A5080629899- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Immune cells in cancer
- Cancer Immunotherapy and Biomarkers
- Neonatal Respiratory Health Research
- Spectroscopy Techniques in Biomedical and Chemical Research
- Immunotherapy and Immune Responses
- Advanced Biosensing Techniques and Applications
- Hematopoietic Stem Cell Transplantation
- Cell death mechanisms and regulation
- Optical Imaging and Spectroscopy Techniques
- Advanced Fluorescence Microscopy Techniques
- Inflammatory Bowel Disease
- Immune responses and vaccinations
- Digital Imaging for Blood Diseases
- Ferroptosis and cancer prognosis
- Immunodeficiency and Autoimmune Disorders
- Cancer, Lipids, and Metabolism
- Skin Protection and Aging
- Pancreatic and Hepatic Oncology Research
- IL-33, ST2, and ILC Pathways
- Prostate Cancer Treatment and Research
- Lung Cancer Research Studies
- Advanced MRI Techniques and Applications
- Prostate Cancer Diagnosis and Treatment
City College of San Francisco
2025
University of Cambridge
2023-2024
University of California, San Francisco
2019-2024
Columbia University Irving Medical Center
2023-2024
Wellcome/MRC Cambridge Stem Cell Institute
2023-2024
University of California System
2021-2024
UCSF Helen Diller Family Comprehensive Cancer Center
2021
Rutgers, The State University of New Jersey
2014-2019
Emory University
1998
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) an anti-integrin antibody that effective for treating UC. VDZ known to inhibit lymphocyte trafficking the intestine, but its broader effects on other cell subsets are less defined. To identify inflammatory cells contribute affected VDZ, we perform single-cell transcriptomic proteomic analyses of peripheral blood colonic biopsies healthy controls patients with UC or therapies....
Anti-TNF antibodies are effective for treating patients with inflammatory bowel disease (IBD), but many fail to respond anti-TNF therapy, highlighting the importance of TNF-independent disease. We previously demonstrated that acute deletion 2 IBD susceptibility genes, A20 (Tnfaip3) and Abin-1 (Tnip1), in intestinal epithelial cells (IECs) sensitized mice both TNF-dependent death. Here we show IEC death after was rescued by germ-free derivation or MyD88, while Trif provided only partial...
Abstract The bone marrow is the main site of blood cell production in adults, however, rare pools hematopoietic stem and progenitor cells with self-renewal differentiation potential have been found extramedullary organs. lung primarily known for its role gas exchange but has recently described as a mice. Here, we show that functional precursors reside extravascular spaces human lung, at frequency similar to marrow, are capable proliferation engraftment. organ-specific gene signature...
In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research are now a key element of toolbox used by scientists to study immune system. However, analysis data generated these approaches often requires clustering algorithms dimensionality reduction representation, which computationally intense difficult evaluate optimize. Here, we present Cytometry Clustering Optimization Evaluation (Cyclone), an pipeline integrating reduction,...
The epidermal growth factor receptor (EGFR) inhibitor cetuximab is the only FDA-approved oncogene-targeting therapy for head and neck squamous cell carcinoma (HNSCC). Despite variable treatment response, no biomarkers exist to stratify patients in HNSCC. Here, we applied unbiased hierarchical clustering reverse-phase protein array molecular profiles from patient-derived xenograft (PDX) tumors revealed 2 PDX clusters defined by networks associated with EGFR resistance. In vivo validation...
Abstract Purpose: Metastatic colorectal cancer (mCRC) is the second leading cause of death worldwide. Roughly 8% mCRC tumors harbor a BRAF(V600E) mutation, associated with worst prognosis and limited treatment options. Most CRC research most clinical trials targeted therapies have narrowly focused on targeting vertical mechanisms MAPK re-activation (i.e., EGFR-MAPK), incremental advances for patients. New approaches are needed to address how therapeutic resistance mediated by coordinated...
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) an anti-integrin antibody that effective for treating UC. VDZ known to inhibit lymphocyte trafficking the intestine, but its broader effects on other cell subsets are less defined. To identify inflammatory cells contribute affected VDZ, we performed single-cell transcriptomic proteomic analyses of peripheral blood colonic biopsies healthy controls patients with UC or...
SUMMARY Cancers display significant heterogeneity with respect to tissue of origin, driver mutations and other features the surrounding tissue. It is likely that persistent tumors differentially engage inherent patterns–here ‘Archetypes’–of immune system, both benefit from a tumor microenvironment (TIME) disengage tumor-targeting. To discover dominant system archetypes, Immunoprofiler Initiative (IPI) processed 364 individual across 12 cancer types using standardized protocols. Computational...
Imaging without fluorescent protein labels or dyes presents significant advantages for studying living cells confounding staining artifacts and with minimal sample preparation. Here, we combine label-free optical scatter imaging digital segmentation processing to create dynamic subcellular masks, which highlight significantly scattering objects within the cells’ cytoplasms. The technique is tested by quantifying organelle morphology redistribution during cell injury induced calcium overload....
In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research are now a key element of toolbox used by scientists to study immune system. However, analysis data generated these approaches often requires clustering algorithms dimensionality reduction representation which computationally intense difficult evaluate optimize. Here we present Cyclone, an pipeline integrating reduction, clustering, evaluation optimization resolution,...
In plant associated pattern-triggered immunity (PTI), pattern-recognition receptors (PRRs) play crucial role in the mechanism of first line defense against pathogenic invasion.Throughout event, PRR binds with microorganism's pathogen-associated molecular pattern (PAMP) and recruit co-receptor protein to initiate primary signal.Although several PRRs have been identified, very few them fully characterized studied so far.PRR Xa21 perceives PAMP RaxX21 activates triggered Oryzae spp (rice).The...
Cancers display significant heterogeneity with respect to tissue of origin, driver mutations and other features the surrounding tissue. It is likely that persistent tumors differentially engage inherent patterns–here ‘Archetypes’–of immune system, both benefit from a tumor microenvironment (TIME) disengage tumor-targeting. To discover dominant system archetypes, Immunoprofiler Initiative (IPI) processed 364 individual across 12 cancer types using standardized protocols. Computational...
We investigate the role of Bax/Bak in altering morphology iBMK cells under baseline and apoptosis conditions. Bax/Bak-null have more predictable structural phenotypes measured with entropy textural features time-lapse optical scatter images.
Abstract The bone marrow is classically viewed as the main site of blood cell production in adults, however, rare pools haematopoietic stem and progenitor cells with self-renewal differentiation potential have been described extramedullary organs. lung primarily known for its role gas exchange but has recently identified a (platelet) mice. Here, we show that functional precursors reside extravascular spaces human lung, at frequency similar to marrow, are capable proliferation engraftment....
Light scattering by subcellular organelles and interfaces such as membranes can be utilized for quantitative measurement of cellular tissue states. The structural information the inferred from light-scattering analyzing signal at a conjugate Fourier plane dark-field imaging system. Via implementation Gabor filters on plane, we selectively allow only certain angles to pass during imaging. These scatter are related spatial frequencies source. So in effect, tuned probe objects size/shape...
Mitochondrial dynamics such as fission, fusion and movement can reveal the physiological status of neurons and, most importantly, serve diagnostic measures for several neurodegenerative diseases. Traditionally fluorescent probes have been used to track mitochondrial in neurons. However, show low transfection efficiency, presenting challenges use genetically-encoded markers. Alternatively, synthetic dyes are shown hinder motility. In addition, all types subject photo-bleaching which precludes...
ABSTRACT Anti-TNF antibodies are effective for treating patients with inflammatory bowel disease (IBD), but many fail to respond anti-TNF therapy, highlighting the importance of TNF-independent disease. We previously demonstrated that acute deletion two IBD susceptibility genes, A20 ( Tnfaip3 ) and Abin-1 Tnip1 ), in intestinal epithelial cells (IECs) sensitizes mice both TNF-dependent death. Here we show IEC death after is rescued by germ-free derivation or MyD88 , while Trif provides only...
No AccessJournal of UrologyUrological Survey: Abstracts: Benign and Malignant Neoplasms Prostate1 Jul 1998Factors Predicting Cancer Detection in Biopsy the Prostatic Fossa After Radical Prostatectomy M.D. Saleem, H. Sanders, M.A. El Naser, R. El-Galley SaleemM.D. Saleem More articles by this author , SandersH. Sanders NaserM.A. Naser El-GalleyR. View All Author Informationhttps://doi.org/10.1016/S0022-5347(01)63112-4AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack...