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  • 1
    Keywords: Medicine ; Oncology ; Human Genetics ; Bioinformatics ; Biomedicine ; Cancer Research ; Bioinformatics ; Human Genetics ; Biomedicine general ; Springer eBooks
    Description / Table of Contents: Introduction: next generation sequencing technology and cancer research -- The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ́€˜dark matteŕ€™ unannotated℗ RNA -- Total RNA-seq of breast cancer in hypoxia -- Altered antisense-to-sense transcript ratios in breast cancer -- Identification of piRNAs in Hela cells by massive parallel sequencing -- Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia -- Whole-Exome Sequencing Identifies FAM20A Mutations as a Cause of Amelogenesis Imperfecta and Gingival Hyperplasia Syndrome -- Whole-exome sequencing in CIC and IDH1/2 contributing to human oligodendroglioma -- Genetic and structural variation in the gastric cancer kinome revealed through targeted deep℗ sequencing -- Tumour evolution inferred by single-cell sequencing -- Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq -- Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNASeq℗ analysis -- Whole genome DNA methylation analysis based on high throughput sequencing technology -- Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors -- High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq -- MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of℗ miRNA action -- Genome-wide identification of polycomb-associated RNAs by RIP-seq -- Single-molecule sequencing: sequence methods to enable accurate quantisation -- Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics℗ in mammalian cells -- Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA -- The genome information process for cancer research: the challenge and perspective -- Index
    Abstract: Next Generation Sequencing (NGS) technology has placed important milestones in the life science and changed the direction in biomedical science inclucing cancer. Scientists around the world are attempting to find the root cause of cancer and they are looking for more direct and effective means to cure cancer. This journey to conquer cancer is more optimistic now with the unfolding of the cancer genome. This book focuses on the application of various NGS in the frontier cancer genome research. The 18 chapters in this volume have been written by scientists with many outstanding contributions in their area and the join effort has created comprehensive insightful view on (1) Overview of next generation sequencing technology in cancer genome research (2) Genome regulation and targeted sequencing in cancer (3) RNA transcriptome (coding and non-coding) in cancer genome (4)The challenges of computational biology for cancer genome study. This book is a state-of-the-art reference to all scientific researchers and onologists who are interested in the understanding of the cancer initiatome at whole genome scale and to those are keen to translate the ‘base pairs to bedside’ for better management of cancer patients in the era of personalized medicine
    Pages: XII, 383 p. 73 illus., 59 illus. in color. : online resource.
    ISBN: 9781461476450
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  • 2
    Keywords: Medicine ; Oncology ; Human Genetics ; Bioinformatics ; Biomedicine ; Cancer Research ; Human Genetics ; Bioinformatics ; Springer eBooks
    Description / Table of Contents: Single-cell next Generation Sequencing and Its Applications in Cancer Biology -- Utility of Next Generation Sequencing in Cancer Drug Development and Clinical Trials -- Next-Generation Sequencing in the Era of Cancer-Targeted Therapies: Towards the Personalised Medicine -- Mutational Similarities Across Cancers: Implications for Research, Diagnostics and Personalized Therapy Design -- Standardized Decision Support in NGS Reports of Somatic Cancer Variants -- Clinical Considerations in the Conduct of Cancer Next Generation Sequencing Testing and Genetic Counselling -- Next Generation Sequencing for Cancer Biomarker Discovery -- Validation and Implementation of Next Generation Sequencing Technologies in a Clinical Molecular Diagnostic Laboratory -- Next Generation Sequencing Technologies and Formalin Fixed Paraffin Embedded Tissue: Application to Clinical Cancer Research -- Applications of NGS to Screen FFPE Tumours for Detecting Fusion Transcripts -- Clinical Application of Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tumors -- ChIP-BS-Sequencing in Cancer Epigenomics -- Integrative Analysis Identifies Transcription Factor-DNA Methylation Relationships and Introduces New Avenues for Translating Cancer Epigenetics Into the Clinic -- Differential Methylation Analysis with Next-Generation Sequencing -- Performance Comparison and Data Analysis Strategies for MicroRNA Profiling in Cancer Research -- Small RNA Sequencing for Squamous Cell Carcinoma Research -- Exome Capture and Capturing Technologies in Cancer Research -- The Landscape of DNA Virus Associations Across Human Malignant Cancers -- Using Next Generation Sequencing to Reveal Patterns of Chromosomal Alterations in Oral Verrucous Carcinoma -- Vironomics: The Study of Viral Genomics in Human Cancer and Disease -- Molecular Typing of Lung Adenocarcinoma on Cytological Samples in the Next Generation Sequencing Era -- Whole Genome/Exome Sequencing in Acute Leukemia: From Research to Clinics -- Next Generation Sequencing Applications in Head and Neck Oncology -- CIC Mutation in Brain Tumor -- Isocitrate Dehydrogenase (IDH) Mutation in Gliomas -- Utilization of Multigene Panels in Hereditary Cancer Predisposition Testing
    Abstract: Next Generation Sequencing in Cancer Research, Volume 2: From Basepairs to Bedsides, the second in the series ́€œNext Generation Sequencing Technology in Cancer Research́€”From Basepairs to Bedsides,́€ is designed to fill the gap between cancer genome research and clinical management of the individual cancer patient. The volume presents the principles of next generation sequencing (NGS) technologies and massively parallel DNA sequencing and their application of the whole genome sequences (WGS), whole exome-seq (WES), RNA-seq, miRNA-seq, and ChIP-seq in cancer research programs and to apply the newly discovered driver genetic alterations for prevention, early diagnosis and genome-oriented precision cancer treatment. Next Generation Sequencing in Cancer Research, Volume 2: From Basepairs to Bedsides brings together the implementation of a wide range of NGS technologies, including single-cell sequencing, in the clinical setting: discovery and validation of cancer biomarkers; standardization of NGS data production; NGS data reporting systems for clinicians; novel anti-cancer therapies ℗ development from NGS data; conducting of clinical trials of newly investigated cancer drugs. It provides compelling evidence to signal a new future for health care and a new standard for cancer care
    Pages: XVIII, 493 p. 78 illus., 70 illus. in color. : online resource.
