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  1. Content type: Research

    Piwi-interacting RNAs (piRNAs) are a class of short (~26–31-nucleotide) non-protein-coding RNAs expressed in the metazoan germline. The piRNA pathway in arthropods is best understood in the ovary of Drosophila me...

    Authors: Maria Ninova, Sam Griffiths-Jones and Matthew Ronshaugen

    Citation: Genome Biology 2017 18:184

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  2. Content type: Research

    Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mam...

    Authors: Daniel Bouyer, Amira Kramdi, Mohamed Kassam, Maren Heese, Arp Schnittger, François Roudier and Vincent Colot

    Citation: Genome Biology 2017 18:179

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  3. Content type: Research

    One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classif...

    Authors: Alexa B. R. McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A. Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi…

    Citation: Genome Biology 2017 18:182

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  4. Content type: Method

    We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin ...

    Authors: Christopher Quince, Tom O. Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E. Darling, Gavin Collins and A. Murat Eren

    Citation: Genome Biology 2017 18:181

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  5. Content type: Research

    The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA poly...

    Authors: Kevin Van Bortle, Douglas H. Phanstiel and Michael P. Snyder

    Citation: Genome Biology 2017 18:180

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  6. Content type: Research

    DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global pa...

    Authors: Yung-Hsin Huang, Jianzhong Su, Yong Lei, Lorenzo Brunetti, Michael C. Gundry, Xiaotian Zhang, Mira Jeong, Wei Li and Margaret A. Goodell

    Citation: Genome Biology 2017 18:176

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  7. Content type: Research

    Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of input...

    Authors: Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey and James Whelan

    Citation: Genome Biology 2017 18:172

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  8. Content type: Research

    Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases.

    Authors: Matthias Heinig, Michiel E. Adriaens, Sebastian Schafer, Hanneke W. M. van Deutekom, Elisabeth M. Lodder, James S. Ware, Valentin Schneider, Leanne E. Felkin, Esther E. Creemers, Benjamin Meder, Hugo A. Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron…

    Citation: Genome Biology 2017 18:170

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  9. Content type: Open Letter

    Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. We show that this information is essential to...

    Authors: Chakravarthi Kanduri, Diana Domanska, Eivind Hovig and Geir Kjetil Sandve

    Citation: Genome Biology 2017 18:175

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  10. Content type: Method

    As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current...

    Authors: Luke Zappia, Belinda Phipson and Alicia Oshlack

    Citation: Genome Biology 2017 18:174

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  11. Content type: Method

    Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-...

    Authors: Yang Eric Li, Mu Xiao, Binbin Shi, Yu-Cheng T. Yang, Dong Wang, Fei Wang, Marco Marcia and Zhi John Lu

    Citation: Genome Biology 2017 18:169

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  12. Content type: Research

    The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the divers...

    Authors: Hamed S. Najafabadi, Michael Garton, Matthew T. Weirauch, Sanie Mnaimneh, Ally Yang, Philip M. Kim and Timothy R. Hughes

    Citation: Genome Biology 2017 18:167

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  13. Content type: Research

    Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most i...

    Authors: Jacki E. Heraud-Farlow, Alistair M. Chalk, Sandra E. Linder, Qin Li, Scott Taylor, Joshua M. White, Lokman Pang, Brian J. Liddicoat, Ankita Gupte, Jin Billy Li and Carl R. Walkley

    Citation: Genome Biology 2017 18:166

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  14. Content type: Software

    Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cell...

    Authors: Mariana Gómez-Schiavon, Liang-Fu Chen, Anne E. West and Nicolas E. Buchler

    Citation: Genome Biology 2017 18:164

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  15. Content type: Research

    Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4+ T cells. Linking such regulatory regions to gene promoters in disease-relevant cell context...

    Authors: Oliver S. Burren, Arcadio Rubio García, Biola-Maria Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas J. Cooper, John J. Lambourne, Ellen Schofield, Xaquin Castro Dopico, Ricardo C. Ferreira, Richard Coulson, Frances Burden, Sophia P. Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini…

    Citation: Genome Biology 2017 18:165

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  16. Content type: Research

    Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential sourc...

    Authors: Hadas Hezroni, Rotem Ben-Tov Perry, Zohar Meir, Gali Housman, Yoav Lubelsky and Igor Ulitsky

    Citation: Genome Biology 2017 18:162

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Page 7 of 247