino H (1992) Freeing phylogenies from artifacts of alignment. Mol Bio Evol 9: 1148-1162 (PDF file)

Laird CD, Lamb MM, Sved J, Thorne J (1991) Modeling the inheritance and expression of the fragile-X syndrome, with emphasis on the X-inactivation imprinting model, pp. 228-251. In ``The Fragile-X Syndrome: Diagnosis, Treatment, and Research,'' R. Hagerman and A. Cronister, eds. John Hopkins University Press. (Review)

Thorne JL, Kishino H, Felsenstein J (1991) An evolutionary model for the maximum likelihood alignment of DNA sequences. J Mol Evol 33:114-124 (PDF file)

Laird CD, Lamb MM, Thorne JL (1990) Two progenitor cells for human oogonia inferred from pedigree data and the X-inactivation imprinting model of the fragile-X syndrome. Am J Hum Genet 46:696-719

Laird CD, Sved J, Thorne J, Lamb MM (1990) The X-inactivation imprinting model of the fragile-X syndrome: Annotated References, 1989. Chromosomes Today, 10:163-165 (Review)

Book Review:

Thorne JL (1997) Review of Molecular Evolution by V.A. Ratner et al. Theoretical Population Biology 51:252-253. (PDF file)

Conference Proceedings:

Kishino, H., Thorne, J.L., Seo, T.-K., Kajitani, Y. (2003) Modeling of variable evolutionary rates to estimate divergence times and adaptive evolution. Proceedings of the Conference Science of Modeling: the 30th Anniversary of Information Criterion (AIC). pp. 297-306.

Goldstein RA, Pollock DD, Thorne JL (2001)  Structures, Phylogenies, and Genomes: The Integrated Study of Protein Evolution.  Pacific Symposium on Biocomputing. 13:164-166.

Kishino H, Thorne JL, Bar-Hen A (1999)  Statistical models of evolution and their comparison.  1998 Proceedings of the Business and Economic Statistics Section of the American Statistical Association, pp. 22-30.

Goldman N, Thorne JL, Jones DT (1997) Hidden Markov models for inferring evolutionary trees and predicting protein secondary structures. Proceedings of the 51st Session of the International Statistical Institute, Istanbul. (invited submission) pp. 233-236.

Thorne JL, Goldman N, Jones DT (1996) Adding protein structure to modelsof protein evolution. IMS Bulletin 25:19.

Thorne JL, Goldman N, Jones DT (1995) Combining protein secondary structure and evolution. DIMACS: Proceedings of Phylogeny Workshop. DIMACS TechnicalReport 95-48 (October 1995), pp. 62-64. (invited submission)

Technical Report:

Thorne JL, Churchill GA. Estimation and Reliability of Molecular Sequence Alignments, 1993. Cornell University BU-1201-M

Software:

I wrote the software "statalign". These programs align pairs of sequences,detect sequence regions of potential functional importance, and infer evolutionary trees.  I also wrote the "multidivtime" software for estimating evolutionary rates and divergence times.

 

J.L. Thorne homepage:  Research Overview    Publications    Research Group, Alumni, & Collaborators    Software (multidivtime)     Teaching