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Books on the topic 'Single cell sequencing data'

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Author: Grafiati
Published: 10 December 2022
Last updated: 29 January 2023

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1

Suzuki, Yutaka, ed. Single Molecule and Single Cell Sequencing. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-6037-4.

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2

Yu, Buwei, Jiaqiang Zhang, Yiming Zeng, Li Li, and Xiangdong Wang, eds. Single-cell Sequencing and Methylation. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-4494-1.

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3

Wang, Xiangdong, ed. Single Cell Sequencing and Systems Immunology. Dordrecht: Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-9753-5.

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4

Loos, Carolin. Analysis of Single-Cell Data. Wiesbaden: Springer Fachmedien Wiesbaden, 2016. http://dx.doi.org/10.1007/978-3-658-13234-7.

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5

Yuan, Guo-Cheng, ed. Computational Methods for Single-Cell Data Analysis. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9057-3.

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6

Mallick, Himel, Lingling An, Mengjie Chen, Pei Wang, and Ni Zhao, eds. Methods for Single-Cell and Microbiome Sequencing Data. Frontiers Media SA, 2022. http://dx.doi.org/10.3389/978-2-88976-280-4.

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7

Chen, Geng, Zhichao Liu, and Cheng Peng, eds. Multimodal and Integrative Analysis of Single-Cell or Bulk Sequencing Data. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88966-668-3.

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8

Yang, Jialiang, Liao Bo, Tuo Zhang, and Yifei Xu, eds. Bioinformatics Analysis of Single Cell Sequencing Data and Applications in Precision Medicine. Frontiers Media SA, 2020. http://dx.doi.org/10.3389/978-2-88963-528-3.

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9

Suzuki, Yutaka. Single Molecule and Single Cell Sequencing. Springer, 2019.

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10

Wang, Xiangdong. Single Cell Sequencing and Systems Immunology. Springer, 2016.

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11

Proserpio, Valentina. Single Cell Methods: Sequencing and Proteomics. Springer New York, 2019.

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12

Proserpio, Valentina. Single Cell Methods: Sequencing and Proteomics. Springer New York, 2020.

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13

Wang, Xiangdong. Single Cell Sequencing and Systems Immunology. Ingramcontent, 2015.

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14

Wang, Xiangdong. Single Cell Sequencing and Systems Immunology. Springer, 2015.

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15

Li, Li, Xiangdong Wang, Jiaqiang Zhang, Buwei Yu, and Yiming Zeng. Single-Cell Sequencing and Methylation: Methods and Clinical Applications. Springer Singapore Pte. Limited, 2021.

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16

Li, Li, Xiangdong Wang, Jiaqiang Zhang, Buwei Yu, and Yiming Zeng. Single-cell Sequencing and Methylation: Methods and Clinical Applications. Springer, 2020.

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17

Yuan, Guo-Cheng. Computational Methods for Single-Cell Data Analysis. Springer New York, 2019.

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18

Yang, Sheng, Shiquan Sun, Xiang Zhou, and Yang Zhao, eds. Integrative Analysis of Genome-Wide Association Studies and Single-Cell Sequencing Studies. Frontier Media SA, 2021. http://dx.doi.org/10.3389/978-2-88971-467-4.

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19

Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.

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The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
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20

Loos, Carolin. Analysis of Single-Cell Data: ODE Constrained Mixture Modeling and Approximate Bayesian Computation. Springer Spektrum, 2016.

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21

Loos, Carolin. Analysis of Single-Cell Data: ODE Constrained Mixture Modeling and Approximate Bayesian Computation. Spektrum Akademischer Verlag GmbH, 2016.

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22

Coleman, William L., and R. Michael Burger. Extracellular Single-Unit Recording and Neuropharmacological Methods. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199939800.003.0003.

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Small biogenic changes in voltage such as action potentials in neurons can be monitored using extracellular single unit recording techniques. This technique allows for investigation of neuronal electrical activity in a manner that is not disruptive to the cell membrane, and individual neurons can be recorded from for extended periods of time. This chapter discusses the basic requirements for an extracellular recording setup, including different types of electrodes, apparatus for controlling electrode position and placement, recording equipment, signal output, data analysis, and the histological confirmation of recording sites usually required for in vivo recordings. A more advanced extracellular recording technique using piggy-back style multibarrel electrodes that allows for localized pharmacological manipulation of neuronal properties is described in detail. Strategies for successful signal isolation, troubleshooting advice such as noise reduction, and suggestions for general laboratory equipment are also discussed.
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23

Henderson, Daniel A., R. J. Boys, Carole J. Proctor, and Darren J. Wilkinson. Linking systems biology models to data: A stochastic kinetic model of p53 oscillations. Edited by Anthony O'Hagan and Mike West. Oxford University Press, 2018. http://dx.doi.org/10.1093/oxfordhb/9780198703174.013.7.

