OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon | OLISSIPO | Progetto | Risultati | H2020 | CORDIS

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Project website
Promotional materials

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

Pubblicazioni

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

Autori: Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel
Pubblicato in: Bioinformatics, Numero 40, 2024, Pagina/e i180-i188, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btae214

Reduced order models of myelinated axonal compartments.

Autori: Daniel Ioan, Ruxandra Bărbulescu, Luis Miguel Silveira, Gabriela Ciuprina
Pubblicato in: Journal of Computational Neuroscience, 2019, ISSN 0929-5313
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10827-019-00726-4

On Finding Optimal (Dynamic) Arborescences

Autori: Joaquim Espada, Alexandre P. Francisco, Tatiana Rocher, Luís M. S. Russo, Cátia Vaz
Pubblicato in: Algorithms, Numero 16, 2023, Pagina/e 559, ISSN 1999-4893
Editore: MDPI Open Access Publishing
DOI: 10.3390/a16120559

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0

Autori: Aurélien Naldi, Céline Hernandez, Wassim Abou-Jaoudé, Pedro T. Monteiro, Claudine Chaouiya, Denis Thieffry
Pubblicato in: Frontiers in Physiology, Numero 9, 2018, ISSN 1664-042X
Editore: Frontiers Research Foundation
DOI: 10.3389/fphys.2018.00646

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

Autori: Marta B. Lopes, Susana Vinga
Pubblicato in: BMC Bioinformatics, Numero 21/1, 2020, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-020-3390-4

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

Autori: Bruno Lourenço, Cátia Vaz, Miguel E. Coimbra, Alexandre P. Francisco
Pubblicato in: SoftwareX, Numero 26, 2024, Pagina/e 101668, ISSN 2352-7110
Editore: Elsevier
DOI: 10.1016/j.softx.2024.101668

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

Autori: 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
Pubblicato in: BMC Bioinformatics, Numero 24, 2023, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-022-05104-z

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

Autori: Pieter Segaert, Marta B Lopes, Sandra Casimiro, Susana Vinga, Peter J Rousseeuw
Pubblicato in: Statistical Methods in Medical Research, 2019, ISSN 0962-2802
Editore: SAGE Publications
DOI: 10.1177/0962280218794722

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

Autori: José Basílio, Bernhard Hochreiter, Bastian Hoesel, Emira Sheshori, Marion Mussbacher, Rudolf Hanel, Johannes A. Schmid
Pubblicato in: Cancers, Numero 14, 2024, Pagina/e 6164, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14246164

SpliceTAPyR - An Efficient Method for Transcriptome Alignment.

Autori: Andreia Sofia Teixeira, Francisco Fernandes and Alexandre P. Francisco
Pubblicato in: International Journal of Foundations of Computer Science, 2018, ISSN 0129-0541
Editore: 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

Autori: Armando M. Fernandes, Andrei B. Utkin, José Eiras-Dias, Jorge Cunha, José Silvestre, Pedro Melo-Pinto
Pubblicato in: Computers and Electronics in Agriculture, Numero 163, 2019, Pagina/e 104855, ISSN 0168-1699
Editore: Elsevier BV
DOI: 10.1016/j.compag.2019.104855

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

Autori: 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
Pubblicato in: Cancer Cell, Numero 41, 2024, Pagina/e 288-303.e6, ISSN 1535-6108
Editore: Cell Press
DOI: 10.1016/j.ccell.2022.12.009

G-bic: generating synthetic benchmarks for biclustering

Autori: Eduardo N. Castanho, João P. Lobo, Rui Henriques, Sara C. Madeira
Pubblicato in: BMC Bioinformatics, Numero 24, 2024, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-023-05587-4

AliClu - Temporal sequence alignment for clustering longitudinal clinical data

Autori: Kishan Rama, Helena Canhão, Alexandra M. Carvalho, Susana Vinga
Pubblicato in: BMC Medical Informatics and Decision Making, Numero 19/1, 2019, ISSN 1472-6947
Editore: BioMed Central
DOI: 10.1186/s12911-019-1013-7

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

Autori: 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
Pubblicato in: Nanomedicine: Nanotechnology, Biology and Medicine, Numero 30, 2020, Pagina/e 102287, ISSN 1549-9634
Editore: Elsevier BV
DOI: 10.1016/j.nano.2020.102287

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

Autori: Alexandre Lemos, Inês Lynce and Pedro T. Monteiro
Pubblicato in: Algorithms for Molecular Biology, 2019, ISSN 1748-7188
Editore: BioMed Central
DOI: 10.1186/s13015-019-0145-8

On logical bifurcation diagrams

Autori: Wassim Abou-Jaoudé, Pedro T. Monteiro
Pubblicato in: Journal of Theoretical Biology, Numero 466, 2019, Pagina/e 39-63, ISSN 0022-5193
Editore: Academic Press
DOI: 10.1016/j.jtbi.2019.01.008

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

Autori: Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
Pubblicato in: The Journal of Supercomputing, Numero 75/7, 2019, Pagina/e 3369-3373, ISSN 0920-8542
Editore: Kluwer Academic Publishers
DOI: 10.1007/s11227-019-02934-2

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

Autori: 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
Pubblicato in: Frontiers in Physiology, Numero 9, 2018, ISSN 1664-042X
Editore: Frontiers Research Foundation
DOI: 10.3389/fphys.2018.00680

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

Autori: 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
Pubblicato in: Genome Biology, Numero 20/1, 2019, ISSN 1474-760X
Editore: 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

Autori: Antje Jensch, Marta B. Lopes, Susana Vinga, Nicole Radde
Pubblicato in: Statistical Methods in Medical Research, Numero 31, 2022, Pagina/e 947-958, ISSN 0962-2802
Editore: SAGE Publications
DOI: 10.1177/09622802211072456

Outlier Detection for Multivariate Time Series Using Dynamic Bayesian Networks

Autori: Jorge L. Serras, Susana Vinga, Alexandra M. Carvalho
Pubblicato in: Applied Sciences, Numero 11/4, 2021, Pagina/e 1955, ISSN 2076-3417
Editore: MDPI
DOI: 10.3390/app11041955

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

Autori: Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Pubblicato in: Microbiome, Numero 7/1, 2019, ISSN 2049-2618
Editore: London: BioMed Central
DOI: 10.1186/s40168-019-0684-8

Triclustering Algorithms for Three-Dimensional Data Analysis

Autori: Rui Henriques, Sara C. Madeira
Pubblicato in: ACM Computing Surveys, Numero 51/5, 2019, Pagina/e 1-43, ISSN 0360-0300
Editore: Association for Computing Machinary, Inc.
DOI: 10.1145/3195833

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

Autori: Sergio Santander-Jiménez, Miguel A. Vega-Rodríguez, Antonio Zahinos-Márquez, Leonel Sousa
Pubblicato in: The Journal of Supercomputing, Numero 76/12, 2020, Pagina/e 9827-9853, ISSN 0920-8542
Editore: Kluwer Academic Publishers
DOI: 10.1007/s11227-020-03225-x

Revision of Boolean Models of Regulatory Networks Using Stable State Observations

Autori: Filipe Gouveia, Inês Lynce, Pedro T. Monteiro
Pubblicato in: Journal of Computational Biology, Numero 27/2, 2020, Pagina/e 144-155, ISSN 1557-8666
Editore: Mary Ann liebert, inc
DOI: 10.1089/cmb.2019.0289

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

Autori: Cláudia S. Constantino, Alexandra M. Carvalho, Susana Vinga
Pubblicato in: BioData Mining, Numero 14, 2024, ISSN 1756-0381
Editore: BioMed Central
DOI: 10.1186/s13040-021-00257-8

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

Autori: Belen Gonzalez-Sanchez, Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
Pubblicato in: Expert Systems with Applications, Numero 136, 2019, Pagina/e 83-93, ISSN 0957-4174
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.eswa.2019.06.031

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

Autori: Mariana Galvão Ferrarini, Irene Ziska, Ricardo Andrade, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César, Arnaud Mary, Susana Vinga, Marie-France Sagot
Pubblicato in: Frontiers in Genetics, Numero 13, 2022, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2022.815476

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

Autori: Leonardo Alexandre, Rafael S. Costa, Lucio Lara Santos, Rui Henriques
Pubblicato in: IEEE Journal of Biomedical and Health Informatics, Numero 25, 2022, Pagina/e 2421-2434, ISSN 2168-2194
Editore: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/jbhi.2021.3064786

Governance of risky public goods under graduated punishment

Autori: Marta C. Couto, Jorge M. Pacheco, Francisco C. Santos
Pubblicato in: Journal of Theoretical Biology, Numero 505, 2020, Pagina/e 110423, ISSN 0022-5193
Editore: 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

