Navegando por Palavras-chave "bioinformatics"
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- ItemSomente MetadadadosBioinformatics Approach to BDNF and BDNF-Related Disorders(Bentham Science Publ Ltd, 2011-06-01) Dias, Alvaro Machado [UNIFESP]; Universidade Federal de São Paulo (UNIFESP); Universidade de São Paulo (USP)Context: Currently, the keyword 'BDNF' retrieves 7388 publications in Pubmed, which point to many directions.Objective: This paper aims to uncover patterns that are hidden under this huge mass of studies and then to review the most prominent sub-topics in 'BDNF and mental health'.Method: Several semi-automatic tools employed, in order to present: 1. A visual representation of BDNF's main molecular pathways; 2. A table with all the components of this pathway that are known to be associated with human diseases; 3. A conceptual map of the whole literature; 4. A histogram of the mental disorders that are known to be associated with BDNF, as well as a review of the literature on each one of these topics.Results: The conceptual map suggests that the field is divided in two major sections: BDNF molecular pathways, receptors, other neurotrophins and neurotransmitters; and BDNF-related disorders. Among the latter, the mental disorders that are mostly related to BDNF are: depression, schizophrenia, Parkinson disease, Alzheimer disease, and bipolar disorder.
- ItemSomente MetadadadosThe DrugAge database of aging-related drugs(Wiley, 2017) Barardo, Diogo; Thornton, Daniel; Thoppil, Harikrishnan; Walsh, Michael; Sharifi, Samim; Ferreira, Susana; Anzic, Andreja; Fernandes, Maria; Monteiro, Patrick; Grum, Tjasa; Cordeiro, Rui; De-Souza, Evandro Araujo [UNIFESP]; Budovsky, Arie; Araujo, Natali; Gruber, Jan; Petrascheck, Michael; Fraifeld, Vadim E.; Zhavoronkov, Alexander; Moskalev, Alexey; de Magalhaes, Joao PedroAging is a major worldwide medical challenge. Not surprisingly, identifying drugs and compounds that extend lifespan in model organisms is a growing research area. Here, we present DrugAge (http://genomics. senescence. info/drugs/), a curated database of lifespan-extending drugs and compounds. At the time of writing, DrugAge contains 1316 entries featuring 418 different compounds from studies across 27 model organisms, including worms, flies, yeast and mice. Data were manually curated from 324 publications. Using drug-gene interaction data, we also performed a functional enrichment analysis of targets of lifespan-extending drugs. Enriched terms include various functional categories related to glutathione and antioxidant activity, ion transport and metabolic processes. In addition, we found a modest but significant overlap between targets of lifespan-extending drugs and known aging-related genes, suggesting that some but not most aging-related pathways have been targeted pharmacologically in longevity studies. DrugAge is freely available online for the scientific community and will be an important resource for biogerontologists.
- ItemSomente MetadadadosAn exploration of the genetic robustness landscape of surface protein families in the human protozoan parasite trypanosoma cruzi(Ieee-inst Electrical Electronics Engineers Inc, 2007-09-01) Azuaje, Francisco; Ramirez, Jose Luis; Silveira, Jos Franco da; Univ Ulster; IDEA; Universidade Federal de São Paulo (UNIFESP)The ability of genes to be robust to mutations at the codon level has been suggested as a key factor for understanding adaptation features. It has been proposed that genes relevant to host-parasite interactions will tend to exhibit high volatility or antirobust patterns, which may be related to the capacity of the parasite to evade the host immune system. We compared two superfamilies of surface proteins, trans-sialidase (TS)-like proteins and putative surface protein dispersed gene family-1 (DGF-1), in the parasite Trypanosoma cruzi in terms of a measure of gene volatility. We proposed alternative codon robustness indicators based on cross entropy and impurity of amino acids encoded by point-mutations, which were compared to a volatility estimator previously published. This allowed us to present a more detailed description of the differences between families. A significant difference was observed in terms of these scores, with the TS-MVar1 and the DGF-1 families showing the highest and lowest gene volatility values respectively. the cross entropy and impurity estimators suggest that the MVar1 levels of volatility are linearly correlated with their capacity to generate diverse sets of amino acids as a consequence of potential mutations. This study indicates the feasibility of applying different measures of genetic robustness to detect variations between potential drug targets at the protein level.
- ItemAcesso aberto (Open Access)A Hybrid Heuristic for the k-medoids Clustering Problem(Assoc Computing Machinery, 2012-01-01) Nascimento, Maria C. V. [UNIFESP]; Toledo, Franklina M. B.; Carvalho, Andre C. P. L. F. de; Soule, T.; Universidade Federal de São Paulo (UNIFESP)Clustering is an important tool for data analysis, since it allows the exploration of datasets with no or very little prior information. Its main goal is to group a set of data based on their similarity (dissimilarity). A well known mathematical formulation for clustering is the k-medoids problem. Current versions of k-medoids rely on heuristics, with good results reported in the literature. However, few methods that analyze the quality of the partitions found by the heuristics have been proposed. in this paper, we propose a hybrid Lagrangian heuristic for the k-medoids. We compare the performance of the proposed Lagrangian heuristic with other heuristics for the k-medoids problem found in literature. Experimental results presented that the proposed Lagrangian heuristic outperformed the other algorithms.
- ItemSomente MetadadadosNeglected Tropical Diseases, Bioinformatics, and Vaccines(Oxford Univ Press Inc, 2015-01-15) Rodrigues, Mauricio Martins [UNIFESP]; Ersching, Jonatan [UNIFESP]; Universidade Federal de São Paulo (UNIFESP)