Searching journal content for articles similar to L. Strausberg and Levy 17 (7): 965.

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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
..., catalyzed by the adenosine deaminase acting on RNA (ADAR) enzymes, is a posttranscriptional process that modifies RNA sequences and diversifies the transcriptome. ADARs bind to double-stranded RNA (dsRNA) and their specificity and efficiency are affected by the structural properties of these substructures...
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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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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: 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: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
...Single-cell transcriptome and meta profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants Juan Deng1,2,7, Ya-Jing Liu1,7, Wen-Tian Wei1, Qi-Xuan Huang1, Li-Ping Zhao3,4, Ling-Yun Luo1, Qi Zhu2, Lin Zhang2, Yuan Chen2, Yan-Ling Ren5, Shan-Gang Jia6...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...as the major determinants of gene expression profiles in male germ cells, we wondered whether they may serve as alternative promoters driving additional expression of reference transcripts in specific cell types. We thus further compared our de novo transcriptome annotation with GENCODE using gffcompare...
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Research: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans
- Seokjin Ham,
- Sieun S. Kim,
- Sangsoon Park,
- Eun Ji E. Kim,
- Sujeong Kwon,
- Hae-Eun H. Park,
- Yoonji Jung,
- and Seung-Jae V. Lee
Genome Res. November/December 2022 32: 2003-2014; Published in Advance November 9, 2022, doi:10.1101/gr.276515.121
...for additional sequence analyses of the 3′ splice sites.Age-dependent up-regulation of intron-derived transcripts and noncoding RNAs matches chronological agingWe then investigated whether the rates of age-dependent deregulation of transcriptome were affected by a longevity-promoting regimen, focusing on daf-2...
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Resource: Recounting the FANTOM CAGE-Associated Transcriptome
- Eddie Luidy Imada,
- Diego Fernando Sanchez,
- Leonardo Collado-Torres,
- Christopher Wilks,
- Tejasvi Matam,
- Wikum Dinalankara,
- Aleksey Stupnikov,
- Francisco Lobo-Pereira,
- Chi-Wai Yip,
- Kayoko Yasuzawa,
- Naoto Kondo,
- Masayoshi Itoh,
- Harukazu Suzuki,
- Takeya Kasukawa,
- Chung-Chau Hon,
- Michiel J.L. de Hoon,
- Jay W. Shin,
- Piero Carninci,
- Andrew E. Jaffe,
- Jeffrey T. Leek,
- Alexander Favorov,
- Gloria R. Franco,
- Ben Langmead,
- and Luigi Marchionni
Genome Res. July 2020 30: 1073-1081; Published in Advance February 20, 2020, doi:10.1101/gr.254656.119
...results demonstrate that the FC-R2 gene expression atlas is a reliable and powerful resource for exploring both the coding and noncoding transcriptome, providing compelling evidence and robust support to the notion that lncRNA gene classes, including enhancers and promoters, despite not being yet fully...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
..., preserving the spatial and morphological context of gene expression. Here, we describe expanding the chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed...
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Resource: An 11-point time course midgut transcriptome across 72 h after bloodfeeding provides detailed temporal resolution of transcript expression in the arbovirus vector, Aedes aegypti
- Hitoshi Tsujimoto and
- Zach N. Adelman
Genome Res. September 2023 33: 1638-1648; Published in Advance October 6, 2023, doi:10.1101/gr.277808.123
...against viruses. Despite its importance, transcriptomic dynamics with fine temporal resolution across the entire digestion cycle have not yet been reported. To fill this gap, we conducted a transcriptomic analysis of A. aegypti female midguts across a 72-h bloodmeal digestion cycle for 11 time points...

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