Benjamin K. Johnson

The paper analyzes bone marrow microenvironment changes in HMA-resistant MDS patients treated with guadecitabine and atezolizumab, finding that long-term survivors show reduced immunosuppressive monocytes and expanded effector lymphocytes.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

This study shows dietary restriction enhances CD8+ T cell ketolysis, improving mitochondrial function and anti-tumor immunity by reducing exhaustion.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

Tranquillyzer is a deep learning framework for processing long-read single-cell RNA-seq data, enabling accurate identification of structural elements and demultiplexing despite sequencing errors and library variability.

The paper introduces scDEEP-mC, a single-cell DNA methylation profiling method, and shows it can identify cell types, X-inactivation states, and replication dynamics with high coverage.

Synthbar adds synthetic cell barcodes to sequencing reads to enable compatibility with computational tools that require them.

STORM-seq improves single-cell RNA sequencing by enhancing detection of non-coding transcripts and transcript-level complexity, revealing new cell states in human fallopian tube epithelium.

Compartmap infers higher-order chromatin structure from scRNA-seq and scATAC-seq data, matching specialized chromatin capture methods and identifying clinically relevant structural alterations in single cells.

This study identifies epigenetic differences between cutaneous and plexiform neurofibromas that drive distinct RAS/MKK/P38 signaling and clinical behavior.