Proteome birthdating reveals age-selectivity of protein ubiquitination

Michael E Meadow, Sarah Broas, Margaret Hoare, Fatemeh Alimohammadi, Kevin A Welle, Kyle Swovick, Jennifer R Hryhorenko, John C. Martinez, Seyed Ali Biashad, Andrei Seluanov, Vera Gorbunova, Abigail Buchwalter, Sina Ghaemmaghami

Mol Cell Proteomics. 2024 May 24:100791.

bioRxiv 2023.10.08.561433

Formylation facilitates the reduction of oxidized initiator methionines

Ruiyue Tan, Margaret Hoare, Philip Bellomio, Sarah Broas, Konttessa Camacho, Kyle Swovick, Kevin A. Welle, Jennifer R. Hryhorenko, Sina Ghaemmaghami

bioRxiv 2024.02.06.579201

Methionine Alkylation as an Approach to Quantify Methionine Oxidation Using Mass Spectrometry

Margaret Hoare, Ruiyue Tan, Kevin A. Welle, Kyle Swovick, Jennifer R. Hryhorenko, Sina Ghaemmaghami

J Am Soc Mass Spectrom. 2024 Feb 7.

bioRxiv 2023.09.21.558873

Long lifetime and tissue-specific accumulation of lamin A/C in Hutchinson-Gilford progeria syndrome

John Hasper, Kevin Welle, Kyle Swovick, Jennifer Hryhorenko, Sina Ghaemmaghami, Abigail Buchwalter

J Cell Biol. 2024 Jan 1.

bioRxiv 2023.02.04.527139


In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response

Xuewen Chen, Augustinus G Haribowo, Alan H Baik, Andrea Fossati, Erica Stevenson, Yiwen R Chen, Nabora S Reyes, Tien Peng, Michael A Matthay, Michela Traglia, Alexander R Pico, Daniel F Jarosz, Abigail Buchwalter, Sina Ghaemmaghami, Danielle L Swaney, Isha H Jain

Sci Adv. 8;9(49) Dec 2023

Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry

Ruiyue Tan, Margaret Hoare, Kevin A. Welle, Kyle Swovick, Jennifer R. Hryhorenko, Sina Ghaemmaghami

Proc Natl Acad Sci U S A. 2023 Aug 8.

bioRxiv 2022.11.07.515500

Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes

John Hasper, Kevin Welle, Jennifer Hryhorenko, Sina Ghaemmaghami, Abigail Buchwalter

Mol Syst Biol. 12;19(4):e11393. Apr 2023


Accurate proteome-wide measurement of methionine oxidation in aging mouse brains

John Q. Bettinger, Matthew Simon, Anatoly Korotkov, Kevin A. Welle, Jennifer R. Hryhorenko, Andrei Seluanov, Vera Gorbunova, Sina Ghaemmaghami

J Proteome Res. 3;21(6):1495-1509. Jun 2022

Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues

Walker EJ, Bettinger JQ, Welle KA, Hryhorenko JR, Molina Vargas AM, O'Connell MR, Ghaemmaghami S

J Biol Chem. 298(5):101872. Mar 2022


Comprehensive Structure-Activity Profiling of Micheliolide and its Targeted Proteome in Leukemia Cells via Probe-Guided Late-Stage C-H Functionalization

Alwaseem H, Giovani S, Crotti M, Welle K, Jordan CT, Ghaemmaghami S, Fasan R

ACS Cent Sci. 26;7(5):841-857. May 2021

MicroRNA-574 regulates FAM210A expression and influences pathological cardiac remodeling

Wu J, Venkata Subbaiah KC, Jiang F, Hedaya O, Mohan A, Yang T, Welle K, Ghaemmaghami S, Tang WHW, Small E, Yan C, Yao P

Mol EMBO Mol Med. 5;13(2):e12710. Feb 2021


Interspecies differences in proteome turnover kinetics are correlated with lifespans and energetic demands

Swovick K, Firsanov D, Welle KA, Hryhorenko JH, Wise JP,George C, Sformo TL, Seluanov A, Gorbunova V, Ghaemmaghami S

Mol Cell Proteomics. 20:100041. Jan 2021

Redox-mediated regulation of an evolutionarily conserved cross-β structure formed by the TDP43 low complexity domain

Lin Y, Zhou X, Kato M, Liu D, Ghaemmaghami S, Tu BP, McKnight SL

Proc Natl Acad Sci U S A. 2020 Nov 3.

bioRxiv 2019.12.24.885962; doi: https://doi.org/10.1101/2019.12.24.885962

Methionine oxidation within the prion protein

Bettinger J, Ghaemmaghami S

Prion. 14(1):193-205. Jul 2020.

