A5035334249- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Epigenetics and DNA Methylation
- Reproductive Biology and Fertility
- Cancer-related molecular mechanisms research
- RNA Interference and Gene Delivery
- Birth, Development, and Health
- RNA regulation and disease
- Advanced biosensing and bioanalysis techniques
- interferon and immune responses
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- MicroRNA in disease regulation
- Machine Learning in Bioinformatics
- Water Quality Monitoring Technologies
- Single-cell and spatial transcriptomics
- Advanced Adaptive Filtering Techniques
- Cancer-related gene regulation
- Robotics and Sensor-Based Localization
- Target Tracking and Data Fusion in Sensor Networks
- Hydrological Forecasting Using AI
- Advanced Neural Network Applications
Institute of Microbiology
2022-2023
Academy of Military Medical Sciences
2023
Nantong University
2023
Xi'an Jiaotong University
2023
Changsha University
2023
Beijing Radiation Center
2010-2021
University of Science and Technology of China
2020-2021
Affiliated Hospital of Shandong University of Traditional Chinese Medicine
2020
Xiangtan University
2014
National University of Defense Technology
2004-2009
Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing silencing through maintenance heterochromatin boundaries or activation blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is only protein implicated in establishment vertebrates. While CTCF has been diverse regulatory functions, studied limited number cell types across human genome. Thus, it not...
Enhancer elements are noncoding stretches of DNA that play key roles in controlling gene expression programmes. Despite major efforts to develop accurate enhancer prediction methods, identifying sequences continues be a challenge the annotation mammalian genomes. One issues is lack large, sufficiently comprehensive and experimentally validated enhancers for humans or other species. Thus, development computational methods based on limited deciphering transcriptional regulatory code encoded...
Abstract Transcriptional enhancers are non-coding segments of DNA that play a central role in the spatiotemporal regulation gene expression programs. However, systematically and precisely predicting remain major challenge. Although existing methods have achieved some success enhancer prediction, they still suffer from many issues. We developed deep learning-based algorithmic framework named PEDLA ( https://github.com/wenjiegroup/PEDLA ), which can directly learn an predictor massively...
N6-methyladenosine (m6A) is the most prevalent epigenetic modification of messenger RNA (mRNA) in higher eukaryotes; this mainly catalyzed by a methyltransferase complex including methyltransferase-like 3 (METTL3) as key factor. Although m6A has been proven to play an essential role diverse biological processes, our knowledge Mettl3 still limited because mutations are lethal embryos both mammals and plants. In study, we knocked down microinjection its specific short interfering RNAs (siRNAs)...
Abstract Mutations in amino acid sequences can provoke changes protein function. Accurate and unsupervised prediction of mutation effects is critical biotechnology biomedicine, but remains a fundamental challenge. To resolve this challenge, here we present Pro tein M utational E ffect P redictor (ProMEP), general multiple sequence alignment-free method that enables zero-shot effects. A multimodal deep representation learning model embedded ProMEP was developed to comprehensively learn both...
Abstract Motivation: The de novo identification of the initiation and termination zones—regions that replicate earlier or later than their upstream downstream neighbours, respectively—remains a key challenge in DNA replication. Results: Building on advances deep learning, we developed novel hybrid architecture combining pre-trained, neural network hidden Markov model (DNN-HMM) for replication domains using timing profiles. Our results demonstrate DNN-HMM can significantly outperform strong,...
Abstract DNase I hypersensitive sites (DHSs) define the accessible chromatin landscape and have revolutionised discovery of distinct cis -regulatory elements in diverse organisms. Here, we report first comprehensive map human transcription factor binding site (TFBS)-clustered regions using Gaussian kernel density estimation based on genome-wide mapping TFBSs 133 cell tissue types. Approximately 1.6 million TFBS-clustered regions, collectively spanning 27.7% genome, were discovered. The TFBS...
Abstract 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 accurate and broadly applicable approaches. Here we develop Optimized Editing Design (OPED), an interpretable nucleotide language model that leverages transfer learning improve its accuracy generalizability for efficiency prediction pegRNAs. Comprehensive validations on various published datasets demonstrate broad...
Lnc2Catlas ( http://lnc2catlas.bioinfotech.org/ ) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class functional lengths over 200 nt and play vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction many human cancers/diseases. It therefore important to understand the underlying relationship between lncRNAs cancers. To this end, we developed compile quantitative associations cancers using three computational...
Abstract 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 based on Smart-seq2 method to perform long-read sequencing. Our analysis describes additional novel transcripts complexity transcriptome, identifying 2280 potential from unannotated loci 6289 splicing isoforms genes. Notably, these transcription start sites are enriched for an active promoter modification,...
The assembly of primordial follicles in mammals represents one the most critical processes ovarian biology. It directly affects number oocytes available to a female throughout her reproductive life. Premature depletion contributes pathology primary insufficiency (POI). To delineate developmental trajectory and regulatory mechanisms during process, we performed RNA-seq on single germ cells from newborn (P0.5) ovaries. Three cell clusters were classified which corresponded three states (germ...
Abstract Aging has many effects on the female reproductive system, among which decreased oocyte quality and impaired embryo developmental potential are most important factors affecting fertility. However, mechanisms underlying aging not yet fully understood. Here, we selected normal reproductively mice constructed a protein expression profile of metaphase II (MII) oocytes from three age groups. A total 187 differentially expressed (DE) proteins were identified, bioinformatics analyses showed...
Abstract Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences enhancer regions. Despite extensive efforts devoted to revealing potential functions and underlying mechanisms eRNAs, it remains an open question whether eRNAs mere transcriptional noise or relevant biologically functional species. Here, we identified catalogue in broad range human cell/tissue types extended our understanding by demonstrating their multi-omic signatures....
An animal model harboring pathogenic mitochondrial DNA (mtDNA) mutations is important to understand the biological links between mtDNA variation and diseases. DdCBE, a DddA-derived cytosine base editor, has been utilized in zebrafish, mice, rats for tC sequence-context targeting human disease modeling. However, other than context cannot be manipulated. Here, we screened combination of different DdCBE pairs at mutation sites with nC (n a, g, or c) identified that left-G1333C (L1333C) + right...
Advances in genome-wide association studies (GWAS) and large-scale sequencing have resulted an impressive growing list of disease- trait-associated genetic variants. Most emphasised the discovery variation coding sequences, however, noncoding regulatory effects responsible for human disease cancer biology been substantially understudied. To better characterise cis-regulatory variation, we performed a comprehensive analysis variants HOT (high-occupancy target) regions, which are considered to...
RNA editing is a post-transcriptional sequence alteration. Current methods have identified sites and facilitated research but require sufficient genomic annotations prior-knowledge-based filtering steps, resulting in cumbersome, time-consuming identification process. Moreover, these limited generalizability applicability species with insufficient or conditions of prior knowledge. We developed DeepRed, deep learning-based method that identifies from primitive sequences without steps...