A5023347218- Inflammatory Bowel Disease
- Single-cell and spatial transcriptomics
- Cancer Immunotherapy and Biomarkers
- Radiomics and Machine Learning in Medical Imaging
- Mycobacterium research and diagnosis
- AI in cancer detection
- Pancreatic and Hepatic Oncology Research
- Immune cells in cancer
- Microscopic Colitis
- Colorectal Cancer Screening and Detection
- Cancer Cells and Metastasis
- Cancer Genomics and Diagnostics
- Immunotherapy and Immune Responses
- Cell Image Analysis Techniques
- Tryptophan and brain disorders
- Artificial Intelligence in Healthcare and Education
- Biomarkers in Disease Mechanisms
- Esophageal Cancer Research and Treatment
- Genetic Syndromes and Imprinting
- Reproductive System and Pregnancy
- Mathematical Biology Tumor Growth
- Smart Agriculture and AI
- Psoriasis: Treatment and Pathogenesis
- Advanced Nanomaterials in Catalysis
- Inflammation biomarkers and pathways
Stony Brook Medicine
2024
Stony Brook University
2019-2023
Stony Brook School
2020-2023
Icahn School of Medicine at Mount Sinai
2016-2020
Tumor-infiltrating lymphocytes (TILs) have been established as a robust prognostic biomarker in breast cancer, with emerging utility predicting treatment response the adjuvant and neoadjuvant settings. In this study, role of TILs overall survival progression-free interval was evaluated two independent cohorts cancer from Cancer Genome Atlas (TCGA BRCA) Carolina Breast Study (UNC CBCS). We utilized machine learning computer vision algorithms to characterize TIL infiltrates digital whole-slide...
Tissue-resident macrophages (TRMs) populate all tissues and play key roles in homeostasis, immunity repair. TRMs express a molecular program that is mostly shaped by tissue cues. However, TRM identity the mechanisms maintain remain poorly understood. We recently found serous-cavity (LPMs) are highly enriched RXR transcripts RXR-response elements. Here, we show RXRs control mouse serous-macrophage regulating chromatin accessibility transcriptional regulation of canonical macrophage genes....
Inflammatory bowel disease (IBD) is a chronic illness characterized by dysregulated immune cascades in the intestines, which Th17 response plays an important role. We demonstrated that mice with intestinal epithelium-specific deletion of Krüppel-like factor 5 (Klf5) developed Th17-dependent colonic inflammation. In absence KLF5, there was aberrant cellular localization phosphorylated STAT3, essential mediator Th17-associated cytokine, IL-22, required for epithelial tissue regeneration....
Background Mass cytometry leverages inductively coupled mass spectrometry to perform high dimensional single cell analyses using antibodies tagged with rare earth isotopes that are considered be largely absent in biological samples. We have recently noted an unusual exception this rule while analyzing tissue samples from patients undergoing surgical resection for early stage lung cancer, and here we present a detailed cytometric characterization of cerium clinical patient sample. Methods...
Inflammatory bowel disease (IBD) is a chronic immune-mediated of the gastrointestinal tract. While therapies exist, response can be limited within patient population. Researchers have thus studied mouse models colitis to further understand pathogenesis and identify new treatment targets. Flow cytometry RNA-sequencing phenotype immune populations with single-cell resolution but provide no spatial context. Spatial context may particularly important in models, due simultaneous presence colonic...
Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal tumors with a predicted five-year survival rate in 2023 12%. Building on prior observations that molecular subtypes correlate and response to treatment, our goal has been understand patterns expression prognostic correlations three reciprocally expressed proteins previously identified as surrogate biomarkers PDAC subtypes. Keratin 17 (K17) 5 (K5) have both basal subtype whereas GATA6, transcription factor...
Abstract Tumors form complex ecosystems that include normal epithelial cells, fibroblasts, blood and lymphatic vessels as well structural components, importantly, immune cells. The density, location, organization of various tumor-infiltrating hematopoietic cells myeloid lymphoid origin can impact tumor growth, spreading, clinical outcome cancers, including non-small cell lung cancer (NSCLC). Here, we propose to characterize the microenvironment tumors using a unique set matched fresh tissue...
Inflammatory bowel disease (IBD) is characterized by chronic, dysregulated inflammation in the gastrointestinal tract. The heterogeneity of IBD reflected through two major subtypes, Crohn's Disease (CD) and Ulcerative Colitis (UC). CD UC differ across symptomatic presentation, histology, immune responses, treatment. While colitis mouse models have been influential deciphering pathogenesis, no single model captures full clinical disease. translational capacity may be augmented shifting to...
Abstract The interaction of tumor, stroma, and immune cells in pancreatic ductal adenocarcinoma (PDAC) is complex difficult to quantify patient samples. Recently, deep learning algorithms have shown successes identifying tumor lymphocytes regions on whole-slide images derived from routinely collected histopathologic specimens. Cancer Genome Atlas (TCGA) particular has generated as well paired molecular data, thus allowing for combined spatial analyses tumor-lymphocyte interactions. We...
Abstract Inflammatory bowel disease (IBD) is a chronic immune-mediated of the gastrointestinal tract. While therapies exist, response can be limited within patient population. As such, researchers have studied mouse models colitis to further understand its pathogenesis and identify new treatment targets. Although bench methods like flow cytometry RNA-sequencing characterize immune responses with single-cell resolution, whole murine colon specimens are processed at once. Given simultaneous...
The combination of data analysis methods, increasing computing capacity, and improved sensors enable quantitative granular, multi-scale, cell-based analyses. We describe the rich set application challenges related to tissue interpretation survey AI methods currently used address these challenges. focus on a particular class targeted human - histopathology aimed at characterization disease state, patient outcome prediction treatment steering.