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OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon

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Publications

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
DOI: 10.1007/s10827-019-00726-4

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
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
DOI: 10.1186/s12859-020-3390-4

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
DOI: 10.1177/0962280218794722

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
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
DOI: 10.1016/j.compag.2019.104855

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
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
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
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
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
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
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
DOI: 10.1186/s13059-019-1772-6

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
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
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
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
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
DOI: 10.1089/cmb.2019.0289

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
DOI: 10.1016/j.eswa.2019.06.031

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
DOI: 10.1016/j.jtbi.2020.110423

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
DOI: 10.3389/fbioe.2020.00962

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
DOI: 10.3390/cancers13051045

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
DOI: 10.1089/cmb.2018.0083

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
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
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
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
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
DOI: 10.1186/s13015-017-0119-7

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
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
DOI: 10.1186/s12859-020-3377-1

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
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
DOI: 10.1186/s12859-019-2937-8

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
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
DOI: 10.1186/s13059-019-1755-7

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
DOI: 10.1111/nph.16544

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
DOI: 10.1093/database/baaa114