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This article discusses the use of a stochastic kinetic model to study protein level oscillations in single living cancer cells, using the p53 and Mdm2 proteins as examples. It describes the refinement of a dynamic stochastic process model of the cellular response to DNA damage and compares this model to time course data on the levels of p53 and Mdm2. The article first provides a biological background on p53 and Mdm2 before explaining how the stochastic kinetic model is constructed. It then introduces the stochastic kinetic model and links it to the data and goes on to apply sophisticated MCMC methods to compute posterior distributions. The results demonstrate that it is possible to develop computationally intensive Markov chain Monte Carlo (MCMC) methods for conducting a Bayesian analysis of an intra-cellular stochastic systems biology model using single-cell time course data.
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24

Marlow, Heather, ed. Evolutionary Development of Marine Larvae. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198786962.003.0002.

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Access to a growing number of marine invertebrates with genetic and genomic tools has broadened our understanding of the diversity of developmental mechanisms, informing our understanding of larval evolution by allowing the identification of shared or divergent programs for the formation of body plan patterning and organ formation. Two such genetic programs are the apical plate patterning network and the hox/parahox trunk and gut patterning network common to larval and adult forms, respectively. While mounting evidence supports an ancient origin at the base of the Bilateria for both adult and larval forms, it is clear that many distinct organs and structures have appeared independently and can be shifted between the larval and adult phase frequently. Future advances in our understanding of larval evolution are likely to emerge from exhaustive studies of marine invertebrate cell types by single-cell sequencing technologies and through the study of the genetic basis of the metamorphic transition.
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25

Pezzella, Francesco, Mahvash Tavassoli, and David J. Kerr, eds. Oxford Textbook of Cancer Biology. Oxford University Press, 2019. http://dx.doi.org/10.1093/med/9780198779452.001.0001.

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The study of the biology of tumours has grown to become markedly interdisciplinary, involving chemists, statisticians, epidemiologists, mathematicians, bioinformaticians, and computer scientists alongside medical scientists. Oxford Textbook of Cancer Biology brings together the developments from different branches of research into one volume. Structured in seven sections, the book starts with a review of the development and biology of multicellular organisms, how they maintain a healthy homeostasis in an individual, and a description of the molecular basis of cancer development. The book then illustrates how, once cells become neoplastic, their signalling network is altered and pathological behaviour follows. Changes that cancer cells can induce in nearby normal tissue are explored, and the new relationship established between them and the stroma is explicated. Finally, the authors illustrate the contribution provided by high throughput techniques to map cancer at different levels, from genomic sequencing to cellular metabolic functions, and how information technology with its vast amounts of data are integrated with traditional cell biology to provide a global view of the disease. The book concludes by summarizing what we know to date about cancer, and in what direction our understanding of cancer is moving.
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26

Bakhtiar, Syeda Marriam, and Erum Dilshad, eds. Omics Technologies for Clinical Diagnosis and Gene Therapy: Medical Applications in Human Genetics. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150795171220101.

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Genetic disorders have been the focus of scientists for a long time. The emergence of next-generation sequencing techniques has ushered a new era in genetics and several developments have occurred in human genetics. The scientific perspective has also been widened with omics technologies that allow researchers to analyze genetic sequences and their expression products. An integrated approach is being used not only for diagnosis but also for disease management and therapeutic purposes. This book highlights emerging areas of omics technology and its application in the diagnosis and management of human genetic disorders. The book covers three areas of research and implementation: 1) Diagnosis (covering conventional strategies to next-generation platforms). This section focuses on the role of in silico analysis, databases and multi-omics of single-cell which will help in designing better management strategies. 2) Disease Management and therapeutic interventions. This section starts with genetic counselling and progresses to more specific techniques such as pharmacogenomics and personalized medicine, gene editing techniques and their applications in gene therapies and regenerative medicine. 3) Case studies. This section discusses the applications and success of all the above-mentioned strategies on selected human disorders. This book serves as a handy reference for students and academics studying advanced omics techniques in biochemistry and molecular genetics as part of courses in life sciences, pharmacology and medicine.
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27

Lewis, Myles, and Tim Vyse. Genetics of connective tissue diseases. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0042.

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The advent of genome-wide association studies (GWAS) has been an exciting breakthrough in our understanding of the genetic aetiology of autoimmune diseases. Substantial overlap has been found in susceptibility genes across multiple diseases, from connective tissue diseases and rheumatoid arthritis (RA) to inflammatory bowel disease, coeliac disease, and psoriasis. Major technological advances now permit genotyping of millions of single nucleotide polymorphisms (SNPs). Group analysis of SNPs by haplotypes, aided by completion of the Hapmap project, has improved our ability to pinpoint causal genetic variants. International collaboration to pool large-scale cohorts of patients has enabled GWAS in systemic lupus erythematosus (SLE), systemic sclerosis and Behçet's disease, with studies in progress for ANCA-associated vasculitis. These 'hypothesis-free' studies have revealed many novel disease-associated genes. In both SLE and systemic sclerosis, identified genes map to known pathways including antigen presentation (MHC, TNFSF4), autoreactivity of B and T lymphocytes (BLK, BANK1), type I interferon production (STAT4, IRF5) and the NFκ‎B pathway (TNIP1). In SLE alone, additional genes appear to be involved in dysregulated apoptotic cell clearance (ITGAM, TREX1, C1q, C4) and recognition of immune complexes (FCGR2A, FCGR3B). Future developments include whole-genome sequencing to identify rare variants, and efforts to understand functional consequences of susceptibility genes. Putative environmental triggers for connective tissue diseases include infectious agents, especially Epstein-Barr virus; cigarette smoking; occupational exposure to toxins including silica; and low vitamin D, due to its immunomodulatory effects. Despite numerous studies looking at toxin exposure and connective tissue diseases, conclusive evidence is lacking, due to either rarity of exposure or rarity of disease.
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28

Divan, Aysha, and Janice A. Royds. 5. Molecular interactions. Oxford University Press, 2016. http://dx.doi.org/10.1093/actrade/9780198723882.003.0005.

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Every nucleated diploid cell in the body, with the exception of B and T cells of the immune system, has the same genome as its originating single fertilized egg. During development, this single cell differentiates into a complex multicellular organism composed of various cells and tissues each carrying out specialized functions. Although each cell contains a genome of data it needs to select the relevant information from this genetic blueprint to fulfil its own specific function. ‘Molecular interactions’ shows that proteins must be produced in the right place and at the right time. This requires regulation of gene expression in conjunction with a myriad of bio-molecular interactions to coordinate this.
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29

Fehse, Boris, Ferdinand Hucho, Sina Bartfeld, Stephan Clemens, Tobias Erb, Heiner Fangerau, Jürgen Hampel, et al., eds. Fünfter Gentechnologiebericht. Nomos Verlagsgesellschaft mbH & Co. KG, 2021. http://dx.doi.org/10.5771/9783748927242.

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In the ‘Fifth Gene Technology Report’, renowned experts provide an overview of current developments and their applications in the dynamically evolving research field of gene and biotechnologies. They examine, among other topics, genetic diagnostics, somatic gene therapy, the development of vaccines, stem cell and organoid research, green gene technology, synthetic biology, gene drives, genome editing, epigenetics and single cell analysis. In addition to reporting on the current state of affairs in this field, the authors also discuss society’s perception of gene technologies and ethical and legal issues relating to them, such as genome edit-ing, cerebral organoids and big data in personalised medicine. Moreover, the interdisciplinary task force ‘Gentechnologiebericht’ (Gene Technology Report) offers recommendations on action that could be taken in relation to the key issues. With contributions by Karla Alex, Sina Bartfeld, Meik Bittkowski, Inge Broer, Lorina Buhr, Stephan Clemens, Wolfgang Van den Daele, Hans-Georg Dederer, Tobias J. Erb, Nina Gasparoni, Heiner Fangerau, Boris Fehse, Jürgen Hampel, Louise Herde, Ferdinand Hucho, Ali Jawaid, Aida Khachatryan, Sarah Kohler, Alma Kolleck, Martin Korte, Cordula Kropp, Alfons Labisch, Markus Lehmkuhl, Melanie Leidecker-Sandmann, Annette Leßmöllmann, Isabelle M. Mansuy, Lilian Marx-Stölting, Andreas Merk, Yannick Milhahn, Fruzsina Molnár-Gábor, Stefan Mundlos, Staffan Müller-Wille, Angela Osterheider, Anja Pichl, Barbara Prainsack, Jens Reich, Marlen Reinschke, Ortwin Renn, Hans-Jörg Rheinberger, Arnold Sauter, Hannah Schickl, Silke Schicktanz, Volker Stollorz, Constanze Störk-Biber, Jochen Taupitz, Jörn Walter, Eva C. Winkler, Martin Zenke and Michael M. Zwick.
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30

