I. Yanai

Mechanical confinement governs phenotypic plasticity in melanoma

This study shows mechanical confinement drives phenotype switching in melanoma via chromatin remodeling mediated by HMGB2.

Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer

The paper identifies adeno-to-squamous transition (AST) as a mechanism of resistance to KRAS inhibitors in LKB1 mutant lung cancer and links KRT6A expression to poor patient outcomes.

Quorum-sensing agr system of Staphylococcus aureus primes gene expression for protection from lethal oxidative stress

This study shows that the agr quorum-sensing system in Staphylococcus aureus primes the bacteria to resist oxidative stress by controlling reactive oxygen species, even when the system is not actively activated.

Drug-induced adaptation along a resistance continuum in cancer cells

This study shows that gradual dose exposure and prolonged treatment drive ovarian cancer cell resistance to targeted therapy through a continuous adaptation process involving transcriptional, epigenetic, and genetic changes.

Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment

The paper identifies recurrent cancer cell states across 15 tumor types and examines their interactions with the tumor microenvironment using single-cell RNA-Seq and spatial transcriptomics.

The genetic basis of tail-loss evolution in humans and apes

This paper identifies an Alu element insertion in the TBXT gene as the genetic mechanism driving tail-loss evolution in hominoids, showing it causes alternative splicing and tail absence in mice.

Spatially resolved transcriptomics reveals the architecture of the tumor/microenvironment interface

This study uses spatial transcriptomics to identify a conserved tumor-microenvironment interface in zebrafish and human melanoma characterized by cilia gene upregulation.

Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma

This study shows that melanoma metastasis is promoted by heterotypic clusters formed between proliferative and invasive cell states, mediated by TFAP2.

Selective attention in hypothesis-driven data analysis

This study shows that hypothesis-driven analysis can limit data exploration, as students without specific hypotheses were more likely to discover unexpected patterns in a dataset.

A population of stress-like cancer cells in melanoma promotes tumorigenesis and confers drug resistance

The paper identifies a stress-like cancer cell state in melanoma that promotes tumorigenesis and drug resistance, validated across zebrafish and human models.

Integrating single-cell RNA-Seq with spatial transcriptomics in pancreatic ductal adenocarcinoma using multimodal intersection analysis

This study integrates single-cell RNA-Seq and spatial transcriptomics data from pancreatic cancer tissue to map cell type spatial distributions and infer tissue architecture.

Widespread transcriptional scanning in the testis modulates gene evolution rates

The paper maps gene expression in human spermatogenesis and finds that expressed genes have fewer germline mutations, suggesting transcriptional scanning reduces DNA damage and influences gene evolution rates.