A5077970112- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Advanced Fluorescence Microscopy Techniques
- Photoreceptor and optogenetics research
- Cancer Research and Treatments
- Microfluidic and Bio-sensing Technologies
- Diabetes Management and Research
- Photosynthetic Processes and Mechanisms
- Immunotherapy and Immune Responses
- Diet and metabolism studies
- vaccines and immunoinformatics approaches
- T-cell and B-cell Immunology
- Immune responses and vaccinations
- Gene Regulatory Network Analysis
- Image Processing Techniques and Applications
- Probiotics and Fermented Foods
- AI in cancer detection
- Light effects on plants
- Inflammatory Bowel Disease
- Genetic diversity and population structure
- Advanced Proteomics Techniques and Applications
- Diabetes and associated disorders
- Horticultural and Viticultural Research
Weizmann Institute of Science
2019-2025
Bacteria were first detected in human tumors more than 100 years ago, but the characterization of tumor microbiome has remained challenging because its low biomass. We undertook a comprehensive analysis microbiome, studying 1526 and their adjacent normal tissues across seven cancer types, including breast, lung, ovary, pancreas, melanoma, bone, brain tumors. found that each type distinct composition breast particularly rich diverse microbiome. The intratumor bacteria are mostly intracellular...
Abstract Multiplexed imaging enables measurement of multiple proteins in situ, offering an unprecedented opportunity to chart various cell types and states tissues. However, classification, the task identifying type individual cells, remains challenging, labor-intensive, limiting throughput. Here, we present CellSighter, a deep-learning based pipeline accelerate classification multiplexed images. Given small training set expert-labeled images, CellSighter outputs label probabilities for all...
OBJECTIVE Previous studies have demonstrated an association between gut microbiota composition and type 1 diabetes (T1D) pathogenesis. However, little is known about the function of microbiome in adults with longstanding T1D or its host glycemic control. RESEARCH DESIGN AND METHODS We performed a metagenomic analysis obtained from fecal samples 74 T1D, 14.6 ± 9.6 years following diagnosis, compared their microbial to 296 age-matched healthy control subjects (1:4 ratio). further analyzed taxa...
Significance The intricate structure of the membrane network that hosts primary steps photosynthesis in plant chloroplasts has intrigued scientists for decades. Here, we used electron tomography to determine this structure. We found is consolidated by arrays right- and left-handed helical structures. Similar arrangements pitch-balanced elements alternating handedness were proposed be present endoplasmic reticulum and, remarkably, ultradense nuclear matter. These thus likely represent a...
Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, particularly powerful. We evaluated the utility varying k-mer lengths for genome comparisons by analyzing their sequence space coverage 5805 genomes KEGG GENOME database. subsequent analyses four spanning relevant range (11, 21, 31, 41), hierarchical clustering 1634 genus-level representative...
We present a novel approach to cell phenotyping for spatial proteomics that addresses the challenge of generalization across diverse datasets with varying marker panels. Our utilizes transformer channel-wise attention create language-informed vision model; this model's semantic understanding underlying panel enables it learn from and adapt heterogeneous datasets. Leveraging curated, dataset type labels spanning literature NIH Human BioMolecular Atlas Program (HuBMAP) consortium, our model...
Abstract Acute graft-versus-host disease (aGVHD) is a significant complication of allogeneic hematopoietic stem cell transplantation (aHSCT), driven by alloreactive donor T cells in the gut. However, roles additional and host this process are not fully understood. We conducted multiplexed imaging on 59 biopsies from patients with gastrointestinal GVHD 10 healthy controls, revealing key pathological changes, including fibrosis, crypt alterations, loss Paneth cells, accumulation endocrine...
Abstract Multiplexed imaging enables measurement of multiple proteins in situ , offering an unprecedented opportunity to chart various cell types and states tissues. However, classification, the task identifying type individual cells, remains challenging, labor-intensive, limiting throughput. Here, we present CellSighter, a deep-learning based pipeline accelerate classification multiplexed images. Given small training set expert-labeled images, CellSighter outputs label probabilities for all...
Abstract Understanding tissue structure and function requires tools that quantify the expression of multiple proteins at single-cell resolution while preserving spatial information. Current imaging technologies use a separate channel for each individual protein, inherently limiting their throughput scalability. Here, we present CombPlex (COMBinatorial multiPLEXing), combinatorial staining platform coupled with an algorithmic framework to exponentially increase number can be measured from C...
Abstract Understanding tissue structure and function requires tools that quantify the expression of multiple proteins at single-cell resolution while preserving spatial information. Current imaging technologies use a separate channel for each individual protein, inherently limiting their throughput scalability. Here, we present CombPlex (COMBinatorial multiPLEXing), combinatorial staining platform coupled with an algorithmic framework to exponentially increase number can be measured from C...
Priming plants with chemical agents has been extensively investigated as a means for improving their tolerance to many biotic and abiotic stresses. Earlier, we showed that priming young avocado (Persea americana Mill cv. 'Hass') trees sodium hydrosulfide (NaHS), donor of hydrogen sulfide, improves the response photosynthesis simulated frost (cold followed by high light) conditions. In current study, performed transcriptome analysis gain insight into molecular 'Hass' leaves frost, or without...
Abstract Changes in cell shape are fundamentally involved signaling, intracellular organization, function, and intercellular interactions within tissues, health disease. Investigating the interplay between protein expression was limited, until recently, by number of proteins that can be imaged simultaneously or population averaging. We combined spatial multiplexed single imaging machine learning to systematically investigate intricate relationships context heterogeneous human cells their...
<b><i>OBJECTIVE </i></b>Previous studies have demonstrated an association between gut microbiota composition and Type 1 diabetes (T1D) pathogenesis. However, little is known about the function of microbiome in adults with longstanding T1D or its host glycemic control. <p><b><i>RESEARCH DESIGN AND METHODS</i></b><i> </i>We performed a metagenomic analysis obtained from fecal samples 74 T1D, 14.6 ± 9.6 years following diagnosis,...
<b><i>OBJECTIVE </i></b>Previous studies have demonstrated an association between gut microbiota composition and Type 1 diabetes (T1D) pathogenesis. However, little is known about the function of microbiome in adults with longstanding T1D or its host glycemic control. <p><b><i>RESEARCH DESIGN AND METHODS</i></b><i> </i>We performed a metagenomic analysis obtained from fecal samples 74 T1D, 14.6 ± 9.6 years following diagnosis,...
Abstract Multiplexed imaging enables measurement of multiple proteins in situ, offering an unprecedented opportunity to chart various cell types and states tissues. However, classification, the task identifying type individual cells, remains challenging, labor-intensive, limiting throughput. Here, we present CellSighter, a deep-learning based pipeline accelerate classification multiplexed images. Given small training set expert-labeled images, CellSighter outputs label probabilities for all...