A5008135101- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Immune Cell Function and Interaction
- Extracellular vesicles in disease
- Genomics and Rare Diseases
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Bacteriophages and microbial interactions
- RNA Research and Splicing
- Retinal Diseases and Treatments
- Retinal Development and Disorders
- Monoclonal and Polyclonal Antibodies Research
- Bioinformatics and Genomic Networks
- Plant and Fungal Interactions Research
- Gene expression and cancer classification
- T-cell and B-cell Immunology
- Viral Infections and Vectors
- Software Engineering Techniques and Practices
- RNA modifications and cancer
- Yersinia bacterium, plague, ectoparasites research
- Algorithms and Data Compression
Georgia State University
2014-2023
University of California, Los Angeles
2019-2022
Samueli Institute
2022
Abstract Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid accurate profiling of the Ig repertoire, including complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types 544 individuals in Genotype-Tissue Expression (GTEx v6) project. Using ImReP GTEx v6 data, generate collection 3.6 million...
Abstract Motivation Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks inference transmission history from viral genomic data often do not consider intra-host diversity pathogens and heavily rely on additional epidemiological data, such as sampling times exposure intervals. This impedes outbreaks highly mutable viruses associated with chronic infections, human immunodeficiency virus hepatitis C virus, whose...
Abstract Motivation: Next-generation high-throughput sequencing has become a state-of-the-art technique in genome assembly. Scaffolding is one of the main stages assembly pipeline. During this stage, contigs assembled from paired-end reads are merged into bigger chains called scaffolds. Because high level statistical noise, chimeric reads, and repeats problem scaffolding challenging task. Current software packages widely vary their quality highly dependent on read data complexity. There no...
Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition state, which can otherwise only be estimated by applying deconvolution methods bulk RNA-Seq estimates. However, it has not yet become widely used tool in population-scale analyses, due its prohibitively high cost. Here we show that given the same budget, statistical power of cell-type-specific expression quantitative trait loci (eQTL) mapping increased through...
Abstract Background Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements technologies, errors present the data still risk confounding downstream analysis and limiting applicability of technologies clinical tools. Computational error correction promises eliminate errors, but relative accuracy algorithms remains unknown. Results In this paper, we evaluate fix across different...
This note presents IsoEM2 and IsoDE2, new versions with enhanced features faster runtime of the IsoEM IsoDE packages for expression level estimation differential expression. estimates fragments per kilobase million (FPKM) transcript (TPM) levels genes isoforms confidence intervals through bootstrapping, while IsoDE2 performs analysis using bootstrap samples generated by IsoEM2. Both tools are available a command line interface as well graphical user (GUI) wrappers Galaxy platform.The source...
High throughput sequencing has spurred the development of metagenomics, which involves direct analysis microbial communities in various environments such as soil, ocean water, and human body. Many existing methods based on marker genes or k-mers have limited sensitivity are too computationally demanding for many users. Additionally, most work metagenomics focused bacteria archaea, neglecting to study other key microbes viruses eukaryotes.Here we present a method, MiCoP (Microbiome Community...
Lyme disease (LD), the most prevalent tick-borne of humans in Northern Hemisphere, is caused by spirochetal bacterium Borreliella burgdorferi ( Bb ) sensu lato complex. In nature, spirochetes are continuously transmitted between Ixodes ticks and mammalian or avian reservoir hosts. Peromyscus leucopus mice considered primary United States. Earlier studies demonstrated that experimentally infected P. do not develop disease. contrast, C3H mice, a widely used laboratory strain Mus musculus LD...
The nuclear RNA exosome is essential for processing and degradation. Here, we show that the nuclear-specific subunit Rrp6p promotes cell survival during heat stress through wall integrity (CWI) pathway, independently of its catalytic activity or association with core exosome. exhibits negative genetic interactions Slt2/Mpk1p Paf1p elongation factors required expression CWI genes stress. Overexpression catalytically inactive exosome-independent mutants can partially rescue growth defect mpk1Δ...
