Agnieszka Kraft

The paper analyzes multiomic data from primary and metastatic esophageal adenocarcinoma tumors to identify cell states and their spatial interactions, linking them to clinical outcomes.

The paper characterizes exosomal RNA cargo in pleural mesothelioma, identifies potential biomarkers, and explores their role in cell communication and prognosis.

CDState infers malignant cell subpopulations from bulk RNA-seq data, revealing gene programs and clinical associations in 33 cancer types.

The paper investigates the impact of mitochondrial content filtering in cancer single-cell studies, finding that high pctMT malignant cells are viable and functionally significant.

The paper introduces ANS, a new gene signature scoring method for scRNA-seq, improving cell annotation by addressing limitations in existing methods and demonstrating strong classification performance.

CanSig benchmarks methods for identifying transcriptional signatures in cancer using scRNA-seq data, finding BBKNN as a leading method with clinically relevant outcomes.

This study examines how structural variants in 26 human populations affect 3D chromatin structure and gene transcription, showing a link between chromatin loops and transcriptional variation.