6 documents found, page 1 of 1
Reconstruction of tissue-specific genome-scale metabolic models for human cance...
Barata, Tânia; Vieira, Vítor; Rodrigues, Rúben André Costa; Neves, Ricardo Pires das; Rocha, MiguelCancer Stem Cells (CSCs) contribute to cancer aggressiveness, metastasis, chemo/radio-therapy resistance, and tumor recurrence. Recent studies emphasized the importance of metabolic reprogramming of CSCs for the maintenance and progression of the cancer phenotype through both the fulfillment of the energetic requirements and the supply of substrates fundamental for fast-cell growth, as well as through metabolit...
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...
BioTMPy: a Deep Learning-based tool to classify biomedical literature
Alves, Nuno; Rodrigues, Rúben André Costa; Rocha, MiguelOver the last few decades, the publication rate has been massively increasing, resulting in a huge number of available scientific documents, which consequently makes the search of relevant information for a certain topic a heavy and time-consuming task. Biomedical Text Mining has been addressing this problem for a while, but there is still space for improvements. For instance, PubMed, which contains now more th...
ViralFP: a web application of viral fusion proteins
Moreira, Pedro; Sequeira, Ana; Pereira, S.; Rodrigues, Rúben André Costa; Rocha, Miguel; Lousa, DianaViral fusion proteins are attached to the membrane of enveloped viruses (a group that includes Coronaviruses, Dengue, HIV and Influenza) and catalyze fusion between the viral and host membranes, enabling the virus to insert its genetic material into the host cell. Given the importance of these biomolecules, this work presents a centralized database containing the most relevant information on viral fusion protei...
Metabolite integration pipeline for the improvement of human metabolic models
Vieira, Vítor; Ferreira, Jorge; Rodrigues, Rúben André Costa; Rocha, MiguelGenome-scale metabolic models (GSMMs) of human cells are predictive tools with great potential for revealing important aspects of cell physiology, disease as well as for the diagnosis and treatment of diseases caused by the deregulation of metabolism. In the past decade, there have been notable efforts to reconstruct models of human metabolism, with five generic GSMMs currently available. Maintaining references...
A model integration pipeline for the improvement of human genome-scale metaboli...
Vieira, Vítor; Ferreira, Jorge; Rodrigues, Rúben André Costa; Liu, Filipe Alexandre Wang; Rocha, MiguelMetabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstructio...