J. P. Townsend

Early NOTCH1 mutation is positively selected but epistatically suppresses evolution of later esophageal squamous-cell carcinoma drivers

The paper shows early NOTCH1 mutations are selected in normal tissue but suppress later cancer driver mutations through epistasis, highlighting stage-specific mutation effects in esophageal cancer.

Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2

This study analyzes selection pressures in SARS-CoV-1 and SARS-CoV-2 genomes near zoonosis, finding strong purifying selection and limited positive selection, except for NSP12 and ORF7a.

Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery

The paper maps 3D genome structures in cancer tissues to identify structural changes and potential biomarkers across cancer progression stages.

Lineage-specific genes are clustered with allorecognition loci and respond to GxE factors regulating the switch from asexual to sexual reproduction in Neurospora

The paper identifies lineage-specific genes (LSGs) in Neurospora crassa that cluster with allorecognition loci and respond to environmental factors regulating the switch from asexual to sexual reproduction.

Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis

This study estimates pairwise and higher-order epistatic effects among somatic cancer mutations using a continuous-time Markov chain model and deconvolution approach in lung adenocarcinoma.

Attribution of Cancer Origins to Endogenous, Exogenous, and Actionable Mutational Processes

The paper attributes cancer origins to endogenous, exogenous, and actionable mutational processes across 23 cancer types, highlighting preventable factors like UV light and tobacco.

Field testing of biohybrid robotic jellyfish to demonstrate enhanced swimming speeds

The paper tests biohybrid robotic jellyfish in natural environments, showing increased swimming speeds compared to lab settings and using a hydrodynamic model to predict performance.

Identifying Modules of Cooperating Cancer Drivers

The paper introduces CRSO to identify cooperating driver combinations in cancer, finding 11 core combinations per cancer type with clinical relevance.

Colloblasts act as a biomechanical sensor for suitable prey in Pleurobrachia

This study investigates the mechanical properties of colloblast adhesive in Pleurobrachia, finding it weak but effective for size-selective prey capture through physical modeling.

Evolutionary analyses guide selection of model systems to investigate proto-oncogene function in ALK and LTK

This paper identifies model organisms for studying ALK and LTK proto-oncogenes by analyzing their evolutionary history and ligand homology across species.

Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

The paper shows that genes for complex multicellularity have converged across distant fungal clades, indicating genomic constraints on evolutionary paths.

Effect sizes of somatic mutations in cancer

The paper estimates effect sizes of recurrent single nucleotide variants in 23 cancer types to quantify their relative importance in cancer growth and therapeutic response.

The likelihood of heterogeneity or additional mutation in KRAS or associated oncogenes to compromise targeting of oncogenic KRAS G12C

The study finds no evidence of resistance-conferring mutations in KRAS or downstream genes in KRAS G12C positive tumors at treatment time, and predicts BRAF mutations as likely resistance mechanisms with existing therapies.