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| Registros recuperados: 1.312 | |
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| Diego Mauricio Riaño-Pachón; Luiz Gustavo Guedes Correa; Bernd Mueller-Roeber. |
| PlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants. The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date, summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the database to additional completed viridiplantae genomes, i.e., the moss _Physcomitrella patens_ and the rice _Oryza sativa_ spp _indica_. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the rhodophyte... |
| Tipo: Poster |
Palavras-chave: Ecology; Bioinformatics; Plant Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1094/version/1 |
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| Shi Huang. |
| Early studies of molecular evolution revealed a correlation between genetic distance and time of species divergence. This observation provoked the molecular clock hypothesis and in turn the ‘Neutral Theory’, which however remains an incomplete explanation since it predicts a constant mutation rate per generation whereas empirical evidence suggests a constant rate per year. Data inconsistent with the molecular clock hypothesis have steadily accumulated in recent years that show no correlation between genetic distance and time of divergence. It has therefore become a challenge to find a testable idea that can reconcile the seemingly conflicting data sets. Here, an inverse relationship between genetic diversity and epigenetic... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Genetics & Genomics; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1751/version/1 |
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| Marcelo Sobottka; Andrew Glenn Hart. |
| It is probable that the distributional structure of DNA sequences arises from the accumulation of many successive stochastic events such as nucleotide deletions, insertions, substitutions and elongations [1, 2, 3, 4, 5, 6, 7]. Although the existence of long-range correlations in non-coding portions of DNA sequences is well established [8, 9, 10, 11], first order Markov chains might well capture aspects of their nucleotide distributions [12]. Here we propose a hidden Markov model based on a coupling of an urn process with a Markov chain to approximate the distributional structure of primitive DNA sequences. Then, by supposing that a bacterial DNA sequence can be derived from uniformly distributed mutations of some primitive DNA, we use the model to explain... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5245/version/1 |
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| Mark Thomas. |
| The European Conditional Mouse Mutagenesis (EUCOMM) project aims to establish a mutant resource containing up to 13,000 conditional mouse mutations in C57BL/6N embryonic stem cells. As part of this resource, up to 8,000 targeted conditional mutations will be generated for genes that can not be readily trapped by random gene trapping methods. Non-symmetrical critical exons are identified as part of the targeting approach, which when deleted produce a knockout (KO) transcript that is susceptible to nonsensemediated decay (NMD). The success of this approach is dependent on detailed and accurate genome annotation, which is provided by the Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute. Based on a combination... |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3181/version/1 |
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| Karuna J. Jaya Sai; Dibyabhaba Pradhan; Amineni Umamaheswari. |
| Human proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects. Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported human YES... |
| Tipo: Poster |
Palavras-chave: Cancer; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4902/version/1 |
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| Ajeet Ajeet. |
| The purpose of present work is to introduce the binding of existing drugs to the trans-disciplinary protein with the help of docking procedures. Docking procedures allows virtually screening a database of compounds and predict the strongest binder based on various scoring functions. This work has been performed with the help of Molegro Virtual docker, in which two drugs are docked with their corresponding and non-corresponding (trans-disciplinary) protein. Results reveals that the protein-ligand interaction energy, hydrogen bond energy and MolDock scores provided by molegro virtual docker, between legands (Levodopa and Acyclovir) and trans-disciplinary proteins have been equivalent or even better than that of between legands and corresponding proteins. |
| Tipo: Manuscript |
Palavras-chave: Pharmacology; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6702/version/1 |
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| Pinar Wennerberg; Sonja Zillner. |
| Formal knowledge about human anatomy, radiology or diseases is necessary to support clinical applications such as medical image search. This machine processable knowledge can be acquired from biomedical domain ontologies, which however, are typically very large and complex models. Thus, their straightforward incorporation into the software applications becomes difficult. In this paper we discuss first ideas on a statistical approach for modularizing large medical ontologies and we prioritize the practical applicability aspect. The underlying assumption is that the application relevant ontology fragments, i.e. modules, can be identified by the statistical analysis of the ontology concepts in the domain corpus. Accordingly, we argue that most frequently... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3522/version/1 |
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| Taras K. Oleksyk. |
| The genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico. This is a critically endangered endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to have its genome sequenced and assembled. A genome of one A. vittata female was sequenced resulting in a total of almost 42.5 billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (<500bp), the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6552/version/1 |
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| Takayuki Tanaka; Yuko Ishizaka; Toru Mitushima; Mizuki Tani; Akiko Toda; Eiichi Toda; Minoru Okada; Hiroshi Yamamoto; Minoru Yamakado. |
| Background: The plasma amino acid profile can be a useful indicator in clinical settings because it changes in response to various metabolic alternations. However, the association between the plasma amino acid profile and body fat accumulation has not been evaluated in humans.Objective: This study aimed to relate plasma amino acids to visceral fat accumulation in humans because excess visceral fat raises the odds ratio of developing metabolic syndrome.Design: A total of 1,449 subjects (985 males and 464 females) who had undergone a comprehensive health screening were enrolled in this study. The visceral fat area (VFA) was determined in each subject using CT imaging. Subjects were then divided into two groups according to VFA: high-VFA (≥100 cm2,... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5560/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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| Rajneesh Prajapat; Avinash Marwal; Anurag Sahu; Rajarshi Kumar Gaur. |
| We retrieved six protein sequences of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A [FJ345402] from GenBank-NCBI (ACJ03821, ACJ03822, ACJ03823, ACJ03824, ACJ03825 and ACJ03826) which were used for computational modeling structure prediction. Ramachandran plot of ACJ03826-AC4 had maximum 73.3% and ACJ03822-AV1 had 71% residues in core region therefore these models cannot be placed in a good quality category. ACJ03824-AC2 had only 18.6% residues in core and 13.6% residues in disallowed regions and therefore it was the least stable protein. Verify-3D graph profile scores for selected ToLCJV proteins were greater than zero. Therefore all the verify-3D graph corresponds to an acceptable environment for the model. Findings of the present study provide a base... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6658/version/1 |
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| Rafal Woycicki; Wojciech Gutman; Zbigniew Przybecki. |
| Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3900/version/1 |
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| Registros recuperados: 1.312 | |
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