Curriculum Vitae

Brazilian Lattes CV
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Experience

• Research Scientist - Exact Sciences, Munich - Germany (Since September/2024).
  

• Post-doc in Computational Proteomics tailored toward Cross-linking Mass Spectrometry - The Liu Lab - Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin - Germany (2020-2024).
  Supervised by Dr. Fan Liu. We have developed Scout for identifying and quantifying cross-linked peptides using cleavable-reagents.

• Data Scientist in Proteomics - Winter lab - CeMM, Vienna - Austria (Jan/2020 - Aug/2020).

• Post-doc in Bioinformatics and Computational Biology - Mass Spectrometry for Biology Unit - Institut Pasteur - Paris, Paris - France (2016-2019). Supervised by Dr. Julia Chamot-Rooke. I've worked on an algorithm for top-down proteomics data analysis.

• Ph.D. in Bioinformatics and Computational Biology - Carlos Chagas Institute - Fundação Oswaldo Cruz (Fiocruz), Curitiba - Brazil. (2013-2016) "Algorithm for identifying cross-linked peptides analyzed by mass spectrometry."
  I've developed with my supervisors, as Ph.D Thesis, a new search engine for identifying and annotating cross-linked peptides, called SIM-XL.
  Visualize our video demonstration to check how SIM-XL works!

• M.Sc. in Computer Science and Systems Engineering - COPPE - Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro - Brazil. (2011-2013) "Computational Method for identifying peptides labeled with phenylisothiocyanate analyzed by liquid chromatography coupled to tandem mass spectrometry" I have developed with Dr. Paulo C. Carvalho as Master's Thesis, a search tool mass spectrometry - SIM (Spectrum Identification Machine), using PSM approach.

Honor & Awards

• Honorable mention in the "Prêmio Capes de Tese 2016" award as one of the top 3 PhD thesis in biological sciences in Brazil, October 2017
  
• One of the best projects presented in the academic journey - ICC/Fiocruz - 2014 & 2015
  
• The best poster in the Masters category - BrProt (Conference) - 2012
  

Reviewer Editor of Frontiers in Chemistry - Chemical Biology journal.

Reviewer of the following journals

• Bioinformatics
• Scientific Reports - Nature
• Journal of Proteomics
• Biochimica et Biophysica Acta - Proteins and Proteomics
• Letters in Drug Design & Discovery
• International Society for Computational Biology - ECCB
• Source Code for Biology and Medicine - BMC

Co-supervisor of MSc and PhD students

• Louise Ulrich Kurt, PhD in Biosciences and Biotechnology at ICC/Fiocruz - Brazil (concluded in 2024)
• Milan Avila Clasen, PhD in Biosciences and Biotechnology at ICC/Fiocruz - Brazil (concluded in 2023)
• Louise Ulrich Kurt, MSc in Biosciences and Biotechnology at ICC/Fiocruz - Brazil (concluded in 2020)
• Milan Avila Clasen, MSc in Biosciences and Biotechnology at ICC/Fiocruz - Brazil (concluded in 2019)

Supervisor of undergraduate students (BSc)

• André Ramos Fernandes da Silva, BSc in Computer Science at UFRJ - Brazil (concluded in 2014)
• Felipe Araújo Teixeira, BSc in Computer Science at UFRJ - Brazil (concluded in 2014)
• Lucas Henning Brisola, BSc in Biomedical informatics at UFPR - Brazil (concluded in 2014)
• Marcos Antonio Serpa de Barros, BSc in Computer Science at UFRJ - Brazil (concluded in 2014)
  

Invited lectures / seminars in computational proteomics

• XII Proteomics Workshop. (virtual). Campinas - SP, Brazil. October 30th to November 1st, 2023.
• International course on Proteome Analysis by Mass Spectrometry – Institut Pasteur de Montevideo – Uruguay. March 21^st to 30^th, 2022. (Total: 54h)
• Top-down Proteomics course at the 7^th Brazilian Conference on Mass Spectrometry – Rio de Janeiro, Brazil. December 7^th, 2018 (Total: 9h)
• International course on Proteome Analysis by Mass Spectrometry – Institut Pasteur de Montevideo – Uruguay. October 15^th to 23^rd, 2018. (Total: 54h)
• Séminaire – Journées Departamentales – DBSC: “Automatic Selection of discriminative top-down mass spectra with DiagnoTop” – Institut Pasteur, Paris – France. December 12^th and 13^th, 2017.
• Séminaire DBSC: “How to identify and annotate cross-linked peptides analyzed by mass spectrometry?” – Institut Pasteur, Paris – France. February 14^th, 2017.
• International course on Proteome Analysis by Mass Spectrometry – Institut Pasteur de Montevideo – Uruguay. November 28^th to December 2^nd, 2016. (Total: 35h)
• VII Proteomics Workshop. Campinas – SP, Brazil. November 10^th and 11^th, 2016. (Total: 15h)
• VI BrMass & 1^st IbMS, course: Proteomics. Rio de Janeiro – Brazil. December 9^th, 2016. (Total: 8h)

Events organization

• Symposium in Proteomics at Fiocruz. Rio de Janeiro, RJ - Brazil. November 7^th, 2014 (Symposium)
  
• 1st Symposium Carlos Chagas Institute in Proteomics. Curitiba, PR - Brazil. July 5^th, 2013 (Symposium)
  

Participation in events

2012-2023

• 71^st American Society for Mass Spectrometry. Houston, USA. June 4^th to 8^th, 2023 - 71^st ASMS (Conference).
  
