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[PMID]:29408272
[Au] Autor:Saif I; Kasmi Y; Allali K; Ennaji MM
[Ad] Endereço:Team of Virology, Oncology and Medical Biotechnologies, Laboratory of Virology, Microbiology, Quality and Biotechnologies/ETB, Faculty of Science sand Technologies-Mohammedia, Hassan II University of Casablanca, Morocco.
[Ti] Título:Prediction of DNA methylation in the promoter of gene suppressor tumor.
[So] Source:Gene;651:166-173, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:The epigenetics methylation of cytosine is the most common epigenetic form in DNA sequences. It is highly concentrated in the promoter regions of the genes, leading to an inactivation of tumor suppressors regardless of their initial function. In this work, we aim to identify the highly methylated regions; the cytosine-phosphate-guanine (CpG) island located on the promoters and/or the first exon gene known for their key roles in the cell cycle, hence the need to study gene-gene interactions. The Frommer and hidden Markov model algorithms are used as computational methods to identify CpG islands with specificity and sensitivity up to 76% and 80%, respectively. The results obtained show, on the one hand, that the genes studied are suspected of developing hypermethylation in the promoter region of the gene involved in the case of a cancer. We then showed that the relative richness in CG results from a high level of methylation. On the other hand, we observe that the gene-gene interaction exhibits co-expression between the chosen genes. This let us to conclude that the hidden Markov model algorithm predicts more specific and valuable information about the hypermethylation in gene as a preventive and diagnostics tools for the personalized medicine; as that the tumor-suppresser-genes have relative co-expression and complementary relations which the hypermethylation affect in the samples studied in our work.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Ilhas de CpG
Metilação de DNA
Genes Supressores de Tumor
Regiões Promotoras Genéticas
[Mh] Termos MeSH secundário: Algoritmos
DNA de Neoplasias
Conjuntos de Dados como Assunto
Epistasia Genética
Seres Humanos
Cadeias de Markov
Modelos Genéticos
Neoplasias/genética
[Pt] Tipo de publicação:EVALUATION STUDIES; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Neoplasm)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180207
[St] Status:MEDLINE


  2 / 57077 MEDLINE  
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[PMID]:29408208
[Au] Autor:Yue J; Wan F; Zhang Q; Wen P; Cheng L; Li P; Guo W
[Ad] Endereço:Beijing University of Chinese Medicine, Yinghuadong Road, Chaoyang District, Beijing, China; Department of Joint Surgery, China-Japan Friendship Hospital, Yinghuadong Road, Chaoyang District, Beijing, China. Electronic address: 20150941122@bucm.edu.cn.
[Ti] Título:Effect of glucocorticoids on miRNA expression spectrum of rat femoral head microcirculation endothelial cells.
[So] Source:Gene;651:126-133, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:The study profiled the differential miRNA expression from femoral head bone microvascular endothelial cells (BMECs) between model group and control group to explore the pathogenesis of steroid-induced osteonecrosis of femoral head (ONFH). Twenty 8-week-old Female Sprague-Dawley (SD) rats were randomly divided into control and model groups. Rats in model group received an intraperitoneal injection of 20-µg/kg lipopolysaccharide (LPS) at an interval of 24 h. Then, 24 h later, rats received three doses of 40-mg/kg methylprednisolone by intramuscular injection at intervals of 24 h. In control group, rats received the same volume of normal saline. After 4 weeks, the femoral heads were sectioned to confirm the establishment of the model. To replicate the animal model ex vivo, BMECs were isolated. Different miRNAs were screened using Agilent Gene Spring GX software, and real-time quantitative polymerase chain reaction (qPCR) was used to confirm the results of miRNA microarray analysis. The differentially expressed miRNA were assessed by bioinformatics analysis. Four differentially expressed miRNAs were identified (two upregulated: miR-132-3p, miR-335 and two down regulated: miR-466b-2-3p, let-7c-1-3p). qPCR results were consistent with the gene-chip results. Steroid-induced ONFH may cause miRNA changes in BMSCs. miR-132-3p and miR-335 may be important in steroid-induced ONFH.
[Mh] Termos MeSH primário: Endotélio Vascular/metabolismo
Necrose da Cabeça do Fêmur/metabolismo
Cabeça do Fêmur/metabolismo
Glucocorticoides/farmacologia
Metilprednisolona/farmacologia
MicroRNAs/biossíntese
[Mh] Termos MeSH secundário: Animais
Células Cultivadas
Biologia Computacional
Modelos Animais de Doenças
Endotélio Vascular/efeitos dos fármacos
Feminino
Cabeça do Fêmur/irrigação sanguínea
Cabeça do Fêmur/efeitos dos fármacos
Necrose da Cabeça do Fêmur/sangue
Necrose da Cabeça do Fêmur/induzido quimicamente
Necrose da Cabeça do Fêmur/patologia
MicroRNAs/genética
Microcirculação
Ratos
Ratos Sprague-Dawley
Reação em Cadeia da Polimerase em Tempo Real
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Glucocorticoids); 0 (MicroRNAs); X4W7ZR7023 (Methylprednisolone)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180207
[St] Status:MEDLINE


