RAMP improves cross-platform proteomics analysis by preserving protein expression order, enhancing cell-type annotation and prediction across multiple cancer types.

bioRxiv · Oct 1, 2026 · PreprintBioinformatics

Arborist: Prioritizing Bulk DNA Inferred Tumor Phylogenies via Low-pass Single-cell DNA Sequencing Data

Leah L. Weber, Chi Yin Ching, Christopher P. Ly, Yidan Pan, Yixiao Cheng, Chunxu Gao, Peter Van Loo

Arborist improves tumor phylogeny reconstruction by integrating bulk DNA-seq and low-pass scDNA-seq data, outperforming existing methods on simulated and biological datasets.

bioRxiv · Feb 28, 2026 · PreprintBioinformatics

Spatial Transcriptomics Reveals Inflammation and Trans-differentiation States of Acute Myeloid Leukemia in Extramedullary and Medullary Tissues

Enes Dasdemir, Ivo Veletić, Christopher P. Ly, Andres Ernesto Quesada, Christopher D. Pacheco, Fatima Zahra Jelloul, Pâmella Borges, Sreyashi Basu, Sonali Jindal, Zhiqiang Wang, Alexander J. Lazar, Khalida Wani, Dinler A. Antunes, Patrick Kevin Reville, Preethi H. Gunaratne, , Hussein A. Abbas

This study uses spatial transcriptomics to analyze AML in both medullary and extramedullary tissues, revealing inflammation and trans-differentiation states.

iScience · Nov 29, 2025Peer-reviewedCancer Biology

Multimodal Spatial Proteomic Profiling in Acute Myeloid Leukemia

Christopher P. Ly, Ivo Veletić, Christopher D. Pacheco, Enes Dasdemir, Fatima Zahra Jelloul, Sammy Ferri Borgogno, Akshay Basi, Javier A. Gomez, Jessica Lynn Root, Patrick Kevin Reville, Sonali Jindal, Sreyashi Basu, Padmanee Sharma, Andres Ernesto Quesada, Carlos Bueso-Ramos, , Hussein A. Abbas

This study uses high-plex spatial proteomics to identify tertiary lymphoid-like structures in AML bone marrow and links them to patient outcomes.

npj Precision Oncology · May 20, 2025Peer-reviewedCancer Biology