    ISBN: 9783319158112
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  • 3
    Keywords: Medicine ; Cancer Research ; Biomedicine ; Cancer Research ; Springer eBooks
    Description / Table of Contents: Non- coding RNAs in DNA Damage Response: Opportunities for Cancer Therapeutics -- MicroRNAs in Breast Cancer: Diagnostic and Therapeutic Potential -- Involvement of miRNAs and Pseudogenes in Cancer -- microRNAs Reprogram Tumor Immune Response -- APOBEC Gene Expression Regulated by microRNAs -- MicroRNAs Changes the Landscape of Cancer Resistance -- MicroRNA, Noise, and Gene Expression Regulation -- Deep Sequencing Reveals a microRNA Expression Signature in Triple-negative Breast Cancer -- Detection of Plasma microRNA Signature in Osteosarcoma Patients -- Identification of E6/E7-dependent microRNAs in HPV-positive Cancer Cells -- Combination of Anti-miRNAs Oligonucleotides with Low Amounts of Chemotherapeutic Agents for Pancreatic Cancer Therapy -- Evaluation of microRNA Delivery in vivo -- Angiogenesis Analysis by in vitro Co-culture Assays in Transwell Chambers in Ovarian Cancer -- Application of Individual qPCR Performance Parameters for Quality Control of Circulating microRNA Data -- Construction of Multi-potent microRNA Sponge and its Functional Evaluation -- microRNA Sequencing Data Analysis Toolkits
    Abstract: This volume details basic principles of experimental and computational methods for the study of microRNAs in cancer research and, therefore, provides a firm grounding for those who wish to develop further applications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, MicroRNA and Cancer: Methods and Protocols, Second Edition℗ aims to ensure successful results in the further study of this vital field
    Pages: XI, 222 p. 21 illus., 17 illus. in color. : online resource.
    Edition: 2nd ed. 2018.
    ISBN: 9781493974351
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  • 4
    ISSN: 1432-072X
    Keywords: Methanobacterium formicicum ; Formate metabolism ; Methanogenesis from formate ; Methanogenesis from H2 ; H2 metabolism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Accumulation of formate to millimolar levels was observed during the growth of Methanobacterium formicicum species on H2−CO2. Hydrogen was also produced during formate metabolism by M. formicicum. The amount of formate accumulated in the medium or the amount H2 released in gas phase was influenced by the bicarbonate concentration. The formate hydrogenlyase system was constitutive but regulated by formate. When methanogenesis was inhibited by addition of 2-bromoethane sulfonate, M. formicicum synthesized formate from H2 plus HCO inf3 sup- or produced H2 from formate to a steady-state level at which point the Gibbs free energy (ΔG′) available for formate synthesis or H2 production was approximately -2 to -3 kJ/reaction. Formate conversion to methane was inhibited in the presence of high H2 pressure. The relative rates of conversion of formate and H2 were apparently controlled by the ΔG′ available for formate synthesis, hydrogen production, methane production from formate and methane production from H2. Results from 14C-tracer tests indicated that a rapid isotopic exchange between HCOO- and HCO inf3 sup- occurred during the growth of M. formicicum on H2−CO2. Data from metabolism of 14C-labelled formate to methane suggested that formate was initially split to H2 and HCO inf3 sup- and then subsequently converted to methane. When molybdate was replaced with tungstate in the growth media, the growth of M. formicicum strain MF on H2−CO2 was inhibited although production of methane was not Formate synthesis from H2 was also inhibited.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 89 (1994), S. 105-121 
    ISSN: 1432-2234
    Keywords: Valence-bond method ; Nonorthogonal problem ; Group theoretical approach
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A new algorithm for nonorthogonalab initio valence bond calculation has been deduced based on the left-coset decomposition of the symmetric groupS N . The strategy in the new approach is that, instead of performing the summation overN! permutations of groupS N , we sum the left cosets, and each coset corresponds to a “positive determinant” of orderN/2 for the evaluation of overlap, or a few positive determinants for Hamiltonian. Therefore, the computation turns into accumulating positive determinants. The expressions for evaluating both overlap and Hamiltonian matrix elements of VB functions are given in detail. Our practice shows that such a positive determinant method is quite attractive and it provides an excellent starting point for developing an even much more efficient algorithm of nonorthogonal VB calculation.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-2242
    Keywords: QTLs ; Joint mapping ; Genetic marker ; Linkage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A previous paper proposed a new method of QTL mapping called joint mapping (JM). Some problems have been found in model fitting and model testing due to the neglect of the correlations among different observations of the dependent variable in this model. The present paper reports a method of solving the problems. The coefficient of correlation between two observations of the dependent variable is derived. A generalized least square (GLS) approach is developed for model fitting and a strategy and procedure of model testing based on a chi-square test is suggested. A simulated example is given. The example shows that the JM method is quite efficient in mapping multiple linked QTLs.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 93 (1996), S. 1156-1160 
