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| Registros recuperados: 1.312 | |
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| Ulrich Bodenhofer; Andreas Kothmeier; Ingrid G. Abfalter; Carsten C. Mahrenholz; Sepp Hochreiter. |
| Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.

In this contribution, we propose a new approach to analyzing... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4708/version/1 |
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| Kojiro Yano. |
| Background:Detection of correlated gene expression is a fundamental process in the characterization of gene functions using microarray data. Commonly used methods such as the Pearson correlation can detect only a fraction of interactions between genes or their products. However, the performance of correlation analysis can be significantly improved either by providing additional biological information or by combining correlation with other techniques that can extract various mathematical or statistical properties of gene expression from microarray data. In this article, I will test the performance of three correlation methods-the Pearson correlation, the rank (Spearman) correlation, and the Mutual Information approach-in detection of protein-protein... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4430/version/1 |
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| Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter. |
| Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4710/version/1 |
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| Maurício V. Kritz; Marcelo T. dos Santos; Sebastián Urrita; Jean-Marc Schwartz. |
| Metabolic networks are among the most widely studied biological systems. The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms. The principles directing the dynamic organisation of reaction fluxes remain poorly understood. Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment. In this work, we investigate the role of fluxes of matter cycling in metabolic networks. First, we introduce a methodology for the computation of cyclic and acyclic fluxes in metabolic networks, adapted from an algorithm initially developed to study cyclic fluxes... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3932/version/1 |
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| Yukio Maruyama; Yoshifumi Kawamura; Takao Isogai; Nobuo Nomura; Naoki Goshima. |
| HGPD ("http://www.HGPD.jp/":http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression data. HGPD was launched in November 2008 and, since then, 33,275 human Gateway entry clones have been constructed from ORFs of full-length cDNAs, thus representing the largest collection in the world. Sequence information and protein expression of Gateway entry clones can also be retrieved from HGPD. The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database ("http://flj.hinv.jp/v01/cgi/index.cgi":http://flj.hinv.jp/v01/cgi/index.cgi), which was constructed as human cDNA sequence analysis database focusing on mRNA... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5070/version/1 |
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| Piotr Dittwald; Anna Gambin. |
| This document presents the original approach for estimating parameters of proteolysis process. Data used to fit the model are taken from mass
spectrometric experiments. For parameters estimation the Levenberg-Marquadt algorithm is used. The motivation for model is a hypothesis
that discrimination between cancer patients and healthy donors can be based on activity of peptide cleaving enzymes (i.e. peptidases). |
| Tipo: Manuscript |
Palavras-chave: Cancer; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4400/version/1 |
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| Vincent S. Smith; Dave Roberts. |
| Recent years have seen the emergence of several major initiatives supporting the development of biodiversity informatics infrastructures. In Europe examples include: EDIT – the European Distributed Institute of Taxonomy; LifeWatch – a biodiversity analytical platform integrating observatories, databases, processing and computational capacity; and SYNTHESYS – funding researcher access to a network of taxonomic collections, laboratories and libraries. These European projects alone represent a spend of approximately 35 Million Euros, with funding contingent on the collaboration of numerous geographically dispersed institutional partners. In this presentation we will review the major informatics products of these initiatives;... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4592/version/1 |
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| Nick Juty. |
| The Systems Biology Ontology (SBO) is composed of hierarchically arranged sets of controlled vocabularies that are commonly used in mathematical modelling, providing an additional layer of semantic information. We present recent developments in SBO, including the ontology's OBO Foundry status, its relationship to SBGN, and detail some of the restructuring work that has been undertaken. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5121/version/1 |
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| Luke McCarthy; Ben Vandervalk; Mark D. Wilkinson. |
| SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: a web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5382/version/1 |
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| Sebastian Bassi; Virginia Gonzalez. |
| Checksum algorithms are used in biological databases for integrity check and identification purposes. CRC64 is the only checksum algorithm already included in Biopython. This work proposes two new implementation of known algorithms (GCG Checksum and SEGUID). There is also an application based on SEGUID: Looking for redundancy between two FASTA files full of protein sequences based only in sequence information, by comparing the SEGUIDs of both files.
The code is shown in the manuscript and may be available at Biopython.org. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/278/version/1 |
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| Bin-Guang Ma. |
| The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function.... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2223/version/1 |
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| Amjesh R; Achuthsankar S. Nair; Sugunan V.S.. |
| Hepatitis C Virus (HCV) infection is a serious cause of chronic liver disease worldwide with more than 170 million infected individuals at a risk of developing significant morbidity and mortality. To date there is no effective drug for the treatment or vaccine to prevent this infection. The present study aims to discover novel inhibitors which target an allosteric binding site of RNA dependent RNA polymerase enzyme of HCV. A structure based virtual screening of Zinc database by computational docking and the post docking analysis of energy calculations and interactions followed by ADMET studies were conducted. Our study revealed 10 compounds which has more potential than the existing inhibitor to be considered as lead compounds.
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| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7055/version/1 |
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| Yeturu Kalidas; Nagasuma Chandra. |
| Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2142/version/1 |
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| Octavio Martinez; Araceli Fernandez-Cortes. |
| When assembling a large quantity of reads in a genomic shotgun project a serious limitation is the amount of random access memory (RAM) of the computers used in the project. This arises because all assembling programs must look at all the overlaps between reads at the same time, using RAM in order to construct contigs, and the memory of the computer can be filled up during this step, causing the abortion of the assembling process.
Here we propose an algorithm that is capable of overcoming any memory limitation by using redundancy of processing and thus producing an increase in computing time but overcoming the memory limitation.
The proposed algorithm consists in dividing the reads in a set of groups which size is half the... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3712/version/1 |
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| Registros recuperados: 1.312 | |
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