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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
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Faculty Participants
| FACULTY | RESEARCH | |
| Tom Anchordoquy, PhD | tom.anchordoquy@cuanschutz.edu | Nanoparticle-mediated gene delivery |
| Bruce Appel, PhD | bruce.appel@cuanschutz.edu | Transcriptional profiling of nerve cell subtypes |
| Yael Aschner, MD | yael.aschner@cuanschutz.edu | Molecular analysis of acute respiratory distress syndrome in bronchoalveolar lavage fluid |
| Rocky Baker, PharmD | rocky.baker@cuanschutz.edu | Single-cell RNAseq to monitor gene expression profiles of HIP-reactive T cells in islet grafts |
| Linda Barlow, PhD | linda.barlow@cuanschutz.edu | RNAseq to define and compare the transcriptomes of taste bud generating epithelial cells to non-sensory tongue epithelium |
| David Bentley, PhD | david.bentley@cuanschutz.edu | Messenger RNA production by RNA polymerase II |
| Joshua Black, PhD | joshua.c.black@cuanschutz.edu | Sequencing technology to uncover intra-tumoral heterogeneity in both transcription and chromosomal copy number across a range of tumors |
| Joe Brzezinski, PhD | joseph.brzezinski@cuanschutz.edu | Transcriptional profiling of retinas undergoing semi-synchronous cone photoreceptor differentiation |
| Matthew Burchill, PhD | matthew.burchill@cuanschutz.edu | Dissection of T lymphocyte activation in nonalcoholic steatohepatitis (NASH) by single-cell RNAseq |
| Eric Clambey, PhD | eric.clambey@cuanschutz.edu | CD4 T cell lineage tracing by single-cell RNAseq |
| Howard Davidson, PhD | howard.davidson@cuanschutz.edu | Advanced single-cell methods to define immune biomarkers in Type 1 diabetes |
| Peter Dempsey, PhD | peter.dempsey@cuanschutz.edu | Population-based analysis of intestinal organoid heterogeneity using CellTagging and scRNAseq |
| James Dylewski, DO | james.dylewski@cuanschutz.edu | Advanced single-cell technologies for investigation of antigen uptake and processing during immune mediated kidney disease |
| Thomas Evans, PhD | tom.evans@cuanschutz.edu | Discovery of direct RNA targets of novel non-coding RNAs |
| Rachel Friedman, PhD | rachel.s.friedman@cuanschutz.edu | Advanced single cell technologies to investigate cell trafficking in type 1 diabetes |
| Austin Gillen, PhD | austingillen@gmail.com | Leveraging single-cell RNAseq to unravel molecular heterogeneity in human disease; analytical software development |
| Berenice Gitomer, PhD | berenice.gitomer@cuanschutz.edu | miRNAs as biomarkers for kidney disease |
| Kirk Hansen, PhD | kirk.hansen@cuanschutz.edu | Development of an ECM atlas to guide regenerative medicine therapies using MULTI-seq |
| Jay Hesselberth, PhD | jay.hesselberth@cuanschutz.edu | Development 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, PhD | joan.hooper@cuanschutz.edu | Genome-wide discovery of differential splicing in RNAseq data sets |
| Elena Hsieh, MD | elena.hsieh@cuanzchutz.edu | Investigation of transcriptional dysregulation in key immune effector cells |
| Ethan Hughes, PhD | ethan.hughes@cuanschutz.edu | Longitudinal in vivo two-photon imaging and single-cell RNA sequencing to characterize the complex dynamics between cortical oligodendrocyte lineage cells and microglia |
| Sujatha Jagannathan, PhD | sujatha.jagannathan@cuanschutz.edu | mRNA surveillance across biological scales - intracellular, tissue-level and human populations |
| Aaron Johnson, PhD | aaron.m.johnson@cuanschutz.edu | Genome-wide chromatin profiling to understand the complex superstructural "neighborhoods" of chromosomes |
| Ross Kedl, PhD | ross.kedl@cuanschutz.edu | In search of Tvacs: single-cell RNAseq comparison between vaccine-elicited and infection-elicited CD8+ T cell responses |
| T. Rajendra Kumar, PhD | raj.kumar@cuanschutz.edu | High throughput genome-wide analysis of pituitary gonadotropes |
| Laurel Lenz, PhD | laurel.lenz@cuanschutz.edu | Regulation and dysregulation of innate immune responses in the context of health and disease |
| Hong Li, PhD | hong.li@cuanschutz.edu | Craniofacial development and orofacial clefting at single-cell resolution |
| Martin McCarter, MD | martin.mccarter@cuanschutz.edu | Molecular characterization of tumor infiltrating myeloid-derived suppressor cells (MDSCs) in human melanoma |
| Timothy McKinsey, PhD | timothy.mckinsey@cuanschutz.edu | Regulation of pathological cardiac gene expression by micro-RNAs |
| Christian Mosimann, PhD | christian.mosimann@cuanschutz.edu | Advanced single-cell technologies to chart cardiovascular progenitor clonality and developmental trajectories in toto |
| Neelanjan Mukherjee, PhD | neelnajan.mukherjee@cuanschutz.edu | Multiplexed RNA sequencing to define temporal aspects of RNA regulation of gene expression |
| Erin Nishimura, PhD | erinnish@colostate.edu | Next generation sequencing and high resolution microscopy to interrogate developmental programs in C. elegans |
| Chad Pearson, PhD | chad.pearson@cuanschutz.edu | Identifying centriolar RNAs in fundamental centrosomal processes and human disease; advanced computational image analysis |
| Eric Pietras, PhD | eric.pietras@cuanschutz.edu | Advanced single-cell technologies for clonal tracking and analysis of hematopoietic stem cells |
| Srinivas Ramachandran, PhD | srinivas.ramachandran@cuanschutz.edu | Temporal and spatial investigation of nucleosome structure and stability during transcription and replication |
| Marino Resendiz, PhD | marino.resendiz@ucdenver.edu | Development of photoactive RNA to manipulate RNA structure in biological systems |
| Diego Restrepo, PhD | diego.restrepo@cuanschutz.edu | Computational neuroscience |
| Olivia Rissland, PhD | olivia.rissland@gmail.com | Transcriptome-wide measurements of mRNA stability |
| Stephen Santoro, PhD | stephen.santoro@cuanschutz.edu | Lineage tracing of odorant receptor fates in olfactory sensory neurons |
| Matthew Sikora, PhD | matthew.sikora@cuanschutz.edu | Single-cell RNAseq to examine functional heterogeneity in estrogen receptor co-regulator activity |
| Matthew Taliaferro, PhD | matthew.taliaferro@cuanschutz.edu | High-throughput experimental and computational analyses of mRNA "zip codes" |
| Matt Taylor, MD, PhD | matthew.taylor@cuanschutz.edu | Large-scale transcriptome analysis of adult and pediatric heart samples |
| Sujatha Venkataraman, PhD | sujatha.venkataraman@cuanschutz.edu | Molecular screening to identify altered epigenetic machinery in neoplastic transformation of pediatric medulloblastoma |
| Quentin Vicens, PhD | quentin.vicens@cuanschutz.edu | Experimental and computational methods for detailed study of RNA viruses |
| Trevor Williams, PhD | trevor.williams@cuanschutz.edu | Small RNA expression during craniofacial development |