Autori: Jorge Oliveira, Miguel Antunes, Claudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia, Pedro T. Monteiro
Pubblicato in: BMC Bioinformatics, Numero 22, 2021, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-021-04312-3

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

Autori: 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
Pubblicato in: Frontiers Bioengineering Biotechnology, 2020, ISSN 2296-4185
Editore: Lausanne: Frontiers Media S.A.
DOI: 10.3389/fbioe.2020.00962

Structured sparsity regularization for analyzing high-dimensional omics data

Autori: Susana Vinga
Pubblicato in: Briefings in Bioinformatics, Numero 22, 2023, Pagina/e 77-87, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbaa122

The Role of Network Science in Glioblastoma

Autori: Marta B. Lopes, Eduarda P. Martins, Susana Vinga, Bruno M. Costa
Pubblicato in: Cancers, Numero 13/5, 2021, Pagina/e 1045, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13051045

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

Autori: André Patrício, Rafael S. Costa, Rui Henriques
Pubblicato in: BMC Medical Genomics, Numero 16, 2023, ISSN 1755-8794
Editore: BioMed Central
DOI: 10.1186/s12920-023-01508-9

Computing RF Tree Distance over Succinct Representations

Autori: António Pedro Branco, Cátia Vaz, Alexandre P. Francisco
Pubblicato in: Algorithms, Numero 17, 2023, Pagina/e 15, ISSN 1999-4893
Editore: MDPI Open Access Publishing
DOI: 10.3390/a17010015

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

Autori: Cátia Vaz, Marta Nascimento, João A Carriço, Tatiana Rocher, Alexandre P Francisco
Pubblicato in: Briefings in Bioinformatics, Numero 22, 2024, ISSN 1477-4054
Editore: Oxford Academic
DOI: 10.1093/bib/bbaa147

Large-Scale Simulations of Bacterial Populations Over Complex Networks

Autori: Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco
Pubblicato in: Journal of Computational Biology, Numero 25/8, 2018, Pagina/e 850-861, ISSN 1557-8666
Editore: 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

Autori: André Patrício, Marta B. Lopes, Pedro Reis Costa, Rafael S. Costa, Rui Henriques, Susana Vinga
Pubblicato in: Toxins, Numero 14, 2024, Pagina/e 679, ISSN 2072-6651
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/toxins14100679

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

Autori: Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
Pubblicato in: BMC Bioinformatics, Numero 19/1, 2018, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-018-2149-7

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

Autori: Sergio Santander-Jimenez, Miguel A. Vega-Rodriguez, Leonel Sousa
Pubblicato in: IEEE Transactions on Evolutionary Computation, Numero 22/6, 2018, Pagina/e 879-893, ISSN 1089-778X
Editore: 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

Autori: Miguel Monteiro, Ana Catarina Fonseca, Ana Teresa Freitas, Teresa Pinho e Melo, Alexandre P. Francisco, Jose M. Ferro, Arlindo L. Oliveira
Pubblicato in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Numero 15/6, 2018, Pagina/e 1953-1959, ISSN 1545-5963
Editore: IEEE Computer Society
DOI: 10.1109/tcbb.2018.2811471

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

Autori: Belen Gonzalez-Sanchez, Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez, José M. Granado-Criado
Pubblicato in: Applied Soft Computing, Numero 74, 2019, Pagina/e 90-98, ISSN 1568-4946
Editore: Elsevier BV
DOI: 10.1016/j.asoc.2018.10.023

Fast phylogenetic inference from typing data

Autori: João A. Carriço, Maxime Crochemore, Alexandre P. Francisco, Solon P. Pissis, Bruno Ribeiro-Gonçalves, Cátia Vaz
Pubblicato in: Algorithms for Molecular Biology, Numero 13/1, 2018, ISSN 1748-7188
Editore: BioMed Central
DOI: 10.1186/s13015-017-0119-7

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

Autori: João Lobo, Rui Henriques, Sara C. Madeira
Pubblicato in: BMC Bioinformatics, Numero 22, 2021, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-020-03925-4

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

Autori: Rafael S. Costa, Susana Vinga
Pubblicato in: Biotechnology Progress, Numero 34/6, 2018, Pagina/e 1344-1354, ISSN 8756-7938
Editore: American Chemical Society
DOI: 10.1002/btpr.2700

