A5037954227- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Plant responses to elevated CO2
- Neurobiology and Insect Physiology Research
- Influenza Virus Research Studies
- Animal Behavior and Reproduction
- Cancer-related molecular mechanisms research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Chromosomal and Genetic Variations
- Plant Stress Responses and Tolerance
- Photosynthetic Processes and Mechanisms
- Viral-associated cancers and disorders
- Plant pathogens and resistance mechanisms
- Soybean genetics and cultivation
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
University of Florida
2021-2024
University of Pittsburgh
2017-2019
SQANTI3 is a tool designed for the quality control, curation and annotation of long-read transcript models obtained with third-generation sequencing technologies. Leveraging its framework, calculates descriptors models, junctions ends. With this information, potential artifacts can be identified replaced reliable sequences. Furthermore, integrated functional feature enables subsequent iso-transcriptomics analyses.
Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and (vRNA) is depicted as a uniform pattern 'beads on string'. Using high-throughput sequencing isolated crosslinking immunoprecipitation (HITS-CLIP), we identified vRNA binding profiles for two H1N1 IAV strains in virions. Contrary to prevailing model packaging, does not bind uniformly A/WSN/1933 A/California/07/2009...
Sweet corn is one of the most important vegetables in United States and Canada. Here, we present a de novo assembly sweet inbred line Ia453 with mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar commercial hybrids developed for processing fresh markets. The ten pseudochromosomes cover 92% total 99% estimated genome size, scaffold N50 222.2 Mb. reference completely assembles large structural variation that created mutant sh2-R allele. Furthermore,...
Abstract The emergence of long-read RNA sequencing (lrRNA-seq) has provided an unprecedented opportunity to analyze transcriptomes at isoform resolution. However, the technology is not free from biases, and transcript models inferred these data require quality control curation. In this study, we introduce SQANTI3, a tool specifically designed perform analysis on constructed using lrRNA-seq data. SQANTI3 provides extensive naming framework describe model diversity in comparison reference...
The genomes of influenza A and B viruses have eight, single-stranded RNA segments that exist in the form a viral ribonucleoprotein complex association with nucleoprotein (NP) an RNA-dependent polymerase complex. We previously used high-throughput sequencing coupled crosslinking immunoprecipitation (HITS-CLIP) to examine where NP binds (vRNA) demonstrated for two H1N1 strains vRNA non-uniform, non-random manner. In this study, we expand on those initial observations describe NP-vRNA binding...
In Drosophila melanogaster and D. simulans head tissue, 60% of orthologous genes show evidence sex-biased expression in at least one species. Of these, ∼39% (2,192) are conserved direction. We hypothesize enrichment open chromatin the sex where we see bias closed opposite sex. Male-biased orthologs significantly enriched for H3K4me3 marks males both species (∼89% male-biased vs. ∼76% unbiased orthologs). Similarly, female-biased females (∼90% ∼73% The sex-bias ratio was similar magnitude...
Abstract Advances in affordable transcriptome sequencing combined with better exon and gene prediction has motivated many to compare transcription across the tree of life. We develop a mathematical framework calculate complexity transcript models. Structural features, i.e. intron retention (IR), donor/acceptor site variation, alternative cassettes, 5′/3′ UTRs, are compared distance between models is calculated nucleotide level precision. All metrics implemented PyPi package, TranD output can...
Abstract Background Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding the functional components genome an untapped wealth knowledge ripe exploration. With “remarkable lack correspondence” between size complexity, there needs to be way quantify across organisms. In this study, we use set metrics that allow evaluating changes using TranD. Results We ascertain if increasing or...
Epstein-Barr virus (EBV) expresses an abundant nuclear noncoding RNA called EBER2, which interacts with and acts as a guide for the host transcription factor PAX5. This ribonucleoprotein complex localizes to terminal repeat (TR) regions of EBV genome via RNA-RNA interactions between EBER2 nascent transcripts originating from these target sites. Given fact that base pairs viral RNA, we developed protocol identify EBER2-interacting RNAs in transcriptome-wide manner. Our approach entails...
Abstract Alternative splicing contributes to organismal complexity. Comparing transcripts between and within species is an important first step toward understanding questions about how evolution of transcript structure changes sub-functionalization. These are confounded with issues data quality availability. The recent explosion affordable long read sequencing mRNA has considerably widened the ability study transcriptional variation in non-model species. In this work, we develop a...
We examine the impact of sustained elevated ozone concentration on leaf transcriptome 5 diverse maize inbred genotypes, which vary in physiological sensitivity to (B73, Mo17, Hp301, C123, and NC338), using long reads assemble transcripts short quantify expression these transcripts. More than 99% reads, assembled transcripts, 97% map both B73 Mo17 reference genomes. Approximately 95% genes with belong known B73-Mo17 syntenic loci 94% are present all temperate lines nested association mapping...
Abstract We propose a new model for the association of chromatin state and sex-bias in expression. hypothesize enrichment open sex where we see expression bias (OS) closed opposite (CO). In this study D. melanogaster simulans head tissue, is associated with H3K4me3 (open mark) males male-biased genes females female-biased both species. Sex-bias also largely conserved direction magnitude between two species on X autosomes. orthologs, ratio more divergent if have H3K27me2me3 marks compared to...
Abstract The genome of Influenza A viruses consists eight negative-sense RNA segments that are bound by viral nucleoprotein (NP). We recently showed NP binding is not uniform along the but exhibits regions enrichment as well depletion. Furthermore, genome-wide profiles distinct even in strains with high sequence similarity, such two H1N1 A/WSN/1933 and A/California/07/2009. Here, we performed interstrain segment swapping experiments either or low congruency binding, which suggested a similar...
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding the functional components genome an untapped wealth knowledge ripe exploration. With "remarkable lack correspondence" between size complexity, there needs to be way quantify across organisms. In this study we use set metrics that allow evaluation changes using TranD. We ascertain if increasing or decreasing transcriptomes at what...
Abstract The maize pangenome has demonstrate large amounts of presence/absence variation and it been hypothesized that contributes to stress response. To uncover whether the observed genetic in physiological response elevated ozone (a secondary air pollutant causes significant crop yield losses) concentration is due genic content, and/or gene expression, we examine impact sustained on leaf tissue from 5 diverse inbred genotypes (B73, Mo17, Hp301, C123, NC338). Analysis long reads...