Quantitative analysis of in vivo methionine oxidation of the human proteome

Bettinger JQ, Welle KA, Hryhorenko JR, Ghaemmaghami S

J Proteome Res. 2020 Feb 7.

bioRxiv 714089; doi: https://doi.org/10.1101/714089 Jul 2019.

Global analysis of protein degradation in prion infected cells

Hutti CR, Welle KA, Hryhorenko JR, Ghaemmaghami S

Sci Rep. 2020;10(1):10800. 2020 Jul 1.

bioRxiv 712927; doi: https://doi.org/10.1101/712927 Jul 2019.


JNK modifies neuronal metabolism to promote proteostasisand longevity

Lifen Wang, Sonnet S. Davis, Martin Borch Jensen, Imilce A. Rodriguez‐Fernandez, Cagsar Apaydin, Gabor Juhasz, Bradford W. Gibson, Birgit Schilling, Arvind Ramanathan, Sina Ghaemmaghami, Heinrich Jasper

Aging Cell. Feb 2019.

Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome

Walker EJ, Bettinger JQ, Welle KA, Hryhorenko JR, Ghaemmaghami S

Proc Natl Acad Sci U S A. 2019 Mar 7.

bioRxiv 467290; doi: https://doi.org/10.1101/467290. Nov 2018.


Developmentally regulated H2Av buffering via dynamic sequestration to lipid droplets in Drosophila embryos

Johnson MR, Stephenson RA, Ghaemmaghami S, Welte MA.

Elife. 2018 Jul 25;7. pii: e36021.

Increased Degradation Rates in the Components of the Mitochondrial Oxidative Phosphorylation Chain in the Cerebellum of Old Mice

Popa-Wagner A, Sandu RE, Cristin C, Uzoni A, Welle KA, Hryhorenko JR, Ghaemmaghami S.

Front Aging Neurosci. 2018 Feb 16;10:32.

Cross-species comparison of proteome turnover kinetics

Swovick K, Welle KA, Hryhorenko J, Seluanov A, Gorbunova V, Ghaemmaghami S.

Mol Cell Proteomics. 2018 Jan 10. pii: mcp.RA117.000574.


Proteome-wide modulation of degradation dynamics in response to growth arrest

Zhang T, Wolfe C, Pierle A, Welle KA, Hryhorenko JR, Ghaemmaghami S.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):E10329-E10338.

Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation

Nadtochiy SM, Wang YT, Zhang J, Nehrke K, Schafer X, Welle K, Ghaemmaghami S, Munger J, Brookes PS.

The Biochemical journal. 2017 Aug 10;474(16):2829-2839.


Biology and genetics of PrP prion strains

Ghaemmaghami S.

Cold Spring Harb Perspect Med. 2016 doi: 10.1101/cshperspect.a026922

Time-resolved analysis of proteome dynamics by TMT-SILAC hyperplexing

Welle KA, Zhang T, Hyrohorenko JR, Shen S, Qu J, Ghaemmaghami S.

Mol Cell Proteomics. 2016 Dec;15(12):3551-3563.

Autophagic Punctum: Global analysis of cellular protein flux quantifies the selectivity of basal autophagy

Zhang T, Ghaemmaghami S.

Autophagy. 2016 Aug 2;12(8):1411-2.

Global analysis of cellular protein flux quantifies the selectivity of basal autophagy

Zhang T, Shen S, Qu J, Ghaemmaghami S.

Cell Rep. 2016 Mar 15;14(10):2426-39.

Ion-current-based temporal proteomic profiling of influenza-A-virus-infected mouse lungs revealed underlying mechanisms of altered integrity of the lung microvascular barrier

Shen S, Li J, Hilchey S, Shen X, Tu C, Qiu X, Ng A, Ghaemmaghami S, Wu H, Zand MS, Qu J.

J Proteome Res. 2016 Feb 5;15(2):540-53

Pre 2016

Analysis of proteome dynamics in mice by isotopic labeling.

Price JC, Ghaemmaghami S.

Methods Mol Biol. 2014;1156:111-31.

Successes and challenges in phenotype-based lead discovery for prion diseases

Ghaemmaghami S, Russo M, Renslo AR.

J Med Chem. 2014 Aug 28;57(16):6919-29.

Kinetics of precursor labeling in SILAC experiments.

Zhang T, Nouri E, Li J, Price JC, Hellerstein M, Qu J, Ghaemmaghami S.

Anal Chem. 2014 Nov 18;86(22):11334-41.

