Searching journal content for articles similar to Imada et al. 30 (7): 1073.

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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...Transcriptome. Genome Res 14: 1719–1725. Kiyosawa H, Yamanaka I, Osato N, Kondo S, Hayashizaki Y, RIKEN GER Group, GSL Members. 2003. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res 13: 1324–34. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G...
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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
...@bcm.eduAbstractThe vast majority of protein-coding genes in the human produce multiple mRNA isoforms through alternative splicing, significantly enhancing the complexity of the transcriptome and proteome. To establish an efficient method for characterizing transcript isoforms within tissue samples, we conducted...
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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
...Genomics and Transcriptomics Laboratory, Biological and Medical Research Center, Heinrich Heine University and West German Genome Center, 40225 Düsseldorf, Germany; 7Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; 8Institute for Pharmaceutical...
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Method: Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads
- Seong Woo Han,
- San Jewell,
- Andrei Thomas-Tikhonenko,
- and Yoseph Barash
Genome Res. October 2024 34: 1624-1635; Published in Advance September 25, 2024, doi:10.1101/gr.278659.123
...These authors contributed equally to this work. Corresponding author: yosephb@upenn.eduAbstractMapping transcriptomic variations using either short- or long-read RNA sequencing is a staple of genomic research. Long reads are able to capture entire isoforms and overcome repetitive regions, whereas short reads...
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Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
- Shristi Pandey,
- Anna J. Moyer,
- and Summer B. Thyme
Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
...signatures of the neuronal cell types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6-day-postfertilization (dpf), 15-dpf, and adult telencephalon...
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Method: High-confidence coding and noncoding transcriptome maps
- Bo-Hyun You,
- Sang-Ho Yoon,
- and Jin-Wu Nam
Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
...Sciences, Hanyang University, Seoul 133791, Republic of Korea The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic s. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed...
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Research: Cellular age explains variation in age-related cell-to-cell transcriptome variability
- Ming Yang,
- Benjamin R. Harrison,
- and Daniel E.L. Promislow
Genome Res. November 2023 33: 1906-1916; Published in Advance November 16, 2023, doi:10.1101/gr.278144.123
...: promislo@uw.eduAbstractOrgans and tissues age at different rates within a single individual. Such asynchrony in aging has been widely observed at multiple levels, from functional hallmarks, such as anatomical structures and physiological processes, to molecular endophenotypes, such as the transcriptome...
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Method: Dissecting and improving gene regulatory network inference using single-cell transcriptome data
- Lingfeng Xue,
- Yan Wu,
- and Yihan Lin
Genome Res. September 2023 33: 1609-1621; Published in Advance August 14, 2023, doi:10.1101/gr.277488.122
..., 100871; 3Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871 Corresponding author: yihan.lin@pku.edu.cnAbstractSingle-cell transcriptome data has been widely used to reconstruct gene regulatory networks (GRNs) controlling...
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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...and interpret the biological significance of the traits used for estimation. Here we present SCALE, a statistical pipeline that quantifies biological aging in different tissues using explainable features learned from literature and single-cell transcriptomic data. Applying SCALE to the “Mouse Aging Cell Atlas...
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Research: LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
- Jan Attig,
- George R. Young,
- Louise Hosie,
- David Perkins,
- Vesela Encheva-Yokoya,
- Jonathan P. Stoye,
- Ambrosius P. Snijders,
- Nicola Ternette,
- and George Kassiotis
Genome Res. October 2019 29: 1578-1590; Published in Advance September 19, 2019, doi:10.1101/gr.248922.119
...of the role of EREs in cancer is currently hampered by gaps in the annotation and quantitation of the transcriptional activity in cancer of the compendium of ERE-overlapping transcripts the human can produce. By using de novo assembly of cancer transcriptomes, we aimed to provide a comprehensive view of LTR...
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