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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

共 879 条记录，以下是341-350 订阅

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CloG: A pipeline for closing gaps in a draft assembly using short reads

CloG: A pipeline for closing gaps in a draft assembly using ...

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ieee International conference on computational Advances in Bio and Medical Sciences (ICCABS)

作者： Xing Yang Daniel Medvin Giri Narasimhan Deborah Yoder-Himes Stephen Lory School of Computing and Information Sciences Bioinformatics Research Group Miami FL USA Microbiology and Molecular Genetics Department Harvard Medical School Boston MA USA

Closing of gaps in draft assemblies using Next Generation Sequencing (NGS) data is becoming increasingly important. In this paper we present CloG, a software pipeline that uses NGS data to close gaps in draft assemblies. Firstly, CloG uses the VELVET assembler to generate a hybrid assembly from a mixture of reads: short reads from the NGS data and the original draft assembly (treated as long reads). It then closes gaps between adjacent contigs by reconciling (i.e., “stitching”) the two assemblies. By exploiting the strengths of both hybrid assembly and stitching reassembly, CloG is able to outperform its contemporaries in closing gaps in the draft assembly of the bacterium Burkholderia dolosa.

关键词： Assembly bioinformatics Genomics Finishing Hybrid power systems Organisms Pipelines

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Latency Minimizing Tasking for Information Processing systems

Latency Minimizing Tasking for Information Processing System...

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ieee International conference on Data Mining Workshops (ICDM Workshops)

作者： James Horey Brent Lagesse Computational Sciences and Engineering Oak Ridge National Laboratory Oak Ridge TN USA

Real-time cyber-physical systems and information processing clusters require system designers to consider the total latency involved in collecting and aggregating data. For example, applications such as wild-fire monitoring require data to be presented to users in a timely manner. However, most models and algorithms for sensor networks have focused on alternative metrics such as energy efficiency. In this paper, we present a new model of sensor network aggregation that focuses on total latency. Our model is flexible and enables users to configure varying transmission and computation time on a node-by-node basis, and thus enables the simulation of complex computational phenomena. In addition, we present results from three tasking algorithms that trade-off local communication for overall latency performance. These algorithms are evaluated in simulated networks of up to 200 nodes.

关键词： Schedules computational modeling Genetic algorithms Information processing Genomics bioinformatics Routing

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Analyzing time-course gene expression data using profile-state hidden Markov model

Analyzing time-course gene expression data using profile-sta...

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ieee International conference on systems Biology

作者： Qiang Huang Ling-Yun Wu Ji-Bin Qu Xiang-Sun Zhang National Center for Mathematics and Interdisciplinary Sciences Institute of Applied Mathematics Academy of Mathematics and Systems Science CAS Beijing 100190 China

ISBN: (纸本)9781457716614

More and more gene expression data are available due to the rapid development of high-throughput experimental techniques such as microarray and next generation sequencing (NGS). The gene expression data analysis is still one of the fundamental tasks in bioinformatics. In this paper, we propose a new profile-state hidden Markov model (HMM) for analyzing time-course gene expression data, which gives a new point of view to explain the variation of gene expression and regulation in different time. This model addresses the bicluster problem in time-course data efficiently and can identify the irregular shape and overlapping biclusters. The comprehensive computational experiments on simulated and real data show that the new method is effective and useful.

关键词： Hidden Markov models bioinformatics Microarray observational data Gene Expression Profiling

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systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data

Systems Approach to Identifying Relevant Pathways from Pheno...

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ieee International conference on bioinformatics and Biomedicine (BIBM)

作者： Julian Dymacek Nancy Lan Guo Mary Babb Randolph Cancer Center West Virginia University Morgantown WV USA

This study presents a novel computational approach to find relevant pathways from dose-dependent time series gene expression data which are significantly associated with a phenotype pattern pathological patterns in the comprehensive evaluation of a database of pathways. Our system uses four steps: 1) identify a set of genes which change significantly in dose or time; 2) find phenotype patterns and gene coefficients for the genes found in step 1; 3) expand to genome-wide coefficients, and 4) identify pathways which are significantly relevant to a phenotype pattern. Our technique finds biologically relevant pathways with and without phenotype- constraints. Our system has been used on genome-wide expression profiles of mouse lungs (n=160) following aspiration of well dispersed multi-walled carbon nanotubes (MWCNT), in order to detect MWCNT-induced lung inflammation and related pathways. The identified significant pathways are supported by evidence in the literature and biological validation.

