A5101855033- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Cancer Genomics and Diagnostics
- Gene Regulatory Network Analysis
- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Ferroptosis and cancer prognosis
- Gene expression and cancer classification
- Cancer, Lipids, and Metabolism
- Cancer-related Molecular Pathways
- Cancer-related molecular mechanisms research
- PARP inhibition in cancer therapy
- Genomics and Rare Diseases
- Microbial Natural Products and Biosynthesis
- Machine Learning in Bioinformatics
- Genetic factors in colorectal cancer
- Radiomics and Machine Learning in Medical Imaging
- Cancer Cells and Metastasis
- PI3K/AKT/mTOR signaling in cancer
- Colorectal Cancer Treatments and Studies
- 14-3-3 protein interactions
- RNA modifications and cancer
- Genetic Associations and Epidemiology
- Nutrition, Genetics, and Disease
University of Pittsburgh
2015-2024
Nanfang Hospital
2014-2024
Southern Medical University
2014-2024
UPMC Hillman Cancer Center
2020-2022
University of Pittsburgh Medical Center
2021
Center for Discovery
2018-2019
ZheJiang Academy of Agricultural Sciences
2017
Union Hospital
2016
Huazhong University of Science and Technology
2016
University of Kentucky
2014
Precision oncology involves identifying drugs that will effectively treat a tumor and then prescribing an optimal clinical treatment regimen. However, most first-line chemotherapy do not have biomarkers to guide their application. For molecularly targeted drugs, using the genomic status of drug target as therapeutic indicator has limitations. In this study, machine learning methods (e.g., deep learning) were used identify informative features from genome-scale omics data train classifiers...
A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental intracellular signals, it further transmits signals control cellular responses, including tightly controlled transcriptional program. An important yet challenging task in systems biology is to reconstruct data-driven manner. In this study, we investigate the utility of deep hierarchical neural networks learning representing organization yeast transcriptomic machinery. We...
Regulatory T (T reg ) cells and cancer-associated fibroblasts (CAFs) jointly promote tumor immune tolerance tumorigenesis. The molecular apparatus that drives cell CAF coordination in the microenvironment (TME) remains elusive. Interleukin 33 (IL-33) has been shown to enhance fibrosis IL1RL1 + accumulation during tumorigenesis tissue repair. We demonstrated signaling greatly dampened antitumor activity of both IL-33 PD-1 blockade. Whole single-cell RNA sequencing (scRNA-seq) analysis...
Fibroblast growth factor receptor 2 (FGFR2) belongs to the FGFR family, which plays an important role in cell growth, invasiveness, motility and angiogenesis. In human breast cancer, expression of FGFR2 is estrogen (ER)-dependent correlates with a lower rate apoptosis. Recently, whole-genome association studies have identified several single-nucleotide polymorphisms (SNPs) as novel cancer susceptibility loci. present study 1049 patients 1073 cancer-free controls, we assessed whether are...
Several variables are associated with the likelihood of isocitrate dehydrogenase 1 or 2 (IDH1/2) mutation in gliomas, though no guidelines yet exist for when testing is warranted, especially an R132H IDH1 immunostain negative. A cohort 89 patients was used to build IDH1/2 prediction models World Health Organization grades II–IV and external 100 validation. Logistic regression backward model selection Akaike information criterion were develop models. multivariable model, incorporating patient...
A combination of fluorouracil, leucovorin, and oxaliplatin (FOLFOX) is the standard for adjuvant therapy resected early-stage colon cancer (CC). Oxaliplatin leads to lasting disabling neurotoxicity. Reserving regimen patients who benefit from would maximize efficacy minimize unnecessary adverse side effects.
Cancer is mainly caused by somatic genome alterations (SGAs). Precision oncology involves identifying and targeting tumor-specific aberrations resulting from causative SGAs. We developed a novel computational framework that finds the likely SGAs in an individual tumor estimates their impact on oncogenic processes, which suggests disease mechanisms are acting tumor. This information can be used to guide precision oncology. report causal inference (TCI) framework, modeling relationships...
Epithelial IFN-β couples radiation-induced intestinal stem cell injury with local inflammation and regeneration.
Distinct transcriptional modules are regulated by specific ceramides.
To better understand a role of eIF4E S209 in oncogenic translation, we generated EIF4ES209A/+ heterozygous knockin (4EKI) HCT 116 human colorectal cancer (CRC) cells. 4EKI had little impact on total levels, cap binding or global but markedly reduced cell growth spheroids and mice, CRC organoid growth. strongly inhibited Myc ATF4 the integrated stress response (ISR)-dependent glutamine metabolic signature, AKT activation proliferation vivo. polyposis ApcMin/+ mice by suppressing protein...
Abstract Motivation: Model organisms play critical roles in biomedical research of human diseases and drug development. An imperative task is to translate information/knowledge acquired from model humans. In this study, we address a trans-species learning problem: predicting cell responses diverse stimuli, based on the rat cells treated with same stimuli. Results: We hypothesized that share common signal-encoding mechanism but employ different proteins transmit signals, developed bimodal...
1. Ventilation controls the indoor environment and is critical for poultry production welfare. also crucial assessing aerial pollutant emissions from industry. Published ventilation data commercial layer houses have been limited, are mostly based on short-term studies, mainly because monitoring airflow large numbers of fans technically challenging. 2. A two-year continuous trial was conducted at two manure belt (A B), each with 250 000 layers 88 130-cm exhaust fans. All were individually...
GWAS have identified variation in the FGFR2 locus as risk factors for breast cancer. Validation studies, however, shown inconsistent results by ethnics and pathological characteristics. To further explore this inconsistency investigate associations of variants with cancer according to intrinsic subtype (Luminal-A, Luminal-B, ER-&PR-&HER2+, triple negative) among Southern Han Chinese women, we genotyped rs1078806, rs1219648, rs2420946, rs2981579, rs2981582 polymorphisms 609 patients 882...
Background: Breast carcinoma is well recognized to be having the highest global occurrence rate among all cancers, being leading cause of cancer mortality in females. The aim this study was elucidate breast at genomic and transcriptomic levels different subtypes so that we can develop more personalized treatments precision medicine obtain better outcomes. Method: In study, an expression profiling dataset downloaded from Gene Expression Omnibus database, GSE45827, re-analyzed compare profiles...
Cancer is a disease of aberrant cellular signaling resulting from somatic genomic alterations (SGAs). Heterogeneous SGA events in tumors lead to tumor-specific system aberrations. We interpret the cancer as causal graphical model, where SGAs affect proteins, propagate their effects through signal transduction, and ultimately change gene expression. To represent such system, we developed deep learning model called redundant-input neural network (RINN) with transparent architecture. Our...
Feed represents two-thirds of the total costs poultry production, especially in developing countries. Improvement feed efficiency would reduce amount required for production (growth or laying), cost, and nitrogenous waste. The most commonly used measures are conversion ratio (FCR) residual intake (RFI). As a more suitable indicator assessing efficiency, RFI is defined as difference between observed expected based on maintenance growth laying. However, genetic biological mechanisms regulating...
Mutant KRAS is a key driver in colorectal cancer (CRC) and promotes Myc translation Myc-dependent stress adaptation proliferation. Here, we report that the combination of two FDA-approved drugs Bortezomib Everolimus (RAD001) (BR) highly efficacious against mutant CRC cells. Mechanistically, combination, not single agent, rapidly depletes protein, mRNA, leads to GCN2- p-eIF2α-dependent cell death through activation extrinsic intrinsic apoptotic pathways. Cell selectively induced cells with...
Cells within a tumor microenvironment (TME) dynamically communicate and influence each other's cellular states through an intercellular communication network (ICN). In cancers, communications underlie immune evasion mechanisms of individual tumors. We developed individualized causal analysis framework for discovering specific ICNs. Using head neck squamous cell carcinoma (HNSCC) tumors as testbed, we first mined single-cell RNA-sequencing data to discover gene expression modules (GEMs) that...
Abstract We report a tumor-specific causal inference (TCI) framework, which discovers causative somatic genome alterations (SGAs) through inferring relationships between SGAs and molecular phenotypes (e.g., transcriptomic, proteomic, or metabolomic changes) within an individual tumor. applied the TCI algorithm to tumors from The Cancer Genome Atlas (TCGA) identified those that causally regulate differentially expressed genes (DEGs) each Overall, 634 cause cancer-related DEGs in significant...
Current understanding of cancer genomes is mainly “gene centric.” However, GWAS have identified some nongenic breast susceptibility loci. Validation studies showed inconsistent results among different populations. To further explore this inconsistency and to investigate associations by intrinsic subtype (Luminal-A, Luminal-B, ER−&PR−&HER2+, triple negative) Southern Han Chinese women, we genotyped five polymorphisms (2q35: rs13387042, 5p12: rs981782 rs4415084, 8q24: rs1562430...
This paper presents a new prototype of web-based query by humming(QbH) system, which is designed specifically for music retrieval on Web applications. Besides the humming input interface, system also provides an alternative interface note strike. Schemes signal processing and indexing, such as inverted index contour snippet are discussed in detail. In addition, preliminary test was provided, showing that performance acceptable search service.
Abstract Background Sauchinone is extracted from the root of Saururus chinensis and exhibits potent antitumor effects in various human cancers. However, how sauchinone involved breast cancer has not been well studied. Methods Cells apoptosis, cell proliferation, cycle distribution were evaluated. Xenograft tumor mouse model was constructed to investigate roles sauchinone. The relevant protein expression detected by western blot. Results We found that significantly reduced proliferation...