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

Autori: Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira, Susana Vinga
Pubblicato in: BMC Bioinformatics, Numero 21/1, 2020, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-020-3377-1

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

Autori: Carolina Barata, Ana Maria Rodrigues, Helena Canhão, Susana Vinga, Alexandra M Carvalho
Pubblicato in: JMIR Medical Informatics, Numero 9, 2021, Pagina/e e26823, ISSN 2291-9694
Editore: JMIR
DOI: 10.2196/26823

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

Autori: Pedro Rodrigues, Rafael S. Costa, Rui Henriques
Pubblicato in: Computers in Biology and Medicine, Numero 146, 2022, Pagina/e 105443, ISSN 0010-4825
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.compbiomed.2022.105443

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

Autori: Sergio Santander-Jiménez, Miguel A. Vega-Rodríguez
Pubblicato in: Ieee Transactions on Parallel and Distributed Systems., 2019, ISSN 1045-9219
Editore: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tpds.2018.2854788

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

Autori: Marta B. Lopes, Sandra Casimiro and Susana Vinga
Pubblicato in: BMC Bioinformatics, 2019, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-019-2937-8

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

Autori: Cruz, Rafaela C.; Costa, Pedro Reis; Vinga, Susana; Krippahl, Ludwig; Lopes, Marta B.
Pubblicato in: Journal of Marine Science and Engineering, Numero 1, 2021, ISSN 2077-1312
Editore: MDPI
DOI: 10.3390/jmse9030283

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

Autori: João Cardoso, Leyla J. Castro, Fajar J. Ekaputra, Marie C. Jacquemot, Marek Suchánek, Tomasz Miksa, José Borbinha
Pubblicato in: Journal of Biomedical Semantics, Numero 13, 2022, ISSN 2041-1480
Editore: Springer Nature
DOI: 10.1186/s13326-022-00274-4

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

Autori: Alexander Joschua Ohnmacht, Anantharamanan Rajamani, Göksu Avar, Ginte Kutkaite, Emanuel Gonçalves, Dieter Saur, Michael Patrick Menden
Pubblicato in: Communications Biology, Numero 6, 2023, ISSN 2399-3642
Editore: Nature
DOI: 10.1038/s42003-023-05198-y

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

Autori: 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
Pubblicato in: Letters in Drug Design & Discovery, 2018, ISSN 1570-1808
Editore: Bentham Science Publishers
DOI: 10.2174/1570180814666170810120150

Benchmarking of alignment-free sequence comparison methods

Autori: 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
Pubblicato in: Genome Biology, Numero 20/1, 2019, ISSN 1474-760X
Editore: BMC
DOI: 10.1186/s13059-019-1755-7

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

Autori: Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
Pubblicato in: Nature Communications, Numero 14, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-39400-w

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

Autori: Luísa Marote Costa, João Colaço, Alexandra M. Carvalho, Susana Vinga, Andreia Sofia Teixeira
Pubblicato in: Journal of Biomedical Informatics, Numero 140, 2024, Pagina/e 104328, ISSN 1532-0464
Editore: 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

Autori: Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Galvão Ferrarini, Susana Vinga, Lilia Boucinha, Marie-France Sagot
Pubblicato in: NAR Genomics and Bioinformatics, 2021, ISSN 2631-9268
Editore: Oxford

Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Autori: 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
Pubblicato in: New Phytologist, Numero 227/1, 2020, Pagina/e 260-273, ISSN 0028-646X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/nph.16544

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

Autori: Marion Mussbacher, Martina Derler, José Basílio, Johannes A. Schmid
Pubblicato in: Frontiers in Immunology, Numero 14, 2023, ISSN 1664-3224
Editore: Frontiers
DOI: 10.3389/fimmu.2023.1134661

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

Autori: 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
Pubblicato in: Cancer Cell, Numero 42, 2024, Pagina/e 301-316.e9, ISSN 1535-6108
Editore: Cell Press
DOI: 10.1016/j.ccell.2023.12.016

Kidney Cancer Biomarker Selection Using Regularized Survival Models

Autori: Carolina Peixoto, Marta Martins, Luís Costa, Susana Vinga
Pubblicato in: Cells, Numero 11, 2024, Pagina/e 2311, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells11152311

SBML2HYB: a Python interface for SBML compatible hybrid modeling

Autori: José Pinto, Rafael S Costa, Leonardo Alexandre, João Ramos, Rui Oliveira
Pubblicato in: Bioinformatics, Numero 39, 2023, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btad044

