Susana Vinga

71 papers A 1B 2C 1Misc 2Journal 39Unranked 26
YearRankTypeTitle / Venue / Authors
2025 J jnl
A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches.
Briefings Bioinform.
Ana Rita Baião, Zhaoxiang Cai, Rebecca C. Poulos, Phillip J. Robinson, Roger R. Reddel, Qing Zhong, Susana Vinga, Emanuel J. V. Gonçalves
2025 J jnl
Fractal Language Modelling by Universal Sequence Maps (USM).
CoRR
Jonas S. Almeida, Daniel E. Russ, Susana Vinga, Ines Duarte, Lee Mason, Praphulla M. S. Bhawsar, Aaron Ge, Arlindo L. Oliveira, Jeya Balaji Balasubramanian
2024 — conf
A robust deep-learning model for fully automatic segmentation of lymphoma lesions on whole-body [
ISBI
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, Susana Vinga, Durval Campos Costa
2023 C conf
Causal Graph Discovery for Explainable Insights on Marine Biotoxin Shellfish Contamination.
IDEAL
Diogo Ribeiro, Filipe Ferraz, Marta B. Lopes, Susana Rodrigues, Pedro Reis Costa, Susana Vinga, Alexandra M. Carvalho
2023 — conf
Comparative Analysis of Machine Learning Models for Time-Series Forecasting of Escherichia Coli Contamination in Portuguese Shellfish Production Areas.
LOD (1)
Filipe Ferraz, Diogo Ribeiro, Marta B. Lopes, Sónia Pedro, Susana Vinga, Alexandra M. Carvalho
2023 — conf
Evaluating the Causal Role of Environmental Data in Shellfish Biotoxin Contamination on the Portuguese Coast.
EPIA (2)
Ana Rita Baião, Carolina Peixoto, Marta B. Lopes, Pedro Reis Costa, Alexandra M. Carvalho, Susana Vinga
2023 J jnl
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization.
BMC Bioinform.
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, Pedro Filipe, Pedro Marques da Costa, Afonso Fernandes, Paula Borralho, Cristina Ferreira, João Malaquias, António Quintela, Shannon Kaplan, Mahdi Golkaram, Michael Salmans, Nafeesa Khan, Raakhee Vijayaraghavan, Shile Zhang, Traci Pawlowski, Jim Godsey, Alex So, Li Liu, Luís Costa, Susana Vinga
2023 J jnl
Using Markov chains and temporal alignment to identify clinical patterns in Dementia.
J. Biomed. Informatics
Luísa Marote Costa, João Pedro Colaço, Alexandra M. Carvalho, Susana Vinga, Andreia Sofia Teixeira
2022 Misc conf
Comparative Evaluation of Classification Indexes and Outlier Detection of Microcytic Anaemias in a Portuguese Sample.
EPIA
Beatriz N. Leitão, Paula Faustino, Susana Vinga
2022 B conf
Tutorial - Machine Learning and Information Theoretic Methods for Molecular Biology and Medicine.
ESANN
Thomas Villmann, Jonas S. Almeida, John A. Lee, Susana Vinga
2021 J jnl
Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis.
BioData Min.
Cláudia S. Constantino, Alexandra M. Carvalho, Susana Vinga
2021 J jnl
Structured sparsity regularization for analyzing high-dimensional omics data.
Briefings Bioinform.
Susana Vinga
2020 — conf
Identification of Common Gene Signatures in Microarray and RNA-Sequencing Data Using Network-Based Regularization.
IWBBIO
Inês Diegues, Susana Vinga, Marta B. Lopes
2020 — conf
Latent Variable Modelling and Variational Inference for scRNA-seq Differential Expression Analysis.
ICCABS
Joana Godinho, Alexandra M. Carvalho, Susana Vinga
2020 J jnl
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering.
BMC Bioinform.
Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira, Susana Vinga
2020 — conf
Network-Based Variable Selection for Survival Outcomes in Oncological Data.
IWBBIO
Eunice Carrasquinha, André Veríssimo, Marta B. Lopes, Susana Vinga
2020 — conf
Predictive Medicine Using Interpretable Recurrent Neural Networks.
ICPR Workshops (1)
André Ferreira, Sara C. Madeira, Marta Gromicho, Mamede de Carvalho, Susana Vinga, Alexandra M. Carvalho
2020 — conf
Sparse Consensus Classification for Discovering Novel Biomarkers in Rheumatoid Arthritis.
LOD (1)
Cláudia S. Constantino, Alexandra M. Carvalho, Susana Vinga
2020 J jnl
Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data.
BMC Bioinform.
Marta B. Lopes, Susana Vinga
2019 J jnl
AliClu - Temporal sequence alignment for clustering longitudinal clinical data.
BMC Medical Informatics Decis. Mak.
