Genomics and Health in the Developing World. by Kumar, Dhavendra

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Systems biology

Table of Contents: “…2.4 Development and Evolution: Comparative Genomics2.5 Functional Genomics/Large-Scale Manipulation of Expression; 2.6 Computational Approaches; 3 Model Organisms for Embryogenomics; 3.1 Non-Mammalian Animals; 3.2 Mammalian; 3.3 Plants; 3.4 Suitability of Approaches for Particular Model Organisms Applied to the Study of Development; 4 Conclusions; References; 4 Interactome; 1 Introduction; 2 Experimental Techniques for DetectingProtein Interactions; 3 Computational Prediction of Protein Interactions; 3.1 Interaction Prediction from the Gene Patterns Across Genomes…”
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Large-scale sequencing : the future of genomic sciences? by Riley, M. A. (Margaret A.)

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Synthetic Biology : Parts, Devices and Applications. by Lee, Sang Yup

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Poultry genetics, breeding, and biotechnology

Table of Contents: “…Incorporating Molecular Information in Breeding Programmes : Applications and Limitations / W.M. Muir -- 29. Comparative Genomics / David W. Burt -- 30. Functional Genomics : Development and Gene Regulation / John Killefer and Hakan Kocamis -- 31. …”
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Rice genetics V : proceedings of the Fifth International Rice Genetics Symposium, the Philippines, 19-23 November 2005

Table of Contents: “…Cover -- Contents -- FOREWORD -- ACKNOWLEDGMENTS -- RICE8212;A MODEL GENOME FOR CEREAL RESEARCH -- Rice as a reference genome and more -- Rice as a reference -- Finding orthologous genes and quantitative trait loci (QTLs) -- Value of rice for cloning genes underlying QTLs -- American wildrice as a case study -- References -- Notes -- The complete rice genome sequence: a gold mine for future rice research -- Overview of the rice genome structure -- Utility of rice genome sequence information -- Conclusions -- References -- Notes -- Annotation of the rice genome -- Construction of a rice transcript assembly -- Repetitive sequences in the rice genome -- TIGR Rice Genome Browser -- Noncoding RNAs -- Mapping of genetic markers and microsatellite repeats -- SNPs and indel identification between indica and japonica -- Conclusions -- References -- Notes -- STRUCTURAL GENOMICS AND RESOURCES -- The Oryza map alignment project (OMAP): a new resource for comparative genomics studies within Oryza -- Results -- Summary, conclusions, and future research -- References -- Notes -- Analysis of oligo hybridization properties by high-resolution tiling microarrays in rice -- Characteristics of the rice genome and its annotation -- Tiling-path microarray analysis in rice -- Using tiling microarrays to experimentally analyze probe hybridization properties -- Experimental design of the high-resolution rice tiling microarray -- Tiling-array raw data processing workflow -- Mapping tiling-array signals to annotated gene models -- Oligo hybridization properties analysis -- Conclusions and prospects -- References -- Notes -- Tissue culture8211;induced mutations and overexpression of full-length cDNAs as a tool for functional analysis of rice genes -- Forward and reverse genetics using Tos17 -- Limitations and future prospects -- References -- Notes -- Analysis of genome sequences from the maternal and paternal parents of an elite rice hybrid -- Rice genome sequences produced through a whole-genome shotgun approach are of high quality -- Preliminary analysis of the PA64S genome assembly -- In search of genes and their variations involved in hybrid vigor -- References -- Notes -- DEVELOPMENTAL BIOLOGY AND GENE REGULATION -- T-DNA tagging for developmental biology -- Results -- Discussion -- References -- Notes -- Novel insights into the genomics of rice root adaptive development -- Rice root system organization, morphology, and anatomy -- Genetic and molecular control of constitutive root development -- Plasticity of root architecture -- Novel tools for investigating root developmental processes -- Conclusions and prospects -- References -- Notes -- Molecular signaling in disease resistance of rice -- Seven OsRac genes in rice -- Downstream factors of OsRac1 signaling in defense response -- Upstream factors of OsRac1 signaling in defense response -- Emerging technologies for the study of molecular signaling in disease resistance of rice -- References -- Notes -- APPLIED GENETICS -- QTLs in rice breeding: examplesfor abiotic stresses -- Development and spread of mega varieties -- Big QTLs versus small QTLs -- A case study of QTL breeding: submergence tolerance -- Using gene markers for QTL introgression -- Implications for breeding for rainfed conditions.…”
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Molecular diagnostics

Table of Contents: “…Molecular Diagnostics and Comparative Genomics in Clinical Microbiology; 31. Genetic Monitoring of Laboratory Rodents; 32. …”
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Colloquium on Computational Biomolecular Science.

