A5055383192- Cancer Genomics and Diagnostics
- Lung Cancer Treatments and Mutations
- RNA modifications and cancer
- Cancer Immunotherapy and Biomarkers
- Legume Nitrogen Fixing Symbiosis
- Cancer-related gene regulation
- Genetic factors in colorectal cancer
- Radiomics and Machine Learning in Medical Imaging
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- Neurogenetic and Muscular Disorders Research
- Plant Gene Expression Analysis
- Ferroptosis and cancer prognosis
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Lung Cancer Diagnosis and Treatment
- Plant nutrient uptake and metabolism
- Genetic Associations and Epidemiology
- Bioinformatics and Genomic Networks
- Plant biochemistry and biosynthesis
- Hereditary Neurological Disorders
- RNA and protein synthesis mechanisms
Peking University
2017-2024
Peking University Third Hospital
2017-2024
Genecast (China)
2019-2024
National Health and Family Planning Commission
2023
Southern Medical University
2020
Science Applications International Corporation (United States)
2013-2014
National Cancer Institute
2014
Division of Cancer Epidemiology and Genetics
2013-2014
Leidos (United States)
2014
Frederick National Laboratory for Cancer Research
2013-2014
Legumes played central roles in the development of agriculture and civilization, today account for approximately one-third world's primary crop production. Unfortunately, most cultivated legumes are poor model systems genomic research. Therefore, Medicago truncatula, which has a relatively small diploid genome, been adopted as species legume genomics. To enhance its value model, we have generated gene expression atlas that provides global view all major organ this species, with special...
Combining whole exome sequencing, transcriptome profiling, and T cell repertoire analysis, we investigate the spatial features of surgically-removed biopsies from multiple loci in tumor masses 15 patients with non-small lung cancer (NSCLC). This revealed that immune microenvironment has high heterogeneity such intratumoral regional variation is as large inter-personal variation. While local total mutational burden (TMB) associated T-cell clonal expansion, anti-tumor cytotoxicity does not...
DNA methylation changes with age. Chronological age predictors built from are termed ‘epigenetic clocks’. The deviation of predicted the actual (‘age acceleration residual’, AAR) has been reported to be associated death. However, it is currently unclear how a better prediction chronological affects such association. In this study, we build multiple based on training samples selected 13,661 (13,402 blood and 259 saliva). We use Lothian Birth Cohorts 1921 (LBC1921) 1936 (LBC1936) examine...
White lupin (Lupinus albus L.) roots efficiently take up and accumulate (heavy) metals, adapt to phosphate deficiency by forming cluster roots, secrete antimicrobial prenylated isoflavones during development. Genomic proteomic approaches were applied identify candidate genes proteins involved in defense metal uptake translocation. A cDNA library was constructed from of white seedlings. Eight thousand clones randomly sequenced assembled into 2,455 unigenes, which annotated based on homologous...
* Arbuscular mycorrhizas (AMs) contribute significantly to soil nutrient uptake in plants. As a consequence of the fungal colonization and deep reorganization shown by arbusculated cells, important impacts on root transcriptome are expected. An Affymetrix GeneChip with 50,000 probe-sets real-time RT-PCR allowed us detect transcriptional changes triggered Lotus japonicus AM fungus Gigaspora margarita, when arbuscules at their maximum (28 d postinoculation (dpi)). early time (4 dpi) was...
Abstract Purpose: We assessed whether perioperative circulating tumor DNA (ctDNA) could be a biomarker for early detection of molecular residual disease (MRD) and prediction postoperative relapse in resected non–small cell lung cancer (NSCLC). Experimental Design: Based on our prospective, multicenter cohort dynamic monitoring ctDNA surgery patients (LUNGCA), we enrolled 950 plasma samples obtained at three time points (before surgery, 3 days 1 month after surgery) 330 stage I–III NSCLC...
Abstract Hop (Humulus lupulus L. Cannabaceae) is an economically important crop for the brewing industry, where it used to impart flavor and aroma beer, has also drawn attention in recent years due its potential pharmaceutical applications. Essential oils (mono- sesquiterpenes), bitter acids (prenylated polyketides), prenylflavonoids are primary phytochemical components that account these traits, all accumulate at high concentrations glandular trichomes of hop cones. To understand molecular...
Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies the model legume species, Medicago truncatula, are instrumental helping to formulate hypotheses about of genes. With rapid growth publically available Affymetrix GeneChip Genome Array data from great range tissues, cell types, conditions, and stress treatments, research community desires an effective bioinformatics system aid efforts interpret genome through functional genomics. We developed...
Tea (Camellia sinensis) is rich in specialized metabolites, especially polyphenolic proanthocyanidins (PAs) and their precursors. To better understand the PA pathway tea, we generated a complementary DNA library from leaf tissue of blister blight-resistant tea cultivar TRI2043 functionally characterized key enzymes responsible for biosynthesis Structural genes encoding involved general phenylpropanoid/flavonoid PA-specific branch were well represented library. Recombinant leucoanthocyanidin...
Immune checkpoint blockade (ICB) immunotherapy induces potent antitumor immunity across multiple solid tumors, although few patients respond well to this therapy. An emerging biomarker for predicting responsiveness ICB is tumor mutational burden (TMB). Although several surrogate biomarkers, including deficient mismatch repair, TP53/KRAS mutations, and comutations in DNA damage response pathways, have been shown be effective the immunotherapy, each positive only a small cohort of candidates,...
Abstract The ARP2/3 complex, a highly conserved nucleator of F-actin, and its activator, the SCAR are essential for growth in plants animals. In this article, we present pathway through which roots Arabidopsis thaliana directly perceive light to promote their elongation. ARP2/3-SCAR complex maintenance longitudinally aligned F-actin arrays crucial components pathway. involvement light-regulated root is supported by our finding that mutants subunit BRK1/HSPC300, or other individual subunits...
Lotus japonicus is a model species for legume genomics. To accelerate functional genomics, we developed Gene Expression Atlas (LjGEA), which provides global view of gene expression in all organ systems this species, including roots, nodules, stems, petioles, leaves, flowers, pods and seeds. Time-series data covering multiple stages developing pod seed are included the LjGEA. In addition, previously published L. Affymetrix database, making it 'one-stop shop' transcriptome analysis species....
To depict the genomic landscape of Chinese early-stage lung squamous cell carcinoma (LUSC) and investigate its correlation with tumor mutation burden (TMB), PD-L1 expression, immune infiltrates. Whole-exome sequencing was performed on 189 surgically resected LUSC. TMB defined as sum nonsynonymous single nucleotide indel variants. CD8+ tumor-infiltrating lymphocyte (TIL) density expression were evaluated by immunohistochemistry. Six infiltrates estimated using an online database. The median...
RNA isolated from the glands of a Delta(9)-tetrahydrocannabinolic acid (THCA)-producing strain Cannabis sativa was used to generate cDNA library containing over 100 000 expressed sequence tags (ESTs). Sequencing 2000 clones resulted in identification 1000 unigenes. Candidate genes for almost every step biochemical pathways leading primary metabolites THCA were identified. Quantitative PCR analysis suggested that many pathway are preferentially glands. Hexanoyl-CoA, one required synthesis,...
Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, signaling and, consequently, growth, development, responses to the environment. To initiate support systematic characterization of transporters model legume Medicago truncatula, we identified 3,830 classified 2,673 these into 113 families 146 subfamilies. Analysis gene expression data for 2,611 129 that are expressed an organ-specific manner, including 50 nodule...
Switchgrass (Panicum virgatum L.) is a perennial C4 grass with the potential to become major bioenergy crop. To help realize this potential, set of RNA-based resources were developed. Expressed sequence tags (ESTs) generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high-quality ESTs 454 sequencing technology, an additional 169 079 Sanger sequences obtained 5' 3' ends 93 312 clones normalized, full-length-enriched cDNA libraries. VS16 assembled...
Building accurate gene regulatory networks (GRNs) from high-throughput expression data is a long-standing challenge. However, with the emergence of new algorithms combined increase transcriptomic availability, it now reachable. To help biologists to investigate relationships, we developed web-based computational service build, analyze and visualize GRNs that govern various biological processes. The web server preloaded all available Affymetrix GeneChip-based annotation three model legume...
Abstract The evolutionary dynamics of tumor‐associated neoantigens carry information about drug sensitivity and resistance to the immune checkpoint blockade (ICB). However, spectrum somatic mutations is highly heterogeneous among patients, making it difficult track by circulating tumor DNA (ctDNA) sequencing using “one size fits all” commercial gene panels. Thus, individually customized panels (ICPs) are needed neoantigen evolution comprehensively during ICB treatment. Dominant predicted...
Burkholderia cepacia complex (Bcc) bacteria are opportunistic pathogens infecting hosts such as cystic fibrosis (CF) patients. Long-term Bcc infection of CF patients' airways has been associated with emergence phenotypic variation. Here we studied two multivorans clonal isolates displaying different morphotypes from a chronically infected patient to evaluate trait development during lung infection. Expression profiling mucoid D2095 and non-mucoid D2214 revealed decreased expression genes...
Addressing the high false-positive rate of conventional low-dose computed tomography (LDCT) for lung cancer diagnosis, efficacy incorporating blood-based noninvasive testing assisting practicing clinician's decision making in diagnosis pulmonary nodules (PNs) is investigated. In this prospective observative study, next generation sequencing- (NGS-) based cell-free DNA (cfDNA) mutation profiling, NGS-based cfDNA methylation and protein biomarker are performed patients with PNs, who diagnosed...
Lipid polymers in plant cell walls, such as cutin and suberin, build recalcitrant hydrophobic protective barriers. Their degradation is of foremost importance for both pathogenic saprophytic fungi. Regardless numerous reports on fungal emulsified fatty acids or cutin, fungi-plant interactions, the pathways involved utilisation suberin remain largely overlooked. As a structural component wall, isolation, general, uses harsh depolymerisation methods that destroy its macromolecular structure....