OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon | OLISSIPO | Projet | Résultats | H2020 | CORDIS

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

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

Publications

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

Auteurs: Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel
Publié dans: Bioinformatics, Numéro 40, 2024, Page(s) i180-i188, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btae214

Reduced order models of myelinated axonal compartments.

Auteurs: Daniel Ioan, Ruxandra Bărbulescu, Luis Miguel Silveira, Gabriela Ciuprina
Publié dans: Journal of Computational Neuroscience, 2019, ISSN 0929-5313
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10827-019-00726-4

On Finding Optimal (Dynamic) Arborescences

Auteurs: Joaquim Espada, Alexandre P. Francisco, Tatiana Rocher, Luís M. S. Russo, Cátia Vaz
Publié dans: Algorithms, Numéro 16, 2023, Page(s) 559, ISSN 1999-4893
Éditeur: MDPI Open Access Publishing
DOI: 10.3390/a16120559

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0

Auteurs: Aurélien Naldi, Céline Hernandez, Wassim Abou-Jaoudé, Pedro T. Monteiro, Claudine Chaouiya, Denis Thieffry
Publié dans: Frontiers in Physiology, Numéro 9, 2018, ISSN 1664-042X
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fphys.2018.00646

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

Auteurs: Marta B. Lopes, Susana Vinga
Publié dans: BMC Bioinformatics, Numéro 21/1, 2020, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-020-3390-4

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

Auteurs: Bruno Lourenço, Cátia Vaz, Miguel E. Coimbra, Alexandre P. Francisco
Publié dans: SoftwareX, Numéro 26, 2024, Page(s) 101668, ISSN 2352-7110
Éditeur: Elsevier
DOI: 10.1016/j.softx.2024.101668

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

Auteurs: 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
Publié dans: BMC Bioinformatics, Numéro 24, 2023, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-022-05104-z

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

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

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

Auteurs: José Basílio, Bernhard Hochreiter, Bastian Hoesel, Emira Sheshori, Marion Mussbacher, Rudolf Hanel, Johannes A. Schmid
Publié dans: Cancers, Numéro 14, 2024, Page(s) 6164, ISSN 2072-6694
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14246164

SpliceTAPyR - An Efficient Method for Transcriptome Alignment.

Auteurs: Andreia Sofia Teixeira, Francisco Fernandes and Alexandre P. Francisco
Publié dans: International Journal of Foundations of Computer Science, 2018, ISSN 0129-0541
Éditeur: 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

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

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

Auteurs: 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
Publié dans: Cancer Cell, Numéro 41, 2024, Page(s) 288-303.e6, ISSN 1535-6108
Éditeur: Cell Press
DOI: 10.1016/j.ccell.2022.12.009

G-bic: generating synthetic benchmarks for biclustering

Auteurs: Eduardo N. Castanho, João P. Lobo, Rui Henriques, Sara C. Madeira
Publié dans: BMC Bioinformatics, Numéro 24, 2024, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-023-05587-4

AliClu - Temporal sequence alignment for clustering longitudinal clinical data

Auteurs: Kishan Rama, Helena Canhão, Alexandra M. Carvalho, Susana Vinga
Publié dans: BMC Medical Informatics and Decision Making, Numéro 19/1, 2019, ISSN 1472-6947
Éditeur: BioMed Central
DOI: 10.1186/s12911-019-1013-7

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

Auteurs: 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
Publié dans: Nanomedicine: Nanotechnology, Biology and Medicine, Numéro 30, 2020, Page(s) 102287, ISSN 1549-9634
Éditeur: Elsevier BV
DOI: 10.1016/j.nano.2020.102287

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

Auteurs: Alexandre Lemos, Inês Lynce and Pedro T. Monteiro
Publié dans: Algorithms for Molecular Biology, 2019, ISSN 1748-7188
Éditeur: BioMed Central
DOI: 10.1186/s13015-019-0145-8

On logical bifurcation diagrams

Auteurs: Wassim Abou-Jaoudé, Pedro T. Monteiro
Publié dans: Journal of Theoretical Biology, Numéro 466, 2019, Page(s) 39-63, ISSN 0022-5193
Éditeur: Academic Press
DOI: 10.1016/j.jtbi.2019.01.008

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

Auteurs: Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
Publié dans: The Journal of Supercomputing, Numéro 75/7, 2019, Page(s) 3369-3373, ISSN 0920-8542
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s11227-019-02934-2

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

Auteurs: 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
Publié dans: Frontiers in Physiology, Numéro 9, 2018, ISSN 1664-042X
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fphys.2018.00680

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

Auteurs: 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
Publié dans: Genome Biology, Numéro 20/1, 2019, ISSN 1474-760X
Éditeur: 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