Table of Contents: “…COLLOQUIUM ON COMPUTATIONAL BIOMOLECULAR SCIENCE -- NATIONAL ACADEMY OF SCIENCES -- COMPLETED NAS COLLOQUIA -- COMPLETED NAS COLLOQUIA -- PROGRAM -- LIST OF ATTENDEES -- Contents -- Computational biomolecular science -- Measuring genome evolution -- Methodological Issues in Comparisons of Genomes -- Comparing Genomes as “Bags of Genesâ€? -- Measuring Correlations Between Genes -- Comparing Rates of Genome Evolution -- SMART, a simple modular architecture research tool: Identification of signaling domains -- METHODS -- RESULTS -- DISCUSSION…”
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Human Gametes and Preimplantation Embryos Assessment and Diagnosis by Gardner, David K.

Table of Contents: “…-- Sperm Morphologic Characteristics and Their Impact on Embryo Quality and Pregnancy Outcome -- Objective Biomarkers of Sperm Development and Fertility: Assessment of Sperm-Zona Pellucida Binding Ability and Hyaluronic Acid Mediated Selection of Sperm for ICSI Fertilization -- Selecting the Best Sperm and Its Implications in Clinical Practice -- The Origins of Aneuploidy in Human Embryos -- Preimplantation Genetic Screening and Diagnosis Using Fluorescent In Situ Hybridization (FISH) -- Single Nucleotide Polymorphisms and Next Generation Sequencing -- Use of Comparative Genomic Hybridization (CGH) and Microarray-CGH for Preimplantation Genetic Screening -- Quantitative SNP Array and Real-Time PCR Based Human Preimplantation Embryo Aneuploidy Screening -- Regulation of Gene Expression in the Oocyte and Early Embryo: Implications for Transcriptomic and Proteomic Embryo Assessment -- Transcriptomics Technology: Promise and Potential Pitfalls -- Transcriptomic Analysis of Cumulus and Granulosa Cells as a Marker of Embryo Viability -- Mass Spectrometry, Proteomics and the Study of Sperm Cell Biology -- Proteomic Analysis of Embryo Viability -- Metabolism of the Viable Human Embryo -- Analysis of Respiration as an Indicator of Oocyte and Embryo Developmental Potential -- Mitochondrial Activity as a Biomarker of Gamete and Embryo Health -- Carbohydrate Analysis and Embryo Viability -- Identification of Viable Embryos by Non-invasive Measurement of Amino Acids in Culture Media -- Metabolomic Profiling of Embryos Using Spectroscopy -- Microfluidic Devices for the Analysis of Gamete and Embryo Physiology.…”
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Phylogenomics : a primer by DeSalle, Rob, Rosenfeld, Jeffrey

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Functional Genomics in Aquaculture. by Saroglia, Marco

Table of Contents: “…Functional Genomics in Aquaculture; Contents; List of Contributors; Preface; Chapter 1 Functional Genomics Research in Aquaculture: Principles and General Approaches; Introduction; The Concept of Functional Genomics; Genes and Gene Functions; Concept of Functional Genomics; Goals of Functional Genomics; Approaches to Functional Genomics; Functional Correlation of Gene Expression Profiling; Functional Correlation of Gene Positions; Expression Quantitative Trait Loci Analysis; Functional Inference by Comparative Genome Analysis; Gene Pathway Analysis.…”
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Molecular Analysis and Genome Discovery. by Rapley, Ralph

