Searching journal content for articles similar to Johnston et al. 29 (8): 1211.

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  1. Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
    • Ju Heon Maeng,
    • H. Josh Jang,
    • Alan Y. Du,
    • Shin-Cheng Tzeng,
    • and Ting Wang
    Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
    ...of the reference proteome database (Purcell et al. 2019; Chong et al. 2020). Recent research expanded the proteome database to include unannotated proteins by mining genomics data, primarily RNA-seq, which revealed peptides that went undetected owing to the limitations of conventional reference proteome approaches...
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  2. Perspective: Cancer cell states and emergent properties of the dynamic tumor system
    • Dalia Barkley,
    • Anjali Rao,
    • Maayan Pour,
    • Gustavo S. França,
    • and Itai Yanai
    Genome Res. October 2021 31: 1719-1727; doi:10.1101/gr.275308.121
    ..., Oh YT, D'Angelo F, Najac RD, Ko A, Frangaj B, Caruso FP, Yu K, Yuan J, et al. 2021. Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities. Nat Cancer 2: 141–156. doi:10.1038/s43018-020-00159-4 ↵Gatenby RA, Vincent TL. 2003. Application...
  3. Method: Accurate estimation of pathway activity in single cells for clustering and differential analysis
    • Daniel Davis,
    • Avishai Wizel,
    • and Yotam Drier
    Genome Res. June 2024 34: 925-936; Published in Advance July 9, 2024, doi:10.1101/gr.278431.123
    ...-documented tool to dissect single-cell-level differences, allowing its users to interrogate tissue physiology and heterogeneity with high sensitivity and accuracy.SiPSiC reveals differential activity of pathways with potential therapeutic implications in SARS-CoV-2-infected cellsWe applied SiPSiC to investigate...
    OPEN ACCESS ARTICLE
  4. Method: A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data
    • Norah Alghamdi,
    • Wennan Chang,
    • Pengtao Dang,
    • Xiaoyu Lu,
    • Changlin Wan,
    • Silpa Gampala,
    • Zhi Huang,
    • Jiashi Wang,
    • Qin Ma,
    • Yong Zang,
    • Melissa Fishel,
    • Sha Cao,
    • and Chi Zhang
    Genome Res. October 2021 31: 1867-1884; Published in Advance July 22, 2021, doi:10.1101/gr.271205.120
    ...governing the mass balance at steady state. The advantage of incorporating FBA into the model is twofold: considering the chemical stoichiometry in FBA could lead to more accurate estimation of the metabolite abundance; and flux estimation for each individual metabolite can be solved, leading to high-resolution...
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  5. Research: Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains
    • Ying-Tao Zhao,
    • Deborah Y. Kwon,
    • Brian S. Johnson,
    • Maria Fasolino,
    • Janine M. Lamonica,
    • Yoon Jung Kim,
    • Boxuan Simen Zhao,
    • Chuan He,
    • Golnaz Vahedi,
    • Tae Hoon Kim,
    • and Zhaolan Zhou
    Genome Res. July 2018 28: 933-942; Published in Advance May 30, 2018, doi:10.1101/gr.233775.117
    ...is that long genes may harbor distinct chromatin domains and higher-order structures compared with short genes (King et al. 2013), which render them vulnerable to the disruption of chromatin regulators. We found that a unique set of long genes, with a median length of 303 kb, harbors BELDs across their entire...
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