Papers
Preprints
2024
Benman W#, Huang Z#, Iyengar P, Wilde D, Mumford TR, Bugaj LJ*. (2024). A temperature-inducible protein module for control of mammalian cell fate. bioRxiv. 10.1101/2024.02.19.581019. bioRxiv Tweetorial
Benman W#, Iyengar P, Mumford TR, Bugaj LJ*. (2024). Multiplexed dynamic control of temperature to probe and observe mammalian cells. bioRxiv. 10.1101/2024.02.18.580877 bioRxiv
2022
Huang, Z, Benman W, Dong L, Bugaj LJ*. (2024) Rapid optogenetic clustering in the cytoplasm with BcLOVclust. Journal of Molecular Biology. 436(3):168452. link bioRxiv Tweetorial.
Pal AA#, Benman W#, Mumford TR, Chow BY, Bugaj LJ*. (2023) Optogenetic clustering and membrane translocation of the BcLOV4 photoreceptor. PNAS. link bioRxiv Tweetorial
Mumford TR, Rae D, Idris A, Gonzalez-Martinez D, Pal AA, Bugaj LJ*. (2024) Simple detection of submicroscopic protein clusters with a phase-separation-based fluorescent reporter. Cell Systems. 15(2):166-179.e7 link bioRxiv Tweetorial Penn GEN
Benman W#, Datta S#, Gonzalez-Martinez D, Lee G, Hooper J, Qian G, Leavitt G, Salloum L, Ho G, Mhatre S, Magaraci MS, Patterson M, Mannickarottu SG, Malani S, Avalos JL, Chow BY, Bugaj LJ*. (2023) High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates. Communications Biology, 6, 1192. doi: 10.1038/s42003-023-05532-4. link bioRxiv Tweetorial
Gonzalez-Martinez D#, Roth L#, Mumford TR, Guan J, Huang B, Tulpule A, Bivona TG, Bugaj LJ*. (2022). Oncogenic protein condensates modulate growth factor perception and drug tolerance. bioRxiv. doi:10.1101/2022.02.02.478845. bioRxiv Tweetorial
Chan A, Wang HH, Haley RM, Song C, Gonzalez-Martinez D, Bugaj LJ, Mitchell MJ*, Tsourkas A*. (2022). Cytosolic delivery of small protein scaffolds enables efficient inhibition of Ras and Myc. Molecular Pharmaceutics. doi: 10.1021/acs.molpharmaceut.1c00798 link
Peer-reviewed
2024
2023
2022
Benman W, Berlew EE, Deng H, Parker C, Kuznetsov IA, Lim B, Siekmann AF, Chow BY, Bugaj LJ*. (2022). Temperature-responsive optogenetic probes of cell signaling. Nature Chemical Biology. doi: 10.1038/s41589-021-00917-0 link Tweetorial Penn News and Views
Truong ME, Bilekova S, Choksi SP, Li W, Bugaj LJ, Xu K, Reiter JF*. (2021). Vertebrate cells differentially interpret ciliary and extraciliary cAMP. Cell. 184 (11), 2911-2926. doi: 10.1016/j.cell.2021.04.002. link
O’Donoghue GP, Bugaj LJ, Anderson W, Daniels KG, Rawlings DJ, Lim WA*. (2021). T cells selectively filter oscillatory signals on the minutes timescale. PNAS. 118(9). doi: 10.1073/pnas.2019285118. link
2021
Berlew EE, Kuznetsov, Yamada KK, Bugaj LJ, Boerckel JD, Chow BY*. (2021). Single-component optogenetic tools for inducible Rho GTPase signaling. Advanced Biology. 5, 2100810. doi: 10.1002/adbi.202100810 link
2020
Rosenbloom AB, Tarczynski M, Lam N, Kane RS*, Bugaj LJ*, Schaffer DV*. (2020). β-catenin Signaling Dynamics Regulate Cell Fate in Differentiating Neural Stem Cells. PNAS. Nov 2020, 202008509. doi: 10.1073/pnas.2008509117. link Tweetorial
Mumford TR, Roth L, Bugaj LJ*. (2020) Reverse and Forward Engineering Multicellular Structures with Optogenetics. Current Opinion in Biomedical Engineering. doi: 10.1016/j.cobme.2020.100250. link
Chen SY, Osimiri LC, Chevalier MW, Bugaj LJ, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H*. (2020). Optogenetic control reveals differential promoter interpretation of transcription factor nuclear translocation dynamics. Cell Systems. doi: 10.1016/j.cels.2020.08.009. link
