Publications
A - Publications
Books
Book chapters (4)
Joana Pinheiro Neto and Duarte Valério and Susana Vinga. Variable order derivatives and bone remodelling in the presence of metastases. Linear and Nonlinear Fractional Order Systems, Elsevier, 2018, Editor: Ahmad Taher Azar and Ahmed G. Radwan and Sundarapandian Vaidyanathan.
Joana Pinheiro Neto and Duarte Valério and Susana Vinga. Variable-order derivatives and bone remodeling in the presence of metastases. Handbook of Fractional Calculus with Applications, vol. 7, Applications in Engineering, Life and Social Sciences, Part A, De Gruyter, 2019. Editors: Dumitru Baleanu and António Mendes Lopes
Rui M. Coelho and Joana P. Neto and Duarte Valério and Susana Vinga. Dynamic biochemical and cellular models of bone physiology: integrating remodelling processes, tumor growth and therapy. The Computational Mechanics of Bone Tissue, Springer, 2020. Editors: Jorge Belinha and Maria-Cristina Manzanares-Céspedes and António Completo.
N. Saraiva-Agostinho, N.L. Barbosa-Morais. Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics. Methods in Molecular Biology, 2117:179-205, 2020. [https://doi.org/10.1007/978-1-0716-0301-7_10]
Papers in national journals
Papers in international journals
Note: All indexed by ISI Web of Science except the 2 marked with *
A. Hartmann and A.R. Neves and J.M. Lemos and S. Vinga, Identification and automatic segmentation of multiphasic cell growth using a linear hybrid model, Mathematical Biosciences, 279(), pp. 83-89, Jul. 2016, . [DOI Article link] [WOS]
J.M. Lemos and D.V. Caiado and R.M. Coelho and S. Vinga, Optimal and receding horizon control of tumor growth in myeloma bone disease, Biomedical Signal Processing and Control, 24(), pp. 128-134, Feb. 2016, . [DOI Article link] [WOS]
R.M. Coelho and J.M. Lemos and I. Alho and D. Valério and A.R. Ferreira and L. Costa and S. Vinga, Dynamic modeling of bone metastasis, microenvironment and therapy Integrating parathyroid hormone (PTH) effect, anti-resorptive and anti-cancer therapy, Journal of Theoretical Biology, 391(), pp. 1-12, Feb. 2016, . [DOI Article link] [WOS]
Veríssimo A., Oliveira A. L., Sagot, M.-F., Vinga, S. (2016) DegreeCox: a network-based regularization method for survival analysis. BMC Bioinformatics, 17(16), 109-121. DOI: 10.1186/s12859-016-1310-4
Tomás E., Vinga, S., & Carvalho A.M. (2017) Unsupervised learning of pharmacokinetic responses. Computational Statistics, 32(2): 409-428. DOI:10.1007/s00180-016-0707-x
* Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet. 2017 Apr 3. doi: 10.1007/s00439-017-1790-y. PMID: 28374191
S. Silva, L. Vanneschi, A.I. Cabral, M.J. Vasconcelos, A semi-supervised genetic programming method for dealing with noisy labels and hidden overfitting, Swarm and Evolutionary Computation, 39, pp. 323-338, April 2018. [DOI Article link]
W. La Cava, S. Silva, K. Danai, L. Spector, L. Vanneschi, J.H. Moore, Multidimensional genetic programming for multiclass classification. Swarm and Evolutionary Computation, in press. [DOI Article link]
A. Rubio-Largo, M. Castelli, L. Vanneschi, M.A. Vega-Rodríguez, A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment, Journal of Computational Biology, 25, 1-14, 2018. [DOI Article link]
M. B. Lopes, A. Veríssimo, E. Carrasquinha, S. Casimiro, N. Beerenwinkel, S. Vinga, Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC Bioinformatics, 2018. [DOI Article link]
E. Carrasquinha, A. Veríssimo, M. B. Lopes, S. Vinga. Identification of influential observations in high-dimensional cancer survival data through the rank product test. BioData Mining, 11(1), 2018. [DOI Article link]
Margarida Sousa, Alexandra M. Carvalho, Polynomial-Time Algorithm for Learning Optimal BFS-Consistent Dynamic Bayesian Networks. Entropy 20(4): 274 (2018).
Rui P. Guerra, Alexandra M. Carvalho, P. Mateus, Model Selection for Clustering of Pharmacokinetic Responses, Computer Methods and Programs in Biomedicine, Vol. 162, No. 2018, pp. 11 - 18, 2018
Joana Pinheiro Neto and Rui Moura Coelho and Duarte Valério and Susana Vinga and Dominik Sierociuk and Wiktor Malesza and Michal Macias and Andrzej Dzielinski. Simplifying biochemical tumorous bone remodeling models through variable order derivatives, Computers & Mathematics with Applications, 75(9) 3147-3157, 2018.
* Luiz Filipe Christ and Duarte Valério and Rui Moura Coelho and Susana Vinga. Models of bone metastases and therapy using fractional derivatives, Journal of Applied Nonlinear Dynamics, 2018, 1, 81-94, 7.
Teles, F. F., & Lemos, J. M. (2019). Cancer therapy optimization based on multiple model adaptive control. Biomedical Signal Processing and Control, 48, 255-264. doi: https://doi.org/10.1016/j.bspc.2018.09.016 [pdf]
P. Segaert, M.B. Lopes, S. Casimiro, S. Vinga, P.J. Rousseeuw. Robust identification of target genes and outliers in triple-negative breast cancer data. Statistical Methods in Medical Research, 28(10–11) 3042-3056, 2018. [DOI Article link]
Loureiro, H., Carrasquinha, E., Alho, I., Ferreira, A. R., Costa, L., Carvalho, A. M., & Vinga, S. (2019). Modelling cancer outcomes of bone metastatic patients: combining survival data with N-Telopeptide of type I collagen (NTX) dynamics through joint models. BMC Medical Informatics and Decision Making, 19. doi:10.1186/s12911-018-0728-1
Duarte Valério and Joana Neto and Susana Vinga. Variable order 3D models of bone remodeling. Bulletin of the Polish Academy of Sciences: Technical Sciences, 67(3) 501-508, 2019.
N. Saraiva-Agostinho, N.L. Barbosa-Morais. psichomics: graphical application for alternative splicing quantification and analysis. Nucleic Acids Research, 47(2):e7, 2019. [DOI Article link]
M. B. Lopes, S. Casimiro, S. Vinga. Twiner: correlation-based regularization for identifying common cancer gene signature. BMC Bioinformatics, 20:356, 2019. [DOI Article link]
Rama, K., Canhao, H., Carvalho, A. M., & Vinga, S. (2019). AliClu - Temporal sequence alignment for clustering longitudinal clinical data. Bmc Medical Informatics and Decision Making, 19(1). doi:10.1186/s12911-019-1013-7
R. Sousa, S. Silva, C. Pesquita. Evolving knowledge graph similarity for supervised learning in complex biomedical domains, BMC Bioinformatics 21 (1), 6, 2020. [DOI Article link]
I. Azzali, L. Vanneschi, I. Bakurov, S. Silva, M. Ivaldi, M. Giacobini. Towards the use of vector based GP to predict physiological time series, Applied Soft Computing, 106097, 2020. [DOI Article link]
L. Muñoz, L. Trujillo, S. Silva. Transfer learning in constructive induction with Genetic Programming, Genetic Programming and Evolvable Machines, 1-41, 2019b. [DOI Article link]doi:10.1007/s10710-019-09368-y
L. Muñoz, L. Trujillo, S. Silva, M. Castelli, L. Vanneschi. Evolving multidimensional transformations for symbolic regression with M3GP, Memetic Computing 11 (2), 111-126, 2019a. [DOI Article link]
Mariano Lemus, João Beirão, Nikola Paunkovic, Alexandra M. Carvalho, Paulo Mateus Information-theoretical criteria for characterizing the earliness of time-series data, Entropy 2020, 22(1), 49; https://doi.org/10.3390/e22010049
//doi.org/10.1186/s12859-018-2149-
B - Communications
Communications in international scientific meetings
Note: The 7 indexed by ISI are marked with ⧫
B. Andrade Costa and J. M. Lemos. Drug Administration Design for Cancer Gompertz Model Based on the Lyapunov Method. CONTROLO 2016 pp 131-141.
Bertinho A. Costa and J. M. Lemos. Control of a prostate cancer model using intermittent androgen suppression. Proc. Controlo 2018, 282-287. Ponta Delgada, Açores, 2018. [pdf].
Duarte Valério, Rui Coelho, and Susana Vinga. Fractional dynamic modelling of bone metastasis, microenvironment and therapy. In International Conference on Fractional Differentiation and its Applications, 2016.
Nuno Saraiva-Agostinho. Shiny App for the Integrated Analysis of Alternative Splicing from Large Transcriptomic Datasets. Oral presentation. European Bioconductor Developer’s Conference 2016. 6-7 December, 2016. Basel, Switzerland.
