A5040871734- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Muscle Physiology and Disorders
- Cardiomyopathy and Myosin Studies
- Cell Adhesion Molecules Research
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- Immune Cell Function and Interaction
- Microbial Community Ecology and Physiology
- Circular RNAs in diseases
- Cancer-related gene regulation
- Genetic Neurodegenerative Diseases
- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- Cellular Mechanics and Interactions
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Bioinformatics and Genomic Networks
- MicroRNA in disease regulation
- RNA regulation and disease
- Neurogenetic and Muscular Disorders Research
- vaccines and immunoinformatics approaches
Peking University First Hospital
2023-2025
Peking University
2023-2025
Institute of Biophysics
2012-2024
Chinese Academy of Sciences
2012-2024
Czech Academy of Sciences, Institute of Biophysics
2017-2024
University of Chinese Academy of Sciences
2012-2015
C/EBPα is a critical transcriptional regulator of adipogenesis. How transcription itself regulated poorly understood, however, and remains key question that needs to be addressed for complete understanding adipogenic development. Here, we identify lncRNA, ADINR (adipogenic differentiation induced noncoding RNA), transcribed from position ∼450 bp upstream the gene, orchestrates in vivo. Depletion leads severe defect rescued by overexpression C/EBPα. Moreover, reveal RNA specifically binds PA1...
Abstract Summary: We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data visualization. BioCircos.js facilitates the development of web-based applications circular visualization various data, such as genomic features, genetic variations, gene expression biomolecular interactions. Availability implementation: its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/. Contact: rschen@ibp.ac.cn Supplementary...
The lack of haplotype reference panels and whole-genome sequencing resources specific to the Chinese population has greatly hindered genetic studies in world's largest population. Here, we present NyuWa genome resource, based on deep (26.2×) 2,999 individuals, construct a panel 5,804 haplotypes 19.3 million variants, which is high-quality publicly available population-specific with thousands samples. Compared other panels, reduces Han imputation error rate by margin ranging from 30% 51%....
Abstract Noncoding RNAs (ncRNAs) play key regulatory roles in biological processes by interacting with other biomolecules. With the development of high-throughput sequencing and experimental technologies, extensive ncRNA interactions have been accumulated. Therefore, we updated NPInter database to a fifth version document these interactions. interaction entries were doubled from 1 100 618 2 596 695 manual literature mining data processing. We integrated global RNA–DNA iMARGI, ChAR-seq...
Short tandem repeats (STRs) are abundant and highly mutagenic in the human genome. Many STR loci have been associated with a range of genetic disorders. However, most population-scale studies on variation humans focused European ancestry cohorts or limited by sequencing depth. Here, we depicted comprehensive map 366,013 polymorphic STRs (pSTRs) constructed from 6487 deeply sequenced genomes, comprising 3983 Chinese samples (~31.5x, NyuWa) 2504 1000 Genomes Project (~33.3x, 1KGP). We found...
Abstract Small proteins specifically refer to consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance has been revealed current years, along with the discovery their diverse functions. However, systematic annotation is still insufficient. SmProt was specially developed provide valuable information on for scientific community. Here we present update SmProt, emphasizes reliability...
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, various cancers. However, MEI resources from large-scale genome sequencing still lacking compared those for SNPs SVs. Here, we report comprehensive map 36 699 non-reference MEIs constructed 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) 2677 the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that...
Long-read sequencing has emerged as a transformative technology in recent years, offering significant potential for the molecular diagnosis of unresolved genetic disorders. Despite its promise, comprehensive detection and clinical annotation genomic variants remain intricate technically demanding. We present SUMMER, an integrated structured workflow specifically designed to process raw Nanopore reads. SUMMER facilitates in-depth analysis multiple variant types, including SNV, SV, short...
Background/Objectives: Drug-induced Guillain–Barré Syndrome (GBS) is a severe complication of pharmacotherapy. Previous research has established connection between certain medications and higher GBS risk. However, large-cohort analysis crucial to reveal underlying biological mechanisms drug-induced GBS. This study aimed evaluate the association various drugs currently accessible in Food Drug Administration Adverse Event Reporting System (FAERS) database explore Methods: We analyzed adverse...
Characterizing natural selection signatures and relationships with phenotype spectra is important for understanding human evolution both biological pathological mechanisms. Here, we identified 24 genetic loci under recent by analyzing rare singletons in 3946 high-depth whole-genome sequencing data of Han Chinese. The include immune-related gene regions (MHC cluster, IGH STING1, PSG), alcohol metabolism-related (ADH1B, ALDH2, ALDH3B2), the olfactory perception OR4C16, which MHC ADH1B ALDH2...
// Guifeng Wei 1,2,* , Huaxia Luo Yu Sun Jiagen Li 3 Liqing Tian 1 Liu 1,2 Lihui Jianjun Jie He and Runsheng Chen 1,4 Bioinformatics Laboratory CAS Key of RNA Biology, Institute Biophysics, Chinese Academy Sciences, Beijing, China 2 University Department Thoracic Surgery, Cancer Hospital, Medical Sciences Peking Union College, 4 Research Network Computational RNCB, * These authors have contributed equally to this work Correspondence to: Chen, email: He, Keywords : ESCC, long noncoding RNAs,...
Abstract Cis-regulatory elements have an important role in human adaptation to the living environment. However, lag population genomic cohort studies and epigenomic studies, hinders research adaptive analysis of cis-regulatory populations. In this study, we collected 4,013 unrelated individuals performed a comprehensive selection genome-wide Han Chinese. total, 12.34% regions are under influence selection, where 1.00% enhancers 2.06% promoters positive 0.06% 0.02% balancing selection. Gene...
Long noncoding RNAs (lncRNAs) are pervasively transcribed in the human genome. Recent studies suggest that involvement of lncRNAs diseases could be far more prevalent than previously appreciated. Here we have identified a lncRNA termed Lnc_bc060912 whose expression is increased lung and other tumors. 1.2 kb length composed two exons. The was repressed by p53. suppressed cell apoptosis. Using recently developed method for RNA-pulldown with formaldehyde cross-linking, found interacted DNA...
Introduction . Small noncoding RNAs have important regulatory functions in different cell pathways. It is believed that most of them mainly play role gene post-transcriptional regulation the cytoplasm. Recent evidence suggests miRNA and siRNA activity nucleus. Here, we show distinct genome-wide sub-cellular localization distribution profiles small human breast cancer cells. Methods We separated nuclei from cytoplasm, identified RNA sequences using a high-throughput sequencing platform. To...
Abstract The identification and characterization of long non-coding RNAs (lncRNAs) in diverse biological processes has recently developed rapidly. large amounts scale consistent with developmental complexity eukaryotes, indicating that most these transcripts may have functions the regulation disorder organisms. In particular, Understanding overall significance lncRNAs cancers still remains limited. Here, we found a nuclear-retained lncRNA, termed Lnc_ASNR (apoptosis suppressing-noncoding...
(Stem Cell Reports 5, 856–865; November 10, 2015) The authors regret that Figure 2D and 3C were incorrect in the originally published article. In 2, upper layer images of for adipogenesis assay incorrect. These did not match lower muddled when created. A corrected 2 appears below. As knockdown ADINR resulted a dramatic adipogenic defect had been shown layered images, confirm these changes do affect interpretation their data or conclusion study. 3, image WDR5 was incorrect, version 3...
Our understanding of the molecular pathogenesis LAMA2 -related muscular dystrophy ( -MD) requires improving. Here, we report phenotype, neuropathology and transcriptomics data (scRNA-seq bulk RNA-seq) a new Lama2 knockout mouse (dy H /dy ) which was created based on human -MD mutation hotspot region using CRISPR-Cas9. The dy mice presented severe phenotype with dystrophy. Mouse brain scRNA-seq showed that gene expressed predominantly specifically in vascular leptomeningeal fibroblasts smooth...
Noncoding RNAs are increasingly being recognized as important players in eukaryote biology. However, despite major efforts mapping the Caenorhabditis elegans transcriptome over last couple of years, nonpolyadenylated and intermediate-size noncoding (is-ncRNAs) still incompletely explored. We have combined an enzymatic approach with full-length RNA-Seq is-ncRNAs C. . A total 473 novel has been identified, which a substantial fraction was associated transcription factor binding sites...
Abstract The lack of Chinese population specific haplotype reference panel and whole genome sequencing resources has greatly hindered the genetics studies in world’s largest population. Here we presented NyuWa resource based on deep (26.2X) 2,999 individuals, constructed 5,804 haplotypes 19.3M variants, which is first publicly available with thousands samples. Compared other panels, reduces Han imputation error rate by range 30% to 51%. Population structure simulation tests supported...
Abstract Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, various cancers. However, MEI resources from large-scale genome sequencing still lacking compared those for SNPs SVs. Here, we report comprehensive map 36,699 non-reference MEIs constructed 5,675 genomes, comprising 2,998 Chinese samples (∼26.2X, NyuWa) 2,677 the 1000 Genomes Project (∼7.4X, 1KGP). We...
Abstract Small proteins specifically refer to consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance has been revealed current years, along with the discovery their diverse functions. However, systematic annotation is still insufficient. SmProt was specially developed provide valuable information on for scientific community. Here we present update SmProt, emphasizes reliability...