A5039402589- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- T-cell and B-cell Immunology
- Cancer Genomics and Diagnostics
- Immune Cell Function and Interaction
- MicroRNA in disease regulation
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- Acute Myeloid Leukemia Research
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Biosensors and Analytical Detection
- Immune cells in cancer
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- CAR-T cell therapy research
- Immunotherapy and Immune Responses
- Genomics and Chromatin Dynamics
- Circular RNAs in diseases
- Developmental Biology and Gene Regulation
- Advanced Fluorescence Microscopy Techniques
- Advanced Biosensing Techniques and Applications
- Extracellular vesicles in disease
- SARS-CoV-2 and COVID-19 Research
- Cancer-related gene regulation
10X Genomics (United States)
2021-2025
New York Genome Center
2017-2024
Icahn School of Medicine at Mount Sinai
2015-2021
Immunai (United States)
2021
Kettering University
2008-2018
Australian National University
2007-2015
Cornell University
2013
The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, unsupervised framework to learn the relative utility each data type in cell, enabling integrative analysis modalities. We apply our procedure a CITE-seq dataset 211,000 human peripheral blood mononuclear cells (PBMCs) with panels...
Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, assign each to its original sample, robustly identify cross-sample "super-load"...
Cellular imbalances of cholesterol and fatty acid metabolism result in pathological processes, including atherosclerosis metabolic syndrome. Recent work from our group others has shown that the intronic microRNAs hsa-miR-33a hsa-miR-33b are located within sterol regulatory element-binding protein-2 -1 genes, respectively, regulate homeostasis concert with their host genes. Here, we show miR-33a -b also genes involved insulin signaling. target key enzymes regulation oxidation, carnitine O...
Abstract The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on data types. Here, we introduce ‘weighted-nearest neighbor’ unsupervised framework to learn the relative utility each type in cell, enabling integrative analysis modalities. We apply our procedure a CITE-seq dataset hundreds thousands human white blood cells...
Single cell transcriptomics (scRNA-seq) has transformed our ability to discover and annotate types states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise measure distinct cellular modalities, including high-dimensional immunophenotypes, chromatin accessibility, spatial positioning, key analytical challenge is integrate these datasets into harmonized atlas that can be used better understand identity function. Here, we develop...
We analyzed the usage and consequences of alternative cleavage polyadenylation (APA) in Drosophila melanogaster by using >1 billion reads stranded mRNA-seq across a variety dissected tissues. Beyond demonstrating that majority fly transcripts are subject to APA, we observed broad trends for 3' untranslated region (UTR) shortening testis lengthening central nervous system (CNS); latter included hundreds unannotated extensions ranging up 18 kb. Extensive northern analyses validated...
Modifications are present on many classes of RNA, including tRNA, rRNA, and mRNA. These modifications modulate diverse biological processes such as genetic recoding mRNA export folding. In addition, can be introduced to RNA molecules using chemical probing strategies that reveal structure dynamics. Many methods exist detect by short-read sequencing; however, limitations read length inherent short-read-based dissociate from their native context, preventing single-molecule modification...
Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, single-cell transcriptomic proteomic sequencing, we discovered 124
A novel Drosophila -based approach resulted in a significant response by patient with KRAS-mutant colorectal cancer.