Peer-reviewed publications                                                                                                                      

1. Addressing the dNTP bottleneck restricting prime editing activity. Pengpeng Liu, Karthikeyan Ponnienselvan, Thomas Nyalile, Sarah Oikemus, Anya Joint, Karen Kelly, Dongsheng Guo, Zexiang Chen, Jeong Min Lee, Charles Emerson, Nathan D. Lawson, Jonathan K. Watts, Erik J. Sontheimer, Jeremy Luban, Scot A. Wolfe. (2024) (First author) (Nature Biotechnology,2024).

2. Transcriptional suppression of sphingolipid catabolism controls pathogen resistance in

C. elegans.  Mohamad A. Nasrallah, Nicholas D. Peterson, Elizabeth S. Szumel, Pengpeng Liu,

Amanda L. Page, Samantha Y. Tse, Khursheed A. Wani, Claire E. Tocheny, Read Pukkila-Worley. PLoS Pathog 19(10): e1011730. (2023)

3. Reducing the inherent auto-inhibition interaction within the pegRNA enhances prime editing efficiency. Karthikeyan Ponnienselvan, Pengpeng Liu, Thomas Nyalile, Sarah Oikemus, Nathan Lawson, Jeremy Luban, Scot Wolfe. Nucleic acids research. (2023) (Co-First author)

4. Genome-wide Profiling of Prime editor off-target sites in vitro and in vivo using PE-tag. Shun-Qing Liang, Pengpeng Liu2*, Karthikeyan Ponnienselvan, Sneha Suresh, Zexiang Chen, Christian Kramme, Pranam Chatterjee, Lihua Julie Zhu, Erik J. Sontheimer, Wen Xue*, Scot A. Wolfe*. Nature Methods. (2023) https://doi.org/10.1038/s41592-023-01859-2 (Co-First author and Co-Corresponding author)

5. Optimization of NLS Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells. Kevin Luk, Pengpeng Liu,Jing Zeng, Yetao Wang,  Stacy A. Maitland, Feston Idrizi, Karthikeyan Ponnienselvan, Lihua Julie Zhu, Jeremy Luban, Daniel E. Bauer, and Scot A. Wolfe. GEN Biotechology. 1: 271-284 (2022) (Co-First author)

6. Enhancing Prime Editing Efficiency and Flexibility with Tethered and Split pegRNAs. Ying Feng, Siyuan Liu, Qiqin Mo, Xiao Xiao, Pengpeng Liu, Hanhui Ma. Protein & Cell. (2022).

7. Efficient Homology-Directed Repair with Circular Single-Stranded DNA Donors. Iyer S, Mir A, Vega-Badillo J, Roscoe BP, Ibraheim R, Zhu LJ, Lee J, Liu P, Luk K, Mintzer E, Guo D, Soares de Brito J, Emerson CP Jr, Zamore PD, Sontheimer EJ, Wolfe SA. CRISPR J. (2022)

8. Adenine Base Editing In Vivo with a Single Adeno-Associated Virus Vector. Han Zhang, Nathan Bamidele, Pengpeng Liu, Ogooluwa Ojelabi, Xin D. Gao, Tomás Rodriguez, Haoyang Cheng, Karen Kelly, Jonathan K. Watts, Jun Xie, Guangping Gao, Scot A. Wolfe, Wen Xue, and Erik J. Sontheimer. GEN Biotechology. 1: 285-299 (2022)

9. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Shun-Qing Liang, Pengpeng Liu, Jordan L. Smith, Esther Mintzer, Stacy Maitland, Xiaolong Dong, Qiyuan Yang, Jonathan Lee, Cole M. Haynes, Lihua Julie. Zhu, Jonathan K. Watts, Erik J. Sontheimer, Scot A. Wolfe*, Wen Xue*. Nature Communications. 13:437-450 (2022) (Co-First author)

10. A flexible split prime editor using truncated reverse transcriptase improves dual AAV delivery in mouse liver.  Chunwei Zheng, Shun-Qing Liang, Bin Liu, Pengpeng Liu, Suet-Yan Kwan, Scot A Wolfe, Wen Xue. Molecular Therapy. 30(3):1343-1351 (2022)

11. mtDNA replication in dysfunctional mitochondria promotes deleterious heteroplasmy via the UPRmt. Qiyuan Yang, Pengpeng Liu, Nadine S Anderson, Tomer Shpilka, YunGuang Du, Nandhitha Uma Naresh, Kevin Luk, Josh Lavelle, Rilee D Zeinert, Peter Chien, Scot A Wolfe, Cole M Haynes. Nature Cell Biology. 24(2):181-193 (2022)

12. ATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1. Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William Mair, Alban Longchamp, Milos Filipovic, Keith Blackwell, Collin Ewald. Nature Communications. 13:967-972 (2022)

13. The KRAB Domain‐Containing Protein ZFP961 Represses Adipose Thermogenesis and Energy Expenditure through Interaction with PPARα. Lei Huang, Pengpeng Liu, Qiyuan Yang, YongXu Wang. Advanced Science. 9(2):e2102949 (2021)

14. 5′-Modifications improve potency and efficacy of DNA donors for precision genome editing. Krishna S Ghanta, Zexiang Chen, Aamir Mir, Gregoriy A Dokshin, Pranathi M Krishnamurthy, Yeonsoo Yoon, Judith Gallant, Ping Xu, Xiao-Ou Zhang, Ahmet Rasit Ozturk, Masahiro Shin, Feston Idrizi, Pengpeng Liu, Hassan Gneid, Alireza Edraki, Nathan D Lawson, Jaime A Rivera-Pérez, Erik J Sontheimer, Jonathan K Watts, Craig C Mello. Elife. 10:e72216 (2021)

15. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Pengpeng Liu, Shun-Qing Liang, Chunwei Zheng, Esther Mintzer, Yan G Zhao, Karthikeyan Ponnienselvan, Aamir Mir, Erik J Sontheimer, Guangping Gao, Terence R Flotte, Scot A Wolfe, Wen Xue. Nature Communications. 12(1):1-13 (2021). (First author)

16. UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import in Caenorhabditis elegans. Tomer Shpilka, YunGuang Du, Qiyuan Yang, Andrew Melber, Nandhitha Uma Naresh, Joshua Lavelle, Sookyung Kim, Pengpeng Liu, Hilla Weidberg, Rui Li, Jun Yu, Lihua Julie Zhu, Lara Strittmatter, Cole M Haynes. Nat Communications. 12(3): 1-11 (2021)

17. Genome-wide detection and analysis of CRISPR-Cas off-targets. Tomás C Rodríguez, Sina Dadafarin, Henry E Pratt, PengPeng Liu, Nadia Amrani, Lihua Julie Zhu. Progress in molecular biology and translational science. 181:31-43 (2021)

18. Innate immunity in the C. elegans intestine is programmed by a neuronal regulator of AWC olfactory neuron development. Kyle J Foster, Hilary K Cheesman, Pengpeng Liu, Nicholas D Peterson, Sarah M Anderson, Read Pukkila-Worley. Cell reports. 31 (1): 107478 (2020)

19. Tissue-restricted genome editing in vivo specified by microRNA-repressible anti-CRISPR proteins. Jooyoung Lee, Haiwei Mou, Raed Ibraheim, Shun-Qing Liang, Pengpeng Liu, Wen Xue, Erik J Sontheimer. RNA. 25(11):1421-1431 (2019)

20. Enhanced Cas12a editing in mammalian cells and zebrafish. Pengpeng Liu, Kevin Luk, Masahiro Shin, Feston Idrizi, Samantha Kwok, Benjamin Roscoe, Esther Mintzer, Sneha Suresh, Kyle Morrison, Josias B Frazão, Mehmet Fatih Bolukbasi, Karthikeyan Ponnienselvan, Jeremy Luban, Lihua Julie Zhu, Nathan D Lawson, Scot A Wolfe. Nucleic acids research. 47 (8):4169-4180 (2019) (First author)

21. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Yuxuan Wu, Jing Zeng, Benjamin P Roscoe, Pengpeng Liu, Qiuming Yao, Cicera R Lazzarotto, Kendell Clement, Mitchel A Cole, Kevin Luk, Cristina Baricordi, Anne H Shen, Chunyan Ren, Erica B Esrick, John P Manis, David M Dorfman, David A Williams, Alessandra Biffi, Carlo Brugnara, Luca Biasco, Christian Brendel, Luca Pinello, Shengdar Q Tsai, Scot A Wolfe, Daniel E Bauer. Nat Medicine. 25 (5):776-783 (2019)

22. Precise therapeutic gene correction by a simple nuclease-induced double-stranded break. Sukanya Iyer, Sneha Suresh, Dongsheng Guo, Katelyn Daman, Jennifer CJ Chen, Pengpeng Liu, Marina Zieger, Kevin Luk, Benjamin P Roscoe, Christian Mueller, Oliver D King, Charles P Emerson, Scot A Wolfe. Nature. 568 (7753):561-565 (2019)

23. The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans. Nicholas D Peterson, Hilary K Cheesman, Pengpeng Liu, Sarah M Anderson, Kyle J Foster, Richa Chhaya, Paola Perrat, Jose Thekkiniath, Qiyuan Yang, Cole M Haynes, Read Pukkila-Worley. PLoS Genetics. 15(1):e1007935-46 (2019)

24. Potent Cas9 inhibition in bacterial and human cells by AcrIIC4 and AcrIIC5 anti-CRISPR proteins. Jooyoung Lee, Aamir Mir, Alireza Edraki, Bianca Garcia, Nadia Amrani, Hannah E Lou, Ildar Gainetdinov, April Pawluk, Raed Ibraheim, Xin D Gao, Pengpeng Liu, Alan R Davidson, Karen L Maxwell, Erik J Sontheimer. MBio. 9 (6):e02321-18 (2018)

25. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Nadia Amrani, Xin D Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E Sasaki, Tong Wu, Paul D Donohoue, Alexander H Settle, Alexandra M Lied, Kyle McGovern, Chris K Fuller, Peter Cameron, Thomas G Fazzio, Lihua Julie Zhu, Scot A Wolfe, Erik J Sontheimer. Genome Biology. 19 (1):1-25 (2018)

26. Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing. Mehmet Fatih Bolukbasi, Pengpeng Liu, Kevin Luk, Samantha F Kwok, Ankit Gupta, Nadia Amrani, Erik J Sontheimer, Lihua Julie Zhu, Scot A Wolfe. Nature Communications. 9(1):1-12 (2018) (Co-First author)

27. Regulation of transcriptionally active genes via the catalytically inactive Cas9 in C. elegans and D. rerio. Lijiang Long, Hong Guo, Di Yao, Kai Xiong, Yongjun Li, Pengpeng Liu, Zuoyan Zhu, Dong Liu. Cell Research. 25:638–641 (2015) (Co-Corresponding author)

28. Heritable/conditional genome editing in C. elegans using a CRISPR-Cas9 feeding system. Pengpeng Liu, Lijiang Long, Kai Xiong, Bo Yu, Nannan Chang, Jing-Wei Xiong, Zuoyan Zhu, Dong Liu. Cell Research. 24:886–889 (2014) (First author)

29. mir-35 is involved in intestine cell G1/S transition and germ cell proliferation in C. elegans. Min Liu, Pengpeng Liu, Li Zhang, Qingchun Cai, Ge Gao, Wenxia Zhang, Zuoyan Zhu, Dong Liu, Qichang Fan. Cell Research. 21:1605–1618  (2011). (Co-First author)