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  1. Research: ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation
    • Lili Tang,
    • Fei Huang,
    • Wuxin You,
    • Ansgar Poetsch,
    • Rafael Henrique Nóbrega,
    • Deborah Mary Power,
    • Tengfei Zhu,
    • Kaiqiang Liu,
    • Hong-Yan Wang,
    • Qian Wang,
    • Xiwen Xu,
    • Bo Feng,
    • Manfred Schartl,
    • and Changwei Shao
    Genome Res. August 2022 32: 1502-1515; Published in Advance August 12, 2022, doi:10.1101/gr.275962.121
    ...and ESD mechanisms, was used to map the dynamic expression pattern of ncRNAs and mRNA in gonads during sex determination and differentiation. Transcript expression patterns shift during the sex differentiation phase, and ceRNA modulation occurs through crosstalk of differentially expressed long nc...
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  2. Research: Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression
    • Sarah K. Sasse,
    • Margaret Gruca,
    • Mary A. Allen,
    • Vineela Kadiyala,
    • Tengyao Song,
    • Fabienne Gally,
    • Arnav Gupta,
    • Miles A. Pufall,
    • Robin D. Dowell,
    • and Anthony N. Gerber
    Genome Res. November 2019 29: 1753-1765; Published in Advance September 13, 2019, doi:10.1101/gr.248187.119
    ...) indicate that both glucocorticoid and TNF signaling exert repressive effects on the other pathway. We subsequently further classified regulatory crosstalk between the two signaling pathways into three dominant clusters. In cluster one (Fig. 2A), comprising 117 genes, dex and TNF cooperated to enhance...
  3. Corrigendum: Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
    • Jennifer Y. Tan,
    • Tamara Sirey,
    • Frantisek Honti,
    • Bryony Graham,
    • Allison Piovesan,
    • Matthias Merkenschlager,
    • Caleb Webber,
    • Chris P. Ponting,
    • and Ana C. Marques
    Genome Res. September 2015 25: 1410.1
    ...; Supplemental Table S8). A single lnceRNA might, therefore, be as likely as an mRNA to regulate post-transcriptionally the transcript abundance of many mRNAs via crosstalk with many miRNAs.” Corrected versions of Supplemental Figure S9 and Supplemental Table S8 are also now provided online. This correction does...
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  4. Research: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
    • Jennifer Y. Tan,
    • Tamara Sirey,
    • Frantisek Honti,
    • Bryony Graham,
    • Allison Piovesan,
    • Matthias Merkenschlager,
    • Caleb Webber,
    • Chris P. Ponting,
    • and Ana C. Marques
    Genome Res. May 2015 25: 655-666; Published in Advance March 19, 2015, doi:10.1101/gr.181974.114
    ...Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells Jennifer Y. Tan 1 , 2 , 3 , Tamara Sirey 1 , 2 , Frantisek Honti 1 , 2 , 3 , Bryony Graham 4 , 5 , Allison Piovesan 6 , Matthias...
  5. Method: Unified integration of spatial transcriptomics across platforms with LLOKI
    • Ellie Haber,
    • Ajinkya Deshpande,
    • Jian Ma,
    • and Spencer Krieger
    Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
    ...clustering and mitigate batch effects; and (3) a new biological conservation loss that maintains the local neighborhood structure from the preintegration embedding space, ensuring that cell-type relationships established by LLOKI-FP are preserved during batch correction. Together, these loss functions enable...
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  6. Resource: A systems view on DNA damage response kinetics in Tetrahymena
    • Emily Nischwitz,
    • Vivien A.C. Schoonenberg,
    • Rachel Mullner,
    • Albert Fradera-Sola,
    • Susanne Zimbelmann,
    • Joshua J. Smith,
    • and Falk Butter
    Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
    ...to the different genotoxic stressors, highlighting unexpected pathway crosstalk. In addition to the comprehensive analysis presented here, the data can be explored via an accessible user interface. Ultimately, our study provides novel insights into the DNA damage response kinetics in Tetrahymena. [Supplemental...
  7. Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
    • Daijun Zhang,
    • Ren Qi,
    • Xun Lan,
    • and Bin Liu
    Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
    ...addressing issues that may arise with traditional spatial coordinate distance measurements at complex domain boundaries. Finally, the corrected 3D neighborhood graph and ST gene expression data are input into a GAE (Fig. 1, step 4). This model learns the latent spatial representation of spots, which reflects...
  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
    ...integrated and clustered cells from the retina and brain, applying batch effect correction, and visualized them using uniform manifold approximation and projection (UMAP) plots generated with the Seurat package (Hafemeister and Satija 2019). Our analysis revealed overlapping microglia cell clusters between...
  9. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...in one of the dimers permits the correct atomic distance for the disulfide to be formed (Bolduc et al. 2021). All PRDX FIEs, including the one identified in LUAD, result in the loss of charged lysine, arginine, or aspartate residues, either by removing lysine or aspartate in PRDX3; therefore...
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  10. 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
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