Publications

2016

Cussiol JR, Dibitetto D, Pellicioli A, Smolka MB. Slx4 scaffolding in homologous recombination and checkpoint control: lessons from yeast. Chromosoma. 2016 May 10. [Epub ahead of print] Review.

Dibitetto D, Ferrari M, Rawal CC, Balint A, Kim T, Zhang Z, Smolka MB, Brown GW, Marini F, Pellicioli A. Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaksNucleic Acids Res. 2016 Jan 29;44(2):669-82. doi: 10.1093/nar/gkv1080. Epub 2015 Oct 20.

Liu Y and Smolka MB. TOPBP1 takes RADical command in recombinational DNA repair. J Cell Biol. 2016 Jan 25;212(3):263-6. doi: 10.1083/jcb.201601028.

Bai G, Smolka MB, Schimenti JC. Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation. PLOS Genetics. 2016 Jan 14;12(1):e1005787. doi: 10.1371/journal.pgen.1005787.

2015

Jablonowski CM, Cussiol JR, Oberly S, Yimit A, Balint A, Kim T, Zhang Z, Brown GW, Smolka MB. Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase. Genetics. 2015 Nov;201(3):937-49. doi: 10.1534/genetics.115.181479. Epub 2015 Sep 11.

Silva JA, Pompeu DG, Smolka MB, Gozzo FC, Comar M Jr, Eberlin MN, Granjeiro PA, Marangoni S. Primary Structure of a Trypsin Inhibitor (Copaifera langsdorffii Trypsin Inhibitor-1) Obtained from C. langsdorffii Seeds. J Biomol Tech. 2015 Sep;26(3): 90–102. doi:  10.7171/jbt.15-2603-002

Zhou X, Sun L, Oliveira F, Qi X, Brown WJ, Smolka M, Sun Y, Hu F. Prosaposin facilitates sortilin independent lysosomal targeting of progranulin. J Cell Biol. 2015 Sep 14;210(6):991-1002. doi: 10.1083/jcb.201502029

Bastos de Oliveira FM, Kim DS, Cussiol JR, Das J, Jeong MC, Doerfler L, Schmidt KH, Yu H, Smolka MB. Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replicationMol Cell. 19 March 2015;57(6): 1-9.

Cussiol JR, Jablonowski CM, Yimit A, Brown GW, Smolka MB. Dampening DNA damage checkpoint signalling via coordinated BRCT domain interactions. EMBO Journal. 15 April 2015;34(8): 975-1142.

Balint A, Kim T, Gallo D, Cussiol JR, Bastos de Oliveira FM, Yimit A, Ou J, Nakato R, Gurevich A, Shirahige K, Smolka MB, Zhang Z, Brown GW. Assembly of Slx4 signaling complexes behind DNA replication forks. EMBO Journal. 13 August 2015;34(16): 2182-97. doi: 10.15252/embj.201591190

2014

Wei X, Das J, Fragoza R, Liang J, Bastos de Oliveira FM, Lee HR, Wang X, Mort M, Stenson PD, Cooper DN, Lipkin SM, Smolka MB, Yu H. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PLoS Genetics. 2014 Dec 11;10(12):e1004819. doi: 10.1371/journal.pgen.1004819. eCollection 2014.

Hsu F, Luo X, Qiu J, Teng YB, Jin J, Smolka MB, Luo ZQ, Mao Y. The Legionella effector SidC defines a unique family of ubiquitin ligases important for bacterial phagosomal remodeling. Proc Natl Acad Sci U S A. 2014 Jul 8. pii: 201402605.

de Oliveira FM, Smolka MB. Identification of DNA damage checkpoint-dependent protein interactions in Saccharomyces cerevisiae using quantitative mass spectrometryMethods Mol Biol. Volume 1156, 2014, pp 251-263.

2013
Viswanatha R, Wayt J, Ohouo PY, Smolka MB, Bretscher A. Interactome analysis reveals ezrin can adopt multiple conformational statesJ Biol Chem. December 2013; 288(49):35437-5.

Scafoglio C, Smolka M, Zhou H, Perissi V, Rosenfeld MG. The Co-Repressor SMRT Delays DNA Damage-Induced Caspase Activation by Repressing Pro-Apoptotic Genes and Modulating the Dynamics of Checkpoint Kinase 2 ActivationPLoS One. May 2013; 8(5):e59986.

Ohouo PY, Bastos de Oliveira FM, Liu Y, Ma CJ, Smolka MB. DNA-repair scaffolds dampen checkpoint signalling by counteracting the adaptor Rad9. Nature. January 2013; 493(7430):120-4.

2012
Ohouo PY, Smolka MB. The many roads to checkpoint activation. Cell Cycle. December 2012. 11(24). [Epub ahead of print]

Viswanatha R, Ohouo PY, Smolka MB, Bretscher A. Local phosphocycling mediated by LOK/SLK restricts ezrin function to the apical aspect of epithelial cells. J Cell Biol. December 2012. 199(6):969-84.  

Smolka MB, Bastos de Oliveira FM, Harris MR, de Bruin RA. The checkpoint transcriptional response: make sure to turn it off once you are satisfied. Cell Cycle. September 2012. 11(17):3166-74.

Oliveira FB, Harris MR, Brazasuskas P, de Bruin RAM, Smolka MB. Linking DNA checkpoint to MBF cell-cycle transcription reveals a distinct class of G1/S genes. EMBO Journal. February 2012.

Travesa A, Kuo D, de Bruin RAM, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR, Ideker T, Wittenberg C.DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1EMBO Journal. February 2012.

2011
Ohouo, PY, Smolka, MB. A touching moment for Smc5/6: from ssDNA binding to repair. Cell Cycle. February 2011. 10(8): 1190-1191. Comment on Roy MA, et al. 

Macgurn JA, Hsu PC, Smolka MB, Emr SD. TORC1 regulates endocytosis via Npr1-mediated phosphoinhibition of a ubiquitin ligase adapter. Cell. November 23, 2011; 147(5):1104-17.

2010
Ohouo, P., Bastos de Oliveira, F. Almeida, B. and Smolka, M. DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response. Molecular Cell. July 2010; 39(2): 300-306.

Smolka, M. Fine-tuning the DNA damage response: protein phosphatase 2A checks on CHK2. Comment on Freeman AK, et al. Cell Cycle 2010; 9:736–47. Cell Cycle. March 2010, 9(4): 736-747.

2009
Wagner, M.V., Smolka, M.B., de Bruin, R.A., Zhou, H., Wittenberg, C., Dowdy, S.F. Whi5 regulation by site specific CDK-phosphorylation in Saccharomyces cerevisiae. PLoS ONE. 2009; 4(1): e4300. Jan. 2009.

2008
Payne, S. H., Yau, M., Smolka, M. B., Tanner, S., Zhou, H. and Bafna, V. Phosphorylation specific MS/MS scoring for rapid and efficient phosphoproteome analysis. J. Proteome Res. 2008, 7(8):3373-3381.

Pham, P., Smolka M. B., Calabrese, P., Landolph, A., Zhang, K., Zhou, H. and Goodman, M. F. Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase. J Biol Chem. 2008.

Albuquerque, C. P.*, Smolka, M. B.*, Eng, J. and Zhou, H. A Multidimensional Chromatography Technology for In-depth Phosphoproteome AnalysisMol Cell Proteomics. 2008, 7(7):1389-96. *These authors contributed equally to this work.

2007
Smolka, M. B., Albuquerque, C. P., Chen, S. and Zhou, H. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. PNAS. 2007, 104(25):10364-9.

Chen, S., Smolka, M. B. and H. Zhou. Mechanism of Dun1 activation by Rad53 phosphorylation in Saccharomyces cerevisiae. J Biol Chem.2007, 282(2):986-95.

