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Training in several Artificial Intelligence / Deep Learning architectures: Large Language Models, Transformers, Convolutional Neural Networks, Diffusion Models, Reinforcement Learning, etc. Experience and assessment of applying Artificial Intelligence / Machine Learning models to several molecular targets: G Protein-Coupled Receptors, Tumor Necrosis Factor Receptors, Bacterial Cell-Division Proteins, Neuronal Synucleins, etc.
Identification

Personal identification

Full name
Francisco Jorge Dias Oliveira Fernandes

Citation names

  • Fernandes, Francisco

Author identifiers

Ciência ID
FC13-981E-E38C
ORCID iD
0000-0003-2546-2669
Google Scholar ID
https://scholar.google.com/citations?user=57TmQHYAAAAJ

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Intermediate (B1) Advanced (C1) Advanced (C1) Intermediate (B1)
Education
Degree Classification
2016/01 - 2018/12
Concluded
 Efficient Algorithms for Protein Docking (Pós-doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2013
Concluded
 Engenharia Informática e de Computadores (Doutoramento)
Major in Bioinformática
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Efficient algorithms to align DNA sequences" (THESIS/DISSERTATION)
 18
2007
Concluded
 Matemática Aplicada e Computação (Mestrado integrado)
Major in Computação
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Detection of Conserved Regions in Genomes using Entropic Profiles" (THESIS/DISSERTATION)
 15
Affiliation

Science

Category
Host institution 		Employer
2019/01 - 2024/12 Contracted Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Others

Category
Host institution 		Employer
2016/01/01 - 2018/12 Pós-Doutoramento Tema: Efficient Algorithms for Protein Docking Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2015/06/01 - 2015/11/01 Bolseiro de pós-doutoramento no âmbito do projecto: DataStorm - Large scale data management in cloud environments (Referência: EXCL/EEIESS/0257/2012) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2008/09/01 - 2013/12/01 Doutoramento em Engenharia Informática e de Computadores Tema: Efficient Algorithms to Align DNA Sequences Universidade de Lisboa Instituto Superior Técnico, Portugal
2009/09/01 - 2009/12/01 Frequência em regime extra-curricular de disciplinas de áreas directamente ligadas à Bioinformática: Bioquímica e Biologia Molecular, Engenharia Biomolecular e Celular, Engenharia Genética, Biologia E Universidade de Lisboa Instituto Superior Técnico, Portugal
2008/01/01 - 2008/07/01 Bolseiro de investigação no âmbito do projecto: ARN - Algorithms for the identification of genetic Regulatory Networks (Referência: PTDC/EIA/67722/2006) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2006/09/01 - 2007/07/01 Frequência de disciplinas da área de Inteligência Artificial do Mestrado em Engenharia Informática e de Computadores em regime Extra-Curricular Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Grant

Designation Funders
2015/06 - 2015/11 DataStorm - Large scale data management in cloud environments
EXCL/EEIESS/0257/2012
Post-doc Fellow
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Concluded
2011/01/01 - 2013/12 TAGS : The power of the short - Tools and Algorithms for next Generation Sequencing applications
info:eu-repo/grantAgreement/FCT/3599-PPCDT/112283/PT
PhD Student Fellow
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded
2008/01/01 - 2008/12 ARN - Algorithms for the identification of genetic Regulatory Networks
info:eu-repo/grantAgreement/FCT/3599-PPCDT/67722/PT
Master Student Fellow
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded

Other

Designation Funders
2021/01/01 - Current ARCADE - Augmenting Rehabilitation Centers with Context-Aware Digital Environments
PTDC/CCI-COM/30274/2017
Post-doc
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Ongoing
2019/05 - 2020/12/31 STREACKER - Skeletal Tracking Enhanced with Anatomically Correct Kinematics for Exergames and Rehabilitation
UTAP-EXPL/CA/0065/2017
Post-doc
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Ongoing
2016/01 - 2016/12 A-MOP - Algorithms for Macro-Molecular Pocket Detection
UTAPEXPL/QEQ-COM/0019/2014
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
Outputs

