Currently, I have 2 articles published or in print at journals while 2 more are in the pipeline. To introduce you to my work, for my published articles, I have also included small snippets below which quickly describe the whole paper.

  1. Shukla C.J., McCorkindale A.L., Gerhardinger C., Korthauer K.D., Cabili M.N., Shechner D.M., Irizarry R.A., Maass P.G., Rinn J.L. High-throughput identification of RNA nuclear enrichment sequences doi: https://doi.org/10.1101/189654

  2. Shukla C.J., Barutcu R.A., Irizarry R.A., Rinn J.L. Analysis of Local and Tandem Repeats in Human and Mouse Genomes Identifies a Novel Sub-Class of lncRNAs (in preparation)

  3. Hacisuleyman E., Shukla C.J., Weiner C.L., Rinn J.L. Function and evolution of local repeats in the Firre locus http://dx.doi.org/10.1038/ncomms11021

  4. McCorkindale A.L., Wahle P., Jungreis I., Menzel P., Shukla C.J., Abreu R.L.P., Irizarry R.A., Meyer I.M., Kellis M., Rinn J.L., Zinzen R.P. Spatiotemporal long noncoding RNA expression during embryonic neurogenesis in Drosophila (in review)

  5. Kimes P., Korthauer K.D., Reyes A., Duvallet C., Subramanian A., Teng M., Shukla C.J., Hicks S.C. A practical guide for methods controlling False Discovery Rates (in preparation)

I recently put a paper on bioRxiv (in print at EMBO currently) describing a new high throughput genomics technique to identify nuclear enrichment sequences. We also develop a new statistical method available in a package called oligoGames to normalize, model and infer from this new dataset. Below I show the first figure from the paper. It describes a schematic of the new experimental technique (panel A), an overview of the analysis (panel B-D) and successful results for two controls in the dataset. I invite you to read the preprint to learn more details

My first research paper was published in March 2016 and described the new local repeats we found in FIRRE lncRNA. Below is an image with all the local repeats we found in FIRRE. In the paper, we demonstrated that Repeat R0 works as an enhancer element while Repeat RRD is neccessary and sufficient as a nuclear localization signal.