Nuno L. Barbosa-Morais. A bioinformatics application for the analysis and visualisation of alternative splicing in cancer. Oral presentation. 4th Post-EURASNET Symposium. 28 September, 2016. Poznan, Poland.
⧫ Silva, H.G., J.M. Lemos, and B.A. Costa, Adaptive Predictive Control Based Therapy of Bone Marrow Cancer. Ifac Papersonline, 2016. 49(13): p. 330-335.
Nuno Saraiva-Agostinho, Nuno L. Barbosa-Morais. Bioinformatics Application for Analysis and Visualisation of Alternative Splicing in Cancer. Poster presentation at EMBO Young Scientists’ Forum 2016. 1-2 September, 2016. Lisbon, Portugal.
Bertinho A. Costa and João M. Lemos. Lyapunov based Control Design for Cancer Gompertz-Logistic Generalized Model Therapy. MED 2017 - 25th Mediterranean Conference on Control and Automation. 3-6 July 2017. [PDF]
⧫ Joana Neto, Rui Moura Coelho, Duarte Valério, Susana Vinga, Dominik Sierociuk, Wiktor Malesza, Michal Macias, and Andrzej Dzielinski. Variable order differential models of bone remodelling. In IFAC World Congress, 2017.IFAC-PapersOnLine, Volume 50, Issue 1, 2017, Pages 8066-8071, [doi].
⧫ U López, L Trujillo, Y Martinez, P Legrand, E Naredo, S Silva. RANSAC-GP: Dealing with Outliers in Symbolic Regression with Genetic Programming, European Conference on Genetic Programming (EuroGP), 114-130, April 2017, Springer.
⧫ W La Cava, S Silva, L Vanneschi, L Spector, J Moore, Genetic programming representations for multi-dimensional feature learning in biomedical classification, European Conference on the Applications of Evolutionary Computation (EvoApps), 158-173, April 2017, Springer.
Marta B. Lopes, A. Veríssimo, E. Carrasquinha and S. Vinga, Consensus outlier detection in triple-negative breast cancer gene expression data. Oral Presentation. Data Science, Statistics & Visualisation (DSSV 2017), 12-14 Jul 2017. Lisboa, Portugal.
Veríssimo A., Carrasquinha E., Lopes M.B., Sagot M.-F., Oliveira A.L., Vinga S. Network-based regularized optimization for cancer survival data analysis. Ascona Workshop 2017 - Statistical Challenges in Single-Cell Biology, ETH Zurich, Switzerland, April 30 - May 5, 2017.
A. Veríssimo, E. Carrasquinha, Marta B. Lopes, A. L. Oliveira, M.-F. Sagot and S. Vinga, Network-based sparse modeling of breast invasive carcinoma survival data, Signal Processing with Adaptive Sparse Structured Representations (SPARS) , May. 2017. Poster presentation. Lisboa, Portugal.
E. Carrasquinha, A. Veríssimo, M. B. Lopes, S. Vinga, Outlier detection in survival analysis: an application to ovarian cancer data. Oral Presentation. 61st World Statistics Congress ISI 2017. 16-21 july 2017. Marraquexe, Morocco
Vanneschi, L., Castelli, M., Manzoni, L., Krawiec, K., Moraglio, A., Silva, S., Gonçalves, I., PSXO: population-wide semantic crossover. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), 257-258, 2017a.
I. Gonçalves, S. Silva, C.M. Fonseca, M. Castelli, Unsure When to Stop? Ask Your Semantic Neighbors. GECCO'17 Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), 929-936, 2017.
⧫ L. Vanneschi, M. Castelli, I. Gonçalves, L. Manzoni, S. Silva, Geometric semantic genetic programming for biomedical applications: A state of the art upgrade. IEEE Congress on Evolutionary Computation (CEC), 177-184, 2017b.
Duarte Valério and Joana Neto and Susana Vinga, Variable order 3D models of bone remodeling. International Conference on Fractional Signals and Systems, 2017, Lodz.
L.M. Gallego-Paez, M. Martins, N. Barbosa-Morais, “CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer”, Poster Presentation, EMBL Conference - Cancer Genomics, EMBL Heidelberg, Germany. November 5-8, 2017.
L.M. Gallego-Paez, M. Martins, N. Barbosa-Morais, “CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer”, Poster Presentation, Forty Years of mRNA Splicing, Cold Spring Harbor Laboratory, NY, USA. October 22-25, 2017.
N. Saraiva-Agostinho, N. Barbosa-Morais, “psichomics - A bioinformatics application for the quantification, analysis and visualisation of alternative splicing from large transcriptomic datasets”, Poster Presentation, Forty Years of mRNA Splicing, Cold Spring Harbor Laboratory, NY, USA. October 22-25, 2017.