  3 / 57077 MEDLINE  
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[PMID]:29389989
[Au] Autor:Almutairy M; Torng E
[Ad] Endereço:Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America.
[Ti] Título:Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.
[So] Source:PLoS One;13(2):e0189960, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.
[Mh] Termos MeSH primário: Biologia Computacional
[Mh] Termos MeSH secundário: Animais
Genoma Humano
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Camundongos
Modelos Teóricos
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180202
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189960


  4 / 57077 MEDLINE  
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[PMID]:28470244
[Au] Autor:Chen X; Jiang ZC; Xie D; Huang DS; Zhao Q; Yan GY; You ZH
[Ad] Endereço:School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China. xingchen@amss.ac.cn.
[Ti] Título:A novel computational model based on super-disease and miRNA for potential miRNA-disease association prediction.
[So] Source:Mol Biosyst;13(6):1202-1212, 2017 May 30.
[Is] ISSN:1742-2051
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:In recent years, more and more studies have indicated that microRNAs (miRNAs) play critical roles in various complex human diseases and could be regarded as important biomarkers for cancer detection in early stages. Developing computational models to predict potential miRNA-disease associations has become a research hotspot for significant reduction of experimental time and cost. Considering the various disadvantages of previous computational models, we proposed a novel computational model based on super-disease and miRNA for potential miRNA-disease association prediction (SDMMDA) to predict potential miRNA-disease associations by integrating known associations, disease semantic similarity, miRNA functional similarity, and Gaussian interaction profile kernel similarity for diseases and miRNAs. SDMMDA could be applied to new diseases without any known associated miRNAs as well as new miRNAs without any known associated diseases. Due to the fact that there are very few known miRNA-disease associations and many associations are 'missing' in the known training dataset, we introduce the concepts of 'super-miRNA' and 'super-disease' to enhance the similarity measures of diseases and miRNAs. These super classes could help in including the missing associations and improving prediction accuracy. As a result, SDMMDA achieved reliable performance with AUCs of 0.9032, 0.8323, and 0.8970 in global leave-one-out cross validation, local leave-one-out cross validation, and 5-fold cross validation, respectively. In addition, esophageal neoplasms, breast neoplasms, and prostate neoplasms were taken as independent case studies, where 46, 43 and 48 out of the top 50 predicted miRNAs were successfully confirmed by recent experimental literature. It is anticipated that SDMMDA would be an important biological resource for experimental guidance.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Simulação por Computador
MicroRNAs/genética
[Mh] Termos MeSH secundário: Algoritmos
Estudos de Associação Genética
Predisposição Genética para Doença/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1039/c6mb00853d


  5 / 57077 MEDLINE  
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[PMID]:28470277
[Au] Autor:Tseng TS; Tsai KC; Chen C
[Ad] Endereço:Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. bmchinp@ibms.sinica.edu.tw.
[Ti] Título:Characterizing the structure-function relationship reveals the mode of action of a novel antimicrobial peptide, P1, from jumper ant Myrmecia pilosula.
[So] Source:Mol Biosyst;13(6):1193-1201, 2017 Jun 01.
[Is] ISSN:1742-2051
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Microbial infections of antibiotic-resistant strains cause serious diseases and have a significant impact on public health worldwide, so novel antimicrobial drugs are urgently needed. Insect venoms, a rich source of bioactive components containing antimicrobial peptides (AMPs), are attractive candidates for new therapeutic agents against microbes. Recently, a novel peptide, P1, identified from the venom of the Australian jumper ant Myrmecia pilosula, showed potent antimicrobial activities against both Gram-negative and Gram-positive bacteria, but its structure-function relationship is unknown. Here, we used biochemical and biophysical techniques coupled with computational simulations to explore the mode of action of P1 interaction with dodecylphosphocholine (DPC) micelles as a model membrane system. Our circular dichroism (CD) and NMR studies revealed an amphipathic α-helical structure for P1 upon interaction with DPC micelles. A paramagnetic relaxation enhancement approach revealed that P1 orients its α-helix segment (F6-G14) into DPC micelles. In addition, the α-helix segment could be essential for membrane permeabilization and antimicrobial activity. Moreover, the arginine residues R8, R11, and R15 significantly contribute to helix formation and membrane-binding affinity. The lysine residue K19 of the C-terminus functionally guides P1 to interact with DPC micelles in the early interaction stage. Our study provides insights into the mode of action of P1, which is valuable in modifying and developing potent AMPs as antibiotic drugs.
[Mh] Termos MeSH primário: Anti-Infecciosos/química
Anti-Infecciosos/farmacologia
Biologia Computacional
[Mh] Termos MeSH secundário: Peptídeos Catiônicos Antimicrobianos/química
Peptídeos Catiônicos Antimicrobianos/farmacologia
Dicroísmo Circular
Bactérias Gram-Negativas/efeitos dos fármacos
Bactérias Gram-Positivas/efeitos dos fármacos
Espectroscopia de Ressonância Magnética
Micelas
Testes de Sensibilidade Microbiana
Estrutura Secundária de Proteína
Relação Estrutura-Atividade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Infective Agents); 0 (Antimicrobial Cationic Peptides); 0 (Micelles)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1039/c6mb00810k


  6 / 57077 MEDLINE  
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[PMID]:28465312
[Au] Autor:Noorani A; Bornschein J; Lynch AG; Secrier M; Achilleos A; Eldridge M; Bower L; Weaver JMJ; Crawte J; Ong CA; Shannon N; MacRae S; Grehan N; Nutzinger B; O'Donovan M; Hardwick R; Tavaré S; Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium
[Ad] Endereço:Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0XZ, United Kingdom.
[Ti] Título:A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.
[So] Source:Genome Res;27(6):902-912, 2017 06.
[Is] ISSN:1549-5469
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, chemoresistant tumor for which the availability and size of pretreatment endoscopic samples are limiting. This study compares whole-genome sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status. Inclusion of samples collected post-chemotherapy increased the proportion of late-stage tumors. When comparing matched pre- and post-chemotherapy samples from 10 cases, the mutational signatures, copy number, and SNV mutational profiles reflect the expected heterogeneity in this disease. Analysis of SNVs in relation to allele-specific copy-number changes pinpoints the common ancestor to a point prior to chemotherapy. For cases in which pre- and post-chemotherapy samples do show substantial differences, the timing of the divergence is near-synchronous with endoreduplication. Comparison across a large prospective cohort (62 treatment-naive, 58 chemotherapy-treated samples) reveals no significant differences in the overall mutation rate, mutation signatures, specific recurrent point mutations, or copy-number events in respect to chemotherapy status. In conclusion, whole-genome sequencing of samples obtained following neoadjuvant chemotherapy is representative of the genomic landscape of esophageal adenocarcinoma. Excluding these samples reduces the material available for cataloging and introduces a bias toward the earlier stages of cancer.
[Mh] Termos MeSH primário: Adenocarcinoma/genética
Antineoplásicos/uso terapêutico
Neoplasias Esofágicas/genética
Regulação Neoplásica da Expressão Gênica
Genoma Humano
Taxa de Mutação
Proteínas de Neoplasias/genética
[Mh] Termos MeSH secundário: Adenocarcinoma/tratamento farmacológico
Adenocarcinoma/metabolismo
Adenocarcinoma/patologia
Idoso
Transformação Celular Neoplásica/genética
Transformação Celular Neoplásica/metabolismo
Transformação Celular Neoplásica/patologia
Biologia Computacional
Variações do Número de Cópias de DNA
Neoplasias Esofágicas/tratamento farmacológico
Neoplasias Esofágicas/metabolismo
Neoplasias Esofágicas/patologia
Esôfago/metabolismo
Esôfago/patologia
Feminino
Perfilação da Expressão Gênica
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Masculino
Meia-Idade
Terapia Neoadjuvante/métodos
Proteínas de Neoplasias/metabolismo
Mutação Puntual
Polimorfismo de Nucleotídeo Único
Estudos Prospectivos
Fatores de Tempo
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antineoplastic Agents); 0 (Neoplasm Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1101/gr.214296.116


