A5019679682- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Gene Regulatory Network Analysis
- COVID-19 Clinical Research Studies
- SARS-CoV-2 and COVID-19 Research
- Generative Adversarial Networks and Image Synthesis
- Topic Modeling
- Long-Term Effects of COVID-19
- Neural Networks and Applications
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Model Reduction and Neural Networks
- Computational Drug Discovery Methods
- Sepsis Diagnosis and Treatment
- Functional Brain Connectivity Studies
- Neuroinflammation and Neurodegeneration Mechanisms
- Advanced Graph Neural Networks
- RNA Research and Splicing
- Immune Cell Function and Interaction
- Gaussian Processes and Bayesian Inference
- HIV Research and Treatment
- Natural Language Processing Techniques
- Music and Audio Processing
- COVID-19 diagnosis using AI
- CRISPR and Genetic Engineering
Yale University
2016-2025
Maastricht University
2015-2024
Cardiovascular Research Center
2020-2023
University of Amsterdam
2010-2019
Memorial Sloan Kettering Cancer Center
2017-2018
University of New Haven
2017
Weizmann Institute of Science
2013-2016
Columbia University
2015-2016
Amsterdam University of Applied Sciences
2015
Amsterdam University of the Arts
2014
Although COVID-19 is considered to be primarily a respiratory disease, SARS-CoV-2 affects multiple organ systems including the central nervous system (CNS). Yet, there no consensus on consequences of CNS infections. Here, we used three independent approaches probe capacity infect brain. First, using human brain organoids, observed clear evidence infection with accompanying metabolic changes in infected and neighboring neurons. However, for type I interferon responses was detected. We...
Abstract Post-acute infection syndromes may develop after acute viral disease 1 . Infection with SARS-CoV-2 can result in the development of a post-acute syndrome known as long COVID. Individuals COVID frequently report unremitting fatigue, post-exertional malaise, and variety cognitive autonomic dysfunctions 2–4 However, biological processes that are associated persistence these symptoms unclear. Here 275 individuals or without were enrolled cross-sectional study included multidimensional...
Abstract Pathologic immune hyperactivation is emerging as a key feature of critical illness in COVID-19, but the mechanisms involved remain poorly understood. We carried out proteomic profiling plasma from cross-sectional and longitudinal cohorts hospitalized patients with COVID-19 analyzed clinical data our health system database more than 3300 patients. Using machine learning algorithm, we identified prominent signature neutrophil activation, including resistin, lipocalin-2, hepatocyte...
Study objectiveThe goal of this study is to create a predictive, interpretable model early hospital respiratory failure among emergency department (ED) patients admitted with coronavirus disease 2019 (COVID-19).MethodsThis was an observational, retrospective, cohort from 9-ED health system adult severe acute syndrome 2 (COVID-19) and oxygen requirement less than or equal 6 L/min. We sought predict within 24 hours admission as defined by greater 10 L/min low-flow device, high-flow noninvasive...
There are currently limited Food and Drug Administration (FDA)-approved drugs vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) infection pathogenesis is critical development therapeutics. To provide insight into viral replication, cell tropism, host–viral interactions SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) experimentally infected human bronchial epithelial cells...
Immunotherapies targeting the immune checkpoint receptor programmed cell death protein 1 (PD-1) have shown remarkable efficacy in treating cancer. CD4+CD25hiFoxP3+ Tregs are critical regulators of responses autoimmunity and malignancies, but functional status human expressing PD-1 remains unclear. We examined molecular features PD-1hi healthy subjects patients with glioblastoma multiforme (GBM), combining assays, RNA sequencing, cytometry by time flight (CyTOF). In both GBM subjects,...
Summary Although COVID-19 is considered to be primarily a respiratory disease, SARS-CoV-2 affects multiple organ systems including the central nervous system (CNS). Yet, there no consensus whether virus can infect brain, or what consequences of CNS infection are. Here, we used three independent approaches probe capacity brain. First, using human brain organoids, observed clear evidence with accompanying metabolic changes in infected and neighboring neurons. However, for type I interferon...
SARS-CoV-2 infection can result in the development of a constellation persistent sequelae following acute disease called post-acute COVID-19 (PASC) or Long COVID 1-3 . Individuals diagnosed with frequently report unremitting fatigue, post-exertional malaise, and variety cognitive autonomic dysfunctions ; however, basic biological mechanisms responsible for these debilitating symptoms are unclear. Here, 215 individuals were included an exploratory, cross-sectional study to perform...
Abstract Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, signatures associated with immunopathology poorly understood. Here we use multi-omics single-cell analysis to probe dynamic hospitalized patients stable or progressive course of COVID-19, explore V(D)J repertoires, and assess cellular effects tocilizumab. Coordinated profiling gene expression cell lineage protein markers shows that S100A hi /HLA-DR lo classical monocytes...
Summary Strong sex differences in the frequencies and manifestations of Long COVID (LC) have been reported with females significantly more likely than males to present LC after acute SARS-CoV-2 infection 1–7 . However, whether immunological traits underlying differ between sexes, such explain differential symptomology is currently unknown. Here, we performed sex-based multi-dimensional immune-endocrine profiling 165 individuals 8 without an exploratory, cross-sectional study identify key...
ABSTRACT Single-cell RNA-sequencing is fast becoming a major technology that revolutionizing biological discovery in fields such as development, immunology and cancer. The ability to simultaneously measure thousands of genes at single cell resolution allows, among other prospects, for the possibility learning gene regulatory networks large scales. However, scRNA-seq technologies suffer from many sources significant technical noise, most prominent which ‘dropout’ due inefficient mRNA capture....
The ability of cells to accurately control gene expression levels in response extracellular cues is limited by the inherently stochastic nature transcriptional regulation. A change transcription factor (TF) activity results changes its targets, but way which cell-to-cell variability (noise) as a function TF activity, and whether targets same behave similarly, not known. Here, we measure noise for 16 native Zap1 that are regulated it through diverse mechanisms. For most activated repressed...
Increase in thrombotic and microvascular complications is emerging to be a key feature of patients with critical illness associated COVID-19 infection. While endotheliopathy thought factor COVID-19-associated coagulopathy, markers indicative this process that are prognostic disease severity have not been well-established patient population. Using plasma profiling COVID-19, we identified circulating segregated severity: angiogenesis (VEGF-A, PDGF-AA PDGF-AB/BB) were elevated hospitalized...
Genetically identical cells exhibit large variability (noise) in gene expression, with important consequences for cellular function. Although the amount of noise decreases and is thus partly determined by mean expression level, extent to which different promoter sequences can deviate away from this trend not fully known. Here, we present a high-throughput method measuring promoter-driven thousands designed synthetic promoters parallel. We use it investigate how encode levels find that...
We have profiled cerebrospinal fluid T cells in healthy individuals and patients with MS using single-cell RNA TCR sequencing.