49 Result(s)

Article

Response to: “Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus”

Shaoming Liang, Yiling Li, Yang Chen, Heng Huang, Sijia Li… in Genome Biology (2024)

Article

Estimating genome-wide DNA methylation heterogeneity with methylation patterns

In a heterogeneous population of cells, individual cells can behave differently and respond variably to the environment. This cellular diversity can be assessed by measuring DNA methylation patterns. The loci ...

Pei-Yu Lin, Ya-Ting Chang, Yu-Chun Huang, Pao-Yang Chen in Epigenetics & Chromatin (2023)

Article

The Quartet Data Portal: integration of community-wide resources for multiomics quality control

The Quartet Data Portal facilitates community access to well-characterized reference materials, reference datasets, and related resources established based on a family of four individuals with identical twins ...

**gcheng Yang, Yaqing Liu, Jun Shang, Qiaochu Chen, Qingwang Chen… in Genome Biology (2023)

Article

Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method

Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch-effect correction algorithms are propose...

Ying Yu, Naixin Zhang, Yuanbang Mai, Luyao Ren, Qiaochu Chen, Zehui Cao… in Genome Biology (2023)

Article

Map** genetic variants for nonsense-mediated mRNA decay regulation across human tissues

Nonsense-mediated mRNA decay (NMD) was originally conceived as an mRNA surveillance mechanism to prevent the production of potentially deleterious truncated proteins. Research also shows NMD is an important po...

Bo Sun, Liang Chen in Genome Biology (2023)

Article

RAD21 is the core subunit of the cohesin complex involved in directing genome organization

The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesi...

Yuao Sun, **n Xu, Wenxue Zhao, Yu Zhang, Keyang Chen, Yongzheng Li… in Genome Biology (2023)

Article

Large-scale analysis of de novo mutations identifies risk genes for female infertility characterized by oocyte and early embryo defects

Oocyte maturation arrest and early embryonic arrest are important reproductive phenotypes resulting in female infertility and cause the recurrent failure of assisted reproductive technology (ART). However, the...

Qun Li, Lin Zhao, Yang Zeng, Yan** Kuang, Yichun Guan, Biaobang Chen… in Genome Biology (2023)

Article

BIND&MODIFY: a long-range method for single-molecule map** of chromatin modifications in eukaryotes

Epigenetic modifications of histones are associated with development and pathogenesis of disease. Existing approaches cannot provide insights into long-range interactions and represent the average chromatin st...

Zhe Weng, Fengying Ruan, Weitian Chen, Zhichao Chen, Yeming **e, Meng Luo… in Genome Biology (2023)

Article

Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing

Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, who...

Fang Chen, **ngyan Wang, Seon-Kyeong Jang, Bryan C. Quach… in Nature Genetics (2023)

Article

The histone modification reader ZCWPW1 promotes double-strand break repair by regulating cross-talk of histone modifications and chromatin accessibility at meiotic hotspots

The PRDM9-dependent histone methylation H3K4me3 and H3K36me3 function in assuring accurate homologous recombination at recombination hotspots in mammals. Beyond histone methylation, H3 lysine 9 acetylation (H3...

Shenli Yuan, Tao Huang, Ziyou Bao, Shiyu Wang, **nyue Wu, Jiang Liu… in Genome Biology (2022)

Article

PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar

Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of ...

Shaofei Tong, Yubo Wang, Ningning Chen, Deyan Wang, Bao Liu, Weiwei Wang… in Genome Biology (2022)

Article

Decoding the multicellular ecosystem of vena caval tumor thrombus in clear cell renal cell carcinoma by single-cell RNA sequencing

Vascular invasion with tumor thrombus frequently occurs in advanced renal cell carcinoma (RCC). Thrombectomy is one of the most challenging surgeries with high rate of perioperative morbidity and mortality. Ho...

Yue Shi, Qi Zhang, Hai Bi, Min Lu, Yezhen Tan, Daojia Zou, Liyuan Ge… in Genome Biology (2022)

Article

Dysregulated lncRNA and mRNA may promote the progression of ischemic stroke via immune and inflammatory pathways: results from RNA sequencing and bioinformatics analysis

Long non-coding RNAs (lncRNAs) are widely involved in gene transcription regulation and which act as epigenetic modifiers in many diseases.

Yingshuang Wang, Feifei Feng, **** Zheng, Lijuan Wang, Yanjun Wang… in Genes & Genomics (2022)

Article

YTHDF1 promotes the proliferation, migration, and invasion of prostate cancer cells by regulating TRIM44

Prostate cancer (PCa) is one of the most common malignancies in men. YTHDF1 may play an important role in promoting PCa progression, but there is no reports to date on YTHDF1 function in PCa.

Weijian Li, Gaohuang Chen, Zhenyu Feng, Baoyi Zhu, Lilin Zhou… in Genes & Genomics (2021)

Article

Transcriptional landscape of highly lignified poplar stems at single-cell resolution

Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic ...

Yang Chen, Shaofei Tong, Yuanzhong Jiang, Fandi Ai, Yanlin Feng… in Genome Biology (2021)

Article

Genomic insights into the origin, domestication and diversification of Brassica juncea

Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly ...

Lei Kang, Lunwen Qian, Ming Zheng, Liyang Chen, Hao Chen, Liu Yang… in Nature Genetics (2021)

Article

Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index

Liquid-liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, qu...

Minglei Shi, Kaiqiang You, Taoyu Chen, Chao Hou, Zhengyu Liang… in Genome Biology (2021)

Article

Publisher Correction: Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis

Zhi-Qiang Chen, Yanjun Zan, Pascal Milesi, Linghua Zhou, Jun Chen… in Genome Biology (2021)

Article

Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis

Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived...

Zhi-Qiang Chen, Yanjun Zan, Pascal Milesi, Linghua Zhou, Jun Chen… in Genome Biology (2021)

Article

Correction to: Profiling transcriptomic changes and signaling pathways in atopic dermatitis 2 by integrative analyses on multiple databases

A correction to this paper has been published: https://doi.org/10.1007/s00438-021-01770-5

Yubin Xu, Saizhen Chen, **guang Chen in Molecular Genetics and Genomics (2021)