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  1. Research

    Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

    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...

    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…

    Genome Biology 2017 18:182

    Published on: 21 September 2017

  2. Method

    DESMAN: a new tool for de novo extraction of strains from metagenomes

    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 ...

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

    Genome Biology 2017 18:181

    Published on: 21 September 2017

  3. Research

    DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A

    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...

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

    Genome Biology 2017 18:176

    Published on: 18 September 2017

  4. Research

    Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination

    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...

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

    Genome Biology 2017 18:172

    Published on: 15 September 2017

  5. Research

    Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy

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

    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…

    Genome Biology 2017 18:170

    Published on: 14 September 2017

  6. Open Letter

    Genome build information is an essential part of genomic track files

    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...

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

    Genome Biology 2017 18:175

    Published on: 14 September 2017

  7. Method

    Splatter: simulation of single-cell RNA sequencing data

    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...

    Luke Zappia, Belinda Phipson and Alicia Oshlack

    Genome Biology 2017 18:174

    Published on: 12 September 2017

  8. Method

    Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA–protein binding sites

    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-...

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

    Genome Biology 2017 18:169

    Published on: 8 September 2017

  9. Research

    Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding

    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...

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

    Genome Biology 2017 18:167

    Published on: 6 September 2017

  10. Research

    Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis

    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...

    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

    Genome Biology 2017 18:166

    Published on: 5 September 2017

  11. Research

    Chromosome contacts in activated T cells identify autoimmune disease candidate genes

    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...

    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…

    Genome Biology 2017 18:165

    Published on: 4 September 2017

  12. Research

    Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean

    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...

    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…

    Genome Biology 2017 18:161

    Published on: 24 August 2017

  13. Research

    Conservation and divergence of small RNA pathways and microRNAs in land plants

    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...

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

    Genome Biology 2017 18:158

    Published on: 23 August 2017

  14. Research

    Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid

    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...

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

    Genome Biology 2017 18:157

    Published on: 22 August 2017

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