complete list of publicationS and citationS

Zhang lab members: marked in bold | # Co-first author | * Corresponding author

2024

  • Thomas SP, Spinelli MM, Rghei AD, Lopes JA, Zielinska N, McLeod BM, Pei Y, Zhang W, Thebaud B, Karimi K, Wootton SK. (2024) Analysis of the impact of pluronic acid on the thermal stability and infectivity of AAV6.2FF. BMC Biotechnology. doi: 10.1186/s12896-024-00853-6

  • Tessier TM#, Chowdhury A#, Stekel Z, Fux J, Sartori MA, Teyra J, Jarvik N, Chung J, Kurinov I, Sicheri F, Sidhu SS, Singer AU*, Zhang W*. (2024) Structural and functional validation of a highly specific Smurf2 inhibitor. Protein Science. https://onlinelibrary.wiley.com/doi/10.1002/pro.4885

2023

  • Thomas SP, Domm JM, van Vloten JP, Xu L, Vadivel A, Yates JGE, Pei Y, Ingrao J, van P Lieshout L, Jackson SR, Minott JA, Achuthan A, Mehrani Y, McAusland TM, Zhang W, Karimi K, Vaughan AE, de Jong J, Kang MH, Thebaud B, Wootton SK. (2023) A promoterless AAV6.2FF-based lung gene editing platform for the correction of surfactant protein B deficiency. Mol Ther. doi: 10.1016/j.ymthe.2023.10.002.

  • Bodrug T, Welsh KA, Bolhuis DL, Paulаkonis E, Martinez-Chacin RC, Liu B, Pinkin N, Bonacci T, Cui L, Xu P, Roscow O, Amann SJ, Grishkovskaya I, Emanuele MJ, Harrison JS, Steimel JP, Hahn KM, Zhang W, Zhong ED, Haselbach D, Brown NG. (2023) Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C). Nat Struct Mol Biol. doi: 10.1038/s41594-023-01105-5.

  • Liu Q#, Mallette E#, Zheng, H, Zhang W*. (2023) Development of an OTUD1 ubiquitin variant inhibitor. Biochemical Journal. doi: 10.1042/BCJ20230119

  • Liang C#, Roscow O#, Zhang W*. (2023) Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade. Cold Spring Harb Protoc. doi: 10.1101/pdb.over107784

2022

  • Sherpa D#, Mueller J#, Karayel O#, Xu P#, Yao Y, Chrustowicz J, Gottemukkala KV, Baumann C, Gross A, Czarnecki O, Zhang W, Gu J, Nilvebrant J, Sidhu SS, Murray PJ, Mann M, Weiss MJ, Schulman BA, Alpi AF. (2022) Modular UBE2H-CTLH E2-E3 complexes regulate erythroid maturation. Elife. 11, e77937. DOI: https://doi.org/10.7554/eLife.77937

  • Liu Q, LaPlante G, Zhang W*. (2022) Targeting the Ubiquitination Cascade for Drug Discovery. Protein Homeostasis in Drug Discovery: A Chemical Biology Perspective. 179-225. John Wiley & Sons. [Book Chapter Edited by Drs. Milka Kostic & Lyn H. Jones] https://doi.org/10.1002/9781119774198.ch5

  • Stekel Z, Sheng Y*, Zhang W*. (2022) The Multifaceted Role of the Ubiquitin Proteasome System in Pathogenesis and Diseases. Biomolecules 12, 925. https://doi.org/10.3390/biom12070925 

  • McClary WD, Catala A, Zhang W, Gamboni F, Dzieciatkowska M, Sidhu SS, D'Alessandro A, Catalano CE. (2022). A designer nanoparticle platform for controlled intracellular delivery of bioactive macromolecules: Inhibition of ubiquitin-specific protease 7 in breast cancer cells. ACS Chemical Biology 17, 1853–1865. DOI: 10.1021/acschembio.2c00256

  • Zuo Y, He J, Liu S, Xu Y, Liu J, Qiao C, Zang L, Sun W, Yuan Y, Zhang H, Chen X, Jin L, Miao Y, Huang F, Ren T, Wang J, Qian F, Zhu C, Zhang W, Liu Y, Xu G, Ma F, Zheng H. (2022) LATS1 is a central signal transmitter for achieving full type-I interferon activity. Science Advances 8, eabj3887. doi: 10.1126/sciadv.abj3887

  • Bhardwaj A, Banh RS, Zhang W, Sidhu SS, Neel BG. (2022) MMD-associated RNF213 SNPs encode dominant-negative alleles that globally impair ubiquitylation. Life Science Alliance 5, e202000807. doi: 10.26508/lsa.202000807

  • Aminu B#, Fux J#, Mallette E, Petersen N, Zhang W*. (2022) Targeted Degradation of 53BP1 Using Ubiquitin Variant Induced Proximity. Biomolecules 12, 479. [Editor’s Choice article]. https://doi.org/10.3390/biom12040479

