Jeffrey L Thorne

Scalable Bayesian Divergence Time Estimation With Ratio Transformations

Ji, X., Fisher, A. A., Su, S., Thorne, J. L., Potter, B., Lemey, P., … Suchard, M. A. (2023, July 17). SYSTEMATIC BIOLOGY.

Convergent evolution of polyploid genomes from across the eukaryotic tree of life

Hao, Y., Fleming, J., Petterson, J., Lyons, E., Edger, P. P., Pires, J. C., … Conant, G. C. (2022, May 10). G3-GENES GENOMES GENETICS, Vol. 5.

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).

Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers A pilot study

EVOLUTION MEDICINE AND PUBLIC HEALTH, 10(1), 221–230.

Measuring Phylogenetic Information of Incomplete Sequence Data

Seo, T.-K., Gascuel, O., & Thorne, J. L. (2021, September 1). SYSTEMATIC BIOLOGY.

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

Campbell, C. R., Tiley, G. P., Poelstra, J. W., Hunnicutt, K. E., Larsen, P. A., Lee, H.-J., … Yoder, A. D. (2021, July 16). HEREDITY.

Improving Cancer Drug Discovery by Studying Cancer across the Tree of Life

MOLECULAR BIOLOGY AND EVOLUTION, 37(1), 11–17.

Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models

JOURNAL OF COMPUTATIONAL BIOLOGY, 27(3), 361–375.

Modeling Dependence in Evolutionary Inference for Proteins

RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, RECOMB 2018, Vol. 10812, pp. 122–137.

A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast

MOLECULAR BIOLOGY AND EVOLUTION, 33(9), 2469–2476.

Grouping substitution types into different relaxed molecular clocks

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

Current Genetics, 61(4), 567–577.

Relaxing the Molecular Clock to Different Degrees for Different Substitution Types

MOLECULAR BIOLOGY AND EVOLUTION, 32(8), 1948–1961.

Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution

EVOLUTIONARY BIOINFORMATICS, 11.

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

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

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

Protein Science, 21(6), 769–785.

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

[Review of ]. Protein Science, 21(6), 769–785.

Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution

GENOME BIOLOGY AND EVOLUTION, 3, 66–74.

History Can Matter: Non-Markovian Behavior of Ancestral Lineages

SYSTEMATIC BIOLOGY, 60(3), 276–290.

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

Gene, 441(1-2), 45–52.

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.

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

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

A tabu search algorithm for maximum parsimony phylogeny inference

EUROPEAN JOURNAL OF OPERATIONAL RESEARCH, 176(3), 1908–1917.

Population genetics without intraspecific data

MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1667–1677.

Protein evolution constraints and model-based techniques to study them

CURRENT OPINION IN STRUCTURAL BIOLOGY, 17(3), 337–341.

Quantifying the impact of protein tertiary structure on molecular evolution

MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1769–1782.

Dependence among sites in RNA evolution

MOLECULAR BIOLOGY AND EVOLUTION, 23(8), 1525–1537.

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

JOURNAL OF MOLECULAR EVOLUTION, 62(6), 682–692.

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.

A Bayesian approach to DNA sequence segmentation - Discussion

Thorne, J. L. (2004, September). BIOMETRICS, Vol. 60, pp. 584–585.

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.

Molecular evidence on plant divergence times

[Review of ]. AMERICAN JOURNAL OF BOTANY, 91(10), 1656–1665.

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

Genome Biology, 4(6), R39–1.

Protein evolution with dependence among codons due to tertiary structure

MOLECULAR BIOLOGY AND EVOLUTION, 20(10), 1692–1704.

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

Systematic Biology, 52(6), 745–756.

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

[Review of ]. GENES & GENETIC SYSTEMS, 78(4), 267–283.

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

BIOINFORMATICS, 18(1), 115–123.

Divergence time and evolutionary rate estimation with multilocus data

SYSTEMATIC BIOLOGY, 51(5), 689–702.

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

Genetics, 160(4), 1283–1293.

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

MOLECULAR BIOLOGY AND EVOLUTION, 18(3), 352–361.

Models of protein sequence evolution and their applications

CURRENT OPINION IN GENETICS & DEVELOPMENT, 10(6), 602–605.

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

Genetics, 149(1), 445–458.

Estimating the rate of evolution of the rate of molecular evolution

MOLECULAR BIOLOGY AND EVOLUTION, 15(12), 1647–1657.

PASSML: combining evolutionary inference and protein secondary structure prediction

BIOINFORMATICS, 14(8), 726–733.