A5034140883- Lung Cancer Research Studies
- Brain Metastases and Treatment
- Lung Cancer Treatments and Mutations
- Cancer Immunotherapy and Biomarkers
- Single-cell and spatial transcriptomics
- Glioma Diagnosis and Treatment
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Immune cells in cancer
- Multiple Myeloma Research and Treatments
- Cancer Genomics and Diagnostics
- Mathematical Biology Tumor Growth
- Cell Image Analysis Techniques
- Computational Drug Discovery Methods
- Ferroptosis and cancer prognosis
- 3D Printing in Biomedical Research
- Cellular Mechanics and Interactions
- Metabolomics and Mass Spectrometry Studies
- Radiomics and Machine Learning in Medical Imaging
- Gene Regulatory Network Analysis
- Dementia and Cognitive Impairment Research
- Lung Cancer Diagnosis and Treatment
- COVID-19 and healthcare impacts
- Receptor Mechanisms and Signaling
- Chronic Kidney Disease and Diabetes
Indiana University – Purdue University Indianapolis
2020-2025
Indiana University School of Medicine
2020-2025
Hubei Normal University
2025
Quanzhou Normal University
2025
Wake Forest University
2015-2024
Indiana University
2022-2024
Hebei Medical University
2022-2024
Fourth Hospital of Hebei Medical University
2024
Chinese Academy of Medical Sciences & Peking Union Medical College
2017-2024
Shanghai Jiao Tong University
2008-2023
N6-methyladenosine (m6A) modification of mRNA is emerging as a vital mechanism regulating RNA function. Here, we show that fragile X mental retardation protein (FMRP) reads m6A to promote nuclear export methylated targets during neural differentiation. Fmr1 knockout (KO) mice delayed progenitor cell cycle progression and extended maintenance proliferating progenitors into postnatal stages, phenocopying methyltransferase Mettl14 conditional KO (cKO) have no modification. RNA-seq m6A-seq...
Mounting evidence supports a role for the immune system in breast cancer outcomes. The ability to distinguish highly immunogenic tumors susceptible anti-tumor immunity from weakly or inherently immune-resistant would guide development of therapeutic strategies cancer. Genomic, transcriptomic and clinical data Cancer Genome Atlas (TCGA) Molecular Taxonomy Breast International Consortium (METABRIC) cohorts were used examine statistical associations between tumor mutational burden (TMB)...
The National COVID Cohort Collaborative (N3C) is a centralized, harmonized, high-granularity electronic health record repository that the largest, most representative COVID-19 cohort to date. This multicenter data set can support robust evidence-based development of predictive and diagnostic tools inform clinical care policy.
Recent development of spatial transcriptomics (ST) is capable associating information at different spots in the tissue section with RNA abundance cells within each spot, which particularly important to understand cytoarchitectures and functions. However, for such ST data, since a spot usually larger than an individual cell, gene expressions measured are from mixture heterogenous cell types. Therefore, data needs be disentangled so as reveal compositions that spot. In this study, we propose...
Variation in risk of adverse clinical outcomes patients with cancer and COVID-19 has been reported from relatively small cohorts. The NCATS' National COVID Cohort Collaborative (N3C) is a centralized data resource representing the largest multicenter cohort cases controls nationwide. We aimed to construct characterize within N3C identify factors for all-cause mortality COVID-19.
To provide real-world evidence on risks and outcomes of breakthrough COVID-19 infections in vaccinated patients with cancer using the largest national cohort cases controls.
Abstract Single-cell omics is the fastest-growing type of genomics data in literature and public repositories. Leveraging growing repository labeled datasets transferring labels from existing to newly generated will empower exploration single-cell data. However, current label transfer methods have limited performance, largely due intrinsic heterogeneity among cell populations extrinsic differences between datasets. Here, we present a robust graph artificial intelligence model, Graph...
Abstract Cell–cell communications are vital for biological signalling and play important roles in complex diseases. Recent advances single-cell spatial transcriptomics (SCST) technologies allow examining the cell communication landscapes hold promise disentangling ligand–receptor (L–R) interactions across cells. However, due to frequent dropout events noisy signals SCST data, it is challenging lack of effective tailored methods accurately infer cellular communications. Herein, decipher...