  • Zhao Y, Tian Y, Pan C, Liang A, Zhang W, Sheng Y. (2022) Target-Based In Silico Screening for Phytoactive Compounds Targeting SARS-CoV-2. Interdisciplinary Sciences: Computational Life Sciences 14, 64-79. https://doi.org/10.1007/s12539-021-00461-4

  • Yuan Y, Miao Y, Ren T, Huang F, Qian L, Chen X, Zuo Y, Zhang HG, He J, Qiao C, Du Q, Wu Q, Zhang W, Zhu C, Xu Y, Wu D, Shi W, Jiang J, Xu G, Zheng H. (2022) High salt activates p97 to reduce host antiviral immunity by restricting Viperin induction. EMBO Reports 23, e53466. https://doi.org/10.15252/embr.202153466

2021

  • Guo Y#, Liu Q#, Mallette E#, Caba C, Hou F, Fux J, LaPlante G, Dong A, Zhang Q, Zheng H, Tong Y*, Zhang W*. (2021) Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1. Journal of Biological Chemistry 297, 101107. https://doi.org/10.1016/j.jbc.2021.101107

  • Roscow O, Zhang W*. (2021) Using phage display to develop ubiquitin variant modulators for E3 ligases. Journal of Visualized Experiments 174, e62950. doi:10.3791/62950

  • LaPlante G, Zhang W*. (2021) Targeting the ubiquitin-proteasome system for cancer therapeutics by small-molecule inhibitors. Cancers 13, 3079. https://doi.org/10.3390/cancers13123079

  • Liang C#, Roscow O#, Zhang W*. (2021) Recent developments in engineering protein-protein interactions using phage display. Protein Engineering, Design and Selection 34, 1-13. https://doi.org/10.1093/protein/gzab014

  • LeBlanc N#, Mallette E#, Zhang W*. (2021) Targeted modulation of E3 ligases using engineered ubiquitin variants. The FEBS Journal 288, 2143-2165. https://doi.org/10.1111/febs.15536 Epub 2020 Sep 10.

  • Liu Q#, Aminu B#, Roscow O, Zhang W*. (2021) Targeting the Ubiquitin Signaling Cascade in Tumor Microenvironment for Cancer Therapy. International Journal of Molecular Sciences 22, 791. https://doi.org/10.3390/ijms22020791

2020

  • Yuan Y, Miao Y, Qian L, Zhang Y, Liu C, Liu J, Zuo Y, Feng Q, Guo T, Zhang L, Chen X, Jin L, Huang F, Zhang H, Zhang W, Li W, Xu G, Zheng H. (2020) Targeting UBE4A Revives Viperin Protein in Epithelium to Enhance Host Antiviral Defense. Molecular Cell 77, 734–747.

  • Yue L#, Wang L#, Du Y, Zhang W, Hamada K, Matsumoto Y, Jin X, Zhou Y, Mikoshiba K, Gill DL, Han S, Wang Y. (2020) Type 3 Inositol 1,4,5-Trisphosphate Receptor is a Crucial Regulator of Calcium Dynamics Mediated by Endoplasmic Reticulum in HEK Cells. Cells 9, 275. doi: 10.3390/cells9020275.

2019

  • Watson ER, Grace CRR, Zhang W, Miller DJ, Davidson IF, Prabu JR, Yu S, Bolhuis DL, Kulko ET, Vollrath R, Haselbach D, Stark H, Peters JM, Brown NG, Sidhu SS, Schulman BA. (2019) Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Proc. Natl. Acad. Sci. U.S.A. 116, 17280-17289.

  • Gabrielsen M#, Buetow L#, Kowalczyk D#, Zhang W, Sidhu SS, Huang DT. (2019) Identification and Characterization of Mutations in Ubiquitin Required for Non-covalent Dimer Formation. Structure 27, 1452-1459.

  • Veggiani G#, Gerpe MCR#, Sidhu SS*, Zhang W*. (2019) Emerging drug development technologies targeting ubiquitination for cancer therapeutics. Pharmacology & Therapeutics 199, 139-154.

2018

  • Zhang W*, Sidhu SS*. (2018) Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries. Methods in Molecular Biology 1844, 101-119. This is a book chapter in: Mayor T., Kleiger G. (eds) The Ubiquitin Proteasome System. Humana Press, New York, NY

  • Zhang W, Sidhu SS. (2018) Allosteric inhibitors hit USP7 hard. Nature Chemical Biology 14, 110-111.

  • Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW. (2018) Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Molecular Cell 70, 211–227.

  • Canny MD, Moatti N, Wan LC, Fradet-Turcotte A, Krasner D, Mateos-Gomez P, Zimmermann M, Orthwein A, Juang YC, Zhang W, Noordermeer SM, Seclen E, Wilson MD, Vorobyov A, Munro M, Ernst A, Ng TF, Cho T, Cannon P, Sidhu SS, Sicheri F, Durocher D. (2018) Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency. Nature Biotechnology 36, 95–102.

2017

  • Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sibbet GJ, Smith BO, Zhang W*, Sidhu SS*, Huang DT*. (2017) A general strategy for discovery of inhibitors and activators of RING and U-box E3 ligases with ubiquitin variants. Molecular Cell 68, 456-470.

  • Zhang W, Ben-David M, Sidhu SS. (2017) Engineering cell signaling modulators from native protein-protein interactions. Current Opinion in Structural Biology 45, 25-35.

  • Zhang W, Sartori MA, Makhnevych T, Federowicz KE, Dong X, Liu L, Nim S, Dong A, Yang J, Li Y, Haddad D, Ernst A, Heerding D, Tong Y, Moffat J, Sidhu SS. (2017) Generation and validation of intracellular inhibitors for USP7 and USP10. Journal of Molecular Biology 429, 3546-3560.

  • Zhang W, Bailey-Elkin BA, Knaap RCM, Khare B, Dalebout TJ, Johnson G, van Kasteren PB, McLeish N, Gu J, He W, Kikkert M, Mark BL, Sidhu SS. (2017) Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. PLoS Pathogens 13(5): e1006372. https://doi.org/10.1371/journal.ppat.1006372

2016

  • Yamaguchi M, Vanderlinden R, Weissmann F, Qiao R, Brown NG, Dube P, Haselbach D, Zhang W, Sidhu SS, Peters JM, Stark H, Schulman BA. (2016) Cryo-EM of mitotic checkpoint complex-bound APC/C reveals reciprocal and conformational regulation of ubiquitin ligation. Molecular Cell 63, 593-607.

  • Brown NG, Vanderlinden R, Watson E, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA. (2016) Dual RING E3 architectures regulate multiubiquitination and ubiquitin chain elongation by APC/C. Cell 165, 1440-1453.

  • Zhang W#, Wu KP#, Sartori MA, Kamadurai HB, Ordureau A, Jiang C, Mercredi PY, Murchie R, Hu J, Persaud A, Mukherjee M, Li N, Doye A, Walker JR, Sheng Y, Hao Z, Li Y, Brown KR, Lemichez E, Chen J, Tong Y, Harper JW, Moffat J, Rotin D, Schulman BA, Sidhu SS. (2016) System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes. Molecular Cell 62, 121-36. ⌘ Highlighted in the issue with accompanied preview: Canadeo LA, Huibregtse JM. (2016) A billion ubiquitin variants to probe and modulate the UPS. Molecular Cell 62, 2-4.

  • Bahn RS, Iorio C, Marcotte R, Xu Y, Cojocari D, Rahman AA, Pawling J, Zhang W, Sinha A, Rose CM, Isasa M, Zhang S, Wu R, Virtanen C, Hitomi T, Habu T, Sidhu SS, Koizumi A, Wilkins SE, Kislinger T, Gygi SP, Schofiled CJ, Dennis JW, Wouters BG, Neel BG. (2016) PTP1B controls non-mitochondrial oxygen consumption by regulating RNF213 to promote tumour survival during hypoxia. Nature Cell Biology 18, 803-813.

  • Strecker J, Gupta GD, Zhang W, Bashkurov M, Landry MC, Pelletier L, Durocher D. (2016) DNA damage signalling targets the kinetochore to promote chromatin mobility. Nature Cell Biology 18, 281–290.

Pre-2016

  • Chung DKC, Chan JNY, Strecker J, Zhang W, Ebrahimi-Ardebili S, Lu T, Abraham KJ, Durocher D, Mekhail K. (2015) Perinuclear tethers license telomeric DSBs for a broad kinesin/NPC-dependent DNA repair process. Nature Communications 6:7742 doi: 10.1038/ncomms8742

  • Zhang W, Sidhu SS. (2014) Development of inhibitors in the ubiquitination cascade. FEBS Letters 588, 356-67.

  • Zhang W, Durocher D. (2010) De novo telomere formation is suppressed by the Mec1-dependent inhibition of Cdc13 accumulation at DNA breaks. Genes & Development 24, 502-15. ⌘ Highly recommended by Drs. Virginia Zakian (Princeton), David Shore (Geneva), and Katherine Friedman (Vanderbilt) on Faculty of 1000. ⌘ Featured as “Top 7 in Cancer Biology” in March 2011 by The Scientist magazine®

  • O'Donnell L, Panier S, Wildenhain J, Tkach JM, Al-Hakim A, Landry MC, Escribano-Diaz C, Szilard RK, Young JT, Munro M, Canny MD, Kolas NK, Zhang W, Harding SM, Ylanko J, Mendez M, Mullin M, Sun T, Habermann B, Datti A, Bristow RG, Gingras AC, Tyers MD, Brown GW, Durocher D. (2010) The MMS22L-TONSL complex mediates recovery from replication stress and homologous recombination. Molecular Cell 40, 619-31.

  • Mao DY, Neculai D, Downey M, Orlicky S, Haffani YZ, Ceccarelli DF, Ho JS, Szilard RK, Zhang W, Ho CS, Wan L, Fares C, Rumpel S, Kurinov I, Arrowsmith CH, Durocher D, Sicheri F. (2008) Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Molecular Cell 32, 259-75.

  • Zhang W, Durocher D. (2008) Dun1 counts on Rad53 to be turned on. Molecular Cell 31, 1-2.