Naresh Doni Jayavelu
A5069678036- COVID-19 Clinical Research Studies
- Long-Term Effects of COVID-19
- SARS-CoV-2 and COVID-19 Research
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- Asthma and respiratory diseases
- Plant Molecular Biology Research
- Plant Stress Responses and Tolerance
- Chromosomal and Genetic Variations
- MicroRNA in disease regulation
- Photosynthetic Processes and Mechanisms
- COVID-19 and Mental Health
- Plant Gene Expression Analysis
- Reproductive Biology and Fertility
- Neural Networks and Applications
- Hearing, Cochlea, Tinnitus, Genetics
- RNA Research and Splicing
- Respiratory Support and Mechanisms
- Respiratory viral infections research
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Monoclonal and Polyclonal Antibodies Research
University of Washington
2017-2025
Benaroya Research Institute
2022-2025
University of Washington Medical Center
2017-2024
Seattle University
2023
Turku Centre for Biotechnology
2016-2017
University of Turku
2016-2017
Åbo Akademi University
2016
Norwegian University of Science and Technology
2013-2015
Abstract Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated female sex distinctive comorbidities. During...
Better understanding of the association between characteristics patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management.
The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1–3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling >15,000 longitudinal blood nasal samples 540 participants the using 14 distinct assays. These unbiased analyses identify cellular molecular signatures present within 72 h hospital admission that...
BACKGROUNDPatients hospitalized for COVID-19 exhibit diverse clinical outcomes, with outcomes some individuals diverging over time even though their initial disease severity appears similar to that of other patients. A systematic evaluation molecular and cellular profiles the full course can link immune programs coordination progression heterogeneity.METHODSWe performed deep immunophenotyping conducted longitudinal multiomics modeling, integrating 10 assays 1,152 Immunophenotyping Assessment...
Abstract Background Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking. Results In this study, we report transcript response 10 A. ecotypes originating from different geographical locations non-freezing stress (10°C). To analyze the transcriptional diversity,...
Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general condition-specific activities TFs their relationships with target genes (TGs), we have used a homogeneous gene expression dataset generated on ten natural ecotypes model plant Arabidopsis thaliana, during five single six combined conditions. Knowledge-based profiles...
Abstract The glycosylation of IgG plays a critical role during human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, activating immune cells and inducing cytokine production. However, the IgM N-glycosylation has not been studied viral infection. analysis from healthy controls hospitalized disease 2019 (COVID-19) patients reveals increased high-mannose sialylation that correlates with COVID-19 severity. These trends are confirmed within SARS-CoV-2-specific...
Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated impact of aging on host immune response in blood and upper airway, as well nasal microbiome prospective, multicenter cohort 1031 vaccine-naïve patients hospitalized COVID-19 between 18 96 years old. We performed mass cytometry, serum protein profiling, anti–severe acute respiratory syndrome 2 (SARS-CoV-2)...
The post-acute sequelae of SARS-CoV-2 (PASC), also known as long COVID, remain a significant health issue that is incompletely understood. Predicting which acutely infected individuals will go on to develop COVID challenging due the lack established biomarkers, clear disease mechanisms, or well-defined sub-phenotypes. Machine learning (ML) models offer potential address this by leveraging clinical data enhance diagnostic precision. We utilized data, including antibody titers and viral load...
Following SARS-CoV-2 infection, ∼10-35% of COVID-19 patients experience long COVID (LC), in which often debilitating symptoms persist for at least three months. Elucidating the biologic underpinnings LC could identify therapeutic opportunities. We utilized machine learning methods on analytes and patient reported outcome surveys provided over 12 months after hospital discharge from >500 hospitalized IMPACC cohort to a multi-omics "recovery factor". participants who experienced had lower...
During mammalian embryogenesis, changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the preimplantation blastocyst (naive) postimplantation epiblast (primed), our data 2iL/I/F naive demonstrate that a substantial portion of known enhancers premarked by H3K4me1, providing an enhanced open chromatin state pluripotency. The enhancer repertoire occupies 9% genome, three times primed cells, can exist broad domains...
Oocyte maturation is a coordinated process that tightly linked to reproductive potential. A better understanding of gene regulation during human oocyte will not only answer an important question in biology, but also facilitate the development vitro technology as fertility treatment. We generated single-cell transcriptome and used our previously published methylome data from oocytes at different stages investigate how genes are regulated maturation, focusing on potential regulatory role...
In the scenario of global warming and climate change, heat stress is a serious threat to crop production worldwide. Being sessile, plants cannot escape from heat. Plants have developed various adaptive mechanisms survive stress. Several studies focused on diversity tolerance levels in divergent Arabidopsis thaliana (A. thaliana) ecotypes, but comprehensive genome scale understanding response still lacking. Here we report transcript responses 10 A. ecotypes (Col, Ler, C24, Cvi, Kas1, An1,...
Human bone marrow stromal cells, or mesenchymal stem cells (BM-MSCs), need expansion prior to use as cell-based therapies in immunological and tissue repair applications. Aging of BM-MSCs induce epigenetic changes that can impact therapeutic outcomes. By applying sequencing-based methods, we reveal the breadth DNA methylation dynamics associated with aging is greater than previously reported. Methylation are enriched at known distal transcription factor binding sites such enhancer elements,...
The inner ear is a complex structure responsible for hearing and balance, organ pathology associated with deafness balance disorders. To evaluate the role of epigenomic dynamics, we performed whole genome bisulfite sequencing at key time points during development maturation mouse sensory epithelium (SE). Our single-nucleotide resolution maps revealed variations in both general characteristics dynamics DNA methylation over time. This allowed us to predict location non-coding regulatory...
Abstract Age is a major risk factor for severe coronavirus disease-2019 (COVID-19), yet the mechanisms responsible this relationship have remained incompletely understood. To address this, we evaluated impact of aging on host and viral dynamics in prospective, multicenter cohort 1,031 patients hospitalized COVID-19, ranging from 18 to 96 years age. We performed blood transcriptomics nasal metatranscriptomics, measured peripheral immune cell populations, inflammatory protein expression,...
Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles the full course can link immune programs coordination progression heterogeneity. In this study, we carried out deep immunophenotyping conducted longitudinal multi-omics modeling integrating ten distinct assays on a total 1,152 IMPACC participants identified several...
Abstract Hospitalized COVID-19 patients exhibit diverse immune responses during acute infection, which are associated with a wide range of clinical outcomes. However, understanding these heterogeneities and their links to various complications, especially long COVID, remains challenge. In this study, we performed unsupervised subtyping longitudinal multi-omics immunophenotyping in over 1,000 hospitalized patients, identifying two critical subtypes linked mortality or mechanical ventilation...
Network component analysis (NCA) became a popular tool to understand complex regulatory networks. The method uses high-throughput gene expression data and priori topology reconstruct transcription factor activity profiles. Current NCA algorithms are constrained by several conditions posed on the network topology, guarantee unique reconstruction (termed compliancy). However, restrictions these pose not necessarily true from biological perspective they force size reduction, pruning potentially...
MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes at the post-transcriptional level in spatiotemporal manner. Several miRNAs identified as prognostic and diagnostic markers many human cancers. Estimation of temporal activities is an important step way to understand complex interactions these regulatory elements with transcription factors (TFs) target (TGs). However, current research on miRNA excludes network dynamics from studies, disregarding element time analysis.In study,...