Shahar Alon
A5103034989- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- Advanced biosensing and bioanalysis techniques
- Advanced Electron Microscopy Techniques and Applications
- RNA Research and Splicing
- Cancer Cells and Metastasis
- RNA regulation and disease
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- MicroRNA in disease regulation
- RNA modifications and cancer
- Cell Image Analysis Techniques
- Cancer-related molecular mechanisms research
- Evolution and Genetic Dynamics
- Retinal Development and Disorders
- Genetic factors in colorectal cancer
- Neuroinflammation and Neurodegeneration Mechanisms
- CAR-T cell therapy research
- Protein Structure and Dynamics
- Breast Cancer Treatment Studies
- Marine and coastal plant biology
- Advanced X-ray Imaging Techniques
Massachusetts Institute of Technology
2015-2025
McGovern Institute for Brain Research
2017-2025
Bar-Ilan University
2012-2024
Ben-Gurion University of the Negev
2024
Engineering Arts (United States)
2021-2022
Howard Hughes Medical Institute
2021
Broad Institute
2021
Institute of Nanotechnology
2021
Harvard–MIT Division of Health Sciences and Technology
2021
Tel Aviv University
2011-2020
Identifying transcript location in cells where specific RNAs occur within a cell or tissue has been limited by technology and imaging capabilities. Expansion microscopy allowed for better visualization of small structures expanding the tissues with polymer- hydrogel-based system. Alon et al. combined expansion long-read situ RNA sequencing, resulting more precise transcripts. This method, termed “ExSeq” was used to detect RNAs, both new transcripts those previously demonstrated localize...
Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, open source computational methods. Using we generated resource 51,926 matched cell images diverse types including lines, xenografts, diagnostic samples with limited...
Abstract A holistic understanding of tissue and organ structure function requires the detection molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous up to 40 antigens transcripts using metal-tagged antibodies but has so far been restricted two-dimensional imaging. Here we report development 3D IMC for multiplexed analysis at single-cell resolution demonstrate utility technology by human breast cancer samples. The resulting...
How cell-to-cell copy number alterations that underpin genomic instability
Adenosine-to-inosine (A-to-I) editing modifies RNA transcripts from their genomic blueprint. A prerequisite for this process is a double-stranded (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it therefore expected that miRNAs affected by A-to-I editing. Editing has potential to add another layer complexity gene regulation pathways, especially if occurs within miRNA–mRNA recognition site. Thus, interest study extent phenomenon. Current...
Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given relatively small number miRNAs improvements in DNA technology, studying profiles multiple samples a single flow cell lane becomes feasible. Multiplexing strategies require marking each library with barcode. Here we report that barcodes introduced through adapter ligation confer significant bias on profiles. This much higher than expected Poisson noise masks differences...
Recent studies have reported the emerging role of microRNAs (miRNAs) in human cancers. We systematically characterized miRNA expression and editing brain, which displays highest number A-to-I RNA sites among tissues, de novo glioblastoma brain cancer. identified 299 miRNAs altered their 24 differently edited compared to tissues. focused on site within miR-589-3p seed. MiR-589-3p is a unique almost fully (∼100%) normal with consistent decrease glioblastoma. The version inhibits cell...
To study structural changes that occur in Abs upon Ag binding, we systematically compared free and bound structures of all 141 crystal the 49 were solved these two forms. We found many far from binding site. Some them may constitute a mechanism for recently suggested allosteric effects Abs. Within site itself, CDR-H3 is only element shows significant binding-related conformational changes; however, this occurs one third Beyond site, associated with relative orientation H L chains both...
Abstract We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method spatially-resolved, targeted, in situ identification of single or multiple targets. BOLORAMIS was demonstrated range cell types human cerebral organoids. Singleplex experiments to detect coding non-coding RNAs iPSCs showed stem-cell signature pattern. Specificity found be 92% as illustrated by clear distinction between mouse...
The heterogeneity of breast cancer plays a major role in drug response and resistance has been extensively characterized at the genomic level. Here, single-cell mass cytometry (BCMC) panel is optimized to identify cell phenotypes their oncogenic signalling states biobank patient-derived tumour xenograft (PDTX) models representing diversity human cancer. BCMC identifies 13 cellular (11 2 murine), associated with both subtypes specific features. Pre-treatment phenotypic composition determinant...
Sleep has been conserved throughout evolution; however, the molecular and neuronal mechanisms of sleep are largely unknown. The hypothalamic hypocretin/orexin (Hcrt) neurons regulate sleep\wake states, feeding, stress, reward. To elucidate mechanism that enables these various functions to identify regulators, we combined fluorescence cell sorting RNA-seq in hcrt:EGFP zebrafish. Dozens Hcrt-neuron–specific transcripts were identified comprehensive high-resolution imaging revealed...
Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology, 27: 261-269, 2013). Near coastal cities or other densely populated areas, coral face a range of additional challenges. While considerable progress has been made understanding responses acute individual stressors (Dominoni Nature Ecology & Evolution, 4: 502-511, 2020), the impacts chronic exposure varying combinations sensory pollutants largely unknown. To investigate...
Abstract Although metastatic disease is the leading cause of cancer-related deaths, its tumor microenvironment remains poorly characterized due to technical and biospecimen limitations. In this study, we assembled a multi-modal spatial cellular map 67 biopsies from 60 patients with breast cancer across diverse clinicopathological features nine anatomic sites detailed clinical annotations. We combined single-cell or single-nucleus RNA sequencing for all panel four expression assays...
Abstract: Methods for highly multiplexed RNA imaging are limited in spatial resolution, and thus their ability to localize transcripts nanoscale subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, long-read untargeted targeted situ sequencing. applied sequencing (ExSeq) mouse brain, yielding readout of thousands genes, including splice variants novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps RNAs throughout dendrites...
Abstract Summary: DREAM: detecting RNA editing associated with microRNAs, is a webserver for the identification of mature microRNA events using deep sequencing data. Raw reads can be provided as input, are aligned against genome and custom scripts process data, search potential sites assess statistical significance findings. The output text file location description all putative detected. Availability implementation: DREAM freely available on web at http://www.cs.tau.ac.il/∼mirnaed/....
The website and database https://snengs.nichd.nih.gov provides RNA sequencing data from multi-species analysis of the pineal glands zebrafish (Danio rerio), chicken (White Leghorn), rat (Rattus novegicus), mouse (Mus musculus), rhesus macaque (Macaca mulatta), human (Homo sapiens); in most cases, retinal are also included along with results a mixture tissues. Studies cover day night conditions; addition, time series over multiple hours, developmental pharmacological experiments on rats...