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  1. Content type: Review

    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

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  2. Content type: Research

    Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ...

    Authors: Emanuel Wyler, Jennifer Menegatti, Vedran Franke, Christine Kocks, Anastasiya Boltengagen, Thomas Hennig, Kathrin Theil, Andrzej Rutkowski, Carmelo Ferrai, Laura Baer, Lisa Kermas, Caroline Friedel, Nikolaus Rajewsky, Altuna Akalin, Lars Dölken, Friedrich Grässer…

    Citation: Genome Biology 2017 18:209

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  3. Content type: Research

    Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding land...

    Authors: Katja Meyer, Tino Köster, Christine Nolte, Claus Weinholdt, Martin Lewinski, Ivo Grosse and Dorothee Staiger

    Citation: Genome Biology 2017 18:204

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  4. Content type: Research

    Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few...

    Authors: Alexandre P. Marand, Shelley H. Jansky, Hainan Zhao, Courtney P. Leisner, Xiaobiao Zhu, Zixian Zeng, Emily Crisovan, Linsey Newton, Andy J. Hamernik, Richard E. Veilleux, C. Robin Buell and Jiming Jiang

    Citation: Genome Biology 2017 18:203

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  5. Content type: Research

    Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of protein variants or to the regulation of gene expression via nonsense-mediated messenger RNA (mRNA) dec...

    Authors: Baptiste Saudemont, Alexandra Popa, Joanna L. Parmley, Vincent Rocher, Corinne Blugeon, Anamaria Necsulea, Eric Meyer and Laurent Duret

    Citation: Genome Biology 2017 18:208

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  6. Content type: Research

    Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5′ cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with indi...

    Authors: Joseph L. Costello, Christopher J. Kershaw, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Christopher M. Grant, Simon J. Hubbard and Graham D. Pavitt

    Citation: Genome Biology 2017 18:201

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  7. Content type: Research

    It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long non-coding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and s...

    Authors: Oskar Marín-Béjar, Aina M. Mas, Jovanna González, Dannys Martinez, Alejandro Athie, Xabier Morales, Mikel Galduroz, Ivan Raimondi, Elena Grossi, Shuling Guo, Ana Rouzaut, Igor Ulitsky and Maite Huarte

    Citation: Genome Biology 2017 18:202

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  8. Content type: Method

    The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method, scDual-Seq, that simultaneously...

    Authors: Gal Avital, Roi Avraham, Amy Fan, Tamar Hashimshony, Deborah T. Hung and Itai Yanai

    Citation: Genome Biology 2017 18:200

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  9. Content type: Method

    Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning a...

    Authors: Dina Hafez, Aslihan Karabacak, Sabrina Krueger, Yih-Chii Hwang, Li-San Wang, Robert P. Zinzen and Uwe Ohler

    Citation: Genome Biology 2017 18:199

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  10. Content type: Research

    Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted fr...

    Authors: Dei M. Elurbe, Sarita S. Paranjpe, Georgios Georgiou, Ila van Kruijsbergen, Ozren Bogdanovic, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen and Gert Jan C. Veenstra

    Citation: Genome Biology 2017 18:198

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  11. Content type: Review

    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

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  12. Content type: Research

    Most cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically...

    Authors: Song Liu, Yuwen Liu, Qin Zhang, Jiayu Wu, Junbo Liang, Shan Yu, Gong-Hong Wei, Kevin P. White and Xiaoyue Wang

    Citation: Genome Biology 2017 18:194

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  13. Content type: Research Highlight

    Concentration is important and not only while driving; a new study indicates how an adjacent genomic element helps to increase the efficiency of a specific adenosine to inosine RNA editing reaction, by providi...

    Authors: Miri Danan-Gotthold and Erez Y. Levanon

    Citation: Genome Biology 2017 18:196

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  14. Content type: Research

    Recombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, ...

    Authors: Yaping Liu, Abhishek Sarkar, Pouya Kheradpour, Jason Ernst and Manolis Kellis

    Citation: Genome Biology 2017 18:193

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  15. Content type: Research

    There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

    Authors: Hung-ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton and Patrick S. Schnable

    Citation: Genome Biology 2017 18:192

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  16. Content type: Method

    High-fidelity SpCas9 variants (eSpCas9 and SpCas9-HF1) have been engineered to reduce off-target effects. We found that changes in guide RNA length induced significant reductions in the editing activities of S...

    Authors: Dingbo Zhang, Huawei Zhang, Tingdong Li, Kunling Chen, Jin-Long Qiu and Caixia Gao

    Citation: Genome Biology 2017 18:191

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  17. Content type: Research

    The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of...

    Authors: Péter István Kulcsár, András Tálas, Krisztina Huszár, Zoltán Ligeti, Eszter Tóth, Nóra Weinhardt, Elfrieda Fodor and Ervin Welker

    Citation: Genome Biology 2017 18:190

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  18. Content type: Research

    The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene r...

    Authors: Roberta Tarallo, Giorgio Giurato, Giuseppina Bruno, Maria Ravo, Francesca Rizzo, Annamaria Salvati, Luca Ricciardi, Giovanna Marchese, Angela Cordella, Teresa Rocco, Valerio Gigantino, Biancamaria Pierri, Giovanni Cimmino, Luciano Milanesi, Concetta Ambrosino, Tuula A. Nyman…

    Citation: Genome Biology 2017 18:189

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  19. Content type: Review

    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

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  20. Content type: Research

    Adenosine to inosine (A-to-I) RNA editing is a post-transcriptional modification catalyzed by the ADAR (adenosine deaminase that acts on RNA) enzymes, which are ubiquitously expressed among metazoans. Technica...

    Authors: Hagit T. Porath, Binyamin A. Knisbacher, Eli Eisenberg and Erez Y. Levanon

    Citation: Genome Biology 2017 18:185

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