Table of Contents: “…Cover; Title Page; Copyright; Preface; Contributors; Chapter 1: Overview of Genotyping; Introduction; Methods for interrogating SNPs; Commercial platforms for SNP genotyping; Practical recommendations; SNP databases; Methylation analysis; Copy number variation analysis; Second generation sequencing technologies; Conclusions; References; Chapter 2: DNA Chip Analysis in Genome Discovery; Introduction; Interrogating a genome; Cross-species hybridization; Comparative genomic hybridization and microarray-based genotyping; Barcodes, DNA microarrays and organism identification; Concluding remarks.…”
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Photosynthesis : genetic, environmental and evolutionary aspects

Table of Contents: “…Danilov and Nils G.A. Ekelund -- 9. Comparative genomic analysis of C[subscript 4] photosynthetic pathway evolution in grasses / Xiyin Wang [and others] -- 10. …”
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Environmental Stress Physiology of Plants and Crop Productivity by Kaur, Tajinder

Table of Contents: “…Role of Plant Growth Regulators in Abiotic Stress Tolerance -- Sakshi Sharma1, Inderpreet Kaur2,* and Avinash Kaur Nagpal3,* -- INTRODUCTION -- ABIOTIC STRESS AND PLANT RESPONSES -- PLANT GROWTH REGULATORS AND THEIR ROLE IN ABIOTIC STRESS TOLERANCE -- Auxins -- Abscisic Acid -- Cytokinins -- Ethylene -- Gibberellins -- Jasmonic Acid -- Brassinosteroids -- Salicylic Acid -- Polyamines -- Strigolactones -- CONCLUSION -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Genomics, Proteomics and Metabolic Approaches against Abiotic Stress -- Harjit Kaur Bajwa1 and Hina Khan1,* -- INTRODUCTION -- GENOMICS APPROACHES AGAINST ABIOTIC STRESS -- Structural Genomics -- Molecular Markers -- Genome Sequencing and Mapping -- Functional Genomics -- Sequencing-Based Approaches -- Hybridization-Based Approaches -- Comparative Genomics -- PROTEOMICS APPROACHES AGAINST ABIOTIC STRESS -- METABOLOMIC APPROACHES AGAINST ABIOTIC STRESS -- CONCLUSION -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- CRISPR/CAS9 Technologies to Enhance Tolerance to Abiotic Stress in Crop Plants -- Ravinder Singh1,*, Rajani Gupta2, Renu Bhardwaj1 and Rattandeep Singh3,* -- INTRODUCTION -- IMPORTANCE OF BREEDING TOWARDS ABIOTIC STRESS TOLERANCE -- GENETIC APPROACHES TO ENHANCE ABIOTIC STRESS TOLERANCES IN PLANTS -- RNA INTERFERENCE (RNAI) APPROACHES TO RESIST ABIOTIC STRESSORS -- CRISPR/CAS9-SINGLE GUIDE RNA (SGRNA) SCHEME FOR GENETIC ENGINEERING -- CRISPR/CAS9 TECHNOLOGIES TO ENHANCE ABIOTIC TOLERANCE TO STRESSORS IN CROP PLANTS -- FUTURE APPROACHES -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Subject Index -- Back Cover.…”
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Alternative Pre-mRNA Splicing : Theory and Protocols

Table of Contents: “…Overview of Splicing Relevant Databases / Pierre de la Grange -- Analysis of RNA Transcripts by High-Throughput RNA Sequencing / Paolo Ribeca, Vincent Lacroix, Michael Sammeth, Roderic Guig̤ -- Identification of Splicing Factor Target Genes by High-Throughput Sequencing / Chaolin Zhang, Michael Q Zhang -- Bioinformatic Analysis of Splicing Events / Zhaiyi Zhang, Stefan Stamm -- Analysis of Pre-mRNA Secondary Structures and Alternative Splicing / Michael Hiller -- Structure Prediction for Alternatively Spliced Proteins / Lukasz Kozlowski, Jerzy Orlowski, Janusz M Bujnicki -- Comparative Genomics Methods for the Prediction of Small RNA-Binding Sites / Rym Kachouri-Lafond, Mihaela Zavolan -- Appendix A1: Yeast Nomenclature Systematic Open Reading Frame (ORF) and Other Genetic Designations -- Appendix A2: Glossary -- Index.…”
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Molecular biology of spirochetes

Table of Contents: “…Kuramitsu and Caroline E. Cameron -- Comparative genomics of borrelia burgdorferi / Sherwood R. …”
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Concise Review of Veterinary Microbiology by Quinn, P. J.

