J. Kaufman

A Community Challenge to Predict Clinical Outcomes After Immune Checkpoint Blockade in Non-Small Cell Lung Cancer

The paper evaluates predictive models for immune checkpoint inhibitor outcomes in NSCLC using clinical trial data from two RCTs, finding that models combining PD-L1, TMB, and immune signatures outperform single biomarkers.

Retrotransposons facilitate tissue-specific horizontal Transfer of circulating tumor DNA

This study shows retrotransposons enable tissue-specific horizontal gene transfer of circulating tumor DNA in cancer cells, influencing treatment response and opening new therapeutic avenues.

Minor differences in peptide presentation between chicken MHC class I molecules can explain differences in disease susceptibility

The paper shows that differences in peptide binding between chicken MHC class I alleles BF2*1901 and BF2*1501 explain their differing susceptibility to Mareks disease.

Differential host response to a herpesvirus: Mareks disease virus peptides on chicken MHC class II molecules are derived from only a few genes and illustrate a new mode of peptide binding

The paper identifies that Mareks disease virus peptides presented by chicken MHC class II molecules come from only four genes, revealing a new peptide binding mode and explaining MHC-driven resistance to the virus.

Monitoring the microbiome for food safety and quality using deep shotgun sequencing

The paper uses deep shotgun sequencing to analyze food microbiomes, identifying microbial genera and observing shifts related to ingredient composition, but finds limited correlation between RNA sequencing and Salmonella growth.

Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera

The paper analyzes ICE and associated cargo genes across 200,000 bacterial genomes, finding ICE genomes are common and linked to AMR gene spread and phenotypic resistance.