Kishan Rama, Helena Canhão, Alexandra M. Carvalho, Susana Vinga
2019 — conf
MSAX: Multivariate Symbolic Aggregate Approximation for Time Series Classification.
CIBB
Manuel Anacleto, Susana Vinga, Alexandra M. Carvalho
2019 J jnl
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 Decis. Mak.
Hugo Loureiro, Eunice Carrasquinha, Irina Alho, Arlindo R. Ferreira, Luís Costa, Alexandra M. Carvalho, Susana Vinga
2019 — conf
On the Role of Hub and Orphan Genes in the Diagnosis of Breast Invasive Carcinoma.
LOD
Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Susana Vinga
2019 — conf
Random Sample Consensus for the Robust Identification of Outliers in Cancer Data.
CIBB
André Veríssimo, Marta B. Lopes, Eunice Carrasquinha, Susana Vinga
2019 J jnl
Twiner: correlation-based regularization for identifying common cancer gene signatures.
BMC Bioinform.
Marta B. Lopes, Sandra Casimiro, Susana Vinga
2019 J jnl
Twiner: correlation-based regularization for identifying common cancer gene signatures.
BMC Bioinform.
Marta B. Lopes, Sandra Casimiro, Susana Vinga
2018 J jnl
Ensemble outlier detection and gene selection in triple-negative breast cancer data.
BMC Bioinform.
Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
2018 J jnl
Identification of influential observations in high-dimensional cancer survival data through the rank product test.
BioData Min.
Eunice Carrasquinha, André Veríssimo, Marta B. Lopes, Susana Vinga
2018 J jnl
Simplifying biochemical tumorous bone remodeling models through variable order derivatives.
Comput. Math. Appl.
Joana P. Neto, Rui Moura Coelho, Duarte Valério, Susana Vinga, Dominik Sierociuk, Wiktor Malesza, Michal Macias, Andrzej Dzielinski
2018 — conf
Unravelling Breast and Prostate Common Gene Signatures by Bayesian Network Learning.
CIBB
João Villa-Brito, Marta B. Lopes, Alexandra M. Carvalho, Susana Vinga
2018 — conf
Variable Selection and Outlier Detection in Regularized Survival Models: Application to Melanoma Gene Expression Data.
LOD
Eunice Carrasquinha, André Veríssimo, Marta B. Lopes, Susana Vinga
2018 — conf
Variational Inference in Probabilistic Single-cell RNA-seq Models.
CIBB
Pedro F. Ferreira, Alexandra M. Carvalho, Susana Vinga
2017 J jnl
Unsupervised learning of pharmacokinetic responses.
Comput. Stat.
Elson Tomás, Susana Vinga, Alexandra M. Carvalho
2016 J jnl
DegreeCox - a network-based regularization method for survival analysis.
BMC Bioinform.
André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga
2016 J jnl
Optimal and receding horizon control of tumor growth in myeloma bone disease.
Biomed. Signal Process. Control.
João Miranda Lemos, Daniela V. Caiado, Rui Coelho, Susana Vinga
2015 Misc conf
Fuzzy Clustering for Incomplete Short Time Series Data.
EPIA
Lúcia P. Cruz, Susana M. Vieira, Susana Vinga
2015 J jnl
Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics.
Comput. Biol. Medicine
András Hartmann, João Miranda Lemos, Susana Vinga
2015 — conf
Outlier Detection in Cox Proportional Hazards Models Based on the Concordance c-Index.
MOD
João Diogo Pinto, Alexandra M. Carvalho, Susana Vinga
2015 — conf
Outlier Detection in Survival Analysis based on the Concordance C-index.
BIOINFORMATICS
João Diogo Pinto, Alexandra M. Carvalho, Susana Vinga
2015 A conf
Polynomial-time algorithm for learning optimal tree-augmented dynamic Bayesian networks.
UAI
José L. Monteiro, Susana Vinga, Alexandra M. Carvalho
2014 J jnl
Editorial: Alignment-free methods in computational biology.
Briefings Bioinform.
Susana Vinga
2014 — conf
Exploring the Cellular Objective in Flux Balance Constraint-Based Models.
CMSB
Rafael S. Costa, Son Nguyen, András Hartmann, Susana Vinga
2014 J jnl
Identifying IIR filter coefficients using particle swarm optimization with application to reconstruction of missing cardiovascular signals.
Eng. Appl. Artif. Intell.
András Hartmann, João Miranda Lemos, Rafael S. Costa, Susana Vinga
2014 J jnl
Information theory applications for biological sequence analysis.
Briefings Bioinform.
Susana Vinga
2014 J jnl
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems.
BMC Syst. Biol.
Rafael S. Costa, André Veríssimo, Susana Vinga
2013 J jnl
BGFit: management and automated fitting of biological growth curves.
BMC Bioinform.
