Google Scholar
Work from the Lu lab at USC
25. A snoRNA-tRNA modification network controls codon-biased cellular states.
Zhang M, Li K, Bai J, Van Damme R, Zhang W, Alba M, Stiles BL, Chen JF and Lu Z*
PNAS, 120 (41) (2023) PDF. Highlighted by GenomeTDCC on Youtube.
24. Ribosome biogenesis controls cranial suture MSC fate via the complement pathway in mouse and human iPSC models.
Jariyasakulroj S, Zhang W, Bai J, Zhang M, Lu Z, Chen JF*.
Stem Cell Reports. 2023.
23. Chemical RNA crosslinking: mechanisms, computational analysis, and biological applications.
Velema WA* and Lu Z*
JACS Au (2023) PDF.
22. Integrated analysis of crosslink-ligation data for the detection of RNA 2D/3D conformations in vivo.
Lee WH, Zhang M and Lu Z*
Methods in Molecular Biology (2023).
21. Chemical crosslinking and ligation methods for in vivo analysis of RNA structures and interactions.
Lee WH, Li K and Lu Z* .
Methods in Enzymology (2023) PDF.
20. Chemical Reversible Crosslinking Enables Measurement of RNA 3D Distances and Alternative Conformations in Cells.
Van Damme R, Li K, Zhang M, Bai J, Lee WH, Yesselman JD, Lu Z* and Velema WA*
Nature Communications, 13:911 (2022) PDF. Recommended by Faculty Opinions, Dr. Janusz Bujnicki (https://facultyopinions.com/article/741670636).
19. Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers.
Zhang M, Hwang IT, Li K, Bai J, Chen JF, Weissman T, Zou JY and Lu Z*
Genome Research, 32: 1-18 (2022) PDF.
18. Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells and virus infections,
Zhang M, Li K, Bai J, Velema WA, Yu C, van Damme R, Lee WH, Corpuz ML, Chen JF, Lu Z*
Nature Communications, 12:2344 (2021) PDF
17. Cerebral organoid and mouse models reveal a RAB39b–PI3K–mTOR pathway-dependent dysregulation of cortical development leading to macrocephaly/autism phenotypes.
Zhang W, Ma L, Yang M, Shao Q, Xu J, Lu Z, Zhao Z, Chen R, Chai Y, Chen JF
Genes & Development 34, 580-597 (2020) PDF.
16. Structural modularity of the XIST ribonucleoprotein complex.
Lu Z*, Guo JK, Wei Y, Dou DR, Zarnegar B, Ma Q, Li R, Zhao Y, Liu F, Choudhry H, Khavari PA, Chang HY
Nature Communications, 11:6163 (2020) PDF.
15. IRIS: A method for predicting in vivo RNA secondary structures using PARIS data. Zhou J, Li P, Zeng W, Ma W, Lu Z, Jiang R, Zhang QC, Jiang T
Quantitative Biology, 1-13 (2020) PDF.
14. Modeling microcephaly with cerebral organoids reveals a WDR62-CEP170-KIF2A pathway promoting cilium disassembly in neural progenitors.
Zhang W, Yang SL, Yang M, Herrlinger S, Shao Q, Collar JL, Fierro E, Shi Y, Liu A, Lu H, Herring BE, Guo ML, Buch S, Zhao Z, Xu J, Lu Z, Chen JF.
Nature Communications. 10:2612 (2019) PDF
Postdoc work at Stanford University
13. The RNA Base-pairing Problem and Base-pairing Solutions.
Lu Z and Chang HY
Cold Spring Harbor Perspectives in Biology (2018). Also as a book chapter in RNA Worlds: New tools for deep exploration, fifth edition. PDF
12. PARIS: psoralen analysis of RNA interactions and structures with high throughput and resolution.
Lu Z, Gong J and Zhang QC
Methods in Molecular Biology: RNA Detection, 59-84 (2018). PDF
11. RISE: a database of RNA Interactome from Sequencing Experiments.
Gong J, Shao D, Xu K, Lu Z, Lu ZJ, Yang YT and Zhang QC (2017)
Nucleic Acid Research, gkx864. PDF
10. Mechanistic insights in X chromosome inactivation.
Lu Z, Carter AC and Chang HY
Philosophical Transactions of the Royal Society B, 372(1733) (2017). PDF
9. RNA duplex map in living cells reveals higher order transcriptome structure.
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)
Cell, 165 (5): 1267-1279. PDF.
Featured on the cover and in a paperclip of Cell (Youtube video: Get an Eye-full (Eiffel)), on the cover of Best of Cell 2016. Highlighted in Nature Methods, Nature Chemical Biology, Molecular Cell and Trends in Biochemical Sciences.
8. Decoding the RNA structurome.
Lu Z, Chang HY
Current Opinion in Structural Biology 36:142- 148 (2016). PDF
PhD work at UNC Chapel Hill
7. Metazoan tRNA introns generate stable circular RNAs in vivo.
Lu Z, Filonov GS, Noto JJ, Schmidt CA, Hatkevich T,Wen Y, Jaffrey SR andMatera AG,
RNA 21:1-12 (2015). PDF
6. Developmental Analysis of Spliceosomal snRNA Isoform Expression.
Lu Z and Matera AG
G3: Genes|Genomes|Genetics 5 (1), 103-110 (2015). PDF
5. RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins.
Lu Z, Guan X, Schmidt CA and Matera AG
Genome Biology 15(1):R7 (2014) . PDF
4. Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments
Lu Z and Matera AG
Nucleic Acid Research doi: 10.1093/nar/gku207 (2014). PDF
3. Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes.
Garcia EL, Lu Z, Meers MP, Praveen K and Matera AG
RNA 19 (11), 1510-1516 (2013) . PDF
Undergrad work at Fudan University
2. REV3L confers chemoresistance to cisplatin in human gliomas: The potential of its RNAi for synergistic therapy.
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
Neuro-Oncology,11: 790-802 (2009). PDF
1. Hypermethylation of hepatic Gck promoter in ageing rats contributes to diabetogenic potential.
Jiang M, Fei J, Lan MS, Lu Z, Liu M, Fan W, Gao X and Lu D,
Diabetologia, 51: 1525-1533 (2008). PDF
Zhipeng Lu Lab @ USC 