• Berlin PostDoc day 2022. Berlin, Germany. November 3^rd, 2022 - PostDoc Day 2022 (Symposium).
  
• 70^th American Society for Mass Spectrometry. Minneapolis, USA. June 5^th to 9^th, 2022 - 70^th ASMS (Conference).
  
• Proteome Analysis by Mass Spectrometry. Montevideo, Uruguay. March 21^st to 30^th, 2022 - International Course - IP Montevideo (Course).
  
• X Proteomics Workshop. (virtual). November 3^rd to 5^th, 2021 - Workshop LNBio (Symposium).
  
• Berlin PostDoc day 2021. Berlin, Germany. November 4^th, 2021 - PostDoc Day 2021 (Symposium).
  
• Berlin PostDoc day 2020. Berlin, Germany. November 13^th, 2020 - PostDoc Day 2020 (Symposium).
  
• 1^st European Top-down Proteomics Symposium. Paris, France. February 12^th to 14^th, 2019 - 1^st EuTDP (Symposium).
  
• 7^th BrMass. Rio de Janeiro, RJ. December 8^th to 12^th, 2018 - 7^th BrMass (Conference).
  
• Proteome Analysis by Mass Spectrometry. Montevideo, Uruguay. October 15^th to 23^rd, 2018 - International Course - IP Montevideo (Course).
  
• 66^th American Society for Mass Spectrometry. San Diego, USA. June 3^rd to 7^th, 2018 - 66^th ASMS (Conference)
  
• Departmental Days of the Department of Structural Biology and Chemistry - Institut Pasteur. Paris, France. December 12^th and 13^th, 2017 (Departamental Journey).
  
• São Paulo School of Advanced Science on Mass Spectrometry - based Proteomics - SPSAS-MS. Campinas, Brazil. August 28^th to September 6^th, 2017 - SPSAS-MS (Workshop)
  
• 65^th American Society for Mass Spectrometry. Indianapolis, USA. June 4^th to 8^th, 2017 - 65^th ASMS (Conference)
  
• VI BrMass & 1^st IbMS. Rio de Janeiro, RJ. December 10^th to 14^th - 6^th, 2016 - BrMass (Conference).
  
• Proteome Analysis by Mass Spectrometry. Montevideo, Uruguay. November 28^th to December 2^nd, 2016 - International Course - IP Montevideo (Course).
  
• VII Proteomics Workshop. Campinas, SP. November 8^th to 11^th, 2016 - Workshop LNBio (Symposium).
  
• 2nd Proteomics meeting of the Brazilian Proteomics Society. Buzios, RJ. December 7^th to 10^th - 2^nd, 2014 - BrProt (Conference)
  
• V BrMass. Campinas, SP. December 7^th to 11^th - 5^th, 2013 - BrMass (Conference).
  
• IV Proteomics Workshop. Campinas, SP. November 6^th and 7^th, 2013 - Workshop LNBio (Symposium).
  
• Advanced topics in Proteomics. Rio de Janeiro, RJ. From October, 29^th to November 1^st, 2013 (Symposium).
  
• 1st Symposium Carlos Chagas Institute in Proteomics. Curitiba, PR. July 5^th, 2013 (Symposium)
  
• São Paulo Advanced School on Bioorganic Chemistry. Araraquara, SP. July 1^st to 5^th, 2013 - ESPCA (Conference)
  
• Implementation and Perspectives of MS-Imaging in Rio de Janeiro, RJ. June 6^th and 7^th, 2013 - MSI 2013 - Rio (Symposium)
  
• 1^st National Meeting of Brazilian Proteomics Society. Rio de Janeiro, RJ. December 10^th, 11^th and 12^th, 2012 - BrProt (Conference)
  
• V Proteomics Forum of Rio de Janeiro. November 29^th and 30^th, 2012 (Conference)
  
• III Proteomics Workshop. Campinas, SP. November 8^th, 2012 - Workshop LNBio (Symposium).
  

Skills

• Operating Systems: Linux, MacOS and Windows
  
• Programming language: C, C#, C++, Java, Python, R, SQL, HTML, Javascript, XML
  
• Databases: MySQL, SQLite, Oracle