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Rosenstein A, Sambathkumar R, Murareanu B, Dhaliwal N, Sun F, Zhao X, Dadvar A, Al-attar R, Chai A, Gulati N, Yin T, Nguyen M, Serra D, Devina T, Gilbert PM, Kunath T, Laflamme M, Ogawa S, Muffat J, Li Y, Protze S, Nostro C and Garton MJ. FAST-STEM: A human pluripotent stem cell engineering toolkit for rapid design-build-test-learn development of human cell-based therapeutic devices. bioRxiv. 2024 May 24.

*Dhaliwal NK, *Weng OY, Dong X, Ahmed M, Bhattacharya A, Nishimura H, Aggarwal A, Choi WWY, Shu Q, Li X, Wilson MD, Moffat J, Wang LY, Muffat J and Li Y. Synergistic hyperactivation of both mTORC1 and mTORC2 underlies the neural abnormalities of PTEN-deficient human neurons and brain organoids. Cell Reports. 2024 May 2.*Co-first authors.

Wang WX, Douglas TR, Zhang H, Bhattacharya A, Rothenbroker M, Tang W, Sun Y, Jia Z, Muffat J, Li Y and Chou LYT. origamiFISH allows universal, label-free single molecular visualization of DNA origami nanodevices across biological samples. Nature Nanotechnology. 2023 July 27.

Ahmed M, Muffat J, Li Y. Understanding neural development and diseases using CRISPR screens in human pluripotent stem cell-derived cultures. Frontiers in Cell and Developmental Biology. 2023 April 10, 10:1158373.

*Bhattacharya A, *Choi WWY, Muffat J, Li Y. Modeling developmental brain diseases using human pluripotent stem cells-derived brain organoids – progress and perspective. Journal of Molecular Biology. 2021 December 6:167386.

*Dhaliwal N, *Choi WWY, Muffat J, Li Y. Modeling PTEN overexpression induced microcephaly in human brain organoids. Molecular Brain. 2021 August 30; 14: 131.

Osborne J, Salta E, Hu H, Shook B, Li Y, Kannan N. Introduction to the community: early-career researchers in the time of COVID-19. Cell Stem Cell. 2021 March 4; 28 (3): 367-369.

Tian A, Muffat J, Li Y. Studying Human Neurodevelopment and Diseases Using 3D Brain Organoids. Journal of Neuroscience. 2020 Feb 5;40(6):1186-1193.

*Li Y, *Muffat J, *Omer Javed A, *Keys HR, Lungjangwa T, Bosch I, Khan M, Virgilio MC, Gehrke L, Sabatini DM, Jaenisch R. Genome-wide CRISPR screen for Zika virus resistance in human neural cells. Proceedings of the National Academy of Sciences USA. 2019 May 7;116(19):9527-9532.

*Omer-Javed A, *Li Y, *Muffat J, Su KC, Cohen MA, Lungjangwa T, Aubourg P, Cheeseman IM, and Jaenisch R. Microcephaly modeling of kinetochore mutation reveals a brain-specific phenotype. Cell Reports. 2018 Oct 9; 25: 368-382.

*Muffat J, *Li Y, *Omer A, Durbin A, Bosch I, Bakiasi G, Gehrke L, and Jaenisch R. Human induced pluripotent stem cell-derived glial cells and neural progenitors display divergent responses to Zika and dengue infections. Proceedings of the National Academy of Sciences USA2018 Jul 3; 115 (27): 7117-7122.

Liu XS, Wu H, Krzisch M, Wu X, Graef J, Muffat J, Hnisz D, Li CH, Yuan B, Xu C, Li Y, Vershkov D, Cacace A, Young RA, and Jaenisch R. Rescue of Fragile X syndrome neurons by DNA methylation editing of the FMR1 gene. Cell. 2018 Feb 22; 172(5): 979-992.e6.

Mellios N, Feldman DA, Sheridan SD, Ip J, Kwok S, Amoah SK, Rosen B, Rodriguez BA, Crawford B, Swaminathan R, Chou S, Li Y, Ziats M, Ernst C, Jaenisch R, Haggerty SJ, and Sur M. MECP2-regulated miRNAs control early human neurogenesis through differential effects on ERK and AKT signaling. Molecular Psychiatry. 2018 Apr; 23 (4): 1051-1065.

*Li Y, *Muffat J, Omer A, Bosch I, Lancaster M, Sur M, Gehrke L, Knoblich J, and Jaenisch R. Induction of expansion and folding in human cerebral organoids. Cell Stem Cell. 2017 Mar 2; 20(3): 385-396.e3.

*Muffat J, *Li Y, and Jaenisch R. CNS disease models with human pluripotent stem cells in the CRISPR age. Current Opinion in Cell Biology. 2016 Dec; 43:96-103.

*Muffat J, *Li Y, Yuan B, Mitalipova M, Omer A, Corcoran S, Bakiasi G, Tsai LH, Aubourg P, Ransohoff RM, and Jaenisch R. Efficient derivation of microglia-like cells from human pluripotent stem cells. Nature Medicine. 2016 Nov; 22(11): 1358-1367.

Li Y, Wang H, Muffat J, Cheng AW, Orlando DA, Loven J, Kwok S, Feldman DA, Bateup HS, Gao Q, Hockemeyer D, Mitalipova M, Lewis CA, Vander Heiden MG, Sur M, Young RA, and Jaenisch R. Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett Syndrome neurons. Cell Stem Cell. 2013 Oct; 13(4): 446-458.

Li Y, Yui D, Luikart BW, McKay R, Li Y, Rubenstein JL, and Parada LF. Conditional ablation of brain-derived neurotrophic factor-TrkB signaling impairs striatal neuron development. Proceedings of the National Academy of Sciences USA. 2012 Sep; 109(38): 15491-6.

Sanchez-Ortiz E, Yui D, Song D, Li Y, Rubenstein JL, Reichardt LF, and Parada LF. TrkA gene ablation in basal forebrain results in dysfunction of the cholinergic circuitry. Journal of Neuroscience. 2012 Mar; 32(12), 4065-4079.

Li Y, Li Y, McKay, RM, Riethmacher D, and Parada LF. Neurofibromin modulates adult hippocampal neurogenesis and behavioral effects of antidepressants. Journal of Neuroscience. 2012 Mar; 32(10), 3529-3539.

*Choi SH, and *Li Y. Elevated levels of BMP6 impair neurogenesis in Alzheimer’s disease. Journal of Neuroscience. 2011 Jan; 31(2): 371-372.

Luikart, BW, Bensen AL, Washburn EK, Perederiy JV, Su KG, Li Y, Kernie SG, Parada LF, and Westbrook GL. miR-132 mediates the integration of newborn neurons into the adult dentate gyrus. PLoS One. 2011; 6(5): e19077.

Choi SH, Li Y, Parada LF, and Sisodia SS. Regulation of hippocampal progenitor cell survival, proliferation and dendritic development by BDNF. Molecular Neurodegeneration. 2009 Dec 21; 4, 52.

Li Y, Luikart BW, Birnbaum S, Chen J, Kwon CH, Kernie SG, Bassel-Duby R, and Parada LF. TrkB regulates hippocampal neurogenesis and governs sensitivity to antidepressive treatment. Neuron. 2008 Aug 14; 59(3), 399-412.

*Lush ME, *Li Y, Kwon CH, Chen J, and Parada LF. Neurofibromin is required for barrel formation in the mouse somatosensory cortex. Journal of Neuroscience. 2008 Feb 13; 28(7), 1580-1587.