Searching journal content for articles similar to Wenger et al. 23 (5): 889.

Displaying results 1-10 of 21

For checked items

view abstracts
download to citation manager

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
...in reconstructing GRNs. As shown in Figure 1C, comprehensive benchmark experiments were conducted to demonstrate the efficacy of PRISM-GRN in reconstructing GRNs and predicting causality. Experiments on data sets with unpaired omics data and limited prior GRN information were performed to demonstrate PRISM...
Select this article
Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...in the SCN central clock that potentially contributes to maintaining its uniquely stable circadian timekeeping.ResultsGenome-wide promoter and enhancer site mapping in the SCN using histone ChIP-seqTo identify DNA regulatory elements influencing gene transcription in the SCN, we focused on SCN...
OPEN ACCESS ARTICLE
Select this article
Research: An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation
- Andrew M. Lerner,
- Austin J. Hepperla,
- Gregory R. Keele,
- Hashem A. Meriesh,
- Hayretin Yumerefendi,
- David Restrepo,
- Seth Zimmerman,
- James E. Bear,
- Brian Kuhlman,
- Ian J. Davis,
- and Brian D. Strahl
Genome Res. November 2020 30: 1605-1617; Published in Advance October 5, 2020, doi:10.1101/gr.264283.120
...shown in G and Supplemental Figure S2B. n = 3 and data represent mean ± SEM. Half-lives were calculated from single exponential fits to the H3K36me3 and H3K36me2 relative abundance data using GraphPad Prism 5.We then evaluated the functional effects of LANS-Set2. LANS-Set2 was introduced into the KLY78...
Select this article
Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...(Supplemental Fig. S9). These findings collectively demonstrate that HBV integration significantly perturbs transcriptional regulation in affected genomic regions.Cis-activating role of HBV-Enh I in oncogene expressionThe cis-regulatory effects of integrated HBV sequences represent a key mechanism driving...
Select this article
Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...TBI at the single-cell level. We observed cell-specific gene expression changes following mTBI and unveiled diverse cell-to-cell interaction networks that influence a wide array of cellular processes. Moreover, we report novel neurogenesis lineage trajectories and related key transcription factors, which we...
Select this article
Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...downstream from MTOR activity. Our results therefore provide the first comprehensive overview of miRNA function in early mouse embryos during the transition into diapause. Among the predicted upstream TFs, NR2F1 has been implicated in cancer dormancy with associated pluripotency signatures (Sosa et al. 2015...
Select this article
Research: A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
...the computational prediction pipeline described in Eveland et al. (2014) that leverages the Search Tool for Occurrences of Regulatory Motifs (STORM) from the Comprehensive Regulatory Element Analysis and Detection (CREAD) suite of tools (Smith et al. 2006). Enrichment scores for 51 distinct position weight matrices...
OPEN ACCESS ARTICLE
Select this article
Methods: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
- Daisuke Komura,
- Fan Shen,
- Shumpei Ishikawa,
- Karen R. Fitch,
- Wenwei Chen,
- Jane Zhang,
- Guoying Liu,
- Sigeo Ihara,
- Hiroshi Nakamura,
- Matthew E. Hurles,
- Charles Lee,
- Stephen W. Scherer,
- Keith W. Jones,
- Michael H. Shapero,
- Jing Huang,
- and Hiroyuki Aburatani
Genome Res. December 2006 16: 1575-1584; Published in Advance November 22, 2006, doi:10.1101/gr.5629106
...for single amplicons. Multiplex real-time PCR reactions were performed using the ABI Prism 7700 Sequence Detection System (Applied Biosystems) and followed the manufacturer’s guidelines and cycling conditions. For normalization, a VIC-labeled TaqMan probe to the RPPH1 locus (RNA moiety of RNase P) was used...
Select this article
Method: INTEGRATE: gene fusion discovery using whole genome and transcriptome data
- Jin Zhang,
- Nicole M. White,
- Heather K. Schmidt,
- Robert S. Fulton,
- Chad Tomlinson,
- Wesley C. Warren,
- Richard K. Wilson,
- and Christopher A. Maher
Genome Res. January 2016 26: 108-118; Published in Advance November 10, 2015, doi:10.1101/gr.186114.114
...variations (SV), a subset of which may produce gene fusions. Despite some successes, existing bioinformatics tools such as BreakDancer (Chen et al. 2009), VariationHunter (Hormozdiari et al. 2010), CREST (Wang et al. 2011), and PRISM (Jiang et al. 2012) are hindered by intra-tumor heterogeneity, alignment...
Select this article
Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...was measured after 5 days using CellTiter-Glo (Promega) and read with an Envision plate reader. AUCs were computed using GraphPad Prism 9 and normalized. Clustering was performed with ConsensusClusterPlus v1.64.0 (Wilkerson and Hayes 2010) using parameters: reps = 1000, pItem = 0.8, pFeature = 1, algorithm...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Wenger et al. 23 (5): 889.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: