Searching journal content for articles similar to Cenik et al..

Displaying results 1-10 of 711

For checked items

view abstracts
download to citation manager

Select this article
Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs Qiuhan Wen1,2, Zhen Wang1, Qi Bao1, Tianli Ding1, Haihan Zhang3, Jianbo Li4, Zhuang Liu5, Jieping Huang2 and Guoqiang Yi1,6,7 1Shenzhen Branch, Guangdong Laboratory of Lingnan...
Select this article
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
...by regulating gene expression, RNA metabolism, and translation. Their dysregulation contributes to the development of human diseases, including cancer. 3-methylcytidine (m3C) primarily occurs in transfer RNA, where it regulates translation, stem cell pluripotency, and mitochondrial function. m3C has also been...
Select this article
Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...,154 cells from all samples passing quality control (QC) for both RNA-seq and ATAC-seq were integrated, clustered, and annotated into 14 cell types (Fig. 2A; Supplemental Fig. S1A). The clustering distinguished nuclei of different cell types by their global pattern of gene expression (for the full list...
Select this article
Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
..., as well as in humans and viruses (Figs. 1⇑–3, 7). Lastly, our models revealed hidden TISs based on mRNA sequences across monocots and dicots, thereby improving gene annotation in plants (Figs. 6, 7). The translation of small or nonAUG TIS-initiated ORFs can expand proteome diversity and produce proteins...
OPEN ACCESS ARTICLE
Select this article
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
...-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent...
Select this article
Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...and identify therapeutic opportunities. Here, we develop a cell type–specific regulatory atlas of the human middle temporal gyrus via leveraging single-nucleus RNA-seq (1,197,032 nuclei) and ATAC-seq (740,875 nuclei) data sets from 84 donors across four stages of AD neuropathological change (ADNC). We observe...
OPEN ACCESS ARTICLE
Select this article
Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...expression (P-value = 4.4 × 10−40), RNA-induced silencing complex (RISC) (P-value = 9.2 × 10−38), DNA-binding transcription factor activity (P-value = 1.6 × 10−13), and structural component of ribosome (P-value = 1.9 × 10−10) (Supplemental Fig. S16).View larger version: In this window In a new window Figure...
OPEN ACCESS ARTICLE
Select this article
Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...batch annotation module built on integrated data; a feature extraction module that captures contextual properties of sSNVs across DNA, RNA, and protein levels; and an analysis module that investigates potential biological mechanisms affected by sSNVs. Fourth, SynMall also continuously curates...
Select this article
Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...regulatory 113 elements across vertebrates. 114 Results 115 In this study we examine the modulation of gene expression, chromatin accessibility and 116 histone modifications in Atlantic salmon following stimulation using poly I:C, a mimic of 117 infection with an RNA virus. A major transcriptomic response...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...) for supervised link prediction in GRN inference, leveraging scRNA-seq data and existing regulatory information to predict latent TF–gene interactions. Similarly, Grace (Wang et al. 2024a) integrates structural causal models with graph neural networks to infer both GRNs and gene causality from scRNA-seq data...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Cenik et al..

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: