A5015367801- Cancer Genomics and Diagnostics
- Lymphoma Diagnosis and Treatment
- Single-cell and spatial transcriptomics
- CAR-T cell therapy research
- RNA modifications and cancer
- Acute Myeloid Leukemia Research
- Radiomics and Machine Learning in Medical Imaging
- Cell Image Analysis Techniques
- Cancer Immunotherapy and Biomarkers
- Immune Cell Function and Interaction
- Cancer Cells and Metastasis
- Cancer, Hypoxia, and Metabolism
- Endometriosis Research and Treatment
- Lung Cancer Treatments and Mutations
- Immunotherapy and Immune Responses
- Gene expression and cancer classification
- Immune cells in cancer
- Bioinformatics and Genomic Networks
- Chromosomal and Genetic Variations
- Computational Drug Discovery Methods
- Epigenetics and DNA Methylation
- Gynecological conditions and treatments
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
Stanford University
2016-2025
Stratford University
2017-2024
Stanford Medicine
2009-2023
Palo Alto University
2010-2023
Palo Alto Institute
2023
Center for Systems Biology
2011-2022
Stanford Cancer Institute
2021
Stanford Health Care
2019
California Institute for Regenerative Medicine
2017
Indiana University – Purdue University Indianapolis
2014
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled TCGA. Across types, we identified six immune subtypes—wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant—characterized differences in macrophage or signatures, Th1:Th2 cell ratio, extent intratumoral heterogeneity, aneuploidy, neoantigen load, overall proliferation, expression immunomodulatory genes,...
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition progenitor stem-cell-like features. Here, we provide novel stemness indices for assessing degree oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic epigenetic feature sets derived from non-transformed pluripotent stem cells their progeny. Using OCLR, were able identify previously undiscovered biological mechanisms...
CD47, a “don't eat me” signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis patient and matched adjacent normal (nontumor) tissue revealed that CD47 overexpressed cancer mRNA expression levels correlated with decreased probability survival multiple types cancer. ligand SIRPα, protein macrophages dendritic In vitro, blockade signaling using targeted monoclonal antibodies enabled macrophage phagocytosis cells were otherwise protected. Administration...
Abstract Background Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences repeats and basic information described in annotations. Updating maintenance the requires specialized tools, we have created made available for use with Repbase, may be useful as template other curated databases. Results We describe software tools RepbaseSubmitter Censor, are designed to facilitate updating screening content Repbase. java-based interface formatting annotating...
Calreticulin-induced phagocytosis of cancer cells can be counterbalanced by CD47 expression.
CAR-T cells rest to get back in the race Chimeric antigen receptor (CAR)–T cells, which are engineered target specific tumor antigens, increasingly used as an immunotherapy. have shown promising results patients, particularly hematologic cancers, but their anticancer activity can be limited by onset of exhaustion and loss effectiveness. Weber et al. characterized phenotypic epigenomic changes associated with cell caused continuous beneficial effects transient periods (see Perspective...
CUTE MYELOID LEUKEMIA(AML) is an aggressive malignancy of the bone marrow characterized by accumulation early myeloid blood cells that fail to mature and differentiate.The course disease marked poor prognosis, frequent relapse, high disease-related mortality. 1,2Recent clinical investigation has focused on identification prognostic subgroups in adult AML with goal guiding patients into risk-adapted therapies.Such determined cytogenetic abnormalities are prognostic, some favorable others...
We consider a setting in which we have treatment and potentially large number of covariates for set observations, wish to model their relationship with an outcome interest. propose simple method modeling interactions between the covariates. The idea is modify covariate way, then fit standard using modified no main effects. show that coupled efficiency augmentation procedure, this produces clinically meaningful estimators variety settings. It can be useful practicing personalized medicine:...
Significance Follicular lymphoma (FL) is a disease characterized by multiple relapses that are linked common progenitor bearing only subset of the mutations found within tumor presents clinically. Inability to cure this may therefore be failure current therapies clear these early tumor-propagating clones. Here we further define genetic hallmarks and model steps in evolution through phylogenetic analysis serial biopsies. This identified CREBBP as events genome enriched cell progenitors...
Abstract Lung squamous cell carcinoma (LSCC) pathogenesis remains incompletely understood, and biomarkers predicting treatment response remain lacking. Here, we describe novel murine LSCC models driven by loss of Trp53 Keap1, both which are frequently mutated in human LSCCs. Homozygous inactivation Keap1 or promoted airway basal stem (ABSC) self-renewal, suggesting that mutations these genes lead to expansion mutant clones. Deletion ABSCs, but not more differentiated tracheal cells, produced...
Hematopoietic tissues in acute myeloid leukemia (AML) patients contain both stem cells (LSC) and residual normal hematopoietic (HSC). The ability to prospectively separate HSC from LSC would enable important scientific clinical investigation including the possibility of purged autologous cell transplants. We report here identification TIM3 as an AML surface marker more highly expressed on multiple specimens than bone marrow HSC. expression was detected all cytogenetic subgroups AML, but...
Abstract Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for transcriptomics limited gene recovery or low resolution. Here we introduce CytoSPACE, an optimization method mapping individual cells from a RNA sequencing atlas to expression profiles. Across diverse platforms and tissue types, show that CytoSPACE outperforms previous methods with respect noise tolerance accuracy, enabling cartography at
We present a comparative proteome analysis of the five complete eukaryotic genomes (human, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana ), focusing on individual and multiple amino acid runs, charge hydrophobic runs. found that human proteins with long runs are often associated diseases; these include glutamine induce neurological disorders, various cancers, categories leukemias (mostly involving chromosomal translocations), an abundance Ca...