Searching journal content for articles similar to Castensson et al. 10 (8): 1219.

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  1. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...targets mRNAs to the mitochondrion (Lee et al. 2009; Caballero et al. 2025), 446 while Sal1, an ADP/ATP transporter, helps maintain mitochondrial ATP levels and inner 447 membrane potential (Traba et al. 2008). Introduction of the MKT1-30G allele into BY led to 448 decreased colony size in multiple...
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  2. Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
    • Xue Dong,
    • Mengzhu Hu,
    • Xiaonan Cui,
    • Wenjian Zhou,
    • Jingtao Cai,
    • Guangyao Mao,
    • and Weiyang Shi
    Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
    ...; Shah et al. 2016; Eng et al. 2019) or in situ mRNA capture (Ståhl et al. 2016; Rodriques et al. 2019; Vickovic et al. 2019; Srivatsan et al. 2021; Stickels et al. 2021; Chen et al. 2022; Russell et al. 2024). The second category targets specific regions of interest (ROIs) with known locations...
  3. Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
    • Aayush Grover,
    • Till Muser,
    • Liine Kasak,
    • Lin Zhang,
    • Ekaterina Krymova,
    • and Valentina Boeva
    Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
    ..., or attention mechanisms, drive performance in these high-resolution predictions. To address these knowledge gaps, we systematically evaluate classic architectural choices and introduce ConvNeXt V2 blocks, originally developed for computer vision, as high-resolution feature extractors in deep learning models...
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  4. Resource: Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types
    • Jill E. Moore,
    • Xiao-Ou Zhang,
    • Shaimae I. Elhajjajy,
    • Kaili Fan,
    • Henry E. Pratt,
    • Fairlie Reese,
    • Ali Mortazavi,
    • and Zhiping Weng
    Genome Res. February 2022 32: 389-402; Published in Advance December 23, 2021, doi:10.1101/gr.275723.121
    ...correction, P < 1.0 × 10−16) (Supplemental Fig. S3P). These results suggest that many of the exonic rPeaks likely are not TSSs and may arise from mRNA recapping (Trotman and Schoenberg 2019).To evaluate the ability of the RAMPAGE assay to detect low-abundance and unstable transcripts, we compared our r...
  5. Method: SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
    • Nevena Cvetesic,
    • Harry G. Leitch,
    • Malgorzata Borkowska,
    • Ferenc Müller,
    • Piero Carninci,
    • Petra Hajkova,
    • and Boris Lenhard
    Genome Res. December 2018 28: 1943-1956; Published in Advance November 7, 2018, doi:10.1101/gr.235937.118
    ..., Kanagawa 230-0045, Japan; 6Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway Corresponding authors: ncvetesi@ic.ac.uk, b.lenhard@imperial.ac.ukAbstractCap analysis of gene expression (CAGE) is a methodology for -wide quantitative mapping of mRNA 5′ ends...
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  6. Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
    • Konstantin Licht,
    • Utkarsh Kapoor,
    • Fabian Amman,
    • Ernesto Picardi,
    • David Martin,
    • Prajakta Bajad,
    • and Michael F. Jantsch
    Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
    ...-containing transcripts and mRNAs. The increase in editing upon splicing inhibition is particularly strong for exonic editing sites with adjacent intronic ECSs. Editing in UTRs does not follow a general trend, as a decrease was observed in bone marrow whereas UTR-editing in primary neurons was not shifted. Differences...
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  7. Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
    • German Nudelman,
    • Antonio Frasca,
    • Brandon Kent,
    • Kirsten C. Sadler,
    • Stuart C. Sealfon,
    • Martin J. Walsh,
    • and Elena Zaslavsky
    Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
    ...extensively used to study embryonic development (Howe et al. 2013). The first stage of zebrafish development is characterized by rapid cleavage of the embryonic cells and is entirely driven by the maternally provided mRNA and proteins as the zygotic is transcriptionally inactive until about 3 h post...
  8. Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
    • Khang Ma and
    • Rinki Ratnapriya
    Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
    ...) High-resolution UMAP plots of microglia, PVMs, and monocytes in the brain. (F) The UMAP plots show that the clusters of microglia, PVMs, and monocytes from both the retina and brain overlap perfectly, indicating a high degree of similarity in their subcluster organization across these two tissues. (RGC...
  9. Method: NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
    • Zhengyu Luo,
    • Ran Zhang,
    • Tengfei Hu,
    • Yuting Zhu,
    • Yueming Wu,
    • Wenfei Li,
    • Zhi Zhang,
    • Xuebiao Yao,
    • Haiyi Liang,
    • and Xiaoyuan Song
    Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
    ...of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China; 4Affiliated Psychological Hospital of Anhui Medical University, Hefei Fourth People's Hospital, Anhui Mental Health Center, Hefei...
  10. Method: Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation
    • Ni Huang,
    • Wei Qiang Seow,
    • Alex Appert,
    • Yan Dong,
    • Przemyslaw Stempor,
    • and Julie Ahringer
    Genome Res. February 2022 32: 357-366; Published in Advance December 21, 2021, doi:10.1101/gr.275669.121
    ...Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into architecture and regulation Ni Huang1,2, Wei Qiang Seow1,2, Alex Appert1, Yan Dong1, Przemyslaw Stempor1 and Julie Ahringer1 1The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1...
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