Alexandra M. Carvalho

Research interests | Publications | Software | Teaching | Short CV

Academic degrees

• Sandwich PhD in Computer Science
  PhD Thesis: Motif representation and discovery
  Supervised by Arlindo L. Oliveira and co-supervised by Marie-France Sagot
  Doutoramento em Engenharia Informática e Computadores
  Instituto Superior Técnico
  Finished in July 2011

• Master in Computer Science
  Master Thesis: Efficient Algorithms for Structured Motif Extraction in DNA Sequences
  Supervised by Arlindo L. Oliveira and co-supervised by Ana T. Freitas
  Mestrado em Engenharia Informática e Computadores
  Instituto Superior Técnico
  Finished in June 2004

• Five year degree in Applied Mathematics
  Diploma Thesis: Category Theory In COQ
  Supervised by Amílcar Sernadas
  Licenciatura em Matemática Aplicada e Computação
  Instituto Superior Técnico
  Finished in July 1998

Professional experience

• Academia
  • Instituto Superior Técnico
    Department of Electrical and Computer Engineering
    Assistant Professor, since July 2011
    Teaching Assistant, from June 2006 to July 2011
  • Instituto Superior Técnico
    Department of Mathematics
    Section of Computer Science
    Teaching Assistant, from September 1998 to February 1999
    Monitor, from September 1997 to August 1998


• Research
  • Instituto de Telecomunicações
    Researcher of PIA Group, since October 2011
  • Instituto de Engenharia de Sistemas e Computadores
    Researcher of KDBio Group, from September 2006 to October 2011
    Researcher of ALGOS group, from March 2003 to August 2006


• Software industry
  • Altitude Software
    Research and development, from May 2000 to August 2002
  • OBLOG Software
    Research and development, from March 1999 to May 2000

Teaching

Find my personal teaching webpage here.

Publications

Find my personal publications webpage here.

Indexed by:

• ISI - Researcher ID profile

• Google scholar citations

Talks

• 5th Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB'18), Invited speaker, Monte da Caparica, Lisboa, Portugal, September 7, 2018.

• 4th International Conference on Machine Learning, Optimization, and Data Science (LOD'18), Learning consistent tree-augmented dynamic Bayesian networks, Volterra, Tuscany, Italy, September 15, 2018.

• 31st Conference on Uncertainty in Artificial Intelligence (UAI'15), Polynomial-time algorithm for learning optimal tree-augmented dynamic Bayesian networks, Amsterdam, Netherlands, July 14, 2015.

• Logic and Computation Seminar, Complete MDL for Bayesian networks, IST, Lisboa, July 19, 2013

• KDBIO Seminar, Scoring functions for learning Bayesian networks, INESC-ID, Lisboa, April 23, 2009

• 11th Symposium on String Processing and Information Retrieval (SPIRE'04), Efficient extraction of structured motifs using box-links, Padova, Italy, October 8, 2004

• Genómica Funcional e Bioinformática, Extraction of structured motifs from DNA sequences, IST, Lisboa, March 24, 2004

• 19th ACM Symposium on Applied Computing (SAC'04), A parallel algorithm for the extraction of structured motifs, Nicosia, Cyprus, March 17, 2004

• Theory of Computation Seminar, A parallel algorithm for the extraction of structured motifs, IST, Lisboa, October 31, 2003

• ALGOS Reading Group, A parallel algorithm for the extraction of structured motifs, INESC-ID, Lisboa, October 17, 2003

• ALGOS Reading Group, Primes in P: an exposition of the AKS algorithm, INESC-ID, Lisboa, April 11, 2003

• Seminar of the Departamento de Informática, Adjunctions in COQ, Universidade do Minho, Braga, May 22, 1998

Grants and awards

• Highly accessed article by BioMed Central, for the paper GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge. Highly accessed articles are those that have been especially highly accessed, relative to their age, and the journal in which they were published.

• Sartorius award for Innovation in Microbiology/Biotechnology, at Micro-Biotec 2007, for the work that lead to the article YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae published in NAR, 2008 (with a number of co-authors, see publication list)

• PhD grant from FCT SFRH/BD/18660/2004, from October 2004 to June 2006

• Grant from BioGrid, FCT Project FEDER POSI/SRI/47778/2002, from September 2003 to September 2004

• Grant from PRODEP program 5/5.2/207/011/PRODEP/98, Diploma Thesis award

Participation in Cientific Projects

• MONET: Multi-omic networks in gliomas, FCT Project PTDC/CCI-BIO/4180/2020

• SmartGlauco: Smart Drug Delivery Device for Glaucoma Treatment, FCT Project PTDC/CTM-REF/2679/2020

• MATISSE: A machine learning-based forecasting system for shellfish safety, FCT Project DSAIPA/DS/0026/2019

• PREDICT: Personalized therapy for rheumatic diseases via machine learning, FCT Project PTDC/CCI-CIF/29877/2017

• PERSEIDS: Personalizing cancer therapy through integrated modeling and decision, FCT Project PTDC/EMS­SIS/0642/2014

• NEUROCLINOMICS2: Unravelling Prognostic Markers in NEUROdegenerative diseases through CLINical and OMICS data integration, FCT Project PTDC/EEI-SII/1937/2014

• CancerSys: Multiscale modeling for personalized therapy of bone metastasis, FCT Project EXPL/EMS-SIS/1954/2013

• InteleGen: Pharmacokinetic/Pharmacogenetic modulation of HIV infection therapy by bayesian and artificial intelligence methods, FCT Project PTDC/DTP-FTO/1747/2012

• PNEUMOPATH: A comprehensive dissection of pneumococcal-host interactions, EU-FP7 (Contract 222983), 2010

• NEUROCLINOMICS: Understanding neurodegenerative diseases throught clinical and omics data integration, FCT Project PTDC/EIA-EIA/111239/2009

• BioHypo: Confronting the clinical relevance of biocide induced antibiotic resistance, EU-FP7 (Contract 227258), 2009

• PneumoSyS: A systems biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease, FCT Project PTDC/SAU-MII/100964/2008

• ARN: Algorithms for the identification of genetic Regulatory Networks, FCT Project PTDC/EIA/67722/2006

• DBYeast: DBYeast: Infrastructures and algorithms for analysis and identification of gene regulatory networks, FCT Project POSC/EIA/57398/2004

• BioGrid: Parallel Algorithms for Gene Annotation, FCT Project FEDER POSI/SRI/47778/2002

• LogComp, PRAXIS XXI Project 2/2.1/TIT/1658/95

Research interests | Publications | Software | Teaching | Short CV