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Genome Research|May 2, 2025
Harnessing agent-based frameworks in CellAgentChat to unravel cell-cell interactions from single-cell and spatial transcriptomicsVishvak Raghavan, Yumin Zheng, Yue Li, et al.Molecular Systems Biology|May 6, 2026
Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgentVishvak Raghavan, Brent Yoon, Gregory J Fonseca, et al.Nature Communications|July 4, 2025
DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction readsKailu Song, Yumin Zheng, Bowen Zhao, et al.Nature Communications|December 10, 2025
SIDISH integrates single-cell and bulk transcriptomics to identify high-risk cells and guide precision therapeutics through in silico perturbationYasmin Jolasun, Kailu Song, Yumin Zheng, et al.Nature Communications|October 11, 2024
MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cellRuohan Wang, Yumin Zheng, Zijian Zhang, et al.Journal of Cachexia, Sarcopenia and Muscle|January 28, 2025
Characterization of SARS-CoV-2 Entry Genes in Skeletal Muscle and Impacts of In Vitro Versus In Vivo InfectionSalyan Bhattarai, Eva Kaufmann, Feng Liang, et al.Cell Systems|April 3, 2026
GFETM: Genome foundation-based embedded topic model for scATAC-seq modelingYimin Fan, Adrien Osakwe, Shi Han, et al.Journal of Magnetic Resonance Imaging : JMRI|December 22, 2023
Assessment of Cerebrovascular Reactivity Using CO2-BOLD MRI: A 15-Year, Single Center ExperienceVishvak Raghavan, Olivia Sobczyk, Ece Su Sayin, et al.Bioengineered|May 19, 2022
lncRNA NEAT1 promotes autophagy of neurons in mice by impairing miR-107-5pLi Dong, Yumin Zheng, Xiaoguang LuoAsian Journal of Neurosurgery|July 8, 2024
Variability of Resting Carbon Dioxide Tension in Patients with Intracranial Steno-occlusive DiseaseEric Plitman, Lashmi Venkatraghavan, Sanket Agrawal, et al.Pageof 819