Searching journal content for articles similar to Goryshin et al. 13 (4): 644.

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  1. Method: Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo
    • Luca Tosti,
    • James Ashmore,
    • Boon Siang Nicholas Tan,
    • Benedetta Carbone,
    • Tapan K. Mistri,
    • Valerie Wilson,
    • Simon R. Tomlinson,
    • and Keisuke Kaji
    Genome Res. April 2018 28: 592-605; Published in Advance March 23, 2018, doi:10.1101/gr.227124.117
    ...–associated genes in ESCs and post-implantation epiblasts (Kojima et al. 2014). Genes whose expression significantly changed 24 h after Pou5f1 deletion in the 7.5-dpc mouse embryo (DeVeale et al. 2013) are indicated in color. (CAV) Epiblast of cavity; (PS) prestreak; (LMS) late mid streak; (LS) late streak; (OB...
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  2. METHODS: An Efficient DNA Sequencing Strategy Based on the Bacteriophage Mu in Vitro DNA Transposition Reaction
    • Saija Haapa,
    • Sini Suomalainen,
    • Simo Eerikäinen,
    • Matti Airaksinen,
    • Lars Paulin,
    • and Harri Savilahti
    Genome Res. March 1, 1999 9: 308-315; doi:10.1101/gr.9.3.308
    ...efficient and easy methodology for DNA sequencing that is based on the bacteriophage Mu in vitro transposition reaction. As a test case, we used the system to determine a 10,288-bp sequence from a mouse genomic locus containing a Kcc2 gene. The respective protein, KCC2, is a K+/Cl− cotransporter...
  3. GENOME METHODS: A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes
    • Scott E. Devine,
    • Stephanie L. Chissoe,
    • Yolanda Eby,
    • Richard K. Wilson,
    • and Jef D. Boeke
    Genome Res. May 1, 1997 7: 551-563; doi:10.1101/gr.7.5.551
    ...functions for the host organism (e.g., see Levis et al. 1993 ). The C. elegans sequencing project began initially with the gene-rich regions of the six C. elegans chromosomes, and has now progressed to regions such as the telomeric arms of these chromosomes. The same genomic regions of organisms...
  4. Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
    • Alexander Zee,
    • Dori Z.Q. Deng,
    • Matthew Adams,
    • Kayla D. Schimke,
    • Russell Corbett-Detig,
    • Shelbi L. Russell,
    • Xuan Zhang,
    • Robert J. Schmitz,
    • and Christopher Vollmers
    Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
    ...for the protein-coding regions of approximately 100 cancer-relevant genes (Fig. 1).View larger version: In this window In a new window Figure 1. Experiment overview. Illumina RNA-seq, ChIP-seq, and Tn5-based genomic libraries (regular and enriched) were generated from different samples. The Illumina libraries...
  5. LETTER: A General Approach for Identifying Distant Regulatory Elements Applied to the Gdf6 Gene
    • Douglas P. Mortlock,
    • Catherine Guenther,
    • and David M. Kingsley
    Genome Res. September 2003 13: 2069-2081; Published in Advance January 1, 2003, doi:10.1101/gr.1306003
    .../exon structure and the protein-coding regions of the genes are highly conserved, the surrounding genomic regions now show little or no sequence homology. This may reflect the tendency of duplicated genes to gain or lose regulatory elements by local deletion, insertion, mutation, transposition, or chromosome...
  6. Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
    • Angelo A. Ruggieri,
    • Luca Livraghi,
    • James J. Lewis,
    • Elizabeth Evans,
    • Francesco Cicconardi,
    • Laura Hebberecht,
    • Yadira Ortiz-Ruiz,
    • Stephen H. Montgomery,
    • Alfredo Ghezzi,
    • José Arcadio Rodriguez-Martinez,
    • Chris D. Jiggins,
    • W. Owen McMillan,
    • Brian A. Counterman,
    • Riccardo Papa,
    • and Steven M. Van Belleghem
    Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
    ...within large inversions can initiate co-adaptation of gene complexes in the rearranged genomic haplotype (e.g., supergenes; Jay et al. 2021; Matschiner et al. 2022). Alternatively, insertion-deletion mutations (indels) can include one or multiple functional genetic elements and studies are starting...
  7. Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
    • Zhoutao Chen,
    • Long Pham,
    • Tsai-Chin Wu,
    • Guoya Mo,
    • Yu Xia,
    • Peter L. Chang,
    • Devin Porter,
    • Tan Phan,
    • Huu Che,
    • Hao Tran,
    • Vikas Bansal,
    • Justin Shaffer,
    • Pedro Belda-Ferre,
    • Greg Humphrey,
    • Rob Knight,
    • Pavel Pevzner,
    • Son Pham,
    • Yong Wang,
    • and Ming Lei
    Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
    ...gene.View this table: In this window In a new window Table 4. Summary of TELL-seq phasing results on nine HLA genes in comparison with the reference dataResolving structural variant call discrepanciesPrevious studies have reported 10 structural variants (i.e., deletions) in NA12878 revealed by other...
  8. Method: Identification of regulatory elements from nascent transcription using dREG
    • Zhong Wang,
    • Tinyi Chu,
    • Lauren A. Choate,
    • and Charles G. Danko
    Genome Res. February 2019 29: 293-303; Published in Advance December 20, 2018, doi:10.1101/gr.238279.118
    ...multiple aspects of gene regulation, including the precise position of regulatory elements, gene expression, and pausing levels using a single genomic experiment. When paired with ChRO-seq (Chu et al. 2018), which applies run-on assays in solid tissues, dREG allows the discovery of regulatory elements...
  9. Methods: De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
    • Josephine A. Reinhardt,
    • David A. Baltrus,
    • Marc T. Nishimura,
    • William R. Jeck,
    • Corbin D. Jones,
    • and Jeffery L. Dangl
    Genome Res. February 2009 19: 294-305; Published in Advance November 17, 2008, doi:10.1101/gr.083311.108
    ...of small insertions and deletions (indels). Such frameshifts inhibit gene prediction in de novo assemblies more than single nucleotide errors. Illumina sequencing is less than one-hundredth the cost of Sanger sequencing, but reads are currently 36 bp in length, preventing significant assembly of even short...
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  10. PERSPECTIVE: Insights on biology and evolution from microbial genome sequencing
    • Claire M. Fraser-Liggett
    Genome Res. December 2005 15: 1603-1610; doi:10.1101/gr.3724205
    .... Bacteriol. 187 : 2426 -2438. ↵ Gogarten, J.P., Doolittle, W.F., and Lawrence, J.G. 2002 . Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19 : 2226 -2238. ↵ Goryshin, I.Y., Naumann, T.A., Apodaca, J., and Reznikoff, W.S. 2003 . Chromosomal deletion formation system based on Tn5 double...
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