Searching journal content for articles similar to Hammer et al. 20 (6): 847.

Displaying results 1-10 of 6093
For checked items
  1. Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
    • Daffodil M. Canson,
    • Michael T. Parsons,
    • Gemma Moir-Meyer,
    • Troy Dumenil,
    • Gemma Montalban,
    • Erica Lin,
    • Terri P. McVeigh,
    • Aimee L. Davidson,
    • Shaun M. Bouckaert,
    • Matt Trau,
    • Darren Korbie,
    • and Amanda B. Spurdle
    Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
    ...additional advantages in that it could test intronic and exonic variants for their effect on exon skipping and alternative splice site usage. Although MaPSy measured these splicing effects for exonic variants only, Vex-seq and MFASS tested intronic and exonic variants but only measured exon skipping...
  2. 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
    ...scoring approach.These findings further demonstrate that LLOKI not only enables effective integration of heterogeneous spatial transcriptomics data but also facilitates the discovery of biologically meaningful gene programs, such as the one defining tumor-infiltrating T cells in ovarian cancer...
    OPEN ACCESS ARTICLE
  3. Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
    • Yidi Deng,
    • Jiadong Mao,
    • Jarny Choi,
    • and Kim-Anh Lê Cao
    Genome Res. April 2026 36: 785-801; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
    ...such as differentiation, proliferation, and responses to environmental stimuli. The emergence of high-throughput sequencing, particularly in transcriptomics in the early 2000s, has enabled rapid and affordable quantification of gene expression. Since then, substantial research efforts have been dedicated to developing...
    OPEN ACCESS ARTICLE
  4. Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
    • Tanner D. Jensen,
    • Bohan Ni,
    • Chloe M. Reuter,
    • John E. Gorzynski,
    • Sarah Fazal,
    • Devon Bonner,
    • Rachel A. Ungar,
    • Pagé C. Goddard,
    • Archana Raja,
    • Euan A. Ashley,
    • Jonathan A. Bernstein,
    • Stephan Zuchner,
    • Undiagnosed Diseases Network,
    • Michael D. Greicius,
    • Stephen B. Montgomery,
    • Michael C. Schatz,
    • Matthew T. Wheeler,
    • and Alexis Battle
    Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
    ...continues to drop, higher read-depth LR-GS could excel at calling both SNV, small variants, and SVs, enabling LR-only tests in the clinic.Beyond variant discovery, our work investigates the functional impact of LR-GS rare SVs and TREs with expression outliers measured from RNA-seq. We reinforce previous...
    OPEN ACCESS ARTICLE
  5. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...of Biomedical Informatics, Columbia University, New York, New York 10032, USA Corresponding author: hagen.u.tilgner@gmail.comAbstractRNA isoform diversity, produced via alternative splicing, and alternative usage of transcription start and poly(A) sites, results in varied transcripts being derived from the same...
    OPEN ACCESS ARTICLE
  6. 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...
  7. Method: Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data
    • Lulu Yan,
    • Jinyu Cheng,
    • Qing Nie,
    • and Xiaoqiang Sun
    Genome Res. June 2025 35: 1400-1414; Published in Advance April 22, 2025, doi:10.1101/gr.279857.124
    ...Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data Lulu Yan1,4, Jinyu Cheng2,4, Qing Nie3 and Xiaoqiang Sun1 1School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China; 2Zhongshan School of Medicine, Sun Yat-sen University...
  8. Method: Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
    • Hang Zhang,
    • Yi Zhang,
    • Kai Ming Ting,
    • Jie Zhang,
    • and Qiuran Zhao
    Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
    ...to this work. Corresponding authors: tingkm@nju.edu.cn, zhangj_ai@nju.edu.cnAbstractSpatial transcriptomics are a collection of technologies that have enabled characterization of gene expression profiles and spatial information in tissue samples. Existing methods for clustering spatial transcriptomics data...
    OPEN ACCESS ARTICLE
  9. Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
    • John Beaulaurier,
    • Lynn Ly,
    • J. Andrew Duty,
    • Carly Tyer,
    • Christian Stevens,
    • Chuan-Tien Hung,
    • Akash Sookdeo,
    • Alex W. Drong,
    • Shreyas Kowdle,
    • Axel Guzman-Solis,
    • Domenico Tortorella,
    • Daniel J. Turner,
    • Sissel Juul,
    • Scott Hickey,
    • and Benhur Lee
    Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
    ...with chronic infections like HIV (Yu and Guan 2014). These findings should be considered when choosing a sequencing platform for future antibody repertoire studies.A matching whole transcriptome library from the MBC gate revealed preferential isoform expression in certain clusters of MBCs, indicating a level...
    OPEN ACCESS ARTICLE
  10. Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
    • Lin Li,
    • Xianbin Su,
    • and Ze-Guang Han
    Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
    .... Recent advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies have empowered the comprehensive characterization of gene programs at both single-cell and spatial resolutions. Here, we present DeCEP, a computational framework designed to characterize context...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research