Sequence Analysis, RNA

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  Subject Areas on Research

  • A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. 
  • A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing. 
  • A Wor1-Like Transcription Factor Is Essential for Virulence of Cryptococcus neoformans. 
  • A class of viral inducer of degradation of the necroptosis adaptor RIPK3 regulates virus-induced inflammation. 
  • A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. 
  • A timecourse analysis of systemic and gonadal effects of temperature on sexual development of the red-eared slider turtle Trachemys scripta elegans. 
  • ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer. 
  • Activation of a nerve injury transcriptional signature in airway-innervating sensory neurons after lipopolysaccharide-induced lung inflammation. 
  • Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High- Altitude Stresses in Tibet. 
  • Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. 
  • An integrated encyclopedia of DNA elements in the human genome. 
  • An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. 
  • Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. 
  • Androgen receptor with short polyglutamine tract preferably enhances Wnt/β-catenin-mediated prostatic tumorigenesis. 
  • Antigen receptor repertoire profiling from RNA-seq data. 
  • Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma. 
  • As above, so below: Whole transcriptome profiling demonstrates strong molecular similarities between avian dorsal and ventral pallial subdivisions. 
  • Assessment of gene expression in peripheral blood using RNAseq before and after weight restoration in anorexia nervosa. 
  • Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. 
  • Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model. 
  • Associations of osteopontin and NT-proBNP with circulating miRNA levels in acute coronary syndrome. 
  • BEARscc determines robustness of single-cell clusters using simulated technical replicates. 
  • Benchmarking association analyses of continuous exposures with RNA-seq in observational studies. 
  • Bimodal age distribution at diagnosis in breast cancer persists across molecular and genomic classifications. 
  • Cell cycle-regulated transcription: effectively using a genomics toolbox. 
  • Cell-Type-Specific Analysis of Molecular Pathology in Autism Identifies Common Genes and Pathways Affected Across Neocortical Regions. 
  • Characterization of 67 kD laminin receptor, a protein whose gene is overexpressed on treatment of cells with anti-benzo[a]pyrene-7,8-diol-9,10-epoxide. 
  • Characterization of hepatocellular adenoma and carcinoma using microRNA profiling and targeted gene sequencing. 
  • Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. 
  • Circular RNAs are abundant, conserved, and associated with ALU repeats. 
  • Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. 
  • Clustering gene expression time series data using an infinite Gaussian process mixture model. 
  • Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila. 
  • Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea. 
  • Comparative RNA sequencing reveals substantial genetic variation in endangered primates. 
  • Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. 
  • Comparing reference-based RNA-Seq mapping methods for non-human primate data. 
  • Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. 
  • Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. 
  • Conserved and divergent expression dynamics during early patterning of the telencephalon in mouse and chick embryos. 
  • Cooperation between the Hepatitis C Virus p7 and NS5B Proteins Enhances Virion Infectivity. 
  • DO-RIP-seq to quantify RNA binding sites transcriptome-wide. 
  • Decoding the noncoding transcripts in human heart failure. 
  • Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. 
  • Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. 
  • Detecting m6A with In Vitro DART-Seq. 
  • Detection of Donor's HIV Strain in HIV-Positive Kidney-Transplant Recipient. 
  • Detection of m6A in single cultured cells using scDART-seq. 
  • Development and Verification of an RNA Sequencing (RNA-Seq) Assay for the Detection of Gene Fusions in Tumors. 
  • DictyBase 2013: integrating multiple Dictyostelid species. 
  • Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. 
  • Differential expression analysis for RNAseq using Poisson mixed models. 
  • Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing. 
  • Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever. 
  • Dissecting the human kidney allograft transcriptome: single-cell RNA sequencing. 
  • Dissecting the in vivo metabolic potential of two human gut acetogens. 
  • Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy. 
  • Dynamic microRNA gene transcription and processing during T cell development. 
  • Dysregulated transcriptional responses to SARS-CoV-2 in the periphery. 
  • EBV BART MicroRNAs Target Multiple Pro-apoptotic Cellular Genes to Promote Epithelial Cell Survival. 
  • Effects of Combined Tristetraprolin/Tumor Necrosis Factor Receptor Deficiency on the Splenic Transcriptome. 
  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. 
  • Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release. 
  • Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. 
  • Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems. 
  • Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq 
  • Evaluation of an RNAseq-Based Immunogenomic Liquid Biopsy Approach in Early-Stage Prostate Cancer. 
  • Evidence for multiple roles for grainyhead-like 2 in the establishment and maintenance of human mucociliary airway epithelium.[corrected]. 
  • Expression and prognostic impact of lncRNAs in acute myeloid leukemia. 
  • Expression of CRISPR/Cas single guide RNAs using small tRNA promoters. 
  • External Quality Assessment Program for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Logistical Considerations. 
  • External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges. 
  • Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination. 
  • Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide. 
  • Gene expression throughout a vertebrate's embryogenesis. 
  • Genetics of gene expression responses to temperature stress in a sea urchin gene network. 
  • Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner. 
  • Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. 
  • Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. 
  • Global impact of RNA splicing on transcriptome remodeling in the heart. 
  • HEART DISEASE. Titin mutations in iPS cells define sarcomere insufficiency as a cause of dilated cardiomyopathy. 
  • High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. 
  • High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. 
  • High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. 
  • Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. 
  • Host cell transcriptome profile during wild-type and attenuated dengue virus infection. 
  • Hybrid error correction and de novo assembly of single-molecule sequencing reads. 
  • Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. 
  • Identification of Host Biomarkers of Epstein-Barr Virus Latency IIb and Latency III. 
  • Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice. 
  • Identification of human short introns. 
  • Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. 
  • Immature excitatory neurons develop during adolescence in the human amygdala. 
  • Improved transcript isoform discovery using ORF graphs. 
  • Influenza A virus-derived siRNAs increase in the absence of NS1 yet fail to inhibit virus replication. 
  • Insensitivity of paediatric HIV-1 subtype C viruses to broadly neutralising monoclonal antibodies raised against subtype B. 
  • Insights into coral bleaching under heat stress from analysis of gene expression in a sea anemone model system. 
  • Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer. 
  • Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. 
  • Lactose drives Enterococcus expansion to promote graft-versus-host disease. 
  • Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging. 
  • Limits in the detection of m6A changes using MeRIP/m6A-seq. 
  • Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. 
  • Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. 
  • MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. 
  • MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root. 
  • Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing. 
  • Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. 
  • Mecp2 regulates tnfa during zebrafish embryonic development and acute inflammation. 
  • Metabolism in the tumor microenvironment: insights from single-cell analysis. 
  • MicroRNA target site identification by integrating sequence and binding information. 
  • MicroRNAs both promote and antagonize longevity in C. elegans. 
  • Molecular Features Underlying Neurodegeneration Identified through In Vitro Modeling of Genetically Diverse Parkinson's Disease Patients. 
  • Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex. 
  • Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. 
  • N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. 
  • Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception. 
  • New tools for studying microglia in the mouse and human CNS. 
  • Non-coding RNA prediction and verification in Saccharomyces cerevisiae. 
  • Novel enriched pathways in superficial malignant peripheral nerve sheath tumours and spindle/desmoplastic melanomas. 
  • Nucleotide bias observed with a short SELEX RNA aptamer library. 
  • Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs. 
  • Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer. 
  • PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. 
  • PCK1 regulates neuroendocrine differentiation in a positive feedback loop of LIF/ZBTB46 signalling in castration-resistant prostate cancer. 
  • Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. 
  • Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. 
  • Pervasive Effects of Aging on Gene Expression in Wild Wolves. 
  • Plasmodium parasite exploits host aquaporin-3 during liver stage malaria infection. 
  • Pol II docking and pausing at growth and stress genes in C. elegans. 
  • Post-transcriptional regulation of myotube elongation and myogenesis by Hoi Polloi. 
  • Postnatally-transmitted HIV-1 Envelope variants have similar neutralization-sensitivity and function to that of nontransmitted breast milk variants. 
  • Predicting gene structure changes resulting from genetic variants via exon definition features. 
  • Progenitor Hyperpolarization Regulates the Sequential Generation of Neuronal Subtypes in the Developing Neocortex. 
  • Programmable RNA sensing for cell monitoring and manipulation. 
  • Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. 
  • Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. 
  • Prurigo Nodularis Is Characterized by Systemic and Cutaneous T Helper 22 Immune Polarization. 
  • Putative biomarkers for predicting tumor sample purity based on gene expression data. 
  • Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq. 
  • RNA sequencing of isolated cell populations expressing human APOL1 G2 risk variant reveals molecular correlates of sickle cell nephropathy in zebrafish podocytes. 
  • RNA-Seq and ChIP-Seq reveal SQSTM1/p62 as a key mediator of JunB suppression of NF-κB-dependent inflammation. 
  • RNA-Seq optimization with eQTL gold standards. 
  • RNA-seq: impact of RNA degradation on transcript quantification. 
  • Real-world Evidence of Diagnostic Testing and Treatment Patterns in US Patients With Breast Cancer With Implications for Treatment Biomarkers From RNA Sequencing Data. 
  • Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. 
  • Repression of Sox9 by Jag1 is continuously required to suppress the default chondrogenic fate of vascular smooth muscle cells. 
  • Retinal Ganglion Cells With a Glaucoma OPTN(E50K) Mutation Exhibit Neurodegenerative Phenotypes when Derived from Three-Dimensional Retinal Organoids. 
  • Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement. 
  • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. 
  • Self-renewing endometrial epithelial organoids of the human uterus. 
  • Sequence basis of Barnacle Cement Nanostructure is Defined by Proteins with Silk Homology. 
  • Simple and inexpensive ribosome profiling analysis of mRNA translation. 
  • Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands. 
  • Single cell transcriptome analysis of mouse carotid body glomus cells. 
  • Single cell transcriptomics in human osteoarthritis synovium and in silico deconvoluted bulk RNA sequencing. 
  • Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. 
  • Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing (DIVA-Seq). 
  • Single-cell RNA sequencing reveals time- and sex-specific responses of mouse spinal cord microglia to peripheral nerve injury and links ApoE to chronic pain. 
  • Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. 
  • Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. 
  • Single-cell analysis of olfactory neurogenesis and differentiation in adult humans. 
  • Single-cell genomics identifies cell type-specific molecular changes in autism. 
  • Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. 
  • Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. 
  • Statistical analysis of RNA backbone. 
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. 
  • Surgical necrotizing enterocolitis in extremely premature neonates is associated with genetic variations in an intergenic region of chromosome 8. 
  • TCF1 links GIPR signaling to the control of beta cell function and survival. 
  • Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula. 
  • The effect of Bacopa monnieri on gene expression levels in SH-SY5Y human neuroblastoma cells. 
  • The genetic architecture of gene expression levels in wild baboons. 
  • The genetic regulatory signature of type 2 diabetes in human skeletal muscle. 
  • The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics. 
  • The relationship of cervical microbiota diversity with race and disparities in preterm birth. 
  • Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. 
  • Trans-splicing reactions by ribozymes. 
  • Transcriptional Profiling of CD8+ CMV-Specific T Cell Functional Subsets Obtained Using a Modified Method for Isolating High-Quality RNA From Fixed and Permeabilized Cells. 
  • Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing. 
  • Transcriptional profiles of JIA patient blood with subsequent poor response to methotrexate. 
  • Transcriptome analysis of adult and fetal trabecular meshwork, cornea, and ciliary body tissues by RNA sequencing. 
  • Transcriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia. 
  • Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. 
  • Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide. 
  • Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. 
  • Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. 
  • Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated. 
  • Whole blood sequencing reveals circulating microRNA associations with high-risk traits in non-ST-segment elevation acute coronary syndrome. 
  • Whole-Genome and Segmental Homozygosity Confirm Errors in Meiosis as Etiology of Struma Ovarii. 
  • miRNA Profile in Three Different Normal Human Ocular Tissues by miRNA-Seq. 
  • scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. 
  • scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells. 
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  Keywords of People

  • Ciofani, Maria, Associate Professor of Immunology, Cell Biology
  • Luftig, Micah Alan, Associate Professor of Molecular Genetics and Microbiology, Cell Biology
  • Reddy, Timothy E, Associate Professor of Biostatistics & Bioinformatics,, Molecular Genetics and Microbiology
  • Wray, Gregory Allan, Professor of Biology, Evolutionary Anthropology