Veríssimo A., Carrasquinha E., Lopes M.B., Oliveira A.L., Sagot M.-F., Vinga S. Regularized survival analysis and feature clustering of TCGA breast cancer data. From Single- to Multiomics: Applications and Challenges in Data Integration, Heidelberg, Germany, November 12-14, 2017.
Veríssimo A., Lopes M. B., Carrasquinha E., Sagot M. -F., Oliveira A. L., Vinga S., Random Sample Consensus (RANSAC) for the robust identification of outliers in transcriptomic data. Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB 2017), Prague - Czech Republic, July 21-25, 2017.
L.M. Gallego-Paez, M. Martins, N. Barbosa-Morais, “CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer”, Poster Presentation, EMBO Practical Course – iCLIP: Genomic views of protein-RNA interactions, Barcelona, Spain, June 3-9, 2018.
M.A. Ferreira, N. Barbosa-Morais, “Profiling the alternative splicing landscape of senescent cells”, Poster Presentation, 25th Biennial Congress of the European Association for Cancer Research (EACR25), Amsterdam, the Netherlands, June 30-July 3, 2018.
L.M. Gallego-Paez, M. Martins, N. Barbosa-Morais, “CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer”, Poster Presentation, 25th Biennial Congress of the European Association for Cancer Research (EACR25), Amsterdam, the Netherlands, June 30-July 3, 2018.
M. B. Lopes, A. Veríssimo, S. Casimiro, E. Carrasquinha, S. Vinga. Network-based penalized logistic regression for the identification of common gene signatures in breast and prostate cancers. Oral Presentation. Data Science, Statistics & Visualisation (DSSV 2018), July 9-11 2018. Vienna, Austria.
P. Segaert, M. B. Lopes, S. Vinga, P. Rousseeuw. Robust identification of target genes and outliers in triple-negative breast cancer data. Oral Presentation. Data Science, Statistics & Visualisation (DSSV 2018), July 9-11 2018. Vienna, Austria.
Miranda, R., Valério, D., Vinga, S., Bone Remodelling, Tumour Growth, and Fractional Order Therapy Predictive Control. International Conference on Fractional Differentiation and its Applications, Amman, 16-18 July, 2018.
Nuno Barbosa-Morais, “CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer”, Oral Presentation, 2nd International Caparica Conference in Splicing, Lisbon, Portugal, July 16-19, 2018.
M.A. Ferreira, N. Barbosa-Morais, “Profiling the alternative splicing landscape of senescent cells”, Oral and Poster Presentation, 2nd International Caparica Conference in Splicing, Lisbon, Portugal, July 16-19, 2018.
N. Saraiva-Agostinho, N. Barbosa-Morais, “psichomics: a bioinformatics application for the quantification, analysis and visualisation of alternative splicing from large transcriptomic datasets”, Poster Presentation, 2nd International Caparica Conference in Splicing, Lisbon, Portugal, July 16-19, 2018.
E. Carrasquinha, A. Veríssimo, M. B. Lopes, S. Vinga. Variable selection of high-dimensional longitudinal data and survival analysis of cancer gene expression data. Poster presentation. 11th European Conference on Mathematical and Theoretical Biology (ECMTB 2018), July 23-27 2018, Lisbon, Portugal. [poster abstract].
Bertinho A. Costa and J. M. Lemos. Control of a prostate cancer model using intermittent androgen suppression. Proc. Controlo 2018, 282-287. Ponta Delgada, Açores, 2018. [pdf].
E. Carrasquinha, A. Veríssimo, M. B. Lopes, S. Vinga. Variable selection and outlier detection in regularised survival models: application to melanoma gene expression data. 4th Annual Conference on Machine Learning, Optimization and Data science (LOD 2018), 2018.
Margarida Sousa, Alexandra M. Carvalho, Learning consistent tree-augmented dynamic Bayesian networks. Internacional Conference on Machine Learning, Optimization, and Data Science – September 13-16, 2018 – Volterra, Tuscany, Italy
Pedro F. Ferreira, Alexandra M. Carvalho, Susana Vinga, Variational inference in probabilistic single-cell RNA-seq models. International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics - Caparica, Portugal, September 6- 8, 2018. https://doi.org/10.1007/978-3-030-34585-3_2
João V. Brito, Marta B. Lopes, Alexandra M. Carvalho, Susana Vinga, Unravelling breast and prostate common gene signatures by Bayesian network learning. International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018) - Caparica, Portugal, September 6-8, 2018. https://doi.org/10.1007/978-3-030-34585-3_25
Carrasquinha E., Lopes M.B., Veríssimo A., Casimiro S., Beerenwinkel N., Vinga S. Ensemble outlier detection in cancer gene expression data. The 17th European Conference on Computational Biology (ECCB 2018), Athens, Greece, September 8-12, 2018. [poster].
