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, ...
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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.
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-sc...
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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.
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 regulator...
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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.
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...
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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.
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 s...
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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.
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....
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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.
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 ...
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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.
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 decisio...
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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.
Complex systems of interactions govern, the structure and function of biomolecules. Mutations that substantially disrupt these interactions are deleterious and should not persist under selection. Yet, several instance...
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ISBN:
(纸本)9781860947834
Complex systems of interactions govern, the structure and function of biomolecules. Mutations that substantially disrupt these interactions are deleterious and should not persist under selection. Yet, several instances have been reported where a variant confirmed as pathogenic in one species is fixed in the orthologs of other species. Here we introduce a novel method for detecting compensatory substitutions for these so-called compensated pathogenic deviations (CPDs), incorporating knowledge of pathogenic variants into a probabilistic method for detecting correlated evolution. The success of this approach is demonstrated for 26 of 31 CPDs observed in mitochondrial transfer RNAs and for one in beta hemoglobin. The detection of multiple compensatory sites is demonstrated for two of these CPDs. The methodology is applicable to comparative sequence data for biomolecules expressed in any alphabet, real or abstract. It provides a widely applicable approach to the prediction of compensatory substitutions for CPDs, avoiding any reliance on rigid non-probabilistic criteria or structural data. The detection of compensatory substitutions that facilitate the substitution of otherwise pathogenic variants offers valuable insight into the molecular constraints imposed on adaptive evolution.
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