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检索条件"丛书名=Series on Advances in Bioinformatics and Computational Biology"

共 62 条记录，以下是1-10 订阅

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computational Systems biology Of Synaptic Plasticity: Modelling Of Biochemical Pathways Related To Memory Formation And Impairement

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丛书名： series on advances in bioinformatics and computational biology

2017年

作者： Kulasiri Don

ISBN: (数字)9781786343383

ISBN: (纸本)9781786343376

This book demonstrates the power of mathematical thinking in understanding the biological complexity that exists within the brain. It looks at the latest research on modelling of biochemical pathways within synapses, and provides a clear background for the study of mathematical models related to systems biology. Discussion then focusses on developments in computational models based on networks linked to synaptic plasticity. The models are used to understand memory formation and impairment and they provide a mathematical basis for memory *** Systems biology of Synaptic Plasticity is a valuable source of knowledge to postgraduate students and researchers in computational systems biology, and as a reference book for various techniques that are needed in modelling biological processes.

关键词： life sciences biology bioinformatics biocomputing computational biology

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Proceedings of the 6th Asia-Pacific bioinformatics Conference : Kyoto, Japan, 14-17 January 2008

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丛书名： series on advances in bioinformatics and computational biology

2008年

作者： Alvis Brazma Satoru Miyano Tatsuya Akutsu.

ISBN: (纸本)9781848161085

High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically, and agriculturally important species, thus enabling large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures, metabolic pathways, and gene expression profiles of normal and diseased tissues are rapidly being generated for human and model *** is therefore gaining importance in the annotation of genomic sequences; the understanding of the interplay among and between genes and proteins; the analysis of the genetic variability of species; the identification of pharmacological targets; and the inference of evolutionary origins, mechanisms, and relationships. This proceedings volume contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics by researchers, professionals, and industry practitioners at the 6th Asia-Pacific bioinformatics Conference held in Kyoto, Japan, in January 2008.

关键词： bioinformatics--Congresses

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Applications of fuzzy logic in bioinformatics /

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2008年

作者： Dong Xu ... [et al.].

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Regulatory Genomics: Proceedings of the 3rd Annual RECOMB Workshop 1st

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丛书名： series on advances in bioinformatics and computational biology:Volume 8

2008年

作者： Wai, Leong Hon Wing-Kin, Sung Eskin, Eleazar

ISBN: (数字)9781908978745

ISBN: (纸本)9781848162518

Research in the field of gene regulation is evolving rapidly in the ever-changing scientific environment. advances in microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics. The study of genomic binding locations of transcription factors has enabled a more comprehensive modeling of regulatory networks. In addition, complete genomic sequences and comparison of numerous related species have demonstrated the conservation of non-coding DNA sequences, which often provide evidence for cis-regulatory binding sites. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks; key to these methods are motif discovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programs are becoming more sophisticated and are beginning to leverage evidence from comparative genomics. These topics and more were discussed at the 3rd Annual RECOMB Workshop on Regulatory Genomics, which brought together more than 90 attendees and included about 22 excellent talks from leading researchers in the field.

关键词： workshop national recomb annual genomics proceedings regulatorybioinformatics Biological Sciences Science

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Proceedings Of The 5th Asia-pacific bioinformatics Conference 1

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丛书名： series on advances in bioinformatics and computational biology

2007年

作者： Francis Y L Chin David Sankoff

ISBN: (数字)9781860947995

ISBN: (纸本)9781860947834

High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically, and agriculturally important species, and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures, and gene expression profiles of normal and diseased tissues are being rapidly generated for human and model organisms. bioinformatics is thus rapidly growing in importance in the annotation of genomic sequences; the understanding of the interplay among and between genes and proteins; the analysis of genetic variability of species; the identification of pharmacological targets; and the inference of evolutionary origins, mechanisms, and relationships. This proceedings volume contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics by researchers, professionals, and industrial practitioners at the 5th Asia-Pacific bioinformatics Conference held in Hong Kong in January 2007.

关键词： Life Sciences biology

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Complexities and algorithms for glycan structure sequencing using tandem mass spectrometry

Complexities and algorithms for glycan structure sequencing ...

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Shan, Baozhen Ma, Bin Mang, Kaizhong Lajoie, Gilles Univ Western Ontario Dept Comp Sci London ON N6A 5B7 Canada Univ Western Ontario Dept Biochem London ON N6A 5B7 Canada

ISBN: (纸本)9781860947834

Determining glycan structures is vital to comprehend cell-matrix, cell-cell, and even intracellular biological events. Glycan structure sequencing, which is to determine the primary structure of a glycan using MS/MS spectrometry, remains one of the most important tasks in proteomics. Analogous to the peptide de novo sequencing, the glycan de novo sequencing is to determine the structure without the aid of a known glycan database. We show in this paper that glycan de novo sequencing is NP-hard. We then provide a heuristic algorithm and develop a software program to solve the problem in practical cases. Experiments on real MS/MS data of glycopeptides demonstrate that our heuristic algorithm gives satisfactory results on practical data.

关键词： Heuristic algorithms

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Simple and fast alignment of metabolic pathways by exploiting local diversity

Simple and fast alignment of metabolic pathways by exploitin...

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5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Wernicke, Sebastian Rasche, Florian Univ Jena Inst Informat Ernst Abbe Pl 2 D-07743 Jena Germany

ISBN: (纸本)9781860947834

An important tool for analyzing metabolic pathways is being able to do homology searches, that is, for a given pattern network one would like to find occurrences of similar (sub)networks within a set of host networks. In the context of metabolic pathways, Pinter et al. [bioinformatics, 2005] recently proposed to solve this computationally hard problem by restricting it to the case where both the pattern and host network are trees. This restriction, however, severely limits the applicability of their algorithm. Here, we propose a novel algorithm that does not restrict the topology of the host or pattern network in any way;instead, we exploit a natural property of metabolic networks that we call "local diversity property," which allows us to obtain a very fast and simple algorithm for the alignment of metabolic pathways. Experiments on a testbed of metabolic pathways extracted from the BIOCYC database indicate that our algorithm is much faster than the restricted algorithm of Pinter et al. and yet has a wider range of applicability and yields new biological insights.

关键词： Metabolism

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Algorithm engineering for color-coding to facilitate signaling pathway detection

Algorithm engineering for color-coding to facilitate signali...

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5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Hueffner, Falk Wernicke, Sebastian Zichner, Thomas Friedrich Schiller Uni Jena Inst Informat Ernst Abbe Pl 2 D-07743 Jena Germany

ISBN: (纸本)9781860947834

To identify linear signaling pathways, Scott et al. [RECOMB, 2005] recently proposed to extract paths with high interaction probabilities from protein interaction networks. They used an algorithmic technique known as color-coding to solve this NP-hard problem;their implementation is capable of finding biologically meaningful pathways of length up to 10 proteins within hours. In this work, we give various novel algorithmic improvements for color-coding, both from a worst-case perspective as well as under practical considerations. Experiments on the interaction networks of yeast and fruit fly as well as a testbed of structurally comparable random networks demonstrate a speedup of the algorithm by orders of magnitude. This allows more complex and larger structures to be identified in reasonable time;finding paths of length up to 13 proteins can even be done in seconds and thus allows for an interactive exploration and evaluation of pathway candidates.

关键词： Proteins

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Inferring gene regulatory networks by machine learning methods

Inferring gene regulatory networks by machine learning metho...

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5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Supper, Jochen Frohlich, Holger Spieth, Christian Drager, Andreas Zell, Andreas Ctr Bioinformat Tubingen ZBIT Sand 1 D-72076 Tubingen Germany

ISBN: (纸本)9781860947834

The ability to measure the transcriptional response after a stimulus has drawn much attention to the underlying gene regulatory networks. Several machine learning related methods, such as Bayesian networks and decision trees, have been proposed to deal with this difficult problem, but rarely a systematic comparison between different algorithms has been performed. In this work, we critically evaluate the application of multiple linear regression, SVMs, decision trees and Bayesian networks to reconstruct the budding yeast cell cycle network. The performance of these methods is assessed by comparing the topology of the reconstructed models to a validation network. This validation network is defined a priori and each interaction is specified by at least one publication. We also investigate the quality of the network reconstruction if a varying amount of gene regulatory dependencies is provided a priori.

关键词： Bayesian networks

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A novel clustering method for analysis of biological networks using maximal components of graphs

A novel clustering method for analysis of biological network...

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5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Hayashida, Morihiro Akutsu, Tatsuya Nagamochi, Hiroshi Kyoto Univ Inst Chem Res Bioinformat Ctr Uji Kyoto 6110011 Japan Kyoto Univ Grad Sch Informat Dept Appl Math & Phys Kyoto Kyoto 6068501 Japan

ISBN: (纸本)9781860947834

This paper proposes a novel clustering method for analyzing biological networks. In this method, each biological network is treated as an undirected graph and edges are weighted based on similarities of nodes. Then, maximal components, which are defined based on edge connectivity, are computed and the nodes are partitioned into clusters by selecting disjoint maximal components. The proposed method was applied to clustering of protein sequences and was compared with conventional clustering methods. The obtained clusters were evaluated using P-values for GO (GeneOntology) terms. The average P-values for the proposed method were better than those for other methods.

关键词： Cluster analysis

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