R. Taylor Raborn
I am an Research Scientist in Mike Lynch's lab in the Biodesign Institute Center for Mechanisms of Evolution at Arizona State University.
My work is principally focused on cis-regulatory regions in eukaryotic genomes, particularly promoter architecture and evolution. I am currently working on several projects in this area, which include:
- Promoter evolution after whole-genome duplication, using the Paramecium aurelia species complex).
- Cis-regulatory sequence differences in populations, using the model system Daphnia pulex.
- Modeling the shape properties of promoters across eukaryotes.
STRIPE-seq: a novel TSS profiling method
I was also recently involved in the development of a new transcription start site (TSS) profiling method, STRIPE-seq. STRIPE-seq (Survey of TRanscription Initiation at Promoter Elements) is a straightforward and efficient method for identifying promoters from small quantities (~100ng and below) of input RNA. The STRIPE-seq preprint can be found here; at present the manuscript is in the latter stages of peer review. Update: the STRIPE-seq paper was just published in Genome Research, and can be found here.
Development of bioinformatics software for analysis of TSS profiling data
To facilitate the analysis of STRIPE-seq and other forms of TSS profiling data, I have authored or contributed to bioinformatics software. This includes TSRchitect, an R Bioconductor package that identifies and provides quantitative information on promoters using aligned TSS profiling data. TSRchitect is available here, and includes a vignette and users guide. My github page is here.
- Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner (2020). Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq. Genome Research. doi:10.1101/gr.261545.120. (Epub ahead of print)
- R. Taylor Raborn, Krishnakumar Sridharan and Volker P. Brendel (2017). TSRchitect: Promoter identification from large-scale TSS profiling data. In Bioconductor v. 3.7. doi:10.18129/B9.bioc.TSRchitect.
- Zhiqiang Ye, Sen Xu, Ken Spitze, Jana Asselman, Xiaoqian Jiang, Matthew S. Ackerman, Jacqueline Lopez, Brent Harker, R. Taylor Raborn, W. Kelley Thomas, Jordan Ramsdell, Michael E. Pfrender, Michael Lynch. (2017) A New Reference Genome Assembly for the Microcrustacean Daphnia pulex. G3: Genes, Genomes, Genetics. 7(5): 1405-1416. doi: 10.1534/g3.116.038638.
- R. Taylor Raborn, Ken Spitze, Volker P. Brendel and Michael Lynch. (2016) Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. GENETICS. 204, 593-612. doi:10.1534/genetics.116.193334.