Publications

PAPERS

    Pubmed list

            *co-corresponding author, #equal contribution

• Meydan, S^#, Barros, G.C.^#, Simões, V., Harley, L., Cizubu, B.K., Guydosh, R.* and Silva, G.M*. The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress  Cell Reports (2023) doi:10.1016/j.celrep.2023.113359

• Mays, A., Byars-Winston, A., Hinton, A.J., ... Silva, G.M., ... Lambert, W.M., and Clemons, W.M. Juneteenth in STEMM and the barriers to equitable science  Cell (2023) doi::10.1016/j.cell.2023.05.016

• Simões, V., Cizubu, B.K.^#, Harley, L.^#, Zhou, Y.E., Pajak, J., Snyder, N.A., Bouvette, J., Borgnia, M.J., Arya, G., Bartesaghi, A. and Silva, G.M. Redox sensitive E2 Rad6 controls cellular response to oxidative stress via K63 ubiquitination of ribosomes  Cell Reports  (2022) doi:10.1016/j.celrep.2022.110860
  • Recognition: DukeToday: Gene Linked to Severe Learning Disabilities Governs Cell Stress Response

• Snyder, N.A and Silva, G.M. Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response  J Biol Chem (2021) doi:10.1016/j.jbc.2021.101077

• Zhou, Y.E., Kastritis, P.L., Dougherty, S.E., Bouvette, J., Hsu, A., Burbaum, L., Mosalaganti, S., Pfeffer, S., Hagen, W.J.H., Förster, F., Borgnia, M.J., Vogel, C., Beck, M., Bartesaghi, A. and Silva, G.M. Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress. Proc Natl Acad Sci U S A (2020) doi:10.1073/pnas.2005301117
  • Press: Collaboration Makes New Discovery Using Cryo-EM

• Blount, J.R., Libohova, K., Silva, G.M., and Todi, S.V. Isoleucine 44 hydrophobic patch controls toxicity of unanchored, linear ubiquitin chains through NF-κB signaling.  Cells (2020) doi: 10.3390/cells9061519

• Dougherty, S.E.^#, Maduka, A.O.^#, Inada, T., and Silva, G.M. Expanding role of ubiquitin in translational control. International Journal of Molecular Sciences (2020) doi: 10.3390/ijms21031151

• Manohar, S., Jacob, S., Wang, J.C., Wiechecki, K.A., Koh, H.W., Simoes, V., Choi, H., Vogel, C., and Silva, G.M. Polyubiquitin chains linked by lysine 48 (K48) selectively targets oxidized proteins in vivo  Antioxidants & Redox Signaling (2019) doi: 10.1089/ars.2019.7826

• Back, S., Gorman, A.W., Vogel, C., and Silva, G.M. Site-specific K63 ubiquitinomics provides insights into translation regulation under stress Journal of Proteome Research (2018) doi: 10.1021/acs.jproteome.8b00623
  • Recognition: PreLights - preprint highlights

• Lin, Y.C., Sekedat, M., Cornell, W.C., Silva, G.M., Okegbe, C., Price-Whelan, A., Vogel, C., and Dietrich, L.E.P. Phenazines regulate Nap-dependent denitrification in Pseudomonas aeruginosa biofilms. Journal of Bacteriology (2018) doi: 10.1128/JB.00031-18.
  • Recognition: Editor's pick spotlight 
  •  Journal's cover image

• Wiechecki, K., Manohar, S., Silva, G.M., Tchourine, K., Jacob, S., Valleriani, A. and Vogel, C. Integrative meta analysis reveals that most yeast proteins are very stable. bioRxiv (2017) doi: 10.1101/165290.
• Silva, G.M., and Vogel, C. Quantifying gene expression: the importance of being subtle. Molecular Systems Biology (2016) doi: 15252/msb.20167325. 

