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  1. Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
    • Krzysztof H. Banecki,
    • Haoxi Chai,
    • Yijun Ruan,
    • and Dariusz Plewczynski
    Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
    ...within cellular genomics, we find significant advances in single-cell analysis. For instance, single-cell RNA sequencing (scRNA-seq) has revolutionized transcriptomics by offering advantages over traditional bulk analysis (Stegle et al. 2015; Bacher and Kendziorski 2016). Single-cell transcriptomics has...
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  2. Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
    • Kehan Lang,
    • Chenyang Jia,
    • Siyu Li,
    • Yi Guo,
    • Dingjun Hu,
    • and Shengquan Chen
    Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
    ...Interdisciplinary Studies, Nankai University, Tianjin 300071, China ↵4 These authors contributed equally to this work. Corresponding author: chenshengquan@nankai.edu.cnAbstractSingle-cell multiomic sequencing technologies have offered unprecedented insights into cellular heterogeneity by jointly profiling gene...
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  3. Method: Quantifying pathological progression from single-cell transcriptomic data with scPSS
    • Samin Rahman Khan,
    • M Saifur Rahman,
    • M. Sohel Rahman,
    • and Md Abul Hassan Samee
    Genome Res. February 2026 36: 375-386; Published in Advance January 14, 2026, doi:10.1101/gr.280411.125
    ..., and .False discovery rate control using Storey's q-valuesWe identify significant pathological shifts at the single-cell level by performing separate hypothesis testing for each cell. To control for false discoveries from multiple hypothesis testing, we apply the q-value method developed by Storey...
  4. Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
    • Meng Wang,
    • Yumei Li,
    • Jun Wang,
    • Soo Hwan Oh,
    • Yexuan Cao,
    • and Rui Chen
    Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
    ...-Iseppi et al. 2021). In our study, we developed a workflow designed to streamline the analysis aspect of high-throughput long-read RNA sequencing data, enabling the identification of transcript isoforms at the single-cell level. Our workflow modified the 10x Genomics scRNA-seq protocol (Gupta et al. 2018...
  5. Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
    • Wenhao Zhang,
    • Lan Cao,
    • Xiaoxuan Gu,
    • Yongyu Long,
    • and Ying Wang
    Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
    ...and target genes (Gao et al. 2023).Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling at the individual cell level, revealing cellular heterogeneity with single-cell resolution and significantly enhancing the understanding of cell type–specific gene regulation (Chen and Liu 2022; Kartha...
  6. Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
    • Qian Qin,
    • Victoria Popic,
    • Kirsty Wienand,
    • Houlin Yu,
    • Emily White,
    • Akanksha Khorgade,
    • Asa Shin,
    • Christophe Georgescu,
    • Catarina D. Campbell,
    • Arthur Dondi,
    • Niko Beerenwinkel,
    • Francisca Vazquez,
    • Aziz M. Al'Khafaji,
    • and Brian J. Haas
    Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
    ...differences in the detection of fusion transcripts based on long- versus short-read sequencing. In these single-cell applications, the 10x Genomics single-cell sequencing libraries were based on 3′-end sequencing, inherently biasing sequencing coverage to the very 3′ ends of sequenced isoforms with Illumina...
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  7. Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
    • Kristine Bilgrav Saether,
    • Angelo Salazar Mantero,
    • Marlene Ek,
    • Maria Pettersson,
    • Elisabeth Syk Lundberg,
    • Christopher M. Grochowski,
    • Claudia M.B. Carvalho,
    • Jesper Eisfeldt,
    • and Anna Lindstrand
    Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
    ...structure of the derivative Chromosome 7 identified in RD_P328. (B) Integrative Genomics Viewer images of short-read sequencing (srGS) and long-read sequencing (lrGS) data for each BPJ. (C) Breakpoint sequences of the two BPJs with the chimeric sequence in the center aligned to the reference sequences shown...
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  8. 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 single-cell technology with the long-range information offered by long-read sequencing has resulted in new insights into the transcriptomes of disease-relevant systems with heterogeneous cell populations. In cancer, transcriptomic variation among cells can be layered on top of genomic variation. Short...
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  9. 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
    ...). Importantly, these HBV integration events, along with their human breakpoints, likely play significant roles in hepatocarcinogenesis and warrant further investigation.Structural variation (SV) analysis was performed on the inserted HBV sequences and revealed inversions, duplications, insertions, and deletions...
  10. Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
    • Kristine Bilgrav Saether,
    • Jesper Eisfeldt,
    • Jesse D. Bengtsson,
    • Ming Yin Lun,
    • Christopher M. Grochowski,
    • Medhat Mahmoud,
    • Hsiao-Tuan Chao,
    • Jill A. Rosenfeld,
    • Pengfei Liu,
    • Marlene Ek,
    • Jakob Schuy,
    • Adam Ameur,
    • Hongzheng Dai,
    • Undiagnosed Diseases Network,
    • James Paul Hwang,
    • Fritz J. Sedlazeck,
    • Weimin Bi,
    • Ronit Marom,
    • Josephine Wincent,
    • Ann Nordgren,
    • Claudia M.B. Carvalho,
    • and Anna Lindstrand
    Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
    ...,102,785–51,230,413 (GRCh38) did not contain any known genes and consists of 51% repeat sequence; 49% interspersed repeats, and 2% simple repeats (Fig. 6C). Discordant reads pairs in srGS and split reads in lrGS were present in the GRCh37 alignment at the 6q16.1 breakpoint, partnering with multiple genomic locations...
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