A5061868538- vaccines and immunoinformatics approaches
- Immunotherapy and Immune Responses
- Monoclonal and Polyclonal Antibodies Research
- Cancer Genomics and Diagnostics
- Pancreatic and Hepatic Oncology Research
- Single-cell and spatial transcriptomics
- Genetic factors in colorectal cancer
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Mesenchymal stem cell research
- Tissue Engineering and Regenerative Medicine
- Cancer, Hypoxia, and Metabolism
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Genomics and Rare Diseases
- Congenital heart defects research
- Nitric Oxide and Endothelin Effects
- Plant Molecular Biology Research
- Gender Diversity and Inequality
- Kruppel-like factors research
- Genetic Syndromes and Imprinting
- Youth Development and Social Support
- Labor Movements and Unions
- Cancer-related gene regulation
- Renal cell carcinoma treatment
Johns Hopkins University
2017-2024
Johns Hopkins Medicine
2017-2024
Center for Drug Evaluation and Research
2024
Chengdu University of Traditional Chinese Medicine
2024
Sichuan University
2013-2024
West China Hospital of Sichuan University
2013-2024
University of Baltimore
2020
University of Illinois Chicago
2018
UCSF Helen Diller Family Comprehensive Cancer Center
2010
University of California, San Francisco
2010
Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response cancer immunotherapy. Current predictors focus on in silico estimation MHC affinity are limited by low predictive value for actual peptide presentation, inadequate support rare alleles, poor scalability high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep neural network method that predicts peptide-MHC...
PURPOSE The modern researcher is confronted with hundreds of published methods to interpret genetic variants. There are databases genes and variants, phenotype-genotype relationships, algorithms that score rank genes, in silico variant effect prediction tools. Because prioritization a multifactorial problem, welcome development the field has been emergence decision support frameworks, which make it easier integrate multiple resources an interactive environment. Current frameworks typically...
Intraductal papillary mucinous neoplasms (IPMNs) are non-invasive precursor lesions that can progress to invasive pancreatic cancer and classified as low-grade or high-grade based on the morphology of neoplastic epithelium. We aimed compare genetic alterations in regions same IPMN order identify molecular underlying progression.We performed multiregion whole exome sequencing tissue samples from 17 IPMNs with both dysplasia (76 regions, including 49 27 dysplasia). reconstructed phylogeny for...
Abstract Intraductal papillary mucinous neoplasms (IPMNs) are precursors to pancreatic cancer; however, little is known about genetic heterogeneity in these lesions. The objective of this study was characterize IPMNs at the single‐cell level. We isolated single cells from fresh tissue ten IPMNs, followed by whole genome amplification and targeted next‐generation sequencing driver genes. then determined genotypes using a novel multi‐sample mutation calling algorithm. Our analyses revealed...
Abstract Background Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as biomarker the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark performance CNV calling by six most recent commonly software tools on their detection accuracy, sensitivity, reproducibility. In comparison to other orthogonal methods, such microarray Bionano, also explore consistency across different technologies...
Abstract Motivation Multi-region sequencing of solid tumors can improve our understanding intratumor subclonal diversity and the evolutionary history mutational events. Due to uncertainty in clonal composition multitude possible ancestral relationships between clones, elucidating most probable from bulk tumor poses statistical computational challenges. Results We developed a Bayesian hierarchical model called PICTograph assigning mutations subclones, enable posterior distributions cancer...
Pancreatic intraepithelial neoplasia (PanIN) is a precursor to pancreatic cancer and represents critical opportunity for interception. However, the number, size, shape, connectivity of PanINs in human tissue samples are largely unknown. In this study, we quantitatively assessed using CODA, novel machine-learning pipeline 3D image analysis that generates quantifiable models large pieces pancreas with single-cell resolution. Using cohort 38 slabs grossly normal from surgical resection...
Endothelial progenitor cells (EPCs) are increasingly becoming a major focus of regenerative medicine research and practice. The present study was undertaken to establish an appropriate procedure for isolation characterization EPCs from Rhesus monkeys research. Selective CD34+ nonselective mononuclear were isolated bone marrow cultured under varying conditions. results showed that better choice high yield the target cells. grew in M 200 than EGM-2, supplementation with fetal bovine serum...
Abstract PURPOSE The modern researcher is confronted with hundreds of published methods to interpret genetic variants. There are databases genes and variants, phenotype-genotype relationships, algorithms that score rank genes, in silic o variant effect prediction tools. Because prioritization a multi-factorial problem, welcome development the field has been emergence decision support frameworks, which make it easier integrate multiple resources an interactive environment. Current frameworks...
10604 Background: It has been estimated that up to 40% of prostate cancer may be attributed inherited genetic susceptibility, yet very few variants have consistently associated with risk and/or adverse outcomes after diagnosis. Moreover, because survival is generally good, developing a second primary (SPC) an important concern. Identifying men at greater SPC will lead improved post-diagnostic surveillance practices and lifestyle behavior modifications. Methods: The current investigation...
: Intraductal papillary mucinous neoplasms (IPMNs) are precursors to pancreatic cancer; however, little is known about genetic heterogeneity in these lesions. We report the first characterization of IPMNs at single-cell level. isolated single cells from fresh tissue ten IPMNs, followed by whole genome amplification and targeted next generation sequencing driver genes. then determined genotypes using a novel multi-sample mutation calling algorithm. Our analyses revealed that different...
Mobilization and homing of bone-marrow mesenchymal stem cells (BMSCs) were observed in acute myocardial ischemic injury, but disappeared a long-term stress along with depressed copper (Cu) concentrations the heart. Cu is required for hypoxia-inducible transcription factor-1 (HIF-1) regulation expression BMSC factors. The present study was to test hypothesis that supplementation recovers signaling system, leading chronic infarct area Male adult New Zealand rabbits subjected coronary artery...
<div>Abstract<p>Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response cancer immunotherapy. Current predictors focus on <i>in silico</i> estimation MHC affinity are limited by low predictive value for actual peptide presentation, inadequate support rare alleles, poor scalability high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep...
<div>Abstract<p>Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response cancer immunotherapy. Current predictors focus on <i>in silico</i> estimation MHC affinity are limited by low predictive value for actual peptide presentation, inadequate support rare alleles, poor scalability high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep...