Cells, the basic units of biological structure and function, vary broadly in type and state. Individual cells are the building blocks of tissues, organs, and organisms. Each tissue contains cells of many types, and cells of each type can switch among biological states. Single-cell genomics, transcriptomics and epigenomics open a whole new era with the possibility to interrogate every cell of an organism in order to decipher the important biological processes that occur within. This has emerged as a ground-breaking technology that has greatly enhanced our understanding of the complexity of gene expression dynamics at a microscopic resolution. It is anticipated that in the next 5-10 years, the wider research community will be routinely employing this powerful technology as a laboratory staple. Single-cell genomics, transcriptomics and epigenomics hold the potential to revolutionize the way we characterize complex cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks. These fascinating advances have opened up a new field of cell population genomics.
Single-cell genomics, transcriptomics and epigenomics research is providing new insights into inter-cellular population genomic diversity, heterogeneity, specialization, taxonomy, spatial and temporal gene regulation, and cellular and organismal development and evolution. It is facilitating plant breeding, understanding of human disease conditions and personalized medicine. This book discusses the perspectives, progress, and promises of single-cell genomics, transcriptomics and epigenomics research and applications in addressing the above and other key biological aspects in all organisms. It establishes the current state-of-the-field and serves as the foundation for future developments in single-cell genomics, transcriptomics, and epigenomics.
Preface
I. Introduction
1 Single-Cell Genomics, Transcriptomics and Epigenomics: Current State and Future PerspectivesProf. Parwinder KaurProf. Om P. RajoraDr. Sarah A. Teichmann, Wellcome Trust Sanger Institute, UK
II. Single-Cell Genomics Technologies and Experimental Designs
2 Single-cell genomicsProf. Stephen R. Quake, Stanford, California 94304, USAProf. Paul Soloway, Cornell University, USADr. Robert Salomon, IBMD, University of Technology, Sydney, Australia
3 Single-cell transcriptomicsDr. Christoph Ziegenhain, Ludwig-Maximilians University, Germany
4 Single-cell epigenomicsProf. Amos Tanay, Weizmann Institute, Israel
5 Single-cell metagenomicsProf. Andrew C. Tolonen, Broad Institute of MIT and Harvard University, USA
6 Single-cell Hi-CProf. Erez Aiden Lieberman and Dr. Olga Dudchenko, Baylor College of Medicine, USA
7 Single-cell ATAC-SeqProf. Paul Soloway, Cornell University, USA
8 Practical considerations for designing single-cell experimentsDr. David Gallgo Ortega, Garvan Institute of Medical Research, Australia
III. Single-Cell Omics Data Analysis and Bioinformatics
9 Visualization of single-cell genomic, transcriptomic and epigenomic data Prof. Evan W Newell, Singapore.Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
10 Addressing the problem of large single-cell genomic, transcriptomic and epigenomic data Dr. Bhavna Hurgobin and Prof. Parwinder Kaur, WAU, Australia
11 Data analysis tools and statistical methods Prof. Alicia Oshlack, WEHI/MCRI, Australia
12 Role of Artificial Intelligence (AI) and deep learning Dr. Andrew Butler, Shiwei Zheng NYGC, New York University, USA
13 Overview of clustering methods and batch effects in single-cell RNA Sequencing Dr. Kim-Anh Le Cao, University of Melbourne, Australia
14 Best practices for single-cell RNA-Seq data analysis Prof. Martin Hemberg, Wellcome Trust Sanger Institute, UK
15 Advanced disease modeling Dr. Paulina M. Strzelecka, Wellcome Trust Sanger Institute, UK
IV. Inter-cellular Population Genomic Diversity, Specialization and Taxonomy
16 Tracking mutations, copy number variations, and chromosomal aberrations at the single-cell level Dr. Stephanie Lauer, NYU, USA
17 Defining cell types and states from single-cell genomics Prof. Cole Trapnell, University of Washington, USA
18 Unravelling single cell heterogeneity using single-cell RNA sequencing and understanding function of cellular specialization Prof. Qiaolin Deng, , Karolinska Institutet, Sweden; Prof. Evan Z. Macosko, Broad Institute of MIT and Harvard, USA
19 Building a taxonomy of the cells Prof. David Scadden, Massachusetts General Hospital/Harvard University, USA
20 Characterization of the epigenetic landscape of cellular populations Prof. Richard Bonneau, New York University, USAProf. Jason D. Buenrostro, Stanford University School of Medicine, USA
21 Microbial population genetics using single-cell genomics Prof. Karin Rengefors, Lund University, Sweden
V. Spatial and Temporal Gene Regulation Dynamics
22 Spatial and temporal gene regulation dynamics at the single-cell level Dr. Andreas Sagner, The Francis Crick Institute, UK
23 Single-cell spatial and temporal gene expression patterns in mice Dr. Chen-Hsiang Yeang, Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan
24 Single-cell spatial and temporal gene expression patterns in humans Prof. Stefan Semrau, Leiden University, The Netherlands
VI. Development, Regeneration and Evolution Perspectives
25 New insights into cellular development and evolution from single-cell genomics Dr. Detlev Arendt, University of Heidelberg, Germany and Dr. Jeff Farrell, Harvard University, USA
26 Assessing embryo development and regeneration via single-cell RNA-Seq Prof. Richard M. Harland, University of California, Berkeley, Berkeley, USA.
27 Reconstructing lineages from single-cell genomics Dr. Michael A. Lodato, Harvard Medical School, USA
VII. Human Diseases and Medicine Perspectives
28 Understanding human diseases using single-cell omics approaches Prof. Rong Fan, Yale University, USA
29 Single-cell omics for personalized medicine Prof. Mikael Benson, Linkoping University, Sweden
30 Advancing understanding of cancer using single-cell transcriptomics Dr. Fatima Valdes Mora, Garvan Institute of Medical Research, Australia
31 Dissecting Alzheimer's disease at the single-cell level Prof. Li-Huei Tsai, Broad Institute of MIT and Harvard, USA
32 Single-cell mass cytometry of differential immune and drug responses Dr. Sean C. Bendall, Stanford University, USA
VIII. Plant Genetics and Breeding Perspectives
33 Challenges and opportunities of single-cell genomics, transcriptomics and epigenomics in plants Prof. Ryan Lister, UWA, Australia
34 Systems biology of plants at the single-cell level Prof. John Schiefelbein, University of Michigan, USA
35 Single-cell genomics for new and enhanced green revolution Dr. Jack Satterlee and Prof. Michael Scanlon, Cornell University, USA
IX. Integration of Single-cell Genomics, Transcriptomics and Epigenomics
36 Single-cell genome, transcriptome and epigenome sequencing Prof. Wolf Reik, Wellcome Trust Sanger Institute, UK
37 Integration and harmonization of single-cell genomic, transcriptomic and epigenomic data Dr. Rahul Satija, NYGC/NYU, USA
38 Integration of single cell RNA-Seq with CRISPR/Cas9 Prof. Alexander F. Schier, Broad Institute of MIT and Harvard, USA
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