Universal sequence map (USM) of arbitrary discrete sequences. - Jonas S. Almeida; Susana Vinga (BMC Bioinform., 2002)

Alignment-free sequence comparison-a review. - Susana Vinga; Jonas S. Almeida (Bioinform., 2003)

Comparative evaluation of word composition distances for the recognition of SCOP relationships. - Susana Vinga; Rodrigo Gouveia-Oliveira; Jonas S. Almeida (Bioinform., 2004)

Computing distribution of scale independent motifs in biological sequences. - Jonas S. Almeida; Susana Vinga (Algorithms Mol. Biol., 2006)

Automated smoother for the numerical decoupling of dynamics models. - Marco Vilela; Carlos Cristiano H. Borges; Susana Vinga; Ana Tereza Ribeiro de Vasconcelos; Helena Santos; Eberhard O. Voit; Jonas S. Almeida (BMC Bioinform., 2007)

Local Renyi entropic profiles of DNA sequences. - Susana Vinga; Jonas S. Almeida (BMC Bioinform., 2007)

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. - Ana C. Casimiro; Susana Vinga; Ana T. Freitas; Arlindo L. Oliveira (BMC Bioinform., 2008)

Parameter optimization in S-system models. - Marco Vilela; I-Chun Chou; Susana Vinga; Ana Tereza Ribeiro de Vasconcelos; Eberhard O. Voit; Jonas S. Almeida (BMC Syst. Biol., 2008)

Biological sequences as pictures - a generic two dimensional solution for iterated maps. - Jonas S. Almeida; Susana Vinga (BMC Bioinform., 2009)

Identification of neutral biochemical network models from time series data. - Marco Vilela; Susana Vinga; Marco Maia; Eberhard O. Voit; Jonas S. Almeida (BMC Syst. Biol., 2009)

A Data Mining Approach for the Detection of High-Risk Breast Cancer Groups. - Orlando Anunciação; Bruno C. Gomes; Susana Vinga; Jorge Gaspar; Arlindo L. Oliveira; José Rueff (IWPACBB, 2010)

Optimization strategies for metabolic networks. - Alexandre Domingues; Susana Vinga; João Miranda Lemos (BMC Syst. Biol., 2010)

Unified Modeling of Several Perturbation Experiments in Systems Biology - A Case Study on the Glucose Uptake of Lactococcus Lactis. - András Hartmann; Susana Vinga; João Miranda Lemos (BIOINFORMATICS, 2011)

Nonlinear MPC of HIV-1 infection with periodic inputs. - Joao V. Pinheiro; João Miranda Lemos; Susana Vinga (CDC/ECC, 2011)

Quantitative Modeling the Saccharomyces cerevisiae FLR1 Regulatory Network Using an S-System Formalism. - Dulce Calçada; Susana Vinga; Ana T. Freitas; Arlindo L. Oliveira (HISB, 2011)

Quantitative Modeling of the Saccharomyces cerevisiae Flr1 regulatory Network Using an S-System Formalism. - Dulce Calçada; Susana Vinga; Ana T. Freitas; Arlindo L. Oliveira (J. Bioinform. Comput. Biol., 2011)

A Survey on Methods for Modeling and Analyzing Integrated Biological Networks. - Nuno Tenazinha; Susana Vinga (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Multi-level Dynamic Modeling in Biological Systems - Application of Hybrid Petri Nets to Network Simulation. - Rafael S. Costa; Daniel Machado; Ana Rute Neves; Susana Vinga (BIOINFORMATICS, 2012)

Identification of Hiv-1 Dynamics - Estimating the Noise Model, Constant and Time-varying Parameters of Long-term Clinical Data. - András Hartmann; Susana Vinga; João Miranda Lemos (BIOINFORMATICS, 2012)

Fractal MapReduce decomposition of sequence alignment. - Jonas S. Almeida; Alexander Grüneberg; Wolfgang Maass 002; Susana Vinga (Algorithms Mol. Biol., 2012)

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis. - Susana Vinga; Alexandra M. Carvalho; Alexandre P. Francisco; Luís M. S. Russo; Jonas S. Almeida (Algorithms Mol. Biol., 2012)

Prediction of Forest Aboveground Biomass: An Exercise on Avoiding Overfitting. - Sara Silva; Vijay Ingalalli; Susana Vinga; João Manuel de Brito Carreiras; Joana B. Melo; Mauro Castelli; Leonardo Vanneschi; Ivo Gonçalves; José Caldas (EvoApplications, 2013)

Hybrid identification of time-varying parameter with particle filtering and expectation maximization. - András Hartmann; Susana Vinga; João Miranda Lemos (MED, 2013)

Parameter estimation and identifiability of a HIV-1 model. - Ana Portêlo; João Miranda Lemos; Susana Vinga; Ruy M. Ribeiro; J. P. Cruz; Emília Valadas (MED, 2013)

