OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon

Project Information

OLISSIPO

Grant agreement ID: 951970

DOI

10.3030/951970

Project closed

EC signature date 27 June 2020

Start date 1 January 2021

End date 30 June 2024

Funded under

• Twinning of research institutions

Total cost

€ 900 000,00

EU contribution

€ 900 000,00

Coordinated by

INESC ID - INSTITUTO DE ENGENHARIADE SISTEMAS E COMPUTADORES, INVESTIGACAO E DESENVOLVIMENTO EM LISBOA
Portugal

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Websites, patent fillings, videos etc. (2)

Project website
Promotional materials

Documents, reports (19)

OLISSIPO impact assessment and forecast
OLISSIPO innovation management and results exploitation plan
Midterm report on Dissemination, communication and outreach activities
Final annual project meeting with the SAB
Final report on organized joint events, schools, workshops and conferences

Profiting from the staff exchange activities and expert visits to Lisbon (WP1, Tasks 1.1-1.3), a series ofComputational Biology seminars and lectures will be implemented. The invited speakers will give a seminaropen to the scientific community, thus increasing the impact of the planned activities. The lectures will takeplace at Instituto Superior Técnico (IST) or at other venues in the Lisbon area ( e.g. Medical School, Faculty ofSciences) and will be published in the communication channels of the University of Lisbon. We expect 3lectures per year. The full programme (dates, scheduling, invited speakers) will be defined and delivered(D2.1).

Mid-term report on activities targeted for Early Stage Researchers
Final report on staff exchanges

Final report on staff exchanges.

Midterm report on research management training activities, impact, and forecast

We will explore, as much as possible, the complementarities and synergies between Tasks5.3 and Tasks 4.3, i.e. , provide training targeting the PI, her team, ESRs, and the associated staff at theINESC-ID units — see also e.g. the training in Scientific Communication for the PI and the ESR, in order toincrease the impact of research activities and raise general public awareness of science and technologyimportance. The impact and forecast of these measures will be evaluated.

Second annual project meeting with the SAB

After all the project meetings, a report will be produced

Midterm report staff exchanges
OLISSIPO management training plan

This task will define several activities for training the INESCID staff the PI and her group in order toincrease the funding opportunities of the team and improve its research profile These activities range fromproject management to proposal writing as well as HR managementBelow is a table with the expected Training the participants involved the major goals and topics covered Thisplan will be reviewed and updated during the first months of the project

OLISSIPO Early Stage Researchers training programme

Profiting from the existing staff exchange programme WP1 Early Stage Researchers ESR will be invited tovisit the other Twinning partners for 13 weeks They will also participate in other OLISSIPO activitiesnamely project meetings and lab retreats and will contribute to the organization of scientific eventsWe will also implement activities to invite ESRs from portuguese speaking countries eg Angola and Brazilto visit INESCID following strictly gender balance issues in the selection of the candidates This aims atexpanding the OLISSIPO network to Africa and South America with impact on the visibility andattractiveness of INESCID and to further expand and strengthen collaborations outside Europe reinforcingLisbon as a key hub between Europe and nonEU countries

Midterm report on organized joint events, schools, workshops and conferences

Profiting from the staff exchange activities and expert visits to Lisbon (WP1, Tasks 1.1-1.3), a series of Computational Biology seminars and lectures will be implemented. The invited speakers will give a seminar open to the scientific community, thus increasing the impact of the planned activities. The lectures will take place at Instituto Superior Técnico (IST) or at other venues in the Lisbon area ( e.g. Medical School, Faculty of Sciences) and will be published in the communication channels of the University of Lisbon. We expect 3 lectures per year. The full programme (dates, scheduling, invited speakers) will be defined and delivered.

