Searching journal content for articles similar to Kan et al. 27 (7): 1099.

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  1. Method: Identification of the shortest species-specific oligonucleotide sequences
    • Ioannis Mouratidis,
    • Maxwell A. Konnaris,
    • Nikol Chantzi,
    • Candace S.Y. Chan,
    • Michail Patsakis,
    • Kimonas Provatas,
    • Austin Montgomery,
    • Fotis A. Baltoumas,
    • Congzhou M. Sha,
    • Manvita Mareboina,
    • Georgios A. Pavlopoulos,
    • Dionysios V. Chartoumpekis,
    • and Ilias Georgakopoulos-Soares
    Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
    ...interactions of living organisms, and developing precise techniques to detect genomic differences between species. Nevertheless, the increase in biological data also necessitates algorithmic advances to capture the most useful information.As species evolve and diverge, they acquire new traits. This leads...
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  2. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ..., Stafforst T. 2019. Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat Biotechnol 37: 133–138. Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD. 2004. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively...
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  3. Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
    • Xiaoyue Duan,
    • Chaolei Chen,
    • Chang Du,
    • Liang Guo,
    • Jun Liu,
    • Naipeng Hou,
    • Pan Li,
    • Xiaolan Qi,
    • Fei Gao,
    • Xuguang Du,
    • Jiangping Song,
    • and Sen Wu
    Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
    ...editing efficiency. This approach led to the successful generation of xenotransplantation pigs with multiple homozygously edited genes in a much shorter time frame than previously achievable.ResultsSurrogate reporters for genomic targetingEfficient selection methods are essential for enhancing multiplex...
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  4. Method: CRISPR-Cas9-mediated pinpoint microbial genome editing aided by target-mismatched sgRNAs
    • Ho Joung Lee,
    • Hyun Ju Kim,
    • and Sang Jun Lee
    Genome Res. May 2020 30: 768-775; Published in Advance April 23, 2020, doi:10.1101/gr.257493.119
    ...–mediated recombineering of oligonucleotides, followed by CRISPR-Cas9 negative selection. Because the lambda Bet protein promotes recombineering of single-stranded DNA (Costantino and Court 2003), Bet-mediated recombineering along with CRISPR-Cas9 facilitated genomic editing of two to three bases in galK, xylA, and lac...
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  5. Method: Accurate analysis of genuine CRISPR editing events with ampliCan
    • Kornel Labun,
    • Xiaoge Guo,
    • Alejandro Chavez,
    • George Church,
    • James A. Gagnon,
    • and Eivind Valen
    Genome Res. May 2019 29: 843-847; Published in Advance March 8, 2019, doi:10.1101/gr.244293.118
    ...-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9: e98186. doi:10.1371/journal.pone.0098186 ↵Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. 2017. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551: 464. doi:10...
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  6. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    ...donors using GangSTR v2.4.3 (https://github.com/gymreklab/GangSTR) and a BED file for 832,380 TR regions (hg38_ver13.bed.gz, https://github.com/gymreklab/GangSTR) (Mousavi et al. 2019). We downloaded an hg38 reference file (resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta, https://console.cloud.google.com/storage/browser/genomics...
  7. Research: Cellular abundance shapes function in piRNA-guided genome defense
    • Pavol Genzor,
    • Parthena Konstantinidou,
    • Daniel Stoyko,
    • Amirhossein Manzourolajdad,
    • Celine Marlin Andrews,
    • Alexandra R. Elchert,
    • Constantinos Stathopoulos,
    • and Astrid D. Haase
    Genome Res. November 2021 31: 2058-2068; Published in Advance October 19, 2021, doi:10.1101/gr.275478.121
    ...allowed us to remove PCR duplicates and precisely quantitate individual piRNA sequences.Generating endogenously tagged Piwi in ovarian somatic sheath cellsOvarian somatic sheath cells were purchased from the Drosophila Genomics Resource Center (DGRC cell line 288) and were grown in Shields and Sang M3...
  8. Method: Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins
    • Sojung Kim,
    • Daesik Kim,
    • Seung Woo Cho,
    • Jungeun Kim,
    • and Jin-Soo Kim
    Genome Res. June 2014 24: 1012-1019; Published in Advance April 2, 2014, doi:10.1101/gr.171322.113
    ...rather than plasmids could facilitate isolation of -modified clones of ES cells or induced pluripotent stem cells. Oligonucleotide-directed editing via homologydirected repair Next,we investigatedwhether RGENRNPs canbe co-transfectedwith homologous donor DNA to achieve editing via homologydirected repair...
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  9. Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
    • Juniper J. Elacqua,
    • Navpreet Ranu,
    • Sarah E. DiIorio,
    • and Paul C. Blainey
    Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
    ..., toxicity, and cell death (Wu et al. 2014; Zhang et al. 2015). In efforts to make precise edits and minimize off-target DSB toxicity, Cas9's engineered nickase variants are an increasing focus in editing applications (Davis and Maizels 2011, 2014; Jinek et al. 2012; Ran et al. 2013; Komor et al. 2016...
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  10. 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
    ...for elucidating how specific genes, their regulatory elements, and other -related components influence physiological processes. Gene editing encompasses various methodologies and involves the targeted insertion, deletion, modification, or replacement of DNA sequences at precise locations within...
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