Convergent replication of mouse synthetic prion strains

Ghaemmaghami S, Colby DW, Nguyen HO, Hayashi S, Oehler A, DeArmond SJ, Prusiner SB.

Am J Pathol. 2013 Mar;182(3):866-74.

Antiprion compounds that reduce PrPSc levels in dividing and stationary-phase cells

Silber BM, Gever JL, Li Z, Gallardo-Godoy A, Renslo AR, Widjaja K, Irwin JJ, Rao S, Jacobson MP, Ghaemmaghami S, Prusiner SB.

Bioorgan Med Chem 2013 Dec 15;21(24):7999-8012.

Strain Specificity and Drug Resistance in Anti- Prion Therapy

Miller-Vedam L, Ghaemmaghami S.

Cur Top Med Chem. 2013;13(19):2397-406.

Compartment modeling for mammalian protein turnover studies by stable isotope metabolic labeling

Guan S, Price JC, Ghaemmaghami S, Prusiner SB, Burlingame AL.

Anal Chem. 2012 May 1;84(9):4014-21.

Pharmacokinetics of quinacrine efflux from mouse brain via the P-glycoprotein efflux transporter

Ahn M, Ghaemmaghami S, Huang Y, Phuan PW, May BC, Giles K, DeArmond SJ, Prusiner SB.

PLoS One. 2012;7(7):e39112.

Intracerebral Infusion of Antisense Oligonucleotides Into Prion-infected Mice

Friberg KN, Hung G, Wancewicz E, Giles K, Black C, Freier S, Bennett F, DeArmond SJ, Freyman Y, Lessard P, Ghaemmaghami S, Prusiner SB.

Mol Ther Nucleic Acids. 2012 February; 1(2): e9.

A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling

Guan S, Price JC, Prusiner SB, Ghaemmaghami S, Burlingame AL.

Mol Cell Proteomics. 2011 Dec;10(12):M111.010728.

Conformational transformation and selection of synthetic prion strains

Ghaemmaghami S, Watts JC, Nguyen HO, Hayashi S, DeArmond SJ, Prusiner SB.

J Mol Biol. 2011 Oct 28;413(3):527-42.

A survey of antiprion compounds reveals the prevalence of non-PrP molecular targets

Poncet-Montange G, St Martin SJ, Bogatova OV, Prusiner SB, Shoichet BK, Ghaemmaghami S.

J Biol Chem. 2011 Aug 5;286(31):27718-28.

Analysis of proteome dynamics in the mouse brain

Price JC, Guan S, Burlingame A, Prusiner SB, Ghaemmaghami S.

Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14508-13.

Chemical induction of misfolded prion protein conformers in cell culture

Ghaemmaghami S, Ullman J, Ahn M, St Martin S, Prusiner SB.

J Biol Chem. 2010 Apr 2;285(14):10415-23.

Discovery of 2-aminothiazoles as potent antiprion compounds

Ghaemmaghami S, May BC, Renslo AR, Prusiner SB.

J Virol. 2010 Apr;84(7):3408-12.

Continuous quinacrine treatment results in the formation of drug-resistant prions

Ghaemmaghami S, Ahn M, Lessard P, Giles K, Legname G, DeArmond SJ, Prusiner SB.

PLoS Pathog. 2009 Nov;5(11):e1000673.

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS.

Science. 2009 Apr 10;324(5924):218-23.

Cell division modulates prion accumulation in cultured cells

Ghaemmaghami S, Phuan PW, Perkins B, Ullman J, May BC, Cohen FE, Prusiner SB.

Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):17971-6.

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS.

Nature. 2006 Jun 15;441(7095):840-6.

Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains

Howson R, Huh WK, Ghaemmaghami S, Falvo JV, Bower K, Belle A, Dephoure N, Wykoff DD, Weissman JS, O'Shea EK.

Comp Funct Genomics. 6(1-2):2-16. 2005

Global analysis of protein expression in yeast

Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS.

Nature. 2003 Oct 16;425(6959):737-41.

A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution

Powell KD, Ghaemmaghami S, Wang MZ, Ma L, Oas TG, Fitzgerald MC.

J Am Chem Soc. 2002 Sep 4;124(35):10256-7.

Quantitative protein stability measurement in vivo

Ghaemmaghami S, Oas TG.

Nat Struct Biol. 2001 Oct;8(10):879-82.

A quantitative, high-throughput screen for protein stability

Ghaemmaghami S, Fitzgerald MC, Oas TG.

Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8296-301.

Folding kinetics of a fluorescent variant of monomeric lambda repressor

Ghaemmaghami S, Word JM, Burton RE, Richardson JS, Oas TG.

Biochemistry. 1998 Jun 23;37(25):9179-85.

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