Abstract Recent advances in high-throughput molecular imaging have pushed spatial transcriptomics technologies to subcellular resolution, which surpasses the limitations of both single-cell RNA-seq and array-based profiling. The multichannel immunohistochemistry images such data provide rich information on cell types, functions, morphologies cellular compartments. In this work, we developed a method, elucidation through image-augmented Graph transformer (SiGra), leverage for revealing...
Abstract Brain metastases is the most common intracranial tumor and account for approximately 20% of all systematic cancer cases. It a leading cause death in advanced-stage cancer, resulting five-year overall survival rate below 10%. Therefore, there critical need to identify effective biomarkers that can support frequent surveillance promote efficient drug guidance brain metastasis. Recently, remarkable breakthroughs single-cell RNA-sequencing (scRNA-seq) technology have advanced our...
The Library of Integrated Network-based Cellular Signatures (LINCS) L1000 big data provide gene expression profiles induced by over 10 000 compounds, shRNAs, and kinase inhibitors using the platform.
Abstract Background The effect of immunotherapy on brain metastasis patients remains incompletely understood. Our goal was to evaluate its survival, neurologic death, and patterns failure after stereotactic radiosurgery (SRS) without prior whole-brain radiation therapy (WBRT) in with lung melanoma primaries metastatic the brain. Methods We performed a retrospective analysis 271 consecutive or treated upfront SRS for metastases between 2013 2018. Of these patients, 101 (37%) received 170...
Unravelling the regulatory programs from single-cell multi-omics data has long been one of major challenges in genomics, especially current emerging field. Currently there is a huge gap between fast-growing and effective methods for integrative analysis these inherent sparse heterogeneous data. In this study, we have developed novel method, Single-cell Multi-omics Gene co-Regulatory algorithm (SMGR), to detect coherent functional signals target genes joint RNA-sequencing (scRNA-seq) assay...
Abstract Spatial cellular authors heterogeneity contributes to differential drug responses in a tumor lesion and potential therapeutic resistance. Recent emerging spatial technologies such as CosMx, MERSCOPE Xenium delineate the gene expression patterns at single cell resolution. This provides unprecedented opportunities identify spatially localized resistance optimize treatment for individual patients. In this work, we present graph-based domain adaptation model, SpaRx, reveal of response...
The clinical value of 3D printed surgical guides in resection and reconstruction malignant bone tumor around the knee joint were studied. For this purpose, a sample 66 patients from October 2013 to 2015 randomly selected further divided into control group observation group, each consisted 33 cases. was treated by conventional whereas, resected with guide. However, tumor-type hinge prosthesis performed both groups then effect compared. Results show that there no significant difference...
Multiple myeloma, the second most common hematological cancer, is currently incurable due to refractory disease relapse and development of multiple drug resistance. We others recently established biophysical model that myeloma initiating (stem) cells (MICs) trigger stiffening their niches via SDF-1/CXCR4 paracrine; The stiffened then promote colonogenesis MICs protect them from treatment. In this work we examined in silico pharmaceutical potential targeting MIC niche stiffness facilitate...
Abstract Immuno-oncology (IO) therapies have transformed the therapeutic landscape of non-small cell lung cancer (NSCLC). However, patient responses to IO are variable and influenced by a heterogeneous combination health, immune, tumor factors. There is pressing need discover distinct NSCLC subgroups that influence response. We developed dee p pa tient graph convolutional n etwork, we call “DeePaN”, complexity across data modalities impacting benefit. DeePaN employs high-dimensional derived...
PurposeMelanoma brain metastases (MBM) occur in ∼50% of melanoma patients. Although both radiation therapy (RT) and immune checkpoint inhibitor (ICI) are used alone or combination for MBM treatment, the role this how these treatments could best be sequenced remains unclear.Methods MaterialsWe conducted a retrospective analysis patients with resected who underwent treatment RT, ICI, RT ICI. Among latter, we specifically investigated differential gene expression via RNA-sequencing between...
The incidence of brain metastasis continues to increase as therapeutic strategies have improved for a number solid tumors. presence is associated with worse prognosis but it unclear if distinctive biomarkers can separate patients at risk CNS related death.We executed single institution retrospective collection from who were diagnosed lung, breast, and other primary metastatic samples sent RNA sequencing, proteomic metabolomic analysis metastasis. outcome was distant failure after definitive...