Searching journal content for articles similar to Lee et al. 35 (12): 2756.

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  1. Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
    • Ran Zhang,
    • Chengxiang Qiu,
    • Galina N. Filippova,
    • Gang Li,
    • Jay Shendure,
    • Jean-Philippe Vert,
    • Xinxian Deng,
    • William Stafford Noble,
    • and Christine M. Disteche
    Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
    ...are unavailable. Sunbear thus enables the projection of single-cell time-series snapshots to multimodal and multicondition views of cellular trajectories.Rapidly improving single-cell sequencing technologies now allows us to characterize diverse and dynamic cellular processes. Multimodal time-series measurements...
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  2. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ..., and the relative proportions of such patterns can provide insights into its mechanisms of formation. Traditional methods based on bisulfite conversion and high-throughput sequencing, such as Illumina, owing to the read size (150 bp) allow epiallele frequency analysis only in high CpG density regions, limiting...
  3. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...(predictive phenotype) because of their “black-box” nature (Novakovsky et al. 2023). For genomic researchers, interpretative information, which is often lacking, can bemore valuable than predictions themselves because it can provide new insights into genetic processes. Traditional linear models, such as -wide...
  4. 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. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
    ...Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read sequencing Kristine Bilgrav Saether,1,2,6 Angelo Salazar Mantero,1,3,6 Marlene Ek,1,3 Maria Pettersson,1,3 Elisabeth Syk Lundberg,1,3 Christopher M. Grochowski,4 Claudia M...
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  5. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ...in pancreatic cancer tumors, while also being essential for pancreatic cancer cell proliferation. Using comparative nanopore direct RNA sequencing, we identify potential METTL2A-mediated m3C sites in poly(A) RNA. These m3C sites are mapped in both messenger RNA and mitochondrial RNA and are enriched in the CC...
  6. 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
    ...with the newer chemistry compared with the previous R9.Clinical genomic applications primarily target genetic variants with functional impact, typically restricting analyses to coding regions, namely, exons. Variants within exons are more likely to produce interpretable functional and phenotypic effects, whereas...
  7. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...-read sequencing technologies are enabling even larger population studies, enhancing our ability to associate genetic variations—particularly those previously undetectable—with human diversity, disease, and other phenotypes. For example, in 2021, the deCODE genetics initiative generated a major large-scale long...
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  8. 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
    ...Dayea Park and Can Cenik Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA Corresponding author: ccenik@austin.utexas.eduAbstractLong-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights...
  9. 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
    ...of microRNA expression analyses is reflected by the existence of thousands of sRNA-seq studies in which matched total RNA-seq data are often unavailable. The lack of paired sequencing experiments limits the analysis of microRNA–gene regulatory networks. Here, we explore whether protein-coding gene...
  10. 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
    ...and is expected to improve the interpretation of transcriptomic data in future genomic studies.RNA sequencing (RNA-seq) has become an essential tool for characterizing transcriptomes (Stark et al. 2019), enabling comprehensive profiling of gene expression, including tissue-specific patterns, disease...
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