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检索条件"任意字段=Proceedings of the IEEE Computational Systems Bioinformatics Conference, CSB"

共 410 条记录，以下是51-60 订阅

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Automatic prediction of functional site regions in low-resolution protein structures

Automatic prediction of functional site regions in low-resol...

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proceedings - 2004 ieee computational systems bioinformatics conference, csb 2004

作者： Sodhi, Jaspreet Singh McGuffin, Liam J. Bryson, Kevin Ward, Jonathan J. Wernisch, Lorenz Jones, David T. Bioinformatics Group Department of Computer Science University College London London United Kingdom

ISBN: (纸本)0769521940

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.

关键词： Proteins

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Profilins, formins and katanins as flagellar proteins of Leishmania spp.: A genome-based, multi-step bioinformatics-driven description

Profilins, formins and katanins as flagellar proteins of Lei...

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7th ieee International conference on bioinformatics and Bioengineering, BIBE

作者： Vasconcelos, Elton J. R. Pacheco, Ana C. L. Gouveia, João J. S. Araújo, Fabiana F. Diniz, Michely C. Kamimura, Michel T. Costa, Marcília P. Maggioni, Rodrigo Araújo-Filho, Raimundo Costa, Raimundo B. De Oliveira, Diana Magalhães Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformáitica - NUGEN Universidade Estadual do Ceará - UECE Fortaleza Ceará Brazil

ISBN: (纸本)1424415098

Flagellum plays a key role in Leishmania motility and sensory reception, and it is essential for parasite migration, invasion and persistence on host tissues. In search for genomic and/or proteomic evidences of flagellar genes/proteins in Leishmania spp., we have used available databases and computational biology tools to predict and distinguish putative flagellar proteins that are either actin-, tubulin-, axoneme- or microtubule-related sequences and, also, probable virulence factors. Here we present results of sequence and structural analyses of profilins, formins and katanins as possible flagellar proteins of Leishmania spp., whose sequences were in silico selected for predicting viable roles on flagellum assembly, disassembly and dynamics in terms of intraflagellar mechanisms. Taken together, our results provide the filrst integrated bioinformatics analyses of Leishmania profilin, katanin and formin genes and their gene products to contribute to a more detailed annotation of these important actin-related proteins not yet properly characterized in flagellate trypanosomatids or in their flagellar activities towards virulence. ©2007 ieee.

关键词： bioinformatics

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Fractal Genomics modeling: A new approach to genomic analysis and biomarker discovery

Fractal Genomics modeling: A new approach to genomic analysi...

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ieee computational systems bioinformatics conference (csb 2004)

作者： Shaw, S Shapshak, P Hlth Discovery Corp Inc Savannah GA 31406 USA

ISBN: (纸本)0769521940

Reverse engineering of genetic networks generally requires establishing correlative behavior within and between a very large number of genes. This becomes a difficult analytical problem for even a few hundred genes and the difficulty tends to grow exponentially as more genes are examined Using a hybrid data analysis method known as Fractal Genomics Modeling (FGM), this problem is reduced to examining correlative behavior within small gene groups that can then be compared and integrated to produce a picture of larger networks using a type of shotgun approach. We have applied FGM toward examining genetic networks involved in HIV infection in the brain. These networks have relevance both to processes related to HIV infection and neurodegenerative disorders. Our preliminary findings have produced conjectures of related pathways and networks as well new candidates for genetic markers in HIV brain infection. Evidence has also been produced which appears to show the presence of a hierarchical network structure within the genes studied We will discuss the background and methodology of FGM as well as our recent findings.

关键词： bioinformatics gene expression fractals network theory scale-free brain HIV infection

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An energy-aware bioinformatics application for assembling short reads in high performance computing systems

An energy-aware bioinformatics application for assembling sh...

