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Reviews

Recent Reviews published in Genome Biology

This list will be updated with all our new Reviews. Genome Biology publishes Reviews that are open access and therefore free to read and share.

  1. Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long...

    Authors: Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie and Quentin Gouil

    Citation: Genome Biology 2020 21:30

    Content type: Review

    Published on:

  2. The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different ty...

    Authors: Zibo Zhao and Ali Shilatifard

    Citation: Genome Biology 2019 20:245

    Content type: Review

    Published on:

  5. Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of geno...

    Authors: Guillaume Bourque, Kathleen H. Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L. Levin, Todd S. Macfarlan, Dixie L. Mager and Cédric Feschotte

    Citation: Genome Biology 2018 19:199

    Content type: Review

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  6. Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools...

    Authors: Mona Schreiber, Nils Stein and Martin Mascher

    Citation: Genome Biology 2018 19:140

    Content type: Review

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  7. “Conservation genomics” encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, ...

    Authors: Megan A. Supple and Beth Shapiro

    Citation: Genome Biology 2018 19:131

    Content type: Review

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  9. Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the res...

    Authors: Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan and Curtis Huttenhower

    Citation: Genome Biology 2017 18:228

    Content type: Review

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  10. A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (ln...

    Authors: Francesco P. Marchese, Ivan Raimondi and Maite Huarte

    Citation: Genome Biology 2017 18:206

    Content type: Review

    Published on:

  12. RNA contains over 150 types of chemical modifications. Although many of these chemical modifications were discovered several decades ago, their functions were not immediately apparent. Discoveries of RNA demet...

    Authors: Phillip J. Hsu, Hailing Shi and Chuan He

    Citation: Genome Biology 2017 18:197

    Content type: Review

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  13. Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of ...

    Authors: Andrzej Zielezinski, Susana Vinga, Jonas Almeida and Wojciech M. Karlowski

    Citation: Genome Biology 2017 18:186

    Content type: Review

    Published on:

  15. Studies on genetic–epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in ...

    Authors: Catherine Do, Alyssa Shearer, Masako Suzuki, Mary Beth Terry, Joel Gelernter, John M. Greally and Benjamin Tycko

    Citation: Genome Biology 2017 18:120

    Content type: Review

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  18. High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which ...

    Authors: Yehudit Hasin, Marcus Seldin and Aldons Lusis

    Citation: Genome Biology 2017 18:83

    Content type: Review

    Published on:

  21. High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation fr...

    Authors: Galip Gürkan Yardımcı and William Stafford Noble

    Citation: Genome Biology 2017 18:26

    Content type: Review

    Published on:

  22. Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on ...

    Authors: Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier and Frank Johannes

    Citation: Genome Biology 2016 17:264

    Content type: Review

    Published on:

    The Erratum to this article has been published in Genome Biology 2017 18:41

  25. Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect size...

    Authors: Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez and Rob Knight

    Citation: Genome Biology 2016 17:217

    Content type: Review

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  26. Chromosome conformation capture (3C)-based techniques have revolutionized the field of nuclear organization, partly replacing DNA FISH as the method of choice for studying three-dimensional chromosome architec...

    Authors: Luca Giorgetti and Edith Heard

    Citation: Genome Biology 2016 17:215

    Content type: Review

    Published on:

  27. We are entering an era of epigenome engineering. The precision manipulation of chromatin and epigenetic modifications provides new ways to interrogate their influence on genome and cell function and to harness...

    Authors: Minhee Park, Albert J. Keung and Ahmad S. Khalil

    Citation: Genome Biology 2016 17:183

    Content type: Review

    Published on:

  29. Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish nove...

    Authors: Patricia Gerdes, Sandra R. Richardson, Dixie L. Mager and Geoffrey J. Faulkner

    Citation: Genome Biology 2016 17:100

    Content type: Review

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  30. Almost 20 % of all infectious human diseases are vector borne and, together, are responsible for over one million deaths per annum. Over the past decade, the decreasing costs of massively parallel sequencing t...

    Authors: David C. Rinker, R. Jason Pitts and Laurence J. Zwiebel

    Citation: Genome Biology 2016 17:95

    Content type: Review

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  31. Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequenc...

    Authors: Lu Wen and Fuchou Tang

    Citation: Genome Biology 2016 17:71

    Content type: Review

    Published on:

  35. We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of

    Authors: Jonathan F. Wendel, Scott A. Jackson, Blake C. Meyers and Rod A. Wing

    Citation: Genome Biology 2016 17:37

    Content type: Review

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  36. RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, ...

    Authors: Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang and Ali Mortazavi

    Citation: Genome Biology 2016 17:13

    Content type: Review

    Published on:

    The Erratum to this article has been published in Genome Biology 2016 17:181