• Da Costa, J., Vitorino, R.; Silva, G.M., Vogel, C., Duarte, A.C., Rocha-Santos, T. A synopsis on Aging – theory, mechanisms and future prospects Ageing Research Reviews 2016, 29:90-112, doi: 10.1016/j.arr.2016.06.005, 

• Toledo, R.A, Qin, Y., Cheng, Z.M., Gao, Q., Iwata, S., Silva, G.M., Prasad, M.L., Ocal, T., Rao, S., Aronin, N., Barontini, M., Bruder, J, Reddick, R. Chen, Y., Aguiar, R.C.T. and Dahia, P.L.M. Recurrent mutations of chromatin remodeling genes and kinase receptors in pheochromocytomas and paragangliomas Clinical Cancer Research 2016, 22:2301-2310 doi: 10.1158/1078-0432

• Silva, GM.,* Wei, W., Manohar, S. and Vogel, C. Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry. NeuroMethods (2015) Humana Press – Springer Science, NY, doi: 10.1007/7657_2015_95 

• Silva, G.M.* and Vogel, C. Mass spectrometry analysis of K63-ubiquitinated targets in response to oxidative stress. Data in Brief 2015, 4:130-134. doi: 10.1016/j.dib.2015.05.002

• Silva, G.M.,* Finley, D. and Vogel, C. K63 ubiquitination is a new modulator of the oxidative stress response. Nature Strucutural & Molecular Biology 2015, 22:116-123.  doi:10.1038/nsmb.2955
   
  • Press: NYU Research News,

  Agencia FAPESP press release
  Redoxoma Newsletter
  ScienceDaily
  Phys.org

• Tchourine, K., Poultney, C., Wang, L., Silva, G.M., Manohar, S., Mueller, C.L. Bonneau, R. and Vogel, C. One third of dynamic gene expression profiles can be predicted by simple rate equations. Mol BioSys 2014 10(11):2850-2862. PubMed PMID: 25111754 

• Demasi, M., Netto L.E., Silva, G.M., Hand, A., de Oliveira, C.L., Bicev, R.N., Gozzo, F. Barros, M.H., Leme, J.M., Ohara, E. Redox regulation of the proteasome via S-glutathionylation. Redox Biol. 2013 2:44-51. PubMed PMID: 24396728 

• Malvezzi, A., Higa, P.M., Amaral, A.T., Silva, G.M., Gozzo, F.C., Ferro, E.S., Castro, L.M., de Rezende, L., Monteiro, G., and Demasi, M. The Cysteine-Rich Protein Thimet Oligopeptidase as a Model of the Structural Requirements for S-glutathiolation and Oxidative Oligomerization. PLoS One 2012 7(6):e39408. PubMed PMID: 22761783

• Silva, G.M., Netto, L.E., Simoes, V., Santos, L.F., Gozzo, F.C., Demasi, M.A., Oliveira, C.L., Bicev, R.N., Klitzke, C.F., Sogayar, M.C. and Demasi, M. Redox Control of 20S Proteasome Gating. Antioxid Redox Signal 2012 16 (11):1183-1194. PubMed PMID: 22229461

Press: Journal's cover image
 FAPESP Agency press release
            

• Vogel, C., Silva, G.M., and Marcotte, E.M. Protein expression regulation under oxidative stress. Mol Cell Proteomics 2011 10(12):M111.009217. PubMed PMID: 21933953
• Silva, G.M., Netto, L.E., Discola, K.F., Piassa-Filho, G.M., Pimenta, D.C., Barcena, J.A., and Demasi, M. Role of glutaredoxin 2 and cytosolic thioredoxins in cysteinyl-based redox modification of the 20S proteasome. FEBS J 2008 275: 2942-2955. PubMed PMID: 18435761

• Netto, L.E., de Oliveira, M.A., Monteiro, G., Demasi, A.P., Cussiol, J.R., Discola, K.F., Demasi, M., Silva, G.M., Alves, S.V., Faria, V.G., et al.. Reactive cysteine in proteins: protein folding, antioxidant defense, redox signaling and more. Comp Biochem Physiol C Toxicol Pharmacol 2007 146:180-193. PubMed PMID:17045551

• Discola, K.F., Oliveira, M.A., Silva, G.M., Barcena, J.A., Porras, P., Padilla, A., Netto, L.E., and Guimaraes, B.G. Crystallization and preliminary X-ray crystallographic studies of glutaredoxin 2 from Saccharomyces cerevisiae in different oxidation states. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005 61:445-447. PubMed PMID: 16511065

• Demasi, M., Silva, G.M., and Netto, L.E. 20 S proteasome from Saccharomyces cerevisiae is responsive to redox modifications and is S-glutathionylated. J Biol Chem 2003 278:679-685. PubMed PMID:12409293