A5086167394- Respiratory viral infections research
- Influenza Virus Research Studies
- Insect symbiosis and bacterial influences
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- interferon and immune responses
- Nematode management and characterization studies
- Immune Cell Function and Interaction
- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- T-cell and B-cell Immunology
- Immune cells in cancer
- CRISPR and Genetic Engineering
- Glioma Diagnosis and Treatment
- Single-cell and spatial transcriptomics
- Immune Response and Inflammation
- Parasites and Host Interactions
- Phytoplasmas and Hemiptera pathogens
- Herpesvirus Infections and Treatments
- Amyotrophic Lateral Sclerosis Research
- Viral Infections and Vectors
- Parasitic Diseases Research and Treatment
- Cancer, Hypoxia, and Metabolism
- Trypanosoma species research and implications
University of Rochester Medical Center
2022-2023
New York University
2017-2022
Columbia University
2014
Columbia University Irving Medical Center
2014
Memorial Sloan Kettering Cancer Center
2010
Background Microbiome studies of the lower airways based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short-chain fatty acids (SCFAs), in have significant impact host's immune tone. Thus, approaches to analyses microbiome are necessary. Methods Here we used upper and airway samples from a research bronchoscopy smoker cohort. In addition, validated our results an experimental mouse model....
Abstract Background The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In context influenza virus infection, interactions between virus, host, resident bacteria with pathogenic potential are known to complicate worsen disease, resulting coinfection increased morbidity mortality infected individuals. When acquire resistance, they more difficult treat global health concern. Characterization ARG expression upper...
Virus and host factors contribute to cell-to-cell variation in viral infections determine the outcome of overall infection. However, extent variability at single-cell level how it impacts virus-host interactions a system are not well understood. To characterize dynamics transcription responses, we used RNA sequencing quantify multiple time points transcriptomes human A549 cells primary bronchial epithelial infected with influenza A virus. We observed substantial between cells, including...
Filarial nematodes can cause debilitating diseases in humans. They have complicated life cycles involving an insect vector and mammalian hosts, they go through a number of developmental molts. While whole genome sequences parasitic worms are now available, very little is known about transcription factor (TF) binding sites their cognate factors that play role regulating development. To address this gap, we developed novel motif prediction pipeline, Emotif Alpha, integrates ten different...
Abstract Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO system while others, filarial parasite Brugia malayi , XY mechanism. We present complete B. genome assembly and define Nigon elements shared with C. which we then map to genomes other more distantly nematodes. find remarkable plasticity chromosome several...
The co-evolution of myxoma virus (MYXV) and the European rabbit occurred independently in Australia Europe from different progenitor viruses. Although this is canonical study evolution virulence, whether genomic phenotypic outcomes MYXV mirror those observed unknown. We addressed question using viruses isolated United Kingdom early epizootic (1954–1955) between 2008–2013. later UK fell into three distinct lineages indicative a long period separation independent evolution. rates evolutionary...
Factors that contribute to enhanced susceptibility severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with A/H3N2 or B and profiled microbiota by target sequencing 16S rRNA gene. identified signature taxonomic groups...
The specific interactions of Mycobacterium tuberculosis (Mtb), the causative agent (TB), and lung microbiota in infection are entirely unexplored. Studies cancer other infectious diseases suggest that there important exchanges occurring between host influence immunological landscape. This can result alterations immune regulation inflammation both locally systemically. To assess whether Mtb modifies microbiome, identify changes microbial abundance diversity as a function pulmonary...
The filarial nematode
Abstract The fundamental basis of how arboviruses evolve in nature and what regulates the adaptive process remain unclear. To address this problem, we established a Zika virus (ZIKV) vector-borne transmission system immunocompromised mice to study evolutionary characteristics ZIKV infection. Using system, defined factors that influence landscape infection show route specific organ microenvironments impact viral diversity defective genome production. In addition, identified emergence mutants...
Lymphatic filariasis affects ∼120 million people and can result in elephantiasis hydrocele. Here, we report the nearly complete genome sequence of best-studied causative agent lymphatic filariasis, Brugia malayi . The assembly contains four autosomes, an X chromosome, only eight gaps but lacks a contiguous for known Y chromosome.
Molecular responses to influenza A virus (IAV) infections vary between mammalian species. To identify conserved and species-specific molecular responses, we perform a comparative study of transcriptomic data derived from blood cells, primary epithelial lung tissues collected IAV-infected humans, ferrets, mice. The in the human host have unique functions such as antigen processing that are not observed mice or ferrets. Highly gene coexpression modules across three species enriched for IAV...
ABSTRACT Virus and host factors contribute to cell-to-cell variation in viral infections determine the outcome of overall infection. However, extent variability at single cell level how it impacts virus-host interactions a systems are not well understood. To characterize dynamics transcription responses, we used single-cell RNA sequencing quantify multiple time points transcriptomes human A549 cells primary bronchial epithelial infected with influenza A virus. We observed substantial between...
Abstract Factors that contribute to enhanced susceptibility severe bacterial disease after influenza infection are not well defined, but likely include the microbiome of respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with A/H3N2 or B and profiled microbiota by target sequencing 16S rRNA gene. identified signature taxonomic groups...
Abstract Filarial nematodes can cause debilitating diseases in humans. They have complicated life cycles involving an insect vector and mammalian hosts, they go through a number of developmental molts. While whole genome sequences parasitic worms are now available, very little is known about transcription factor (TF) binding sites their cognate factors that play role regulating development. To address this gap, we developed novel motif prediction pipeline, Emotif Alpha, integrates ten...
Abstract Tissue-resident memory CD8 T cells (TRM) principally reside in peripheral nonlymphoid tissues, such as lung and skin, confer protection against a variety of illnesses ranging from infections to cancers. The functions different cell subsets have been linked with distinct metabolic pathways differ other subsets. For example, skin-derived undergo fatty acid oxidation oxidative phosphorylation greater degree than circulating naive cells. Lung TRMs defined by the cell-surface expression...
Abstract The filarial nematode Brugia malayi represents a leading cause of disability in the developing world, causing lymphatic filariasis nearly 40 million people. Currently available drugs are not well-suited to mass drug administration efforts, so new treatments urgently required. One potential vulnerability is endosymbiotic bacteria Wolbachia —present many filariae—which vital worm. Genome scale metabolic networks have been used study prokaryotes and protists proven valuable identifying...