Searching journal content for articles similar to Collins et al. 22 (10): 2067.

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  1. Method: Targeted chromosomal deletions and inversions in zebrafish
    • Ankit Gupta,
    • Victoria L. Hall,
    • Fatma O. Kok,
    • Masahiro Shin,
    • Joseph C. McNulty,
    • Nathan D. Lawson,
    • and Scot A. Wolfe
    Genome Res. June 2013 23: 1008-1017; Published in Advance March 11, 2013, doi:10.1101/gr.154070.112
    ..., StempleDL. 2012. Incorporating RNA-seq data into the zebrafish Ensembl genebuild. Genome Res 22: 2067–2078. Cristea S, Freyvert Y, Santiago Y, Holmes MC, Urnov FD, Gregory PD, Cost GJ. 2013. In vivo cleavage of transgene donors promotes nucleasemediated targeted integration. Biotechnol Bioeng 110: 871...
  2. Research: Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
    • Juan J. Tena,
    • Cristina González-Aguilera,
    • Ana Fernández-Miñán,
    • Javier Vázquez-Marín,
    • Helena Parra-Acero,
    • Joe W. Cross,
    • Peter W.J. Rigby,
    • Jaime J. Carvajal,
    • Joachim Wittbrodt,
    • José L. Gómez-Skarmeta,
    • and Juan R. Martínez-Morales
    Genome Res. July 2014 24: 1075-1085; Published in Advance April 7, 2014, doi:10.1101/gr.163915.113
    .... To that end, we performed ChIP-seq experiments with specific antibodies against H3K4me3 (histone 3 lysine 4 trimethylation) and H3K27ac (Fig. 3A). The reads obtained from sequencing of immunoprecipitated DNA were aligned to the medaka (oryLat2 assembly, Ensembl) (Flicek et al. 2013). Then, we used the H3K4me3...
  3. Resource: Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation
    • Kang Du,
    • Martin Pippel,
    • Susanne Kneitz,
    • Romain Feron,
    • Irene da Cruz,
    • Sylke Winkler,
    • Brigitta Wilde,
    • Edgar G. Avila Luna,
    • Gene Myers,
    • Yann Guiguen,
    • Constantino Macias Garcia,
    • and Manfred Schartl
    Genome Res. March 2022 32: 583-594; Published in Advance January 26, 2022, doi:10.1101/gr.275826.121
    ...RNAs (ncRNAs) were annotated using the method adapted from Ensembl (http://useast.ensembl.org/info//genebuild/ncrna.html).Details of the procedures are provided in Supplemental Methods (Genome annotation).Orthology assignmentOrthology of genes was assigned by a clustering of sequence similarity...
  4. Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
    • Ian T. Fiddes,
    • Joel Armstrong,
    • Mark Diekhans,
    • Stefanie Nachtweide,
    • Zev N. Kronenberg,
    • Jason G. Underwood,
    • David Gordon,
    • Dent Earl,
    • Thomas Keane,
    • Evan E. Eichler,
    • David Haussler,
    • Mario Stanke,
    • and Benedict Paten
    Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
    ...rabbit (oryCun2), Egyptian jerboa (jacJac1), and human (hg38) as outgroups. To provide hints to AUGUSTUS, RNA-seq data were obtained from the NCBI Sequence Read Archive (SRA) (Supplemental Table S2; Cortez et al. 2014; Fushan et al. 2015; Liu et al. 2016). For comparison we used existing Ensembl and Ref...
  5. Perspective: Functional transcriptomics in the post-ENCODE era
    • Jonathan M. Mudge,
    • Adam Frankish,
    • and Jennifer Harrow
    Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
    ...(the gene set of the ENCODE project [The ENCODE Project Consortium 2012]) represents a merge between manually annotated HAVANA and computationally derived Ensembl models, with annotation taking place on the sequence. In contrast, while RefSeq also combines manual and automated processes, most human...
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  6. Method: Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Yann Surget-Groba and
    • Juan I. Montoya-Burgos
    Genome Res. October 2010 20: 1432-1440; Published in Advance August 6, 2010, doi:10.1101/gr.103846.109
    ...conducted on a simulated 35-bp RNA-seq data set based on the set of zebrafish cDNA from Ensembl (Supplemental Table S1). As expected, the average coverage of assembled contigs increases with increasing k-mer values on both the real (Table 2) and the simulated (Supplemental Table S2) data sets. However...
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