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  • 1
    Online Resource
    Online Resource
    Introduction to Bio-Ontologies. (2011)
    London :CRC Press LLC,
    Details
    Keywords: Bioinformatics. ; Ontologies (Information retrieval). ; Electronic books.
    Description / Table of Contents: Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications. The first part of the book defines ontology and bio-ontologies. It also explains the importance of mathematical logic for understanding concepts of inference in bio-ontologies, discusses the probability and statistics topics necessary for understanding ontology algorithms, and describes ontology languages, including OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL. The second part covers significant bio-ontologies and their applications. The book presents the Gene Ontology; upper-level ontologies, such as the Basic Formal Ontology and the Relation Ontology; and current bio-ontologies, including several anatomy ontologies, Chemical Entities of Biological Interest, Sequence Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology. The third part of the text introduces the major graph-based algorithms for bio-ontologies. The authors discuss how these algorithms are used in overrepresentation analysis, model-based procedures, semantic similarity analysis, and Bayesian networks for molecular biology and biomedical applications. With a focus on computational reasoning topics, the final part describes the ontology languages of the Semantic Web and their applications for inference. It covers the formal semantics of RDF and RDFS, OWL inference rules, a key inference algorithm, the SPARQL query language, and the state of the art for querying OWL ontologies. Web Resource Software and data designed to complement material in the text are available on the book's website: http://bio-ontologies-book.org The site provides the R Robo package developed for the book, along with a
    Type of Medium: Online Resource
    Pages: 1 online resource (514 pages)
    Edition: 1st ed.
    ISBN: 9781439836668
    Series Statement: Chapman and Hall/CRC Mathematical and Computational Biology Series
    URL: https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=1633237
    DDC: 610.285
    Language: English
    Note: Front Cover -- Dedication -- Preface -- Contents -- List of Figures -- List of Tables -- Symbol Description -- I. Basic Concepts -- 1. Ontologies and Applications of Ontologies in Biomedicine -- 2. Mathematical Logic and Inference -- 3. Probability Theory and Statistics for Bio-Ontologies -- 4. Ontology Languages -- II. Bio-Ontologies -- 5. The Gene Ontology -- 6. Upper-Level Ontologies -- 7. A Selective Survey of Bio-Ontologies -- III. Graph Algorithms for Bio-Ontologies -- 8. Overrepresentation Analysis -- 9. Model-Based Approaches to GO Analysis -- 10. Semantic Similarity -- 11. Frequency-Aware Bayesian Network Searches in Attribute Ontologies -- IV. Inference in Ontologies -- 12. Inference in the Gene Ontology -- 13. RDFS Semantics and Inference -- 14. Inference in OWL Ontologies -- 15. Algorithmic Foundations of Computational Inference -- 16. SPARQL -- Appendices -- A. An Overview of R -- B. Information Content and Entropy -- C. W3C Standards: XML, URIs, and RDF -- D. W3C Standards: OWL -- Glossary -- C -- D -- F -- H -- J -- M -- N -- O -- P -- Q -- R -- T -- W -- Bibliography.
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  • 2
    Online Resource
    Online Resource
    Computational Exome and Genome Analysis. (2017)
    Milton :CRC Press LLC,
    Details
    Keywords: Exome. ; Electronic books.
    Description / Table of Contents: This book provides a practical introduction to the major areas in the field of computational exome and genome sequencing, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.
    Type of Medium: Online Resource
    Pages: 1 online resource (575 pages)
    Edition: 1st ed.
    ISBN: 9781351650816
    Series Statement: Chapman and Hall/CRC Computational Biology Series
    URL: https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=5046645
    DDC: 572.86
    Language: English
    Note: Cover -- Half Title -- Series Editor -- Published Titles -- Title -- Copyright -- Dedication -- Contents -- Who is this book for? -- Preface -- Contributors -- Part I Introduction -- Chapter 1 Introduction: Whole Exome and Genome Sequencing -- Chapter 2 NGS Technology -- Chapter 3 Illumina Technology -- Chapter 4 Data -- Part II Raw Data Processing -- Chapter 5 FASTQ Format -- Chapter 6 Raw Data: Quality Control -- Chapter 7 Trimming -- Part III Alignment -- Chapter 8 Alignment: Mapping Reads to the Reference Genome -- Chapter 9 SAM/BAM Format -- Chapter 10 Postprocessing the Alignment -- Chapter 11 Alignment Data: Quality Control -- Part IV Variant Calling -- Chapter 12 Variant Calling and Quality- Based Filtering -- Chapter 13 Variant Call Format (VCF) -- Chapter 14 Jannovar -- Chapter 15 Variant Annotation -- Chapter 16 Variant Calling: Quality Control -- Chapter 17 Integrative Genomics Viewer (IGV): Visualizing Alignments and Variants -- Chapter 18 De Novo Variants -- Chapter 19 Structural Variation -- Part V Variant Filtering -- Chapter 20 Pedigree and Linkage Analysis -- Chapter 21 Intersection Analysis and Rare Variant Association Studies -- Chapter 22 Variant Frequency Analysis -- Chapter 23 Variant Pathogenicity Prediction -- Part VI Prioritization -- Chapter 24 Variant Prioritization -- Chapter 25 Prioritization by Random Walk Analysis -- Chapter 26 Phenotype Analysis -- Chapter 27 Exomiser and Genomiser -- Chapter 28 Medical Interpretation -- Part VII Cancer -- Chapter 29 A (Very) Short Introduction to Cancer -- Chapter 30 Somatic Variants in Cancer -- Chapter 31 Tumor Evolution and Sample Purity -- Chapter 32 Driver Mutations and Mutational Signatures -- Appendix A Hints and Answers -- References -- Index.
