Works (35)

2018 article

Modeling Dependence in Evolutionary Inference for Proteins

RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, RECOMB 2018.

By: G. Larson, J. Thorne & S. Schmidler

Source: Web Of Science
Added: March 18, 2019

2016 journal article

A A phylogenetic approach finds abundant interlocus gene conversion in yeast

Molecular Biology and Evolution, 33(9), 2469–2476.

By: X. Ji, A. Griffing & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2016 journal article

Grouping substitution types into different relaxed molecular clocks

By: H. Lee, H. Kishino, N. Rodrigue & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2015 journal article

Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species

Current Genetics, 61(4), 567–577.

By: E. Lassiter, C. Russ, C. Nusbaum, Q. Zeng, A. Saville, R. Olarte, I. Carbone, C. Hu ...

Source: NC State University Libraries
Added: August 6, 2018

2015 journal article

Relaxing the molecular clock to different degrees for different substitution types

Molecular Biology and Evolution, 32(8), 1948–1961.

By: H. Lee, N. Rodrigue & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2015 journal article

Roles of solvent accessibility and gene expression in modeling protein sequence evolution

Evolutionary Bioinformatics, 11.

By: K. Wang, S. Yu, X. Ji, C. Lakner, A. Griffing & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2014 journal article

Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution

Bayesian Phylogenetics: Methods, Algorithms, and Applications, 247–275.

By: A. Hobolth & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2012 review

The interface of protein structure, protein biophysics, and molecular evolution

Protein Science.

By: D. Liberles, S. Teichmann, I. Bahar, U. Bastolla, J. Bloom, E. Bornberg-Bauer, L. Colwell, A. Koning ...

Source: NC State University Libraries
Added: August 6, 2018

2011 journal article

Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution

Genome Biology and Evolution, 3, 66–74.

By: K. Yokoyama, J. Thorne & G. Wray

Source: NC State University Libraries
Added: August 6, 2018

2011 journal article

History can matter: Non-Markovian behavior of ancestral lineages

Systematic Biology, 60(3), 276–290.

By: R. Cartwright, N. Lartillot & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2009 journal article

Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci

Gene, 441(1-2), 45–52.

By: S. Choi, E. Stone, H. Kishino & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

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(1512), 3931–3939.

By: S. Choi, B. Redelings & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors

Molecular Phylogenetics and Evolution, 49(1), 327–342.

By: Q. Xiang, J. Thorne, T. Seo, W. Zhang, D. Thomas & R. Ricklefs

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

A A tabu search algorithm for maximum parsimony phylogeny inference

European Journal of Operational Research, 176(3), 1908–1917.

By: Y. Lin, S. Fang & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

Population genetics without intraspecific data

Molecular Biology and Evolution, 24(8), 1667–1677.

By: J. Thorne, S. Choi, J. Yu, P. Higgs & H. Kishino

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

Protein evolution constraints and model-based techniques to study them

Current Opinion in Structural Biology, 17(3), 337–341.

By: J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

Quantifying the impact of protein tertiary structure on molecular evolution

Molecular Biology and Evolution, 24(8), 1769–1782.

By: S. Choi, A. Hobolth, D. Robinson, H. Kishino & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

Dependence among sites in RNA evolution

Molecular Biology and Evolution, 23(8), 1525–1537.

By: J. Yu & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

Testing for spatial clustering of amino acid replacements within protein tertiary structure

Journal of Molecular Evolution, 62(6), 682–692.

By: J. Yu & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

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.

By: T. Seo, H. Kishino & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

A A Bayesian approach to DNA sequence segmentation - Discussion

Biometrics, 60(3), 584–585.

By: J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

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.

By: T. Seo, H. Kishino & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

Molecular evidence on plant divergence times

American Journal of Botany, 91(10), 1656–1665.

By: M. Sanderson, J. Thorne, N. Wikstrom & K. Bremer

Source: NC State University Libraries
Added: August 6, 2018

2003 journal article

Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach

Genome Biology, 4(6), R39–1.

By: E. Scholl, J. Thorne, J. McCarter & D. Bird

Source: NC State University Libraries
Added: August 6, 2018

2003 journal article

Protein evolution with dependence among codons due to tertiary structure.

Molecular Biology and Evolution, 20(10), 1692–1704.

By: D. Robinson, D. Jones, H. Kishino, N. Goldman & J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

2003 journal article

Time flies, a new molecular time-scale for brachyceran fly evolution without a clock

Systematic Biology, 52(6), 745–756.

By: B. Wiegmann, D. Yeates, J. Thorne & H. Kishino

Source: NC State University Libraries
Added: August 6, 2018

2003 journal article

Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution

Genes & Genetic Systems, 78(4), 267–283.

By: M. Hasegawa, J. Thorne & H. Kishino

Source: NC State University Libraries
Added: August 6, 2018

2002 journal article

A A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times

Bioinformatics, 18(1), 115–123.

By: T. Seo, J. Thorne, M. Hasegawa & H. Kishino

Source: NC State University Libraries
Added: August 6, 2018

2002 journal article

Divergence time and evolutionary rate estimation with multilocus data

Systematic Biology, 51(5), 689–702.

By: J. Thorne & H. Kishino

Source: NC State University Libraries
Added: August 6, 2018

2002 journal article

Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach

Genetics, 160(4), 1283–1293.

By: T. Seo, J. Thorne, M. Hasegawa & H. Kishino

Source: NC State University Libraries
Added: August 6, 2018

2001 journal article

Performance of a divergence time estimation method under a probabilistic model of rate evolution

Molecular Biology and Evolution, 18(3), 352–361.

By: H. Kishino, J. Thorne & W. Bruno

Source: NC State University Libraries
Added: August 6, 2018

2000 journal article

Models of protein sequence evolution and their applications

Current Opinion in Genetics & Development, 10(6), 602–605.

By: J. Thorne

Source: NC State University Libraries
Added: August 6, 2018

1998 journal article

Assessing the impact of secondary structure and solvent accessibility on protein evolution

Genetics, 149(1), 445–458.

By: N. Goldman, J. Thorne & D. Jones

Source: NC State University Libraries
Added: August 6, 2018

1998 journal article

Estimating the rate of evolution of the rate of molecular evolution

Molecular Biology and Evolution, 15(12), 1647–1657.

By: J. Thorne, H. Kishino & I. Painter

Source: NC State University Libraries
Added: August 6, 2018

1998 journal article

PASSML: combining evolutionary inference and protein secondary structure prediction

Bioinformatics, 14(8), 726–733.

By: P. Lio, N. Goldman, J. Thorne & D. Jones

Source: NC State University Libraries
Added: August 6, 2018