Publications by authors named "Joshua D Welch"

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Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis.
Yuki Matsushita, Jialin Liu, Angel Ka Yan Chu, Chiaki Tsutsumi-Arai, Mizuki Nagata, Yuki Arai, Wanida Ono, Kouhei Yamamoto, Thomas L Saunders, Joshua D Welch

Nat Commun· April 2023

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Inferring differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data with MultiVeloVAE.
Chen Li, Yichen Gu, Maria C Virgilio, Kun H Lee, Kathleen L Collins, Joshua D Welch

Nat Commun· November 2025

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HPV integration in head and neck cancer: downstream splicing events and expression ratios linked with poor outcomes.
Shiting Li, Shaomiao Xia, Maria Lawas, Aishani Kulshreshtha, Bailey F Garb, Joshua D Welch

Clin Cancer Res· November 2025

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VISTA-FISH: Video Imaging with Spatial-Temporal Analysis by Fluorescent In Situ Hybridization.
Kun H Lee, Mingjia Yao, Javid Ghaemmaghami, Cynthia J DeLong, Neil Zhao, Joshua D Welch

bioRxiv· November 2025

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Reprogramming the Immune Suppressive Tumor Microenvironment in Glioma Enhances the Efficacy of Immune-Mediated Gene Therapy.
Brandon L McClellan, Jorge A Peña Agudelo, Anzar A Mujeeb, Ali A Dabaja, Ziwen Zhu, Joshua D Welch

bioRxiv· November 2025

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Molecular effects of transposable element sequences in mammalian cells.
Ming-Ching C Wen, Joshua D Welch

Genome Biol· November 2025

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Predicting the structural impact of human alternative splicing.
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch

Genome Biol· September 2025

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Autophagy Upregulation in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma Uncovers a Novel Therapeutic Target.
Felipe J Núñez, Kaushik Banerjee, Anzar A Mujeeb, Ava Mauser, Claire E Tronrud, Joshua D Welch

Res Sq· September 2025

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PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations.
Hengshi Yu, Weizhou Qian, Yuxuan Song, Joshua D Welch

Mol Syst Biol· August 2025

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A Hedgehog-Foxf axis coordinates dental follicle-derived alveolar bone formation.
Mizuki Nagata, Gaurav T Gadhvi, Taishi Komori, Yuki Arai, Chiaki Tsutsumi-Arai, Joshua D Welch

Nat Commun· July 2025

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Wnt-directed CXCL12-expressing apical papilla progenitor cells drive tooth root formation.
Mizuki Nagata, Gaurav T Gadhvi, Taishi Komori, Yuki Arai, Hiroaki Manabe, Joshua D Welch

Nat Commun· July 2025

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Topological velocity inference from spatial transcriptomic data.
Yichen Gu, Jialin Liu, Kun H Lee, Chen Li, Lu Lu, Joshua D Welch

Nat Biotechnol· July 2025

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Epigenetic Reprogramming of Autophagy Leads to Uncovering a Novel Therapeutic Target for Mutant IDH1 Astrocytomas.
Felipe J Núñez, Kaushik Banerjee, Anzar A Mujeeb, Ava Mauser, Claire E Tronrud, Joshua D Welch

bioRxiv· June 2025

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Evidence for Transcriptomic Conservation Between the Main Cells of the Prostate-Like Accessory Gland and Basal Cells of the Mammalian Prostate.
S Jaimian Church, April R Kriebel, Joshua D Welch, Laura A Buttitta

bioRxiv· June 2025

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Single-cell multi-omic analysis of mesenchymal cells reveals molecular signatures and putative regulators of lung allograft fibrosis.
Lu Lu, A Patrick McLinden, Natalie M Walker, Ragini Vittal, Yichen Wang, Joshua D Welch

bioRxiv· June 2025

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Lung CD4 resident memory T cells use airway secretory cells to stimulate and regulate onset of allergic airway neutrophilic disease.
Vijay Raaj Ravi, Filiz T Korkmaz, Carolina Lyon De Ana, Lu Lu, Feng-Zhi Shao, Joshua D Welch

Cell Rep· March 2025

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Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Boyan Bonev, Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M Ryan Corces, Joshua D Welch

Nat Neurosci· January 2025

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HPV integration in head and neck cancer: downstream splicing events and expression ratios linked with poor outcomes.
Shiting Li, Shaomiao Xia, Maria Lawas, Aishani Kulshreshtha, Bailey F Garb, Joshua D Welch

bioRxiv· January 2025

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Linking transcriptome and morphology in bone cells at cellular resolution with generative AI.
Lu Lu, Noriaki Ono, Joshua D Welch

J Bone Miner Res· December 2024

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Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Boyan Bonev, Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M Ryan Corces, Joshua D Welch

Nat Neurosci· December 2024

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Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks.
Chao Gao, Joshua D Welch

Bioinformatics· December 2024

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TET2 promotes tumor antigen presentation and T cell IFN-γ, which is enhanced by vitamin C.
Meng Cheng, Angel Ka Yan Chu, Zhijun Li, Shiyue Yang, Matthew D Smith, Joshua D Welch

JCI Insight· November 2024

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LUMIC: Latent diffUsion for Multiplexed Images of Cells.
Albert Hung, Charles J Zhang, Jonathan Z Sexton, Matthew J O'Meara, Joshua D Welch

bioRxiv· November 2024

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HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages.
Maria C Virgilio, Barkha Ramnani, Thomas Chen, W Miguel Disbennett, Jay Lubow, Joshua D Welch

Nat Commun· June 2024

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Integrating single-cell multimodal epigenomic data using 1D-convolutional neural networks.
Chao Gao, Joshua D Welch

bioRxiv· February 2024

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Predicting the Structural Impact of Human Alternative Splicing.
Yuxuan Song, Chengxin Zhang, Gilbert S Omenn, Matthew J O'Meara, Joshua D Welch

bioRxiv· December 2023

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