26 Result(s)

Article

Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering

Mutations in amino acid sequences can provoke changes in protein function. Accurate and unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but remains a fundamental chall...

Peng Cheng, Cong Mao, ** Tang, Sen Yang, Yu Cheng, Wuke Wang, Qiuxi Gu… in Cell Research (2024)

Article

Design of prime-editing guide RNAs with deep transfer learning

Prime editors (PEs) are promising genome-editing tools, but effective optimization of prime-editing guide RNA (pegRNA) design remains a challenge owing to the lack of accurate and broadly applicable approaches...

Feng Liu, Shuhong Huang, Jiongsong Hu, **aozhou Chen… in Nature Machine Intelligence (2023)

Article

Cytosine and adenine deaminase base-editors induce broad and nonspecific changes in gene expression and splicing

Cytosine or adenine base editors (CBEs or ABEs) hold great promise in therapeutic applications because they enable the precise conversion of targeted base changes without generating of double-strand breaks. Ho...

Jiao Fan, Yige Ding, Chao Ren, Ziguo Song, Jie Yuan, Qiuzhen Chen… in Communications Biology (2021)

Article

Author Correction: High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22148-6

Yunbo Qiao, Chao Ren, Shisheng Huang, Jie Yuan, **ngchen Liu… in Nature Communications (2021)

Article

High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing

The transcriptome of the preimplantation mouse embryo has been previously annotated by short-read sequencing, with limited coverage and accuracy. Here we utilize a low-cell number transcriptome based on the Sm...

Yunbo Qiao, Chao Ren, Shisheng Huang, Jie Yuan, **ngchen Liu… in Nature Communications (2020)

Article

Differential roles of Stella in the modulation of DNA methylation during oocyte and zygotic development

Longsen Han, Chao Ren, Jun Zhang, Wenjie Shu, Qiang Wang in Cell Discovery (2019)

Article

The landscape of the A-to-I RNA editome from 462 human genomes

A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological processes in metazoans. However, how and to what extent A-to-I editing diversifies and s...

Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, **aochen Bo, Wenjie Shu in Scientific Reports (2018)

Article

Publisher Correction: Embryonic defects induced by maternal obesity in mice derive from Stella insufficiency in oocytes

In the version of this article originally published, the positions of Wenjie Shu and Qiang Wang in the author list were reversed and incorrect images were displayed in the HTML for Supplementary Figs. 1–12. Th...

Longsen Han, Chao Ren, Ling Li, **aoyan Li, Juan Ge, Haichao Wang… in Nature Genetics (2018)

Article

Accurate identification of RNA editing sites from primitive sequence with deep neural networks

RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filter...

Zhangyi Ouyang, Feng Liu, Chenghui Zhao, Chao Ren, Gaole An… in Scientific Reports (2018)

Article

Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers

Lnc2Catlas (http://lnc2catlas.bioinfotech.org/) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional n...

Chao Ren, Gaole An, Chenghui Zhao, Zhangyi Ouyang, **aochen Bo… in Scientific Reports (2018)

Article

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and un...

Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao… in Scientific Reports (2017)

Article

Genome-wide identification and characterisation of HOT regions in the human genome

HOT (high-occupancy target) regions, which are bound by a surprisingly large number of transcription factors, are considered to be among the most intriguing findings of recent years. An improved understanding ...

Hao Li, Feng Liu, Chao Ren, **aochen Bo, Wenjie Shu in BMC Genomics (2016)

Article

PEDLA: predicting enhancers with a deep learning-based algorithmic framework

Transcriptional enhancers are non-coding segments of DNA that play a central role in the spatiotemporal regulation of gene expression programs. However, systematically and precisely predicting enhancers remain...

Feng Liu, Hao Li, Chao Ren, **aochen Bo, Wenjie Shu in Scientific Reports (2016)

Article

Functional annotation of HOT regions in the human genome: implications for human disease and cancer

Advances in genome-wide association studies (GWAS) and large-scale sequencing studies have resulted in an impressive and growing list of disease- and trait-associated genetic variants. Most studies have emphas...

Hao Li, Hebing Chen, Feng Liu, Chao Ren, Shengqi Wang, **aochen Bo… in Scientific Reports (2015)

Article

An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape

DNase I hypersensitive sites (DHSs) define the accessible chromatin landscape and have revolutionised the discovery of distinct cis-regulatory elements in diverse organisms. Here, we report the first comprehensiv...

Hebing Chen, Hao Li, Feng Liu, **aofei Zheng, Shengqi Wang… in Scientific Reports (2015)

Article

Correlation between sequence conservation and structural thermodynamics of microRNA precursors from human, mouse, and chicken genomes

Previous studies have shown that microRNA precursors (pre-miRNAs) have considerably more stable secondary structures than other native RNAs (tRNA, rRNA, and mRNA) and artificial RNA sequences. However, pre-miR...

Ming Ni, Wenjie Shu, **aochen Bo, Shengqi Wang, Songgang Li in BMC Evolutionary Biology (2010)