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Marcus Bustamante  Smolka


EDUCATION
2003 - 2008 - Post-doc - Ludwig Institute for Cancer Research, San Diego, USA
1998 - 2002 - Ph.D. - Biochemistry and Molecular Biology - State University of Campinas, Brazil
1997 - 1998 - Master’s - Biochemistry - State University of Campinas, Brazil
1993 - 1996 - B. S. - Biological Sciences - State University of Campinas, Brazil

RESEARCH AND PROFESSIONAL POSITIONS
2014 - present - Associate professor Weill Institute / Dept. of Molecular Biology and Genetics, Cornell University, USA
2016 - present - Director of graduate studies - Field of Biochemistry, Molecular and Cell Biology, Cornell University, USA
2008 - 2014 - Assistant professor - Weill Institute / Dept. of Molecular Biology and Genetics, Cornell University, USA
2003 - 2008 - Postdoctoral fellow - PI: Dr. Huilin Zhou Ludwig - Institute for Cancer Research, San Diego, USA
2000 - 2001 - Graduate fellow - PI: Dr. Ruedi Aebersold - Institute for Systems Biology, Seattle, USA
1998 - 2002 - Graduate research - PI: Dr. Jose Camilo Novello - Laboratory of Protein Chemistry, State University of Campinas, Brazil

PUBLICATIONS
1. Lanz M, Oberly S, Sanford E, Sharma S, Chabes A, Smolka MB. Separable Roles for Mec1/ATR in Genome Maintenance and DNA replication. Genes & Development (2018). PMID: 29899143.
2. Kim D, Liu Y, Oberly S, Freire R, Smolka MB. ATR-mediated Proteome Remodeling is a Major Determinant of Homologous Recombination Capacity in Cancer Cells. Nucleic Acids Res. (2018). PMID: 30010936.
3. Bastos de Oliveira FM, Kim D, Lanz M, Smolka MB. Quantitative Analysis of DNA Damage Signaling Responses to Chemical and Genetic Perturbations. Methods Molecular Biology (2018) 1672:645-660. PMID: 29043653.
4. Liu Y, Cussiol JR, Dibitetto D, Sims J, Twayana S, Weiss RS, Freire R, Marini F, Pellicioli A, Smolka MB. TOPBP1/Dpb11 Plays a Conserved Role in Homologous Recombination DNA Repair Through the Coordinated Recruitment of 53BP1/Rad9. J. Cell Biology (2017) Mar 6;216(3):623-639. PMID: 28228534.
5. Cabrera E, Hernández-Pérez S, Koundrioukoff S, Debatisse M, Kim D, Smolka MB, Freire R, Gillespie DA. PERK inhibits DNA replication during the Unfolded Protein Response via Claspin and Chk1. Oncogene. (2017) PMID: 27375025
6. Bai G, Smolka MB, Schimenti JC. Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation. PLoS Genet. (2016) 12(1):e1005787. PMID: 26765334
7. Sullivan PM, Zhou X, Robins AM, Paushter DH, Kim D, Smolka MB, Hu F. The ALS/FTLD associated protein C9orf72 associates with SMCR8 and WDR41 to regulate the autophagy-lysosome pathway. Acta Neuropathol Commun. (2016) 18;4(1):51. PMID: 27193190
8. 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 breaks. Nucleic Acids Res. (2016) 44(2):669-82. PMID: 26490958. PMCID: PMC4737138.
9. Cussiol JR, Jablonowski CM, Yimit A, Brown GW, Smolka MB. Dampening DNA damage checkpoint signalling via coordinated BRCT domain interactions. EMBO J. (2015) PMID: 25896509
10. Bastos de Oliveira FM, Kim D, Cussiol JR, Das J, Jeong MC, Doerfler L, Schmidt KH, Yu H, Smolka MB. Phosphoproteomics Reveals Distinct Modes of Mec1/ATR Signaling during DNA Replication. Molecular Cell. (2015) Mar 19;57(6):1124-32. PMID: 25752575
11. 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) Sep 11. PMID: 26362319.
12. Zhou X, Sun L, Bastos de Oliveira F, Qi X, Brown WJ, Smolka MB, Sun Y, Hu F. Prosaposin facilitates sortilin-independent lysosomal trafficking of progranulin. J Cell Biol. (2015) Sep 14;210(6):991-1002. PMID: 26370502.
13. 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 J. (2015) Jun 25. pii: e201591190.
14. 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) 26(3):90-102.
15. 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 Genet. (2014) Dec 11;10(12):e1004819. PMID: 25502805
16. 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. PNAS (2014) Jul 22;111(29):10538-43. PMID: 25006264.
17. de Oliveira FM, Smolka MB. Identification of DNA damage checkpoint-dependent protein interactions in Saccharomyces cerevisiae using quantitative mass spectrometry. Methods Mol Biol (2014). 1156:251-63. PMID: 24791994.
18. Viswanatha R, Wayt J, Ohouo P, Smolka MB and Bretscher A. (2013) Interactome analysis reveals ezrin can adopt multiple conformational states. J Biol Chem 288(49):35437-51.
19. Ohouo P, Liu Y, Oliveira FM, Ma CW and Smolka MB. (2013) DNA Repair Scaffolds Dampen Checkpoint Signaling by Counteracting the Rad9 Adaptor. Nature 493(7430):120-4.
20. Scafoglio C, Smolka M, Zhou H, Perissi V and Rosenfeld MG. (2013) The co-repressor SMRT delays DNA damage-induced caspase activation by repressing pro apoptotic genes and modulating the dynamics of checkpoint kinase 2 activation. PLoS One. 8(5):e59986.
21. Viswanatha R, Ohouo PY, Smolka MB and Bretscher A. (2012) Local phosphocycling mediated by LOK/SLK restricts ezrin function to the apical aspect of epithelial cells. J Cell Biol. 199(6):969-84.
22. Bastos de Oliveira FM, Harris MR, Brazauskas P, de Bruin RA and Smolka MB. (2012) Linking DNA replication checkpoint to MBF cell-cycle transcription reveals a distinct class of G1/S genes. EMBO J. 31(7):1798-810.
23. Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR 3rd, Ideker T and Wittenberg C. (2012) DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO J. 31(7):1811-22.
24. MacGurn JA, Hsu PC, Smolka MB and Emr SD. (2011) TORC1 regulates endocytosis via Npr1-mediated Phosphoinhibition of a ubiquitin ligase adaptor. Cell 147(5):1104-17.
25. Ohouo P, Oliveira FM, Almeida BS and Smolka MB. (2010) DNA Damage Signaling Recruits the Rtt107-Slx4 Scaffolds via Dpb11 to Mediate Replication Stress Response. Molecular Cell 30;39(2):300-6.
26. Wagner MV, Smolka MB, de Bruin RA, Zhou H, Wittenberg C and Dowdy SF. (2009) Whi5 Regulation by Site Specific CDK-Phosphorylation in Saccharomyces cerevisiae. PLoS ONE 4(1):e4300. (NOTE: work done prior to my arrival at Cornell)
27. Payne SH, Yau M, Smolka MB, Tanner S, Zhou H and Bafna V. (2008) Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis. J Proteome Res. 7(8):3373-3381.
28. Pham P, Smolka MB, Calabrese P, Landolph A, Zhang K, Zhou H and Goodman MF. (2008) Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase. J Biol Chem 283(25):17428-39.
29. Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J and Zhou H. (2008) A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 7(7):1389-96.
30. Smolka MB, Albuquerque CP, Chen S and Zhou H. (2007) Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. PNAS 104(25):10364-9.
31. Chen S, Smolka MB and Zhou H. (2007) Mechanism of Dun1 activation by Rad53 phosphorylation in Saccharomyces cerevisiae. J Biol Chem 282(2):986-95.
32. Martins D, Astua-Monge G, Coletta-Filho HD, Winck FV, Baldasso PA, Oliveira BM, Marangoni S, Machado MA, Novello JC and Smolka MB. (2007) Absence of Classical Heat Shock Response in the Citrus Pathogen Xylella fastidiosa. Curr Microbiol 54(2):119-23.
33. Smolka MB, Chen S, Maddox PS, Enserink JM, Albuquerque CP, Wei XX, Schmidt KH, Desai A, Kolodner RD and Zhou H. (2006) An FHA Domain-Mediated Protein Interaction Network of Rad53 Reveals its Role in Polarized Cell Growth. J Cell Biol. 175(5):743-53.
34. Enserink JM, Smolka MB, Zhou H and Kolodner RD (2006) Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. J Cell Biol. 175(5):729-41.
35. Smolka MB, Albuquerque CP, Chen SH, Schmidt KH, Wei XX, Kolodner RD and Zhou H (2005). Dynamic Changes in Protein-Protein Interaction and Protein Phosphorylation Probed with Amine-reactive Isotope Tag. Mol Cell Proteomics 4(9):1358-69.
36. Macedo ML, Freire Md, Martins LT, Martinez DS, Gomes VM, Smolka MB, Toyama MH, Marangoni S and Coelho LC. (2004) Novel protein from Labramia bojeri A. DC. seeds homologue to Kunitz-type trypsin inhibitor with lectin-like properties. J Agric Food Chem 52(25):7548-54.
37. Smolka MB, Martins-de-Souza D, Winck FV, Santoro CE, Castellari RR, Ferrari F, Brum IJ, Galembeck E, Della Coletta Filho H, Machado MA, Marangoni S and Novello JC. (2003) Proteome Analysis of the Plant Pathogen Xylella fastidiosa Reveals Major Cellular and Extracellular Proteins and a Peculiar Codon Bias Distribution. Proteomics 3:224-37.
38. Smolka M, Zhou H and Aebersold R. (2002) Quantitative Protein Profiling Using Two-dimensional Gel Electrophoresis, Isotope-coded Affinity Tag Labeling, and Mass Spectrometry. Mol Cell Proteomics 1:19-29.
39. Smolka MB, Zhou H, Purkayastha S and Aebersold R. (2001) Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal Biochem 297:25-31.
40. Freire MG, Machado OL, Smolka MB, Marangoni S, Novello JC and Macedo ML. (2001) Isolation and characterization of isolectins from Talisia esculenta seeds. J Protein Chem 20:495-500.
41. Smolka MB, Zoppi CC, Alves AA, Silveira LR, Marangoni S, Pereira-Da-Silva L, Novello JC and Macedo DV. (2000) HSP72 as a complementary protection against oxidative stress induced by exercise in the soleus muscle of rats. Am J Physiol Regul Integr Comp Physiol 279(5):R1539-45.
42. Smolka MB, Marangoni S, Oliveira B and Novello JC. (1998) Purification and partial characterization of a thrombin-like enzyme, balterobin, from the venom of Bothrops alternatus. Toxicon 36(7):1059-63.

