Masanao Yajima

Defining mutational signatures of lung cancer-associated carcinogens through in vitro exposure of human airway epithelial cells

This study uses in vitro exposure of human airway epithelial cells to genotoxic carcinogens to define mutational signatures associated with lung cancer.

A gene program association study (GPAS) delineates novel patterns of lineage plasticity and aggressiveness in non-small cell lung cancer

The paper introduces GPAS to analyze gene co-expression modules in NSCLC, identifying lineage plasticity and aggressiveness patterns across different cancer subtypes.

Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro

The paper identifies and removes background noise in CITE-seq data using DecontPro, a Bayesian model that improves clustering specificity and reduces contamination from spongelets and ambient ADTs.

Interactive analysis of single-cell data using flexible workflows with SCTK2.0

SCTK2.0 provides an integrated toolkit for scRNA-seq analysis with a graphical interface, enabling non-programmers to perform end-to-end workflows and generate reproducible reports.

Celda: A Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data

Celda identifies transcriptional modules and cell subpopulations in scRNA-seq data, outperforming existing methods in detecting biological programs and cell types.

Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data

The paper introduces a pipeline for generating, visualizing, and reporting quality control metrics for scRNA-seq data, improving standardization across platforms.

The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the discovery, prediction, and exploration of mutational signatures

The paper introduces musicatk, a toolkit for analyzing mutational signatures, enabling preprocessing, analysis, visualization, and comparison to COSMIC database.

Protein kinase C is a key target for attenuation of Leigh syndrome by rapamycin

The paper identifies PKC as a therapeutic target for treating mitochondrial disease by analyzing proteomic and phosphoproteomic changes in a mouse model of Leigh syndrome.

Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program

This study uses scRNA-seq to show chronic opioid use suppresses antiviral gene programs in immune cells, both acutely and chronically, highlighting potential immune system harm.

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

DecontX is a Bayesian method to remove ambient RNA contamination in scRNA-seq data, improving cell cluster separation and marker gene accuracy.

Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK)

The paper introduces SCTK, an interactive scRNA-Seq analysis tool with command-line and GUI interfaces for handling complex single-cell data.