Table of Contents: “…Molecular hybridization -- Chapter 5: Laboratory diagnosis of bacterial disease -- Chapter 6: Molecular subtyping of bacteria -- Comparative genomic hybridization -- Restriction fragment length polymorphism analysis -- PCR-based subtyping methods -- DNA sequence-based subtyping methods -- Whole bacterial genome sequencing -- Chapter 7: Antibacterial agents -- Chapter 8: Antimicrobial susceptibility testing -- Chapter 9: Bacterial resistance to antimicrobial drugs -- Chapter 10: Bacterial infections -- Chapter 11: Structure and components of the immune system -- Innate immunity…”
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Space exploration research

Table of Contents: “…ELEGANS MUTAGENESIS TESTING SYSTEMS ""; ""ARRAY COMPARATIVE GENOMIC HYBRIDIZATION (ACGH) AS AN AID TO HIGH RESOLUTION GENOMIC ANALYSIS OF MUTATED GENOMES ""; ""CONCLUSION ""; ""REFERENCES ""; ""STRUCTURE AND TRANSPORT OF THE MARTIAN SURFACE MATERIAL ""; ""ABSTRACT ""; ""1. …”
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Translational Genomics for Crop Breeding : Volume 2 - Improvement for Abiotic Stress, Quality and Yield Improvement. by Varshney, Rajeev

Table of Contents: “…Introduction -- Rice and Drought -- The Current Drought-Tolerance Improvement Strategy at the International Rice Research Institute (IRRI) -- Direct Selection for Grain Yield is Achieved with Proper Drought Treatments -- Identification of Large-Effect QTLs for Grain Yield under Drought -- Major Rice QTLs Reported for Grain Yield under Drought -- QTL x Environment and QTL x Genotype Interactions -- Effect of Drought Yield QTLs on Multiple Yield-Related Traits under Drought -- Candidate Gene Content and Comparative Genomics of Drought Yield QTLs -- Physiology Studies to Characterize the Mechanisms by Which Major-Effect QTLs Confer Improved Yield under Drought -- Perspectives -- Novel Marker-Assisted Breeding Approaches -- Collaborative Strategies of Breeding and Physiology for Improvement of Drought Tolerance in Rice -- Summary -- References -- Chapter 5 Molecular Breeding for Phosphorus-efficient Rice -- Introduction -- Plant Responses to P Deficiency -- Phosphorus in Rice Cropping Systems -- Breeding Targets Related to P Efficiency in Rice -- The Pup1 QTL and Its Application in Molecular Breeding -- Pup1-specific Molecular Markers -- Evaluation of Pup1 in Different Genetic Backgrounds and Environments -- Phenotyping for Low-P Tolerance -- Outlook and Perspectives -- References -- Chapter 6 Aluminum Tolerance in Sorghum and Maize -- Introduction -- Importance of Acid Soils in Limiting Worldwide Agriculture -- Progress on Physiology of Crop Al Tolerance -- Progress on the Molecular Biology of Crop Al Tolerance -- Sorghum Al Tolerance -- Historical Aspects of Aluminum Tolerance in Sorghum -- The AltSB Locus in Sorghum -- Genetic Diversity for Al Tolerance in Sorghum -- Molecular and Physiological Basis of Al Tolerance Conferred by AltSB -- The Relationship between Population Structure and Al Tolerance in Sorghum.…”
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Genetics of Bone Biology and Skeletal Disease. by Thakker, Rajesh V.

