35 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

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

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

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

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

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subty**, and classification, their direct biological impacts at the individual gene leve...

Justin Williams, Beisi Xu, Daniel Putnam, Andrew Thrasher, Chunliang Li… in Genome Biology (2021)

Article

Publisher Correction: Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics

An amendment to this paper has been published and can be accessed via the original article.

Kwangbom Choi, Yang Chen, Daniel A. Skelly, Gary A. Churchill in Genome Biology (2020)

Article

sgBE: a structure-guided design of sgRNA architecture specifies base editing window and enables simultaneous conversion of cytosine and adenosine

We present a base editing system, in which base editors are attached to different sites of sgRNA scaffold (sgBE). Each independent sgBE has its own specific editing pattern for a given target site. Among teste...

Yanhong Wang, Lifang Zhou, Rui Tao, Nan Liu, Jie Long, Fengming Qin… in Genome Biology (2020)

Article

Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics

Single-cell RNA sequencing is a powerful tool for characterizing cellular heterogeneity in gene expression. However, high variability and a large number of zero counts present challenges for analysis and inter...

Kwangbom Choi, Yang Chen, Daniel A. Skelly, Gary A. Churchill in Genome Biology (2020)

Article

Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer

Malignant transformation and progression of cancer are driven by the co-evolution of cancer cells and their dysregulated tumor microenvironment (TME). Recent studies on immunotherapy demonstrate the efficacy i...

Jian Chen, Yun Tan, Fenghuan Sun, Likun Hou, Chi Zhang, Tao Ge… in Genome Biology (2020)

Article

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

An important challenge in pre-processing data from droplet-based single-cell RNA sequencing protocols is distinguishing barcodes associated with real cells from those binding background reads. Existing methods...

Zijian Ni, Shuyang Chen, Jared Brown, Christina Kendziorski in Genome Biology (2020)