关键词： bioinformatics Genomics Lungs Gene expression Mice Time series analysis Pathology

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Evolutionary sequence divergence predicts protein sub-cellular localization signals

Evolutionary sequence divergence predicts protein sub-cellul...

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ieee International conference on systems Biology

作者： Yoshinori Fukasawa Ross KK Leung Stephen KW Tsui Paul Horton Department of Computational Biology Graduate School of Frontier Sciences University of Tokyo Kashiwa Japan Hong Kong Bioinformatics Centre and School of Biomedical Sciences Chinese University of Hong Kong Shatin China Computational Biology Research Center Advanced Industrial Science and Technology Tokyo Japan

Protein sub-cellular localization is a central problem in understanding cell biology and has been the focus of intense research. In order to predict localization from amino acid sequence a myriad of features have been tried: including amino acid composition, sequence similarity, the presence of certain motifs or domains, and many others. Surprisingly, sequence conservation of sorting motifs has not yet been employed, despite its extensive use for tasks such as the prediction of transcription factor binding sites. Here, we flip the problem around, and present a proof of concept for the idea that the lack of sequence conservation can be a useful feature for localization prediction.

关键词： Proteins Amino acids Sorting Entropy Educational institutions Accuracy Protein engineering

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Protein Structure Visualization by Dimension Reduction and Texture Mapping

Protein Structure Visualization by Dimension Reduction and T...

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ieee International conference on bioinformatics and Biomedicine (BIBM)

作者： Heng Yang Rehman Qureshi Ahmet Sacan Center of Integrated Bioinformatics School of Biomedical Engineering Science and Health Systems Drexel University Philadelphia PA USA

Among the biological macromolecules, proteins have attracted special attention from the scientific community due to their rich functional roles. The ability to visualize and manipulate macromolecular structures on graphical display devices has facilitated the identification and analysis of these macromolecules. Structural analyses of the proteins often provide important insights into their biochemical functions. However, such analysis is often limited by the representation of protein structures and the corresponding computational resource requirements. In this study, we focus on the molecular surface of the proteins and investigate computationally and visually effective representations to serve a number of visualization and analysis purposes. Specifically, we "unfold" the protein surface onto a planar space, while preserving the local surface features as much as possible. In contrast to classical cartographic projections, our approach is able to preserve local shape features. Several biochemical properties associated with each surface point are mapped to generate a two dimensional map of these features. The 3D-2D mapping of the surface vertices has also been utilized to texture-map an arbitrary image back onto the protein structure to facilitate the visualization of the 3D structure.

关键词： Proteins Three dimensional displays Surface topography Protein engineering Solvents Shape Surface texture

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A Profile of Today's SBML-Compatible Software

A Profile of Today's SBML-Compatible Software

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ieee International conference on E-Science Workshops

作者： Michael Hucka Frank T. Bergmann Sarah M. Keating Lucian P. Smith California Institute of Technology Pasadena CA USA EMBL European Bioinformatics Institute Hinxton Cambridge UK University of Washington Seattle WA USA

computational systems biologists today have a healthy selection of software resources to help them do research. Many software packages, especially those concerned with computational modeling, have adopted SBML (the systems Biology Markup Language) as a machine-readable format to permit users to exchange models. Our group has a keen interest in understanding the landscape of SBML support. To help us ascertain the state of modern SBML-compatible software, in mid-2011 we initiated a survey of software packages that support SBML. Here we report the preliminary survey results. Based on 81 packages for which we have data so far, we summarize the trends in six areas: (1) What are the major types of functionality offered by the software systems? (2) What mathematical frameworks do they support? (3) What are their SBML-specific capabilities? (4) What other standards do they support besides SBML? (5) What are their characteristics with respect to run-time environments? And finally, (6) what are the availability and licensing terms?

关键词： Software tools Analytical models Mathematical model Software systems systems biology Biological system modeling

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Insect navigation and communication in flight and migration: A potential model for joining and collision avoidance in MAVs and mobile robots fleet control

Insect navigation and communication in flight and migration:...

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2011 ieee Aerospace conference, AERO 2011

作者： Ma, Zhanshan Krings, Axel W. Millar, Richard Wang, Feng Chao, Jun Computational Biology and Bioinformatics Lab. KIZ Chinese Academy of Sciences China Computer Science Department University of Idaho Moscow ID 83843 United States Department of Systems Engineering Naval Postgraduate School Patuxent River NAS MD United States Computer Science Department Kunming Univ. of Science and Technology Kunming 650223 China Chinese Academy of Sciences Kunming 650223 China Computer Science Dept. iBEST University of Idaho United States

ISBN: (纸本)9781424473502

The human being should be awarded the championship of navigation on the planet, on the virtues that they not only have invented and manufactured the compass, GPS, aircraft, vessel, spacecraft, but also have demonstrated exceptional non-instrumental navigation skills. The Austronesian expansion from the Asian mainland into the Pacific performed by the Pacific navigators, who eventually populated the most remote islands of the Pacific about 4000 years ago, is a vivid example (Wehner 1998). However, animals, especially flying birds and insects are strong contenders. Monarch butterflies can migrate up to 2000 miles from their reproductive sites in the eastern US and Canada to their over-wintering sites in the forests of Mexico, and it is postulated that they may possess a biological equivalent of a low-resolution GPS system that is based on the magnetic field of the earth. In fact, even the long-legged ants (Cataglyphis fortis) in the Saharan desert use the dead-reckoning navigation strategy, which is attributed to the Polynesians, but the ants apparently have acquired the capability much earlier, given the relative short evolutionary history of humans. In this article, we briefly review the state-of-the-art research on insect navigation and communication used in flight and communication, with the objective to inspire cross-disciplinary studies in aerospace engineering, biology and computer science. After a brief review, we overview and identify seven cross-disciplinary research topics that may draw on inspirations from insect navigation and communication in flight and migration. These topics include: ants colony inspired swarm intelligence, honeybee inspired group decision-making, insect sociobiology, MAV/mobile robot flight control and remote control of insect flights, optimal migration strategy, Quorum sensing, and joining and collision avoidance for MAV fleet control. An interesting question one may pose is: given the rich and advanced navigation and communication t

关键词： Global positioning system

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Constant penalty functions to simplify optimization of the Choquet integral under constraints

Constant penalty functions to simplify optimization of the C...

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ieee International conference on Fuzzy systems (FUZZ-ieee)

作者： Tanja Magoč Center of Bioinformatics and Computational Biology University of Maryland College Park MD USA

The Choquet integral have been used in many decision making problems as the optimization function that needs to be maximized or minimized. The complexity of these optimization problems is often increased by numerous constraints that are imposed to the solution. Several methods have been developed for optimization under constraints, one of them being penalty functions method. This method transforms a constrained optimization problem in an equivalent unconstrained optimization problem by adding penalties to the solutions that do not satisfy one of more constraints. Penalty functions method is an iterative process, which adjusts penalty functions in each iteration, often yielding a large number of iterations until a satisfying solution is found. To speed the process of the Choquet integral optimization under constraints, we propose to use constant penalty functions. This approach requires only one iteration, and is therefore much faster than the generic penalty function method. In this paper, we derive the constant penalty function that guarantees that the optimal solution found in the first iteration satisfies all constraints.

关键词： Optimization Decision making Indexes Safety Complexity theory Investments Minimization

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Model based clustering approach for identifying structural variation using next generation sequencing data

Model based clustering approach for identifying structural v...

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ieee International conference on computational Advances in Bio and Medical Sciences (ICCABS)

作者： Yoon Soo Pyon Matthew Hayes Jing Li Department of Electrical Engineering and Computer Science Case Western Reserve University Cleveland OH USA Joint Institute of Systems Biology College of Computer Science & Technology Jilin University Changchun China

Structural variation (SV) has been reported to be associated with numerous diseases such as cancer. With the advent of next generation sequencing (NGS) technologies, various types of SV can be potentially identified. We propose a model based clustering approach utilizing a set of features defined for each type of SV event. Our method, termed SVMiner, not only provides a probability score for each candidate, but also predicts the heterozygosity of genomic deletions. Experiments on genome-wide deep sequencing data have demonstrated that SVMiner is robust against the variability of a single cluster feature, and it performs well when classifying validated SV events with accentuated features.

关键词： bioinformatics Genomics Prediction algorithms Biological cells Clustering algorithms Sensitivity Humans

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