Publications

Book chapter
  1. Javier Montoya; Francisco Fernandes; Ana Teresa Freitas. "Microbiome Classification in Colon Cancer Patients Using Chaos Game Representations and CNN Models". In Lecture Notes in Computer Science. 2024.
    10.1007/978-3-031-64636-2_22
Conference paper
  1. André Salgado; Fernandes, Francisco; Ana Teresa Freitas. "CSA-MEM: Enhancing Circular DNA Multiple Alignment Through Text Indexing Algorithms". Paper presented in Bioinformatics Research and Applications: 19th International Symposium, ISBRA 2023, Wroclaw, 2023.
    Published • 10.1007/978-981-99-7074-2_41
  2. Seabra, Miguel; Fernandes, Francisco; Lopes, Daniel Simões; Pereira, João Madeiras. "Position Based Rigid Body Simulation: A comparison of physics simulators for games". 2023.
    Published • 10.24132/csrn.3301.59
  3. Milagros Jaén Vargas; Karla Reyes Leiva; Francisco Fernandes; Sérgio Gonçalves; Miguel Silva; Daniel Simões Lopes; José Javier Olmedo. "A Deep Learning Approach to Recognize Human Activity using Inertial Sensors and Motion Capture Systems". Paper presented in 7th International Conference on Fuzzy Systems and Data Mining, 2021.
    Published • 10.3233/FAIA210196
  4. Fernandes, Francisco; Santos, João; Lopes, Daniel; Ferreira, Alfredo. "PuzzleDock: An Immersive Protein Docking Environment". Paper presented in International Conference on Graphics and Interaction (ICGI2018), 2018.
  5. Fernandes, Francisco; Ferreira, Alfredo. "An experimental shape matching approach for protein docking". Paper presented in EG 3DOR 16: 9th Eurographics Workshop on 3D Object Retrieval, 2016.
    10.2312/3dor.20161083
  6. Coimbra, Miguel E.; Fernandes, Francisco; Russo, Luís M. S.; Freitas, Ana T.. "Parallel efficient aligner of pyrosequencing reads". 2013.
    10.1145/2488551.2488593
  7. Fernandes, Francisco; Fonseca, Paulo; Russo, Luís; Oliveira, Arlindo. "An efficient data representation for large scale genome re-sequencing". Paper presented in 13t th International Meeting on Human Genome Variation and Complex Genome Analysis (HGV2012), 2012.
  8. Fernandes, Francisco; Paulo G. S. da Fonseca; Luís M. S. Russo; Arlindo L. Oliveira; Ana T. Freitas. "Efficient High-throughput Read Mapping For Re-sequencing Applications". Paper presented in Bioinformatics Open Days, 2012.
  9. Fernandes, Francisco; Paulo G. S. da Fonseca; Luís M. S. Russo; Arlindo L. Oliveira; Ana T. Freitas. "TAPYR: An efficient high-throughput sequence aligner for re-sequencing applications". Paper presented in 7th Internation Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-Meeting 2011), 2011.
  10. Dário Abdulrehman; Fernandes, Francisco; Sofia Pinto; Ana T. Freitas. "YEASTRACT Semantic Web Services". Paper presented in 3º INForum - Simpósio de Informática, 2011.
  11. Fernandes, Francisco; Luisa Pereira; Ana Teresa Freitas. "CIRCALIGN: A new algorithm to align multiple mitochondrial genomes". Paper presented in Jornadas de Bioinformatica 2009, 2009.
  12. Fernandes, Francisco; Ana T. Freitas; Jonas S. Almeida; Susana Vinga. "ENTROPIC PROFILER – efficient whole genome analysis using information theory and statistical concepts". Paper presented in ISMB/ECCB09 - 17th Annual International Conference on Intelligent Systems for Molecular Biology - 8th European Conference on Computational Biology, 2009.
Conference poster
  1. Fernandes, Francisco; Luisa Pereira; Ana T. Freitas. "An efficient algorithm to align multiple circular genomes". Paper presented in RECOMB2010: 14th International Conference on Research in Computational Molecular Biology, 2010.
Journal article
  1. Duarte, Alexandre; Fernandes, Francisco; Pereira, João M.; Moreira, Catarina; Nascimento, Jacinto C.; Jorge, Joaquim. "SelfReDepth: Self-Supervised Real-Time Depth Restoration for Consumer-Grade Sensors". Journal of Real-Time Image Processing 21 4 (2024): http://dx.doi.org/10.1007/s11554-024-01491-z.
    Open access • Published • 10.1007/s11554-024-01491-z
  2. Francisco Fernandes; Ivo Roupa; Sérgio B. Gonçalves; Gonçalo Moita; Miguel Tavares da Silva; João Pereira; Joaquim Jorge; Richard R. Neptune; Daniel Simões Lopes. "Sticks and STONES may build my bones: Deep learning reconstruction of limb rotations in stick figures". Pattern Recognition Letters (2023): https://doi.org/10.1016/j.patrec.2022.12.012.
    10.1016/j.patrec.2022.12.012
  3. Jaén-Vargas, Milagros; Reyes Leiva, Karla Miriam; Fernandes, Francisco; Barroso Gonçalves, Sérgio; Tavares Silva, Miguel; Lopes, Daniel Simões; Serrano Olmedo, José Javier. "Effects of sliding window variation in the performance of acceleration-based human activity recognition using deep learning models". PeerJ Computer Science 8 (2022): e1052. http://dx.doi.org/10.7717/peerj-cs.1052.
    Open access • Published • 10.7717/peerj-cs.1052
  4. Dias, Sérgio; Simões, Tiago; Fernandes, Francisco; Martins, Ana Mafalda; Ferreira, Alfredo; Jorge, Joaquim; Gomes, Abel J. P.. "CavBench: A benchmark for protein cavity detection methods". PLOS ONE 14 10 (2019): e0223596. http://dx.doi.org/10.1371/journal.pone.0223596.
    10.1371/journal.pone.0223596
  5. Teixeira, Andreia Sofia; Fernandes, Francisco; Francisco, Alexandre P.. "SpliceTAPyR - An Efficient Method for Transcriptome Alignment". International Journal of Foundations of Computer Science 29 08 (2018): 1297-1310. http://dx.doi.org/10.1142/s0129054118430049.