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2012 10th Annual International conference on High Performance Computing and Simulation, HPCS 2012

作者： Warnke, Julia Pawaskar, Sachin Ali, Hesham College of Information Science and Technology University of Nebraska at Omaha Omaha NE 68182 United States

ISBN: (纸本)9781467323598

Current biomedical technologies are producing massive amounts of data on an unprecedented scale. The increasing complexity and growth rate of biological data has made bioinformatics data processing and analysis a key and computationally intensive task. High performance computing (HPC) has been successfully applied to major bioinformatics applications to reduce computational burden. However, a naïve approach for developing parallel bioinformatics applications may achieve a high degree of parallelism while unnecessarily expending computational resources and consuming high levels of energy. As the wealth of biological data and associated computational burden continues to increase, there has become a need for the development of energy efficient computational approaches in the bioinformatics domain. To address this issue, we have developed an energy-aware scheduling (EAS) model to run computationally intensive applications that takes both deadline requirements and energy factors into consideration. An example of a computationally demanding process that would benefit from our scheduling model is the assembly of short sequencing reads produced by next generation sequencing technologies. Next generation sequencing produces a very large number of short DNA reads from a biological sample. Multiple overlapping fragments must be aligned and merged into long stretches of contiguous sequence before any useful information can be gathered. The assembly problem is extremely difficult due to the complex nature of underlying genome structure and inherent biological error present in current sequencing technologies. We apply our EAS model to a newly proposed assembly algorithm called Merge and Traverse, giving us the ability to generate speedup profiles. Our EAS model was also able to dynamically adjust the number of nodes needed to meet given deadlines for different sets of reads. © 2012 ieee.

关键词： bioinformatics

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An information fusion approach to controlling complexity in bioinformatics research

An information fusion approach to controlling complexity in ...

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ieee computational systems bioinformatics conference, csb Workshops and Poster Abstracts

作者： B. Olsson P. Nilsson B. Gawronska A. Persson T. Ziemke S.F. Andler School of Humanities and Informatics Sweden School of Life Sciences South Korea School of Technology and Society University of Skövde Skovde Sweden School of Humanities and Informatics Japan

Information Fusion (IF) is about combining, or fusing, information from different sources in order to facilitate our understanding of a complex system and thereby provide insights that could not be gained from any of the individual data sources in isolation. We argue in this paper that there is a need for applying an IF approach in bioinformatics research, since the aim of bioinformatics is to understand complex biological systems using many different data sources providing complementary views of the system. We illustrate this argument with two application examples, where IF-based bioinformatics is applied to the study of stem cell differentiation and lipid digestion, respectively. We also discuss the use of automated information extraction from text sources, which is an essential component of a bioinformatics IF approach, given the abundant literature.

关键词： bioinformatics Databases Sensor fusion Informatics Biological systems Stem cells Lipidomics Data mining Robot sensing systems Biosensors

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3rd International Work-conference on bioinformatics and Biomedical Engineering, IWBBIO 2015

3rd International Work-Conference on Bioinformatics and Biom...

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3rd International Work-conference on bioinformatics and Biomedical Engineering, IWBBIO 2015

ISBN: (纸本)9783319164793

The proceedings contain 70 papers. The special focus in this conference is on eHealth, Next generation sequencing and sequence analysis, Quantitative and systems pharmacology, Hidden markov model (HMM) for biological sequence modeling, Advances in computational intelligence for bioinformatics and biomedicine and Tools for next generation sequencing data analysis. The topics include: e-health informed foreign patient and physician communication;empirical analysis of the effect of eHealth on medical expenditures of patients with chronic diseases;impact of health apps in health and computer science publications. a systematic review from 2010 to 2014;local search for multi objective multiple sequence alignment;alignment free frequency based distance measures for promoter sequence comparison;energy-efficient architecture for DP local sequence alignment;successes and pitfalls in scoring molecular interactions;the use of random forest to predict binding affinity in docking;strong inhomogeneity in triplet distribution alongside a genome;predicting sub-cellular location of proteins based on hierarchical clustering and hidden markov models;risk quantification of multigenic conditions for SNP array based direct-to-consumer genomic services;computational inference in systems biology;a price we pay for inexact dimensionality reduction;DEgenes hunter - a self-customised gene expression analysis workflow for non-model organisms;bioinformatics analyses to separate species specific mrnas from unknown sequences in de novo assembled transcriptomes;evaluation of combined genome assemblies;nucleotide sequence alignment and compression via shortest unique substring and modeling of the urothelium with an agent based approach.

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6th International conference on Practical Applications of computational Biology and bioinformatics

6th International Conference on Practical Applications of Co...

