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San Diego Nathan Shock Center

Publications

Salk Institute for Biological Studies - San Diego Nathan Shock Center - Publications

Publications

Fiscal Year 4

  1. Lande K, Williams AE. PCBS: an R package for fast and accurate analysis of bisulfate sequencing data. bioRxiv [Preprint]. 2024 May 28: 2024.05.23.595620. doi: 10.1101/2024.05.23.595620.
  2. Rockhold JD, Marszalkowski H, Sannella M, Gibney K, Murphy L, Zukowski E, Kalantar GH, SantaCruz-Calvo S, Hart SN, Kuhn MK, Yu J, Stefanik O, Chase G, Proctor EA, Hasturk H, Nikolajczyk BS, Bharath LP*. Everolimus alleviates CD4+ T cell inflammation by regulating autophagy and cellular redox homeostasis. Geroscience. 2024 May 18. doi: 10.1007/s11357-024-01187-z. Epub ahead of print. PMID: 38761287.
  3. Reina J, Vallmajo-Martin Q, Ning J, Michi AN, Yeung K, Wahl GM, Hunter T. LHPP expression in triple-negative breast cancer promotes tumor growth and metastasis by modulating the tumor microenvironment. bioRxiv [Preprint]. 2024 Apr 23:2024.04.19.590151. doi: 10.1101/2024.04.19.590151. PMID: 38712081; PMCID: PMC11071390.
  4. Boussaty EC, Ninoyu Y, Andrade LR, Li Q, Takeya R, Sumimoto H, Ohyama T, Wahlin KJ, Manor U, Friedman RA. Altered Fhod3 expression involved in progressive high-frequency hearing loss via dysregulation of actin polymerization stoichiometry in the cuticular plate. PLoS Genet. 2024 Mar 18;20(3):e1011211. doi: 10.1371/journal.pgen.1011211. PMID: 38498576; PMCID: PMC10977885.
  5. Wang M, Zhang L, Novak SW, Yu J, Gallina IS, Xu LL, Lim CK, Fernandes S, Shokhirev MN, Williams AE, Saxena MD, Coorapati S, Parylak SL, Quintero C, Molina E, Andrade LR, Manor U, Gage FH. Morphological diversification and functional maturation of human astrocytes in glia-enriched cortical organoid transplanted in mouse brain. Nat Biotechnol. 2024 Feb 28. doi: 10.1038/s41587-024-02157-8. Epub ahead of print. PMID: 38418648.
  6. Park JH, Sahbaz BD, Pekhale K, Chu X, Okur MN, Grati M, Isgrig K, Chien W, Chrysostomou E, Sullivan L, Croteau DL, Manor U, Bohr VA. Early-Onset Hearing Loss in Mouse Models of Alzheimer's Disease and Increased DNA Damage in the Cochlea. Aging Biol. 2024;1:20240025. doi: 10.59368/agingbio.20240025. Epub 2024 Feb 20. PMID: 38500536; PMCID: PMC10948084.
  7. Newman LE, Weiser Novak S, Rojas GR, Tadepalle N, Schiavon CR, Grotjahn DA, Towers CG, Tremblay MÈ, Donnelly MP, Ghosh S, Medina M, Rocha S, Rodriguez-Enriquez R, Chevez JA, Lemersal I, Manor U, Shadel GS. Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal. Nat Cell Biol. 2024 Feb;26(2):194-206. doi: 10.1038/s41556-023-01343-1. Epub 2024 Feb 8. PMID: 38332353; PMCID: PMC11026068.
  8. Priessner M, Gaboriau DCA, Sheridan A, Lenn T, Garzon-Coral C, Dunn AR, Chubb JR, Tousley AM, Majzner RG, Manor U, Vilar R, Laine RF. Content-aware frame interpolation (CAFI): deep learning-based temporal super-resolution for fast bioimaging. Nat Methods. 2024 Feb;21(2):322-330. doi: 10.1038/s41592-023-02138-w. Epub 2024 Jan 18. PMID: 38238557; PMCID: PMC10864186.
  9. Jolis M, Praturu A, Sharpee TO. A bayesian approach to non-Metric hyperbolic multi-dimensional scaling. bioRxiv [Preprint]. 2023 Dec 11: 2023.12.08.570871. doi: 10.1101/2023.12.08.570871.
