Searching journal content for articles similar to Stamatoyannopoulos 22 (9): 1602.

Displaying results 1-10 of 3889
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  1. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
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  2. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...). These findings suggest that C. nigoni populations may experience substantially higher selection pressure from pathogens in their native environments compared with C. briggsae populations.Genes encoding Cullin-E3 ubiquitin-ligase-adaptors are major contributors to both gene family and genomic sequence divergence...
  3. 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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  4. Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
    • Sophia N. Lee,
    • Erin C. Banda,
    • Lu Qiao,
    • Sarah L. Thompson,
    • Karan Singh,
    • Ryan A. Hagenson,
    • Teresa Davoli,
    • Stefan F. Pinter,
    • and Jason M. Sheltzer
    Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
    ...Sophia N. Lee1, Erin C. Banda2,5, Lu Qiao1,5, Sarah L. Thompson1, Karan Singh3, Ryan A. Hagenson1, Teresa Davoli3, Stefan F. Pinter2,4 and Jason M. Sheltzer1 1Yale University School of Medicine, New Haven, Connecticut 06510, USA; 2Department of Genetics and Genome Sciences, UCONN Health, University...
  5. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...such as compaction and accessibility, whereas endogenous DNA allows for in cellulo analysis under physiological conditions. Similarly, proteins can be purified and studied in vitro, expressed exogenously from a plasmid, or endogenously produced within the cell from genomic DNA. Although plasmid-based expression...
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  6. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ...Ruhollah Shemirani1, Gillian M. Belbin1,9, Sinead Cullina1,2, Christa Caggiano1, Christopher R. Gignoux3,4, Noah Zaitlen5,6,7 and Eimear E. Kenny1,2,8 1Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 2Department of Genetics and Genomic Sciences...
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  7. 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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  8. Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
    • Judith Arres,
    • Santosh Elavalli,
    • Shalini Behl,
    • Daniel Matias Sanchez,
    • Ayesha Al Ali,
    • Abdelrahman Ahmed Yehia Abdelaziz Saad,
    • Azza Attia,
    • Cyla Minas,
    • Sharika Pariyachery,
    • Shariq Ahmed,
    • Fatmah Aldhuhoori,
    • Nitu Thulasidharan,
    • Gurunath Katagi,
    • Omar Soliman,
    • Shilp Purohit,
    • Vinay Kusuma,
    • Raony Cardenas,
    • Thyago Cardoso,
    • Luis F. Paulin,
    • Philippe Sanio,
    • Joseph Mafofo,
    • Haiguo Wu,
    • Val Zvereff,
    • Albarah El-Khani,
    • Fahed Al Marzooqi,
    • Tiago R. Magalhães,
    • Fritz J. Sedlazeck,
    • and Javier Quilez
    Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
    ...1, Raony Cardenas1, Thyago Cardoso1, Luis F. Paulin2, Philippe Sanio2, Joseph Mafofo1, Haiguo Wu1, Val Zvereff1, Albarah El-Khani1, Fahed Al Marzooqi1, Tiago R. Magalhães1, Fritz J. Sedlazeck2,3,4 and Javier Quilez1 1M42, Abu Dhabi, United Arab Emirates; 2Human Genome Sequencing Center, Baylor...
  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
    ...an overly large window size, which might lose fine-grained structure) and encoding efficiency (not using an excessively small window size, which would require a large bottleneck to capture all local information). In our analysis, w = 2500 results in a good compromise between capturing local genomic...
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  10. Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
    • Zhitao Huang,
    • Ruiqing Zheng,
    • Pengzhen Jia,
    • Xuhua Yan,
    • Jinmiao Chen,
    • and Min Li
    Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
    ..., scSHEFT leverages a deep learning framework to dynamically learn representations from all three data types. On one hand, scSHEFT employs peak-specific encoder to embed the peak count data, helping to preserve the information in original peak features. On the other hand, scSHEFT employs gene...
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