C. Sahinalp

Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones

The paper models gene expression adaptation in tumor subclones using stochastic processes and finds non-genetic mechanisms drive subclonal evolution and treatment response.

Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History

This paper introduces DETOPT, a method for accurately placing SNVs affected by CNAs in tumor progression trees, showing improved accuracy on simulated data and biologically plausible results on breast cancer metastases.

Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms

The paper analyzes melanoma clonal sublines to uncover how intratumoral heterogeneity drives resistance to immunotherapy.

MAIT cells have a negative impact on glioblastoma

The paper identifies MAIT cells as immunosuppressive in glioblastoma, correlating their presence with poor patient survival and immune suppressive gene upregulation.

Proteogenomic analysis unveils the HLA Class I presented immunopeptidome in melanoma and EGFR mutant lung adenocarcinoma

The paper identifies HLA Class I-presented peptides in melanoma and EGFR mutant lung adenocarcinoma using proteogenomic analysis, revealing neopeptides and post-translationally modified peptides for potential immunotherapy.

scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations

The paper develops a computational pipeline to identify microbial reads in scRNA-seq data and finds that microbial reads are enriched in myeloid cells with proinflammatory transcriptional changes.