Alexander Bagaev

Benchmarking of bulk transcriptomic harmonization tools in a multi-platform B-cell lymphoma cohort identifies feature-specific quantile normalization and surrogate variable analysis as top-performing methods

Across 7,174 multi-platform lymphoma transcriptomes, only surrogate variable analysis and feature-specific quantile normalization corrected batch effects while keeping subtype and normal B-cell differences; top-scoring MNN erased biomarker correlations.

AI-based separation of malignant cell- and microenvironment-specific gene expression from bulk RNA sequencing enhances biomarker interpretation

Helenus separates malignant and microenvironment gene expression from bulk RNA-seq to improve biomarker interpretation in cancer.

A simple circuit to sustain intact tumor microenvironments for complex drug interrogations

The paper develops a perfusion circuit system to preserve tumor microenvironments in 3D patient-derived tumor models for up to 48 hours, enabling complex drug interrogations.

Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma

This study identifies high-quality neoantigens in follicular lymphoma patients using WES and RNA-Seq, and initiates a clinical trial of personalized neoantigen vaccines combined with PD-1 blockade.

Single Cell Resolution Spatial Mapping of Human Hematopoiesis Reveals Aging-Associated Topographic Remodeling

This study maps human hematopoiesis at single-cell resolution, revealing aging-associated topographic remodeling in bone marrow.