First annual project meeting with the SAB

These meetings will have the participation of the Scientific Advisory Board SABIn the first kickoff meeting the OLISSIPO Project Handbook will be presented and discussed D61 It includes all internal communication procedures such as contacts document management and dissemination among the partners templates reporting scheduling updated workplanstravellingactivities and also reviewedKey Performance Indicators KPI

OLISSIPO outreach activities programme
Evolution of the publications in hign impact journals in the relevant research fields
OLISSIPO Short-term staff exchange plan

OLISSIPO Shortterm staff exchange plan

Final report on activities targeted for Early Stage Researchers
OLISSIPO Schools, and Workshops, and Invited lecture series programme

OLISSIPO Schools and Workshops and Invited lecture series programme M2To be updated throughout the whole duration of the project

Publications

Peer reviewed articles (74)

Oncotree2vec — a method for embedding and clustering of tumor mutation trees

Author(s): Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel
Published in: Bioinformatics, Issue 40, 2024, Page(s) i180-i188, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btae214

Reduced order models of myelinated axonal compartments.

Author(s): Daniel Ioan, Ruxandra Bărbulescu, Luis Miguel Silveira, Gabriela Ciuprina
Published in: Journal of Computational Neuroscience, 2019, ISSN 0929-5313
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10827-019-00726-4

On Finding Optimal (Dynamic) Arborescences

Author(s): Joaquim Espada, Alexandre P. Francisco, Tatiana Rocher, Luís M. S. Russo, Cátia Vaz
Published in: Algorithms, Issue 16, 2023, Page(s) 559, ISSN 1999-4893
Publisher: MDPI Open Access Publishing
DOI: 10.3390/a16120559

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0

Author(s): Aurélien Naldi, Céline Hernandez, Wassim Abou-Jaoudé, Pedro T. Monteiro, Claudine Chaouiya, Denis Thieffry
Published in: Frontiers in Physiology, Issue 9, 2018, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2018.00646

Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data

Author(s): Marta B. Lopes, Susana Vinga
Published in: BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-3390-4

phyloDB: A framework for large-scale phylogenetic analysis of sequence based typing data

Author(s): Bruno Lourenço, Cátia Vaz, Miguel E. Coimbra, Alexandre P. Francisco
Published in: SoftwareX, Issue 26, 2024, Page(s) 101668, ISSN 2352-7110
Publisher: Elsevier
DOI: 10.1016/j.softx.2024.101668

Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization

Author(s): 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 Vijayara
Published in: BMC Bioinformatics, Issue 24, 2023, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-05104-z

Robust identification of target genes and outliers in triple-negative breast cancer data.

Author(s): Pieter Segaert, Marta B Lopes, Sandra Casimiro, Susana Vinga, Peter J Rousseeuw
Published in: Statistical Methods in Medical Research, 2019, ISSN 0962-2802
Publisher: SAGE Publications
DOI: 10.1177/0962280218794722

Antagonistic Functions of Androgen Receptor and NF-κB in Prostate Cancer—Experimental and Computational Analyses

Author(s): José Basílio, Bernhard Hochreiter, Bastian Hoesel, Emira Sheshori, Marion Mussbacher, Rudolf Hanel, Johannes A. Schmid
Published in: Cancers, Issue 14, 2024, Page(s) 6164, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14246164

SpliceTAPyR - An Efficient Method for Transcriptome Alignment.

Author(s): Andreia Sofia Teixeira, Francisco Fernandes and Alexandre P. Francisco
Published in: International Journal of Foundations of Computer Science, 2018, ISSN 0129-0541
Publisher: World Scientific Publishing Co
DOI: 10.1142/s0129054118430049

Grapevine variety identification using “Big Data” collected with miniaturized spectrometer combined with support vector machines and convolutional neural networks

Author(s): Armando M. Fernandes, Andrei B. Utkin, José Eiras-Dias, Jorge Cunha, José Silvestre, Pedro Melo-Pinto
Published in: Computers and Electronics in Agriculture, Issue 163, 2019, Page(s) 104855, ISSN 0168-1699
Publisher: Elsevier BV
DOI: 10.1016/j.compag.2019.104855

Base editing screens map mutations affecting interferon-γ signaling in cancer

Author(s): Matthew A. Coelho, Sarah Cooper, Magdalena E. Strauss, Emre Karakoc, Shriram Bhosle, Emanuel Gonçalves, Gabriele Picco, Thomas Burgold, Chiara M. Cattaneo, Vivien Veninga, Sarah Consonni, Cansu Dinçer, Sara F. Vieira, Freddy Gibson, Syd Barthorpe, Claire Hardy, Joel Rein, Mark Thomas, John Marioni, Emile E. Voest, Andrew Bassett, Mathew J. Garnett
Published in: Cancer Cell, Issue 41, 2024, Page(s) 288-303.e6, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2022.12.009

G-bic: generating synthetic benchmarks for biclustering

Author(s): Eduardo N. Castanho, João P. Lobo, Rui Henriques, Sara C. Madeira
Published in: BMC Bioinformatics, Issue 24, 2024, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-023-05587-4

AliClu - Temporal sequence alignment for clustering longitudinal clinical data

Author(s): Kishan Rama, Helena Canhão, Alexandra M. Carvalho, Susana Vinga
Published in: BMC Medical Informatics and Decision Making, Issue 19/1, 2019, ISSN 1472-6947
Publisher: BioMed Central
DOI: 10.1186/s12911-019-1013-7

Point-of-care quantification of serum cellular fibronectin levels for stratification of ischemic stroke patients

Author(s): Elisabete Fernandes, Tomás Sobrino, Verónica C. Martins, Ignacio Lopez-loureiro, Francisco Campos, José Germano, Manuel Rodríguez-Pérez, Susana Cardoso, Dmitri Y. Petrovykh, José Castillo, Paulo P. Freitas
Published in: Nanomedicine: Nanotechnology, Biology and Medicine, Issue 30, 2020, Page(s) 102287, ISSN 1549-9634
Publisher: Elsevier BV
DOI: 10.1016/j.nano.2020.102287

Repairing Boolean logical models from time-series data using Answer Set Programming.

Author(s): Alexandre Lemos, Inês Lynce and Pedro T. Monteiro
Published in: Algorithms for Molecular Biology, 2019, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-019-0145-8

On logical bifurcation diagrams

Author(s): Wassim Abou-Jaoudé, Pedro T. Monteiro
Published in: Journal of Theoretical Biology, Issue 466, 2019, Page(s) 39-63, ISSN 0022-5193
Publisher: Academic Press
DOI: 10.1016/j.jtbi.2019.01.008

Parallel computing in bioinformatics: a view from high-performance, heterogeneous, and cloud computing

Author(s): Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
Published in: The Journal of Supercomputing, Issue 75/7, 2019, Page(s) 3369-3373, ISSN 0920-8542
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11227-019-02934-2

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Author(s): Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé
Published in: Frontiers in Physiology, Issue 9, 2018, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2018.00680

The bio.tools registry of software tools and data resources for the life sciences

Author(s): Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondrášek, Hedi Peterson, Ahto Salumets, Inge Jonassen, Rob Hooft, Tommi Nyrönen, Alfonso Valencia, Salvador Capella, Josep Gelpí, Federico Zambell
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
Publisher: London: BioMed Central Ltd
DOI: 10.1186/s13059-019-1772-6

ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data

Author(s): Antje Jensch, Marta B. Lopes, Susana Vinga, Nicole Radde
Published in: Statistical Methods in Medical Research, Issue 31, 2022, Page(s) 947-958, ISSN 0962-2802
Publisher: SAGE Publications
DOI: 10.1177/09622802211072456

Outlier Detection for Multivariate Time Series Using Dynamic Bayesian Networks

Author(s): Jorge L. Serras, Susana Vinga, Alexandra M. Carvalho
Published in: Applied Sciences, Issue 11/4, 2021, Page(s) 1955, ISSN 2076-3417
Publisher: MDPI
DOI: 10.3390/app11041955

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

Author(s): Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Published in: Microbiome, Issue 7/1, 2019, ISSN 2049-2618
Publisher: London: BioMed Central
DOI: 10.1186/s40168-019-0684-8

Triclustering Algorithms for Three-Dimensional Data Analysis

Author(s): Rui Henriques, Sara C. Madeira
Published in: ACM Computing Surveys, Issue 51/5, 2019, Page(s) 1-43, ISSN 0360-0300
Publisher: Association for Computing Machinary, Inc.
DOI: 10.1145/3195833

GPU acceleration of Fitch’s parsimony on protein data: from Kepler to Turing

Author(s): Sergio Santander-Jiménez, Miguel A. Vega-Rodríguez, Antonio Zahinos-Márquez, Leonel Sousa
Published in: The Journal of Supercomputing, Issue 76/12, 2020, Page(s) 9827-9853, ISSN 0920-8542
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11227-020-03225-x

Revision of Boolean Models of Regulatory Networks Using Stable State Observations

Author(s): Filipe Gouveia, Inês Lynce, Pedro T. Monteiro
Published in: Journal of Computational Biology, Issue 27/2, 2020, Page(s) 144-155, ISSN 1557-8666
Publisher: Mary Ann liebert, inc
DOI: 10.1089/cmb.2019.0289

Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis

Author(s): Cláudia S. Constantino, Alexandra M. Carvalho, Susana Vinga
Published in: BioData Mining, Issue 14, 2024, ISSN 1756-0381
Publisher: BioMed Central
DOI: 10.1186/s13040-021-00257-8

Multi-objective memetic meta-heuristic algorithm for encoding the same protein with multiple genes

Author(s): Belen Gonzalez-Sanchez, Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
Published in: Expert Systems with Applications, Issue 136, 2019, Page(s) 83-93, ISSN 0957-4174
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.eswa.2019.06.031

Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Author(s): Mariana Galvão Ferrarini, Irene Ziska, Ricardo Andrade, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César, Arnaud Mary, Susana Vinga, Marie-France Sagot
Published in: Frontiers in Genetics, Issue 13, 2022, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2022.815476

Mining Pre-Surgical Patterns Able to Discriminate Post-Surgical Outcomes in the Oncological Domain

Author(s): Leonardo Alexandre, Rafael S. Costa, Lucio Lara Santos, Rui Henriques
Published in: IEEE Journal of Biomedical and Health Informatics, Issue 25, 2022, Page(s) 2421-2434, ISSN 2168-2194
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/jbhi.2021.3064786

Governance of risky public goods under graduated punishment

Author(s): Marta C. Couto, Jorge M. Pacheco, Francisco C. Santos
Published in: Journal of Theoretical Biology, Issue 505, 2020, Page(s) 110423, ISSN 0022-5193
Publisher: Academic Press
DOI: 10.1016/j.jtbi.2020.110423

From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon

Author(s): Jorge Oliveira, Miguel Antunes, Claudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia, Pedro T. Monteiro
Published in: BMC Bioinformatics, Issue 22, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04312-3

Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes.

Author(s): W. J. Araújo, J. S. Oliveira, S. C. S. Araújo, C. F. Minnicelli, R. C. B. Silva-Portela, M. M. B. da Fonseca, J. F. Freitas, K. K. Silva-Barbalho, A. P. Napp, J. E. S. Pereira, M. C. R. Peralba, L. M. P. Passaglia, M. H. Vainstein and L. F. Agnez-Lima
Published in: Frontiers Bioengineering Biotechnology, 2020, ISSN 2296-4185
Publisher: Lausanne: Frontiers Media S.A.
DOI: 10.3389/fbioe.2020.00962

Structured sparsity regularization for analyzing high-dimensional omics data

Author(s): Susana Vinga
Published in: Briefings in Bioinformatics, Issue 22, 2023, Page(s) 77-87, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa122

The Role of Network Science in Glioblastoma

Author(s): Marta B. Lopes, Eduarda P. Martins, Susana Vinga, Bruno M. Costa
Published in: Cancers, Issue 13/5, 2021, Page(s) 1045, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13051045