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6th International conference on Practical Applications of computational Biology and bioinformatics, PACBB'12

ISBN: (纸本)9783642288388

The proceedings contain 32 papers. The topics discussed include: prognostic prediction using clinical expression time series: towards a supervised learning approach based on meta-biclusters;parallel e-CCC-biclustering: mining approximate temporal patterns in gene expression time series using parallel biclustering;parameter influence in genetic algorithm optimization of support vectormachines;biological knowledge integration in DNA microarray gene expression classification based on rough set theory;quantitative assessment of estimation approaches for mining over incomplete data in complex biomedical spaces: a case study on cerebral aneurysms;case-based reasoning to classify endodontic retreatments;a comparative analysis of balancing techniques and attribute reduction algorithms;sliced model checking for phylogenetic analysis;and a systematic approach to the interrogation and sharing of standardized biofilm signatures.

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Integrating biomolecular analysis and visual programming: Flexibility and interactivity in the design of bioinformatics tools 36

Integrating biomolecular analysis and visual programming: Fl...

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36th Annual Hawaii International conference on System Sciences, HICSS 2003

作者： Stoffler, D. Coon, S.I. Huey, R. Olson, A.J. Sanner, M.F. Scripps Research Institute 10550 North Torrey Pines Road San DiegoCA92037 United States

ISBN: (纸本)0769518745

One of the challenges in bio-computing is to enable the efficient use of a wide variety of rapidly evolving computational methods to simulate, analyze and understand complex interactions of molecular systems. Our laboratory is interested in the development of novel computational technologies and in the application of these technologies to the analysis and understanding of complex biological systems. We have been using the Python programming language as a platform to develop reusable and interoperable components dealing with different aspects of structural bioinformatics. These components are the basic building blocks from which several domain specific applications have been developed. In this paper we describe the integration of two applications developed in our laboratory: PMV and a visual-programming environment. PMV is a general purpose, command-driven molecular visualization and manipulation program built from reusable software components. The visual-programming environment enables a user to build interactively networks describing novel combinations of computational methods. We describe several applications demonstrating the synergy created by combining these two programs. © 2003 ieee.

关键词： computational methods

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bioinformatics approach for exploring MS/MS proteomics data

Bioinformatics approach for exploring MS/MS proteomics data

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38th Annual Hawaii International conference on System Sciences, HICSS 2005

作者： Singhal, Mudita Klicker, Kyle Chin, George Trease, Lynn Stephan, Eric Gracio, Deborah

The use of computer tools and technologies is unavoidable when it comes to conducting mass spectrometry (MS) research at any significant level. This is mainly due to the large volume of MS data and the processing rates required. Most of the existing tools focus on one particular task: be it storing and maintaining the data or visualizing the dataset to draw inferences from the data. But for the researcher the problem of manually retrieving a large dataset from a datasource and customizing it for a particular visualization application is a daunting task in itself. This paper describes the computational Cell Environment (CCE) which is a problem-solving environment for systems biology that provides uniform and integrated access to distributed, heterogeneous biological data sources and analysis applications, through a multi-tiered architecture. This paper also illustrates the necessity for such a tool by discussing its usage in proteomics research being performed on the diseased and normal states of Deinococcus Radiodurans along with corresponding curated data collected from community resources.

关键词： Database systems

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International conference on Practical Applications of computational Biology and bioinformatics PACBB, 2016

International Conference on Practical Applications of Comput...

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International conference on Practical Applications of computational Biology and bioinformatics PACBB, 2016

ISBN: (纸本)9783319401256

The proceedings contain 22 papers. The special focus in this conference is on Data and Text Mining. The topics include: Intelligent systems for predictive modelling in cheminformatics;a challenge for deep learning;visual exploratory assessment of class C GPCR extracellular domains discrimination capabilities;development of a machine learning framework for biomedical text mining;sequence retriever for known, discovered, and user-specified molecular fragments;sensitivity, specificity and prioritization of gene set analysis when applying different ranking metrics;deep data analysis of a large microarray collection for leukemia biomarker identification;systematic evaluation of gene expression data analysis methods using benchmark data;a clustering-based method for gene selection to classify tissue samples in lung cancer;large-scale transcriptomic approaches for characterization of post-transcriptional control of gene expression;ultra-fast fuzzy whole genome alignment;exploring the high performance computing-enablement of a suite of gene-knockout based genetic engineering applications;an application that executes parallelized pipelines to analyse next-generation sequencing data;exceptional symmetry profile;a computation tool for the estimation of biomass composition from genomic and transcriptomic information;role of nerve growth factor signaling in cancer cell proliferation and survival using a reachability analysis approach;a hybrid of harmony search and minimization of metabolic adjustment for optimization of succinic acid production;a web-based application for network reconstruction and visualization of cytometry data and reconstruction of metabolic models for liver cancer cells.

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