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  • 3
    Electronic Resource
    Electronic Resource
    Two recurrent nonsense mutations and a 4 bp deletion in a quasi-symmetric element in exon 37 of the NF1 gene (1995)
    Springer
    Human genetics 〈Berlin〉 96 (1995), S. 95-98 
    Details
    ISSN: 1432-1203
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract We screened a total of 92 unrelated patients with neurofibromatosis type 1 (NF1) for mutations in exon 37 of the NF1 gene, by using temperature gradient gel electrophoresis. Two novel mutations were found: a 4 bp deletion in a so-called quasi-symmetric element (6789delTTAC) and a recurrent nonsense mutation, which was identified in two unrelated patients, at codon 2264 (C6792A). The independent origin of the latter mutation in two families was confirmed by haplotype analysis. The nonsense mutation and the 4 bp deletion are both predicted to lead to a truncated protein product lacking the Cterminal 20% (aproximately) of its sequence. The occurrence of three independent mutations among 92 NF1 patients at codons 2263–2264 (exon 37) suggests that a specific search for mutations in this area should be undertaken in screening programs for NF1 mutations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00214193
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  • 4
    Electronic Resource
    Electronic Resource
    Species-specific detection of Legionella using polymerase chain reaction and reverse dot-blotting (1996)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 140 (1996), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract Legionella pneumophila and some other Legionella species are capable of causing Legionnaire's disease, a potentially fatal pneumonia. The identification of legionellae by standard laboratory techniques such as culture is difficult and time-consuming. In the present work, the DNA sequence of the 23S-5S spacer region was determined for 43 Legionella isolates, and the sequence information was used to develop a species-specific detection system using PCR and reverse dot-blotting which employs just one PCR amplicon to perform genus- and species-specific detection. L. pneumophila serogroups 1–16 as well as 21 non-pneumophila isolates could be identified and differentiated at the species level using this system.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1996.tb08323.x
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  • 5
    Electronic Resource
    Electronic Resource
    Bipolar clamping improves the sensitivity of mutation detection by temperature gradient gel electrophoresis (1998)
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 1347-1350 
    Details
    ISSN: 0173-0835
    Keywords: Temperature gradient gel electrophoresis ; Psoralen ; Bipolar clamping ; Heteroduplex ; Melting ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Temperature gradient gel electrophoresis (TGGE) is a rapid and sensitive screening method for point mutations and other small DNA alterations. Usually a polymerase chain reaction (PCR)-product of 150 to 500 bp that has been clamped at one end by a psoralen molecule or a “GC-clamp” is tested for abnormal melting characteristics by electrophoresis in a temperature gradient. Under optimal conditions, a heterozygous mutation within the fragment is detected through the presence of three additional bands in the TGGE gel, the mutant homoduplex and two heteroduplex bands. However, the ideal pattern of four sharp bands is not always found due to inconsistencies in melting behavior along the sequence of the DNA fragment under study. Some of these fragments show fuzzy bands that may impede or even prevent the detection of a mutation. Here, we describe a method to overcome this problem by utilizing one psoralen clamp at each end of the PCR product. Using TGGE assays established for exons 16, 17, and 18 of the NF1 gene and for exon 14 of the FBN1 gene as examples, we show that bipolar clamping may transform blurred bands into sharp ones and may visualize mutations that could not be detected by conventional single-sided clamping.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150190824
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  • 6
    Electronic Resource
    Electronic Resource
    Three novel mutations of the NF1 gene detected by temperature gradient gel electrophoresis of exons 5 and 8 (1996)
    Weinheim : Wiley-Blackwell
    Electrophoresis 17 (1996), S. 1559-1563 
    Details
    ISSN: 0173-0835
    Keywords: Temperature gradient gel electrophoresis ; Denaturing gradient gel electrophoresis ; Neurofibromatosis gene ; Mutation analysis ; Exon skipping ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: We screened a total of 100 unrelated patients with neurofibromatosis type 1 (NF1) for mutations in exons 5 and 8 of the NF1 gene using temperature gradient gel electrophoresis (TGGE). Careful interpretation of exon 5 TGGE patterns was necessary due to interference by an exonic polymorphism. Three novel mutations were identified: a stop mutation in exon 5 (Q239X) caused by a C→T transition at cDNA nucleotide position 715, a transition at the invariant G of the splice accceptor site in intron 4c (G655-1A), and a transversion at the invariant G of the splice donor site in intron 8 (G1185+1T). Analysis of mRNA revealed the predicted abnormal splice products. While skipping of exon 5 causes a shift in the reading frame with a premature stop codon downstream in the middle of exon 6, skipping of exon 8 leads to an in-frame deletion with the predicted protein product being shortened by 41 amino acids.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150171011
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