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| Registros recuperados: 1.312 | |
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| Smrita Singh. |
| In the postgenomic era, computational methods are being used in diverse areas like drug discovery, robotics, weather forecasting etc. Computational methods are incorporated with various programmes that are further instructed with complex algorithms based on different logistic approaches. Artificial neural network is one of them to be utilized in various molecular dynamics and simulation studies. Therefore, it is essential to understand the basic logic while programming in order to troubleshoot the computational methods. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6623/version/1 |
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| Benoit H. Dessailly; Oliver C. Redfern; Christine A. Orengo. |
| The structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein function.
A few protein domain superfamilies have been shown to account for unexpectedly large numbers of proteins encoded in fully sequenced genomes. These large superfamilies are generally very diverse, spanning a wide range of functions,... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2214/version/1 |
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| Gaurav Pandey; Gowtham Atluri; Michael Steinbach; Vipin Kumar. |
| An application of great interest in microarray data analysis is the identification of a group of genes that show very similar patterns of expression in a data set, and are expected to represent groups of genes that perform common/similar functions, also known as functional modules. Although clustering offers a natural solution to this problem, it suffers from the limitation that it uses all the conditions to compare two genes, whereas only a subset of them may be relevant. Association analysis offers an alternative route for finding such groups of genes that may be co-expressed only over a subset of the experimental conditions used to prepare the data set. The techniques in this field attempt to find groups of data objects that contain coherent values... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2184/version/1 |
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| Rodrick Wallace. |
| The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, trajectory found on Earth. Are many of these life forms likely to be conscious in ways that we would recognize? Almost certainly. Will many conscious entities develop high order technology? Less likely. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is straightforward. |
| Tipo: Manuscript |
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5286/version/1 |
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| Brad Nicholas; Michael J. Owen; Dawn C. Wimpory; Thomas Caspari. |
| Intronic single nucleotide polymorphisms (SNPs) in the clock genes _npas2_ and _per1_ and the homeobox gene _en2_ are reported to be associated with autism. This bioinformatics analysis of the intronic regions which contain the autism-associated SNPs rs1861972 and rs1861973 in _en2_, rs1811399 in _npas2_, and rs885747 in _per1_, shows that these regions encode RNA transcripts with predicted structural characteristics of microRNAs. These microRNA-like structures are disrupted _in silico_ by the presence of the autism enriched alleles of rs1861972, rs1861973, rs1811399 and rs885747 specifically, as compared with the minor alleles of these SNPs. The predicted gene targets of these microRNA-like structures include genes reported to be implicated in autism... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2366/version/1 |
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| Naoki Sato. |
| Development of new generation sequencers enabled genome sequencing feasible for every organism in a laboratory. A typical data flow of de novo seuqencing includes (1) assembly of sequence reads, (2) estimation of open reading frames, (3) annotation of proteins, and (4) finding RNA genes. The annotation is normally performed by BLASTP searches against several different databases. However, it is usually hard to find a plausible annotation by just looking at the results of BLASTP searches.

Here I propose a potentially automatic method of annotation that exploits automatic protein clustering using the software GCLUST, which estimates proper similarity threshold for each list of homologs using ‘entropy-optimized... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5086/version/1 |
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| The HAPMAP Team; The PROSITE Team; Edouard de Castro; Alan Bridge; UniProt Consortium. |
| The development of next generation sequencing technologies promises a massive increase in the rate of submission of new protein sequences to sequence databases such as the Universal Protein Resource Knowledge Base, UniProtKB. At UniProtKB/Swiss-Prot we propose to meet this challenge by continuing to expand and develop systems for the automatic propagation of existing annotation to newly submitted protein sequences. These developments will promote the standardization of ortholog annotation both across and within kingdoms and significantly enhance our ability to accurately annotate new protein sequences which are being produced at an ever increasing rate.
