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  1. Method

    A tandem simulation framework for predicting mapping quality

    Read alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is ...

    Ben Langmead

    Genome Biology 2017 18:152

    Published on: 10 August 2017

  2. Method

    A statistical framework for analyzing deep mutational scanning data

    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...

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

    Genome Biology 2017 18:150

    Published on: 7 August 2017

  3. Method

    stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

    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...

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

    Genome Biology 2017 18:151

    Published on: 7 August 2017

  4. Research

    Large scale genomic reorganization of topological domains at the HoxD locus

    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...

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

    Genome Biology 2017 18:149

    Published on: 7 August 2017

  5. Method

    SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

    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...

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

    Genome Biology 2017 18:148

    Published on: 4 August 2017

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

  6. Research

    An interaction map of circulating metabolites, immune gene networks, and their genetic regulation

    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 ...

    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…

    Genome Biology 2017 18:146

    Published on: 1 August 2017

  7. Research

    A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)-creating mutation

    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...

    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

    Genome Biology 2017 18:144

    Published on: 28 July 2017

  8. Research

    Population and allelic variation of A-to-I RNA editing in human transcriptomes

    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...

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

    Genome Biology 2017 18:143

    Published on: 28 July 2017

  9. Method

    ReMixT: clone-specific genomic structure estimation in cancer

    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...

    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

    Genome Biology 2017 18:140

    Published on: 27 July 2017

  10. Research

    Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

    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...

    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…

    Genome Biology 2017 18:142

    Published on: 27 July 2017

  11. Method

    Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

    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...

    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

    Genome Biology 2017 18:141

    Published on: 27 July 2017

  12. Research

    Characterization of background noise in capture-based targeted sequencing data

    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...

    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

    Genome Biology 2017 18:136

    Published on: 21 July 2017

  13. Research

    Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

    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,...

    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

    Genome Biology 2017 18:137

    Published on: 21 July 2017

  14. Research

    Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

    The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the eme...

    Catriona P. Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D. Bentley, Angela M. Kearns and Matthew T. G. Holden

    Genome Biology 2017 18:130

    Published on: 20 July 2017

  15. Research

    MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity

    Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we ...

    David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling…

    Genome Biology 2017 18:131

    Published on: 6 July 2017

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