A5028692805- Bioinformatics and Genomic Networks
- Cancer-related molecular mechanisms research
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Radiomics and Machine Learning in Medical Imaging
- Gene expression and cancer classification
- MicroRNA in disease regulation
- Single-cell and spatial transcriptomics
- Influenza Virus Research Studies
- Gut microbiota and health
- vaccines and immunoinformatics approaches
- Cancer Diagnosis and Treatment
- SARS-CoV-2 and COVID-19 Research
- RNA Research and Splicing
- Extracellular vesicles in disease
- Cancer Immunotherapy and Biomarkers
- Protein Structure and Dynamics
- COVID-19 Clinical Research Studies
- AI in cancer detection
- CRISPR and Genetic Engineering
- Genetics, Aging, and Longevity in Model Organisms
Cipher Gene (China)
2019-2025
Zhejiang University
2025
First Affiliated Hospital Zhejiang University
2025
Southern California University for Professional Studies
2025
University of Southern California
2025
Changzhou University
2024
Institute of Process Engineering
2024
Chinese Academy of Sciences
2009-2024
Changsha Medical University
2017-2024
Mississippi State University
2012-2024
Expression, genetic variation, and tissues Human genomes show extensive variation across individuals, but we have only just started documenting the effects of this on regulation gene expression. Furthermore, a few been examined per variant. In order to examine how expression varies among within Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative traits that affect determined which these...
Expression, genetic variation, and tissues Human genomes show extensive variation across individuals, but we have only just started documenting the effects of this on regulation gene expression. Furthermore, a few been examined per variant. In order to examine how expression varies among within Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative traits that affect determined which these...
Recent studies have uncovered thousands of long non-coding RNAs (lncRNAs) in human pancreatic β cells. cell lncRNAs are often type specific and exhibit dynamic regulation during differentiation or upon changing glucose concentrations. Although these features hint at a role gene diabetes, the function remains largely unknown. In this study, we investigated cell-specific transcription factors using transcript knockdowns co-expression network analysis. This revealed that concert with to...
Abstract Aging is one of the most important biological processes and a known risk factor for many age-related diseases in human. Studying transcriptomic changes tissues across whole body can provide valuable information holistic understanding this fundamental process. In work, we catalogue gene expression nine from nearly two hundred individuals collected by Genotype-Tissue Expression (GTEx) project. general, find aging signatures are very tissue specific. However, enrichment some well-known...
HER2-positive breast cancer is a highly heterogeneous tumor, and about 30% of patients still suffer from recurrence metastasis after trastuzumab targeted therapy. Predicting individual prognosis great significance for the further development precise With continuous computer technology, more attention has been paid to computer-aided diagnosis prediction based on Hematoxylin Eosin (H&E) pathological images, which are available all undergone surgical treatment. In this study, we first enrolled...
Drug repositioning is an efficient and promising strategy for traditional drug discovery development. Many research efforts are focused on utilizing deep-learning approaches based a heterogeneous network modeling complex drug-disease associations. Similar to latent factor models, which directly factorize associations, they assume the neighbors independent of each other in thus tend be ineffective capture localized information. In this study, we propose novel neighborhood interaction-based...
Gene regulatory network (GRN) inference based on genomic data is one of the most actively pursued computational biological problems. Because different types usually provide complementary information regarding underlying GRN, a model that integrates big diverse expected to increase both power and accuracy GRN inference. Towards this goal, we propose novel algorithm named iRafNet: integrative random forest for gene inference.iRafNet flexible, unified framework allows from heterogeneous data,...
Tail-anchored (TA) proteins contain a single transmembrane domain (TMD) at the C-terminus that anchors them to membranes of organelles where they mediate critical cellular processes. Accordingly, mutations in genes encoding TA have been identified number severe inherited disorders. Despite importance correctly targeting protein its appropriate membrane, mechanisms and signals involved are not fully understood. In this study, we identify additional peroxisomal proteins, discover more present...
The CRISPR/Cas9 system is a creative and innovative gene editing biotechnology tool in genetic engineering. Although several achievements have been attained using the system, it still challenge to avoid off-target effects improve efficacy. Previous efforts on evaluating efficacy designing guide RNA mainly focused DNA properties. However, some features not characterized but can be reflected by protein properties, such as disorder sequence conservation. In this paper, we provided computational...
Carcinoma of unknown primary (CUP) is a type metastatic cancer, the tumor site which cannot be identified. CUP occupies approximately 5% cancer incidences in United States with usually unfavorable prognosis, making it big threat to public health. Traditional methods identify tissue-of-origin (TOO) like immunohistochemistry can only deal around 20% patients. In recent years, more and studies suggest that promising solve problem by integrating machine learning techniques biomedical data...
Abstract The 2019 coronavirus disease (COVID-19) outbreak caused by the SARS-CoV-2 virus is an ongoing global health emergency. However, virus’ pathogenesis remains unclear, and there no cure for disease. We investigated dynamic changes of blood immune response in patients with COVID-19 at different stages using 5’ gene expression, T cell receptor (TCR), B receptors (BCR) V(D)J transcriptome analysis a single-cell resolution. obtained mRNA sequencing (scRNA-seq) data 341,420 peripheral...
Lonicera japonica is a typical Chinese herbal medicine. We previously reported method to isolate polysaccharides from (LJP). In this study, we first performed qualitative analysis of LJP using the Fourier Transform Infrared Spectrometer (FT-IR) and explored monosaccharide composition pre-column derivatization high performance liquid chromatography (HPLC) method. then investigated immunomodulatory function in cyclophosphamide (CTX)-induced immunosuppressed mouse models. The results showed...
Metastatic cancers require further diagnosis to determine their primary tumor sites. However, the tissue-of-origin for around 5% tumors could not be identified by routine medical according a statistics in United States. With development of machine learning techniques and accumulation big cancer data from The Cancer Genome Atlas (TCGA) Gene Expression Omnibus (GEO), it is now feasible predict computational tools. inherits characteristics its tissue-of-origin, both gene expression profile...
In this study, we proposed an ensemble learning method, simultaneously integrating a low-rank matrix completion model and ridge regression to predict anticancer drug response on cancer cell lines. The was applied two benchmark datasets, including the Cancer Cell Line Encyclopedia (CCLE) Genomics of Drug Sensitivity in (GDSC). As previous studies suggest, dual-layer integrated line-drug network one best models by far outperformed most state-of-the-art models. Thus, performed head-to-head...
A novel coronavirus, named COVID-19, has become one of the most prevalent and severe infectious diseases in human history. Currently, there are only very few vaccines therapeutic drugs against their efficacies yet to be tested. Drug repurposing aims explore new applications approved drugs, which can significantly reduce time cost compared with de novo drug discovery. In this study, we built a virus-drug dataset, included 34 viruses, 210 437 confirmed related pairs from existing literature....
Tumor mutational burden (TMB) is an indicator of the efficacy and prognosis immune checkpoint therapy in colorectal cancer (CRC). In general, patients with higher TMB values are more likely to benefit from immunotherapy. Though whole-exome sequencing considered gold standard for determining TMB, it difficult be applied clinical practice due its high cost. There also a few DNA panel-based methods estimate TMB; however, their detection cost high, associated wet-lab experiments usually take...
Abstract Drug repositioning, the strategy of redirecting existing drugs to new therapeutic purposes, is pivotal in accelerating drug discovery. While many studies have engaged modeling complex drug–disease associations, they often overlook relevance between different node embeddings. Consequently, we propose a novel weighted local information augmented graph neural network model, termed DRAGNN, for repositioning. Specifically, DRAGNN firstly incorporates attention mechanism dynamically...