Searching journal content for articles similar to Li et al. 31 (1): 13.

Displaying results 1-10 of 5505
For checked items
  1. 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...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  2. Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
    • Kejia Wen,
    • Lijuan Yang,
    • Tuanlin Xiong,
    • Chao Di,
    • Danhui Ma,
    • Menghua Wu,
    • Zhaoyu Xue,
    • Xuedi Zhang,
    • Li Long,
    • Weimin Zhang,
    • Jiaying Zhang,
    • Xiaolin Bi,
    • Junbiao Dai,
    • Qiangfeng Zhang,
    • Zhi John Lu,
    • and Guanjun Gao
    Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
    ...Critical roles of long noncoding RNAs in Drosophila spermatogenesis Kejia Wen 1 , 6 , Lijuan Yang 1 , 2 , 6 , Tuanlin Xiong 1 , 6 , Chao Di 1 , Danhui Ma 1 , Menghua Wu 1 , Zhaoyu Xue 1 , Xuedi Zhang 1...
  3. 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
    ...of repetitive sequences to the spermatogenic transcriptome.We set out to create a more complete catalog of genes expressed during postreplicative spermatogenesis by isolating several specific cell types, performing a deep-coverage, paired-end RNA-seq analysis and generating a de novo annotation for genes...
    OPEN ACCESS ARTICLE
  4. Method: Accurate assembly of circular RNAs with TERRACE
    • Tasfia Zahin,
    • Qian Shi,
    • Xiaofei Carl Zang,
    • and Mingfu Shao
    Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
    ...full-length circular RNA isoforms in human transcriptomes. Nat Commun 12: 266. doi:10.1038/s41467-020-20459-8 ↵Yang W, Du WW, Li X, Yee AJ, Yang BB. 2016. Foxo3 activity promoted by non-coding effects of circular RNA and Foxo3 pseudogene in the inhibition of tumor growth and angiogenesis. Oncogene 35...
  5. Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
    • Wenli Xu,
    • Chang Liu,
    • Bing Deng,
    • Penghui Lin,
    • Zhenghua Sun,
    • Anrui Liu,
    • Jiajia Xuan,
    • Yuying Li,
    • Keren Zhou,
    • Xiaoqin Zhang,
    • Qiaojuan Huang,
    • Hui Zhou,
    • Qingyu He,
    • Bin Li,
    • Lianghu Qu,
    • and Jianhua Yang
    Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
    ...-encoded microproteins to the TP53 pathway, leading to a better understanding on the complexity of TP53 regulatory network.View larger version: In this window In a new window Figure 7. The expanded TP53 network. Network of the main TP53-inducible coding and noncoding RNAs in human cells as found in this screen. LncRNAs...
  6. Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
    • Michiel de Hoon,
    • Alessandro Bonetti,
    • Charles Plessy,
    • Yoshinari Ando,
    • Chung-Chau Hon,
    • Yuri Ishizu,
    • Masayoshi Itoh,
    • Sachi Kato,
    • Dongyan Lin,
    • Sho Maekawa,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Jay W. Shin,
    • Jens Stolte,
    • Ana Maria Suzuki,
    • Michihira Tagami,
    • Hazuki Takahashi,
    • Supat Thongjuea,
    • Alistair R.R. Forrest,
    • Yoshihide Hayashizaki,
    • Juha Kere,
    • and Piero Carninci
    Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
    .... 2012. 5′ End–centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 7: 542–561. doi:10.1038/nprot.2012.005 ↵Uszczynska-Ratajczak B, Lagarde J, Frankish A, Guigó R, Johnson R. 2018. Towards a complete map of the human long non-coding RNA transcriptome...
    OPEN ACCESS ARTICLE
  7. Resource: Functional annotation of human long noncoding RNAs via molecular phenotyping
    • Jordan A. Ramilowski,
    • Chi Wai Yip,
    • Saumya Agrawal,
    • Jen-Chien Chang,
    • Yari Ciani,
    • Ivan V. Kulakovskiy,
    • Mickaël Mendez,
    • Jasmine Li Ching Ooi,
    • John F. Ouyang,
    • Nick Parkinson,
    • Andreas Petri,
    • Leonie Roos,
    • Jessica Severin,
    • Kayoko Yasuzawa,
    • Imad Abugessaisa,
    • Altuna Akalin,
    • Ivan V. Antonov,
    • Erik Arner,
    • Alessandro Bonetti,
    • Hidemasa Bono,
    • Beatrice Borsari,
    • Frank Brombacher,
    • Christopher J.F. Cameron,
    • Carlo Vittorio Cannistraci,
    • Ryan Cardenas,
    • Melissa Cardon,
    • Howard Chang,
    • Josée Dostie,
    • Luca Ducoli,
    • Alexander Favorov,
    • Alexandre Fort,
    • Diego Garrido,
    • Noa Gil,
    • Juliette Gimenez,
    • Reto Guler,
    • Lusy Handoko,
    • Jayson Harshbarger,
    • Akira Hasegawa,
    • Yuki Hasegawa,
    • Kosuke Hashimoto,
    • Norihito Hayatsu,
    • Peter Heutink,
    • Tetsuro Hirose,
    • Eddie L. Imada,
    • Masayoshi Itoh,
    • Bogumil Kaczkowski,
    • Aditi Kanhere,
    • Emily Kawabata,
    • Hideya Kawaji,
    • Tsugumi Kawashima,
    • S. Thomas Kelly,
    • Miki Kojima,
    • Naoto Kondo,
    • Haruhiko Koseki,
    • Tsukasa Kouno,
    • Anton Kratz,
    • Mariola Kurowska-Stolarska,
    • Andrew Tae Jun Kwon,
    • Jeffrey Leek,
    • Andreas Lennartsson,
    • Marina Lizio,
    • Fernando López-Redondo,
    • Joachim Luginbühl,
    • Shiori Maeda,
    • Vsevolod J. Makeev,
    • Luigi Marchionni,
    • Yulia A. Medvedeva,
    • Aki Minoda,
    • Ferenc Müller,
    • Manuel Muñoz-Aguirre,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Kazuhiro R. Nitta,
    • Shuhei Noguchi,
    • Yukihiko Noro,
    • Ramil Nurtdinov,
    • Yasushi Okazaki,
    • Valerio Orlando,
    • Denis Paquette,
    • Callum J.C. Parr,
    • Owen J.L. Rackham,
    • Patrizia Rizzu,
    • Diego Fernando Sánchez Martinez,
    • Albin Sandelin,
    • Pillay Sanjana,
    • Colin A.M. Semple,
    • Youtaro Shibayama,
    • Divya M. Sivaraman,
    • Takahiro Suzuki,
    • Suzannah C. Szumowski,
    • Michihira Tagami,
    • Martin S. Taylor,
    • Chikashi Terao,
    • Malte Thodberg,
    • Supat Thongjuea,
    • Vidisha Tripathi,
    • Igor Ulitsky,
    • Roberto Verardo,
    • Ilya E. Vorontsov,
    • Chinatsu Yamamoto,
    • Robert S. Young,
    • J. Kenneth Baillie,
    • Alistair R.R. Forrest,
    • Roderic Guigó,
    • Michael M. Hoffman,
    • Chung Chau Hon,
    • Takeya Kasukawa,
    • Sakari Kauppinen,
    • Juha Kere,
    • Boris Lenhard,
    • Claudio Schneider,
    • Harukazu Suzuki,
    • Ken Yagi,
    • Michiel J.L. de Hoon,
    • Jay W. Shin,
    • and Piero Carninci
    Genome Res. July 2020 30: 1060-1072; Published in Advance July 27, 2020, doi:10.1101/gr.254219.119
    ...suitable for functional screenings of our lncRNA (62% found in the nuclear compartment). Besides, the dynamics of secondary effects mediated by different levels of knockdown from different technologies are likely to be observed as discordance when considering the whole transcriptome, where this kind...
    OPEN ACCESS ARTICLE
  8. Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
    • Junling Shi,
    • Jiaqi Xu,
    • Jun Ma,
    • and Feng He
    Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
    ...of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang 310058, China; 4Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China Corresponding authors: jun_ma@zju.edu.cn, feng_he@zju.edu.cnAbstractA class of noncoding RNAs...
  9. 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
    ...) and myelodysplastic syndromes (MDSs). These mutations have different effects on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge on SF3B1 mutation effects on RNA splicing and its contribution to patient survival...
    OPEN ACCESS ARTICLE
  10. Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
    • Richard D.W. Kelly,
    • Kristy R. Stengel,
    • Aditya Chandru,
    • Lyndsey C. Johnson,
    • Scott W. Hiebert,
    • and Shaun M. Cowley
    Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
    ...inhibitor JQ1 (Fig. 4). PRO-seq allows high-resolution mapping of active RNA polymerases across the at both coding and noncoding regions and provides information on both the abundance and directionality of transcripts. Analysis of the transcriptome in LBH589-treated ESCs revealed that the majority of genes...
    OPEN ACCESS ARTICLE
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research