Searching journal content for articles similar to Thomas et al. 11 (7): 1227.

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  1. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ...to increase the stability of results in case of strong technical variation and batch effects. UCell is solely based on Mann–Whitney U statistics (Andreatta and Carmona 2021) and is expected to be robust against technical variation as it only uses per-cell gene rank information. JASMINE computes scores...
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  2. Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
    • Tianyu Liu,
    • Tinglin Huang,
    • Wengong Jin,
    • Tinyi Chu,
    • Rex Ying,
    • and Hongyu Zhao
    Genome Res. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...models to jointly denoise and impute spatial transcriptomic data. Our results demonstrate that spRefine yields more robust cell- and spot-level representations after denoising and imputation, substantially improving data integration. In addition, spRefine serves as a strong framework for model...
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  3. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...of H3K27me3 and the acquisition of H3K27ac, which marks active enhancers (Barral and 307 Déjardin, 2023). (5) Active Regulatory Elements (Enhancers/Promoters): Regions displaying 308 strong ATAC-seq and H3K27ac signals, reflecting robust regulatory activity and heightened 309 chromatin accessibility...
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  4. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...expected per human (The 1000 Genomes Project Consortium 2015). Tools that detect SNVs and indels are broadly categorized into two major approaches: traditional statistical methods and machine learning-based techniques. An example of a statistical method is Longshot, which utilizes the Pair-Hidden Markov...
  5. Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
    • Michelle Kudron,
    • Louis Gevirtzman,
    • Alec Victorsen,
    • Bridget C. Lear,
    • Jiahao Gao,
    • Jinrui Xu,
    • Swapna Samanta,
    • Emily Frink,
    • Adri Tran-Pearson,
    • Chau Huynh,
    • Dionne Vafeados,
    • Ann Hammonds,
    • William Fisher,
    • Martha Wall,
    • Greg Wesseling,
    • Vanessa Hernandez,
    • Zhichun Lin,
    • Mary Kasparian,
    • Kevin White,
    • Ravi Allada,
    • Mark Gerstein,
    • LaDeana Hillier,
    • Susan E. Celniker,
    • Valerie Reinke,
    • and Robert H. Waterston
    Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
    ...depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data...
  6. Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
    • Irmgard U. Haussmann,
    • Thomas C. Dix,
    • David W.J. McQuarrie,
    • Veronica Dezi,
    • Abdullah I. Hans,
    • Roland Arnold,
    • and Matthias Soller
    Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
    ...to be correct for high-efficiency cleavage leading to models incorporating weighing of features and/or thermodynamics of secondary structures (Hsu et al. 2013; Doench et al. 2014, 2016; Gagnon et al. 2014; Ren et al. 2014; Wang et al. 2014; Chari et al. 2015; Farboud and Meyer 2015; Hart et al. 2015; Housden et...
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  7. Research: Historical RNA expression profiles from the extinct Tasmanian tiger
    • Emilio Mármol-Sánchez,
    • Bastian Fromm,
    • Nikolay Oskolkov,
    • Zoé Pochon,
    • Panagiotis Kalogeropoulos,
    • Eli Eriksson,
    • Inna Biryukova,
    • Vaishnovi Sekar,
    • Erik Ersmark,
    • Björn Andersson,
    • Love Dalén,
    • and Marc R. Friedländer
    Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
    ...and skin tissues (Fig. 3B,C). This provides further support for the robustness of our analyses and confirms that the thylacine is indeed the primary source of our RNA sequencing data.There were very few RNA reads assigned to prokaryotes or viral species, and their abundance profiles differed between muscle...
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  8. Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
    • Pengfei Lv,
    • Xingzhuo Yang,
    • Xianguo Zhao,
    • Zhangwu Zhao,
    • and Juan Du
    Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
    ...mechanisms in diapause regulation, it remains unclear whether dynamic -wide profiles of epigenetic modifications exist during this process. By investigating multiple histone modifications, we have discovered the essential roles of H3K9me3 and H3K27me3 during diapause of the Asian corn borer. Building upon...
  9. Method: A statistical physics approach for disease module detection
    • Xu-Wen Wang,
    • Dandi Qiao,
    • Michael H. Cho,
    • Dawn L. DeMeo,
    • Edwin K. Silverman,
    • and Yang-Yu Liu
    Genome Res. October 2022 32: 1918-1929; Published in Advance October 11, 2022, doi:10.1101/gr.276690.122
    ...diseases. We found that RFIM, ROBUST, DOMINO, and DIAMOnD are the four most efficient methods, which require significantly shorter running time than ModuleDiscoverer and Hierarchical HotNet (see Fig. 2). Moreover, we found that RFIM shows lower time complexity than other methods across different...
  10. Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
    • Ting-Ying Wu,
    • Ya-Ru Li,
    • Kai-Jyun Chang,
    • Jhen-Cheng Fang,
    • Daisuke Urano,
    • and Ming-Jung Liu
    Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
    ...predicted the four types of Arabidopsis TISs with F1 scores ranging from 0.73 to 0.87 (Fig. 1F, orange; Supplemental Fig. S2B; Supplemental Table S1), showing the robustness of the established ML workflow in identifying TIS prediction models across plants. We observed similar patterns using Arabidopsis...
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