Common treatment, common variant: evolutionary prediction of functional pharmacogenomic variants
Journal of Personalized Medicine (accepted) | (https://doi.org/10.3390/jpm11020131)
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
Molecular Ecology Resources | 21:122–136
Molecular and morphological clocks for estimating evolutionary divergence times
Research Square | (https://doi.org/10.21203/rs.3.rs-29165/v1)
An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic
bioRxiv | (https://doi.org/10.1101/2020.09.24.311845)
Efficient Methods for Dating Evolutionary Divergences
In The Molecular Evolutionary Clock | 197–219
Molecular Memories of a Cambrian Fossil
The American Biology Teacher | 82:586–595
The bits and bytes of biology: digitalization fuels an emerging generative platform for biological innovation
Handbook of Digital Innovation | 253
Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats
Current Biology | 30:(18 pp)
Interactive effect of TLR SNPs and exposure to sexually transmitted infections on prostate cancer risk in Jamaican men
The Prostate | 80:1365–1372
Where did SARS-CoV-2 come from?
Molecular Biology and Evolution | 37:2463–2464
Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated
Bioinformatics | 36:i884–i894
PathFinder: Bayesian inference of clone migration histories in cancer
Bioinformatics | 36:i675–i683
TreeMap: A structured approach to fine mapping of eQTL variants
Bioinformatics (in revision) | (https://doi.org/10.1101/2020.05.31.125880)
Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity
Cells Reports | 32:(13 pp)
Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics
Molecular Biology and Evolution | 37:1819–1831
Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data
Scientific Reports | 10:3498 (21 pp)
A new method for inferring timetrees from temporally sampled molecular sequences
PLoS Computational Biology | 16:(24 pp)
Somatic Selection Distinguishes Oncogenes and Tumor Suppressor Genes
Bioinformatics | 36:1712–1717
The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution
Annual Review of Biophysics | 49:267–288
Molecular biology and evolution of cancer: from discovery to action
Molecular Biology and Evolution | 37:320–326
Molecular Evolutionary Genetics Analysis (MEGA) for macOS
Molecular Biology and Evolution | 37:1237–1239
Reliable confidence intervals for RelTime estimates of evolutionary divergence times
Molecular Biology and Evolution | 37:280–290
Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach
Cancers | 11:12 (14 pp)
Adventures in Evolution: The Narrative of Tardigrada, Trundlers in Time
The American Biology Teacher | 81:543–552
Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans
BMC Genetics | 20:52 (14 pp)
On estimating evolutionary probabilities of population variants
BMC Evolutionary Biology | 19:133 (14 pp)
A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies
Molecular Biology and Evolution | 36:811–824
Biological relevance of computationally predicted pathogenicity of noncoding variants
Nature Communications | 10:330 (11 pp)
Accurate timetrees require accurate calibrations
Proceedings of the National Academy of Sciences (USA) | 115:E9510–E9511
Computational enhancement of single-cell sequences for inferring tumor evolution
Bioinformatics | 34:i917–i926
Predicting clone genotypes from tumor bulk sequencing of multiple samples
Bioinformatics | 34:4017–4026
Adaptive landscape of protein variation in human exomes
Molecular Biology and Evolution | 35:2015–2025
RelTime relaxes the strict molecular clock throughout the phylogeny
Genome Biology and Evolution | 10:1631–1636
Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates
Molecular Biology and Evolution | 35:1770–1782
MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms
Molecular Biology and Evolution | 35:1547–1549
Neutral theory, disease mutations, and personal exomes
Molecular Biology and Evolution | 35:1297–1303
Somatic evolutionary timings of driver mutations
BMC Cancer | 18:85 (10 pp)
FlyExpress 7: an integrated discovery platform to study coexpressed genes using in situ hybridization images in Drosophila
Genes, Genomes, Genetics (G3) | 7:2791–2797
TimeTree: A resource for timelines, timetrees, and divergence times
Molecular Biology and Evolution | 34:1812–1819
The reliability and stability of an inferred phylogenetic tree from empirical data
Molecular Biology and Evolution | 34:718–723
Fast and accurate estimates of divergence times from big data
Molecular Biology and Evolution | 34:45–50