  10. Zukowski E, Sannella M, Rockhold JD, Kalantar GH, Yu J, SantaCruz-Calvo S, Kuhn MK, Hah N, Ouyang L, Wang TW, Murphy L, Marszalkowski H, Gibney K, Drummond MJ, Proctor EA, Hasturk H, Nikolajczyk BS, Bharath LP*. STAT3 modulates CD4+ T mitochondrial dynamics and function in aging. Aging Cell. 2023 Nov;22(11):e13996. doi: 10.1111/acel.13996. Epub 2023 Oct 13. PMID: 37837188; PMCID: PMC10652300.
  11. Alvarez-Kuglen M, Rodriguez D, Qin H, Ninomiya K, Fiengo L, Farhy C, Hsu WM, Havas A, Feng GS, Roberts AJ, Anderson RM, Serrano M, Adams PD, Sharpee TO, Terskikh AV. Imaging-based chromatin and epigenetic age, ImAge, quantitates aging and rejuvenation. Res Sq [Preprint]. 2023 Nov 7:rs.3.rs-3479973. doi: 10.21203/rs.3.rs-3479973/v1. PMID: 37986947; PMCID: PMC10659560.
  12. Victorelli S, Salmonowicz H, Chapman J, Martini H, Vizioli MG, Riley JS, Cloix C, Hall-Younger E, Machado Espindola-Netto J, Jurk D, Lagnado AB, Sales Gomez L, Farr JN, Saul D, Reed R, Kelly G, Eppard M, Greaves LC, Dou Z, Pirius N, Szczepanowska K, Porritt RA, Huang H, Huang TY, Mann DA, Masuda CA, Khosla S, Dai H, Kaufmann SH, Zacharioudakis E, Gavathiotis E, LeBrasseur NK, Lei X, Sainz AG, Korolchuk VI, Adams PD, Shadel GS, Tait SWG, Passos JF. Apoptotic stress causes mtDNA release during senescence and drives the SASP. Nature. 2023 Oct;622(7983):627-636. doi: 10.1038/s41586-023-06621-4. Epub 2023 Oct 11. Erratum in: Nature. 2024 Jan;625(7995):E15. PMID: 37821702; PMCID: PMC10584674.
  13. Mangalhara KC, Varanasi SK, Johnson MA, Burns MJ, Rojas GR, Esparza Moltó PB, Sainz AG, Tadepalle N, Abbott KL, Mendiratta G, Chen D, Farsakoglu Y, Kunchok T, Hoffmann FA, Parisi B, Rincon M, Vander Heiden MG, Bosenberg M, Hargreaves DC, Kaech SM, Shadel GS. Manipulating mitochondrial electron flow enhances tumor immunogenicity. Science. 2023 Sep 22;381(6664):1316-1323. doi: 10.1126/science.abq1053. Epub 2023 Sep 21. PMID: 37733872; PMCID: PMC11034774.
  14. Alvarez-Kuglen M, Rodriguez D, Qin H, Ninomiya K, Fiengo L, Farhy C, Hsu WM, Havas A, Feng GS, Roberts AJ, Anderson RM, Serrano M, Adams PD, Sharpee TO, Terskikh AV. ImAge: an imaging approach to quantitate aging and rejuvenation. bioRxiv [Preprint]. 2023 Sep 4: 2022.10.16.512441. doi: 10.1101/2022.10.16.512441.
  15. Gatti P, Schiavon C, Manor U, Germain M. Mitochondria- and ER-associated actin are required for mitochondrial fusion. bioRxiv [Preprint]. 2023 Jun 13:2023.06.13.544768. doi: 10.1101/2023.06.13.544768. PMID: 37398222; PMCID: PMC10312652.
  16. Delcroix V*, Mauduit O, Lee HS, Ivanova A, Umazume T, Knox SM, de Paiva CS, Dartt DA, Makarenkova HP. The First Transcriptomic Atlas of the Adult Lacrimal Gland Reveals Epithelial Complexity and Identifies Novel Progenitor Cells in Mice. Cells. 2023 May 21;12(10):1435. doi: 10.3390/cells12101435. PMID: 37408269; PMCID: PMC10216974.
  17. Malik N, Ferreira BI, Hollstein PE, Curtis SD, Trefts E, Weiser Novak S, Yu J, Gilson R, Hellberg K, Fang L, Sheridan A, Hah N, Shadel GS, Manor U, Shaw RJ. Induction of lysosomal and mitochondrial biogenesis by AMPK phosphorylation of FNIP1. Science. 2023 Apr 21;380(6642):eabj5559. doi: 10.1126/science.abj5559. Epub 2023 Apr 21. PMID: 37079666; PMCID: PMC10794112.

Fiscal Year 3

  1. Nassour J, Aguiar LG, Correia A, Schmidt TT, Mainz L, Przetocka S, Haggblom C, Tadepalle N, Williams A, Shokhirev MN, Akincilar SC, Tergaonkar V, Shadel GS, Karlseder J. Telomere-to-mitochondria signalling by ZBP1 mediates replicative crisis. Nature. 2023 Feb;614(7949):767-773. doi: 10.1038/s41586-023-05710-8. Epub 2023 Feb 8. PMID: 36755096; PMCID: PMC9946831.
  2. Zhang H, Rich PD, Lee AK, Sharpee TO. Hippocampal spatial representations exhibit a hyperbolic geometry that expands with experience. Nat Neurosci. 2023 Jan;26(1):131-139. doi: 10.1038/s41593-022-01212-4. Epub 2022 Dec 29. PMID: 36581729; PMCID: PMC9829541.
  3. Rowekamp RJ, Sharpee TO. Quadratic computations maintain neural specificity to natural stimuli across stages of visual processing. bioRxiv [Preprint]. 2022 Nov 18: 2022.11.17.516970. doi: 10.1101/2022.11.17.516970.
  4. Praturu A, Sharpee TO. A bayseian approach to hyperbolic multi-dimensional scaling. bioRxiv [Preprint]. 2022 Oct 16: 2022.10.12.511940. doi: 10.1101/2022.10.12.511940.
  5. Zhou Y, Sharpee TO. Using Global t-SNE to Preserve Intercluster Data Structure. Neural Comput. 2022 Jul 14;34(8):1637-1651. doi: 10.1162/neco_a_01504. PMID: 35798323; PMCID: PMC10010455.

Fiscal Year 2

  1. Liu Z, Hu X, Liang Y, Yu J, Li H, Shokhirev MN, Zheng Y. Glucocorticoid signaling and regulatory T cells cooperate to maintain the hair-follicle stem-cell niche. Nat Immunol. 2022 Jul;23(7):1086-1097. doi: 10.1038/s41590-022-01244-9. Epub 2022 Jun 23. PMID: 35739197; PMCID: PMC9283297.
  2. Heard KJ, Shokhirev MN, Becronis C, Fredlender C, Zahid N, Le AT, Ji Y, Skime M, Nelson T, Hall-Flavin D, Weinshilboum R, Gage FH, Vadodaria KC. Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients. Transl Psychiatry. 2021 Nov 30;11(1):608. doi: 10.1038/s41398-021-01733-9. PMID: 34848679; PMCID: PMC8632962.
  3. Farhy-Tselnicker I, Boisvert MM, Liu H, Dowling C, Erikson GA, Blanco-Suarez E, Farhy C, Shokhirev MN, Ecker JR, Allen NJ. Activity-dependent modulation of synapse-regulating genes in astrocytes. Elife. 2021 Sep 8;10:e70514. doi: 10.7554/eLife.70514. PMID: 34494546; PMCID: PMC8497060.
  4. Shadel GS, Adams PD, Berggren WT, Diedrich JK, Diffenderfer KE, Gage FH, Hah N, Hansen M, Hetzer MW, Molina AJA, Manor U, Marek K, O'Keefe DD, Pinto AFM, Sacco A, Sharpee TO, Shokriev MN, Zambetti S. The San Diego Nathan Shock Center: tackling the heterogeneity of aging. Geroscience. 2021 Oct;43(5):2139-2148. doi: 10.1007/s11357-021-00426-x. Epub 2021 Aug 9. PMID: 34370163; PMCID: PMC8599742.
  5. Johnson AA, Shokhirev MN, Lehallier B. The protein inputs of an ultra-predictive aging clock represent viable anti-aging drug targets. Ageing Res Rev. 2021 Sep;70:101404. doi: 10.1016/j.arr.2021.101404. Epub 2021 Jul 6. PMID: 34242807.

Fiscal Year 1

  1. Hsu WM, Kastner DB, Baccus SA, Sharpee TO. How inhibitory neurons increase information transmission under threshold modulation. Cell Rep. 2021 May 25;35(8):109158. doi: 10.1016/j.celrep.2021.109158. PMID: 34038717; PMCID: PMC8846953.
  2. Zhou Y, Sharpee TO. Hyperbolic geometry of gene expression. iScience. 2021 Feb 24;24(3):102225. doi: 10.1016/j.isci.2021.102225. PMID: 33748711; PMCID: PMC7970362.

Bold and Underline = SD-NSC Team Members
Bold = SD-NSC Affiliates; * indicates Pilot Grant Awardees