Auteurs: Antje Jensch, Marta B. Lopes, Susana Vinga, Nicole Radde
Publié dans: Statistical Methods in Medical Research, Numéro 31, 2022, Page(s) 947-958, ISSN 0962-2802
Éditeur: SAGE Publications
DOI: 10.1177/09622802211072456

Outlier Detection for Multivariate Time Series Using Dynamic Bayesian Networks

Auteurs: Jorge L. Serras, Susana Vinga, Alexandra M. Carvalho
Publié dans: Applied Sciences, Numéro 11/4, 2021, Page(s) 1955, ISSN 2076-3417
Éditeur: MDPI
DOI: 10.3390/app11041955

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

Auteurs: Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Publié dans: Microbiome, Numéro 7/1, 2019, ISSN 2049-2618
Éditeur: London: BioMed Central
DOI: 10.1186/s40168-019-0684-8

Triclustering Algorithms for Three-Dimensional Data Analysis

Auteurs: Rui Henriques, Sara C. Madeira
Publié dans: ACM Computing Surveys, Numéro 51/5, 2019, Page(s) 1-43, ISSN 0360-0300
Éditeur: Association for Computing Machinary, Inc.
DOI: 10.1145/3195833

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

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

Revision of Boolean Models of Regulatory Networks Using Stable State Observations

Auteurs: Filipe Gouveia, Inês Lynce, Pedro T. Monteiro
Publié dans: Journal of Computational Biology, Numéro 27/2, 2020, Page(s) 144-155, ISSN 1557-8666
Éditeur: Mary Ann liebert, inc
DOI: 10.1089/cmb.2019.0289

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

Auteurs: Cláudia S. Constantino, Alexandra M. Carvalho, Susana Vinga
Publié dans: BioData Mining, Numéro 14, 2024, ISSN 1756-0381
Éditeur: BioMed Central
DOI: 10.1186/s13040-021-00257-8

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

Auteurs: Belen Gonzalez-Sanchez, Miguel A. Vega-Rodríguez, Sergio Santander-Jiménez
Publié dans: Expert Systems with Applications, Numéro 136, 2019, Page(s) 83-93, ISSN 0957-4174
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.eswa.2019.06.031

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

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

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

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

Governance of risky public goods under graduated punishment

Auteurs: Marta C. Couto, Jorge M. Pacheco, Francisco C. Santos
Publié dans: Journal of Theoretical Biology, Numéro 505, 2020, Page(s) 110423, ISSN 0022-5193
Éditeur: 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

Auteurs: Jorge Oliveira, Miguel Antunes, Claudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia, Pedro T. Monteiro
Publié dans: BMC Bioinformatics, Numéro 22, 2021, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-021-04312-3

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

Auteurs: 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
Publié dans: Frontiers Bioengineering Biotechnology, 2020, ISSN 2296-4185
Éditeur: Lausanne: Frontiers Media S.A.
DOI: 10.3389/fbioe.2020.00962

Structured sparsity regularization for analyzing high-dimensional omics data

Auteurs: Susana Vinga
Publié dans: Briefings in Bioinformatics, Numéro 22, 2023, Page(s) 77-87, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbaa122

The Role of Network Science in Glioblastoma

Auteurs: Marta B. Lopes, Eduarda P. Martins, Susana Vinga, Bruno M. Costa
Publié dans: Cancers, Numéro 13/5, 2021, Page(s) 1045, ISSN 2072-6694
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13051045

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

Auteurs: André Patrício, Rafael S. Costa, Rui Henriques
Publié dans: BMC Medical Genomics, Numéro 16, 2023, ISSN 1755-8794
Éditeur: BioMed Central
DOI: 10.1186/s12920-023-01508-9

Computing RF Tree Distance over Succinct Representations

Auteurs: António Pedro Branco, Cátia Vaz, Alexandre P. Francisco
Publié dans: Algorithms, Numéro 17, 2023, Page(s) 15, ISSN 1999-4893
Éditeur: MDPI Open Access Publishing
DOI: 10.3390/a17010015

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

Auteurs: Cátia Vaz, Marta Nascimento, João A Carriço, Tatiana Rocher, Alexandre P Francisco
Publié dans: Briefings in Bioinformatics, Numéro 22, 2024, ISSN 1477-4054
Éditeur: Oxford Academic
DOI: 10.1093/bib/bbaa147

Large-Scale Simulations of Bacterial Populations Over Complex Networks

Auteurs: Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco
Publié dans: Journal of Computational Biology, Numéro 25/8, 2018, Page(s) 850-861, ISSN 1557-8666
Éditeur: 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

