I am a rock climber and a former PhD student at the Systems Engineering in Life Sciences in INESC-ID (Lisbon, Portugal) and at the Erable team in INRIA (Lyon, France). I am interested in applying modeling and machine learning techniques to biological problems. My research mostly focus on Systems Biology, with emphasis in engineering applications to the life sciences.

The core of my research work was to create new models that use known biological networks to better predict the outcome of cancer patients.

I am also driven to create collaborative solutions to facilitate communications between team members and across areas. BGFit is a great example and I look forward to continue my research and create real-world applications that are used by people and are an asset when solving problems.

I was awarded a PhD Grant by FCT to research machine learning techniques in Cancer, Sepsis and HIV at University of Lisbon and the Université Claude Bernard - Lyon 1 - (SFRH/BD/97415/2013).

"To give anything less than your best is to sacrifice the gift", Steve Prefontaine

Relevant software contributions

glmSparseNet: Network and sparse regression modelling package for R (avaible at BioConductor)
loose.rock: Bioinformatics R Package (available at CRAN)
Yakyak: Hangouts messaging app
BGFit: Data modeling collaborative web app
KimoSyS: Systems Biology collaborative web app

Education

1. 2014-2020
3. Técnico Lisboa, University of Lisbon
4. PhD in Information Systems and Computer Enginnering
5. Title: Adaptive Clinical Decision Support System for Personalized Medicine
6. Supervisor: Prof.ª Susana Vinga
7. Co-supervisor: Prof.ª Marie-France Sagot, Prof. Arlindo Oliveira
1. Graduated in 2009
3. Técnico Lisboa, University of Lisbon
4. Master in Information Systems and Computer Engineering
5. Title: Content-based image retrieval systems and high-dimensional
6. Supervisor: Andreas Wichert
1. Graduated in 2008
3. Técnico Lisboa, University of Lisbon
4. Bachelor in Information Systems and Computer Engineering

Projects

SOUND- Sep. 2015 to Aug. 2018 -Create the bioinformatic tools for statistically informed use of personal genomic and other ‘omic data in medicine, including cancers and rare metabolic diseases. (European Union H2020 - 633974)
BacHBerry- Nov. 2013 to Oct. 2016 -BACterial Hosts for production of Bioactive phenolics from bERRY fruits (European Union FP7- 613793)
CancerSys- Apr. 2013 - Mar. 2014 -Multiscale modeling for personalized therapy of bone metastasis (EXPL/EMS-SIS/1954/2013)
Intelegen- Jun. 2013 - May 2015 -Pharmacokinetic/Pharmacogenetic modulation of HIV infection therapy by bayesian and artificial intelligence methods (PTDC/DTP-FTO/1747/2012)
PneumoSys- Apr. 2010 - Sep. 2013 -A systems biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease (PTDC/SAU-MII/100964/2008)

Publications

Journal

1. Veríssimo, André;
2. Oliveira, Arlindo L.;
3. Sagot, Marie-France;
4. Vinga, Susana;
5. "DegreeCox – a network-based regularization method for survival analysis".
6. (2016)
7. BMC Bioinformatics.
8. Volume 17
9. Issue S16
10. page 109–121
11. 10.1186/s12859-016-1310-4
1. Veríssimo, André;
2. Paixão, Laura;
3. Neves, Ana R.;
4. Vinga, Susana;
5. "BGFit: management and automated fitting of biological growth curves".
6. (2013)
7. BMC Bioinformatics.
8. Volume 14
9. Issue 1
10. page 283
11. 10.1186/1471-2105-14-283
1. Costa, Rafael S.;
2. Veríssimo, André;
3. Vinga, Susana;
4. "KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems".
5. (2014)
6. BMC Systems Biology.
7. Volume 8
8. Issue 1
9. page 85
10. 10.1186/s12918-014-0085-3
1. Paixão, Laura;
2. Oliveira, Joana;
3. Veríssimo, André;
4. Vinga, Susana;
5. Lourenço, Eva C.;
6. Ventura, M. Rita;
7. Kjos, Morten;
8. Veening, Jan-Willem;
9. Fernandes, Vitor E.;
10. Andrew, Peter W.;
11. Yesilkaya, Hasan;
12. Neves, Ana R.;
13. "Host Glycan Sugar-Specific Pathways in Streptococcus pneumonia: Galactose as a Key Sugar in Colonisation and Infection".
14. (2015)
15. 10.1371/journal.pone.0127483
1. "BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits".
2. (2018)
3. Phytochemistry Reviews.
4. Volume 17
5. Issue 2
6. page 291-326
7. 10.1007/s11101-017-9532-2

Conference

1. Veríssimo, André;
2. Carrasquinha, Eunice;
3. Lopes, Marta B.;
4. Vinga, Susana;
5. "Random sample consensus for the robust identification of outliers in cancer data".
6. (2019)
7. CIBB - International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics.
8. September 4 - 6, 2019.
9. Bergamo, Italy.
1. Veríssimo, André;
2. Carrasquinha, Eunice;
3. Lopes, Marta B.;
4. Oliveira, Arlindo L.;
5. Sagot, Marie-France;
6. Vinga, Susana;
7. "Network-based sparse modeling of breast invasive carcinoma survival data, Signal Processing with Adaptive Sparse Structured Representations".
8. (2017)
9. SPARS - Signal Processing with Adaptive Sparse Structured Representations.
10. June 5 - 8, 2017.
11. Lisbon, Portugal.

Poster

1. Veríssimo, André;
2. Lopes, Marta B.;
3. Carrasquinha, Eunice;
4. Sagot, Marie-France;
5. Oliveira, Arlindo L.;
6. Vinga, Susana;
7. "Random Sample Consensus (RANSAC) for the robust identification of outliers in transcriptomic data".
8. (2017)
9. Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB 2017).
10. July 21-25, 2017.
11. Prague, Czech Republic.
1. Veríssimo, André;
2. Carrasquinha, Eunice;
3. Lopes, Marta B.;
4. Oliveira, Arlindo L.;
5. Sagot, Marie-France;
6. Vinga, Susana;
7. "Regularized survival analysis and feature clustering of TCGA breast cancer data".
8. (2017)
9. From Single- to Multiomics: Applications and Challenges in Data Integration.
10. November 12-14, 2017.
11. Heidelberg, Germany.
1. Veríssimo, André;
2. Carrasquinha, Eunice;
3. Lopes, Marta B.;
4. Sagot, Marie-France;
5. Oliveira, Arlindo L.;
6. Vinga, Susana;
7. "Network-based regularized optimization for cancer survival data analysis".
8. (2017)
9. Ascona Workshop - Statistical Challenges in Single-Cell Biology.
10. April 30 - May 5 2017.
11. ETH Zurich, Switzerland.

Professional Experience

1. Oct. 2012 - Sep. 2013
2. Vice-President at GASTagus
4. Coordinator at GASTagus responsible for the internal collaborative platforms, communication and financial management.
  
  GASTagus is a non-profit organization that manages over 130 volunteers during all-year round, preparing them for a one month volunteer project in Angola, Cabo Verde, São Tomé e Príncipe, Mozambique and Brasil.
1. Dec. 2011 - Nov. 2012
2. Research Fellow at INESC-ID
4. Researcher at INESC-ID in Knowledge Discovery and Bioinformatics (KDBIO) group. In this position we developed BGFit as a web application to manage timeseries data sets and uses matlab in the backend to model the data.
1. Sep. 2010 - Dec. 2011
2. Consultant at Deloitte
4. Consultant at Deloitte’s Consulting division, in Manufacturing, Consumer Business, Energy and Resources industries on the Enterprise Applications service line.
  
  Professional experience in the logistics and operations processes. Those projects, took place mostly in manufacturing and consumer business organizations, across multiple business sectors and countries, such as, Portugal and Angola.
  
  Comprehending several business areas, particularly in Production Planning, Materials Management and Plant Maintenance, as well as in the design and implementation of solutions for Enterprise Resource Planning (ERP)
1. Feb. 2010 - Sep. 2010
2. Junior Consultant at Karma
4. Junior consultant at Karma consulting in the public sector service line.
  
  Professional experience in logistics and information systems design working with Portugal's public sector entities as a software engineer specialized in Java development.

This website was generated using averissimo/website (layout inspired by Adrian Dalca's page).

André Veríssimo

PhD Student