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Timothy L. Downing

Title(s)Assistant Professor, Biomedical Engineering
SchoolSamueli School of Engineering
Address2408 Engineering III
Zot 2730
Irvine CA 92697
Phone(949) 824-8744
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    Collapse Research 
    Collapse research activities and funding
    Spatial epigenomics: A new framework for overcoming mechanical heterogeneity in solid tumors
    NIH DP2CA250382Sep 19, 2019 - May 31, 2024
    Role: Principal Investigator
    Epigenetic regulation of macrophage response to biomaterial implants
    NIH R21EB027840Apr 18, 2019 - Jan 31, 2021
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Nucleosome placement and polymer mechanics explain genomic contacts on 100 kb scales. Nucleic Acids Res. 2025 Jul 19; 53(14). Corrette J, Li J, Shao H, Veerasubramanian PK, Spakowitz A, Downing TL, Allard J. PMID: 40705928; PMCID: PMC12288874.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Bacteria detect neutrophils via a system that responds to hypochlorous acid and flow. bioRxiv. 2025 May 23. Foik IP, Shu R, Abbondante S, Kasallis SJ, Urban LA, Huang AP, Duong L, Marshall ME, Pearlman E, Downing TL, Siryaporn A. PMID: 40475492; PMCID: PMC12139993.
      View in: PubMed   Mentions:
    3. Nucleosome placement and polymer mechanics explain genomic contacts on 100kbp scales. bioRxiv. 2025 May 03. Corrette J, Li J, Shao H, Veerasubramanian PK, Spakowitz A, Downing TL, Allard J. PMID: 39386659; PMCID: PMC11463500.
      View in: PubMed   Mentions:
    4. Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read sequencing. bioRxiv. 2025 Mar 11. Trinh A, Akhtar N, Bonsu K, Laszik N, Mendelevich A, Wen T, Morival JLP, Diune KE, Frazeur M, Vega JE, Gimelbrant AA, Read EL, Downing TL. PMID: 40161794; PMCID: PMC11952338.
      View in: PubMed   Mentions:
    5. Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa. Viruses. 2024 04 03; 16(4). Haga IR, Shih BB, Tore G, Polo N, Ribeca P, Gombo-Ochir D, Shura G, Tserenchimed T, Enkhbold B, Purevtseren D, Ulziibat G, Damdinjav B, Yimer L, Bari FD, Gizaw D, Adedeji AJ, Atai RB, Adole JA, Dogonyaro BB, Kumarawadu PL, Batten C, Corla A, Freimanis GL, Tennakoon C, Law A, Lycett S, Downing T, Beard PM. PMID: 38675899; PMCID: PMC11053774.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCellsPHPublic Health
    6. Biphasic regulation of epigenetic state by matrix stiffness during cell reprogramming. Sci Adv. 2024 02 16; 10(7):eadk0639. Song Y, Soto J, Wong SY, Wu Y, Hoffman T, Akhtar N, Norris S, Chu J, Park H, Kelkhoff DO, Ang CE, Wernig M, Kasko A, Downing TL, Poo MM, Li S. PMID: 38354231; PMCID: PMC10866547.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    7. A primer on correlation-based dimension reduction methods for multi-omics analysis. J R Soc Interface. 2023 10; 20(207):20230344. Downing T, Angelopoulos N. PMID: 37817584; PMCID: PMC10565429.
      View in: PubMed   Mentions: 3     Fields:    
    8. Reduction of Intracellular Tension and Cell Adhesion Promotes Open Chromatin Structure and Enhances Cell Reprogramming. Adv Sci (Weinh). 2023 08; 10(24):e2300152. Soto J, Song Y, Wu Y, Chen B, Park H, Akhtar N, Wang PY, Hoffman T, Ly C, Sia J, Wong S, Kelkhoff DO, Chu J, Poo MM, Downing TL, Rowat AC, Li S. PMID: 37357983; PMCID: PMC10460843.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    9. Targeting the ADPKD methylome using nanoparticle-mediated combination therapy. APL Bioeng. 2023 Jun; 7(2):026111. Trinh A, Huang Y, Shao H, Ram A, Morival J, Wang J, Chung EJ, Downing TL. PMID: 37305656; PMCID: PMC10257530.
