The Genetic Foundations of Convergent Traits
Nature Reviews Genetics | (16 pp)
Epistasis plays a limited role in driving entrenchment during neutral protein evolution
Genome Biology | revision in review
Nutrigenomics: From Epicure to Epigenetics - Engaging Students with Nutrition Through the Human Genome
The American Biology Teacher | accepted
Treemble: A Graphical Tool to Generate Newick Strings from Phylogenetic Tree Images
Bioinformatics
An Evolutionary Metric for Estimating PhyloAges from Bulk Sequencing of Hematopoietic Stem Cells Reveals the Tempo of Blood Aging in Cancer and Longevity
Journal of Molecular Evolution | 94:177–189
Evolutionary dynamics of early and late mutational signatures in metastatic cancer
Frontiers in Bioinformatics | 6:(10 pp)
Transformer-based Hi-C Upscaling Reveals 3D Genome Structure at Low-resolution Sequencing
Cell Genomics | submitted
The Big Evolution of the Little Phage: Teaching biological interdependency through a virus
The American Biology Teacher | 88:93–102
A collaborative genomics platform for T1D research in Eastern and Central Europe
Metabologia | in submission
R3F: An R Package for Evolutionary Dates, Rates, and Priors using Relative Rate Framework
arXiv | (available)
Enabling Data-driven Discoveries in Evolutionary Genetics and Genomics
Genetics | 230:iyaf084 (4 pp)
MEGA 12.1: Cross-platform release for macOS and Linux operating systems
Journal of Molecular Evolution | 94:14–18
Evolutionary Sparse Learning Reveals the Shared Genetic Basis of Convergent Traits
Nature Communications | 16:3217 (14 pp)
Robust and Efficient Method for Estimating Confidence Limits for Phylogenomic Inferences of Organismal Relationships
Molecular Biology and Evolution | 42:msaf296 (11 pp)
MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols using MEGA software
Molecular Biology and Evolution | 42:msaf101 (5 pp)
Genome Assembly of Arctica islandica, the Longest-Lived Non-Colonial Animal Species
Animals | 15:ani15050690 (13 pp)
MyESL: A software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics
Molecular Biology and Evolution | 42:msaf224 (16 pp)
Integrating Phylogenies with Chronology to Assemble the Tree of Life
Frontiers in Bioinformatics | 5:1571568 (14 pp)
STICI: Split-Transformer with Integrated Convolutions for Genotype Imputation
Nature Communications | 16:(14 pp)
Teaching Biology & Evolution Through the Watery Matrix of Life: A Genomic Medicine Perspective
The American Biology Teacher | 87:84–92
Completing a Molecular Timetree of Afrotheria
Frontiers in Bioinformatics | 5:1710926 (9 pp)
GenoPath: A Pipeline to Infer Tumor Clone Composition, Mutational History, and Metastatic Cell Migration Events from Tumor DNA Sequencing Data
Frontiers in Bioinformatics | 5:1615834 (10 pp)
MEGA12: Molecular Evolutionary Genetics Analysis version 12 for Adaptive and Green Computing
Molecular Biology and Evolution | 41:msae263 (9 pp)
Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning
Molecular Biology and Evolution | 41:msae131 (13 pp)
Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells
Molecular Biology and Evolution | 41:msad279 (11 pp)
Visualizing Genomic Medicine: An Introduction to General Biology
The American Biology Teacher | 86:265–273 (9 pp)
Of Phylogenies and Tumors: Cancer as a Model System to Teach Evolution
The American Biology Teacher | 86:62–70 (9 pp)
Completing a Molecular Timetree of Primates
Frontiers in Bioinformatics | 4:1495417 (6 pp)
Some Mechanistic Underpinnings of Molecular Adaptations of SARS-COV-2 Spike Protein by Integrating Candidate Adaptive Polymorphisms with Protein Dynamics
eLife | 12:RP92063 (25 pp)
Analyses of Allele Age and Fitness Impact Reveal Human Beneficial Alleles to be Older than Neutral Controls
eLife | 13:RP93258 (27 pp)
Computational Reproducibility of Molecular Phylogenies
Molecular Biology and Evolution | 40:msad165 (9 pp)
Completing a Molecular Timetree of Apes and Monkeys
Frontiers in Bioinformatics | 3:1284744 (8 pp)
Molecular Timetrees using Relaxed Clocks and Uncertain Phylogenies
Frontiers in Bioinformatics | 3:1225807 (13 pp)
The Origin of Eukaryotes and Rise in Complexity were Synchronous with the Rise in Oxygen
Frontiers in Bioinformatics | 3:1233281 (10 pp)
Discovering Research Articles Containing Evolutionary Timetrees by Machine Learning
Bioinformatics | 39:btad035 (7 pp)
Improving Cellular Phylogenies through the Integrated Use of Mutation Order and Optimality Principles
Computational and Structural Biotechnology Journal | 21:3894–3903
Bootstrap Confidence for Molecular Evolutionary Estimates from Tumor Bulk Sequencing Data
Frontiers in Bioinformatics | 3:1090730 (11 pp)
Protein Dynamics Provide Mechanistic Insights about Epistasis among Common Missense Polymorphisms
Biophysical Journal | 122:2938–2947
Gene Expression Study of Breast Cancer using Welch Satterthwaite t-test, Kaplan-Meier Estimator Plot and Huber Loss Robust Regression Model
Journal of King Saud University - Science | 35:102447 (9 pp)
Masatoshi Nei (1931–2023)
Nature Ecology & Evolution | 7:(2 pp)
Masatoshi Nei (1931–2023)
Molecular Biology and Evolution | 40:msad149 (5 pp)
Embracing Green Computing in Molecular Phylogenetics
Molecular Biology and Evolution | 39:msac043 (4 pp)
TimeTree 5: An Expanded Resource for Species Divergence Times
Molecular Biology and Evolution | 39:msac174 (6 pp)
Taming the Selection of Optimal Substitution Models in Phylogenomics by Site Subsampling and Upsampling
Molecular Biology and Evolution | 39:msac236 (8 pp)
TopHap: Rapid Inference of Key Phylogenetic Structures from Common Haplotypes in Large Genome Collections with Limited Diversity
Bioinformatics | 38:2719–2726
Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution
Molecular Biology and Evolution | 39:msac106 (11 pp)
Dynamic Coupling of Residues within Proteins as a Mechanistic Foundation of Many Enigmatic Pathogenic Missense Variants
PLoS Computational Biology | 18:e1010006 (22 pp)
Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts
Molecular Biology and Evolution | 39:msac038 (11 pp)
Storyboarding for Biology: An Authentic STEAM Experience
The American Biology Teacher | 84:328–335
Epistasis Storyboarded
The American Biology Teacher | 84:562–569
Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models
Cancers | 14:4326 (13 pp)
A Phylogenetic Approach to Study the Evolution of Somatic Mutational Processes in Cancer
Communications Biology | 5:617 (11 pp)
MOCA for Integrated Analysis of Gene Expression and Genetic Variation in Single Cells
Frontiers in Genetics | 13:831040 (8 pp)
Waiting for the Truth: Is Reluctance in Accepting an Early Origin Hypothesis for SARS-CoV-2 Delaying Our Understanding of Viral Emergence?
BMJ Global Health | 7:e008386 (8 pp)
Molecular Evidence for SARS-CoV-2 in Samples Collected from Patients with Morbilliform Eruptions since Late Summer 2019 in Lombardy, Northern Italy
Environmental Research | 215:113979 (9 pp)
Development of "Biosearch System" for Biobank Management and Storage of Disease Associated Genetic Information
Journal of King Saud University - Science | 34:101760 (10 pp)
An Evolutionary Portrait of the Progenitor SARS-CoV-2 and its Dominant Offshoots in COVID-19 Pandemic
Molecular Biology and Evolution | 38:3046–3059
Evolutionary Sparse Learning for Phylogenomics
Molecular Biology and Evolution | 38:4674–4682
Fast and Accurate Bootstrap Confidence Limits on Genome-scale Phylogenies using Little Bootstraps
Nature Computational Science | 1:573–577
Tumors are Evolutionary Island-like Ecosystems
Genome Biology and Evolution | 13:evab276 (11 pp)
Migrations of Cancer Cells through the Lens of Phylogenetic Biogeography
Scientific Reports | 11:17184 (13 pp)
Data-driven Speciation Tree Prior for Better Species Divergence Times in Calibration-poor Molecular Phylogenies
Bioinformatics | 37:i102–i110
Epistasis Produces an Excess of Invariant Sites in Neutral Molecular Evolution
Proceedings of the National Academy of Sciences (USA) | 118:e2018767118
MEGA11: Molecular Evolutionary Genetics Analysis Version 11
Molecular Biology and Evolution | 38:3022–3027
Molecular Dating for Phylogenies Containing a Mix of Populations and Species by Using Bayesian and RelTime Approaches
Molecular Ecology Resources | 21:122–136
How to Build a Super Predator: From Genotype to Phenotype
The American Biology Teacher | 83:138–146
Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating
Genome Biology and Evolution | 13:evab251 (14 pp)
Molecular and Morphological Clocks for Estimating Evolutionary Divergence Times
BMC Ecology and Evolution | 21:83 (15 pp)
Deep Low-Shot Learning for Biological Image Classification and Visualization from Limited Training Samples
IEEE Transactions on Neural Networks and Learning Systems | (11 pp)
Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants
Journal of Personalized Medicine | 11:131 (13 pp)
TreeMap: A Structured Approach to Fine Mapping of eQTL Variants
Bioinformatics | 37:1125–1134
The Durability of Immunity against Reinfection by SARS-CoV-2: A Comparative Evolutionary Study
The Lancet Microbe | 12:e666–e675
The Somatic Molecular Evolution of Cancer: Mutation, Selection, and Epistasis
Progress in Biophysics and Molecular Biology | 165:56–65
PathFinder: Bayesian Inference of Clone Migration Histories in Cancer
Bioinformatics | 36:i675–i683
Efficient Methods for Dating Evolutionary Divergences
in The Molecular Evolutionary Clock (ed. Ho) [Springer] | 197–219
Where Did SARS-CoV-2 Come From?
Molecular Biology and Evolution | 37:2463–2464
Molecular Evolutionary Genetics Analysis (MEGA) for macOS
Molecular Biology and Evolution | 37:1237–1239
A New Method for Inferring Timetrees from Temporally Sampled Molecular Sequences
PLoS Computational Biology | 16:e1007046 (24 pp)
Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times
Molecular Biology and Evolution | 37:280–290
Power and Pitfalls of Computational Methods for Inferring Clone Phylogenies and Mutation Orders from Bulk Sequencing Data
Scientific Reports | 10:3498 (21 pp)
Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics
Molecular Biology and Evolution | 37:1819–1831
Using a GTR+Gamma Substitution Model for Dating Sequence Divergence when Stationarity and Time-reversibility Assumptions are Violated
Bioinformatics | 36:i884–i894
The Bits and Bytes of Biology: Digitalization Fuels an Emerging Generative Platform for Biological Innovation
Handbook of Digital Innovation (ed. Nambisan, Lyytinen, Yoo) [Edward Elgar] | 253–265
Molecular Memories of a Cambrian Fossil
The American Biology Teacher | 82:586–595
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 | 80:4329–4341.e4
Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity
Cell Reports | 32:(13 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
Deep Model Based Transfer and Multi-task Learning for Biological Image Analysis
IEEE Transactions on Big Data | 6:322–333