Searching journal content for articles similar to Craig et al. 19 (11): 2075.

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  1. Resource: A large-scale zebrafish gene knockout resource for the genome-wide study of gene function
    • Gaurav K. Varshney,
    • Jing Lu,
    • Derek E. Gildea,
    • Haigen Huang,
    • Wuhong Pei,
    • Zhongan Yang,
    • Sunny C. Huang,
    • David Schoenfeld,
    • Nam H. Pho,
    • David Casero,
    • Takashi Hirase,
    • Deborah Mosbrook-Davis,
    • Suiyuan Zhang,
    • Li-En Jao,
    • Bo Zhang,
    • Ian G. Woods,
    • Steven Zimmerman,
    • Alexander F. Schier,
    • Tyra G. Wolfsberg,
    • Matteo Pellegrini,
    • Shawn M. Burgess,
    • and Shuo Lin
    Genome Res. April 2013 23: 727-735; Published in Advance February 4, 2013, doi:10.1101/gr.151464.112
    ...A large-scale zebrafish gene knockout resource for the genome-wide study of gene function Gaurav K. Varshney 1 , 8 , Jing Lu 2 , 3 , 8 , Derek E. Gildea 4 , Haigen Huang 3 , Wuhong Pei 1 , Zhongan Yang 3 , Sunny C. Huang...
  2. Method: MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq
    • Jonathon T. Hill,
    • Bradley L. Demarest,
    • Brent W. Bisgrove,
    • Bushra Gorsi,
    • Yi-Chu Su,
    • and H. Joseph Yost
    Genome Res. April 2013 23: 687-697; Published in Advance January 8, 2013, doi:10.1101/gr.146936.112
    ...organisms, such as Drosophila and Caenorhabditis elegans, that are amenable to both forward genetic screens and pooled RNA-seq experiments. Thus, MMAPPR is a rapid, cost-efficient, and highly automated pipeline, available to perform mutant mapping in any organism with a well-assembled . [Supplemental...
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  3. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...hypersensitivity), high nucleosomal turnover (e.g., high levels of rapid-turnover histones H2A.Z and H3.3), specific epigenetic markers (e.g., high ratio of H3K4me1 and H3K4me2 to H3K4me3, high ratio of 5hmC to 5mC, enrichment of H3K27ac), chromatin loops in direct contact with the core promoter (enrichment...
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  4. Method: Multiplexed shotgun genotyping for rapid and efficient genetic mapping
    • Peter Andolfatto,
    • Dan Davison,
    • Deniz Erezyilmaz,
    • Tina T. Hu,
    • Joshua Mast,
    • Tomoko Sunayama-Morita,
    • and David L. Stern
    Genome Res. April 2011 21: 610-617; Published in Advance January 13, 2011, doi:10.1101/gr.115402.110
    ...even when s are ‘‘assembled’’ by alignment to a known sequence. For example, the D. simulans project involved placement of most contigs onto Figure 2. Genome-wide ancestry assignment for a representative individual. (A) The ancestry states are shown for all major chromosome arms for a representative...
  5. Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
    • Marzia Rossato,
    • Luca Marcolungo,
    • Luca De Antoni,
    • Giulia Lopatriello,
    • Elisa Bellucci,
    • Gaia Cortinovis,
    • Giulia Frascarelli,
    • Laura Nanni,
    • Elena Bitocchi,
    • Valerio Di Vittori,
    • Leonardo Vincenzi,
    • Filippo Lucchini,
    • Kirstin E. Bett,
    • Larissa Ramsay,
    • David James Konkin,
    • Massimo Delledonne,
    • and Roberto Papa
    Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
    ...of SAMtools and BCFtools. GigaScience 10: giab008. doi:10.1093/gigascience/giab008 ↵Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12: 499–510. doi:10.1038/nrg3012 ↵Deng T, Zhang P...
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  6. Methods: Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
    • Michael R. Miller,
    • Joseph P. Dunham,
    • Angel Amores,
    • William A. Cresko,
    • and Eric A. Johnson
    Genome Res. February 2007 17: 240-248; Published in Advance December 22, 2006, doi:10.1101/gr.5681207
    ...R estriction site a ssociated D NA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allows RAD tags to serve as genetic markers...
  7. Method: Copolymerization of single-cell nucleic acids into balls of acrylamide gel
    • Siran Li,
    • Jude Kendall,
    • Sarah Park,
    • Zihua Wang,
    • Joan Alexander,
    • Andrea Moffitt,
    • Nissim Ranade,
    • Cassidy Danyko,
    • Bruno Gegenhuber,
    • Stephan Fischer,
    • Brian D. Robinson,
    • Herbert Lepor,
    • Jessica Tollkuhn,
    • Jesse Gillis,
    • Eric Brouzes,
    • Alex Krasnitz,
    • Dan Levy,
    • and Michael Wigler
    Genome Res. January 2020 30: 49-61; Published in Advance November 14, 2019, doi:10.1101/gr.253047.119
    ...-BAGs). Unlike other “cell bead” ideas (Tamminen and Virta 2015; Andor et al. 2018), in C-BAGs the first copy of nuclei acids is covalently bound to the gel matrix and individually tagged by a split-and-pool strategy.The apparatus is inexpensive, and we estimate the cost per cell to be $0.50 when performed...
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  8. Perspective: Tagmentation-based single-cell genomics
    • Andrew C. Adey
    Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
    ...is of less value than a rapid workflow.The removal of Tn5 effectively releases the two end fragments from one another that were generated during the reaction, each receiving one of the adapters from the transposome complex and retaining one strand of the 9-bp region in between the two cut sites. Extension...
  9. Method: HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay
    • Jia Lv,
    • Wenqian Jiao,
    • Haobing Guo,
    • Pingping Liu,
    • Ruijia Wang,
    • Lingling Zhang,
    • Qifan Zeng,
    • Xiaoli Hu,
    • Zhenmin Bao,
    • and Shi Wang
    Genome Res. December 2018 28: 1919-1930; Published in Advance November 8, 2018, doi:10.1101/gr.235820.118
    ....Recent advances in next-generation sequencing (NGS) technologies now allow rapid and affordable generation of extensive genomic resources in numerous less-studied organisms and offer opportunities to address many scientific questions with unprecedented power and precision (Levy and Myers 2016). During the last...
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  10. Method: Time course regulatory analysis based on paired expression and chromatin accessibility data
    • Zhana Duren,
    • Xi Chen,
    • Jingxue Xin,
    • Yong Wang,
    • and Wing Hung Wong
    Genome Res. April 2020 30: 622-634; Published in Advance March 18, 2020, doi:10.1101/gr.257063.119
    ...are large changes in chromatin accessibility, which then induces subsequent gene expression changes in the time course.View larger version: In this window In a new window Figure 2. Genome-wide profiling of gene expression and chromatin accessibility during RA induction reveals landscape for RA...
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