      View in: PubMed   Mentions: 5  
    10. Mechanosensation to inflammation: Roles for YAP/TAZ in innate immune cells. Sci Signal. 2023 05 02; 16(783):eadc9656. Meli VS, Veerasubramanian PK, Downing TL, Wang W, Liu WF. PMID: 37130167; PMCID: PMC10625748.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    11. DNA Methylation Dynamics During Esophageal Epithelial Regeneration Following Repair with Acellular Silk Fibroin Grafts in Rat. Adv Biol (Weinh). 2023 05; 7(5):e2200160. Urban LA, Li J, Gundogdu G, Trinh A, Shao H, Nguyen T, Mauney JR, Downing TL. PMID: 36658732; PMCID: PMC10401397.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    12. Locally correlated kinetics of post-replication DNA methylation reveals processivity and region specificity in DNA methylation maintenance. J R Soc Interface. 2022 Oct; 19(195):20220415. Ren H, Taylor RB, Downing TL, Read EL. PMID: 36285438; PMCID: PMC9597173.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    13. Characterization of Macrophage and Cytokine Interactions with Biomaterials Used in Negative-Pressure Wound Therapy. Bioengineering (Basel). 2021 Dec 22; 9(1). Veerasubramanian PK, Joe VC, Liu WF, Downing TL. PMID: 35049711; PMCID: PMC8773312.
      View in: PubMed   Mentions: 4  
    14. Towards spheroid-omics. Nat Methods. 2021 11; 18(11):1283-1285. Downing TL. PMID: 34732905.
      View in: PubMed   Mentions: 1     Fields:    
    15. A Src-H3 acetylation signaling axis integrates macrophage mechanosensation with inflammatory response. Biomaterials. 2021 12; 279:121236. Veerasubramanian PK, Shao H, Meli VS, Phan TAQ, Luu TU, Liu WF, Downing TL. PMID: 34753038; PMCID: PMC8939266.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    16. Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus. Neurobiol Aging. 2021 12; 108:223-235. Chinn CA, Ren H, Morival JLP, Nie Q, Wood MA, Downing TL. PMID: 34598831; PMCID: PMC9186538.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    17. DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies. Clin Epigenetics. 2021 07 10; 13(1):139. Morival JLP, Widyastuti HP, Nguyen CHH, Zaragoza MV, Downing TL. PMID: 34246298; PMCID: PMC8272901.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    18. The impact of age-related hypomethylated DNA on immune signaling upon cellular demise. Trends Immunol. 2021 06; 42(6):464-468. Urban LA, Trinh A, Pearlman E, Siryaporn A, Downing TL. PMID: 33994111; PMCID: PMC9650629.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    19. YAP-mediated mechanotransduction tunes the macrophage inflammatory response. Sci Adv. 2020 12; 6(49). Meli VS, Atcha H, Veerasubramanian PK, Nagalla RR, Luu TU, Chen EY, Guerrero-Juarez CF, Yamaga K, Pandori W, Hsieh JY, Downing TL, Fruman DA, Lodoen MB, Plikus MV, Wang W, Liu WF. PMID: 33277245; PMCID: PMC7717914.
      View in: PubMed   Mentions: 129     Fields:    Translation:HumansCells
    20. Biophysical and epigenetic regulation of cancer stemness, invasiveness and immune action. Curr Tissue Microenviron Rep. 2020 Dec; 1(4):277-300. Veerasubramanian PK, Trinh A, Akhtar N, Liu WF, Downing TL. PMID: 33817661; PMCID: PMC8015331.
      View in: PubMed   Mentions: 8  
    21. Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation. PLoS Comput Biol. 2020 04; 16(4):e1007195. Busto-Moner L, Morival J, Ren H, Fahim A, Reitz Z, Downing TL, Read EL. PMID: 32275652; PMCID: PMC7176288.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    22. Global genome diversity of the Leishmania donovani complex. Elife. 2020 03 25; 9. Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, Dujardin JC, Sanders MJ, Mauricio I, Miles MA, Schnur LF, Jaffe CL, Nasereddin A, Schallig H, Yeo M, Bhattacharyya T, Alam MZ, Berriman M, Wirth T, Schönian G, Cotton JA. PMID: 32209228; PMCID: PMC7105377.
      View in: PubMed   Mentions: 69     Fields:    Translation:Animals
    23. Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana. Mol Biol Evol. 2019 06 01; 36(6):1239-1253. Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O'Connell MJ, Spillane C. PMID: 30913563; PMCID: PMC6526901.
      View in: PubMed   Mentions: 10     Fields:    Translation:Animals
    24. Biophysical regulation of macrophages in health and disease. J Leukoc Biol. 2019 08; 106(2):283-299. Meli VS, Veerasubramanian PK, Atcha H, Reitz Z, Downing TL, Liu WF. PMID: 30861205; PMCID: PMC7001617.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    25. Author Correction: Global delay in nascent strand DNA methylation. Nat Struct Mol Biol. 2018 04; 25(4):355. Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. PMID: 29581568.
      View in: PubMed   Mentions: 1     Fields:    
    26. Global delay in nascent strand DNA methylation. Nat Struct Mol Biol. 2018 04; 25(4):327-332. Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. PMID: 29531288; PMCID: PMC5889353.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    27. Mechanoresponsive stem cells to target cancer metastases through biophysical cues. Sci Transl Med. 2017 07 26; 9(400). Liu L, Zhang SX, Liao W, Farhoodi HP, Wong CW, Chen CC, Ségaliny AI, Chacko JV, Nguyen LP, Lu M, Polovin G, Pone EJ, Downing TL, Lawson DA, Digman MA, Zhao W. PMID: 28747514; PMCID: PMC5890431.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    28. Leishmania infections: Molecular targets and diagnosis. Mol Aspects Med. 2017 Oct; 57:1-29. Akhoundi M, Downing T, Votýpka J, Kuhls K, Lukeš J, Cannet A, Ravel C, Marty P, Delaunay P, Kasbari M, Granouillac B, Gradoni L, Sereno D. PMID: 28159546.
      View in: PubMed   Mentions: 150     Fields:    Translation:HumansAnimalsPHPublic Health
    29. Redeploying β-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections. J Infect Dis. 2017 Jan 01; 215(1):80-87. Waters EM, Rudkin JK, Coughlan S, Clair GC, Adkins JN, Gore S, Xia G, Black NS, Downing T, O'Neill E, Kadioglu A, O'Gara JP. PMID: 28077586; PMCID: PMC5225249.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    30. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. Elife. 2016 Mar 22; 5. Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, Rai K, Uranw S, Bhattarai NR, Khanal B, Prajapati VK, Sharma S, Stark O, Schönian G, De Koning HP, Settimo L, Vanhollebeke B, Roy S, Ostyn B, Boelaert M, Maes L, Berriman M, Dujardin JC, Cotton JA. PMID: 27003289; PMCID: PMC4811772.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansAnimalsPHPublic Health
    31. The triploid East African Highland Banana (EAHB) genepool is genetically uniform arising from a single ancestral clone that underwent population expansion by vegetative propagation. Theor Appl Genet. 2016 Mar; 129(3):547-61. Kitavi M, Downing T, Lorenzen J, Karamura D, Onyango M, Nyine M, Ferguson M, Spillane C. PMID: 26743524.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    32. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. PLoS Genet. 2014 Jan; 10(1):e1004092. Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodova M, Volf P, Berriman M, Cotton JA, Smith DF. PMID: 24453988; PMCID: PMC3894156.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    33. Biophysical regulation of epigenetic state and cell reprogramming. Nat Mater. 2013 Dec; 12(12):1154-62. Downing TL, Soto J, Morez C, Houssin T, Fritz A, Yuan F, Chu J, Patel S, Schaffer DV, Li S. PMID: 24141451; PMCID: PMC9675045.
      View in: PubMed   Mentions: 209     Fields:    Translation:HumansAnimalsCells
    34. Human induced pluripotent stem cell-derived neural crest stem cells integrate into the injured spinal cord in the fetal lamb model of myelomeningocele. J Pediatr Surg. 2013 Jan; 48(1):158-63. Saadai P, Wang A, Nout YS, Downing TL, Lofberg K, Beattie MS, Bresnahan JC, Li S, Farmer DL. PMID: 23331809.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimalsCells
    35. Drug-eluting microfibrous patches for the local delivery of rolipram in spinal cord repair. J Control Release. 2012 Aug 10; 161(3):910-7. Downing TL, Wang A, Yan ZQ, Nout Y, Lee AL, Beattie MS, Bresnahan JC, Farmer DL, Li S. PMID: 22634093; PMCID: PMC3698241.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    36. Prenatal repair of myelomeningocele with aligned nanofibrous scaffolds-a pilot study in sheep. J Pediatr Surg. 2011 Dec; 46(12):2279-83. Saadai P, Nout YS, Encinas J, Wang A, Downing TL, Beattie MS, Bresnahan JC, Li S, Farmer DL. PMID: 22152865.
      View in: PubMed   Mentions: 21     Fields:    Translation:Animals
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