Searching journal content for articles similar to Warren et al. 21 (5): 790.

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  1. Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
    • Artem Mikelov,
    • George Nefediev,
    • Alexander Tashkeev,
    • Oscar L. Rodriguez,
    • Diego Aguilar Ortmans,
    • Valeriia Skatova,
    • Mark Izraelson,
    • Alexey N. Davydov,
    • Stanislav Poslavsky,
    • Souad Rahmouni,
    • Corey T. Watson,
    • Dmitriy Chudakov,
    • Scott D. Boyd,
    • and Dmitry Bolotin
    Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
    ...@milaboratories.comAbstractAllelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research...
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  2. 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
    ...overexpression analysis overlapped with SPC and SNC genes, respectively. The small overlap potentially reflects distinct biological contexts of HEK-293T cells and peripheral nerves.Targets of multiple miRNAs were enriched in the upregulated genes. Importantly, among the top 20 miRNAs, miR-9, miR-651, miR-520a-5p...
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  3. Research: Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
    • Blandine C. Mercier,
    • Emmanuel Labaronne,
    • David Cluet,
    • Laura Guiguettaz,
    • Nicolas Fontrodona,
    • Alicia Bicknell,
    • Antoine Corbin,
    • Mélanie Wencker,
    • Fabien Aube,
    • Laurent Modolo,
    • Karina Jouravleva,
    • Didier Auboeuf,
    • Melissa J. Moore,
    • and Emiliano P. Ricci
    Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
    ...determinants of TDD magnitude. Consistently, all transcripts that undergo changes in ribosome density within their coding sequence upon T cell activation display a corresponding change in their TDD level. Moreover, we reveal a dynamic modulation in the relationship between GC3 content and TDD upon T cell...
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  4. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...
  5. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...-associated changes, and cell type–specific signatures (Glinos et al. 2022). Short-read sequencing remains the most widely used method for large-scale studies (Djebali et al. 2012) due to its ability to capture even low-abundance transcripts with high base-calling accuracy through massively parallel read generation...
  6. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent...
  7. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...RNA–mRNA pairs. For a dual mRNA/miRNA profile, we recommend sequencing the ≥25 nucleotide fraction at 5 million or more reads. To confirm the utility of this approach, we apply our method to breast cancer sRNA-seq data sets lacking total RNA-seq data and achieve 75% recall and 64% accuracy comparing inferred...
  8. Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    • Wei-Hao Lee,
    • Lechuan Li,
    • Ruth Dannenfelser,
    • and Vicky Yao
    Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
    ...to determine which signatures are most relevant to each label. Subsequently, we can directly visualize the relevant component of Hstimulation to reveal which cell types are predominantly affected by the condition (Fig. 3C). The low-dimensional representation visualizes the cell embeddings, with colors...
  9. Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
    • Kangli Wang,
    • Weikun Xia,
    • Yingli Gu,
    • Songpeng Zu,
    • Qian Yang,
    • Maria Luisa Amaral,
    • Yaozhi Wang,
    • Allen Wang,
    • Xiang-Dong Fu,
    • William C. Mobley,
    • and Bing Ren
    Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
    ...in the microglia data set. We observed a significant enrichment of upregulated DEGs in these signatures (Fig. 2D), and signature scores displayed a clear trend of increasing expression with age (Fig. 2E).Functional enrichment analysis of age-associated DEGs revealed that upregulated DEGs in several subclasses were...
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  10. Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
    • An Wang,
    • Stephanie Hicks,
    • Donald Geman,
    • and Laurent Younes
    Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
    ...signatures from rare sources of variability. To facilitate the discovery of genes associated with all sources of transcriptomic variability, we introduce geneCover, a label-free correlation-based marker gene selection method designed for single-cell RNA sequencing and spatial transcriptomics data. gene...
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