Restoring sensation after injury or disease requires a reproducible method for generating large quantities of bona fide somatosensory interneurons. Toward this goal, we assess the mechanisms by which dorsal spinal interneurons (dIs; dI1-dI6) can be derived from mouse embryonic stem cells (mESCs). Using two developmentally relevant growth factors, retinoic acid (RA) and bone morphogenetic protein (BMP) 4, recapitulate complete in vivo program dI differentiation through neuromesodermal...
Assessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions. This usually inferred from microarray expression data. Wide availability of NGS technology has triggered demand for bioinformatics tools capable analyzing directly RNA-Seq In this paper we introduce XPathway, set that compares mapping contigs assembled reads KEGG pathways. The XPathway analysis based on expectation maximization and topological properties graphs. have been...
Abstract Assay-based approaches provide a detailed view of the adaptive immune system by profiling immunoglobulin (Ig) receptor repertoires. However, these methods carry high cost and lack scale standard RNA sequencing (RNA-Seq). Here we report development ImReP, novel computational method for rapid accurate repertoire from regular RNA-Seq data. ImReP can also accurately assemble complementary determining regions 3 (CDR3s), most variable Ig receptors. We applied our to 8,555 samples across...
The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of factors ATOH7 Neurog2 human ES cell-derived organoids. Single cell transcriptome analyses identify three states proliferating progenitors: pre-neurogenic, neurogenic, cycle-exiting progenitors. Each shows different expression profile feed into a postmitotic heterozygous neuroblast pool...
Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome long repeats. An accurate assessment tools take account multiple locations same contig on reference rather than matching repeat single best location. This makes mapping inferred scaffoldings onto problem....
Single-cell RNA-sequencing (scRNA-seq) is a set of technologies used to profile gene expression at the level individual cells. Although throughput scRNA-seq experiments steadily growing in terms number cells, large datasets are not yet commonly generated owing prohibitively high costs. Integrating multiple into one can improve power experiments, and efficient integration very important for downstream analyses such as identifying cell-type-specific eQTLs. State-of-the-art methods based on...
Abstract One of the most important steps in genome assembly is scaffolding. Increasing length sequencing reads allows assembling short genomes but long repeat-rich remains one interesting and challenging problems bioinformatics. There a high demand developing computational approaches for repeat aware In this paper, we propose novel repeat-aware scaffolder BATISCAF based on optimization formulation filtering out repeated contigs. Our experiments with five benchmarking datasets show that...
Abstract Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to simultaneously measure cellular composition and state which impossible with bulk profiling approaches. However, it has not yet become widely used tool in population-scale analyses, due its prohibitively high cost. Here we show that given the same budget, statistical power of cell-type-specific expression quantitative trait loci (eQTL) mapping can be increased through low-coverage per-cell sequencing more samples...
Scaffolding is the important stage of genome assembly consisting orienting and ordering contigs based on read pairs. We present a scalable scaffolding algorithm that finds most likely contig orientation using integer linear program solved by non-serial dynamic programming approach. then formulate problem finding as an optimization propose novel improving over our previous tool SILP2.
In this article, we present our novel pipeline for analysis of metabolic activity using a microbial community's metatranscriptome sequence data set validation. Our method is based on expectation-maximization (EM) algorithm and provides enzyme expression pathway levels. Further expanding analysis, consider individual enzymatic compute participation coefficients to approximate the more accurately. We apply EM pathways metatranscriptomic plankton community from surface waters Northern Gulf...
Abstract Background Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements technologies, errors present the data still risk confounding downstream analysis and limiting applicability of technologies clinical tools. Computational error-correction promises eliminate errors, but relative accuracy error correction algorithms remains unknown. Results In this paper, we evaluate fix...
Abstract Summary Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome, long repeats. An accurate assessment tools take account multiple locations same contig on reference rather than matching repeat single best location. This makes mapping inferred...