On the challenges of predicting treatment response in Hodgkin’s Lymphoma using transcriptomic data

Author(s): André Patrício, Rafael S. Costa, Rui Henriques
Published in: BMC Medical Genomics, Issue 16, 2023, ISSN 1755-8794
Publisher: BioMed Central
DOI: 10.1186/s12920-023-01508-9

Computing RF Tree Distance over Succinct Representations

Author(s): António Pedro Branco, Cátia Vaz, Alexandre P. Francisco
Published in: Algorithms, Issue 17, 2023, Page(s) 15, ISSN 1999-4893
Publisher: MDPI Open Access Publishing
DOI: 10.3390/a17010015

Distance-based phylogenetic inference from typing data: a unifying view

Author(s): Cátia Vaz, Marta Nascimento, João A Carriço, Tatiana Rocher, Alexandre P Francisco
Published in: Briefings in Bioinformatics, Issue 22, 2024, ISSN 1477-4054
Publisher: Oxford Academic
DOI: 10.1093/bib/bbaa147

Large-Scale Simulations of Bacterial Populations Over Complex Networks

Author(s): Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco
Published in: Journal of Computational Biology, Issue 25/8, 2018, Page(s) 850-861, ISSN 1557-8666
Publisher: Mary Ann Liebert, Inc.
DOI: 10.1089/cmb.2018.0083

Time-Lagged Correlation Analysis of Shellfish Toxicity Reveals Predictive Links to Adjacent Areas, Species, and Environmental Conditions

Author(s): André Patrício, Marta B. Lopes, Pedro Reis Costa, Rafael S. Costa, Rui Henriques, Susana Vinga
Published in: Toxins, Issue 14, 2024, Page(s) 679, ISSN 2072-6651
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/toxins14100679

Ensemble outlier detection and gene selection in triple-negative breast cancer data

Author(s): Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
Published in: BMC Bioinformatics, Issue 19/1, 2018, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-018-2149-7

Multiobjective Frog-Leaping Optimization for the Study of Ancestral Relationships in Protein Data

Author(s): Sergio Santander-Jimenez, Miguel A. Vega-Rodriguez, Leonel Sousa
Published in: IEEE Transactions on Evolutionary Computation, Issue 22/6, 2018, Page(s) 879-893, ISSN 1089-778X
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tevc.2017.2774599

Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients

Author(s): Miguel Monteiro, Ana Catarina Fonseca, Ana Teresa Freitas, Teresa Pinho e Melo, Alexandre P. Francisco, Jose M. Ferro, Arlindo L. Oliveira
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Issue 15/6, 2018, Page(s) 1953-1959, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2018.2811471

Multi-Objective Artificial Bee Colony for designing multiple genes encoding the same protein

Author(s): Belen Gonzalez-Sanchez, Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez, José M. Granado-Criado
Published in: Applied Soft Computing, Issue 74, 2019, Page(s) 90-98, ISSN 1568-4946
Publisher: Elsevier BV
DOI: 10.1016/j.asoc.2018.10.023

Fast phylogenetic inference from typing data

Author(s): João A. Carriço, Maxime Crochemore, Alexandre P. Francisco, Solon P. Pissis, Bruno Ribeiro-Gonçalves, Cátia Vaz
Published in: Algorithms for Molecular Biology, Issue 13/1, 2018, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-017-0119-7

G-Tric: generating three-way synthetic datasets with triclustering solutions

Author(s): João Lobo, Rui Henriques, Sara C. Madeira
Published in: BMC Bioinformatics, Issue 22, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03925-4

Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data

Author(s): Rafael S. Costa, Susana Vinga
Published in: Biotechnology Progress, Issue 34/6, 2018, Page(s) 1344-1354, ISSN 8756-7938
Publisher: American Chemical Society
DOI: 10.1002/btpr.2700

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Author(s): Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira, Susana Vinga
Published in: BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-3377-1

Predicting Biologic Therapy Outcome of Patients With Spondyloarthritis: Joint Models for Longitudinal and Survival Analysis

