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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.

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  2. In biomedical research, validating a scientific discovery hinges on the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility remain imprecise....

    Authors: Pelin Icer Baykal, Paweł Piotr Łabaj, Florian Markowetz, Lynn M. Schriml, Daniel J. Stekhoven, Serghei Mangul and Niko Beerenwinkel
    Citation: Genome Biology 2024 25:213
    Content type: Review Published on:

  3. Genomic data holds huge potential for medical progress but requires strict safety measures due to its sensitive nature to comply with data protection laws. This conflict is especially pronounced in genome-wide...

    Authors: Alissa Brauneck, Louisa Schmalhorst, Stefan Weiss, Linda Baumbach, Uwe Völker, David Ellinghaus, Jan Baumbach and Gabriele Buchholtz
    Citation: Genome Biology 2024 25:154
    Content type: Review Published on:

    The Author Correction to this article has been published in Genome Biology 2024 25:160

  4. Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of geno...

    Authors: Jacob Montgomery, Sarah Morran, Dana R. MacGregor, J. Scott McElroy, Paul Neve, Célia Neto, Martin M. Vila-Aiub, Maria Victoria Sandoval, Analia I. Menéndez, Julia M. Kreiner, Longjiang Fan, Ana L. Caicedo, Peter J. Maughan, Bianca Assis Barbosa Martins, Jagoda Mika, Alberto Collavo…
    Citation: Genome Biology 2024 25:139
    Content type: Review Published on:

  5. The history of yeast Saccharomyces cerevisiae, aka brewer’s or baker’s yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, ye...

    Authors: Hamid Kian Gaikani, Monika Stolar, Divya Kriti, Corey Nislow and Guri Giaever
    Citation: Genome Biology 2024 25:10
    Content type: Review Published on:

  6. Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges imped...

    Authors: Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks and Kristen R. Maynard
    Citation: Genome Biology 2023 24:288
    Content type: Review Published on:

  7. Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future ...

    Authors: Sina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, Fritz J. Sedlazeck and Medhat Mahmoud
    Citation: Genome Biology 2023 24:221
    Content type: Review Published on:

  8. It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend fra...

    Authors: Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux and Camille Marchet
    Citation: Genome Biology 2023 24:133
    Content type: Review Published on:

  9. Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be “silent,” but mounting evidence has revealed that these variants can cause RNA and prote...

    Authors: Brian C. Lin, Upendra Katneni, Katarzyna I. Jankowska, Douglas Meyer and Chava Kimchi-Sarfaty
    Citation: Genome Biology 2023 24:126
    Content type: Review Published on:

  11. Ageing is inherent to all human beings, yet why we age remains a hotly contested topic. Most mechanistic explanations of ageing posit that ageing is caused by the accumulation of one or more forms of molecular...

    Authors: João Pedro de Magalhães
    Citation: Genome Biology 2023 24:51
    Content type: Review Published on:

  12. The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary struc...

    Authors: Ilias Georgakopoulos-Soares, Candace S. Y. Chan, Nadav Ahituv and Martin Hemberg
    Citation: Genome Biology 2022 23:159
    Content type: Review Published on:

    The Author Correction to this article has been published in Genome Biology 2022 23:164

  16. Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptom...

    Authors: Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol C. Shetty, Anup Mahurkar and Julie C. Dunning Hotopp
    Citation: Genome Biology 2021 22:121
    Content type: Review Published on:

  17. Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromo...

    Authors: Ruqian Lyu, Vanessa Tsui, Davis J. McCarthy and Wayne Crismani
    Citation: Genome Biology 2021 22:112
    Content type: Review Published on:

  18. Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs ar...

    Authors: Anil Panigrahi and Bert W. O’Malley
    Citation: Genome Biology 2021 22:108
    Content type: Review Published on:

  22. Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to ...

    Authors: Rafael Della Coletta, Yinjie Qiu, Shujun Ou, Matthew B. Hufford and Candice N. Hirsch
    Citation: Genome Biology 2021 22:3
    Content type: Review Published on:

  23. 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:

  24. 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:

  27. 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 Published on:

  28. 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 Published on:

  29. “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 Published on:

  31. 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 Published on:

  32. 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:

  34. 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 Published on:

  35. 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:

  37. 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 Published on:

  40. 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:

  43. 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:

  44. 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

  47. 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 Published on:

  48. 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:

  49. 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: