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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...
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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
..., rely on short reads and offer the ability to transcriptomically compare different cell types but are limited in their ability to measure differential isoform expression. More recently, long-read sequencing methods have been combined with single-cell and spatial technologies in order to characterize...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
....beerenwinkel@bsse.ethz.chAbstractIn cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging...
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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
...in long-term memory consolidation (Zhang et al. 2018; Yasuda et al. 2022). We next asked if we can validate our single-cell data and the absence of CAMK2A-expressing cells in E-YTH but not in E-YTHmut hippocampi. Although our single-cell data did not reveal any CAMK2A-expressing cells following E...
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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
...predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can systematically miss or misrepresent certain types of alterations, especially structural variants, complex rearrangements, and alterations within repetitive regions. Long...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...mediated by mutated SF3B1 in CLL (bulk or single cell) (Tang et al. 2020; Peng et al. 2024) and MDS (single-cell) (Cortés-López et al. 2023).Here, we used long-read Iso-Seq (Pacific Biosciences [PacBio]) sequencing of 44 patients to investigate the impact of SF3B1 mutations on alternative splicing. Our...
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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
...al. 2022; Kong et al. 2023). Many sequencing-based approaches, using short- or long-read sequencing platforms, map RNA modifications across the transcriptome, revealing their patterns in normal and disease states across various cell types, tissues, organisms, and under different environmental...
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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...V, Wienand K, Yu H, White E, Khorgade A, Shin A, Georgescu C, Campbell CD, Dondi A, et al. 2025. Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution. Genome Res (this issue) 35: 967–986. doi:10.1101/gr.279200.124 ↵Rafehi H...
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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
...) recombination, somatic hypermutation, and class-switch recombination than can be derived from bulk analyses (Dudley et al. 2005; Di Noia and Neuberger 2007; Papalexi and Satija 2018; Jaffe et al. 2022). Single-cell sequencing using long-read approaches can produce reads that span entire transcripts, removing...
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Method: End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
- Alan Derr,
- Chaoxing Yang,
- Rapolas Zilionis,
- Alexey Sergushichev,
- David M. Blodgett,
- Sambra Redick,
- Rita Bortell,
- Jeremy Luban,
- David M. Harlan,
- Sebastian Kadener,
- Dale L. Greiner,
- Allon Klein,
- Maxim N. Artyomov,
- and Manuel Garber
Genome Res. October 2016 26: 1397-1410; Published in Advance July 28, 2016, doi:10.1101/gr.207902.116
...that these extensions resulted in the highest correlationwith full length (Supplemental Fig. S3B). End-sequencing reveals a global change to long 3′ UTR usage upon LPS stimulation Control of gene expression is complex, often involving many different processes (Moore 2005). Alternative promoter and polyadenylation usage...
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