A5042618575- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Gene Regulatory Network Analysis
- Intensive Care Unit Cognitive Disorders
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Gut microbiota and health
- Nosocomial Infections in ICU
- Respiratory Support and Mechanisms
- Chromosomal and Genetic Variations
- Circular RNAs in diseases
- Extracellular vesicles in disease
- IL-33, ST2, and ILC Pathways
- Neonatal Respiratory Health Research
University of Pittsburgh
2016-2025
University of Florida
2022-2025
University of Florida Health
2024
Carnegie Mellon University
2016-2024
Florida College
2023-2024
Johns Hopkins University
2023
Tsinghua University
2023
UPMC Montefiore
2023
University of Pittsburgh Medical Center
2005-2023
Massachusetts General Hospital
2023
The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for investigation many developmental cellular processes common to higher eukaryotes, including humans. We have determined nucleotide sequence nearly all ∼120-megabase euchromatic portion genome using whole-genome shotgun sequencing strategy supported by extensive clone-based high-quality bacterial artificial chromosome physical map. Efforts are under way close remaining...
A comprehensive understanding of the changes in gene expression cell types involved idiopathic pulmonary fibrosis (IPF) will shed light on mechanisms underlying loss alveolar epithelial cells and development honeycomb cysts fibroblastic foci. We sought to understand IPF lung transcriptomes gain insight into innate immune aspects pathogenesis. investigated pathogenesis using single-cell RNA-sequencing fresh explants, comparing human fibrotic lower lobes reflecting late disease, upper early...
Tumor heterogeneity of high-grade glioma (HGG) is recognized by four clinically relevant subtypes based on core gene signatures. However, molecular signaling in stem cells (GSCs) individual HGG poorly characterized. Here we identified and characterized two mutually exclusive GSC with distinct dysregulated pathways. Analysis mRNA profiles distinguished proneural (PN) from mesenchymal (Mes) GSCs revealed a pronounced correlation the corresponding PN or Mes HGGs. displayed more aggressive...
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and usually lethal fibrotic lung disease characterized by profound changes in epithelial cell phenotype fibroblast proliferation.To determine expression role of microRNAs IPF.RNA from 10 control IPF tissues was hybridized on Agilent microRNA microarrays results were confirmed quantitative real-time polymerase chain reaction situ hybridization. SMAD3 binding to the let-7d promoter chromatin immunoprecipitation, electrophoretic...
STAMP is a newly developed web server that designed to support the study of DNA-binding motifs. may be used query motifs against databases known motifs; software aligns input chosen database (or alternatively user-provided dataset), and lists highest-scoring matches are returned. Such similarity-search functionality expected facilitate identification transcription factors potentially interact with discovered also automatically builds multiple alignments, familial binding profiles similarity...
Background MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms able to predict miRNA genes their targets, but transcription regulation is still under investigation. It generally believed that intragenic (located introns or exons genes) co-transcribed with host most intergenic transcribed from own polymerase II (Pol II) promoter. However, the length primary...
Abstract Skin and lung fibrosis in systemic sclerosis (SSc) is driven by myofibroblasts, alpha-smooth muscle actin expressing cells. The number of myofibroblasts SSc skin correlates with the modified Rodnan score, most widely used clinical measure disease severity. Murine models indicate that can arise from a variety different cell types, but their origin has remained uncertain. Utilizing single RNA-sequencing, we define dermal fibroblast populations transcriptome changes, comparing to...
Chronic obstructive pulmonary disease (COPD) remains a major cause of morbidity and mortality. Present-day diagnostic criteria are largely based solely on spirometric criteria. Accumulating evidence has identified substantial number individuals without COPD who suffer from respiratory symptoms and/or increased There is clear need for an expanded definition that linked to physiologic, structural (computed tomography [CT]) clinical disease. Using data the Genetic Epidemiology study (COPDGene
Man and Stormo Bulyk et al. recently presented their results on the study of DNA binding af®nity proteins.In both these studies main conclusion is that additivity assumption, usually applied in methods to search for sites, not true.In ®rst study, analysis data from Mnt repressor protein bound all possible (sub)targets at positions 16 17 site, showed those are independent.In second authors analysed wild-type mouse EGR1 four variants differing middle ®nger.The proteins was measured 64...
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence have become popular way to graphically represent DNA and amino acid patterns set of aligned sequences. Each position the alignment represented by column stacked symbols with its total height reflecting information content in this position. Currently, available web servers are able create logo images sequences, but none them weighted directly energy measurements or other With advent high-throughput...
ComiR is a web tool for combinatorial microRNA (miRNA) target prediction. Given an messenger RNA (mRNA) in human, mouse, fly or worm genomes, computes the potential of being targeted by set miRNAs, each which can have zero, one more targets on its 3′untranslated region. In determining regulatory mRNA from uses user-provided miRNA expression levels combination appropriate thermodynamic modeling and machine learning techniques to make accurate predictions. For gene, returns probability...
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The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum) sequence construct map of a major histocompatibility complex (MHC). MHC is most gene-dense region and critical immunity reproductive success. bridges phylogenetic gap between eutherian mammals minimal essential birds. Here we show that opossum gene dense complex, as in humans, but shares more organizational features with...
To develop a systems biology model of fibrosis progression within the human lung we performed RNA sequencing and microRNA analysis on 95 samples obtained from 10 idiopathic pulmonary (IPF) 6 control lungs. Extent in each sample was assessed by microCT-measured alveolar surface density (ASD) confirmed histology. Regulatory gene expression networks were identified using linear mixed-effect models dynamic regulatory events miner (DREM). Differential core set genes increased or decreased before...
mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA microRNA (miRNA) gene regulatory networks. combines sequence information with expression data analysis to create disease-specific, genome-wide network. A prior, static network has been constructed all human mouse genes. It consists of computationally predicted transcription factor (TF)-gene associations miRNA target predictions. The prior supplemented known interactions from the literature. Dynamic TF-...
Objectives: Classification of patients with acute respiratory distress syndrome into hyper- and hypoinflammatory subphenotypes using plasma biomarkers may facilitate more effective targeted therapy. We examined whether established are present not only in but also at risk for (ARFA) then assessed the prognostic information baseline subphenotyping on evolution host-response clinical outcomes. Design: Prospective, observational cohort study. Setting: Medical ICU a tertiary academic medical...
Rationale: Host inflammatory responses have been strongly associated with adverse outcomes in critically ill patients, but the biologic underpinnings of such heterogeneous not defined.Objectives: We examined whether respiratory tract microbiome profiles are host inflammation and clinical acute failure.Methods: collected oral swabs, endotracheal aspirates (ETAs), plasma samples from mechanically ventilated patients. performed 16S ribosomal RNA gene sequencing to characterize upper lower...
Alterations in lipid metabolism have the potential to be markers as well drivers of pathobiology acute critical illness. Here, we took advantage temporal precision offered by trauma a common cause illness identify dynamic patterns circulating lipidome critically ill humans. The major findings include an early loss all classes lipids followed delayed and selective lipogenesis patients destined remain ill. previously reported survival benefit thawed plasma administration was associated with...
Critical illness can significantly alter the composition and function of human microbiome, but few studies have examined these changes over time. Here, we conduct a comprehensive analysis oral, lung, gut microbiota in 479 mechanically ventilated patients (223 females, 256 males) with acute respiratory failure. We use advanced DNA sequencing technologies, including Illumina amplicon (utilizing 16S ITS rRNA genes for bacteria fungi, respectively, all sample types) Nanopore metagenomics lung...
Abstract We have established a collection of 2460 lethal or semi-lethal mutant lines using procedure thought to insert single P elements into vital genes on the third chromosome Drosophila melanogaster. More than 1200 randomly selected were examined by in situ hybridization and 90% found contain insertions at sites that mark 89% all lettered subdivisions Bridges' map. A set chromosomal deficiencies collectively uncover ~25% euchromatin 3 reveal mutations 468 corresponding 145 complementation...
Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression neighbouring genes. The evolution TF binding preference has been subject recent studies, in which generalized profiles have introduced used to improve prediction new target sites. Generalized are generated by aligning merging individual related TFs. However, distance metrics alignment algorithms compare not yet fully explored or optimized. As result, depend on...
ABSTRACT Digital transcript subtraction (DTS) was developed to subtract in silico known human sequences from expression library data sets, leaving candidate nonhuman for further analysis. This approach requires precise discrimination between and cDNA sequences. Database comparisons show high likelihood that small viral can be successfully distinguished DTS analysis of 9,026 20-bp tags an BCBL-1 cells infected with Kaposi's sarcoma-associated herpesvirus (KSHV) resolved all but three Two...
MicroRNA s (miRNAs) are small non-coding single-stranded RNAs (20–23 nts) that known to act as post-transcriptional and translational regulators of gene expression. Although, they were initially overlooked, their role in many important biological processes, such development, cell differentiation, cancer has been established recent times. In spite significance, the identification miRNA genes newly sequenced organisms is still based, a large degree, on extensive use evolutionary conservation,...
Mixed graphical models (MGMs) are learned over a combination of continuous and discrete variables. variable types common in biomedical datasets. MGMs consist parameterized joint probability density, which implies network structure these heterogeneous The reveals direct associations between the variables density allows one to ask arbitrary probabilistic questions on data. This information can be used for feature selection, classification other important tasks. We studied properties MGM...