About Me

Although always open to new opportunities, the academic life fascinates me. Facing challenges every day, elaborating answers to find more questions, learning, teaching, collaborating. In especial, the quest to understand the molecular mechanisms of life guides my thoughts. My favorite approach to pursue this quest is to map the networks of reactions that underlie biological processes and try to simulate them on computers.

Outside the academy, I’m a passionate mountaineer. Being in touch with nature recharge my batteries and clean my mind. The route to the summit teaches me things that books can not, and when I reach there, I can see how big and small we are at the same time.

Paulo Burke on the Rocks
  • Name:

    Paulo E. P. Burke
  • Age:

    27 Years
  • Phone:

    +55 11 99773 1987
  • E-mail:

    pauloepburke@gmail.com
  • Address:

    São Carlos, São Paulo, Brazil
Download CV

Research Interests

My research currently focuses on the development of simulation methods for complex biochemical systems such as models of integrated cellular processes. I'm also interested in the modeling and analysis of biological networks, and network science in general.

Publications

2019

Interdisciplinary Relationships Between Biological and Physical Sciences

Burke, Paulo E. P.; Costa, Luciano da F. ; Interdisciplinary Relationships Between Biological and Physical Sciences. , arXiv, 2019.

arXiv:1905.03298

2017

Biological Networks Border Detection

Burke, Paulo E. P.; Comin, Cesar Henrique ; Nascimento, Filipi ; Costa, Luciano da F. . Biological Networks Border Detection. Integrative Biology, v. 9, p. 947-955, 2017.

DOI: 10.1039/c7ib00161d

2016

Whole-Cell Representation Using Complex Networks

Burke, Paulo E. P.; Campos, Claudia B. de L.; Quiles, Marcos G. . Whole-Cell Representation Using Complex Networks. Master's Dissertation, Federal University of São Paulo, 2016.

PDF

Toward community standards and software for whole-cell modeling

Waltemath, Dagmar; Karr, Jonathan; Bergmann, Frank; Chelliah, Vijayalakshmi; Hucka, Michael; Krantz, Marcus; Liebermeister, Wolfram; Mendes, Pedro; Myers, Chris; Pir, Pinar; Alaybeyoglu, Begum; Aranganathan, Naveen; Baghalian, Kambiz; Bittig, Arne; Burke, Paulo; Cantarelli, Matteo; et al. ; Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering (Print), v. PP, p. 1-1, 2016.

DOI: 10.1109/TBME.2016.2560762

A geographically-aware complex network approach for foot-and-mouth disease phylodynamics

Carvalho, Luiz M. F. ; Santos, Leonardo B. L. ; Burke, Paulo E. P. ; Quiles, Marcos ; Silveira, Waldemir de C. . A geographically-aware complex network approach for foot-and-mouth disease phylodynamics. 6th International Conference on Nonlinear Science and Complexity, 2016.

DOI: 10.20906/CPS/NSC2016-0047

2011

Modularity and Computational Performance of Genetic Algorithims

Burke, Paulo E. P.; Pereira, Alisson R. ; Santos, Denilson P. S. dos . Modularity and Computational Performance of Genetic Algorithms. Brazilian Conference on Dynamics, Control and Applications, p. 266, 2011.

DOI: 10.5540/dincon.2011.001.1.0068

Resume

Grants and
awards

Travel Fellowship Award

July 2019

Awarded by ISCB with the covering of traveling expenses to attend the Intelligent Systems for Molecular Biology and the European Conference on Computational Biology 2019.

Best Presentation Award

February 2019

Awarded with "Best Presentation Award" in the Graduate Program on Bioinformatics' Workshop 2019 held at USP, São Paulo, Brazil.

Whole-Cell Modeling Second Edition

December 2015

Selected to continue working on the Whole-Cell model started in the first edition in March of the same year at the University of Utah, Salt Lake City, USA.

Whole-Cell Modeling Summer School

March 2015

Granted with full expenses cover to participate on the implementation of a Whole-Cell model using Systems Biology standards such as SBML. Member of the team which performed the integration of the model's subsystems. The event was held at University of Rostock, Rostock, Germany.

Regional Programming Marathon Winner

June 2014

Member of the winning team of the regional phase of the SBPC Programming Marathon. Classified for the national contest.

Academic Experience

Ph.D. Student

March 2017 - Today

Currently, I’m a Ph.D. student at the University of São Paulo under the supervision of Professor Luciano da Fontoura Costa.

Master in Computer Science

August 2014 - December 2016

Degree achieved under the supervision of Professor Marcos G. Quiles and Prof. Claudia B. L. Campos. The dissertation is entitled "Whole-Cell Representation Using Complex Networks".

Bachelor in Science and Technology

March 2012 - June 2014

Three-year Interdisciplinary Bachelor at the Federal University of São Paulo concluded with one semester in advance. My final global score of 8.4/10 which made me the 4º student of 200 of my class. The interdisciplinary character of the course gave me good abilities in both physical and biological areas.

Scientific Internship on Complex Networks

October 2013 - February 2014

Worked on the development of a Complex Network Visualization Tool under the supervision of Professor Marcos G. Quiles at the Federal University of São Paulo.

Scientific Internship on Molecular Dynamics

September 2012 - September 2013

Computational screening of inhibitors for CRISPR using Molecular Dynamics under the supervision of Professor Martin Wurtelle at the Federal University of São Paulo.

Scientific Internship on Molecular Biology

May 2012 - September 2013

Heterogeneous protein expression and structural characterization of the CRISPR system from thermophilic organisms under the supervision of Professor Martin Wurtelle at the Federal University of São Paulo.

Scientific Internship on Orbital Dynamics

January 2012 - May 2012

Atmospheric re-entrance of debris simulation under the supervision of Marcelo Lopes at the National Institute of Space Research.

Computer Engineering

August 2010 - December 2011

Started Computer Engineering course at ETEP but changed for a better University with more opportunities in science.

Web Design

February 2007 - June 2010

Web Design technical course at ETEP.

Work Experience

Educational Designer

June 2010 - December 2011

Development of educational media for engineering courses at ETEP.

Graphical Designer

February-May 2010

Production of graphic content and web developer at Amprimart.