A5042529830- Single-cell and spatial transcriptomics
- T-cell and B-cell Immunology
- Influenza Virus Research Studies
- interferon and immune responses
- Respiratory viral infections research
- CAR-T cell therapy research
- CRISPR and Genetic Engineering
- Extracellular vesicles in disease
- Gene Regulatory Network Analysis
- Cancer Genomics and Diagnostics
- Immune cells in cancer
- Cell Image Analysis Techniques
- Advanced Fluorescence Microscopy Techniques
- Gene expression and cancer classification
- Neuroinflammation and Neurodegeneration Mechanisms
- RNA Research and Splicing
- Immunotherapy and Immune Responses
- RNA and protein synthesis mechanisms
- Biomedical and Engineering Education
- Natural Language Processing Techniques
- Abdominal Surgery and Complications
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- Mycobacterium research and diagnosis
- Biomedical Ethics and Regulation
Cambridge University Hospitals NHS Foundation Trust
2024
Fred Hutch Cancer Center
2022-2023
Duke University
2023
Howard Hughes Medical Institute
2023
University of Washington
2023
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2023
New York Genome Center
2017-2021
New York University
2017-2021
Genomics (United Kingdom)
2021
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...
What's in a drop of blood? Blood contains many types cells, including immune system components. Immune cells used to be characterized by marker-based assays, but now classification relies on the genes that express. Villani et al. deep sequencing at single-cell level and unbiased clustering define six dendritic cell four monocyte populations. This refined analysis has identified, among others, previously unknown population potently activates T cells. Further culture revealed possible...
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...
Droplet-based single-cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While this approach offers the exciting promise to deconvolute heterogeneity in diseased tissues, lack of cost-effective and user-friendly instrumentation hindered widespread adoption droplet microfluidic techniques. To address this, we developed 3D-printed, low-cost control instrument deploy it clinical environment perform transcriptome profiling disaggregated synovial tissue...
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...
Article15 March 2018Open Access Transparent process Molecular transitions in early progenitors during human cord blood hematopoiesis Shiwei Zheng New York Genome Center, York, NY, USA Center for Genomics and Systems Biology, University, Search more papers by this author Efthymia Papalexi Andrew Butler William Stephenson Rahul Satija Corresponding Author [email protected] orcid.org/0000-0001-9448-8833 Information Zheng1,2, Papalexi1,2, Butler1,2, Stephenson1 *,1,2 1New 2Center *Corresponding...
ABSTRACT Single cell RNA-seq (scRNA-seq) has emerged as a transformative tool to discover and define cellular phenotypes. While computational scRNA-seq methods are currently well suited for experiments representing single condition, technology, or species, analyzing multiple datasets simultaneously raises new challenges. In particular, traditional analytical workflows struggle align subpopulations that present across datasets, limiting the possibility integrated comparative analysis. Here,...
The ultimate success of a viral infection at the cellular level is determined by number progeny virions produced. However, most single-cell studies quantify expression transcripts and proteins, rather than amount released from infected cells. Here, we overcome this limitation simultaneously measuring transcription production single influenza virus-infected cells embedding nucleotide barcodes in genome. We find that are poorly correlated transcribe mRNA do not produce often represent aberrant...
scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods limited by a reliance on pre-existing cell type labels or difficulties in identifying markers rare cells. We introduce an iterative approach, geneBasis, for selecting optimal panel, each newly added captures maximum distance between true manifold and constructed currently...
ABSTRACT The expression of inhibitory immune checkpoint molecules such as PD-L1 is frequently observed in human cancers and can lead to the suppression T cell-mediated responses. Here we apply ECCITE-seq, a technology which combines pooled CRISPR screens with single-cell mRNA surface protein measurements, explore molecular networks that regulate expression. We also develop computational framework, mixscape , substantially improves signal-to-noise ratio perturbation by identifying removing...
Abstract Droplet-based single cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While these approaches offer the exciting promise to deconvolute heterogeneity in diseased tissues, lack of cost-effective, reliable, and user-friendly instrumentation hindered widespread adoption droplet microfluidic techniques. To address this, we have developed control instrument that can be easily assembled from 3D printed parts commercially available components...
ABSTRACT Diverse subsets of cortical interneurons play a particularly important role in the stability neural circuits underlying cognitive and higher order brain functions, yet our understanding how this diversity is generated far from complete. We applied massively parallel single-cell RNA-seq to profile developmental time course interneuron development, measuring transcriptomes over 60,000 progenitors during their maturation ganglionic eminences embryonic migration into cortex. While...
The ultimate success of a viral infection at the cellular level is determined by number progeny virions produced. However, most single-cell studies quantify expression transcripts and proteins, rather than amount released from infected cells. Here, we overcome this limitation simultaneously measuring transcription production single influenza virus-infected cells embedding nucleotide barcodes in genome. We find that are poorly correlated transcribe mRNA do not produce often represent aberrant...
Abstract The ultimate success of a viral infection at the cellular level is determined by number progeny virions produced. However, most single-cell studies quantify expression transcripts and proteins, rather than amount released from infected cells. Here we overcome this limitation simultaneously measuring transcription production single influenza-virus-infected cells embedding nucleotide barcodes in genome. We find that are poorly correlated transcribe mRNA do not produce progeny, often...
Abstract Background Upper gastro-intestinal (GI) perforations and leaks affect roughly 2,800 patients annually in the UK. They can occur spontaneously, as a complication of medical intervention, or be due to trauma. Mortality rates are around 20%, rising 50% if diagnosis treatment is delayed. Around third cases fall into delayed category. Traditionally, management this group involved surgery with long hospital stays poor outcomes. Our Unit has adopted EVT first line for these cases, using an...
The ultimate success of a viral infection at the cellular level is determined by number progeny virions produced. However, most single-cell studies quantify expression transcripts and proteins, rather than amount released from infected cells. Here we overcome this limitation simultaneously measuring transcription production single influenza-virus-infected cells embedding nucleotide barcodes in genome. We find that are poorly correlated transcribe mRNA do not produce progeny, often represent...