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Genomics & Functional Genomics

  • CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms
    Open Access
    CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms

    Erich Brunner, Ryohei Yagi, Marc Debrunner, Dezirae Beck-Schneider, Alexa Burger, Eliane Escher, Christian Mosimann, George Hausmann, Konrad Basler

    Erich Brunner ... Konrad Basler

    Published 13 June 2019

    CRISPR–Cas9 enables recombination between homologous chromosome arms at predefined sites and also underscores the need for caution when applying CRISPR technologies in translational medicine.

  • Rate of brain aging and <em>APOE ε4</em> are synergistic risk factors for Alzheimer’s disease
    Open Access
    Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s disease

    Christin A Glorioso, Andreas R Pfenning, Sam S Lee, David A Bennett, Etienne L Sibille, Manolis Kellis, Leonard P Guarente

    Christin A Glorioso ... Leonard P Guarente

    Published 27 May 2019

    This study describes a gauge for brain aging predictive of cognitive decline and Alzheimer's disease synergistic with the APOE ε4 allele.

  • A network of human functional gene interactions from knockout fitness screens in cancer cells
    Open Access
    A network of human functional gene interactions from knockout fitness screens in cancer cells

    Eiru Kim, Merve Dede, Walter F Lenoir, Gang Wang, Sanjana Srinivasan, Medina Colic, Traver Hart

    Eiru Kim ... Traver Hart

    Published 12 April 2019

    The function of human genes can be strongly inferred from their knockout fitness profiles across hundreds of CRISPR screens, illuminating the modular organization of the cell.

  • Intra-individual methylomics detects the impact of early-life adversity
    Open Access
    Intra-individual methylomics detects the impact of early-life adversity

    Shan Jiang, Noriko Kamei, Jessica L Bolton, Xinyi Ma, Hal S Stern, Tallie Z Baram, Ali Mortazavi

    Shan Jiang ... Ali Mortazavi

    Published 1 April 2019

    This study shows that methylation profile changes across time in the same individual distinguish a stressful experience from typical infancy, providing a potential predictive marker of vulnerability to disease.

  • Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
    Open Access
    Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements

    Verena Thormann, Laura V Glaser, Maika C Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H Meijsing

    Verena Thormann ... Sebastiaan H Meijsing

    Published 13 March 2019

    This study shows that addition of a single transcription factor binding site can be sufficient to convert a gene into a glucocorticoid receptor target.

  • A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
    Open Access
    A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

    Charlotte Soneson, Michael I Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D Robinson

    Charlotte Soneson ... Mark D Robinson

    Published 17 January 2019

    Comparison of observed exon–exon junction counts to those predicted from estimated transcript abundances can identify genes with misannotated or misquantified transcripts.

  • Evolution of gene expression levels in the male reproductive organs of <em>Anopheles</em> mosquitoes
    Open Access
    Evolution of gene expression levels in the male reproductive organs of Anopheles mosquitoes

    Abril Izquierdo, Martin Fahrenberger, Tania Persampieri, Mark Q Benedict, Tom Giles, Flaminia Catteruccia, Richard D Emes, Tania Dottorini

    Abril Izquierdo ... Tania Dottorini

    Published 2 January 2019

    Expression patterns of transcripts in reproductive tissues reveal the phylogeny of the An. gambiae complex and are indicative of molecular function, transcription regulatory networks, and protein–protein interaction networks.

  • Optimized ChIP-seq method facilitates transcription factor profiling in human tumors
    Open Access
    Optimized ChIP-seq method facilitates transcription factor profiling in human tumors

    Abhishek A Singh, Karianne Schuurman, Ekaterina Nevedomskaya, Suzan Stelloo, Simon Linder, Marjolein Droog, Yongsoo Kim, Joyce Sanders, Henk van der Poel, Andries M Bergman, Lodewyk FA Wessels, Wilbert Zwart

    Abhishek A Singh ... Wilbert Zwart

    Published 28 December 2018

    This study presents an optimized ChIP-seq protocol to enhance transcription factor profiling in human tumours, enabling the analysis of highly challenging samples, including core needle biopsies.

  • Re-annotation of eight <em>Drosophila</em> genomes
    Open Access
    Re-annotation of eight Drosophila genomes

    Haiwang Yang, Maria Jaime, Maxi Polihronakis, Kelvin Kanegawa, Therese Markow, Kenneth Kaneshiro, Brian Oliver

    Haiwang Yang ... Brian Oliver

    Published 24 December 2018

    Using a well-annotated genome to inform the annotation of genomes in a phylogeny.

  • A carnivorous plant genetic map: pitcher/insect-capture QTL on a genetic linkage map of <em>Sarracenia</em>
    Open Access
    A carnivorous plant genetic map: pitcher/insect-capture QTL on a genetic linkage map of Sarracenia

    Russell L Malmberg, Willie L Rogers, Magdy S Alabady

    Russell L Malmberg ... Magdy S Alabady

    Published 29 November 2018

    This study presents the first genetic map for a carnivorous plant, mapping 64 QTLs in Sarracenia to provide the genetic basis for differences between the pitfall and lobster-trap insect-capture strategies.

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