Auteurs: André Patrício, Marta B. Lopes, Pedro Reis Costa, Rafael S. Costa, Rui Henriques, Susana Vinga
Publié dans: Toxins, Numéro 14, 2024, Page(s) 679, ISSN 2072-6651
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/toxins14100679

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

Auteurs: Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
Publié dans: BMC Bioinformatics, Numéro 19/1, 2018, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-018-2149-7

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

Auteurs: Sergio Santander-Jimenez, Miguel A. Vega-Rodriguez, Leonel Sousa
Publié dans: IEEE Transactions on Evolutionary Computation, Numéro 22/6, 2018, Page(s) 879-893, ISSN 1089-778X
Éditeur: 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

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

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

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

Fast phylogenetic inference from typing data

Auteurs: João A. Carriço, Maxime Crochemore, Alexandre P. Francisco, Solon P. Pissis, Bruno Ribeiro-Gonçalves, Cátia Vaz
Publié dans: Algorithms for Molecular Biology, Numéro 13/1, 2018, ISSN 1748-7188
Éditeur: BioMed Central
DOI: 10.1186/s13015-017-0119-7

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

Auteurs: João Lobo, Rui Henriques, Sara C. Madeira
Publié dans: BMC Bioinformatics, Numéro 22, 2021, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-020-03925-4

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

Auteurs: Rafael S. Costa, Susana Vinga
Publié dans: Biotechnology Progress, Numéro 34/6, 2018, Page(s) 1344-1354, ISSN 8756-7938
Éditeur: American Chemical Society
DOI: 10.1002/btpr.2700

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

Auteurs: Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira, Susana Vinga
Publié dans: BMC Bioinformatics, Numéro 21/1, 2020, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-020-3377-1

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

Auteurs: Carolina Barata, Ana Maria Rodrigues, Helena Canhão, Susana Vinga, Alexandra M Carvalho
Publié dans: JMIR Medical Informatics, Numéro 9, 2021, Page(s) e26823, ISSN 2291-9694
Éditeur: JMIR
DOI: 10.2196/26823

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

Auteurs: Pedro Rodrigues, Rafael S. Costa, Rui Henriques
Publié dans: Computers in Biology and Medicine, Numéro 146, 2022, Page(s) 105443, ISSN 0010-4825
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.compbiomed.2022.105443

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

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

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

Auteurs: Marta B. Lopes, Sandra Casimiro and Susana Vinga
Publié dans: BMC Bioinformatics, 2019, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-019-2937-8

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

Auteurs: Cruz, Rafaela C.; Costa, Pedro Reis; Vinga, Susana; Krippahl, Ludwig; Lopes, Marta B.
Publié dans: Journal of Marine Science and Engineering, Numéro 1, 2021, ISSN 2077-1312
Éditeur: MDPI
DOI: 10.3390/jmse9030283

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

Auteurs: João Cardoso, Leyla J. Castro, Fajar J. Ekaputra, Marie C. Jacquemot, Marek Suchánek, Tomasz Miksa, José Borbinha
Publié dans: Journal of Biomedical Semantics, Numéro 13, 2022, ISSN 2041-1480
Éditeur: Springer Nature
DOI: 10.1186/s13326-022-00274-4

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

Auteurs: Alexander Joschua Ohnmacht, Anantharamanan Rajamani, Göksu Avar, Ginte Kutkaite, Emanuel Gonçalves, Dieter Saur, Michael Patrick Menden
Publié dans: Communications Biology, Numéro 6, 2023, ISSN 2399-3642
Éditeur: Nature
DOI: 10.1038/s42003-023-05198-y

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

Auteurs: 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
Publié dans: Letters in Drug Design & Discovery, 2018, ISSN 1570-1808
Éditeur: Bentham Science Publishers
DOI: 10.2174/1570180814666170810120150

Benchmarking of alignment-free sequence comparison methods

Auteurs: 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
Publié dans: Genome Biology, Numéro 20/1, 2019, ISSN 1474-760X
Éditeur: BMC
DOI: 10.1186/s13059-019-1755-7

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

Auteurs: Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
Publié dans: Nature Communications, Numéro 14, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-39400-w

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

Auteurs: Luísa Marote Costa, João Colaço, Alexandra M. Carvalho, Susana Vinga, Andreia Sofia Teixeira
Publié dans: Journal of Biomedical Informatics, Numéro 140, 2024, Page(s) 104328, ISSN 1532-0464
Éditeur: 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

Auteurs: Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Galvão Ferrarini, Susana Vinga, Lilia Boucinha, Marie-France Sagot
Publié dans: NAR Genomics and Bioinformatics, 2021, ISSN 2631-9268
Éditeur: Oxford

Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Auteurs: 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
Publié dans: New Phytologist, Numéro 227/1, 2020, Page(s) 260-273, ISSN 0028-646X
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/nph.16544

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

Auteurs: Marion Mussbacher, Martina Derler, José Basílio, Johannes A. Schmid
Publié dans: Frontiers in Immunology, Numéro 14, 2023, ISSN 1664-3224
Éditeur: Frontiers
DOI: 10.3389/fimmu.2023.1134661

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

Auteurs: 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
Publié dans: Cancer Cell, Numéro 42, 2024, Page(s) 301-316.e9, ISSN 1535-6108
Éditeur: Cell Press
DOI: 10.1016/j.ccell.2023.12.016

Kidney Cancer Biomarker Selection Using Regularized Survival Models

Auteurs: Carolina Peixoto, Marta Martins, Luís Costa, Susana Vinga
Publié dans: Cells, Numéro 11, 2024, Page(s) 2311, ISSN 2073-4409
Éditeur: MDPI
DOI: 10.3390/cells11152311

SBML2HYB: a Python interface for SBML compatible hybrid modeling

Auteurs: José Pinto, Rafael S Costa, Leonardo Alexandre, João Ramos, Rui Oliveira
Publié dans: Bioinformatics, Numéro 39, 2023, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad044

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

Auteurs: Roberta Coletti, Mónica Leiria de Mendonça, Susana Vinga, Marta B. Lopes
Publié dans: Bioinformatics and Biology Insights, Numéro 18, 2024, ISSN 1177-9322
Éditeur: Libertas Academica
DOI: 10.1177/11779322241271535

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

Auteurs: Leonardo Alexandre, Rafael S. Costa, Rui Henriques
Publié dans: BMC Bioinformatics, Numéro 22, 2021, ISSN 1471-2105
Éditeur: 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

Auteurs: Daniel M. Gonçalves, Rui Henriques, Rafael S. Costa
Publié dans: Computational and Structural Biotechnology Journal, Numéro 21, 2024, Page(s) 4960-4973, ISSN 2001-0370
Éditeur: 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

Auteurs: Marion Mussbacher, José Basílio, Barbora Belakova, Anita Pirabe, Elisabeth Ableitner, Manuel Campos-Medina, Johannes A. Schmid
Publié dans: Cells, Numéro 13, 2024, Page(s) 773, ISSN 2073-4409
Éditeur: MDPI
DOI: 10.3390/cells13090773

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

Auteurs: Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta
Publié dans: Biosystems, Numéro 207, 2023, Page(s) 104453, ISSN 0303-2647
Éditeur: Elsevier BV
DOI: 10.1016/j.biosystems.2021.104453

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

Auteurs: John Zobolas, Pedro T. Monteiro, Martin Kuiper, Åsmund Flobak
Publié dans: Journal of Theoretical Biology, Numéro 538, 2024, Page(s) 111025, ISSN 0022-5193
Éditeur: Academic Press
DOI: 10.1016/j.jtbi.2022.111025

CorkOakDB—The Cork Oak Genome Database Portal

Auteurs: Cirenia Arias-Baldrich, Marta Contreiras Silva, Filippo Bergeretti, Inês Chaves, Célia Miguel, Nelson J M Saibo, Daniel Sobral, Daniel Faria, Pedro M Barros
Publié dans: Database, Numéro 2020, 2020, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baaa114

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

Auteurs: Susana C. Gomes; Susana Vinga; Rui Henriques
Publié dans: Volume 13, Numéro 1, 2021, Page(s) MDPI, ISSN 2073-4441
Éditeur: 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

Auteurs: Neto, Joana Pinheiro; Alho, Irina; Costa, Luis; Casimiro, Sandra; Valério, Duarte; Vinga, Susana
Publié dans: Journal of Mathematical Biology, Numéro 1, 2021, ISSN 0303-6812
Éditeur: Springer Verlag
DOI: 10.1007/s00285-021-01666-3

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

Auteurs: Beatriz N. Leitão, Paula Faustino, Susana Vinga
Publié dans: Lecture Notes in Computer Science, Progress in Artificial Intelligence, 2022, Page(s) 219-231
Éditeur: 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

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

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

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

Causal Graph Discovery for Explainable Insights on Marine Biotoxin Shellfish Contamination

Auteurs: Diogo Ribeiro, Filipe Ferraz, Marta B. Lopes, Susana Rodrigues, Pedro Reis Costa, Susana Vinga, Alexandra M. Carvalho
Publié dans: Lecture Notes in Computer Science, Intelligent Data Engineering and Automated Learning – IDEAL 2023, 2023, Page(s) 483-494
Éditeur: 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

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

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