This study identifies MYST acetyltransferases as therapeutic targets in SETBP1-mutant leukemia, showing that MYST inhibitors reduce target gene expression and improve survival in mouse models.

bioRxiv · Jan 8, 2026 · PreprintCancer Biology

Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing

Jack Humphrey, Erica Brophy, Roman Kosoy, Biao Zeng, Elena Coccia, Daniele Mattei, Ashvin Ravi, Tatsuhiko Naito, Anastasia G. Efthymiou, Elisa Navarro, Claudia De Sanctis, Victoria Flores Almazan, Benjamin Z. Muller, Gijsje J. L. Snijders, Amanda Allan, , Towfique Raj

The paper presents a long-read RNA-seq atlas of microglia isoforms, identifying novel isoforms and their associations with genetic risk loci in Alzheimer's and Parkinson's disease.

Nature Genetics · Mar 1, 2025Peer-reviewedGenetic & Genomic Medicine

Robust collection and processing for label-free single voxel proteomics

Reta Birhanu Kitata, Marija Veličković, Zhangyang Xu, Rui Zhao, David Scholten, Rosalie Chu, Danny Orton, William Chrisler, Tong Zhang, Jeremy Abraham Mathews, Benjamin M. Bumgarner, Demirkan Besim Gursel, Ronald Jay Moore, Paul Piehowski, Tao Liu, , Tujin Shi

This paper introduces a method for label-free single voxel proteomics using wcSOP, enabling spatial resolution of protein expression in tissue samples.

Nature Communications · Jan 13, 2025Peer-reviewedMolecular Biology

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes

Steven E. Schutzer, Tao Liu, Chia‐Feng Tsai, Vladislav Petyuk, Athena Schepmoes, Yi-Ting Wang, Karl Weitz, Jonas Bergquist, Richard D. Smith, Benjamin H. Natelson

The paper compares cerebrospinal fluid proteomes of ME/CFS patients with and without fibromyalgia, finding no significant differences, suggesting they may not be distinct conditions.

Annals of Medicine · Sep 18, 2023Peer-reviewedNeuroscience

Robust, sensitive, and quantitative single-cell proteomics based on ion mobility filtering

Jongmin Jacob Woo, Gérémy Clair, Sarah Williams, Song Feng, Chia‐Feng Tsai, Ronald Jay Moore, William Chrisler, Richard D. Smith, Ryan Kelly, Ljiljana Paša‐Tolić, Charles K. Ansong, Ying Zhu

This paper introduces TIFF, a method enhancing single-cell proteomics sensitivity and accuracy by filtering background ions and using 3D MS1 feature matching, achieving deep proteome analysis in single cells.

Cell Systems · Mar 16, 2022Peer-reviewedSystems Biology

Motif-centric phosphoproteomics to target kinase-mediated signaling pathways

Chia‐Feng Tsai, Kosuke Ogata, Naoyuki Sugiyama, Yasushi Ishihama

The paper introduces a motif-centric phosphoproteomics approach to quantify phosphorylation pathways using in vitro kinase reactions and isobaric labeling, demonstrating selective quantification of over 7,000 tyrosine phosphorylation sites.

Cell Reports Methods · Jan 1, 2022Peer-reviewedSystems Biology

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Jongmin Jacob Woo, Sarah Williams, Lye Meng Markillie, Song Feng, Chia‐Feng Tsai, Victor Aguilera-Vazquez, Ryan L. Sontag, Ronald Jay Moore, Dehong Hu, Hardeep S. Mehta, Joshua Cantlon-Bruce, Tao Liu, Joshua Adkins, Richard D. Smith, Gérémy Clair, , Ying Zhu

This paper introduces a nested nanowell chip to improve single-cell proteomics throughput and robustness, demonstrating the ability to quantify ~1500 proteins from ~100 cells with low abundance variation.

Nature Communications · Oct 29, 2021Peer-reviewedSystems Biology