Martins, D., Astua-Monge, G., Coletta-Filho, H. D., Winck, F. V., Baldasso, P. A., Oliveira, B. M., Marangoni, S., Machado, M. A., Novello, J. C. and Smolka, M. B. Absence of Classical Heat Shock Response in the Citrus Pathogen Xylella fastidiosaCurr Microbiol. 2007, 54(2):119-23.

2006
Smolka, M. B., Chen, S., Maddox, P. S., Enserink, J. M., Albuquerque, C. P., Wei, X. X., Schmidt, K. H., Desai, A., Kolodner, R. D. and Zhou, H. An FHA Domain-Mediated Protein Interaction Network of Rad53 Reveals its Role in Polarized Cell Growth. J Cell Biol. 2006, 175(5):743-53.

Enserink, J. M., Smolka, M. B., Zhou, H. and Kolodner, R. D. Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiaeJ Cell Biol. 2006, 175(5):729-41.

Pereira D. R., Martins D., Winck FV, Smolka M. B., Nishimura N. F., Rabelo-Goncalves E. M., Hara N. H., Marangoni S., Zeitune J. M. and Novello J. C. Comparative analysis of two-dimensional electrophoresis maps (2-DE) of Helicobacter pylori from Brazilian patients with chronic gastritis and duodenal ulcer: a preliminary reportRev Inst Med Trop Sao Paulo. 2006, 48(3):175-7.

2005
Smolka, M. B., Albuquerque, C. P., Chen, S. H., Schmidt, K. H., Wei, X. X., Kolodner, R. D. and Zhou, H. Dynamic Changes in Protein-Protein Interaction and Protein Phosphorylation Probed with Amine-reactive Isotope TagMol Cell Proteomics 2005, 4(9):1358-69.

2004
Macedo, M. L, Freire, M. G., Martins, L. T., Martinez, D. S., Gomes, V. M., Smolka, M. B., Toyama, M. H., Marangoni, S. and Coelho, L. C. Novel protein from Labramia bojeri A. DC. seeds homologue to Kunitz-type trypsin inhibitor with lectin-like propertiesJ Agric Food Chem.2004, 52(25):7548-54.

2003
Smolka, M. B., Martins, D., Winck, F. V., Santoro, C. E., Castellari, R. R., Ferrari, F., Brum, I. J., Galembeck, E., Coletta-Filho, H. D., Machado, M. A., Marangoni, S. and Novello, J. C.. Proteome Analysis of the Plant Pathogen Xylella fastidiosa Reveals Major Cellular and Extracellular Proteins and a Peculiar Codon Bias DistributionProteomics. 2003, 3:224-37.

2002
Smolka, M., Zhou, H. and Aebersold, R. Quantitative Protein Profiling Using Two-dimensional Gel Electrophoresis, Isotope-coded Affinity Tag Labeling, and Mass SpectrometryMol Cell Proteomics. 2002, 1:19-29.

2001
Smolka, M. B., Zhou, H., Purkayastha, S. and Aebersold, R. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysisAnalytical Biochem. 2001, 297:25-31.

Freire, M. G., Machado, O. L., Smolka, M. B., Marangoni, S., Novello, J. C. and Macedo, M. L. Isolation and characterization of isolectins from Talisia esculenta seedsJ Protein Chem. 2001, 20:495-500.

2000
Smolka, M. B., Zoppi, C. C, Alves, A. A., Silveira, L. R., Marangoni, S., Pereira-Da-Silva, L., Novello, J. C. and Macedo, D. V. HSP72 as a complementary protection against oxidative stress induced by exercise in the soleus muscle of ratsAm J Physiology 2000, 279(5):R1539-45.

1998
Smolka, M. B., Marangoni, S., Oliveira, B. and Novello, J. C. Purification and partial characterization of a thrombin-like enzyme, balterobin, from the venom of Bothrops alternatusToxicon. 1998, 36(7):1059-63.

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