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  1. Research

    RNF40 regulates gene expression in an epigenetic context-dependent manner

    Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an ex...

    Wanhua Xie, Sankari Nagarajan, Simon J. Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri and Steven A. Johnsen

    Genome Biology 2017 18:32

    Published on: 16 February 2017

  2. Research

    Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

    The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contamina...

    Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Özgür Bayram, Tiziano Benocci, Susanna A. Braus-Stromeyer, Camila Caldana, David Cánovas…

    Genome Biology 2017 18:28

    Published on: 14 February 2017

  3. Research

    Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

    The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a sm...

    Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca…

    Genome Biology 2017 18:27

    Published on: 13 February 2017

  4. Review

    Software tools for visualizing Hi-C data

    High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation fr...

    Galip Gürkan Yardımcı and William Stafford Noble

    Genome Biology 2017 18:26

    Published on: 3 February 2017

  5. Research

    Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects

    The CRISPR-Cas9 system is a widely utilized platform for transgenic animal production in various species, although its off-target effects should be addressed. Several applications of this tool have been propos...

    Yuanpeng Gao, Haibo Wu, Yongsheng Wang, Xin Liu, Linlin Chen, Qian Li, Chenchen Cui, Xu Liu, Jingcheng Zhang and Yong Zhang

    Genome Biology 2017 18:13

    Published on: 1 February 2017

  6. Correspondence

    Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies

    Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methyl...

    Mohammad W. Hattab, Andrey A. Shabalin, Shaunna L. Clark, Min Zhao, Gaurav Kumar, Robin F. Chan, Lin Ying Xie, Rick Jansen, Laura K. M. Han, Patrik K. E. Magnusson, Gerard van Grootheest, Christina M. Hultman, Brenda W. J. H. Penninx, Karolina A. Aberg and Edwin J. C. G. van den Oord

    Genome Biology 2017 18:24

    Published on: 30 January 2017

  7. Correspondence

    Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies

    We thank Hattab and colleagues for their correspondence and their investigation of cell-type mixture correction methods in methyl-CG binding domain sequencing. Here, we speculate on why surrogate variable anal...

    Kevin McGregor, Aurélie Labbe and Celia M. T. Greenwood

    Genome Biology 2017 18:25

    Published on: 30 January 2017

  8. Research

    Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania

    5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping o...

    Fumiko Kawasaki, Dario Beraldi, Robyn E. Hardisty, Gordon R. McInroy, Pieter van Delft and Shankar Balasubramanian

    Genome Biology 2017 18:23

    Published on: 30 January 2017

  9. Editorial

    Human disease genomics: from variants to biology

    We summarize the remarkable progress that has been made in the identification and functional characterization of DNA sequence variants associated with disease.

    Mark I. McCarthy and Daniel G. MacArthur

    Genome Biology 2017 18:20

    Published on: 30 January 2017

  10. Research

    Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing

    Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson’s disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated pa...

    Iris E. Jansen, Hui Ye, Sasja Heetveld, Marie C. Lechler, Helen Michels, Renée I. Seinstra, Steven J. Lubbe, Valérie Drouet, Suzanne Lesage, Elisa Majounie, J. Raphael Gibbs, Mike A. Nalls, Mina Ryten, Juan A. Botia, Jana Vandrovcova, Javier Simon-Sanchez…

    Genome Biology 2017 18:22

    Published on: 30 January 2017

  11. Method

    Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts

    Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational...

    Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia and Philippe Collas

    Genome Biology 2017 18:21

    Published on: 30 January 2017

  12. Research

    Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

    A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability.

    Simone Ecker, Lu Chen, Vera Pancaldi, Frederik O. Bagger, José María Fernández, Enrique Carrillo de Santa Pau, David Juan, Alice L. Mann, Stephen Watt, Francesco Paolo Casale, Nikos Sidiropoulos, Nicolas Rapin, Angelika Merkel, Hendrik G. Stunnenberg, Oliver Stegle, Mattia Frontini…

    Genome Biology 2017 18:18

    Published on: 26 January 2017

  13. Research

    Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies

    Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenoty...

    Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Sai-xia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael L. Feolo, Nataliya R. Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy Heard-Costa, Han Chen, Po-ching Liu, Richard Wang, Kimberly A. Woodhouse…

    Genome Biology 2017 18:16

    Published on: 25 January 2017

  14. Research

    Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation

    Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the i...

    Irene Cantone, Gopuraja Dharmalingam, Yi-Wah Chan, Anne-Celine Kohler, Boris Lenhard, Matthias Merkenschlager and Amanda G. Fisher

    Genome Biology 2017 18:2

    Published on: 25 January 2017

  15. Research

    Single-cell epigenomic variability reveals functional cancer heterogeneity

    Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is dif...

    Ulrike M. Litzenburger, Jason D. Buenrostro, Beijing Wu, Ying Shen, Nathan C. Sheffield, Arwa Kathiria, William J. Greenleaf and Howard Y. Chang

    Genome Biology 2017 18:15

    Published on: 24 January 2017

  16. Research

    Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis

    Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. Th...

    Ganesan Velmurugan, Tharmarajan Ramprasath, Krishnan Swaminathan, Gilles Mithieux, Jeyaprakash Rajendhran, Mani Dhivakar, Ayothi Parthasarathy, D.D. Venkatesh Babu, Leishman John Thumburaj, Allen J. Freddy, Vasudevan Dinakaran, Shanavas Syed Mohamed Puhari, Balakrishnan Rekha, Yacob Jenifer Christy, Sivakumar Anusha, Ganesan Divya…

    Genome Biology 2017 18:8

    Published on: 24 January 2017

  17. Research

    Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus

    In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatme...

    Xuan Liu, Emily Speranza, César Muñoz-Fontela, Sam Haldenby, Natasha Y. Rickett, Isabel Garcia-Dorival, Yongxiang Fang, Yper Hall, Elsa-Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny…

    Genome Biology 2017 18:4

    Published on: 19 January 2017

  18. Research

    Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

    Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illnes...

    Agata Wesolowska-Andersen, Jamie L. Everman, Rebecca Davidson, Cydney Rios, Rachelle Herrin, Celeste Eng, William J. Janssen, Andrew H. Liu, Sam S. Oh, Rajesh Kumar, Tasha E. Fingerlin, Jose Rodriguez-Santana, Esteban G. Burchard and Max A. Seibold

    Genome Biology 2017 18:12

    Published on: 19 January 2017

  19. Erratum

    Erratum to: The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

    Alexie Papanicolaou, Marc F. Schetelig, Peter Arensburger, Peter W. Atkinson, Joshua B. Benoit, Kostas Bourtzis, Pedro Castañera, John P. Cavanaugh, Hsu Chao, Christopher Childers, Ingrid Curril, Huyen Dinh, HarshaVardhan Doddapaneni, Amanda Dolan, Shannon Dugan, Markus Friedrich…

    Genome Biology 2017 18:11

    Published on: 18 January 2017

    The original article was published in Genome Biology 2016 17:192

  20. Method

    iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations

    The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet...

    Siqi Liang, Nathaniel D. Tippens, Yaoda Zhou, Matthew Mort, Peter D. Stenson, David N. Cooper and Haiyuan Yu

    Genome Biology 2017 18:10

    Published on: 18 January 2017

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