André Veríssimo, Laura Paixão, Ana Rita Neves, Susana Vinga
2013 — conf
Hybrid identification of time-varying parameter with particle filtering and expectation maximization.
MED
András Hartmann, Susana Vinga, João Miranda Lemos
2013 — conf
Parameter estimation and identifiability of a HIV-1 model.
MED
Ana Portêlo, João Miranda Lemos, Susana Vinga, Ruy M. Ribeiro, J. P. Cruz, Emília Valadas
2013 B conf
Prediction of Forest Aboveground Biomass: An Exercise on Avoiding Overfitting.
EvoApplications
Sara Silva, Vijay Ingalalli, Susana Vinga, João Manuel de Brito Carreiras, Joana B. Melo, Mauro Castelli, Leonardo Vanneschi, Ivo Gonçalves, José Caldas
2012 J jnl
Fractal MapReduce decomposition of sequence alignment.
Algorithms Mol. Biol.
Jonas S. Almeida, Alexander Grüneberg, Wolfgang Maass, Susana Vinga
2012 — conf
Identification of Hiv-1 Dynamics - Estimating the Noise Model, Constant and Time-varying Parameters of Long-term Clinical Data.
BIOINFORMATICS
András Hartmann, Susana Vinga, João Miranda Lemos
2012 — conf
Multi-level Dynamic Modeling in Biological Systems - Application of Hybrid Petri Nets to Network Simulation.
BIOINFORMATICS
Rafael S. Costa, Daniel Machado, Ana Rute Neves, Susana Vinga
2012 J jnl
Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.
Algorithms Mol. Biol.
Susana Vinga, Alexandra M. Carvalho, Alexandre P. Francisco, Luís M. S. Russo, Jonas S. Almeida
2011 J jnl
A Survey on Methods for Modeling and Analyzing Integrated Biological Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Nuno Tenazinha, Susana Vinga
2011 — conf
Nonlinear MPC of HIV-1 infection with periodic inputs.
CDC/ECC
Joao V. Pinheiro, João Miranda Lemos, Susana Vinga
2011 J jnl
Quantitative Modeling of the
J. Bioinform. Comput. Biol.
Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira
2011 — conf
Quantitative Modeling the Saccharomyces cerevisiae FLR1 Regulatory Network Using an S-System Formalism.
HISB
Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira
2011 — conf
Unified Modeling of Several Perturbation Experiments in Systems Biology - A Case Study on the Glucose Uptake of Lactococcus Lactis.
BIOINFORMATICS
András Hartmann, Susana Vinga, João Miranda Lemos
2010 — conf
A Data Mining Approach for the Detection of High-Risk Breast Cancer Groups.
IWPACBB
Orlando Anunciação, Bruno C. Gomes, Susana Vinga, Jorge Gaspar, Arlindo L. Oliveira, José Rueff
2010 J jnl
Optimization strategies for metabolic networks.
BMC Syst. Biol.
Alexandre Domingues, Susana Vinga, João Miranda Lemos
2009 J jnl
Biological sequences as pictures - a generic two dimensional solution for iterated maps.
BMC Bioinform.
Jonas S. Almeida, Susana Vinga
2009 J jnl
Identification of neutral biochemical network models from time series data.
BMC Syst. Biol.
Marco Vilela, Susana Vinga, Marco Maia, Eberhard O. Voit, Jonas S. Almeida
2009 — conf
Optimization strategies for metabolic networks.
ECC
Alexandre Domingues, João Miranda Lemos, Susana Vinga
2008 J jnl
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.
BMC Bioinform.
Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira
2008 J jnl
Parameter optimization in S-system models.
BMC Syst. Biol.
Marco Vilela, I-Chun Chou, Susana Vinga, Ana Tereza Ribeiro de Vasconcelos, Eberhard O. Voit, Jonas S. Almeida
2007 J jnl
Automated smoother for the numerical decoupling of dynamics models.
BMC Bioinform.
Marco Vilela, Carlos Cristiano H. Borges, Susana Vinga, Ana Tereza Ribeiro de Vasconcelos, Helena Santos, Eberhard O. Voit, Jonas S. Almeida
2007 J jnl
Local Renyi entropic profiles of DNA sequences.
BMC Bioinform.
Susana Vinga, Jonas S. Almeida
2006 J jnl
Computing distribution of scale independent motifs in biological sequences.
Algorithms Mol. Biol.
Jonas S. Almeida, Susana Vinga
2004 J jnl
Comparative evaluation of word composition distances for the recognition of SCOP relationships.
Bioinform.
Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida
2003 J jnl
Alignment-free sequence comparison-a review.
Bioinform.
Susana Vinga, Jonas S. Almeida
2002 J jnl
Universal sequence map (USM) of arbitrary discrete sequences.
BMC Bioinform.
Jonas S. Almeida, Susana Vinga