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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. MEETING REPORT

    Genome Informatics 2016

    A report on the Genome Informatics conference, held at the Wellcome Genome Campus Conference Centre, Hinxton, United Kingdom, 19–22 September 2016.

    Davide Chicco and Michael M. Hoffman

    Genome Biology 2017 18:5

    Published on: 16 January 2017

  7. Method

    GAVIN: Gene-Aware Variant INterpretation for medical sequencing

    We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele freque...

    K. Joeri van der Velde, Eddy N. de Boer, Cleo C. van Diemen, Birgit Sikkema-Raddatz, Kristin M. Abbott, Alain Knopperts, Lude Franke, Rolf H. Sijmons, Tom J. de Koning, Cisca Wijmenga, Richard J. Sinke and Morris A. Swertz

    Genome Biology 2017 18:6

    Published on: 16 January 2017

  8. Research

    Insights into the design and interpretation of iCLIP experiments

    Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different co...

    Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W. Hentze, Andreas E. Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R. Sibley, Kathi Zarnack and Jernej Ule

    Genome Biology 2017 18:7

    Published on: 16 January 2017

  9. Research

    Identifying aggressive prostate cancer foci using a DNA methylation classifier

    Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive d...

    Kamilla Mundbjerg, Sameer Chopra, Mehrdad Alemozaffar, Christopher Duymich, Ranjani Lakshminarasimhan, Peter W. Nichols, Manju Aron, Kimberly D. Siegmund, Osamu Ukimura, Monish Aron, ‬Mariana Stern, Parkash Gill, John D. Carpten, Torben F. Ørntoft, Karina D. Sørensen, Daniel J. Weisenberger…

    Genome Biology 2017 18:3

    Published on: 12 January 2017

  10. Research

    Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

    Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosi...

    Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura and Alexandra Lusser

    Genome Biology 2017 18:1

    Published on: 5 January 2017

  11. Research Highlight

    The incredible complexity of RNA splicing

    Alternative splice isoforms are common and important and have been shown to impact many human diseases. A new study by Nellore et al. offers a comprehensive study of splice junctions in humans by re-analyzing ...

    Christelle Robert and Mick Watson

    Genome Biology 2016 17:265

    Published on: 30 December 2016

  12. Research

    Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

    Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects l...

    Abhinav Nellore, Andrew E. Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A. Phillips III, Nishika Karbhari, Kasper D. Hansen, Ben Langmead and Jeffrey T. Leek

    Genome Biology 2016 17:266

    Published on: 30 December 2016

  13. Research Highlight

    TET enzymes: double agents in the transposable element–host genome conflict

    The mouse genome is replete with retrotransposon sequences, from evolutionarily young elements with mutagenic potential that must be controlled, to inactive molecular fossils whose sequences can be domesticate...

    Patricia Gerdes, Sandra R. Richardson and Geoffrey J. Faulkner

    Genome Biology 2016 17:259

    Published on: 20 December 2016

  14. Research

    The genome of the Gulf pipefish enables understanding of evolutionary innovations

    Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuin...

    C. M. Small, S. Bassham, J. Catchen, A. Amores, A. M. Fuiten, R. S. Brown, A. G. Jones and W. A. Cresko

    Genome Biology 2016 17:258

    Published on: 20 December 2016

  15. Review

    Methylome evolution in plants

    Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on ...

    Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier and Frank Johannes

    Genome Biology 2016 17:264

    Published on: 20 December 2016

  16. Software

    IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

    Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated an...

    Shaman Narayanasamy, Yohan Jarosz, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes

    Genome Biology 2016 17:260

    Published on: 16 December 2016

  17. Research

    Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

    Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective con...

    Federico Abascal, André Corvelo, Fernando Cruz, José L. Villanueva-Cañas, Anna Vlasova, Marina Marcet-Houben, Begoña Martínez-Cruz, Jade Yu Cheng, Pablo Prieto, Víctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frias, Paolo Ribeca…

    Genome Biology 2016 17:251

    Published on: 14 December 2016

  18. Research

    Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery

    The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated ...

    Andree Delahaye-Duriez, Prashant Srivastava, Kirill Shkura, Sarah R. Langley, Liisi Laaniste, Aida Moreno-Moral, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Elena V. Gazina, Kay Richards, Steven Petrou, Rafal M. Kaminski, Enrico Petretto and Michael R. Johnson

    Genome Biology 2016 17:245

    Published on: 13 December 2016

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