A5081216012- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- COVID-19 Clinical Research Studies
- Extracellular vesicles in disease
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Microfluidic and Bio-sensing Technologies
- SARS-CoV-2 and COVID-19 Research
- Forensic and Genetic Research
- Forest Insect Ecology and Management
- Respiratory viral infections research
- Plant Virus Research Studies
- Cervical Cancer and HPV Research
- interferon and immune responses
- Cell Image Analysis Techniques
- Genomics and Phylogenetic Studies
- Pneumonia and Respiratory Infections
- RNA modifications and cancer
- Micro and Nano Robotics
- Plant and Fungal Interactions Research
- Immune cells in cancer
- Mathematical Biology Tumor Growth
Princeton University
2024-2025
Stanford University
2017-2024
Biotechnology Institute
2005
University of Maryland, College Park
2005
Rutgers, The State University of New Jersey
1996
Albert Einstein College of Medicine
1996
Although it is well known that the ancestors of modern humans and Neanderthals admixed, effects gene flow on Neanderthal genome are not understood. We develop methods to estimate amount human-introgressed sequences in apply whole-genome sequence data from 2000 three Neanderthals. have 2.5 3.7% human ancestry, we leverage revise estimates ancestry humans, show population sizes were significantly smaller than previously estimated, identify two distinct waves into Our provide insights genetic...
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects SARS-CoV-2 virus by productively infecting healthy human lung tissue using scRNA-seq reconstruct the transcriptional program “infection pseudotime” for individual cell types. predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands viral RNA molecules, taking over 60% transcriptome forming...
Risk factors for cervicovaginal human papillomavirus (HPV) infection were investigated in 604 college women. HPV was detected 168 (27.8%) ofthe subjects by L1 consensus primer polymerase chain reaction, Southern blot hybridization, or both. Significant independent risk (P < .05) included age (odds ratios [DRs]: 2.6 21-23 years old and 1.6 >23, vs. ⩽0;20), ethnicity (DRs: 3.2 black, 2.2 Hispanic, white/other), number of lifetime male vaginal sex partners 4.5 2, 5.8 3 4, 10.3 ⩾5, 1), living...
Although somatic mutations are fundamentally important to human biology, disease, and aging, many outstanding questions remain about their rates, spectrum, determinants in apparently healthy tissues. Here, we performed high-coverage exome sequencing on 265 samples from 14 GTEx donors sampled for a median of 17.5 tissues per donor (spanning 46 total tissues). Using novel probabilistic method tailored the unique structure our data, identified 8,470 variants. We leverage compendium quantify...
ABSTRACT Early stages of deadly respiratory diseases such as COVID-19 have been challenging to elucidate due lack an experimental system that recapitulates the cellular and structural complexity human lung while allowing precise control over disease initiation systematic interrogation molecular events at resolution. Here we show healthy slices cultured ex vivo can be productively infected with SARS-CoV-2, tropism virus its distinct dynamic effects on host cell gene expression determined by...
Gene fusions are known to play critical roles in tumor pathogenesis. Yet, sensitive and specific algorithms detect gene cancer do not currently exist. In this paper, we present a new statistical algorithm, MACHETE (Mismatched Alignment CHimEra Tracking Engine), which achieves highly detection of from RNA-Seq data, including the highest Positive Predictive Value (PPV) compared current state-of-the-art, as assessed simulated data. We show that best performing published either find large...
Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Furthermore, these link to isoform expression, especially 3’ Untranslated Region (UTR) regulation. The recent introduction of genome-wide spatial transcriptomics techniques enables the potential test if is regulated in situ pervasively. In order do this, robust statistical measures alternative poly-adenylation (APA) at...
Summary Three indigenous field strains of the chestnut blight fungus, Cryphonectria parasitica collected in 1996 from a test site Meshomasic State Forest, Connecticut, USA, were engineered to contain chromosomally integrated full‐length infectious cDNA copy severe, virulence‐attenuating hypovirus CHV1‐EP713. These transgenic hypovirulent introduced into after it had been clear‐cut, as sprayed conidia multiple applications over 4 years, beginning 1997. Evidence was obtained for cytoplasmic...
During COVID19 and other viral pandemics, rapid generation of host pathogen genomic data is critical to tracking infection informing therapies. There an urgent need for efficient approaches this at scale. We have developed a scalable, high throughput approach generate fidelity low pass whole genome HLA sequencing, genomes, representation human transcriptome from single nasopharyngeal swabs patients.
Abstract Myriad mechanisms diversify the sequence content of eukaryotic transcripts at both DNA and RNA levels, leading to profound functional consequences. Examples this diversity include splicing V(D)J recombination. Currently, these are detected using fragmented bioinformatic tools that require predefining a form transcript diversification rely on alignment an incomplete reference genome, filtering out unaligned sequences, potentially crucial for novel discoveries. Here, we present...
Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Further, these link to isoform expression, especially 3’ Untranslated Region (UTR) regulation. The recent introduction of genome-wide spatial transcriptomics techniques enable the potential test if is regulated in situ pervasively. In order do this, robust statistical measures alternative poly-adenylation (APA) at single cell...
Abstract Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Further, these link to isoform expression, especially 3’ Untranslated Region (UTR) regulation. The recent introduction of genome-wide spatial transcriptomics techniques enable the potential test if is regulated in situ pervasively. In order do this, robust statistical measures alternative poly-adenylation (APA) at...
Myriad mechanisms diversify the sequence content of eukaryotic transcripts at both DNA and RNA levels, leading to profound functional consequences. Examples this diversity include splicing V(D)J recombination. Currently, these are detected using fragmented bioinformatic tools that require a predefined form transcript diversification rely on alignment an incomplete reference genome, filtering out unaligned sequences which can be among most interesting. Here, we develop NOMAD+, new analytic...
Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Furthermore, these link to isoform expression, especially 3’ Untranslated Region (UTR) regulation. The recent introduction of genome-wide spatial transcriptomics techniques enables the potential test if is regulated in situ pervasively. In order do this, robust statistical measures alternative poly-adenylation (APA) at...