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RNA Technology and Bioinformatics



The RNA Technology and Bioinformatics Group within the RNA Bioscience Initiative develops new molecular and bioinformatic methods to analyze RNA sequence, diversity, nascent transcription, structure, and localization.

Cutting-edge RNA technologies and computational methods fuel new discoveries, advancing the field of RNA biology across disciplines. Recent advances include:

  • New methods for analysis of RNA from complex cell populations and single cells
  • Improved computational approaches to support large-scale RNA sequencing efforts
  • Technologies to define RNA abundance and sub-cellular localization
  • Molecular tagging that allows tracking of nucleic acids, proteins and other macromolecules in cells and tissues
RNA Technology and Informatics

Faculty Participants

FACULTYEMAILRESEARCH
Tom Anchordoquy, PhDtom.anchordoquy@cuanschutz.eduNanoparticle-mediated gene delivery
Bruce Appel, PhDbruce.appel@cuanschutz.eduTranscriptional profiling of nerve cell subtypes 
Yael Aschner, MDyael.aschner@cuanschutz.eduMolecular analysis of acute respiratory distress syndrome in bronchoalveolar lavage fluid
Rocky Baker, PharmDrocky.baker@cuanschutz.eduSingle-cell RNAseq to monitor gene expression profiles of HIP-reactive T cells in islet grafts 
Linda Barlow, PhDlinda.barlow@cuanschutz.eduRNAseq to define and compare the transcriptomes of taste bud generating epithelial cells to non-sensory tongue epithelium
David Bentley, PhDdavid.bentley@cuanschutz.eduMessenger RNA Production by RNA polymerase II
Joshua Black, PhDjoshua.c.black@cuanschutz.eduSequencing technology to uncover intra-tumoral heterogeneity in both transcription and chromosomal copy number across a range of tumors
Joe Brzezinski, PhDjoseph.brzezinski@cuanschutz.eduTranscriptional profiling of retinas undergoing semi-synchronous cone photoreceptor differentiation
Matthew Burchill, PhDmatthew.burchill@cuanschutz.eduDissection of T lymphocyte activation in nonalcoholic steatohepatitis (NASH) by single-cell RNAseq
Eric Clambey, PhDeric.clambey@cuanschutz.eduCD4 T cell lineage tracing by single-cell RNAseq
Randall Cohrs, PhDrandall.cohrs@cuanschutz.eduVaricella Zoster transcript mapping in latently infected human ganglia
Howard Davidson, PhDhoward.davidson@cuanschutz.eduAdvanced single-cell methods to define immune biomarkers in Type 1 diabetes
Richard Davis, PhDrichard.davis@cuanschutz.eduProgrammed DNA elimination and RNA metabolism
Peter Dempsey, PhDpeter.dempsey@cuanschutz.eduPopulation-based analysis of intestinal organoid heterogeneity using CellTagging and scRNAseq
James Dylewski, DOjames.dylewski@cuanschutz.eduAdvanced single-cell technologies for investigation of antigen uptake and processing during immune mediated kidney disease
Thomas Evans, PhDtom.evans@cuanschutz.eduDiscovery of direct RNA targets of novel non-coding RNAs
Rachel Friedman, PhDrachel.s.friedman@cuanschutz.eduAdvanced single cell technologies to investigate cell trafficking in type 1 diabetes
Austin Gillen, PhDaustingillen@gmail.comLeveraging single-cell RNAseq to unravel molecular heterogeneity in human disease; analytical software development
Berenice Gitomer, PhDberenice.gitomer@cuanschutz.edumiRNAs as biomarkers for kidney disease
Kirk Hansen, PhDkirk.hansen@cuanschutz.eduDevelopment of an ECM atlas to guide regenerative medicine therapies using MULTI-seq
Jay Hesselberth, PhDjay.hesselberth@cuanschutz.eduDevelopment of new molecular and computational methods to advance single-cell analysis, including approaches to measure biochemical activities, to understand molecular dissemination in vivo, and to improve the analysis of cell-type-specific gene expression patterns
Joan Hooper, PhDjoan.hooper@cuanschutz.eduGenome-wide discovery of differential splicing in RNAseq data sets
Elena Hsieh, MDelena.hsieh@cuanzchutz.eduInvestigation of transcriptional dysregulation in key immune effector cells
Ethan Hughes, PhDethan.hughes@cuanschutz.eduLongitudinal in vivo two-photon imaging and single-cell RNA sequencing to characterize the complex dynamics between cortical oligodendrocyte lineage cells and microglia
Sujatha Jagannathan, PhDsujatha.jagannathan@cuanschutz.edumRNA surveillance across biological scales - intracellular, tissue-level and human populations
Aaron Johnson, PhDaaron.m.johnson@cuanschutz.eduGenome-wide chromatin profiling to understand the complex superstructural "neighborhoods" of chromosomes
Ross Kedl, PhDross.kedl@cuanschutz.eduIn search of Tvacs: single-cell RNAseq comparison between vaccine-elicited and infection-elicited CD8+ T cell responses
Jeffrey Kieft, PhDjeffrey.kieft@cuanschutz.eduCreate and improve tools to study RNA, particularly RNA structure
T. Rajendra Kumar, PhDraj.kumar@cuanschutz.eduHigh throughput genome-wide analysis of pituitary gonadotropes
Laurel Lenz, PhDlaurel.lenz@cuanschutz.eduRegulation and dysregulation of innate immune responses in the context of health and disease
Hong Li, PhDhong.li@cuanschutz.eduCraniofacial development and orofacial clefting at single-cell resolution
Sandy Martin, PhDsandy.martin@cuanschutz.eduInvestigation of mRNA transcript isoform dynamics
Martin McCarter, MDmartin.mccarter@cuanschutz.eduMolecular characterization of tumor infiltrating myeloid-derived suppressor cells (MDSCs) in human melanoma
Timothy McKinsey, PhDtimothy.mckinsey@cuanschutz.eduRegulation of pathological cardiac gene expression by micro-RNAs
Christian Mosimann, PhDchristian.mosimann@cuanschutz.eduAdvanced single-cell technologies to chart cardiovascular progenitor clonality and developmental trajectories in toto 
Neelanjan Mukherjee, PhDneelnajan.mukherjee@cuanschutz.eduMultiplexed RNA sequencing to define temporal aspects of RNA regulation of gene expression
Erin Nishimura, PhDerinnish@colostate.eduNext generation sequencing and high resolution microscopy to interrogate developmental programs in C. elegans
Chad Pearson, PhDchad.pearson@cuanschutz.eduIdentifying centriolar RNAs in fundamental centrosomal processes and human disease; advanced computational image analysis 
Eric Pietras, PhDeric.pietras@cuanschutz.eduAdvanced single-cell technologies for clonal tracking and analysis of hematopoietic stem cells
Srinivas Ramachandran, PhDsrinivas.ramachandran@cuanschutz.eduTemporal and spatial investigation of nucleosome structure and stability during transcription and replication 
Marino Resendiz, PhDmarino.resendiz@ucdenver.eduDevelopment of photoactive RNA to manipulate RNA structure in biological systems
Diego Restrepo, PhDdiego.restrepo@cuanschutz.eduComputational neuroscience
Olivia Rissland, PhDolivia.rissland@gmail.comTranscriptome-wide measurements of mRNA stability
Stephen Santoro, PhDstephen.santoro@cuanschutz.eduLineage tracing of odorant receptor fates in olfactory sensory neurons
Matthew Sikora, PhDmatthew.sikora@cuanschutz.eduSingle-cell RNAseq to examine functional heterogeneity in estrogen receptor co-regulator activity
Matthew Taliaferro, PhDmatthew.taliaferro@cuanschutz.eduHigh-throughput experimental and computational analyses of mRNA "zip codes"
Matt Taylor, MD, PhDmatthew.taylor@cuanschutz.eduLarge-scale transcriptome analysis of adult and pediatric heart samples
Sujatha Venkataraman, PhDsujatha.venkataraman@cuanschutz.eduMolecular screening to identify altered epigenetic machinery in neoplastic transformation of pediatric medulloblastoma
Quentin Vicens, PhDquentin.vicens@cuanschutz.eduExperimental and computational methods for detailed study of RNA viruses
Trevor Williams, PhDtrevor.williams@cuanschutz.eduSmall RNA expression during craniofacial development
Tuoqi Wu , PhDtuoqi.wu@cuanschutz.eduIdentification of transcriptional expression signatures of CAR T cells with long-term anti-tumor immunity using endogenous TCR sequences as molecular barcodes