Searching journal content for articles similar to Lee et al. 22 (1): 9.

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  1. Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
    • Siyuan Chen,
    • Jiuming Wang,
    • Inkyung Jung,
    • Zhaowen Qiu,
    • Xin Gao,
    • and Yu Li
    Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
    ...from only a few given cell types (Nagano et al. 2017; Ramani et al. 2017; Li et al. 2019; Kim et al. 2020) to thousands of cells (Lee et al. 2019; Liu et al. 2021; Tan et al. 2021) from multiple complex tissues, leading to an exponential increase in analysis time. Therefore, detecting -wide chromatin...
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  2. Method: Inferring chromatin-bound protein complexes from genome-wide binding assays
    • Eugenia G. Giannopoulou and
    • Olivier Elemento
    Genome Res. August 2013 23: 1295-1306; Published in Advance April 3, 2013, doi:10.1101/gr.149419.112
    ...expression from combinatorial binding. (A) Peaks from multiple experiments (TFs, HMs) are merged into nonoverlapping CREs, within the same cell type. (B) For each CRE, the normalized reads intensity in each experiment is estimated. The RC matrix is then produced, representing the CREs in rows, and the reads...
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  3. Resource: Diverse alternative back-splicing and alternative splicing landscape of circular RNAs
    • Xiao-Ou Zhang,
    • Rui Dong,
    • Yang Zhang,
    • Jia-Lin Zhang,
    • Zheng Luo,
    • Jun Zhang,
    • Ling-Ling Chen,
    • and Li Yang
    Genome Res. September 2016 26: 1277-1287; Published in Advance June 30, 2016, doi:10.1101/gr.202895.115
    ...mechanism that can enlarge the diversity of circRNAs. It is well known that most multiexonic genes undergo alternative splicing to generate multiple (linear) mRNAs (Nilsen and Graveley 2010). Thus, alternative splicing can also expand the diversity of circRNAs. For example, some cassette exons are more...
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  4. Research: Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
    • Nathan C. Sheffield,
    • Robert E. Thurman,
    • Lingyun Song,
    • Alexias Safi,
    • John A. Stamatoyannopoulos,
    • Boris Lenhard,
    • Gregory E. Crawford,
    • and Terrence S. Furey
    Genome Res. May 2013 23: 777-788; Published in Advance March 12, 2013, doi:10.1101/gr.152140.112
    ...Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions Nathan C. Sheffield 1 , 2 , Robert E. Thurman 3 , Lingyun Song 2 , Alexias Safi 2 , John A...
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  5. Method: Heterogeneity of transcription factor binding specificity models within and across cell lines
    • Mahfuza Sharmin,
    • Héctor Corrada Bravo,
    • and Sridhar Hannenhalli
    Genome Res. August 2016 26: 1110-1123; Published in Advance June 16, 2016, doi:10.1101/gr.199166.115
    ...of TF occupancy. However, approaches thus far have assumed a uniform TF binding model to explain genome-wide cell-type–specific binding sites. Therefore, the cell type heterogeneity of TF occupancy models, as well as the extent to which binding rules underlying a TF's occupancy are shared across cell...
  6. Research: Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium
    • Gue Su Chang,
    • Angelika A. Noegel,
    • Travis N. Mavrich,
    • Rolf Müller,
    • Lynn Tomsho,
    • Elissa Ward,
    • Marius Felder,
    • Cizhong Jiang,
    • Ludwig Eichinger,
    • Gernot Glöckner,
    • Stephan C. Schuster,
    • and B. Franklin Pugh
    Genome Res. June 2012 22: 1098-1106; Published in Advance March 20, 2012, doi:10.1101/gr.131649.111
    ...and cell type differentiation. The major transition of gene expression during development occurs 4–6 h after onset of starvation (Van Driessche et al. 2002). This transition not only comprises the turning on of developmental genes but also a shutdown of basic cellular functions. At this stage, the cells...
  7. Research: DNA replication and transcription programs respond to the same chromatin cues
    • Yoav Lubelsky,
    • Joseph A. Prinz,
    • Leyna DeNapoli,
    • Yulong Li,
    • Jason A. Belsky,
    • and David M. MacAlpine
    Genome Res. July 2014 24: 1102-1114; Published in Advance July 1, 2014, doi:10.1101/gr.160010.113
    ..., and replication, suggesting that the higher order organization of the in the nucleus is also an important modulator of the transcription and DNA replication programs (Ryba et al. 2010). The replication program is dynamic, responding to developmental and cell-type-specific signals. Embryonic cells replicate...
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  8. Research: Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
    • Sharmistha Pal,
    • Ravi Gupta,
    • Hyunsoo Kim,
    • Priyankara Wickramasinghe,
    • Valérie Baubet,
    • Louise C. Showe,
    • Nadia Dahmane,
    • and Ramana V. Davuluri
    Genome Res. August 2011 21: 1260-1272; Published in Advance June 28, 2011, doi:10.1101/gr.120535.111
    ...such as cell differentiation or migration (Zervas et al. 2005). A critical aspect of its development (proliferation and differentiation of the major cell type, the granule neurons) occurs during postnatal stages, and some genes that are important for normal development are known to express multiple transcripts...
  9. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...of a transcript, and there is a bias toward the ends of a transcript (most often the 3′ end). Relatively few reads cover an exon junction. (B) With long-read sequencing, a read covers all or most of a transcript, including multiple exon junctions. This enables comparisons between cell types in terms...
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  10. Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
    • Alexander J. Ritter,
    • Jolene M. Draper,
    • Christopher Vollmers,
    • and Jeremy R. Sanford
    Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
    ...in each cell type exhibited association with particular subcellular fractions relative to the cytosol. Of the multi-isoform genes, 27% and 19% exhibited significant differential isoform sedimentation in ESCs and NPCs, respectively. Alternative promoter usage and internal exon skipping accounted...
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