Publications
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 Aug 9. doi: 10.1007/s11357-021-00426-x. Epub ahead of print. PMID: 34370163.
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.
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.
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.
Schwartz RE, Shokhirev MN, Andrade LR, Gutkind JS, Iglesias-Bartolome R, Shadel GS. Insights into epithelial cell senescence from transcriptome and secretome analysis of human oral keratinocytes. Aging (Albany NY). 2021 Feb 12;13(4):4747-4777. doi: 10.18632/aging.202658. Epub 2021 Feb 12. PMID: 33601339; PMCID: PMC7950289.
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.
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.
Currais A, Huang L, Petrascheck M, Maher P, Schubert D. A chemical biology approach to identifying molecular pathways associated with aging. Geroscience. 2021 Feb;43(1):353-365. doi: 10.1007/s11357-020-00238-5. Epub 2020 Jul 23. PMID: 32705410; PMCID: PMC8050149.
Shokhirev MN, Johnson AA. Modeling the human aging transcriptome across tissues, health status, and sex. Aging Cell. 2021 Jan;20(1):e13280. doi: 10.1111/acel.13280. Epub 2020 Dec 18. PMID: 33336875; PMCID: PMC7811842.
Huang L, Currais A, Shokhirev MN. SUMMER, a shiny utility for metabolomics and multiomics exploratory research. Metabolomics. 2020 Dec 9;16(12):126. doi: 10.1007/s11306-020-01750-7. PMID: 33294943; PMCID: PMC7723939.
Lehallier B, Shokhirev MN, Wyss-Coray T, Johnson AA. Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. Aging Cell. 2020 Nov;19(11):e13256. doi: 10.1111/acel.13256. Epub 2020 Oct 8. PMID: 33031577; PMCID: PMC7681068.
Huang L, McClatchy DB, Maher P, Liang Z, Diedrich JK, Soriano-Castell D, Goldberg J, Shokhirev M, Yates JR 3rd, Schubert D, Currais A. Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death. Cell Death Dis. 2020 Oct 6;11(10):828. doi: 10.1038/s41419-020-03020-9. PMID: 33024077; PMCID: PMC7538552.
Bersini S, Schulte R, Huang L, Tsai H, Hetzer MW. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. Elife. 2020 Sep 8;9:e54383. doi: 10.7554/eLife.54383. PMID: 32896271; PMCID: PMC7478891.
Johnson AA, Shokhirev MN, Wyss-Coray T, Lehallier B. Systematic review and analysis of human proteomics aging studies unveils a novel proteomic aging clock and identifies key processes that change with age. Ageing Res Rev. 2020 Jul;60:101070. doi: 10.1016/j.arr.2020.101070. Epub 2020 Apr 18. PMID: 32311500.
Kepchia D, Huang L, Dargusch R, Rissman RA, Shokhirev MN, Fischer W, Schubert D. Diverse proteins aggregate in mild cognitive impairment and Alzheimer's disease brain. Alzheimers Res Ther. 2020 Jun 19;12(1):75. doi: 10.1186/s13195-020-00641-2. PMID: 32560738; PMCID: PMC7305608.
Bersini S, Arrojo E Drigo R, Huang L, Shokhirev MN, Hetzer MW. Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease. Adv Biosyst. 2020 May;4(5):e2000044. doi: 10.1002/adbi.202000044. Epub 2020 Mar 17. PMID: 32402127.
Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol. 2020 Apr;16(4):458-468. doi: 10.1038/s41589-019-0425-0. Epub 2019 Dec 9. PMID: 31819274; PMCID: PMC7085969.
Currais A, Huang L, Goldberg J, Petrascheck M, Ates G, Pinto-Duarte A, Shokhirev MN, Schubert D, Maher P. Elevating acetyl-CoA levels reduces aspects of brain aging. Elife. 2019 Nov 19;8:e47866. doi: 10.7554/eLife.47866. PMID: 31742554; PMCID: PMC6882557.
Johnson AA, Shokhirev MN, Shoshitaishvili B. Revamping the evolutionary theories of aging. Ageing Res Rev. 2019 Nov;55:100947. doi: 10.1016/j.arr.2019.100947. Epub 2019 Aug 23. PMID: 31449890.
Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer MW, Navlakha S. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biol. 2018 Dec 20;19(1):221. doi: 10.1186/s13059-018-1599-6. PMID: 30567591; PMCID: PMC6300908.
Kurita M, Araoka T, Hishida T, O'Keefe DD, Takahashi Y, Sakamoto A, Sakurai M, Suzuki K, Wu J, Yamamoto M, Hernandez-Benitez R, Ocampo A, Reddy P, Shokhirev MN, Magistretti P, Núñez Delicado E, Eto H, Harii K, Izpisua Belmonte JC. In vivo reprogramming of wound-resident cells generates skin epithelial tissue. Nature. 2018 Sep;561(7722):243-247. doi: 10.1038/s41586-018-0477-4. Epub 2018 Sep 5. PMID: 30185909.
Boisvert MM, Erikson GA, Shokhirev MN, Allen NJ. The Aging Astrocyte Transcriptome from Multiple Regions of the Mouse Brain. Cell Rep. 2018 Jan 2;22(1):269-285. doi: 10.1016/j.celrep.2017.12.039. PMID: 29298427; PMCID: PMC5783200.
Mertens J, Herdy JR, Traxler L, Schafer ST, Schlachetzki JCM, Böhnke L, Reid DA, Lee H, Zangwill D, Fernandes DP, Agarwal RK, Lucciola R, Zhou-Yang L, Karbacher L, Edenhofer F, Stern S, Horvath S, Paquola ACM, Glass CK, Yuan SH, Ku M, Szücs A, Goldstein LSB, Galasko D, Gage FH. Age-dependent instability of mature neuronal fate in induced neurons from Alzheimer's patients. Cell Stem Cell. 2021 Sep 2;28(9):1533-1548.e6. doi: 10.1016/j.stem.2021.04.004. Epub 2021 Apr 27. PMID: 33910058; PMCID: PMC8423435.
Bersini S, Schulte R, Huang L, Tsai H, Hetzer MW. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. Elife. 2020 Sep 8;9:e54383. doi: 10.7554/eLife.54383. PMID: 32896271; PMCID: PMC7478891.
