Proteome-wide analysis of the oxidation state of initiator methionines
R. Tan, M. Hoare, S. Bryan, S. Ghaemmaghami
Methods Enzymol (2025)
The yeast Mkt1/Pbp1 complex promotes adaptive responses to respiratory growth
D. Caballero, B. M. Sutter, Z. Xing, C. Wang, E. Choo, Y. Wang, Y.-S. Yang, S. Ghaemmaghami, A. Lemoff, B. P. Tu
J Cell Biol (2025)
Pervasive divergence in protein thermostability is mediated by both structural changes and cellular environments
N. Walunjkar, T. Y. Lai, N. Akhter, J. H. Miller, J. Q. Bettinger, E. Marcus, E. M. Phizicky, S. Ghaemmaghami, J. C. Fay
Mol Biol Evol (2025)
Taurine from tumour niche drives glycolysis to promote leukaemogenesis
S. Sharma, B. J. Rodems, C. D. Baker, C. M. Kaszuba, E. I. Franco, B. R. Smith, T. Ito, K. Swovick, K. Welle, Y. Zhang, P. Rock, F. A. Chaves, S. Ghaemmaghami, L. M. Calvi, A. Ganguly, W. R. Burack, M. W. Becker, J. L. Liesveld, P. S. Brookes, J. C. Munger, C. T. Jordan, J. M. Ashton, J. Bajaj
Nature (2025)
Antibiotic treatment modulates Escherichia coli-derived bacterial extracellular vesicle (BEV) production and their capacity to upregulate ICAM-1 in human endothelial cells
L. P. Widom, P. Torabian, A. C. Wojehowski, S. Ghaemmaghami, L. V. Michel, T. R. Gaborski
bioRxiv (2025)
Proteome Birthdating: A Single-Sample Approach for Measuring Global Turnover Dynamics and "Protein Age"
M. E. Meadow, S. Broas, M. Hoare, M. Ahmed, F. Alimohammadi, K. A. Welle, K. Swovick, J. R. Hryhorenko, A. Jain, J. C. Martinez, A. Seluanov, V. Gorbunova, A. Buchwalter, S. Ghaemmaghami
Bio Protoc (2025)
O-GlcNAc modifications regulate lamin A tail processing
K. Augspurger, E. Martin, J. Maynard, K. Welle, S. Ghaemmaghami, A. Burlingame, B. Panning, A. Buchwalter
bioRxiv (2025)
Formylation facilitates the reduction of oxidized initiator methionines
R. Tan, M. Hoare, P. Bellomio, S. Broas, K. Camacho, K. Swovick, K. A. Welle, J. R. Hryhorenko, S. Ghaemmaghami
Proc Natl Acad Sci U S A (2024)
Enzymatic synthesis of isotopically labeled hydrogen peroxide for mass spectrometry-based applications
M. Hoare, R. Tan, I. Militi, K. A. Welle, K. Swovick, J. R. Hryhorenko, S. Ghaemmaghami
J Am Soc Mass Spectrom (2024)
Proteome birthdating reveals age-selectivity of protein ubiquitination
M. E. Meadow, S. Broas, M. Hoare, F. Alimohammadi, K. A. Welle, K. Swovick, J. R. Hryhorenko, J. C. Martinez, S. A. Biashad, A. Seluanov, V. Gorbunova, A. Buchwalter, S. Ghaemmaghami
Mol Cell Proteomics (2024)
Methionine Alkylation as an Approach to Quantify Methionine Oxidation Using Mass Spectrometry
M. Hoare, R. Tan, K. A. Welle, K. Swovick, J. R. Hryhorenko, S. Ghaemmaghami
J Am Soc Mass Spectrom (2024)
Long lifetime and tissue-specific accumulation of lamin A/C in Hutchinson-Gilford progeria syndrome
J. Hasper, K. Welle, K. Swovick, J. Hryhorenko, S. Ghaemmaghami, A. Buchwalter
J Cell Biol (2024)
In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response
X. Chen, A. G. Haribowo, A. H. Baik, A. Fossati, E. Stevenson, Y. R. Chen, N. S. Reyes, T. Peng, M. A. Matthay, M. Traglia, A. R. Pico, D. F. Jarosz, A. Buchwalter, S. Ghaemmaghami, D. L. Swaney, I. H. Jain
Sci Adv (2023)
Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry
R. Tan, M. Hoare, K. A. Welle, K. Swovick, J. R. Hryhorenko, S. Ghaemmaghami
Proc Natl Acad Sci U S A (2023)
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes
J. Hasper, K. Welle, J. Hryhorenko, S. Ghaemmaghami, A. Buchwalter
Mol Syst Biol (2023)
Accurate proteome-wide measurement of methionine oxidation in aging mouse brains
J. Q. Bettinger, M. Simon, A. Korotkov, K. A. Welle, J. R. Hryhorenko, A. Seluanov, V. Gorbunova, S. Ghaemmaghami
J Proteome Res (2022)
Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues
E. J. Walker, J. Q. Bettinger, K. A. Welle, J. R. Hryhorenko, A. M. Molina Vargas, M. R. O'Connell, S. Ghaemmaghami
