Publications by authors named "Timothy Downing"

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Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data.
Junhao Gu, Nandor Laszik, Christopher E Miles, Jun Allard, Timothy L Downing

Bioinformatics· November 2025

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Nucleosome placement and polymer mechanics explain genomic contacts on 100 kb scales.
John Corrette, Jiachun Li, Hanjuan Shao, Praveen Krishna Veerasubramanian, Andrew Spakowitz, Timothy L Downing

Nucleic Acids Res· July 2025

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Nucleosome placement and polymer mechanics explain genomic contacts on 100kbp scales.
John Corrette, Jiachun Li, Hanjuan Shao, Praveen Krishna Veerasubramanian, Andrew Spakowitz, Timothy L Downing

bioRxiv· May 2025

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Bacteria detect neutrophils via a system that responds to hypochlorous acid and flow.
Ilona P Foik, Runhang Shu, Serena Abbondante, Summer J Kasallis, Lauren A Urban, Timothy L Downing

bioRxiv· May 2025

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Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read sequencing.
Annie Trinh, Navied Akhtar, Kwadwo Bonsu, Nandor Laszik, Asia Mendelevich, Timothy L Downing

bioRxiv· March 2025

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Biphasic regulation of epigenetic state by matrix stiffness during cell reprogramming.
Yang Song, Jennifer Soto, Sze Yue Wong, Yifan Wu, Tyler Hoffman, Timothy L Downing

Sci Adv· February 2024

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Reduction of Intracellular Tension and Cell Adhesion Promotes Open Chromatin Structure and Enhances Cell Reprogramming.
Jennifer Soto, Yang Song, Yifan Wu, Binru Chen, Hyungju Park, Timothy L Downing

Adv Sci (Weinh)· August 2023

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Targeting the ADPKD methylome using nanoparticle-mediated combination therapy.
Annie Trinh, Yi Huang, Hanjuan Shao, Aparna Ram, Julien Morival, Timothy L Downing

APL Bioeng· June 2023

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DNA Methylation Dynamics During Esophageal Epithelial Regeneration Following Repair with Acellular Silk Fibroin Grafts in Rat.
Lauren A Urban, Jiachun Li, Gokhan Gundogdu, Annie Trinh, Hanjuan Shao, Timothy L Downing

Adv Biol (Weinh)· May 2023

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Mechanosensation to inflammation: Roles for YAP/TAZ in innate immune cells.
Vijaykumar S Meli, Praveen Krishna Veerasubramanian, Timothy L Downing, Wenqi Wang, Wendy F Liu

Sci Signal· May 2023

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Locally correlated kinetics of post-replication DNA methylation reveals processivity and region specificity in DNA methylation maintenance.
Honglei Ren, Robert B Taylor, Timothy L Downing, Elizabeth L Read

J R Soc Interface· October 2022

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Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus.
Carlene A Chinn, Honglei Ren, Julien L P Morival, Qing Nie, Marcelo A Wood, Timothy L Downing

Neurobiol Aging· December 2021

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A Src-H3 acetylation signaling axis integrates macrophage mechanosensation with inflammatory response.
Praveen Krishna Veerasubramanian, Hanjuan Shao, Vijaykumar S Meli, Tri Andrew Q Phan, Thuy U Luu, Timothy L Downing

Biomaterials· December 2021

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Characterization of Macrophage and Cytokine Interactions with Biomaterials Used in Negative-Pressure Wound Therapy.
Praveen Krishna Veerasubramanian, Victor C Joe, Wendy F Liu, Timothy L Downing

Bioengineering (Basel)· December 2021

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Towards spheroid-omics.
Timothy L Downing

Nat Methods· November 2021

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DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies.
Julien L P Morival, Halida P Widyastuti, Cecilia H H Nguyen, Michael V Zaragoza, Timothy L Downing

Clin Epigenetics· July 2021

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The impact of age-related hypomethylated DNA on immune signaling upon cellular demise.
Lauren A Urban, Annie Trinh, Eric Pearlman, Albert Siryaporn, Timothy L Downing

Trends Immunol· June 2021

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YAP-mediated mechanotransduction tunes the macrophage inflammatory response.
Vijaykumar S Meli, Hamza Atcha, Praveen Krishna Veerasubramanian, Raji R Nagalla, Thuy U Luu, Timothy L Downing

Sci Adv· December 2020

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Biophysical and epigenetic regulation of cancer stemness, invasiveness and immune action.
Praveen Krishna Veerasubramanian, Annie Trinh, Navied Akhtar, Wendy F Liu, Timothy L Downing

Curr Tissue Microenviron Rep· December 2020

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Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation.
Luis Busto-Moner, Julien Morival, Honglei Ren, Arjang Fahim, Zachary Reitz, Timothy L Downing

PLoS Comput Biol· April 2020

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Metabolism of the neurotoxic amino acid β-N-methylamino-L-alanine in human cell culture models.
Simoné Downing, Rianita Van Onselen, Gabré Kemp, Timothy Grant Downing

Toxicon· October 2019

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Biophysical regulation of macrophages in health and disease.
Vijaykumar S Meli, Praveen K Veerasubramanian, Hamza Atcha, Zachary Reitz, Timothy L Downing

J Leukoc Biol· August 2019

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Dose-Dependent Adult Neurodegeneration in a Rat Model After Neonatal Exposure to β-N-Methylamino-L-Alanine.
Laura Scott, Timothy Downing

Neurotox Res· April 2019

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Global delay in nascent strand DNA methylation.
Jocelyn Charlton, Timothy L Downing, Zachary D Smith, Hongcang Gu, Kendell Clement

Nat Struct Mol Biol· April 2018

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Author Correction: Global delay in nascent strand DNA methylation.
Jocelyn Charlton, Timothy L Downing, Zachary D Smith, Hongcang Gu, Kendell Clement

Nat Struct Mol Biol· April 2018

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