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| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3215/version/1 |
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| Trevor G. Marshall. |
| The US CDC believes that 65% of all infections in developed countries may be caused by pathogens in biofilms. Electron Microscopy has shown that these bacterial communities can evade phagocytosis, and persist in the cytoplasm of monocytes, macrophages, lymphocytes and neutrophils. Three decades ago, Wirostko _et al._ found such intraphagocytic communities in Crohn’s disease, Juvenile Rheumatoid Arthritis and Sarcoidosis. However, the mechanism(s) by which such persistent bacteria could evade the immune system have remained elusive. Recently, 16S RNA from species of gliding bacteria never thought to be able to survive _in vivo_, have been found in surgically removed biofilms. This study set out to identify whether the genomes of these gliding... |
| Tipo: Poster |
Palavras-chave: Immunology; Microbiology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/164/version/1 |
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| Djordje Bajic; Juan F. Poyatos. |
| Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression. This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6729/version/1 |
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| Ramírez Sánchez, Obed. |
| Los factores de transcripción (FTs) son proteínas que incrementan o disminuyen la tasa transcripcional de uno o varios genes. Los FTs desempeñan un papel fundamental en el control de casi todos los procesos biológicos: crecimiento, metabolismo, respuesta a factores ambientales, etc. En plantas cultivadas, son de particular importancia aquellos relacionados con la respuesta al estrés (sequía, salinidad, bajas temperaturas, plagas, enfermedades, etc.). La identificación de FTs, su posterior anotación y la construcción de bases de datos públicas constituye un importante recurso para el estudio de los procesos que controlan la expresión génica. Se construyó la base de datos FT-MTS que contiene información de 13,975 genes identificados como FTs en los genomas... |
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Palavras-chave: Regulación transcripcional; Anotación funcional; Bioinformática; Transcriptional regulation; Functional annotation; Bioinformatics; Cómputo aplicado; Maestría. |
| Ano: 2012 |
URL: http://hdl.handle.net/10521/689 |
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| Vladimir Mironov. |
| We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that individual store performance was quite query specific. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second, and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5417/version/1 |
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| Warren Kibbe. |
| Research databases, clinical systems, and lab systems all have different standards, formats and drivers for data capture, operation, analysis and integration. For interdisciplinary nutritional researchers, however, there is a dependence on all of these areas and technologies. While building and integrating these systems can be difficult, using agile practices including short iterations, testing and continuous integration methods, and close engagement with all stakeholders to create useful systems for translational research. Interoperability also requires good data standards, including the use of structured data dictionaries and existing data standards such as HL7, UMLS, LOINC, ICD, and OBO foundry ontologies. |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5197/version/1 |
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| Kaushal Kumar Bhati; Vijay Kumar Singh. |
| Glycine Betaine is a quaternary amino compound that accumulates in stress conditions, mainly abiotic stresses like drought and salinity & synthesized by the two-step oxidation of choline via the intermediate betaine aldehyde, catalyzed by Choline monooxygenase and Betaine aldehyde dehydrogenase (BADH).
The sequence analysis of key enzymes of Glycine betaine biosynthesis i.e. BADH was carried out using various online proteomic tools available on Expasy and EBL, and then homologous modeling of this enzyme was performed using automated mode SWISS-MODEL & GENO 3D and models were analyzed on QMEAN. This was an attempt to find the possible model of BADH, because no physical model of BADH is yet available on... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Plant Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6360/version/1 |
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| Dagmar Köhn; Nicolas Le Novère; Christian Knüpfer. |
| Computational models are becoming more and more the central scientific paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of... |
| Tipo: Poster |
Palavras-chave: Molecular Cell Biology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3137/version/1 |
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| A. Patrice Seyed. |
| This paper examines the primitive relations (dependence, quality, and constitution) of the BFO and DOLCE upper ontologies, employed in developing domain ontologies of the biomedical sciences. The strengths in both upper ontologies are examined, which sets a framework for developing a common upper ontology that utilizes the assets of both. |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3481/version/1 |
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| Guang-Zhong Wang; Martin J. Lercher. |
| Among eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced genome-wide weak positive selection on amino acid composition to increase protein thermostability. |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/2974/version/1 |
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| Arpit Tandon; A Naqvi; Nitin Chitranshi; Siddharth Sinha. |
| Crystal Structure of cytochrome p450 2B4 has 476 amino acids, through docking approach we have attempted to explain the specificity of CYP2B4, total 28 imidazole drug were used for the studies as antifungal drugs in which bound bifonazole (reference) shows the binding energy of -8.67 kcal/mol .Compound Miconazole shows the minimum binding energy of -10.45 kcal/mol. The 2B4-bifonazole structure identified 10 residues (ALA 298, GLY 299, GLU 301, THR 302, ILE 363, VAL 292) within 6.5 Å of the active site of bifonazole. GLU 301, THR 302 are also located in 6.5 Å of the bound ligand in 2B4 structure. Due to the presence of the multiple binding substrates in cytochrome p450, it acts as the major target of many drugs in xenobiotic... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4314/version/1 |
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| Registros recuperados: 1.312 | |
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