OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon | OLISSIPO | Project | Results | H2020 | CORDIS

Livrables

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

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
OLISSIPO Short-term staff exchange plan

OLISSIPO Shortterm staff exchange plan

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon

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