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| Trish Whetzel. |
| In order to effectively search, retrieve, and analyze data oftentimes it is curated and tagged with ontology terms. However, the amount of effort to curate the existing set of data resources is beyond the limits of purely manual curation. We present three ontology-based tools developed by the National Center for Biomedical Ontology to enhance the curation workflow: Ontology Widgets, Notes, and the Annotator. The Ontology Widgets provide a mechanism to use ontologies in Web-based forms without the need to locally parse and store the ontology. The widgets provide a variety of functionality including term autocompletion and ontology visualization. The Ontology Widgets are implemented for all BioPortal ontologies, including those from the OBO Foundry and... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5213/version/1 |
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| Asif Husain Naqvi; Hardik H. Sheth; Vijay Kumar; Suchindran H S; Vivek Gupta. |
| The tumor suppressor protein p53 is a transcription factor that plays a key role in the prevention of cancer development. The p53 cancer mutation Y220C induces formation of a cavity on the protein's surface that can accommodate stabilizing small molecules. We have attempted with the help of virtual screening and molecular docking approach using Lamarckian Genetic Algorithm to elucidate the extent of specificity of p53 cancer mutation Y220C towards different class of Phenothiazines (an anti-cancer agent). 

The 393 residue p53 tumor suppressor protein exists in a dynamic equilibrium to form homotetramers. Each chain comprises several functional domains. The N terminal part of the protein consists of the... |
| Tipo: Presentation |
Palavras-chave: Cancer; Pharmacology; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6135/version/1 |
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| Liao Y. Chen. |
| Atomic force microscopes and optical tweezers afford direct probe into the inner working of single biomolecules by mechanically unfolding them.^1-15^ Critical to the success of this type of probe is to correctly extract the free energy differences between the various conformations of a protein/nucleic acid along its forced unfolding pathways. Current studies rely on the Jarzynski equality^16^ (JE) or its undergirding Crooks fluctuation theorem^17^ (CFT), even though questions remain on its validity^17-19^ and on its accuracy.^13,20-21^ The validity of JE relies on the assumption of microscopic reversibility.^17,18^ The dynamics of biomolecules, however, is Langevin stochastic in nature. The frictional force in the Langevin equation breaks the time reversal... |
| Tipo: Manuscript |
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1911/version/1 |
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| Peter Ralph; Graham Coop; Carl Boettiger. |
| Phylogenetic comparative methods have become all but ubiquitous in only a few decades, forcing us to reconsider if information from a phylogenetic tree can justify the results. Existing approaches to this question have been inadequate and do not scale with tree size or the ability to resolve branches. For instance, selection between phylogenetic models typically based on information criteria fails to adequately reflect this uncertainty, and can lead to preference for arbitrarily complicated models. Common measures of phylogenetic signal tend to characterize the goodness-of-fit of a Brownian motion model to the data, rather than indicate whether the data is sufficient to confidently distinguish between different hypotheses. We present a Monte Carlo based... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6453/version/1 |
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| Michael Hucka. |
| SBML is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations.

The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional "packages" that add topic-specific features to the Core to support more specialized models and application areas. In this presentation, I provide a very brief overview of SBML Level 3 activity areas. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5011/version/1 |
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| Kameshwar R. Ayasolla; Ravi K. R. Kalathur; Matthias E. Futschik. |
| Although the disease causing gene huntingtin has been known for some time, the exact cause of neuronal cell death during _Huntington's disease_ (HD) remains unknown. One potential mechanism contributing to the massive loss of neurons in HD brains might be the _Unfolded Protein Response_ (UPR) which is activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). As an adaptive response, UPR upregulates transcription of chaperones, temporarily attenuating new translation and activates protein degradation via the proteasome. However, at high levels of ER stress, UPR signalling can contribute to neuronal apoptosis.

Our primary aims include (a) construction of the UPR signalling network, (b)... |
| Tipo: Poster |
Palavras-chave: Neuroscience; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7078/version/1 |
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| Jaina Mistry; Penny Cogghill; Sean Eddy; Rob Finn; John Tate; Alex Bateman. |
| Pfam is a database of conserved protein families or domains commonly used for genome annotation and sequence classification. It comprises two parts: (1) Pfam-A families, which are fully annotated and consist of a representative seed alignment, HMMs, and a full alignment comprising all sequences that score above the curated threshold; (2) Pfam-B families, which are automatically generated clusters of domains not matched by Pfam-A but that often indicate conserved sequence regions. Pfam release 23.0 predicts at least one Pfam-A domain on 74% of the sequences in UniProtKB, and predicts either a Pfam-A or Pfam-B domain on 93% of the sequences in UniProtKB.

With the ever increasing rate of deposition of new proteins of all... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3194/version/1 |
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| Roderic Page; Michael Charleston. |
| TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling’s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling’s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1030/version/1 |
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| Martina Kutmon; Nicolas Rodriguez. |
| The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. Recently a prototype has been developed with OSGi to achieve a more modular framework structure. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules. SBFC allows anyone to easily add new... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6370/version/1 |
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| Rodrick Wallace. |
| Tlusty's topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. Unlike the genetic case, two protein folding codes are found, a 'normal' globular and a 'pathological' amyloid version. The underlying normal 'protein folding code error network' is found to have one major, highly dominant, 'spherical' component, a minor attachment handle in the Morse Theory sense, and as many as three additional subminor handles. The basic amyloid folding code error network appears to be more complicated, of genus two, giving the eightfold symmetry of the steric zipper. Like many before us, we conjecture that the elaborate... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4665/version/1 |
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| M Shankaracharya; Suchitra Kumari; Ambarish S. Vidyarthi. |
| Hepatitis is deadly, and the fifth leading cause of death after heart disease, stroke, chest disease and cancer. Worldwide, 1.5 million deaths per year have been estimated. Detection of hepatitis is a big problem for general practitioners. An expert doctor commonly makes decisions by evaluating the current test results of a patient or by comparing the patient with others with the same condition with reference to the previous decisions. Many machine learning and data mining techniques have been designed for the automatic diagnosis of hepatitis. However, no one tool is available to the general population for the diagnosis of Hepatitis. Hence, a graphical user interface-enabled tool needs to be developed, through which medical practitioners can feed patient... |
| Tipo: Poster |
Palavras-chave: Biotechnology; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7093/version/1 |
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| Diego Mauricio Riaño-Pachón; Axel Nagel; Robert Wagner; Elke Weber; Birgit Kersten. |
| GabiPD ("http://gabi.rzpd.de":http://gabi.rzpd.de) was established within GABI-I and further developed in GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics, transcriptomics, proteomics, metabolomics) are incorporated in GabiPD, representing 14 different biological species. Last year GabiPD moved to the Max Planck Institute of Molecular Plant Physiology. In the progressing GABI-FUTURE phase, the GabiPD team has been creating a more integrative data view, expanding the tools and information provided by our well-known GreenCards. Links to different... |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Plant Biology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1684/version/1 |
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| Pedro Beltrao. |
| It has been previously shown [1] that _S. cerevisiae_ proteins preferentially interact with proteins of the same estimated likely time of origin. To study this observation further, the protein interaction networks of _S. cerevisiae_ and _H. sapiens_ were analyzed taking into account an estimate for the age of the proteins in these species. These estimates were obtained by studying the presence and absence of putative orthologs in other eukaryotic species. In this work preliminary results are described that point to a dependence of the likelihood of protein interaction on the proteins’ age. The probability of two proteins interactions was found to be linearly dependent on the time the proteins have co-existed in the species. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/22/version/1 |
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| Registros recuperados: 1.312 | |
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