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