    ISSN: 1432-2242
    Keywords: QTL ; Joint mapping ; F2 population ; Genetic marker ; Linkage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper, the theory of joint mapping of quantitative trait loci is extended to F2 populations. Two independent regression equations, related to the additive and dominance effects respectively, are derived. Therefore, there are three alternative strategies for mapping QTLs, called additive-based mapping (ABM), dominance-based mapping (DBM) and additive-dominance-based mapping (ADBM). Simulation results have shown that ADBM is the most appropriate in most situations.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Two types of methanogenic granules capable of high chemical oxygen demand removal rates were developed in laboratory-scale upflow reactors at 35° C. One granule type (R-granules) had a rod-type Methanothrix-like species as the predominant species whereas the other (F-granules) had a filament-type M. soehngenii-like acetate-utilizer as the predominant species. These two types of granules were compared in terms of operational performance, physical-chemical characteristics and microbial population. The R-granules had a higher density [65–70 vs 39–43 g suspended solids (SS)/l], specific gravity (1.03 vs 1.01) and specific volumetric methane production rate (180 vs 120 l CH4/l granules per day) than the F-granules. Acetate, propionate and butyrate degraders in both types of granules had similar specific growth rates. The most probable number enumeration indicated that both types of granule had the same population levels (cells/g SS) in terms of methanogens (H2-CO2-, formate- and acetate-utilizing) and syntrophic acetogens. Hydrolytic-fermentative bacteria were present in greater number in the F-granules than in the R-granules. The R-granules had a higher cell density than the F-granules. The differences in operational performance were due mainly to their different microbial composition, especially the predominant acetate-utilizing methanogens in the granules. The long-filamentous M. soehngenii-like rods in the F-granules appeared to be responsible for their lower density and large-sized granules.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The microbial species composition of methanogenic granules developed on an acetate-propionate-butyrate mixture was characterized. The granules contained high numbers of adhesive methanogens (1012/g dry weight) and butyrate-, isobutyrate-, and propionate-degrading syntrophic acetogens (1011/g dry weight), but low numbers of hydrolytic-fermentative bacteria (109/g dry weight). Prevalent methanogens in the granules included: Methanobacterium formicicum strain T1N and RF, Methanosarcina mazei strain T18, Methanospirillum hungatei strain BD, and a non-filamentous, bamboo-shaped rod species, Methanothrix/Methanosaeta-like strain M7. Prevalent syntrophic acetogens included: a butyrate-degrading Syntrophospora bryantii-like strain BH, a butyrate-isobutyrate degrading non-spore-forming rod, strain IB, a propionate-degrading sporeforming oval-shaped species, strain PT, and a propionate-degrading none-spore-forming sulfate-reducing rod species, strain PW, which was able to grow syntrophically with an H2-utilizing methanogen. Sulfate-reducing bacteria did not play a significant role in the metabolism of H2, formate, acetate and butyrate but they were involved in propionate degradation.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Two types of mesophilic methanogenic granules (R- and F-granules) were developed on different synthetic feeds containing acetate, propionate and butyrate as major carbon sources and their metabolic properties were characterized. The metabolic activities of granules on acetate, formate and H2-CO2 were related to the feed composition used for their development. These granules performed a reversible reaction between H2 production from formate and formate synthesis from H2 plus bicarbonate. Both types of granules exhibited high activity on normal and branched volatile fatty acids with three to five carbons and low activity on ethanol and glucose. The granules performed a reversible isomerization between isobutyrate and butyrate during butyrate or isobutyrate degradation. Valerate and 2-methylbutyrate were produced and consumed during propionate-butyrate degradation. The respective apparent K m (mm) for various substrates in disrupted R- and F-granules was: acetate, 0.43 and 0.41; propionate, 0.056 and 0.038; butyrate, 0.15 and 0.19; isobutyrate, 0.12 and 0.19; valerate, 0.15 and 0.098. Both granules had an optimum temperature range from 40 to 50° C for H2-CO2 and formate utilization and 40° C for acetate, propionate and butyrate utilization and a similar optimum pH.
    Type of Medium: Electronic Resource
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