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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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  17. Content type: Research

    Soybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both corr...

    Authors: Chao Fang, Yanming Ma, Shiwen Wu, Zhi Liu, Zheng Wang, Rui Yang, Guanghui Hu, Zhengkui Zhou, Hong Yu, Min Zhang, Yi Pan, Guoan Zhou, Haixiang Ren, Weiguang Du, Hongrui Yan, Yanping Wang…

    Citation: Genome Biology 2017 18:161

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  18. Content type: Research

    As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. Ho...

    Authors: Chenjiang You, Jie Cui, Hui Wang, Xinping Qi, Li-Yaung Kuo, Hong Ma, Lei Gao, Beixin Mo and Xuemei Chen

    Citation: Genome Biology 2017 18:158

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  19. Content type: Research

    The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation...

    Authors: Wangsheng Zhu, Bo Hu, Claude Becker, Ezgi Süheyla Doğan, Kenneth Wayne Berendzen, Detlef Weigel and Chang Liu

    Citation: Genome Biology 2017 18:157

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  20. Content type: Research

    Differences in DNA methylation can arise as epialleles, which are loci that differ in chromatin state and are inherited over generations. Epialleles offer an additional source of variation that can affect phen...

    Authors: Brigitte T. Hofmeister, Kevin Lee, Nicholas A. Rohr, David W. Hall and Robert J. Schmitz

    Citation: Genome Biology 2017 18:155

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  21. Content type: Research

    Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characteriz...

    Authors: Amin Emad, Junmei Cairns, Krishna R. Kalari, Liewei Wang and Saurabh Sinha

    Citation: Genome Biology 2017 18:153

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  22. Content type: Method

    Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error est...

    Authors: Alan F. Rubin, Hannah Gelman, Nathan Lucas, Sandra M. Bajjalieh, Anthony T. Papenfuss, Terence P. Speed and Douglas M. Fowler

    Citation: Genome Biology 2017 18:150

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    The Correction to this article has been published in Genome Biology 2018 19:17

  23. Content type: Method

    RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene leve...

    Authors: Koen Van den Berge, Charlotte Soneson, Mark D. Robinson and Lieven Clement

    Citation: Genome Biology 2017 18:151

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  24. Content type: Research

    The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activat...

    Authors: Pierre J. Fabre, Marion Leleu, Benjamin H. Mormann, Lucille Lopez-Delisle, Daan Noordermeer, Leonardo Beccari and Denis Duboule

    Citation: Genome Biology 2017 18:149

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  25. Content type: Method

    Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTran...

    Authors: Nadia M. Davidson, Anthony D. K. Hawkins and Alicia Oshlack

    Citation: Genome Biology 2017 18:148

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    The Erratum to this article has been published in Genome Biology 2017 18:160

  26. Content type: Research

    Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic ...

    Authors: Artika P. Nath, Scott C. Ritchie, Sean G. Byars, Liam G. Fearnley, Aki S. Havulinna, Anni Joensuu, Antti J. Kangas, Pasi Soininen, Annika Wennerström, Lili Milani, Andres Metspalu, Satu Männistö, Peter Würtz, Johannes Kettunen, Emma Raitoharju, Mika Kähönen…

    Citation: Genome Biology 2017 18:146

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  27. Content type: Research

    Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate a...

    Authors: Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo and Frank Alber

    Citation: Genome Biology 2017 18:145

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  28. Content type: Research

    Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations as...

    Authors: Nisha Patel, Arif O. Khan, Maher Al-Saif, Walid N. Moghrabi, Balsam M. AlMaarik, Niema Ibrahim, Firdous Abdulwahab, Mais Hashem, Tarfa Alshidi, Eman Alobeid, Rana A. Alomar, Saad Al-Harbi, Mohamed Abouelhoda, Khalid S. A. Khabar and Fowzan S. Alkuraya

    Citation: Genome Biology 2017 18:144

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  29. Content type: Research

    A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism f...

    Authors: Eddie Park, Jiguang Guo, Shihao Shen, Levon Demirdjian, Ying Nian Wu, Lan Lin and Yi Xing

    Citation: Genome Biology 2017 18:143

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  30. Content type: Method

    Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequen...

    Authors: Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp and Sohrab P. Shah

    Citation: Genome Biology 2017 18:140

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    The Correction to this article has been published in Genome Biology 2017 18:188

  31. Content type: Research

    The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence show...

    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 18:142

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    The Correction to this article has been published in Genome Biology 2017 18:214

  32. Content type: Method

    We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation ch...

    Authors: Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin and Ekta Khurana

    Citation: Genome Biology 2017 18:141

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  33. Content type: Research

    Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are charact...

    Authors: Gahee Park, Joo Kyung Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung K. D. Kim, Yeon Jeong Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Hyuck Lee, Dae-Soon Son, Woong-Yang Park and Donghyun Park

    Citation: Genome Biology 2017 18:136

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  34. Content type: Research

    While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...

    Authors: Rurika Oka, Johan Zicola, Blaise Weber, Sarah N. Anderson, Charlie Hodgman, Jonathan I. Gent, Jan-Jaap Wesselink, Nathan M. Springer, Huub C. J. Hoefsloot, Franziska Turck and Maike Stam

    Citation: Genome Biology 2017 18:137

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