Berlew EE, Kuznetsov IA, Yamada K., Bugaj LJ, Chow BY* (2020). Optogenetic Rac1 engineered from membrane lipid-binding RGS-LOV for inducible lamellipodia formation. Photochemical and Photobiological Sciences. doi: 10.1039/c9pp00434c. link
Bugaj LJ* and Lim WA. (2019). High-throughput multicolor optogenetics in microwell plates. Nature Protocols. doi: 10.1038/s41596-019-0178-y. link Tweetorial
2019
2018
Bugaj LJ, Sabnis AJ, Mitchell A, Garbarino JE, Toettcher JE*, Bivona TG*, Lim WA*. (2018) Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras/Erk pathway. Science. Aug 31. link Tweetorial News and Views
2017
Bugaj LJ, O’Donoghue GP, Lim WA*. (2017) Interrogating Cellular Perception and Decision Making with Optogenetic Tools. J Cell Biol. Dec 21. link
2016
Gordley RM, Bugaj LJ, Lim WA*. (2016) Modular engineering of cellular signalling proteins and networks. Curr Opin Struct Biol. 13(39), 106-114. link
2015
Bugaj LJ, Mesuda CK, Varedi M, Kane RS*, Schaffer DV*. (2015) Regulation of endogenous transmembrane receptors through optogenetic Cry2 clustering. Nature Communications. 6, Article 6898. link
2014
Yousef H, Morgenthaler A, Schlesinger C, Bugaj LJ, Conboy I*, Schaffer DV*. (2014). Age-Associated Increase in BMP Signaling inhibits Hippocampal Neurogenesis. Stem Cells. Published Online 12/1/2014. link
Yousef H, Conboy M, Morgnethaler A, Schlesinger C, Bugaj LJ, Paliwal P, Greer C, Conboy I*, Schaffer DV*. (2014). Systemic attenuation of TGF-β1 pathway in old mice simultaneously rejuvenates neurogenesis and myogenesis by down-modulating MHC I β2 microglobulin. Oncotarget. 6(14), 11959-11978. link
2013
Bugaj LJ, Choksi AT, Mesuda CK, Kane RS*, Schaffer DV*. (2013). Optogenetic protein clustering and signaling activation in mammalian cells. Nature Methods. 10(3), 249-25. link
Cao J, Arha M, Sudrik C, Bugaj LJ, Schaffer DV, Kane RS*. (2013). Light-inducible Activation of Target mRNA Translation in Mammalian Cells. Chem Commun, 49(75), 8338-8340. link
2012
Bugaj LJ and Schaffer DV*. (2012). Bringing next generation therapeutics to the clinic through synthetic biology. Curr Opin Chem Biol. 16(3-4), 355-361. link
Khan M, Steppan J, Schuleri K, Ryoo S, Tuday E, Bugaj L, Santhanam L, Berkowitz T, Nyhan D, Shoukas AA, Berkowitz DE*. (2012) Upregulation of arginase-II contributes to decreased age-related myocardial contractile reserve. Eur J Appl Physiol. 112(8), 2933-2941. link
White AR, Ryoo S, Bugaj L, Attarzadeh DO, Thiyagarajan S, Chen K, Attwater S, Abbot B, Li D, Champion HC, Shoukas AA, Nyhan D, Hare JM, Berkowitz DE, Tuday EC*. (2010). Early changes in vasoreactivity after simulated microgravity are due to an upregulation of the endothelium-dependent nitric oxide/cGMP pathway. Eur J Appl Physiol. 110(2), 395-404. link
2010
2009
Kim JH, Bugaj LJ, Bivalacqua T, Ryoo SS, Oh YJ, Soucy KG, Santhanam L, Camara A, Sikka G, Nyhan D, Shoukas AA, Champion HC, Berkowitz DE*. (2009). Arginase Inhibition Restores NOS Coupling and Reverses Endothelial Dysfunction and Vascular Stiffness in Old Rats. J Appl Physiol. 107(4), 1249-57. link
2006
Steppan J, Ryoo S, Schuleri KH, Gregg C, Hasan RK, White AR, Bugaj LJ, Khan M, Santhanam L, Nyhan D, Shoukas A, Hare J, Berkowitz DE*. (2006). Arginase modulates myocardial contractility by a NOS-1 dependent mechanism. PNAS. 103(12),4759-4764. link