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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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

  14. 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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  15. 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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  16. 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

Page 7 of 247