Bioinformatics for geneticists
edited by Michael R. Barnes and Ian C. Gray
Publisher: Hoboken, NJ : Wiley, c2003.
ISBN: 0470843942
Edition: (PBK.)
Notes:
Introduction: The Role of Genetic Bioinformatics / Michael R. Barnes,
Ian C. Gray -- Genetics in the post-genome era--the role of
bioinformatics -- Knowledge management and expansion -- Data
management and mining -- Genetic study designs -- Physical locus
analysis -- Selecting candidate genes for analysis -- Progressing
from candidate gene to disease-susceptibility gene -- Comparative
genetics and genomics -- Internet Resources for the Geneticist /
Michael R. Barnes, Christopher Southan -- Sub-division of biological
data on the internet -- Searching the internet for genetic
information -- Which web search engine? -- Search syntax: the
mathematics of search engine use -- Boolean searching -- Searching
scientific literature--getting to 'state of the art' -- Searching
full-text journals -- Searching the heart of the biological
internet--sequences and genomic data -- Nucleotide and protein
sequence databases -- Biological sequence databases--primary and
secondary -- Human Genetic Variation: Databases and Concepts /
Michael R. Barnes -- Forms and mechanisms of genetic variation --
Databases of human genetic variation -- SNP databases -- Mutation
databases -- Genetic marker and microsatellite databases --
Non-nuclear and somatic mutation databases -- Tools for SNP and
mutation visualization--the genomic context -- Tools for SNP and
mutation visualization--the gene context -- Finding, Delineating and
Analysing Genes / Christopher Southan -- The evidence cascade for
gene products -- Shortcomings of the standard gene model -- Locating
known genes on the Golden Path -- Gene portal inspection -- Locating
genes which are not present in the Golden Path -- Analysing a novel
gene -- Comprehensive database searching -- The Impact of Complete
Genome Sequences on Genetics -- Assembling a View of the Human Genome
/ Colin A. Semple -- Genomic sequence assembly -- Annotation from a
distance: the generalities -- Annotation up close and personal: the
specifics -- Annotation: the next generation -- Mouse and Rat Genome
Informatics / Judith A. Blake, Janan Eppig, Carol J. Bult -- The
model organism databases for mouse and rat -- Mouse genetic and
physical maps -- Rat genetic and physical maps -- Genome sequence
resources -- Comparative genomics -- From genotype to phenotype --
Functional genomics -- Rodent disease models -- Genetic and Physical
Map Resources--An Integrated View / Michael R. Barnes -- Genetic maps
-- Physical maps -- Physical contig maps -- The role of physical and
genetic maps in draft sequence curation -- The human genome
sequence--the ultimate physical map? -- QC of genomic DNA--resolution
of marker order and gap sizes -- Tools and databases for map analysis
and integration -- Bioinformatics for Genetic Study Design -- From
Linkage Peak to Culprit Gene: Following Up Linkage Analysis of
Complex Phenotypes with Population-based Association Studies / Ian C.
Gray -- Theoretical and practical considerations -- A practical
approach to locus refinement and candidate gene identification --
Genetic Studies from Genomic Sequence / Michael R. Barnes -- Defining
the locus -- Case study 1: Identification and extraction of a genomic
sequence between two markers -- Case study 2: Checking the integrity
of a genomic sequence between two markers -- Case study 3: Definition
of known and novel genes across a genomic region -- Case study 4:
Candidate gene selection--building biological rationale around genes
-- Case study 5: Known and novel marker identification -- Case study
6: Genetic/physical locus characterization and marker panel design --
SNP Discovery and PCR-based Assay Design: From In Silico Data to the
Laboratory Experiment / Ellen Vieux, Gabor Marth, Pui Kwok -- SNP
identification -- PCR primer design -- Broader PCR assay design
issues -- Primer selection -- Problems related to SNP assay
validation -- Tools for Statistical Analysis of Genetic Data / Aruna
Bansal, Peter R. Boyd, Ralph McGinnis -- Linkage analysis --
Association analysis -- Haplotype Reconstruction -- Linkage
disequilibrium -- Quantitative Trait Locus (QTL) mapping in
experimental crosses -- Biological Sequence Analysis and
Characterization -- Predictive Functional Analysis of Polymorphisms:
An Overview / Michael R. Barnes -- Principles of predictive
functional analysis of polymorphisms -- The anatomy of promoter
regions and regulatory elements -- The anatomy of genes --
Pseudogenes and regulatory mRNA -- Analysis of novel regulatory
elements and motifs in nucleotide sequences -- Functional analysis on
non-synonymous coding polymorphisms -- A note of caution on the
prioritization of in silico predictions for further laboratory
investigation -- Functional In Silico Analysis of Non-coding SNPs /
Thomas Werner -- General structure of chromatin-associated DNA --
General functions of regulatory regions -- Transcription Factor
binding sites (TF-sites) -- Structural elements -- Organizational
principles of regulatory regions -- RNA processing -- SNPs in
regulatory regions -- Evaluation of non-coding SNPs -- SNPs and
regulatory networks -- SNPs may affect the expression of a gene only
in specific tissues -- In silico detection and evaluation of
regulatory SNPs -- Getting promoter sequences -- Identification of
relevant regulatory elements -- Estimation of functional consequences
of regulatory SNPs -- Amino Acid Properties and Consequences of
Substitutions / Matthew J. Betts, Robert B. Russell -- Protein
features relevant to amino acid behaviour -- Amino acid
classifications -- Properties of the amino acids -- Amino acid quick
reference -- Studies of how mutations affect function -- A summary of
the thought process -- Genetics/Genomics Interfaces -- Gene
Expression Informatics and Analysis / Antoine H. C. van Kampen, Jan
M. Ruijter, Barbera D. C. van Schaik, Huib N. Caron, Rogier Versteeg
-- Technologies for the measurement of gene expression -- The Cancer
Genome Anatomy Project (CGAP) -- Processing of SAGE data --
Integration of biological databases for the construction of the HTM
-- The Human Transcriptome Map -- Regions of Increased Gene
Expression (RIDGES) -- Proteomic Informatics / Jerome Wojcik,
Alexandre Hamburger -- Proteomic informatics -- Experimental
workflow: classical proteomics -- Protein interaction networks --
Building protein interaction networks -- False negatives and false
positives -- Analysing interaction networks -- Cell pathways --
Prediction of protein networks -- Assessment and validation of
predictions -- Exploiting protein networks -- Deducing prediction
rules from networks -- Concluding Remarks: Final Thoughts and Future
Trends / Michael R. Barnes, Ian C. Gray -- How many genes? -- Mapping
the genome and gaining a view of the full depth of human variation --
Holistic analysis of complex traits.
Book Details:
Language: eng
Physical Description: xiv, 408 p. : ill. ; 24 cm.
Edition Info: (PBK.)
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