Author(s): Carolina Barata, Ana Maria Rodrigues, Helena Canhão, Susana Vinga, Alexandra M Carvalho
Published in: JMIR Medical Informatics, Issue 9, 2021, Page(s) e26823, ISSN 2291-9694
Publisher: JMIR
DOI: 10.2196/26823

Enrichment analysis on regulatory subspaces: A novel direction for the superior description of cellular responses to SARS-CoV-2

Author(s): Pedro Rodrigues, Rafael S. Costa, Rui Henriques
Published in: Computers in Biology and Medicine, Issue 146, 2022, Page(s) 105443, ISSN 0010-4825
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compbiomed.2022.105443

Comparative Analysis of Intra-Algorithm Parallel Multiobjective Evolutionary Algorithms: Taxonomy Implications on Bioinformatics Scenarios.

Author(s): Sergio Santander-Jiménez, Miguel A. Vega-Rodríguez
Published in: Ieee Transactions on Parallel and Distributed Systems., 2019, ISSN 1045-9219
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tpds.2018.2854788

Twiner: correlation-based regularization for identifying common cancer gene signatures.

Author(s): Marta B. Lopes, Sandra Casimiro and Susana Vinga
Published in: BMC Bioinformatics, 2019, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-019-2937-8

A review of recent machine learning advances for forecasting harmful algal blooms and shellfish contamination

Author(s): Cruz, Rafaela C.; Costa, Pedro Reis; Vinga, Susana; Krippahl, Ludwig; Lopes, Marta B.
Published in: Journal of Marine Science and Engineering, Issue 1, 2021, ISSN 2077-1312
Publisher: MDPI
DOI: 10.3390/jmse9030283

DCSO: towards an ontology for machine-actionable data management plans

Author(s): João Cardoso, Leyla J. Castro, Fajar J. Ekaputra, Marie C. Jacquemot, Marek Suchánek, Tomasz Miksa, José Borbinha
Published in: Journal of Biomedical Semantics, Issue 13, 2022, ISSN 2041-1480
Publisher: Springer Nature
DOI: 10.1186/s13326-022-00274-4

The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity

Author(s): Alexander Joschua Ohnmacht, Anantharamanan Rajamani, Göksu Avar, Ginte Kutkaite, Emanuel Gonçalves, Dieter Saur, Michael Patrick Menden
Published in: Communications Biology, Issue 6, 2023, ISSN 2399-3642
Publisher: Nature
DOI: 10.1038/s42003-023-05198-y

Computational Approach to the Discovery of Phytochemical Molecules with Therapeutic Potential Targets to the PKCZ protein

Author(s): Poliany G. Freitas, Thiago C. Elias, Icaro A. Pinto, Luciano T. Costa, Paulo V.S.D. de Carvalho, Daniel de Q. Omote, Ihosvany Camps, Tati Ishikawa, Helen A. Arcuri, Susana Vinga, Arlindo L. Oliveira, Walter F.A. Junior, Nelson J.F. da Silveira
Published in: Letters in Drug Design & Discovery, 2018, ISSN 1570-1808
Publisher: Bentham Science Publishers
DOI: 10.2174/1570180814666170810120150

Benchmarking of alignment-free sequence comparison methods

Author(s): Andrzej Zielezinski, Hani Z. Girgis, Guillaume Bernard, Chris-Andre Leimeister, Kujin Tang, Thomas Dencker, Anna Katharina Lau, Sophie Röhling, Jae Jin Choi, Michael S. Waterman, Matteo Comin, Sung-Hou Kim, Susana Vinga, Jonas S. Almeida, Cheong Xin Chan, Benjamin T. James, Fengzhu Sun, Burkhard Morgenstern, Wojciech M. Karlowski
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
Publisher: BMC
DOI: 10.1186/s13059-019-1755-7

Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees

Author(s): Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
Published in: Nature Communications, Issue 14, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-39400-w

Using Markov chains and temporal alignment to identify clinical patterns in Dementia

Author(s): Luísa Marote Costa, João Colaço, Alexandra M. Carvalho, Susana Vinga, Andreia Sofia Teixeira
Published in: Journal of Biomedical Informatics, Issue 140, 2024, Page(s) 104328, ISSN 1532-0464
Publisher: Academic Press
DOI: 10.1016/j.jbi.2023.104328

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Author(s): Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Galvão Ferrarini, Susana Vinga, Lilia Boucinha, Marie-France Sagot
Published in: NAR Genomics and Bioinformatics, 2021, ISSN 2631-9268
Publisher: Oxford

Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Author(s): Evangelia A. Papoutsoglou, Daniel Faria, Daniel Arend, Elizabeth Arnaud, Ioannis N. Athanasiadis, Inês Chaves, Frederik Coppens, Guillaume Cornut, Bruno V. Costa, Hanna Ćwiek‐Kupczyńska, Bert Droesbeke, Richard Finkers, Kristina Gruden, Astrid Junker, Graham J. King, Paweł Krajewski, Matthias Lange, Marie‐Angélique Laporte, Célia Michotey, Markus Oppermann, Richard Ostler, Hendrik Poorte
Published in: New Phytologist, Issue 227/1, 2020, Page(s) 260-273, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.16544

NF-κB in monocytes and macrophages – an inflammatory master regulator in multitalented immune cells

Author(s): Marion Mussbacher, Martina Derler, José Basílio, Johannes A. Schmid
Published in: Frontiers in Immunology, Issue 14, 2023, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2023.1134661

A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization

Author(s): Clare Pacini, Emma Duncan, Emanuel Gonçalves, James Gilbert, Shriram Bhosle, Stuart Horswell, Emre Karakoc, Howard Lightfoot, Ed Curry, Francesc Muyas, Monsif Bouaboula, Chandra Sekhar Pedamallu, Isidro Cortes-Ciriano, Fiona M. Behan, Lykourgos-Panagiotis Zalmas, Andrew Barthorpe, Hayley Francies, Steve Rowley, Jack Pollard, Pedro Beltrao, Leopold Parts, Francesco Iorio, Mathew J. Garnett
Published in: Cancer Cell, Issue 42, 2024, Page(s) 301-316.e9, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2023.12.016

Kidney Cancer Biomarker Selection Using Regularized Survival Models

Author(s): Carolina Peixoto, Marta Martins, Luís Costa, Susana Vinga
Published in: Cells, Issue 11, 2024, Page(s) 2311, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells11152311

SBML2HYB: a Python interface for SBML compatible hybrid modeling

Author(s): José Pinto, Rafael S Costa, Leonardo Alexandre, João Ramos, Rui Oliveira
Published in: Bioinformatics, Issue 39, 2023, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad044

Inferring Diagnostic and Prognostic Gene Expression Signatures Across WHO Glioma Classifications: A Network-Based Approach

Author(s): Roberta Coletti, Mónica Leiria de Mendonça, Susana Vinga, Marta B. Lopes
Published in: Bioinformatics and Biology Insights, Issue 18, 2024, ISSN 1177-9322
Publisher: Libertas Academica
DOI: 10.1177/11779322241271535

DI2: prior-free and multi-item discretization of biological data and its applications

Author(s): Leonardo Alexandre, Rafael S. Costa, Rui Henriques
Published in: BMC Bioinformatics, Issue 22, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04329-8

Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches

Author(s): Daniel M. Gonçalves, Rui Henriques, Rafael S. Costa
Published in: Computational and Structural Biotechnology Journal, Issue 21, 2024, Page(s) 4960-4973, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2023.10.002

Effects of Chronic Inflammatory Activation of Murine and Human Arterial Endothelial Cells at Normal Lipoprotein and Cholesterol Levels In Vivo and In Vitro

Author(s): Marion Mussbacher, José Basílio, Barbora Belakova, Anita Pirabe, Elisabeth Ableitner, Manuel Campos-Medina, Johannes A. Schmid
Published in: Cells, Issue 13, 2024, Page(s) 773, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells13090773

Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells

Author(s): Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta
Published in: Biosystems, Issue 207, 2023, Page(s) 104453, ISSN 0303-2647
Publisher: Elsevier BV
DOI: 10.1016/j.biosystems.2021.104453

Boolean function metrics can assist modelers to check and choose logical rules

Author(s): John Zobolas, Pedro T. Monteiro, Martin Kuiper, Åsmund Flobak
Published in: Journal of Theoretical Biology, Issue 538, 2024, Page(s) 111025, ISSN 0022-5193
Publisher: Academic Press
DOI: 10.1016/j.jtbi.2022.111025

CorkOakDB—The Cork Oak Genome Database Portal

Author(s): Cirenia Arias-Baldrich, Marta Contreiras Silva, Filippo Bergeretti, Inês Chaves, Célia Miguel, Nelson J M Saibo, Daniel Sobral, Daniel Faria, Pedro M Barros
Published in: Database, Issue 2020, 2020, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baaa114

Spatiotemporal Correlation Feature Spaces to Support Anomaly Detection in Water Distribution Networks

Author(s): Susana C. Gomes; Susana Vinga; Rui Henriques
Published in: Volume 13, Issue 1, 2021, Page(s) MDPI, ISSN 2073-4441
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/w13182551

Dynamic modeling of bone remodeling, osteolytic metastasis and PK/PD therapy: introducing variable order derivatives as a simplification technique

Author(s): Neto, Joana Pinheiro; Alho, Irina; Costa, Luis; Casimiro, Sandra; Valério, Duarte; Vinga, Susana
Published in: Journal of Mathematical Biology, Issue 1, 2021, ISSN 0303-6812
Publisher: Springer Verlag
DOI: 10.1007/s00285-021-01666-3

Book chapters (5)

Comparative Evaluation of Classification Indexes and Outlier Detection of Microcytic Anaemias in a Portuguese Sample

Author(s): Beatriz N. Leitão, Paula Faustino, Susana Vinga
Published in: Lecture Notes in Computer Science, Progress in Artificial Intelligence, 2022, Page(s) 219-231
Publisher: Springer International Publishing
DOI: 10.1007/978-3-031-16474-3_19

Evaluating the Causal Role of Environmental Data in Shellfish Biotoxin Contamination on the Portuguese Coast

Author(s): Ana Rita Baião, Carolina Peixoto, Marta B. Lopes, Pedro Reis Costa, Alexandra M. Carvalho, Susana Vinga
Published in: Lecture Notes in Computer Science, Progress in Artificial Intelligence, 2023, Page(s) 325-337
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-49011-8_26

Latent Variable Modelling and Variational Inference for scRNA-seq Differential Expression Analysis

Author(s): Joana Godinho, Alexandra M. Carvalho, Susana Vinga
Published in: Lecture Notes in Computer Science, Computational Advances in Bio and Medical Sciences, 2021, Page(s) 56-68
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-79290-9_6

Causal Graph Discovery for Explainable Insights on Marine Biotoxin Shellfish Contamination

Author(s): Diogo Ribeiro, Filipe Ferraz, Marta B. Lopes, Susana Rodrigues, Pedro Reis Costa, Susana Vinga, Alexandra M. Carvalho
Published in: Lecture Notes in Computer Science, Intelligent Data Engineering and Automated Learning – IDEAL 2023, 2023, Page(s) 483-494
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-48232-8_44

Comparative Analysis of Machine Learning Models for Time-Series Forecasting of Escherichia Coli Contamination in Portuguese Shellfish Production Areas

Author(s): Filipe Ferraz, Diogo Ribeiro, Marta B. Lopes, Sónia Pedro, Susana Vinga, Alexandra M. Carvalho
Published in: Lecture Notes in Computer Science, Machine Learning, Optimization, and Data Science, 2024, Page(s) 174-188
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-53969-5_14