M.A. Ferreira, N. Barbosa-Morais, “Profiling the alternative splicing landscape of senescent cells”, Poster Presentation, EMBO/EMBL Symposium: The Complex Life of RNA, Heidelberg, Germany, October 3-6, 2018.
N. Saraiva-Agostinho, N. Barbosa-Morais, “psichomics: a bioinformatics application for the quantification, analysis and visualisation of alternative splicing from large transcriptomic datasets”, Poster Presentation, EMBO/EMBL Symposium: The Complex Life of RNA, Heidelberg, Germany, October 3-6, 2018.
L.M. Gallego-Paez, M. Martins, N. Barbosa-Morais, “CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer”, Poster Presentation, EMBO Workshop – RNA and genome maintenance: Cooperation and conflict management, Mainz, Germany, October 10-13, 2018.
Nuno Barbosa-Morais, “Biologist-intelligible alternative splicing analysis of RNA-seq data”. Oral presentation, BIRS/CMO workshop on Statistical and Computational Challenges in High-Throughput Genomics with Application to Precision Medicine, Oaxaca, Mexico, November 6, 2018.
N. Saraiva-Agostinho, N. Barbosa-Morais, “psichomics: a bioinformatics application for the quantification, analysis and visualisation of alternative splicing from large transcriptomic datasets”, Poster Presentation, EMBO VIZBI 2019, Heidelberg, Germany, March 13-15, 2019.
M.A. Ferreira, N. Barbosa-Morais, “Profiling the alternative splicing landscape of senescent cells”, Poster Presentation, 24th Annual RNA Society Meeting - RNA 2019, Krakow, Poland, June 11-16, 2019.
A. Veríssimo, M. B. Lopes, E. Carrasquinha, S. Vinga,. International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019) - September 4-6, Bergamo, Italy, 2019
M.A. Ferreira, N. Barbosa-Morais, “Profiling the alternative splicing landscape of senescent cells”, Poster Presentation, International Cell Senescence Association 2019 Conference: Cellular Senescence - the bright & dark side, Athens, Greece, September 9-12, 2019.
Peixoto C., Martins M., Lopes M.B., Veríssimo A., Costa L., Vinga S. Sparse models and network-based regularizers for the analysis of RNA-seq data from colorectal cancer. EMBO WORKSHOP - Precision Health: Molecular Basis, Technology and Digital Health, Heidelberg, Germany, November 13-16, 2019. [poster]
M. B. Lopes, A. Veríssimo, E. Carrasquinha, S. Vinga. On the role of hub and orphan genes in the diagnosis of breast invasive carcinoma. 5th Annual Conference on Machine Learning, Optimization and Data science (LOD 2019), September 10-13, Siena, Italy, 2019.
Manuel Anacleto, Susana Vinga, Alexandra M. Carvalho. MSAX: Multivariate symbolic aggregate approximation for time series classification. In Computational Intelligence methods for Bioinformatics and Biostatistics. CIBB 2019, Revised Selected Papers, Springer, accepted.
J.E. Batista, N.M. Rodrigues, S. Silva. To adapt or not to adapt, or the beauty of random settings, Genetic and Evolutionary Computation Conference Companion, 336-337, 2019.
I. Azzali, L. Vanneschi, S. Silva, I. Bakurov, M. Giacobini. A Vectorial Approach to Genetic Programming, European Conference on Genetic Programming, 213-227, 2019.
⧫ Vinga, S., Bridging computer science and bioengineering for the multiscale modeling of biological systems. Annals of Medicine, 2019. 51: p. S28-S29. [Keynote speaker].
Communications in national scientific meetings (9)
Luiz Filipe Christ, Duarte Valério, Rui Moura Coelho, and Susana Vinga. Models of bone metastases using fractional derivatives. In CEM 2016 — Mechanical Engineering Conference, Porto, 2016.
Nuno Saraiva-Agostinho. psichomics: Alternative Splicing Quantification, Analysis and Visualisation in Cancer Data. Oral presentation. Bioinformatics Open Days 2017. 22-24 February, 2017. Braga, Portugal.
Mariana Ferreira, Nuno Barbosa-Morais. Profiling the alternative splicing landscape of senescent cells. Poster presentation. 3rd ASPIC International Congress. 10-11 May, 2018. Lisbon, Portugal.
Lina Gallego-Paez, Marta Martins, Nuno Barbosa-Morais. CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer. Poster presentation. 3rd ASPIC International Congress. 10-11 May, 2018. Lisbon, Portugal.
Mariana Ferreira, Nuno Barbosa-Morais. Profiling the alternative splicing landscape of senescent cells. Poster presentation. XII CAML PhD Students’ Meeting, Instituto de Medicina Molecular João Lobo Antunes. 23-25 May, 2018. Lisbon, Portugal.
Mariana Ferreira, Nuno Barbosa-Morais. Profiling the alternative splicing landscape of senescent cells. Oral presentation. VIII National RNA Meeting: ptRNA2019. 25 January, 2019. Porto, Portugal.
Nuno Barbosa-Morais. CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer. Oral presentation. VIII National RNA Meeting: ptRNA2019. 25 January, 2019. Porto, Portugal.
Mariana Ferreira, Nuno Barbosa-Morais. Profiling the alternative splicing landscape of senescent cells. Poster presentation. XIII CAML PhD Students’ Meeting, Instituto de Medicina Molecular João Lobo Antunes. 15-17 May, 2019. Lisbon, Portugal.
Nuno Barbosa-Morais. Tumour transcriptomes reveal a prognostic alternative splicing signature in colorectal cancer. Oral presentation. 23rd Annual Meeting of the Portuguese Human Genetics Society. 15 November, 2019. Coimbra, Portugal.
Nuno Saraiva-Agostinho. psichomics: Alternative Splicing Quantification, Analysis and Visualisation in Cancer Data. Oral presentation. Bioinformatics Open Days 2017. 22-24 February, 2017. Braga, Portugal.
C - Reports (5)
E. Pacheco (2016) A review of models for cancer chemotherapy based on Optimal Control. Internship Report. INESC-ID, Technical report 16/2016 [PDF]
E. Carrasquinha, A. Veríssimo, S. Vinga. Consensus outlier detection in survival analysis using the rank product test. bioRxiv 421917. doi: https://doi.org/10.1101/421917
Joana Godinho, Alexandra M. Carvalho, Susana Vinga. Latent variable modelling and variational inference for scRNA-seq differential expression analysis. bioRxiv 719856; doi: https://doi.org/10.1101/719856
Pedro F. Ferreira, Alexandra M. Carvalho, Susana Vinga. Scalable probabilistic matrix factorization for single-cell RNA-seq analysis. bioRxiv 496810; doi: https://doi.org/10.1101/496810
André Veríssimo, Eunice Carrasquinha, Marta B. Lopes, Arlindo L. Oliveira, Marie-France Sagot, Susana Vinga. Sparse network-based regularization for the analysis of patientomics high-dimensional survival data. bioRxiv 403402; doi: https://doi.org/10.1101/403402
D - Organization of seminars and conferences (10)
Barbosa-Morais, NL. “What transcriptomes tell us about disease”. Seminar, ITQB, Oeiras, Portugal. 6 February 2018.
Ferreira, MA. "betAS: beta distribution-based method for differential alternative splicing analyses". Seminar, Computational Biology and Bioinformatics Seminars, Instituto de Medicina Molecular. March 21, 2018.
Barbosa-Morais, NL. “Computational biology and what transcriptomes tell us about disease”. Seminar, Prossyga 2018, Porto, Portugal. 12 May 2018.
Barbosa-Morais, NL. “What transcriptomes tell us about disease”. Seminar, MRC London Institute of Medical Sciences, London, UK. 25 July 2018.
Barbosa-Morais, NL. "Bioinformatics in the translation of cancer transcriptomics". Lecture, V Semana da Bioengenharia, Instituto Superior Técnico, Lisbon, Portugal. 18 March 2019.
Barbosa-Morais, NL. "Bioinformatics in the translation of cancer transcriptomics". Lecture, Biozentrum, University of Basel, Switzerland. 13 May 2019.
Barbosa-Morais, NL. "Bioinformatics - Computational biology in the translation of cancer 'omics’". Lecture, Masters in Biomedical Research, NOVA Medical School, Lisbon, Portugal. 18 October 2019.
Barbosa-Morais, NL. “What transcriptomes tell us about disease”. Seminar, Department of Bioengineering, Instituto Superior Técnico, Lisbon, Portugal. 21 May 2019.
Vinga S (2018) Bridging computer science and bioengineering for the multiscale modeling of biological systems (Keynote). 3rd International Congress of the CiiEM. Almada, Portugal, June 20-22, 2018.
Vinga S (2019) Computational Biology: bridging computer science and bioengineering for modeling multiscale systems. Molecular Biomarkers and Technologies, PhD Program in Medicines and Pharmaceutical Innovation. Faculdade de Farmácia, ULisboa, Portugal. 8-12 July 2019.
E - Advanced training
Doctoral theses (1)
Luis Muñoz Delgado (2019). Multidimensional Transformations of the Feature Space with Genetic Programming. PhD Thesis, Instituto Tecnológico de Tijuana, Mexico. (Supervisors: Leonardo Trujillo and Sara Silva).
Master's theses (30)
Joana de Castro Capacete. Biochemical and biomechanic integrated modeling of bone. MSc Biomedical Engineering, IST-UL. (Supervisors: S Vinga, J Folgado). 14 Nov 2016.
Ricardo Miguel de Oliveira Moreira. Localização Automática do Núcleo Subtalâmico para Estimulação Cerebral Profunda na Doença de Parkinson. MSc Mechanical Engineering, IST-UL. (Supervisors: J Martins, S. Vinga). 18 Nov 2016.
Joana Catarina Lopes Pinheiro Carreira Neto. Dynamic Modeling of Bone Remodeling, Tumor Growth and Therapy: Simplifying and Diffusing with Variable Order Derivatives. MSc Mechanical Engineering, IST-UL. (Supervisors: D. Valério, S. Vinga). 15 Mar 2017.
Miguel Serpa Branco Faustino. Cancer patients stratification using multivariate clustering analysis for therapy optimization. MSc Mechanical Engineering, IST-UL. (Supervisors: S. Vinga and S. Vieira). 5 Jun 2017.
Massimo Amicone. Survival Analysis and Feature Selection in Ovarian Cancer. International Master in Bioinformatics School of Science. University of Bologna, Italy. (Supervisors: S Vinga, E. Capriotti). July 2017.
Hugo Daniel Paes Loureiro Santos Ambrósio. Robust machine learning methods for survival analysis. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, S. Vinga). 4 Dec 2017.
Cátia Sofia Tadeu Botas. Time series and forecasting. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, S. Vinga). 29 Nov 2017.
Margarida Sousa. Advances in Probabilistic Graphical Models. MSc in Applied Mathematics, IST-UL. (Supervisors: A. M. Carvalho, M. A. T. Figueiredo, P Mateus). 2017
Francisco Teles. Cancer therapy optimization based on unsupervised learning and multiple model adaptive control. M. Sc. Dissertation, Instituto Superior Técnico, 2017. (Supervisor: JM Lemos) [. [pdf]]
Elisa Pacheco. Cancer therapies based on optimal control methods. M. Sc. Dissertation, Instituto Superior Técnico, 2017. [pdf]..(Supervisor: JM Lemos)
Rui Guerra. Clustering of pharmacokinetic responses. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, P. Mateus). 2017
João Beirão. Early prediction from short time series data through multivariate correlations. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, P. Mateus). 2017.
Kishan Rameshchandra Rama. Temporal sequence alignment and agglomerative clustering for the analysis of medical longitudinal data. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: S. Vinga, A. M. Carvalho). 22 Jun 2018.
Ana Raquel Lopes Miranda. Studying bone remodeling for better cancer therapies. MSc Mechanical Engineering, IST-UL. (Supervisors: S Vinga, D Valério). 27 Jun 2018.
João Araújo Delgado Villa de Brito. Unravelling breast and prostate common gene signatures by Bayesian network learning. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: S. Vinga, A. M. Carvalho). 20 Jul 2018.
Pedro Miguel Falé Ferreira. Probabilistic Modelling of Single-cell Transcriptomics. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: S. Vinga, A. M. Carvalho). 31 Oct 2018.
João Pedro Lourenço dos Santos Belfo. Optimal Impulsive Control for Cancer Therapy. MSc Thesis in Electrical and Computer Engineering. Instituto Superior Técnico. (Supervisor: J Miranda Lemos). Oct 2018. [pdf]
Pedro Jorge Estrela Martinho. Network-based Regularization for Survival Analysis. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: S. Vinga, A. M. Carvalho). 23 Nov 2018.
Luís Bernardo de Brito Mendes Rei. Unveiling Interpretable Behavior In Two-Way High-Dimensional Clinical Data. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: S. Vinga, A. M. Carvalho). 23 Nov 2018.
Jorge Luís Fuzeta Serras. Outlier detection for multivariate time series. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: S. Vinga, A. M. Carvalho). 29 Nov 2018.
