Jeffrey P. Townsend

Stepwise Evolution and Epistatic Interaction of Driver Mutations from Endometrial Hyperplasia to Carcinoma

This study analyzes the evolutionary dynamics of driver mutations during endometrial hyperplasia to carcinoma progression, revealing differences in selection pressures and epistatic interactions between mutation pairs.

Signal, noise, and bias in phylogenetic inference:potential and limits to the resolution of phylogenetic trees in the phylogenomic era

The paper analyzes how phylogenetic signal, noise, and bias affect tree resolution in phylogenomics and shows their divergent scaling properties with character sampling.

Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types

TEATIME estimates evolutionary parameters and fitness diversity from bulk sequencing data, revealing patterns of intratumor heterogeneity across 33 cancer types.

Deconvolving mutation and selection reveals stage-specific drivers of thyroid cancer

This study quantifies cancer-driving mutations in thyroid cancer stages by analyzing selection pressures, revealing stage-specific drivers of tumorigenesis and metastasis.

Somatic evolution of prostate cancer: mutation, selection, and epistasis across disease stages

This study quantifies mutation rates, selection coefficients, and epistatic interactions across prostate cancer stages, revealing dynamic selective pressures and therapeutic implications.

AURKA inhibition amplifies DNA replication stress to foster WEE1 kinase dependency and synergistic antitumor effects with WEE1 inhibition in cancers

This study shows that AURKA inhibition increases DNA replication stress in TP53-mutated cancers, creating a dependency on WEE1 that can be exploited with combined AURKA and WEE1 inhibition to enhance antitumor effects.

Comparative transcriptional analysis reveals gene expression changes in spore germination of opportunistic pathogenic fungi

This study compares gene expression during spore germination across fungal pathogens and non-pathogens to identify expression divergence linked to pathogenicity.

DMEM and EMEM are suitable surrogate media to mimic host environment and expand leptospiral pathogenesis studies using in vitro tools

This paper identifies DMEM and EMEM as better in vitro media for studying leptospiral pathogenesis compared to EMJH and HAN by mimicking host gene expression profiles.

Entrenchment and contingency in neutral protein evolution with epistasis

The paper shows that protein evolution with epistasis and purifying selection does not lead to entrenchment, and that rate variation is due to epistasis, not historical contingency.

Tobacco smoke alters the trajectory of lung adenocarcinoma evolution via effects on somatic selection and epistasis

This paper quantifies how tobacco smoke alters somatic selection and epistasis in lung adenocarcinoma, showing distinct mutation selection pressures in smokers and non-smokers.

Cancer relevance of human genes

The paper identifies cancer-relevant genes by analyzing their proximity to core cancer genes in protein-protein interaction networks, finding that genes closer to cancer genes show greater functional importance in cancer biology.

Identifying Combinations of Cancer Drivers in Individual Patients

This paper introduces CRSO to identify cancer driver combinations in individual patients, showing that rule-based analysis improves outcome prediction compared to single-alteration analysis.

Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum

The paper identifies sexual stage-induced lncRNAs in Fusarium graminearum and explores their relationship with gene silencing and transcriptional activity during sexual development.

The Moran coalescent in a discrete one-dimensional spatial model

This study analyzes a Moran coalescent in a one-dimensional spatial model, showing that spatial structure increases genetic divergence and affects coalescent probabilities and times.

Genomic and gene-expression comparisons among phage-resistant type-IV pilus mutants of Pseudomonas syringae pathovar phaseolicola

The paper compares genomic and gene expression differences among phage-resistant Pseudomonas syringae pv. phaseolicola mutants with varying type IV pilus expression.