Curriculum Vitae

Jeffrey Loren Thorne
Bioinformatics Research Center, Box 7566
North Carolina State University
Raleigh NC 27695-7566


B.S. in Mathematics and Molecular Biology, University of Wisconsin-Madison, May 1986.

Ph. D. in Genetics, University of Washington, December 1991.

Research Experience:

Professor: June 2005 - present, Genetics Department (75% appointment) and Statistics Department (25% appointment), North Carolina State University.

Associate Professor: July 2001 - June 2005, Genetics Department (75% appointment) and Statistics Department (25% appointment), North Carolina State University

Associate Professor: July 1999 - June 2001, Statistics Department, North Carolina State University.

Assistant Professor: June 1993 - June 1999, Statistics Department, North Carolina State University.

Postdoctoral Associate: January 1992 - April 1993, Biometrics Unit, Cornell University. Dr. Gary Churchill, advisor.

Graduate Student: September 1986 - December 1991, Department of Genetics, University of Washington. Dr. Joseph Felsenstein, advisor.

Undergraduate Research Assistant: May 1984 - August 1986, Department of Entomology, University of Wisconsin-Madison. Dr. J.M. Scriber, advisor

Teaching Experience:

Organizer and teacher of DNA and protein sequence analysis mini-courses, Summer Institute in Statistical Genetics, North Carolina State University (annually since 1995).

Bioinformatics II (a graduate course on methodology for analyzing data relevant to molecular biology, annually since 2000)

Principles of Genetics (an honors-level undergraduate course co-taught with Dr. Laura Mathies, 2005, 2006)

Co-instructor of workshop on ``Techniques in Bioinformatics and Comparative Genomics''.  Biopharmaceutical Technology Center Inst. Madison, WI. (1999,2000, 2001).

Computational Molecular Evolution (co-taught with Dr. William Atchley 1995,1997, 2001, 2003, 2005; co-taught with Dr. Spencer Muse 1999), Departments of Statistics and Genetics, North Carolina State University.

Viral Evolution Colloquium (2002)

Introduction to Statistics for Engineers, Department of Statistics, North Carolina State University.

Introduction to Statistical Inference and Regression, Department of Statistics, North Carolina State University.

Probability and Statistics for the Physical Sciences, Department of Statistics, North Carolina State University.

Introductory Genetics (Teaching Assistant to Dr. David Stadler), Department of Genetics, University of Washington.

Human Genetics (Teaching Assistant to Dr. Stan Gartler), Department of Genetics, University of Washington.


John Michael Kohler Foundation Scholarship, 8/81 to 5/83

B.S. with Distinction, University of Wisconsin-Madison, 5/86

University of Washington Graduate School Recruitment Fellowship, 9/86 to 9/87

National Science Foundation Graduate Fellowship, 9/87 to 9/90

Sloan Foundation Young Investigator Award in Molecular Evolution

Rosenbaum Fellowship, Isaac Newton Institute, Cambridge U.K., 1998 (declined)

Wissenschaftskolleg fellowship to support sabbatical participation during the 2006-2007 academic year in the ``Phylogenetic Biology'' program that will be held in Berlin Germany.

Grants Awarded (dollar amounts include direct and indirect costs):

"Likelihood Alignment and Evolutionary Models", National Institutes of Health, 9/1/93 - 8/31/95,  $62,214

"Variation of Preferred Residues Among Sequence Sites", Alfred P. Sloan Foundation, 9/1/95 - 11/30/96, $100,000

"Statistical Analyses of Sequences", National Institutes of Health, 12/1/96 - 11/30/00 (an independently reviewed portion of the N.C.S.U. program project grant in Statistical and Quantitative Genetics, $243,557 of total $4,919,029 award)

"Evolution of Evolutionary Rates: A Genomic Perspective", National Science Foundation, 5/15/00 - 5/14/03, $35,730

"Genomic dissection of a Nematode-Plant interaction: A tool to study plant biology" (co-PI with lead P.I. D. Bird and 3 other co-P.I.'s) National Science Foundation, 9/1/00 - 8/31/03,  $2,607,827.

"Molecular Phylogenetics and a Time Scale for Diversification of the Higher Flies (Diptera: Eremoneura)'' (co-P.I. with lead P.I.  B. Wiegmann) National Science Foundation, 4/1/01 - 3/31/05,  $255,000

"Deep arthropod phylogeny from 120 targetted nuclear coding-region sequences"(co-P.I. with lead P.I. C. Cunningham and 3 other co-P.I.'s) National Science Foundation, 10/1/01-9/30/06, $1,345,000 ($163,250 subcontract to J.L Thorne for 10/1/01 - 9/30/05)

"Development of hierarchical models of genomic evolution and mapping, and algorithms for their analysis" (P.I. Hirohisa Kishino)  Japan Science and Technology Corporation, 2/22/02 -10/31/04, subcontract of $240,904 to J.L. Thorne.

"The Genome Research Network: A database and analytical tools" (P.I. J.L. Thorne), Philip Morris Co.  12/15/2003-12/31/2005, $1,092,688

"Estimating Divergence Times and Evolutionary Rates" (P.I. J.L. Thorne), National Science Foundation, 4/01/2005-3/31/2007, $150,000

"Evolutionary inferences from protein-coding genes" (P.I. J.L. Thorne), National Institutes of Health, 8/1/2005-7/31/2009, $455,000 in direct costs


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)

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)

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)

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

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

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)

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

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)

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).

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.

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)

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)

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)

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.

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., Kishino, H. (2007) Population genetics without intraspecific data. Mol. Biol. Evol. 24:1667-1677.

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.

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

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:

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)

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

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.

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.

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, 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.

Technical Report:

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


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.


Chair, N.C.S.U. Undergraduate Admissions Committee (2001-2002 AcademicYear)

Contributing Editor, Current Index to Statistics (Summer 1995 - Spring 2000)

Member, N.S.F. Computational Biology Review Panel (1997, 1998, 1999)

Member, N.S.F. Information Technology Research Panel  (2000)

Member, N.I.H. Genome Study Section, Informatics  (Fall 2000, Spring 2002)

Member, N.I.E.H.S. Toxicogenomics Panel (Spring 2002)

Associate Editor, Systematic Biology (2001-2004)

Editorial Board member for Systematic Biology (2004-present)

"Honorary" Editorial Board Member for Evolutionary Bioinformatics (2004-present)

Faculty Member in Evolutionary/Comparative Genetics, Faculty of 1000 (2004-present)

Editorial Board Member, Journal of Experimental Zoology-B: Molecular and Developmental Evolution (2006-present).

Associate Editor, Molecular Biology and Evolution (2007-present).