A5100392447- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- RNA modifications and cancer
- Genomics and Rare Diseases
- RNA Research and Splicing
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- Biomedical Text Mining and Ontologies
- Epigenetics and DNA Methylation
- Genomic variations and chromosomal abnormalities
- Computational Drug Discovery Methods
- Chromosomal and Genetic Variations
- Gene Regulatory Network Analysis
- Algorithms and Data Compression
- Circular RNAs in diseases
- Single-cell and spatial transcriptomics
- Genetic Associations and Epidemiology
- Molecular Biology Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Genetic diversity and population structure
Harbin Institute of Technology
2016-2025
Third Hospital of Hebei Medical University
2022-2025
Hebei Medical University
2022-2025
Zhengzhou Institute of Machinery
2024
Ministry of Education of the People's Republic of China
2024
Heilongjiang Institute of Technology
2015-2024
Peking Union Medical College Hospital
2022-2024
Chinese Academy of Medical Sciences & Peking Union Medical College
2022-2024
Anhui Medical University
2024
National Clinical Research Center for Digestive Diseases
2024
Abstract Motivation Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence regions high heterozygosity often results assemblers creating two copies rather than one copy a region, leading to breaks contiguity compromising downstream steps such as gene annotation. Several tools have been developed resolve this problem. they either focus only on removing...
'miR2Disease', a manually curated database, aims at providing comprehensive resource of microRNA deregulation in various human diseases. The current version miR2Disease documents 1939 relationships between 299 microRNAs and 94 diseases by reviewing more than 600 published papers. Around one-seventh the microRNA–disease represent pathogenic roles deregulated disease. Each entry contains detailed information on relationship, including ID, disease name, brief description an expression pattern...
The identification of disease-related microRNAs is vital for understanding the pathogenesis diseases at molecular level, and critical designing specific tools diagnosis, treatment prevention. Experimental poses considerable difficulties. Computational analysis microRNA-disease associations an important complementary means prioritizing further experimental examination. Herein, we devised a computational model to infer potential by entire human microRNAome interest. We tested on 270 known...
Abstract Long-read sequencing is promising for the comprehensive discovery of structural variations (SVs). However, it still non-trivial to achieve high yields and performance simultaneously due complex SV signatures implied by noisy long reads. We propose cuteSV, a sensitive, fast, scalable long-read-based detection approach. cuteSV uses tailored methods collect various types SVs employs clustering-and-refinement method implement sensitive detection. Benchmarks on simulated real long-read...
The identification of disease-related microRNAs is vital for understanding the pathogenesis disease at molecular level and may lead to design specific tools diagnosis, treatment prevention. Experimental poses difficulties. Computational prediction microRNA-disease associations one complementary means. However, major issue in microRNA studies lack bioinformatics programs accurately predict associations. Herein, we present a machine-learning-based approach distinguishing positive from negative...
Copy number variation (CNV) has been found to play an important role in human disease. Next-generation sequencing technology, including whole-genome (WGS) and whole-exome (WES), become a primary strategy for studying the genetic basis of Several CNV calling tools have recently developed on WES data. However, comparative performance these using real data remains unclear. An objective evaluation study practical research situations would be beneficial. Here, we evaluated four well-known...
Abstract Circular RNAs (circRNAs) have emerged as an important class of functional RNA molecules. Short-read sequencing (RNA-seq) is a widely used strategy to identify circRNAs. However, inherent limitation short-read RNA-seq that it does not experimentally determine the full-length sequences and exact exonic compositions Here, we report isoCirc, for circRNA isoforms, using rolling circle amplification followed by nanopore long-read sequencing. We describe integrated computational pipeline...
The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation potential functions lncRNA genes is helpful guide further experimental studies on lncRNAs. In this study, based expression correlation between lncRNAs and protein-coding across 19 normal tissues, we used hypergeometric test annotate a single or set with significantly enriched functional terms among that...
Background Measuring similarity between diseases plays an important role in disease-related molecular function research. Functional associations genes and semantic are often used to identify pairs of similar from different perspectives. Currently, it is still a challenge exploit both them calculate disease similarity. Therefore, new method (SemFunSim) that integrates functional association proposed address the issue. Methods SemFunSim designed as follows. First all, FunSim (Functional...
Long non-coding RNAs (lncRNAs) have emerged as critical regulators of genes at epigenetic, transcriptional and post-transcriptional levels, yet what are regulated by a specific lncRNA remains to be characterized. To assess the effects on gene expression, an increasing number researchers profiled genome-wide or individual expression level change after knocking down overexpressing lncRNA. Herein, we describe curated database named LncRNA2Target, which stores lncRNA-to-target is publicly...
We present a kind of harmonic mode locking bound-state solitons in fiber laser based on molybdenum disulfide (MoS(2)) saturable absorber (SA). The locker is fabricated by depositing MoS(2) nanosheets D-shaped (DF). In the laser, two form pulses with temporal separation 3.4 ps, and are equally distributed at repetition rate 125 MHz, corresponding to 14th harmonics fundamental cavity (8.968 MHz). Single- multiple-pulses emissions also observed changing pump power optimizing DF SA. Our...
Abstract Motivation: The development of high-throughput sequencing technologies has enabled novel methods for detecting structural variants (SVs). Current are typically based on depth coverage or pair-end mapping clusters. However, most these only report an approximate location each SV, rather than exact breakpoints. Results: We have developed pair-read informed split (PRISM), a method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses...
As high-throughput sequencing (HTS) technology becomes ubiquitous and the volume of data continues to rise, HTS read alignment is becoming increasingly rate-limiting, which keeps pressing development novel approaches. Moreover, promising applications require aligning reads multiple genomes instead a single reference; however, it still not viable for state-of-the-art aligners align large numbers genomes.We propose de Bruijn Graph-based Aligner (deBGA), an innovative graph-based...
Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to motifs containing highly methylated CpGs both in vitro vivo. Identification such elucidation their physiological roles now become an important stepping-stone toward understanding mechanisms underlying methylation-mediated biological processes, which have...
Abstract Spatial transcriptomics unveils the complex dynamics of cell regulation and transcriptomes, but it is typically cost-prohibitive. Predicting spatial gene expression from histological images via artificial intelligence offers a more affordable option, yet existing methods fall short in extracting deep-level information pathological images. In this paper, we present THItoGene, hybrid neural network that utilizes dynamic convolutional capsule networks to adaptively sense potential...
Prostate cancer is one of the leading causes death in men. Androgen ablation, most commonly-used therapy for progressive prostate cancer, ineffective once cells become androgen-independent. The regulatory mechanisms that cause this transition (from androgen-dependent to androgen-independent) remain unknown. In study, based on microarray data comparing global gene expression patterns tissue between and -independent patients, we indentify a set transcription factors microRNAs potentially such...
Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large‐scale sequencing efforts. Using genome‐scale pooled shRNA screening technology, we mapped negative genetic interactions across a set isogenic cell lines and confirmed hundreds these in orthogonal co‐culture competition assays generate high‐confidence interaction network differentially essential or differential essentiality (DiE) genes. The uncovered examples conserved...
Colorectal cancer pathogenesis remains incompletely understood. Here, we report that the heterochromatin protein HP1γ is upregulated commonly in human colorectal cancer, where it promotes cell proliferation vitro and vivo. Gene-expression promoter-binding experiments demonstrated directly regulated CDKN1A (p21(Waf1/Cip1)) a manner associated with methylation of histone H3K9 on its promoter. We identified miR-30a as tumor-suppressive microRNA targets vivo to specifically suppress growth mouse...
The alignment of long-read RNA sequencing reads is non-trivial due to high errors and complicated gene structures. We propose deSALT, a tailored two-pass approach, which constructs graph-based skeletons infer exons uses them generate spliced reference sequences produce refined alignments. deSALT addresses several difficult technical issues, such as small errors, break through bottlenecks long RNA-seq read alignment. Benchmarks demonstrate that has greater ability accurate homogeneous...
Abstract Non-coding RNAs (ncRNAs) participate in multiple biological processes associated with cancers as tumor suppressors or oncogenic drivers. Due to their high stability plasma, urine, and many other fluids, ncRNAs have the potential serve key biomarkers for early diagnosis screening of cancers. During cancer progression, heterogeneity plays a crucial role, it is particularly important understand gene expression patterns individual cells. With development single-cell RNA sequencing...
With the advance of large-scale omics technologies, it is now feasible to reversely engineer underlying genetic networks that describe complex interplays molecular elements lead diseases. Current networking approaches are mainly focusing on building at large without probing interaction mechanisms specific a physiological or disease condition. The aim this study was thus develop such novel approach based relevance concept, which ideal reveal integrative effects multiple genes in circuit for...
Identifying the genes associated to human diseases is crucial for disease diagnosis and drug design. Computational approaches, esp. network-based have been recently developed identify disease-related effectively from existing biomedical networks. Meanwhile, advance in biotechnology enables researchers produce multi-omics data, enriching our understanding on diseases, revealing complex relationships between diseases. However, none of computational approaches able integrate huge amount omics...