Sara Cristina Pontes Vieira, Analysis of heterogeneous and high-dimensional data of rheumatic diseases patients through clustering methods. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, S. Vinga). Nov 2019.
João Henrique Fialho Rodrigues, Time series analysis using restricted Boltzmann machines and dynamic Bayesian networks. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, P. Mateus). Nov 2019.
Manuel Pereira da Conceição Monteiro Anacleto, MSAX: Multivariate symbolic aggregate approximation for time series classification. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, S. Vinga). Nov 2019.
Guilherme Reis de Moura, Time series data imputation - Comparison of Dynamic Time Warping with Needleman-Wunsch algorithm. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, S. Vinga). Nov 2019.
Joana de Oliveira Mira Godinho, Latent variable modelling and variational inference for single-cell RNA-seq differential expression analysis. MSc in Computer Science (MEEC), IST-UL. (Supervisors: S. Vinga, A. M. Carvalho). Oct 2019.
Rita Sousa, Evolving meaning: using Genetic Programming to learn similarity perspectives for mining biomedical data, Master in Bioinformatics and Computational Biology, Faculdade de Ciências, University of Lisbon (Jul 2019). Supervisors: Cátia Pesquita and Sara Silva
Maria Inês Cotrim de Vilhena Diegues. Identification of common gene signatures in microarray and RNA-sequencing data using network-based regularization. MSc Biomedical Engineering (Supervisors: S Vinga, M Lopes). 13 Nov 2019.
Renata Isabel Jónatas Quintino. Prediction of Treatment Response in Patients with Multiple Myeloma undergoing Chemotherapy using MRI derived Imaging Biomarkers. MEBiol. (Supervisors: S Vinga, N Papanikolaou). 27 Nov 2019.
António Maria Forsado Martins Gonçalves. Computational analysis of isoform level regulation in T helper cells (Supervisors: S Vinga, L Graça). 2 Dec 2019.
Xia Anbang. Latent factors of Mult-Omics data and Clustering. MSc in Electrical and Computer Engineering (MEEC), IST-UL. (Supervisors: A. M. Carvalho, S Vinga). 18 Dec 2019.
Others (2)
Patricia Malea Ochoa. Dynamic Modeling of Bone Remodeling, Tumor Growth and Therapy. Bachelor Thesis in Industrial Tecnologies Engineering, Universidad Politecnica de Valencia, Spain. (Supervisors: D Valério and S Vinga). Jun 2017.
Antje Jensch. University of Stuttgart, Germany. Ensemble methods for omics data analysis. 11 Feb – 5 Apr 2019. Internship.
F - Models (1)
Ricardo Moreira, Jorge Martins. A software tool for automatic segmentation of the hip bones. IDMEC, IST, 2017.
G - Computational applications (11)
Joao Pinto, André Veríssimo, Alexandra M. Carvalho, Susana Vinga (2018) survBootOutliers: Concordance Based Bootstrap Methods for Outlier Detection in Survival Analysis. R package. CRAN - https://cran.r-project.org/web/packages/survBootOutliers/
A. Veríssimo (maintainer), MB Lopes, E Carrasquinha, S Vinga. glmSparseNet - Network Centrality Metrics for Elastic-Net Regularized Models - https://doi.org/doi:10.18129/B9.bioc.glmSparseNet
Saraiva-Agostinho N and Barbosa-Morais N (2019). psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation. R package version 3.1.0 https://github.com/nuno-agostinho/psichomics
Jorge Serras. Outlier detection in multivariate time series: METEOR - https://jorgeserras.shinyapps.io/outlierdetection/
João Beirão. Early classification in multivariate time series: MCEC - https://joaopbeirao.github.io/MCECalgorithm/
Margarida Sousa. Consistent and BFS-consistent k-graph dynamic Bayesian networks: cDBN and bcDBN https://margaridanarsousa.github.io/learn_cDBN/
Samuel Arcadinho. Clustering with dynamic Bayesian multinets: DBMs https://ssamdav.github.io/learnDBM/
Missing value imputation with dynamic Bayesian networks: MVI with DBNs https://ssamdav.github.io/learnDBN/
João Rodrigues. Combing BoLtzmAnn Machines with Dynamic Bayesian nEtworks: BLADE https://github.com/joaor96/BLADE
Joana Godinho. SIngle-cEll differeNtial Analysis: SIENA - https://github.com/JoanaGodinho/SIENA
Pedro Falé Ferreira. Extended ZINBayes: ext-ZINBayes https://github.com/pedrofale/zinbayes