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

Autori: Roberta Coletti, Mónica Leiria de Mendonça, Susana Vinga, Marta B. Lopes
Pubblicato in: Bioinformatics and Biology Insights, Numero 18, 2024, ISSN 1177-9322
Editore: Libertas Academica
DOI: 10.1177/11779322241271535

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

Autori: Leonardo Alexandre, Rafael S. Costa, Rui Henriques
Pubblicato in: BMC Bioinformatics, Numero 22, 2021, ISSN 1471-2105
Editore: 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

Autori: Daniel M. Gonçalves, Rui Henriques, Rafael S. Costa
Pubblicato in: Computational and Structural Biotechnology Journal, Numero 21, 2024, Pagina/e 4960-4973, ISSN 2001-0370
Editore: 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

Autori: Marion Mussbacher, José Basílio, Barbora Belakova, Anita Pirabe, Elisabeth Ableitner, Manuel Campos-Medina, Johannes A. Schmid
Pubblicato in: Cells, Numero 13, 2024, Pagina/e 773, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells13090773

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

Autori: Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta
Pubblicato in: Biosystems, Numero 207, 2023, Pagina/e 104453, ISSN 0303-2647
Editore: Elsevier BV
DOI: 10.1016/j.biosystems.2021.104453

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

Autori: John Zobolas, Pedro T. Monteiro, Martin Kuiper, Åsmund Flobak
Pubblicato in: Journal of Theoretical Biology, Numero 538, 2024, Pagina/e 111025, ISSN 0022-5193
Editore: Academic Press
DOI: 10.1016/j.jtbi.2022.111025

CorkOakDB—The Cork Oak Genome Database Portal

Autori: Cirenia Arias-Baldrich, Marta Contreiras Silva, Filippo Bergeretti, Inês Chaves, Célia Miguel, Nelson J M Saibo, Daniel Sobral, Daniel Faria, Pedro M Barros
Pubblicato in: Database, Numero 2020, 2020, ISSN 1758-0463
Editore: Oxford University Press
DOI: 10.1093/database/baaa114

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

Autori: Susana C. Gomes; Susana Vinga; Rui Henriques
Pubblicato in: Volume 13, Numero 1, 2021, Pagina/e MDPI, ISSN 2073-4441
Editore: 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

Autori: Neto, Joana Pinheiro; Alho, Irina; Costa, Luis; Casimiro, Sandra; Valério, Duarte; Vinga, Susana
Pubblicato in: Journal of Mathematical Biology, Numero 1, 2021, ISSN 0303-6812
Editore: Springer Verlag
DOI: 10.1007/s00285-021-01666-3

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

Autori: Beatriz N. Leitão, Paula Faustino, Susana Vinga
Pubblicato in: Lecture Notes in Computer Science, Progress in Artificial Intelligence, 2022, Pagina/e 219-231
Editore: 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

Autori: Ana Rita Baião, Carolina Peixoto, Marta B. Lopes, Pedro Reis Costa, Alexandra M. Carvalho, Susana Vinga
Pubblicato in: Lecture Notes in Computer Science, Progress in Artificial Intelligence, 2023, Pagina/e 325-337
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-031-49011-8_26

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

Autori: Joana Godinho, Alexandra M. Carvalho, Susana Vinga
Pubblicato in: Lecture Notes in Computer Science, Computational Advances in Bio and Medical Sciences, 2021, Pagina/e 56-68
Editore: Springer International Publishing
DOI: 10.1007/978-3-030-79290-9_6

Causal Graph Discovery for Explainable Insights on Marine Biotoxin Shellfish Contamination

Autori: Diogo Ribeiro, Filipe Ferraz, Marta B. Lopes, Susana Rodrigues, Pedro Reis Costa, Susana Vinga, Alexandra M. Carvalho
Pubblicato in: Lecture Notes in Computer Science, Intelligent Data Engineering and Automated Learning – IDEAL 2023, 2023, Pagina/e 483-494
Editore: 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

Autori: Filipe Ferraz, Diogo Ribeiro, Marta B. Lopes, Sónia Pedro, Susana Vinga, Alexandra M. Carvalho
Pubblicato in: Lecture Notes in Computer Science, Machine Learning, Optimization, and Data Science, 2024, Pagina/e 174-188
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-031-53969-5_14

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