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Page 6 of 126

  1. Content type: Correction

    Upon publication of the original article [1], it was noted that references 11 and 22 were miscited in the reference list.

    Authors: Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai…

    Citation: Genome Biology 2017 18:214

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    The original article was published in Genome Biology 2017 18:142

  2. Content type: Method

    Single-cell RNA-sequencing (scRNA-seq) allows studying heterogeneity in gene expression in large cell populations. Such heterogeneity can arise due to technical or biological factors, making decomposing source...

    Authors: Florian Buettner, Naruemon Pratanwanich, Davis J. McCarthy, John C. Marioni and Oliver Stegle

    Citation: Genome Biology 2017 18:212

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  3. Content type: Research

    Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-r...

    Authors: Seungill Kim, Jieun Park, Seon-In Yeom, Yong-Min Kim, Eunyoung Seo, Ki-Tae Kim, Myung-Shin Kim, Je Min Lee, Kyeongchae Cheong, Ho-Sub Shin, Saet-Byul Kim, Koeun Han, Jundae Lee, Minkyu Park, Hyun-Ah Lee, Hye-Young Lee…

    Citation: Genome Biology 2017 18:210

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  4. 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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  5. 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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  6. 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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  7. Content type: Research

    Polycomb Repressive Complexes 2 (PRC2) are multi-protein chromatin modifiers that are evolutionarily conserved among eukaryotes and play key roles in the regulation of gene expression, notably through the trim...

    Authors: Claudia Chica, Alexandra Louis, Hugues Roest Crollius, Vincent Colot and François Roudier

    Citation: Genome Biology 2017 18:207

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  8. Content type: Research

    All mRNAs are bound in vivo by proteins to form mRNA–protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, ...

    Authors: Olivia S. Rissland, Alexander O. Subtelny, Miranda Wang, Andrew Lugowski, Beth Nicholson, John D. Laver, Sachdev S. Sidhu, Craig A. Smibert, Howard D. Lipshitz and David P. Bartel

    Citation: Genome Biology 2017 18:211

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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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