Invited reviews and commentaries:
43. Cussiol JR, Dibitetto D, Pellicioli A, Smolka MB. Slx4 scaffolding in homologous recombination and checkpoint control: lessons from yeast. Chromosoma. (2017). PMID: 27165041. NIHMS ID: NIHMS792796.
44. Liu Y, Smolka MB. TOPBP1 takes RADical command in recombinational DNA repair. J Cell Biol. (2016) Feb 1;212(3):263-6. PMID: 26811424. PMCID:PMC4748579
45. Ohouo PY and Smolka MB. The many roads to checkpoint activation. (2012) Cell Cycle 11(24).
46. Smolka MB, Bastos de Oliveira FM, Harris MR and de Bruin RA. (2012) The Checkpoint Transcriptional Response: Make Sure to Turn it Off Once You are Satisfied. Cell Cycle 11(17):3166-74.
47. Ohouo PY and Smolka MB. (2011) A touching moment for Smc5/6: From ssDNA binding to repair. Cell Cycle 10(8).
48. Smolka MB. (2010) Fine-tuning the DNA damage response: protein phosphatase 2A checks on CHK2. Cell Cycle 9(5):862-3.

PATENTS
1. U.S. Provisional Patent Application Serial No. 62/679,340, filed June 1, 2018 for “USE OF CHRONIC TREATMENT WITH ATR OR CHK1 INHIBITORS TO SENSITIZE CANCER CELLS TO PARP INHIBITORS OR GENOTOXINS”. Cornell Reference No.: 8183-01-US
2. US & Foreign patent (United States Patent 7045296) for entitled: "Process for Analyzing Protein Samples"

SEMINARS (LAST 5 YEARS)
1. IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation. “Deconstructing the DNA Damage Signaling Network” – Milan, Italy. June, 2018.
2. Friedrich Miescher Institute. “Deconstructing the DNA Damage Signaling Network” – Basel, Switzerland. May, 2018.
3. Rutgers Cancer Institute of New Jersey - Department of Genetics and Development: “Deconstructing the DNA Damage Signaling Network” – New York, NY. February, 2018.
4. Columbia - Department of Genetics and Development: “Deconstructing the DNA Damage Signaling Network” – New York, NY. January, 2018.
5. Duke University School of Medicine - Department of Pharmacology and Cancer Biology: “Deconstructing the DNA Damage Signaling Network” – Durham, NC. November, 2017.
6. NYU School of Medicine - Biochemistry and Molecular Pharmacology Seminar Series: “Deconstructing the DNA Damage Signaling Network” – New York, NY. October, 2017.
7. Cold Spring Harbor Eukaryotic DNA Replication & Genome Maintenance meeting: “Positive and Negative Control of Homologous Recombination via TOPBP1 Shapes Genome Stability in S-phase”. Cold spring Harbor, NY. September, 2017.
8. FASEB Genetic Recombination & Genome Rearrangements: “Positive and Negative Control of Homologous Recombination via TOPBP1 Shapes Genome Stability in S-phase”. Steamboat Springs, Colorado. July, 2017.
9. University of Pennsylvania - UPENN, Department of Cancer Biology - Perelman School of Medicine: “Deconstructing the DNA Damage Signaling Network” – Philadelphia, USA. January, 2017.
10. Memorial Sloan Kettering Cancer Center: Department of Molecular Biology: “Deconstructing the DNA Damage Signaling Network” – New York, USA. October, 2016.
11. Keynote speaker: 6th Conference of the Brazilian Mass Spectrometry Society / 1st Ibero American Conference on Mass Spectrometry: “Proteomics of Signaling Networks". Rio de Janeiro, Brazil. December, 2016.
12. University of Toronto: “Probing kinase action in Genome Maintenance pathways” – Toronto, Canada. September, 2016.
13. Cold Spring Harbor Laboratory Proteomics Course: “Investigating Signaling Networks with Quantitative Proteomics” – Cold Spring Harbor, NY. June, 2016.
14. Wright State University: “Probing kinase action in DNA repair and cancer pathways” – Dayton, OH, USA. March, 2016.
15. New Horizons in Medicinal Chemistry of Protein Kinases Workshop: “Probing kinase action and inhibition in vivo” – Sao Paulo, Brazil. March, 2016.
16. State University of Sao Paulo: “Probing kinase action in DNA repair and cancer pathways” – Sao Paulo, Brazil. March, 2016.
17. UNICAMP: “Probing kinase action in DNA repair and cancer pathways” – Campinas, Brazil. March, 2016.
18. Pennsylvania State University College of Medicine: “Phosphorylation Networks and Genome Maintenance” – Hershey, PA. October, 2015.
19. Centro de Biologia Molecular Severo Ochoa: “Genome Integrity: Rethinking Checkpoints” – Spain. July, 2015.
20. Hospital Universitario de Canarias: “Genome Integrity: Rethinking Checkpoints” – Spain. July, 2015.
21. University of South Florida - Department of Cell Biology, Microbiology and Molecular Biology: “Genome Integrity: Rethinking Checkpoints” – Tampa, FL. November, 2014.
22. Gordon Research Conference on Genomic Instability: “Non-canonical Modes of Mec1/ATR Action during DNA replication” - Hong Kong. July, 2014.
23. Stanford University - “Uncovering the DNA Damage Signaling Network: Proteomics Points the Way” – Palo Alto, CA. June, 2014.
24. NYU School of Medicine - Biochemistry and Molecular Pharmacology Seminar Series: “The DNA Damage Signaling Network: From Proteomics to Mechanisms of Tolerance to Replication Stress” – New York, NY. December, 2013.
25. McMaster University: “The DNA Damage Signaling Network: From Proteomics to Mechanisms of Tolerance to Replication Stress” – New York, NY. December, 2013.
26. Gordon Research Conference on Posttranslational Modification Networks: “The DNA Damage Signaling Network” - Hong Kong. July, 2013.
27. Cold Spring Harbor Laboratory Proteomics Course: “Investigating Signaling Networks with Quantitative Proteomics” - Cold Spring Harbor, NY. July, 2013.
28. Distinguished Scientist Lecture Series - IRIC - Université de Montréal: “Coordination of Replication Stress Responses via Checkpoint Kinases” - Canada. May, 2013.
29. McGill University: “The DNA Damage Signaling Network: From Proteomics to Mechanisms of Tolerance to Replication Stress” - Canada. May, 2013.
30. Workshop: Advanced Topics in Genomics and Cell Biology: “The DNA Damage Signaling Network: From Phosphoproteomics to Cancer” - Unicamp, Brazil. May, 2013

HONORS AND PROFESSIONAL SERVICE
1995 - 1997 - Scholarship Scientific Initiation: CNPq, Brazil
1997 - 1999 - Fellowship Master's: CNPq, Brazil
1999 - 2002 - Fellowship PhD: FAPESP, Brazil
2008 - Member, American Society for Biochemistry and Molecular Biology
2010 - Member, American Society of Mass Spectrometry
2010 - Associate Editor, Scientific Reports – Nature NPG
2010 - Associate Editor, G3 – Genes, Genomes and Genetics
2011 - 2015 - Research Scholar Award - American Cancer Society - USA
2013 - Peer Review Committee on DNA Mechanisms in Cancer - American Cancer Society
2015 - Member, Center for Reproductive Genomics - Cornell
2015 - Guest Editor, Plos Genetics
2016 - Director of Graduate Studies – Field of Biochemistry, Molecular and Cell Biology
2016 - Reviewer for NIH study section: Molecular Genetics A (MGA), Ad hoc
2017 - Guest Editor, eLife
2017 - Reviewer for Special Emphasis Panel ZCA1 TCRB-T (J3) S – NCI/NIH, Ad hoc
2018 - Reviewer for NIH study section: Cellular Signaling and Regul. Systems (CSRS), Ad hoc
2018 - Reviewer for NASA Space Biology Cellular & Molecular Biology Panel

RESEARCH SUPPORT
Active:

RO1 GM 097272A (PI: Smolka)
National Institute of Health (NIGMS)
Period: 09/01/2011 – 04/30/2021
Title: "CELLULAR RESPONSES TO REPLICATION STRESS"
Role: Principal investigator
Total cost: $ 1,332,000

R01 GM 123018 (PI: Smolka)
National Institute of Health (NIGMS)
Period: 01/01/2018 – 12/31/2021
Title: “MECHANISMS OF HETEROCHROMATIN REPLICATION”
Role: Principal investigator
Total cost: $ 1,204,000

R01 HD 095296-01 (Co-PIs: Smolka/Weiss)
National Institute of Health (NICHD)
04/01/2018 – 03/31/2023
Title: “Coordination of ATR Signaling for Genetic Quality Control, Silencing, and DNA Repair During Meiosis”
Role: Co-PI
Total cost: $ 2,809,000

R01 NS 088448 (PI: Hu)
National Institute of Health (NIH)
Period: 08/1/2014 - 07/31/2019
Title: "FUNCTION OF TMEM106B IN NEURODEGENERATION"
Role: Co-investigator
Total cost: $ 1,757,666

R01 GM 116964 (PI: Mao)
National Institute of Health (NIGMS)
Period: 09/01/2016 – 08/31/2020
Title: "THE MECHANISM OF A NOVEL FAMILY OF BACTERIAL UBIQUITIN E3 LIGASES IMPORTANT FOR PHAGOSOME REMODELING"
Role: Co-investigator
Total cost: $ 1,200,154

R01 GM 039066 (PI: Bretscher)
National Institute of Health (NIGMS)
Period: 09/01/2015 – 08/31/2019
Title: "MICROFILAMENTS IN THE YEAST SACCHAROMYCES CEREVISIAE"
Role: Collaborator
Total cost: $ 1,521,133

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