Searching journal content for articles similar to Koonin 7 (5): 418.

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  1. Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
    • Elina Abaev-Schneiderman,
    • Linh Nguyen,
    • Raz Shalev,
    • Tzofit Elbaz Biton,
    • Anand Chopra,
    • Giritharan Jagadeesan,
    • Daniel Sevilla-Sanchez,
    • Nili Tickotsky Moskovitz,
    • Liron Levin,
    • Michal Feldman,
    • Capucine Van Rechem,
    • and Dan Levy
    Genome Res. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
    ...polymerization and smooth muscle contraction. Here, we show that the genomic distribution of ACTB is SETD3-dependent and that this regulation modulates the transcription of genes involved in cell adhesion and mRNA translation in colorectal cancer cells. Proteomic analyses reveal that ACTB and SETD3 interact...
  2. Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
    • Yali Zhang,
    • Yayi Zhou,
    • Yangyang Chen,
    • Xueyu Wang,
    • Boyan Hu,
    • Shahid Siddique,
    • Romnick A. Latina,
    • Veronica I. Casey,
    • Dexin Bo,
    • Yucheng Liao,
    • Min Zhang,
    • Ming Sun,
    • Fengjuan Zhang,
    • and Dadong Dai
    Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
    ...Illumina short-reads data to assemble the A. avenae . We assessed the ploidy of A. avenae and confirmed it to be diploid (Supplemental Fig. S2A). The haploid size was estimated to be ∼173 Mb (Supplemental Fig. S2B). Furthermore, k-mer–based analyses revealed a high level of genomic heterozygosity (∼6...
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  3. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ....edu.cnAbstractPredicting phenotypes from genomic mutations remains a major genetic challenge. Traditional statistical methods (such as GBLUP and BayesR) have limitations, including reliance on artificial prior assumptions, and hard to capture epistatic effects. Machine learning (ML) has emerged as a powerful alternative for genomic...
  4. 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
    ...downloaded from National Cancer Institute’s Genomic Data Commons portal (Heath et al. 2021). Signal P-value bigWig files were then generated using the ENCODE’s ATAC-seq processing pipeline (https://doi.org/10.5281/zenodo.211733). All data sets used in this study are listed in Supplemental Table S1...
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  5. 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
    ...when corresponding single-cell data are not available. To verify the applicability of our devised signature in bulk tumors, we used RNA-seq from The Cancer Genome Atlas (TCGA) data sets and scored both our cancer-cell EMT and hallmark EMT signatures.Scores of the ANS-derived signature showed higher...
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  6. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...David R. Lougheed1,2, Tomi Pastinen3 and Guillaume Bourque1,2,4 1Canadian Centre for Computational Genomics, Montréal, Québec H3A 0G1, Canada; 2Department of Human Genetics, McGill University, Montréal, Québec H3A 0G1, Canada; 3Genomic Medicine Center, Children's Mercy Hospital and Research...
  7. Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
    • Qinhu Zhang,
    • Siguo Wang,
    • Zhipeng Li,
    • Wenzheng Bao,
    • Wenjian Liu,
    • and De-Shuang Huang
    Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
    ...Qinhu Zhang1,2, Siguo Wang1, Zhipeng Li1, Wenzheng Bao3, Wenjian Liu4 and De-Shuang Huang1,5 1Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo 315201, China; 2Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China; 3School...
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  8. Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
    • Kevin S. O'Leary,
    • Meng-Yen Li,
    • Kevyn Jackson,
    • Lijie Shi,
    • Elena Ezhkova,
    • Bernice E. Morrow,
    • and Deyou Zheng
    Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
    OPEN ACCESS ARTICLE
  9. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ..., Barcelona 08034, Spain; 3Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, USA; 4Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; 5Institute for Computational and Mathematical Engineering...
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  10. Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
    • Vikram S. Shivakumar and
    • Ben Langmead
    Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
    ...1.4 to define genic and protein-coding regions; Morales et al. 2022). We also found 1410 (13.6%) elements spanned intron–exon boundaries. These results are consistent with previously reported genomic distributions of ultraconserved elements in humans (Cummins et al. 2024), highlighting the potential...
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