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  1. Content type: Research

    The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation ...

    Authors: Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter W. J. Rigby, Damien P. Devos, Jose L. Gómez-Skarmeta and Jaime J. Carvajal

    Citation: Genome Biology 2017 18:106

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  2. Content type: Research

    The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversificat...

    Authors: Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A. M. Martin, Peter W. H. Holland, Simen R. Sandve and Daniel J. Macqueen

    Citation: Genome Biology 2017 18:111

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  3. Content type: Research

    The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations...

    Authors: Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G. Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi…

    Citation: Genome Biology 2017 18:110

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  4. Content type: Method

    CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exo...

    Authors: Haiwei Mou, Jordan L. Smith, Lingtao Peng, Hao Yin, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M. Ozata, Yingxiang Li, Daniel G. Anderson, Charles P. Emerson, Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng…

    Citation: Genome Biology 2017 18:108

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  5. Content type: Correspondence

    Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that hav...

    Authors: Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Ken Pendavis, Shane C. Burgess, Manfred Grabherr, Miriam Friedman-Einat and Leif Andersson

    Citation: Genome Biology 2017 18:112

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  6. Content type: Research

    Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out f...

    Authors: Agnieszka P. Lipinska, Nicholas R. T. Toda, Svenja Heesch, Akira F. Peters, J. Mark Cock and Susana M. Coelho

    Citation: Genome Biology 2017 18:104

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  7. Content type: Research

    The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and...

    Authors: Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He and Heng Zhang

    Citation: Genome Biology 2017 18:103

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  8. Content type: Research

    Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produc...

    Authors: Qingxin Song, Tianzhen Zhang, David M. Stelly and Z. Jeffrey Chen

    Citation: Genome Biology 2017 18:99

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  9. Content type: Method

    We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide m...

    Authors: Gleb Kuznetsov, Daniel B. Goodman, Gabriel T. Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J. Lajoie and George M. Church

    Citation: Genome Biology 2017 18:100

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  10. Content type: Software

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a...

    Authors: Daniel B. Goodman, Gleb Kuznetsov, Marc J. Lajoie, Brian W. Ahern, Michael G. Napolitano, Kevin Y. Chen, Changping Chen and George M. Church

    Citation: Genome Biology 2017 18:101

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  11. Content type: Research

    Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that ...

    Authors: Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu…

    Citation: Genome Biology 2017 18:98

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  12. Content type: Research Highlight

    Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.

    Authors: Gabriel J. Sandoval and William C. Hahn

    Citation: Genome Biology 2017 18:95

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  13. Content type: Research

    Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enri...

    Authors: Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen and Frédéric Berger

    Citation: Genome Biology 2017 18:94

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  14. Content type: Research

    Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Condit...

    Authors: Rolen M. Quadros, Hiromi Miura, Donald W. Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P. Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M. Buckley, Parthasarathy Seshacharyulu, Surinder K. Batra, Mark A. Behlke, Sarah A. Zeiner, Ashley M. Jacobi…

    Citation: Genome Biology 2017 18:92

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