News Archive

Study identifying novel post-transcriptional regualtors of root hair cell fate published

Our study identifying novel post-transcriptional regulators of root hair cell fate is now published in Developmental Cell! We also are the cover article for this issue!

Congratulations, Shawn on a great study. Also, a huge thank you to our fantastic collaborative team.
A press release about this work can be found through the following link.


Study describing our genome-wide Topoisomerase cleavage assay published

Our collaborative study where we and the Felix lab developed a high-throughput sequencing-based approach for mapping TOP2A cleavage on a genome-wide scale is now online at Genome Research. This was a true labor of love to get this study to completion, but I could not be happier to have this assay finally published!

Congrats to Xiang and James for getting this study passed the finish line!


Structure probing approach review published

June 7, 2016

Our review chapter on RNA secondary structure probing is now online. You can find it at the following.

Great job Ian, Nate, and Sager!!!

Structure Surfer now available

May 17, 2016

A new tool for visualizing and comparing the high-throughput sequencing-based RNA secondary structure data for mammals developed by the Gregory Lab is now available for use at the following URL.

The manuscript desribing this tool/database is also now published in BMC Bioinformatics, and can be found at the following link.…

Review article on conservation and function of RNA secondary structure in plants now available

May 13, 2016

Our review article “The conservation and function of RNA secondary strucutre in plants” is now available in Annual Reviews in Plant Biology. The article can be found at the following.

Up-to-date Gregory Lab news

December 11, 2015

To keep up to date on the happenings in the Gregory Lab follow our twitter account @bdgPhD.

Review on high-throughput probing of plant RNA secondary structure now available

June 26, 2015

A review article by #GregoryLab members Shawn Foley and Lee Vandivier describes the recent findings from high-throughput probing of RNA secondary structure in the plant transcriptome. We focus on the methods used for these analyses and the findings that have been uncovered from such studies. For those interested, the paper can be found by clicking the following web link or by contacting us for an emailed copy.

Structure mapping protocol now available

April 13, 2015

For those interested in our plant RNA secondary structure mapping protocol, a detailed methodology including analytical pipeline can be found at the following.

Good luck and #HappyStructuring!!

2015-01-05 (2)

February 3, 2015

Congratulations to Sager and Shawn! Their Molecular Cell paper is now online. In this study, we reveal the patterns of RNA secondary structure and RNA-binding protein interaction sites in the Arabidopsis nucleus. It is online now at: For those interested in the datasets and affiliated data browsers please go to the following link:


February 3, 2015

Very nice press release about our recent Molecular Cell paper can be found at the following site:


February 3, 2015

Methods paper describing the use of PIP-seq to profile RBP-binding sites transcriptome-wide in HEK293T cells. Those interested can find the paper here: doi: 10.1016/j.ymeth.2014.10.021. The RBP binding site lists are provided as Supplemental Tables for those that are interested in those datasets. This is Ian Silverman’s second first author paper from the lab. Congrats Ian!

News archive

February 3, 2015


Collaborative study with Chen lab to find Pol IV transcripts in Arabidopsis published in Genome Research. If interested, paper can be found here: doi: 10.1101/gr.182238.114.


Yih-Chii’s second first author paper published in Bioinformatics. Congrats Yih-Chii! In this manuscript, we describe HIPPIE, which is an analytical pipeline for identifying enhancer-promoter pairs using Hi-C datasets. Paper can be found here: doi: 10.1093/bioinformatics/btu801.


Collaborative study focusing on a quality control system that monitors microRNA biogenesis in mammals with the Mourelatos lab published in Mol. Cell . If interested the paper can be found here:


Congratulations to Dr. Fan Li on receiving the the Saul Winegrad Award for Outstanding Dissertation for the GCB program!


Congratulations to our award winning undergraduate Sarah Foster on he Churchill Scholarship! Another wonderful accomplishment by a fantastic student. For more information on Sarah’s awards see the following news article:


Congratulations to Ian and Fan on their recent Genome Biol. paper where we describe PIP-seq, which is our novel approach for transcriptome-wide identification of protein-RNA interaction sites in eukaryotic transcriptomes. This manuscript can be found here:


Nice Penn News piece about our novel PIP-seq methodology can be found here:


Congratulations to Ian Silverman! He has won a poster prize at both the CAMB and Genetics Dept. Symposiums this fall by presenting his work on PIP-seq development, which is a global RNA-binding protein footprinting technique. His paper describing this work is coming soon!


A huge congratulations to Dr. Fan Li, who successfully defended his thesis yesterday. Welcome to the Ph.D. club, Fan!


Congratulations to Paul and Fanny on their Methods paper now online. This manuscript provides a detailed description on how to utilize our software CoRAL for classifying RNAs using RNA sequencing data.


Congratulations to Paul, Fanny, and Ian on their RNA paper now online. This study describes our development of the software that we call HAMR, which can be used to identify and annotate many different kinds of modification sites in RNA molecules using high-throughput RNA sequencing data.


Collaborative study with the Weiss lab on transcriptomic analysis of murine coronavirus-infected mice spinal cords published in PLoS ONE


Collaborative epigenomics study with the Berger lab online now at Genes Dev. See Publications for citation.


Congratulations to Matthew and Nate on their paper in Methods where we have made major improvements to our GMUCT protocol. The manuscript describes GMUCT 2.0, which we use on Arabidopsis flower buds and 3 different human cell lines.


Congrats to Fanny Leung and Paul Ryvkin on their paper online now at Nucleic Acids Research where the Gregory, Ungar, and Wang labs collaborated to develop a method that allows more comprehensive classification of non-coding RNAs using smRNA-seq data. The paper can be found here:


Congratulations to Lee on his recent Plant Signaling and Behavior paper were we show that Arabidopsis mRNA secondary structure likely also has effects on protein maturation and expression.


Congratulations to undergraduate research assistant Sarah Foster on being named a Goldwater Scholar! We are all so very proud of your wonderful accomplishment.


Congratulations to Anissa Alexander on her NSF predoctoral fellowship award, and to Lee Vandivier for being named an honorable mention for this prize. We are all very proud of both of you!


We would like to thank the NSF (and our PO Dr. Susannah Gal) for the new grant award that will allow us to analyze RNA-protein interaction sites transcriptome-wide in multiple plant species.


Congrats to Yih-Chii Hwang and Qi Zheng on their paper online now at Nucleic Acids Research where the Gregory and Wang labs collaborated to develop a method that allows comprehensive identification of enhancer – promoter interactions using Hi-C data. The paper can be found here: ijkey=j5Pz4MCJjwUL3ho&keytype=ref


Nice article about the research in the Gregory lab can be found here:


Collaborative study on vsiRNA processing by Drosophila melanogaster Dcr-2 with the Cherry lab now published in PLoS ONE. The paper can be found here:


Congrats to Ian and Fan for their nice review about plant RNA secondary structure and RNA-binding proteins for Plant Science that is now available online at:


Congratulations to Fan and Qi on their recently accepted Plant Cell paper. In this study, we uncovered that RNA secondary structure has significant regulatory effects on gene expression in Arabidopsis thaliana. If interested, you can find the paper here:


Collaborative study with the Wierzbicki lab on AGO4 targeting in Arabidopsis now online at The Plant Journal.


Collaborative study with the Mourelatos lab on piRNA biogenesis and function now online at Nature Structural and Molecular Biology.


Congratulations to Lee on his Cell and Molecular Biology T32 Award. Congrats, Lee!


We thank the Gordon and Betty Moore Foundation for their support to the Gregory and Lyon labs to fund the development of the EPIC-CoGe Browser, which will be an easy-to-use web-based system to store, access, and visualize Arabidopsis epigenetic data in a comparative genomics context. For more information, see this press release (…)


For anybody interested in the structure score data for Drosophila and C. elegans mRNAs, all of this data is available for download here:


Congratulations to Ian on his Genetics T32 Award. Congrats, Ian!


Fan and Paul’s paper on a new web-based tool for RNA-seq analysis in the context of secondary structure (SAVoR) is now online at Nucleic Acids Research: doi: 10.1093/nar/gks310.


Congratulations to Fan and Qi for their paper in Cell Reports on global analysis of secondary structure in Drosophila and C. elegans!!!


If you are interested in accessing our high-throughput RNA sequencing data and models of RNA secondary structure, please visit our webbrowsers at:


Welcome our new lab members, Ian, Nate and Ammar!


Gregory Lab awarded NSF Career Award for characterizing RDR substrates.

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