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)
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)
Completing a Molecular Timetree of Primates
Frontiers in Bioinformatics | 4:(accepted)
MEGA12: Molecular Evolutionary Genetics Analysis version 12 for adaptive and green computing
Molecular Biology and Evolution | (in review)
MyESL: Sparse learning in molecular evolution and phylogenetic analysis
Bioinformatics | (in review)
STICI: Split-Transformer with Integrated Convolutions for Imputation
Nature Communications | (in revision)
Evolutionary Sparse Learning Reveals the Shared Genetic Basis of Convergent Traits
bioRxiv | (in revision)
Integrating Phylogenies with Chronology to Assemble the Tree of Life
Bioinformatics | (in revision)
R3F: An R Package for Evolutionary Dates, Rates, and Priors using Relative Rate Framework
bioRxiv | (available)
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