J Biol Chem (2022)
Comprehensive Structure-Activity Profiling of Micheliolide and its Targeted Proteome in Leukemia Cells via Probe-Guided Late-Stage C-H Functionalization
H. Alwaseem, S. Giovani, M. Crotti, K. W. Welle, C. T. Jordan, S. Ghaemmaghami, R. Fasan
ACS Cent Sci (2021)
MicroRNA-574 regulates FAM210A expression and influences pathological cardiac remodeling
J. Wu, K. C. Venkata Subbaiah, F. Jiang, O. Hedaya, A. Mohan, T. Yang, K. Welle, S. Ghaemmaghami, W. H. W. Tang, E. Small, C. Yan, P. Yao
Mol EMBO Mol Med (2021)
Interspecies differences in proteome turnover kinetics are correlated with lifespans and energetic demands
K. Swovick, D. Firsanov, K. A. Welle, J. H. Hryhorenko, J. P. Wise, C. George, T. L. Sformo, A. Seluanov, V. Gorbunova, S. Ghaemmaghami
Mol Cell Proteomics (2021)
Redox-mediated regulation of an evolutionarily conserved cross-β structure formed by the TDP43 low complexity domain
Y. Lin, X. Zhou, M. Kato, D. Liu, S. Ghaemmaghami, B. P. Tu, S. L. McKnight
Proc Natl Acad Sci U S A (2020)
Methionine oxidation within the prion protein
J. Bettinger, S. Ghaemmaghami
Prion (2020)
Quantitative analysis of in vivo methionine oxidation of the human proteome
J. Q. Bettinger, K. A. Welle, J. R. Hryhorenko, S. Ghaemmaghami
J Proteome Res (2020)
Global analysis of protein degradation in prion infected cells
C. R. Hutti, K. A. Welle, J. R. Hryhorenko, S. Ghaemmaghami
Sci Rep (2020)
JNK modifies neuronal metabolism to promote proteostasisand longevity
L. Wang, S. S. Davis, M. B. Jensen, I. A. Rodriguez-Fernandez, C. Apaydin, G. Juhasz, B. W. Gibson, B. Schilling, A. Ramanathan, S. Ghaemmaghami, H. Jasper
Aging Cell (2019)
Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome
E. J. Walker, J. Q. Bettinger, K. A. Welle, J. R. Hryhorenko, S. Ghaemmaghami
Proc Natl Acad Sci U S A (2019)
Developmentally regulated H2Av buffering via dynamic sequestration to lipid droplets in Drosophila embryos
M. R. Johnson, R. A. Stephenson, S. Ghaemmaghami, M. A. Welte
Elife (2018)
Increased Degradation Rates in the Components of the
Mitochondrial Oxidative Phosphorylation Chain in the Cerebellum of Old Mice
A. Popa-Wagner, R. E. Sandu, C. Cristin, A. Uzoni, K. A. Welle, J. R. Hryhorenko,
S. Ghaemmaghami
Front Aging Neurosci (2018)
Cross-species comparison of proteome turnover kinetics
K. Swovick, K. A. Welle, J. Hryhorenko, A. Seluanov, V. Gorbunova, S. Ghaemmaghami
Mol Cell Proteomics (2018)
Proteome-wide modulation of degradation dynamics in response to growth arrest
T. Zhang, C. Wolfe, A. Pierle, K. A. Welle, J. R. Hryhorenko, S. Ghaemmaghami
Proc Natl Acad Sci U S A (2017)
Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation
S. M. Nadtochiy, Y. T. Wang, J. Zhang, K. Nehrke, X. Schafer, K. Welle, S. Ghaemmaghami, J. Munger, P. S. Brookes
The Biochemical journal (2017)
Time-resolved analysis of proteome dynamics by TMT-SILAC hyperplexing
K. A. Welle, T. Zhang, J. R. Hyrohorenko, S. Shen, J. Qu, S. Ghaemmaghami
Mol Cell Proteomics (2016)
Autophagic Punctum: Global analysis of cellular protein flux quantifies the selectivity of basal autophagy
T. Zhang, S. Ghaemmaghami
Autophagy (2016)
Global analysis of cellular protein flux quantifies the selectivity of basal autophagy
T. Zhang, S. Shen, J. Qu, S. Ghaemmaghami
Cell Rep (2016)
Ion-current-based temporal proteomic profiling of influenza-A-virus-infected mouse lungs revealed underlying mechanisms of altered integrity of the lung microvascular barrier
S. Shen, J. Li, S. Hilchey, X. Shen, C. Tu, X. Qiu, A. Ng, S. Ghaemmaghami, H. Wu, M. S. Zand, J. Qu
J Proteome Res (2016)
Successes and challenges in phenotype-based lead discovery for prion diseases
S. Ghaemmaghami, M. Russo, A. R. Renslo
J Med Chem (2014)
Kinetics of precursor labeling in SILAC experiments.
T. Zhang, E. Nouri, J. Li, J. C. Price, M. Hellerstein, J. Qu, S. Ghaemmaghami
Anal Chem (2014)
Convergent replication of mouse synthetic prion strains
S. Ghaemmaghami, D. W. Colby, H. O. Nguyen, S. Hayashi, A. Oehler, S. J. DeArmond, S. B. Prusiner
Am J Pathol (2013)
Antiprion compounds that reduce PrPSc levels in dividing and stationary-phase cells
B. M. Silber, J. L. Gever, Z. Li, A. Gallardo-Godoy, A. R. Renslo, K. Widjaja, J. J. Irwin, S. Rao, M. P. Jacobson, S. Ghaemmaghami, S. B. Prusiner
Bioorgan Med Chem (2013)
Strain Specificity and Drug Resistance in Anti- Prion Therapy
L. Miller-Vedam, S. Ghaemmaghami
Cur Top Med Chem (2013)
Compartment modeling for mammalian protein turnover studies by stable isotope metabolic labeling
S. Guan, J. C. Price, S. Ghaemmaghami, S. B. Prusiner, A. L. Burlingame
Anal Chem (2012)
Pharmacokinetics of quinacrine efflux from mouse brain via the P-glycoprotein efflux transporter
M. Ahn, S. Ghaemmaghami, Y. Huang, P. W. Phuan, B. C. May, K. Giles, S. J. DeArmond, S. B. Prusiner
PLoS One (2012)
Intracerebral Infusion of Antisense Oligonucleotides Into Prion-infected Mice
K. N. Friberg, G. Hung, E. Wancewicz, K. Giles, C. Black, S. Freier, F. Bennett, S. J. DeArmond, Y. Freyman, P. Lessard, S. Ghaemmaghami, S. B. Prusiner
Mol Ther Nucleic Acids (2012)
A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling
S. Guan, J. C. Price, S. B. Prusiner, S. Ghaemmaghami, A. L. Burlingame
Mol Cell Proteomics (2011)
Conformational transformation and selection of synthetic prion strains
S. Ghaemmaghami, J. C. Watts, H. O. Nguyen, S. Hayashi, S. J. DeArmond, S. B. Prusiner
J Mol Biol (2011)
A survey of antiprion compounds reveals the prevalence of non-PrP molecular targets
G. Poncet-Montange, S. J. St Martin, O. V. Bogatova, S. B. Prusiner, B. K. Shoichet, S. Ghaemmaghami
J Biol Chem (2011)
Chemical induction of misfolded prion protein conformers in cell culture
S. Ghaemmaghami, J. Ullman, M. Ahn, S. St Martin, S. B. Prusiner
J Biol Chem (2010)
Discovery of 2-aminothiazoles as potent antiprion compounds
S. Ghaemmaghami, B. C. May, A. R. Renslo, S. B. Prusiner
J Virol (2010)
Continuous quinacrine treatment results in the formation of drug-resistant prions
S. Ghaemmaghami, M. Ahn, P. Lessard, K. Giles, G. Legname, S. J. DeArmond, S. B. Prusiner
PLoS Pathog (2009)
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
N. T. Ingolia, S. Ghaemmaghami, J. R. Newman, J. S. Weissman
Science (2009)
Cell division modulates prion accumulation in cultured cells
S. Ghaemmaghami, P. W. Phuan, B. Perkins, J. Ullman, B. C. May, F. E. Cohen, S. B. Prusiner
Proc Natl Acad Sci U S A (2007)
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
J. R. Newman, S. Ghaemmaghami, J. Ihmels, D. K. Breslow, M. Noble, J. L. DeRisi, J. S. Weissman
Nature (2006)
Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains
R. Howson, W. K. Huh, S. Ghaemmaghami, J. V. Falvo, K. Bower, A. Belle, N. Dephoure, D. D. Wykoff, J. S. Weissman, E. K. O'Shea
Comp Funct Genomics (2005)
Global analysis of protein expression in yeast
S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O'Shea, J. S. Weissman
Nature (2003)
A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution
K. D. Powell, S. Ghaemmaghami, M. Z. Wang, L. Ma, T. G. Oas, M. C. Fitzgerald
J Am Chem Soc (2002)
Folding kinetics of a fluorescent variant of monomeric lambda repressor
S. Ghaemmaghami, J. M. Word, R. E. Burton, J. S. Richardson, T. G. Oas
Biochemistry (1998)