BGFit: management and automated fitting of biological growth curves. - André Veríssimo; Laura Paixão; Ana Rita Neves; Susana Vinga (BMC Bioinform., 2013)

Exploring the Cellular Objective in Flux Balance Constraint-Based Models. - Rafael S. Costa; Son Nguyen; András Hartmann; Susana Vinga (CMSB, 2014)

Editorial: Alignment-free methods in computational biology. - Susana Vinga (Briefings Bioinform., 2014)

Information theory applications for biological sequence analysis. - Susana Vinga (Briefings Bioinform., 2014)

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. - Rafael S. Costa; André Veríssimo; Susana Vinga (BMC Syst. Biol., 2014)

Identifying IIR filter coefficients using particle swarm optimization with application to reconstruction of missing cardiovascular signals. - András Hartmann; João Miranda Lemos; Rafael S. Costa; Susana Vinga (Eng. Appl. Artif. Intell., 2014)

Outlier Detection in Survival Analysis based on the Concordance C-index. - João Diogo Pinto; Alexandra M. Carvalho; Susana Vinga (BIOINFORMATICS, 2015)

Fuzzy Clustering for Incomplete Short Time Series Data. - Lúcia P. Cruz; Susana M. Vieira; Susana Vinga (EPIA, 2015)

Outlier Detection in Cox Proportional Hazards Models Based on the Concordance c-Index. - João Diogo Pinto; Alexandra M. Carvalho; Susana Vinga (MOD, 2015)

Polynomial-time algorithm for learning optimal tree-augmented dynamic Bayesian networks. - José L. Monteiro; Susana Vinga; Alexandra M. Carvalho (UAI, 2015)

Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics. - András Hartmann; João Miranda Lemos; Susana Vinga (Comput. Biol. Medicine, 2015)

DegreeCox - a network-based regularization method for survival analysis. - André Veríssimo; Arlindo Limede Oliveira; Marie-France Sagot; Susana Vinga (BMC Bioinform., 2016)

Optimal and receding horizon control of tumor growth in myeloma bone disease. - João Miranda Lemos; Daniela V. Caiado; Rui Coelho; Susana Vinga (Biomed. Signal Process. Control., 2016)

Unsupervised learning of pharmacokinetic responses. - Elson Tomás; Susana Vinga; Alexandra M. Carvalho (Comput. Stat., 2017)

Variational Inference in Probabilistic Single-cell RNA-seq Models. - Pedro F. Ferreira; Alexandra M. Carvalho; Susana Vinga (CIBB, 2018)

Unravelling Breast and Prostate Common Gene Signatures by Bayesian Network Learning. - João Villa-Brito; Marta B. Lopes; Alexandra M. Carvalho; Susana Vinga (CIBB, 2018)

Variable Selection and Outlier Detection in Regularized Survival Models: Application to Melanoma Gene Expression Data. - Eunice Carrasquinha; André Veríssimo; Marta B. Lopes; Susana Vinga (LOD, 2018)

Identification of influential observations in high-dimensional cancer survival data through the rank product test. - Eunice Carrasquinha; André Veríssimo; Marta B. Lopes; Susana Vinga (BioData Min., 2018)

Ensemble outlier detection and gene selection in triple-negative breast cancer data. - Marta B. Lopes; André Veríssimo; Eunice Carrasquinha; Sandra Casimiro; Niko Beerenwinkel; Susana Vinga (BMC Bioinform., 2018)

Simplifying biochemical tumorous bone remodeling models through variable order derivatives. - Joana P. Neto 002; Rui Moura Coelho; Duarte Valério; Susana Vinga; Dominik Sierociuk; Wiktor Malesza; Michal Macias; Andrzej Dzielinski (Comput. Math. Appl., 2018)

MSAX: Multivariate Symbolic Aggregate Approximation for Time Series Classification. - Manuel Anacleto; Susana Vinga; Alexandra M. Carvalho (CIBB, 2019)

Random Sample Consensus for the Robust Identification of Outliers in Cancer Data. - André Veríssimo; Marta B. Lopes; Eunice Carrasquinha; Susana Vinga (CIBB, 2019)

On the Role of Hub and Orphan Genes in the Diagnosis of Breast Invasive Carcinoma. - Marta B. Lopes; André Veríssimo; Eunice Carrasquinha; Susana Vinga (LOD, 2019)

Twiner: correlation-based regularization for identifying common cancer gene signatures. - Marta B. Lopes; Sandra Casimiro; Susana Vinga (BMC Bioinform., 2019)

Modelling cancer outcomes of bone metastatic patients: combining survival data with N-Telopeptide of type I collagen (NTX) dynamics through joint models. - Hugo Loureiro; Eunice Carrasquinha; Irina Alho; Arlindo R. Ferreira; Luís Costa; Alexandra M. Carvalho; Susana Vinga (BMC Medical Informatics Decis. Mak., 2019)

AliClu - Temporal sequence alignment for clustering longitudinal clinical data. - Kishan Rama; Helena Canhão; Alexandra M. Carvalho; Susana Vinga (BMC Medical Informatics Decis. Mak., 2019)

Latent Variable Modelling and Variational Inference for scRNA-seq Differential Expression Analysis. - Joana Godinho; Alexandra M. Carvalho; Susana Vinga (ICCABS, 2020)

Predictive Medicine Using Interpretable Recurrent Neural Networks. - André Ferreira; Sara C. Madeira; Marta Gromicho; Mamede de Carvalho; Susana Vinga; Alexandra M. Carvalho (ICPR Workshops (1), 2020)

Network-Based Variable Selection for Survival Outcomes in Oncological Data. - Eunice Carrasquinha; André Veríssimo; Marta B. Lopes; Susana Vinga (IWBBIO, 2020)

Identification of Common Gene Signatures in Microarray and RNA-Sequencing Data Using Network-Based Regularization. - Inês Diegues; Susana Vinga; Marta B. Lopes (IWBBIO, 2020)

Sparse Consensus Classification for Discovering Novel Biomarkers in Rheumatoid Arthritis. - Cláudia S. Constantino; Alexandra M. Carvalho; Susana Vinga (LOD (1), 2020)

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering. - Ricardo Andrade; Mahdi Doostmohammadi; João L. Santos; Marie-France Sagot; Nuno P. Mira; Susana Vinga (BMC Bioinform., 2020)

Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data. - Marta B. Lopes; Susana Vinga (BMC Bioinform., 2020)

Structured sparsity regularization for analyzing high-dimensional omics data. - Susana Vinga (Briefings Bioinform., 2021)

Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis. - Cláudia S. Constantino; Alexandra M. Carvalho; Susana Vinga (BioData Min., 2021)

Comparative Evaluation of Classification Indexes and Outlier Detection of Microcytic Anaemias in a Portuguese Sample. - Beatriz N. Leitão; Paula Faustino; Susana Vinga (EPIA, 2022)

Tutorial - Machine Learning and Information Theoretic Methods for Molecular Biology and Medicine. - Thomas Villmann; Jonas S. Almeida; John A. Lee; Susana Vinga (ESANN, 2022)

Evaluating the Causal Role of Environmental Data in Shellfish Biotoxin Contamination on the Portuguese Coast. - Ana Rita Baião; Carolina Peixoto; Marta B. Lopes; Pedro Reis Costa; Alexandra M. Carvalho; Susana Vinga (EPIA (2), 2023)

Causal Graph Discovery for Explainable Insights on Marine Biotoxin Shellfish Contamination. - Diogo Ribeiro; Filipe Ferraz; Marta B. Lopes; Susana Rodrigues; Pedro Reis Costa; Susana Vinga; Alexandra M. Carvalho (IDEAL, 2023)

Comparative Analysis of Machine Learning Models for Time-Series Forecasting of Escherichia Coli Contamination in Portuguese Shellfish Production Areas. - Filipe Ferraz; Diogo Ribeiro; Marta B. Lopes; Sónia Pedro; Susana Vinga; Alexandra M. Carvalho (LOD (1), 2023)

Using Markov chains and temporal alignment to identify clinical patterns in Dementia. - Luísa Marote Costa; João Pedro Colaço; Alexandra M. Carvalho; Susana Vinga; Andreia Sofia Teixeira (J. Biomed. Informatics, 2023)

Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization. - Carolina Peixoto; Marta B. Lopes; Marta Martins; Sandra Casimiro; Daniel Sobral; Ana Rita Grosso; Catarina Abreu; Daniela Macedo; Ana Lúcia Costa; Helena Pais; Cecília Alvim; André Mansinho; et al. (BMC Bioinform., 2023)

A robust deep-learning model for fully automatic segmentation of lymphoma lesions on whole-body [18F]FDG PET/CT images. - Cláudia S. Constantino; Francisco P. M. Oliveira; Sónia Leocádio; Mariana Silva; Carla Oliveira; Joana Correia Castanheira; Ângelo Silva; Sofia Vaz; Ricardo Teixeira; Manuel Neves; Paulo Lúcio; Cristina João; et al. (ISBI, 2024)

A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches. - Ana R. Baião; Zhaoxiang Cai; Rebecca C. Poulos; Phillip J. Robinson; Roger R. Reddel; Qing Zhong 002; Susana Vinga; Emanuel Gonçalves (Briefings Bioinform., 2025)

Fractal Language Modelling by Universal Sequence Maps (USM). - Jonas S. Almeida; Daniel E. Russ; Susana Vinga; Ines Duarte; Lee Mason; Praphulla M. S. Bhawsar; Aaron Ge; Arlindo L. Oliveira; Jeya Balaji Balasubramanian (CoRR, 2025)