A5020167764- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- Gene expression and cancer classification
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- MicroRNA in disease regulation
- COVID-19 Clinical Research Studies
- Plant Disease Resistance and Genetics
- Metabolomics and Mass Spectrometry Studies
- CRISPR and Genetic Engineering
- Mitochondrial Function and Pathology
- Cancer-related molecular mechanisms research
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Plant and Fungal Interactions Research
- Microbial Community Ecology and Physiology
- Photosynthetic Processes and Mechanisms
- Extracellular vesicles in disease
- Long-Term Effects of COVID-19
- Protist diversity and phylogeny
- Gene Regulatory Network Analysis
- Biomarkers in Disease Mechanisms
- Fungal and yeast genetics research
- Single-cell and spatial transcriptomics
Iowa State University
2018-2024
Illumina (United States)
2023
Jawaharlal Nehru University
2015-2019
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed gene expression in nasopharyngeal autopsy tissues from patients with disease 2019 (COVID-19). In samples declining titers, the virus blocked transcription of a subset nuclear DNA (nDNA)–encoded OXPHOS genes, induced microRNA 2392, activated HIF-1α induce glycolysis, immune defenses...
Long non-coding RNAs (lncRNAs) make up a significant portion of and are involved in variety biological processes. Accurate identification/annotation lncRNAs is the primary step for gaining deeper insights into their functions. In this study, we report novel tool, PLncPRO, prediction plants using transcriptome data. PLncPRO based on machine learning uses random forest algorithm to classify coding long transcripts. has better accuracy as compared other existing tools particularly well-suited...
Highlights•In silico predictions of miR-2392 as a miRNA involved with SARS-CoV-2•Overexpression produces similar biological response COVID-19 infection•miR-2392 is confirmed to circulate in serum and urine patients COVID-19•Development initiated potential antiviral therapeutic against COVID-19SummaryMicroRNAs (miRNAs) are small non-coding RNAs post-transcriptional gene regulation that have major impact on many diseases provide an exciting avenue toward therapeutics. From patient...
Searching for open reading frames is a routine task and critical step prior to annotating protein coding regions in newly sequenced genomes or de novo transcriptome assemblies. With the tremendous increase genomic transcriptomic data, faster tools are needed handle large input datasets. These should be versatile enough fine-tune search criteria allow efficient downstream analysis. Here we present new python based tool, orfipy, which allows user flexibly sequences. The rapid fully...
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling 646 nasopharyngeal swabs 39 patient autopsy tissues to define body-wide transcriptome changes in response COVID-19. We then match data with spatial protein...
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal dynamics of through transcription profiles nasopharyngeal autopsy samples from patients infected rodent models. While bioenergetics is repressed viral portal entry, it up regulated lung tissues deceased patients. In most disease stages organs, discrete OXPHOS functions are blocked by virus, this countered host broadly...
Abstract Our previous research revealed a key microRNA signature that is associated with spaceflight can be used as biomarker and to develop countermeasure treatments mitigate the damage caused by space radiation. Here, we expand on this work determine biological factors rescued treatment. We performed RNA-sequencing transcriptomic analysis 3D microvessel cell cultures exposed simulated deep radiation (0.5 Gy of Galactic Cosmic Radiation) without antagonists three microRNAs: miR-16-5p,...
Abstract Motivation The goal of phylostratigraphy is to infer the evolutionary origin each gene in an organism. This done by searching for homologs within increasingly broad clades. deepest clade that contains a homolog protein(s) encoded gene’s phylostratum. Results We have created general R-based framework, phylostratr, estimate phylostratum every species. program fully automates analysis: selecting species balanced representation, retrieving sequences, building databases, inferring...
Abstract Proteins encoded by newly-emerged genes (‘orphan genes’) share no sequence similarity with proteins in any other species. They provide organisms a reservoir of genetic elements to quickly respond changing selection pressures. Here, we systematically assess the ability five gene prediction pipelines accurately predict genomes according phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer structures machine learning. Direct Inference is an...
The diverse and growing omics data in public domains provide researchers with tremendous opportunity to extract hidden, yet undiscovered, knowledge. However, the vast majority of archived remain unused. Here, we present MetaOmGraph (MOG), a free, open-source, standalone software for exploratory analysis massive datasets. Researchers, without coding, can interactively visualize evaluate context its metadata, honing-in on groups samples or genes based attributes such as expression values,...
Unlike dicots, the robust root system in grass species largely originates from stem base during postembryonic development. The mechanisms by which plant hormone signaling pathways control architecture of adventitious remain unknown. Here, we studied modulations global genes activity developing rice genome-wide RNA sequencing response to external auxin and cytokinin cues. We further analyzed spatiotemporal regulations key developmental regulators emerged our transcriptome analysis....
Abstract The COVID-19 pandemic has affected African American populations disproportionately with respect to prevalence, and mortality. Expression profiles represent snapshots of combined genetic, socio-environmental (including socioeconomic environmental factors), physiological effects on the molecular phenotype. As such, they have potential improve biological understanding differences among populations, provide therapeutic biomarkers mitigation strategies. Here, we undertook a large-scale...
With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations existing genes, many others de novo non-genic regions the genome. If these survive across speciations, then extant organisms will contain a patchwork whose ancestors first appeared at different times. Standard phylostratigraphy, technique partitioning by their age, based solely on protein similarity algorithms. However, this approach relies negative...
Abstract The availability of terabytes RNA-Seq data and continuous emergence new analysis tools, enable unprecedented biological insight. There is a pressing requirement for framework that allows fast, efficient, manageable, reproducible analysis. We have developed Python package, (pyrpipe), enables straightforward development flexible, easy-to-debug computational pipelines purely in Python, an object-oriented manner. pyrpipe provides access to popular within via high-level APIs. Pipelines...
Abstract The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused 2.5 deaths worldwide. Yet, the molecular mechanisms underlying clinical manifestations of COVID-19, as well what distinguishes them from common seasonal influenza other lung injury states such Distress (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling 646 nasopharyngeal swabs 39 patient autopsy tissues, matched...
The orphan gene of SARS-CoV-2, ORF10, is the least studied in virus responsible for COVID-19 pandemic. Recent experimentation indicated ORF10 expression moderates innate immunity vitro. However, whether affects humans remained unknown. We determine that sequence identical to Wuhan-Hu-1 ancestral haplotype 95% genomes across five variants concern (VOC). Four are associated with less virulent clinical outcomes human host: three these affect protein structure, one RNA structural dynamics....
The “dark transcriptome” can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression 6,692 genes and 29,354 unannotated open reading frames (ORFs) in Saccharomyces cerevisiae genome across diverse environmental, genetic developmental conditions (3,457 RNA-Seq samples). Over 30% highly ORFs have translation evidence. Phylostratigraphic analysis infers most these would encode species-specific proteins (“orphan-ORFs”); hundreds mean...
Advancement in sequence data generation technologies are churning out voluminous omics and posing a massive challenge to annotate the biological functional features. Sequence from well studied model organism Saccharomyces cerevisiae has been commonly used test validate silico prediction methods. DNA replication is critical step cellular process location where this originates genomic landscape generally referred as origin of replication. In paper we investigate application bidirectional Long...
ABSTRACT The availability of terabytes RNA-Seq data and continuous emergence new analysis tools, enable unprecedented biological insight. However, implementing pipelines in a reproducible, flexible manner is challenging as gets bigger more complex. Thus, there pressing requirement for frameworks that allows fast, efficient, easy-to-manage, reproducibile analysis. Simple scripting has many challenges drawbacks. We have developed python package, Pipeliner ( pyrpipe ) enables straightforward...
ABSTRACT Proteins encoded by newly-emerged genes (“orphan genes”) share no sequence similarity with proteins in any other species. They provide organisms a reservoir of genetic elements to quickly respond changing selection pressures. Here, we systematically assess the ability five gene annotation pipelines accurately predict genomes according phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer structures machine learning. Direct Inference is an...
The diverse and growing omics data in public domains provide researchers with a tremendous opportunity to extract hidden knowledge. However, the challenge of providing domain experts easy access these big has resulted vast majority archived remaining unused. Here, we present MetaOmGraph (MOG), free, open-source, standalone software for exploratory analysis massive datasets by scientific researchers. Using MOG, researcher can interactively visualize statistically analyze data, context its...
Abstract The “dark transcriptome” can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression 6,692 genes and 29,354 unannotated ORFs in Saccharomyces cerevisiae genome across diverse environmental, genetic developmental conditions (3,457 RNA-Seq samples). Over 48% have translation evidence. Phylostratigraphic analysis infers most these would encode species-specific proteins (“orphan-ORFs”); hundreds mean comparable to These data...
Summary MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we discovered circulating miRNA, miR-2392, is directly with SARS-CoV-2 machinery during host infection. Specifically, show miR-2392 key driving downstream suppression of mitochondrial expression, increasing inflammation, glycolysis, hypoxia as well...
Abstract Motivation The goal of phylostratigraphy is to infer the evolutionary origin each gene in an organism. Currently, there are no general pipelines for this task. We present R package, phylostratr , fill gap, making high-quality phylostratigraphic analysis accessible non-specialists. Results Phylostratigraphic entails searching homologs within increasingly broad clades. highest clade that contains all a gene’s phylostratum. have created R-based framework, estimating phylostratum every...