Table of Contents: “…4.3 -- Detection of Chromosomal Abnormalities, Copy Number Variations, and Mutations Causing Disease4.3.1 -- Karyotype -- 4.3.2 -- Fluorescence In Situ Hybridization (FISH) -- 4.3.3 -- Multiplex-Ligation Dependent Probe Amplification (MLPA) -- 4.3.4 -- Whole Genome Arrays -- 4.3.5 -- Microarray-Comparative Genomic Hybridization (aCGH) -- 4.3.6 -- Single Nucleotide Polymorphism Arrays -- 4.3.7 -- Single Gene Testing (Sanger Sequencing) -- 4.3.8 -- Next-Generation Sequencing or Second-Generation Sequencing…”
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Diabetes mellitus research advances

Table of Contents: “…Direct Methods (Based on Molecular Biology) -- 5.1.1. Comparative Genomics -- 5.1.2. Pharmacological Methods and Pharmacogenetics -- 5.1.3. …”
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Cancer Cytogenetics : Chromosomal and Molecular Genetic Aberrations of Tumor Cells. by Heim, Sverre

Table of Contents: “…"Omics" and gene expression-based methodologiesComparative genomic hybridization-based methodology; Protein-based methodologies; DNA-mediated transformation methodology; Clinic-based methodology; Next-generation sequencing-based methodologies; Conclusion; References; Chapter 6 Acute myeloid leukemia; Most AML harbor clonal chromosomal abnormalities; Impact of age; Impact of previous treatment/genotoxic exposure; Impact of gender; Impact of geographic/ethnic origin; Impact of constitutional genetics; Characteristic chromosomal abnormalities in AML; t(1; 3)(p36; q21) [RPN1-PRDM16]; t(1; 21)(p36.…”
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Advances in statistical bioinformatics : models and integrative inference for high-throughput data

Table of Contents: “…""Contents""; ""List of Contributors""; ""Preface""; ""1 An Introduction to Next-Generation Biological Platforms""; ""Virginia Mohlere, Wenting Wang, and Ganiraju Manyam""; ""1.1 Introduction""; ""1.2 The Biology of Gene Silencing""; ""1.2.1 DNA Methylation""; ""1.2.2 RNA Interference""; ""1.3 High-Throughput Profiling""; ""1.3.1 Molecular Inversion Probe Arrays""; ""1.3.2 Array Comparative Genomic Hybridization (aCGH)""; ""1.3.3 Genome-Wide Association Studies""; ""1.3.4 Reverse-Phase Protein Array""; ""1.4 Next-Generation Sequencing""; ""1.4.1 Whole-Genome and Whole-Exome Sequencing""…”
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Biomedical informatics in translational research

Table of Contents: “…5.1 Introduction5.2 Genomic Technologies Used for DNA Analysis; 5.2.1 DNA Sequencing; 5.2.1.2 Biomedical Informatics Requirements; 5.2.1.3 Future Directions; 5.2.2 Genotyping; 5.2.2.1 Array Technologies; 5.2.2.2 Technological Assessment of Genotyping; 5.2.2.3 Affymetrix Genotyping SNP Assay Workflow; 5.2.2.4 QA/SOP Issues; 5.2.2.5 Biomedical Informatics Requirements; 5.2.2.6 Future Directions; 5.2.3 Array-Based Comparative Genomic Hybridization; 5.2.3.1 Technological Assessment of Chromosomal Rearrangements; 5.2.3.2 Example Platform; 5.2.3.3 QA/SOP Issues.…”
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Mathematics of evolution and phylogeny

Table of Contents: “….; 8.3.5 Topñdown approach and leftñright properties of rooted duplication trees -- 8.3.6 Counting duplication histories -- 8.3.7 Counting simple event duplication trees -- 8.3.8 Counting (unrestricted) duplication trees -- 8.4 Inferring duplication trees from sequence data -- 8.4.1 Preamble -- 8.4.2 Computational hardness of duplication tree inference -- 8.4.3 Distance-based inference of simple event duplication trees -- 8.4.4 A simple parsimony heuristic to infer unrestricted duplication trees -- 8.4.5 Simple distance-based heuristic to infer unrestricted duplication trees -- 8.5 Simulation comparison and prospects -- Acknowledgements -- 9 Conserved segment statistics and rearrangement inferences in comparative genomics -- 9.1 Introduction -- 9.2 Genetic (recombinational) distance -- 9.3 Gene counts -- 9.4 The inference problem -- 9.5 What can we infer from conserved segments? …”
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Insect molecular genetics : an introduction to principles and applications by Hoy, Marjorie A.

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Genomic medicine : principles and practice

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