    10.1142/s0129054118430049
  6. Simões, Tiago; Lopes, Daniel; Dias, Sérgio; Fernandes, Francisco; Pereira, João; Jorge, Joaquim; Bajaj, Chandrajit; Gomes, Abel. "Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey". Computer Graphics Forum 36 8 (2017): 643-683. http://dx.doi.org/10.1111/cgf.13158.
    10.1111/cgf.13158
  7. Fernandes F; Freitas AT. "slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array.". (2014): http://europepmc.org/abstract/med/24336412.
    10.1093/bioinformatics/btt706
  8. Fernandes F; da Fonseca PG; Russo LM; Oliveira AL; Freitas AT. "Efficient alignment of pyrosequencing reads for re-sequencing applications.". (2011): http://europepmc.org/abstract/med/21672185.
    10.1186/1471-2105-12-163
  9. Fernandes F; Pereira L; Freitas AT. "CSA: an efficient algorithm to improve circular DNA multiple alignment.". (2009): http://europepmc.org/abstract/med/19627599.
    10.1186/1471-2105-10-230
  10. Fernandes F; Freitas AT; Almeida JS; Vinga S. "Entropic Profiler - detection of conservation in genomes using information theory.". (2009): http://europepmc.org/abstract/med/19416538.
    10.1186/1756-0500-2-72
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/06/01 Recent Artificial Intelligence tools and architectures for Structural Biology BioData.pt TALKS: 3D BioTalks | Session 3
BioData.pt (Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2024/01 - Current Detecting Defects in Ceramic Dishware using Deep Learning
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - Current Técnicas de Deep Learning para Reconstruir o Movimento de Avatars em Realidade Virtual
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - Current Targeting the RANK-TRAF6 Axis: A Molecular Approach
Co-supervisor
 Biotecnologia (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - 2024/10/22 Weapon Model Classification using Deep Learning
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - 2024/09 Microbiome Classification in Colon Cancer Patients using Chaos Game Representations and CNN models
Co-supervisor
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2023/11 Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/01 - 2022/12 Characterization of the protein-protein interactions of M. tuberculosis divisome proteins expressed in E. coli
Co-supervisor
 Engenharia Biológica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09 - 2022/11 Rigid Body Simulation with Extended Position Based Dynamics
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09 - 2022/11 Kinect Noise Removal with Deep Learning
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09 - 2022/11 Fast Photorealistic Rendering of Protein Representations
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09 - 2022/11 Force Field Calculation for Biomolecules
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09 - 2022/11 Reconstruction of Avatar Motion in Virtual Reality with Machine Learning
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/01 - 2017/11/09 Acoplamento de Proteínas em Ambiente Imersivo
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023/07/18 O Impacto da Personalidade em Interfaces de Gamificação
(Thesis) Arguer
 Viktoriya Limonova (Master)
Instituto Superior de Tecnologias Avançadas de Lisboa, Portugal
2023/05/16 A new generation of user-friendly and machine learning-accelerated methods for protein pKa calculations
(Thesis) Arguer
 Pedro de Brito Pires Santos Reis (PhD)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2021/09/24 Prediction of postoperative complications in oncology patients using fuzzy logic-based machine learning
(Thesis) Arguer
 André Aguiar de Matos de Lima Miranda (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020/06/17 Cerebellum Model for Movement Coordination
(Thesis) Arguer
 Leonardo Filipe Farinha Marques (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/10/31 Strategies to Accelerate Deformable and Rigid Bodies Simulation: A non-polygonal approach to contact detection
(Thesis) Arguer
 José Pedro Carapuça Serrano (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2024/01/04 - 2024/01/04 Biological Image Analysis using Explainable Deep Learning Doctoral Program in Experimental Biology and Biomedicine (Doutoramento) Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2024/01/04 - 2024/01/04 Protein Folding and Peptide Design with AlphaFold and RFdiffusion Doctoral Program in Experimental Biology and Biomedicine (Doutoramento) Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2023/10/20 - 2023/10/20 Working with Linux 3D-BioInfo-PT Introductory Workshop (Outros) Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2023/06/15 - 2023/06/15 Deep Learning for Protein Sequence and Structure 3D-BioInfo-PT Advanced Workshop (Outros) Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2022/12/19 - 2022/12/19 Machine Learning Demystified 3D-BioInfo-PT Intermediate Workshop (Outros) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Distinctions

Other distinction

2012 Artigo "Dez exemplos que mostram a qualidade da ciência nacional em 2011" (Público 01/01/2012)
2011 Artigo "Portugueses são os mais rápidos do mundo a montar genomas" (Expresso 27/08/2011)
2011 Nominee for Best INESC-ID PhD Student
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal