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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, PhD[email protected]Nanoparticle-mediated gene delivery
Bruce Appel, PhD[email protected]Transcriptional profiling of nerve cell subtypes 
Yael Aschner, MD[email protected]Molecular analysis of acute respiratory distress syndrome in bronchoalveolar lavage fluid
Rocky Baker, PharmD[email protected]Single-cell RNAseq to monitor gene expression profiles of HIP-reactive T cells in islet grafts 
Linda Barlow, PhD[email protected]RNAseq to define and compare the transcriptomes of taste bud generating epithelial cells to non-sensory tongue epithelium
David Bentley, PhD[email protected]Messenger RNA production by RNA polymerase II
Joshua Black, PhD[email protected]Sequencing technology to uncover intra-tumoral heterogeneity in both transcription and chromosomal copy number across a range of tumors
Joe Brzezinski, PhD[email protected]Transcriptional profiling of retinas undergoing semi-synchronous cone photoreceptor differentiation
Matthew Burchill, PhD[email protected]Dissection of T lymphocyte activation in nonalcoholic steatohepatitis (NASH) by single-cell RNAseq
Eric Clambey, PhD[email protected]CD4 T cell lineage tracing by single-cell RNAseq
Howard Davidson, PhD[email protected]Advanced single-cell methods to define immune biomarkers in Type 1 diabetes
Peter Dempsey, PhD[email protected]Population-based analysis of intestinal organoid heterogeneity using CellTagging and scRNAseq
James Dylewski, DO[email protected]Advanced single-cell technologies for investigation of antigen uptake and processing during immune mediated kidney disease
Thomas Evans, PhD[email protected]Discovery of direct RNA targets of novel non-coding RNAs
Rachel Friedman, PhD[email protected]Advanced single cell technologies to investigate cell trafficking in type 1 diabetes
Austin Gillen, PhD[email protected]Leveraging single-cell RNAseq to unravel molecular heterogeneity in human disease; analytical software development
Berenice Gitomer, PhD[email protected]miRNAs as biomarkers for kidney disease
Kirk Hansen, PhD[email protected]Development of an ECM atlas to guide regenerative medicine therapies using MULTI-seq
Jay Hesselberth, PhD[email protected]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[email protected]Genome-wide discovery of differential splicing in RNAseq data sets
Elena Hsieh, MD[email protected]Investigation of transcriptional dysregulation in key immune effector cells
Ethan Hughes, PhD[email protected]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[email protected]mRNA surveillance across biological scales - intracellular, tissue-level and human populations
Aaron Johnson, PhD[email protected]Genome-wide chromatin profiling to understand the complex superstructural "neighborhoods" of chromosomes
Ross Kedl, PhD[email protected]In search of Tvacs: single-cell RNAseq comparison between vaccine-elicited and infection-elicited CD8+ T cell responses
T. Rajendra Kumar, PhD[email protected]High throughput genome-wide analysis of pituitary gonadotropes
Laurel Lenz, PhD[email protected]Regulation and dysregulation of innate immune responses in the context of health and disease
Hong Li, PhD[email protected]Craniofacial development and orofacial clefting at single-cell resolution
Martin McCarter, MD[email protected]Molecular characterization of tumor infiltrating myeloid-derived suppressor cells (MDSCs) in human melanoma
Timothy McKinsey, PhD[email protected]Regulation of pathological cardiac gene expression by micro-RNAs
Christian Mosimann, PhD[email protected]Advanced single-cell technologies to chart cardiovascular progenitor clonality and developmental trajectories in toto 
Neelanjan Mukherjee, PhD[email protected]Multiplexed RNA sequencing to define temporal aspects of RNA regulation of gene expression
Erin Nishimura, PhD[email protected]Next generation sequencing and high resolution microscopy to interrogate developmental programs in C. elegans
Chad Pearson, PhD[email protected]Identifying centriolar RNAs in fundamental centrosomal processes and human disease; advanced computational image analysis 
Eric Pietras, PhD[email protected]Advanced single-cell technologies for clonal tracking and analysis of hematopoietic stem cells
Srinivas Ramachandran, PhD[email protected]Temporal and spatial investigation of nucleosome structure and stability during transcription and replication 
Marino Resendiz, PhD[email protected]Development of photoactive RNA to manipulate RNA structure in biological systems
Diego Restrepo, PhD[email protected]Computational neuroscience
Olivia Rissland, PhD[email protected]Transcriptome-wide measurements of mRNA stability
Stephen Santoro, PhD[email protected]Lineage tracing of odorant receptor fates in olfactory sensory neurons
Matthew Sikora, PhD[email protected]Single-cell RNAseq to examine functional heterogeneity in estrogen receptor co-regulator activity
Matthew Taliaferro, PhD[email protected]High-throughput experimental and computational analyses of mRNA "zip codes"
Matt Taylor, MD, PhD[email protected]Large-scale transcriptome analysis of adult and pediatric heart samples
Sujatha Venkataraman, PhD[email protected]Molecular screening to identify altered epigenetic machinery in neoplastic transformation of pediatric medulloblastoma
Quentin Vicens, PhD[email protected]Experimental and computational methods for detailed study of RNA viruses
Trevor Williams, PhD[email protected]Small RNA expression during craniofacial development
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