Zhipeng  Lu

Zhipeng Lu, PhD

Assistant Professor, Pharmacology and Pharmaceutical Sciences

Research Topics

  1. RNA structures and interactions
  2. Chemical tools for RNA
  3. RNA in genetic and infectious diseases
  4. Computational biology

Contact Information


BS. 2008 Biology - Fudan University
PhD. 2014 Biology - UNC Chapel Hill
Postdoctoral Research
Fellowship: 2014-2018 Stanford University

Zhipeng Lu


Dr. Lu received his B.S. in Biology from Fudan University in 2008. He earned his Ph.D. in Biology with Professor Greg Matera at UNC Chapel Hill in 2014. During his PhD work, Dr. Lu discovered novel RNA-protein interactions and new forms of circular RNAs. Dr. Lu conducted postdoctoral training with Professor Howard Y. Chang at Stanford University from 2014 to 2018. His postdoctoral work established a general strategy to determine RNA secondary structures and interactions in living cells.

Dr. Lu’s work on noncoding RNA structures led to the discovery of drug target that has been employed to develop drugs to treat X-linked genetic diseases. His work was featured on the cover of Cell, on the cover of Best of Cell 2016.

Dr. Lu joined the faculty in the Department of Pharmacology and Pharmaceutical Sciences at USC School of Pharmacy as an Assistant Professor in 2018. Dr. Lu’s research contributions have been recognized by several awards, including the Damon Runyon-Sohn Pediatric Cancer Award (Layton Family Fellow), Stanford’s Jump Start Award for Excellence in Research, RNA Society Scaringe Award, and NIH Pathway to Independence Award (K99 /R00, NHGRI)


RNA molecules fold into structures and intermolecular interactions to execute a second layer of genetic instructions beyond encoding proteins. Functions of RNA structures are pervasive and diverse, including many levels of gene regulation, guiding, scaffolding and catalysis. RNA molecules are directly involved in a variety of human diseases, such as genetic disorders resulting from mutations in noncoding RNAs, RNA binding proteins, and infections caused by RNA viruses (like HIV, HCV, Ebola, etc.).

Dr. Lu's research combines computational, chemical and biological approaches, and aims to elucidate the fundamental mechanisms of “RNA machines.” These studies will lead to new understanding and therapies targeting human diseases. In particular, the Lu lab is interested in the following areas of research:

1. New technologies for the analysis of RNA structures and interactions.
2. Organizing principle of RNA in live Cells: a molecular social network.
3. RNA structures and interactions in gene expression.
4. RNA structures and interactions in genetic and infectious diseases.

Selected Projects/Publications

Lu Z and Chang HY (2018) The RNA Base-pairing Problem and Base-pairing Solutions. Cold Spring Harbor Perspectives in Biology, in press. Also as a book chapter in RNA Worlds: New tools for deep exploration, fifth edition.

Lu Z, Gong J and Zhang QC (2018) PARIS: psoralen analysis of RNA interactions and structures with high throughput and resolution. Methods in Molecular Biology, in press.

Gong J, Shao D, Xu K, Lu Z, Lu ZJ, Yang YT and Zhang QC (2017 ) RISE: a database of RNA Interactome from Sequencing Experiments. Nucleic Acid Research, gkx864

Lu Z, Carter AC and Chang HY (2017) Mechanistic insights in X chromosome inactivation. Philosophical Transactions of the Royal Society B, 372(1733).

Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY (2016) RNA duplex map in living cells reveals higher order transcriptome structure. Cell, 165 (5):  1267- 1279. Featured on the cover and in a paperclip of Cell (Youtube video: Get an Eye-full (Eiffel), https://www.youtube.com/watch?v=1GXibPeUUGQ), on the cover of Best of Cell 2016. Highlighted in Nature Methods, Nature Chemical Biology, Molecular Cell and Trends in Biochemical Sciences.

Lu Z, Chang HY (2016) Decoding the RNA structurome. Current Opinion in Structural Biology 36: 142-148

Lu Z, Filonov GS, Noto JJ, Schmidt CA, Hatkevich T,Wen Y, Jaffrey SR and Matera AG, (2015) Metazoan tRNA introns generate stable circular RNAs in vivo. RNA 21: 1- 12

Lu Z and Matera AG, (2015) Developmental Analysis of Spliceosomal snRNA Isoform Expression. G3:Genes|Genomes|Genetics  5 ( 1),  103- 110

Lu Z, Guan X, Schmidt CA and Matera AG, (2014) RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins. Genome Biology 15(1):R7

Lu Z and Matera AG, (2014) Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments. Nucleic Acid Research doi: 10.1093/nar/gku 207

Garcia EL, Lu Z, Meers MP, Praveen K and Matera AG, (2013) Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes. RNA 19 (11), 1510- 1516

Wang H, Zhang SY, Wang S, Lu J, Wu W, Weng L, Chen D, Zhang Y, Lu Z, Yang J, Chen Y, Zhang X, Chen X, Xi C, Lu D, Zhao S, (2009) REV3L confers chemoresistance to cisplatin in human gliomas: The potential of its RNAi for synergistic therapy. Neuro-Oncology 11:790- 802.

Jiang M, Fei J, Lan MS, Lu Z, Liu M, Fan W, Gao X and Lu D, (2008). Hypermethylation of hepatic Gck promoter in ageing rats contributes to diabetogenic potential. Diabetologia, 51:1525-1533