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The European Reference Genome Atlas: piloting a decentralised approach to equit...
Mc Cartney, Ann M.; Formenti, Giulio; Mouton, Alice; De Panis, Diego; Marins, Luísa S.; Leitão, Henrique G.; Diedericks, Genevieve; Kirangwa, JosephA genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the ...
The European Reference Genome Atlas: piloting a decentralised approach to equit...
Mc Cartney, Ann M.; Formenti, Giulio; Mouton, Alice; De Panis, Diego; Marins, Luísa S.; Leitão, Henrique G.; Diedericks, Genevieve; Kirangwa, JosephA genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the ...
The European Reference Genome Atlas: piloting a decentralised approach to equit...
Mc Cartney, Ann M.; Formenti, Giulio; Mouton, Alice; De Panis, Diego; Marins, Luísa S; Leitão, Henrique; Diedericks, Genevieve; KIRANGWA, JOSEPHABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome P...
merlin, an improved framework for the reconstruction of high-quality genome-sca...
Capela, João; Lagoa, Davide Rafael Santos; Rodrigues, Rúben André Costa; Cunha, Emanuel Rodrigues; Cruz, Fernando; Barbosa, Ana; Bastos, J.; Lima, DiogoGenome-scale metabolic models have been recognised as useful tools for better understanding living organisms metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned versi...
BioISO: an objective-oriented application for assisting the curation of genome-...
Cruz, Fernando; Capela, João; Ferreira, Eugénio C.; Rocha, Miguel; Dias, OscarAs the reconstruction of Genome-Scale Metabolic Models becomes standard practice in systems biology, the number of organisms having at least one metabolic model at the genome-scale is peaking at an unprecedented scale. The automation of several laborious tasks, such as gap-finding and gap-filling, allowed to develop GSMMs for poorly described organisms. However, such models quality can be compromised by the aut...
Reconciliation of regulatory data: the regulatory networks of Escherichia coli ...
Lima, Diogo; Cruz, Fernando; Rocha, Miguel; Dias, OscarMultiple efforts have been made to comprehend the regulatory machinery of model prokaryotic organisms, such as Escherichia coli and Bacillus subtilis. However, the lack of unification of published regulatory data reduces the potential of reconstructing whole genome transcriptional regulatory networks. The work hereby discussed, focuses on the retrieval and integration of relevant regulatory data from multiple r...
merlin v4. 0: an updated platform for the reconstruction of high-quality genome...
Capela, João; Lagoa, D.; Rodrigues, Rúben; Cunha, Emanuel; Cruz, Fernando; Barbosa, Ana; Bastos, J.; Lima, Diogo; Ferreira, Eugénio C.; Rocha, MiguelGenome-scale metabolic models have been recognised as useful tools for better understanding living organisms metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models reconstruction process, conjugating manual and automatic procedures while leveraging the users expertise with a curation-oriented graphical interface. An updated and redesigned version...
Towards the reconstruction of integrated genome-scale models of metabolism and ...
Cruz, Fernando; Lima, Diogo; Faria, José P.; Rocha, Miguel; Dias, OscarThe reconstruction of integrated genome-scale models of metabolism and gene expression has been a challenge for a while now. In fact, various methods that allow integrating reconstructions of Transcriptional Regulatory Networks, gene expression data or both into Genome-Scale Metabolic Models have been proposed. Several of these methods are surveyed in this article, which allowed identifying their strengths and ...
A review of methods for the reconstruction and analysis of integrated genome-sc...
Cruz, Fernando; Faria, José Pedro; Rocha, Miguel; Rocha, Isabel; Dias, OscarThe current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the pers...
Estudo comparativo do comportamento enológico de leveduras
Cruz, Fernando; Bessa, António; Andrade, João Verdial; Estevinho, Leticia M.Anexo; Actualmente e comum utilizar leveduras comerciais na fermentação alcoólica por forma a garantir uma maior homogeneidade e um melhor controlo, ano após ano, de alguns parâmetros da fermentação alcoólica dos mostos.