  7 / 57077 MEDLINE  
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[PMID]:29240813
[Au] Autor:Yashar A; Denison RN
[Ad] Endereço:Department of Psychology and Center for Neural Science, New York University, New York, New York, United States of America.
[Ti] Título:Feature reliability determines specificity and transfer of perceptual learning in orientation search.
[So] Source:PLoS Comput Biol;13(12):e1005882, 2017 12.
[Is] ISSN:1553-7358
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Training can modify the visual system to produce a substantial improvement on perceptual tasks and therefore has applications for treating visual deficits. Visual perceptual learning (VPL) is often specific to the trained feature, which gives insight into processes underlying brain plasticity, but limits VPL's effectiveness in rehabilitation. Under what circumstances VPL transfers to untrained stimuli is poorly understood. Here we report a qualitatively new phenomenon: intrinsic variation in the representation of features determines the transfer of VPL. Orientations around cardinal are represented more reliably than orientations around oblique in V1, which has been linked to behavioral consequences such as visual search asymmetries. We studied VPL for visual search of near-cardinal or oblique targets among distractors of the other orientation while controlling for other display and task attributes, including task precision, task difficulty, and stimulus exposure. Learning was the same in all training conditions; however, transfer depended on the orientation of the target, with full transfer of learning from near-cardinal to oblique targets but not the reverse. To evaluate the idea that representational reliability was the key difference between the orientations in determining VPL transfer, we created a model that combined orientation-dependent reliability, improvement of reliability with learning, and an optimal search strategy. Modeling suggested that not only search asymmetries but also the asymmetric transfer of VPL depended on preexisting differences between the reliability of near-cardinal and oblique representations. Transfer asymmetries in model behavior also depended on having different learning rates for targets and distractors, such that greater learning for low-reliability distractors facilitated transfer. These findings suggest that training on sensory features with intrinsically low reliability may maximize the generalizability of learning in complex visual environments.
[Mh] Termos MeSH primário: Orientação/fisiologia
Transferência de Experiência (Psicologia)/fisiologia
Percepção Visual/fisiologia
[Mh] Termos MeSH secundário: Adulto
Encéfalo/fisiologia
Biologia Computacional
Feminino
Seres Humanos
Aprendizagem/fisiologia
Masculino
Modelos Neurológicos
Modelos Psicológicos
Plasticidade Neuronal/fisiologia
Estimulação Luminosa
Reprodutibilidade dos Testes
Aprendizagem Espacial/fisiologia
Análise e Desempenho de Tarefas
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171215
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pcbi.1005882


  8 / 57077 MEDLINE  
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[PMID]:29244015
[Au] Autor:Crosby RW; Williams TL
[Ad] Endereço:Department of Computer Science, College of Charleston, Charleston, SC, USA. crosbyrw@cofc.edu.
[Ti] Título:Fast algorithms for computing phylogenetic divergence time.
[So] Source:BMC Bioinformatics;18(Suppl 15):514, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet scale well to studies with hundreds of taxa and thousands of DNA base pairs. For example a study of 349 primate taxa was estimated to require over 9 months of processing time. In this work, we present a new algorithm, AncestralAge, that significantly improves the performance of the divergence time process. RESULTS: As part of AncestralAge, we demonstrate a new method for the computation of phylogenetic likelihood and our experiments show a 90% improvement in likelihood computation time on the aforementioned dataset of 349 primates taxa with over 60,000 DNA base pairs. Additionally, we show that our new method for the computation of the Bayesian prior on node ages reduces the running time for this computation on the 349 taxa dataset by 99%. CONCLUSION: Through the use of these new algorithms we open up the ability to perform divergence time inference on large phylogenetic studies.
[Mh] Termos MeSH primário: Algoritmos
Biologia Computacional/métodos
Filogenia
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Animais
Primatas/classificação
Primatas/genética
Software
Fatores de Tempo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1916-1


  9 / 57077 MEDLINE  
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[PMID]:29244013
[Au] Autor:Zhao C; Sahni S
[Ad] Endereço:Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, FL, USA. czhao@cise.ufl.edu.
[Ti] Título:Cache and energy efficient algorithms for Nussinov's RNA Folding.
[So] Source:BMC Bioinformatics;18(Suppl 15):518, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. RESULTS: Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. CONCLUSION: Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.
[Mh] Termos MeSH primário: Algoritmos
Biologia Computacional/métodos
Dobramento de RNA
RNA
[Mh] Termos MeSH secundário: Conformação de Ácido Nucleico
RNA/química
RNA/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1917-0


  10 / 57077 MEDLINE  
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[PMID]:29244012
[Au] Autor:Jelínek J; Skoda P; Hoksza D
[Ad] Endereço:Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, Czech Republic. jelinek@ksi.mff.cuni.cz.
[Ti] Título:Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.
[So] Source:BMC Bioinformatics;18(Suppl 15):492, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. RESULTS: We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. CONCLUSION: In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.
[Mh] Termos MeSH primário: Aminoácidos
Bases de Conhecimento
Mapeamento de Interação de Proteínas/métodos
Proteínas
Software
[Mh] Termos MeSH secundário: Aminoácidos/química
Aminoácidos/metabolismo
Biologia Computacional
Bases de Dados de Proteínas
Modelos Estatísticos
Proteínas/química
Proteínas/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1921-4



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