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. 

<b>Preface</b><br><b>I. Introduction</b><b><br></b>1Single-Cell Genomics, Transcriptomics and Epigenomics: Current State and Future PerspectivesProf. Parwinder KaurProf. Om P. RajoraDr. Sarah A. Teichmann, Wellcome Trust Sanger Institute, UK<br><b>II.Single-Cell Genomics Technologies and Experimental Designs</b><br>2Single-cell genomicsProf. Stephen R. Quake, Stanford, California 94304, USAProf. Paul Soloway, Cornell University, USADr. Robert Salomon, IBMD, University of Technology, Sydney, Australia<br>3Single-cell transcriptomicsDr. Christoph Ziegenhain, Ludwig-Maximilians University, Germany<br>4Single-cell epigenomicsProf. Amos Tanay, Weizmann Institute,  Israel<br>5Single-cell metagenomicsProf. Andrew C. Tolonen, Broad Institute of MIT and Harvard University, USA<br>6Single-cell Hi-CProf. Erez Aiden Lieberman and Dr. Olga Dudchenko, Baylor College of Medicine, USA<br>7Single-cell ATAC-SeqProf. Paul Soloway, Cornell University, USA<br>8Practical considerations for designing single-cell experimentsDr. David Gallgo Ortega, Garvan Institute of Medical Research, Australia<br><b>III.Single-Cell Omics Data Analysis and Bioinformatics  </b><br>9Visualization of single-cell genomic, transcriptomic and epigenomic dataProf. Evan W Newell, Singapore.Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.<br>10Addressing the problem of large single-cell genomic, transcriptomic and epigenomic data Dr. Bhavna Hurgobin and Prof. Parwinder Kaur, WAU, Australia<br>11Data analysis tools and statistical methodsProf. Alicia Oshlack, WEHI/MCRI, Australia<br>12Role of Artificial Intelligence (AI) and deep learningDr. Andrew Butler, Shiwei Zheng NYGC, New York University, USA<br>13Overview of clustering methods and batch effects in single-cell RNA SequencingDr. Kim-Anh Le Cao, University of Melbourne, Australia<br>14Best practices for single-cell RNA-Seq data analysisProf. Martin Hemberg, Wellcome Trust Sanger Institute, UK<br>15Advanced disease modelingDr. Paulina M. Strzelecka, Wellcome Trust Sanger Institute, UK<br><b>IV.Inter-cellular Population Genomic Diversity, Specialization and Taxonomy</b><br>16Tracking mutations, copy number variations, and chromosomal aberrations at the single-cell levelDr. Stephanie Lauer, NYU, USA<br>17Defining cell types and states from single-cell genomicsProf. Cole Trapnell, University of Washington, USA<br>18Unravelling single cell heterogeneity using single-cell RNA sequencing and understanding function of cellular specializationProf. Qiaolin Deng, , Karolinska Institutet, Sweden; Prof. Evan Z. Macosko, Broad Institute of MIT and Harvard, USA<br>19Building a taxonomy of the cellsProf. David Scadden, Massachusetts General Hospital/Harvard University, USA<br>20Characterization of the epigenetic landscape of cellular populationsProf. Richard Bonneau, New York University, USAProf. Jason D. Buenrostro, Stanford University School of Medicine, USA<br>21Microbial population genetics using single-cell genomicsProf. Karin Rengefors, Lund University, Sweden<br><b>V.Spatial and Temporal Gene Regulation Dynamics</b><br>22Spatial and temporal gene regulation dynamics at the single-cell level  Dr. Andreas Sagner, The Francis Crick Institute, UK<br>23Single-cell spatial and temporal gene expression patterns in miceDr. Chen-Hsiang Yeang, Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan<br>24Single-cell spatial and temporal gene expression patterns in humansProf. Stefan Semrau, Leiden University, The Netherlands<br><b>VI.Development, Regeneration and Evolution Perspectives</b><br>25New insights into cellular development and evolution from single-cell genomicsDr. Detlev Arendt, University of Heidelberg, Germany and Dr. Jeff Farrell, Harvard University, USA<br>26Assessing embryo development and regeneration via single-cell RNA-SeqProf. Richard M. Harland, University of California, Berkeley, Berkeley, USA.<br>27Reconstructing lineages from single-cell genomicsDr. Michael A. Lodato, Harvard Medical School, USA<br><b>VII.Human Diseases and Medicine Perspectives</b><br>28Understanding human diseases using single-cell omics approachesProf. Rong Fan, Yale University, USA<br>29Single-cell omics for personalized medicineProf. Mikael Benson, Linkoping University, Sweden<br>30Advancing understanding of cancer using single-cell transcriptomicsDr. Fatima Valdes Mora, Garvan Institute of Medical Research, Australia<br>31Dissecting Alzheimer's disease at the single-cell levelProf. Li-Huei Tsai, Broad Institute of MIT and Harvard, USA<br>32Single-cell mass cytometry of differential immune and drug responsesDr. Sean C. Bendall, Stanford University, USA<br><b>VIII.Plant Genetics and Breeding Perspectives</b><br>33Challenges and opportunities of single-cell genomics, transcriptomics and epigenomics in plantsProf. Ryan Lister, UWA, Australia<br>34Systems biology of plants at the single-cell levelProf. John Schiefelbein, University of Michigan, USA<br>35Single-cell genomics for new and enhanced green revolutionDr. Jack Satterlee and Prof. Michael Scanlon, Cornell University, USA<br><b>IX.Integration of Single-cell Genomics, Transcriptomics and Epigenomics</b><br>36Single-cell genome, transcriptome and epigenome sequencingProf. Wolf Reik, Wellcome Trust Sanger Institute, UK<br>37Integration and harmonization of single-cell genomic, transcriptomic and epigenomic dataDr. Rahul Satija, NYGC/NYU, USA<br>38Integration of single cell RNA-Seq with CRISPR/Cas9Prof. Alexander F. Schier, Broad Institute of MIT and Harvard, USA<br><b>Index</b>