Wendling, Fabrice, and Fernando H. Lopes da Silva. Dynamics of EEGs as Signals of Neuronal Populations. Edited by Donald L. Schomer and Fernando H. Lopes da Silva. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190228484.003.0003.

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This chapter gives an overview of approaches used to understand the generation of electroencephalographic (EEG) signals using computational models. The basic concept is that appropriate modeling of neuronal networks, based on relevant anatomical and physiological data, allows researchers to test hypotheses about the nature of EEG signals. Here these models are considered at different levels of complexity. The first level is based on single cell biophysical properties anchored in classic Hodgkin-Huxley theory. The second level emphasizes on detailed neuronal networks and their role in generating different kinds of EEG oscillations. At the third level are models derived from the Wilson-Cowan approach, which constitutes the backbone of neural mass models. Another part of the chapter is dedicated to models of epileptiform activities. Finally, the themes of nonlinear dynamic systems and topological models in EEG generation are discussed.
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31

Ieropoulos, Ioannis A., Pablo Ledezma, Giacomo Scandroglio, Chris Melhuish, and John Greenman. Energy and metabolism. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199674923.003.0006.

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Energy resulting from metabolism is essential for any living system—from single-cell to multicellular organisms. This also applies to symbiotic robots (SymBots), which function utilizing the energy (electricity) generated by living microorganisms. In the context of living technologies, artificial symbiosis between the living and the artificial entities of the machine becomes vital for the whole system. If the living entity stops generating energy, the mechatronic system ceases to work yet it is the mechatronic system that provides the microbes with food, and gets rid of their waste. This chapter presents and discusses SymBots, based on EcoBots that operate using Microbial Fuel Cells as onboard living energy devices. The interface between science and engineering is exemplified through the study and optimization of MFCs, producing the necessary data for technological implementation. Biological inspiration stems from living organisms metabolizing and adapting to the environment (homeostasis), which is the main process transferred to engineering.
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32

Perrien, Mary, and Maureen L. O’Keefe. Disciplinary infractions and restricted housing. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199360574.003.0014.

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Misbehavior occurs within jails and prisons. It is generally handled by a formal disciplinary process. Symptoms and impairments associated with mental illness may play a role in such misbehaviour. One of the many concerns in correctional settings is the use of restricted housing units. Segregation units function as the prison within a prison. Designed for the dangerous and violent offender who cannot be managed safely within the general prison environment, segregation is characterized by single-cell confinement, with minimum time out of cell for showers and exercise (e.g., 5 hours per week). Other features include highly restricted movement, limited contact with others, and few privileges and services. Segregation has been criticized as an inhumane practice due to the degree of social isolation. Specifically, the lack of treatment, programs, and activities to engage the mind; restricted personal contact; lack of control over light and sound; lack of windows; and little or no access to the outdoors are considered to be more extreme than is required for the safe operation of prisons. The most significant issue is whether prisoners are able to psychologically adapt to the austere conditions for long periods, particularly those with mental illness. Because mentally ill inmates may be more prone to rule infractions due to manifestation of their illness, they are more likely to be segregated unless specific rules prohibit their placement. This chapter reviews segregation practices, the data on the potential impact of segregated housing on mental illness, and the role of psychiatry in the disciplinary process.
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33

Perrien, Mary, and Maureen L. O’Keefe. Disciplinary infractions and restricted housing. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199360574.003.0014_update_001.

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Misbehavior occurs within jails and prisons. It is generally handled by a formal disciplinary process. Symptoms and impairments associated with mental illness may play a role in such misbehaviour. One of the many concerns in correctional settings is the use of restricted housing units. Segregation units function as the prison within a prison. Designed for the dangerous and violent offender who cannot be managed safely within the general prison environment, segregation is characterized by single-cell confinement, with minimum time out of cell for showers and exercise (e.g., 5 hours per week). Other features include highly restricted movement, limited contact with others, and few privileges and services. Segregation has been criticized as an inhumane practice due to the degree of social isolation. Specifically, the lack of treatment, programs, and activities to engage the mind; restricted personal contact; lack of control over light and sound; lack of windows; and little or no access to the outdoors are considered to be more extreme than is required for the safe operation of prisons. The most significant issue is whether prisoners are able to psychologically adapt to the austere conditions for long periods, particularly those with mental illness. Because mentally ill inmates may be more prone to rule infractions due to manifestation of their illness, they are more likely to be segregated unless specific rules prohibit their placement. This chapter reviews segregation practices, the data on the potential impact of segregated housing on mental illness, and the role of psychiatry in the disciplinary process.
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34

Katirji, Bashar. Electromyography in Clinical Practice. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780190603434.001.0001.

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Clinical Electromyography in Clinical Practice provides case-based learning of clinical Electromyography (EMG) with a main mission of reducing the gap between theory and practice in the field of electrodiagnostic medicine. The book format includes four introductory chapters that acquaint the discipline and scope of the EMG Examination to the beginners. This include chapters on nerve conduction studies, needle EMG, and specialized testing including late responses, repetitive nerve stimulation and single fiber EMG. Discussion on the electrodiagnostic and clinical EMG findings in the numerous neuromuscular disorders including anterior horn cell disorders, peripheral neuropathies, neuromuscular junction disorders and myopathies. The second part of the book includes comprehensive presentations of 27 cases that encompass the most common disorders encountered in the EMG laboratory and are presented in a similar layout. These are subdivided into (1) focal disorders of the lower extremity, (2) focal disorders of the upper extremity, and (3) generalized neuromuscular disorders. The book focuses on problem solving through analysis of the data obtained on nerve conduction studies and needle EMG. This is meant to be a bedside analysis of data, similar to what occurs in the EMG laboratory on a daily basis. The exact values obtained on nerve conduction studies are examined and the details of the findings on needle EMG are studied. A final diagnosis is then made. This is followed by a detailed discussion of the clinical and electrodiagnostic findings of the disorder. Clinical Electromyography in Clinical Practice is an ideal book for physicians interested in learning and mastering the clinical practice of clinical EMG. This includes specialists in the field of neurology, physical medicine and rehabilitation, orthopedics, hand surgery, neurosurgery, spine, rheumatology and pain management.
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35

Rai, Dibya Prakash, ed. Advanced Materials and Nano Systems: Theory and Experiment - Part 2. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150499611220201.

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The discovery of new materials and the manipulation of their exotic properties for device fabrication is crucial for advancing technology. Nanoscience, and the creation of nanomaterials have taken materials science and electronics to new heights for the benefit of mankind. Advanced Materials and Nanosystems: Theory and Experiment covers several topics of nanoscience research. The compiled chapters aim to update students, teachers, and scientists by highlighting modern developments in materials science theory and experiments. The significant role of new materials in future technology is also demonstrated. The book serves as a reference for curriculum development in technical institutions and research programs in the field of physics, chemistry and applied areas of science like materials science, chemical engineering and electronics. This part covers 12 topics in these areas: 1. Recent advancements in nanotechnology: a human health Perspective 2. An exploratory study on characteristics of SWIRL of AlGaAs/GaAs in advanced bio based nanotechnological systems 3. Electronic structure of the half-Heusler ScAuSn, LuAuSn and their superlattice 4. Recent trends in nanosystems 5. Improvement of performance of single and multicrystalline silicon solar cell using low-temperature surface passivation layer and antireflection coating 6. Advanced materials and nanosystems 7. Effect of nanostructure-materials on optical properties of some rare earth ions doped in silica matrix 8. Nd2Fe14B and SmCO5: a permanent magnet for magnetic data storage and data transfer technology 9. Visible light induced photocatalytic activity of MWCNTS decorated sulfide based nano photocatalysts 10. Organic solar cells 11. Neodymium doped lithium borosilicate glasses 12. Comprehensive quantum mechanical study of structural features, reactivity, molecular properties and wave function-based characteristics of capmatinib
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