Johns Hopkins School of Medicine

Blackshaw S, Qian J, and Hyde D. New pathways to neurogenesis: insights from injury-induced retinal regeneration. Bioessays 2024 e2400133.

Le N, Pulya R, Palazzo I, Kim Y, Blackshaw S*, and Hoang T* (*indicates corresponding author).  Generation of retinal neurons from mammalian Muller glia by suppression of Notch signaling.  Science Advances 2024 10:eadn2091.

Qian C, Xin Y, Qi C, Wang H, Dong BC, Zack D, Blackshaw S, Hattar S, Zhou F, and Qian J.  Intercellular communication analysis identifies Oprm1 as a neuroprotective factor for retinal ganglion cells. Nature Communications 2024 15:2206.

Emmerich K, Hageter J, Hoang T, Liu P, Ceisel A, Thierer J, Chunawala Z, Nimmagadda Z, Palazzo I, Matthews F, Zhang L, White DT, Rodriquez R, Graziano G, Marcos P, May A, Mulligan T, Reibman B, Saxena MT, Qian J, Blackshaw S, Horstick, and Mumm JS. Molecular regulation of retinal regeneration is context-specific. Development 2024 dev.202754.

Lyu P, Iribarne M, Serjanov D, Zhai Y, Hoang T, Palazzo I, Qian J, Hyde DR, and Blackshaw S. Convergent and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. Nature Communications, 2023 14:8477

Hoang T, Kim DW, Appel H, Ozawa M, Zheng S, Kim J, and Blackshaw S.  Ptbp1 deletion does not induce astrocyte-to-neuron conversion in adult mouse brain.  Nature, 2023 618 E1:7.

Santiago CP, Gimmen M, Lu Y, McNally M, Duncan LH, Creamer TJ, Orzolek LD, Blackshaw S* and Singh M* (*indicates corresponding author).  Comparative analysis of single-cell and single-nucleus RNA-sequencing in a rabbit model of induced proliferative vitreoretinopathy. Ophthal Sci, 2023 3:100335.

Zhang X, Leavey P, Appel H, Makrides N, and Blackshaw S. Molecular mechanisms controlling vertebrate retinal patterning, neurogenesis, and cell fate specification.  Trends in Genetics 2023, 39:736-757.

Liu YV, Santiago CP, Sogunro A, Konar GK, Hu MW, McNally MM, Lu Y, Li Z, Agakishiev D, Hussey K, Hadyniak S, Teng D, Qian J, Jiang Z, Johnston RJ Jr.*, Blackshaw S*, Singh MS* (*indicates corresponding author).  Transretinal invasion of astrocytes and brain/spinal cord-like cells arising from transplanted human retinal organoids. Stem Cell Reports, 2023 5:1138-54.

Le N, Appel H, Pannullo N, Hoang T, and Blackshaw S. Ectopic insert-dependent neuronal expression of GFAP promoter-driven AAV constructs in adult mouse retina. Frontiers in Cell and Developmental Biology 2022, doi: 10.3389/fcell.2022.914386. 

Ling J, Bygrave A, Santiago CP, Trinh V, Carmen R, Yu M, Li Y, Han J, Taneja K, Liu Y, Dongmo R, Babola T, Parker P, Jiang L, Leavey P, Smith J, Vistein R, Gimmen M, Dubner B, Teodorescu P, Kanold P, Bergles D, Langmead B, Sun S, Nielsen K, Peachey N, Singh M, Dalton W, Rajaii F, Huganir R, and Blackshaw S. Cell-specific regulation of gene expression using splicing-dependent frameshifting. Nature Communications (2022) 13:5773.

Kim DW, Place E, Chinnaiya K, Manning E, Sun C, Dai W, Burbridge S, Placzek M, and Blackshaw S. Single cell analysis of early hypothalamic regionalization and neurogenesis in chick.  Cell Reports (2022) 38:110251.

Blackshaw S.  Why has the ability to regenerate following CNS injury been repeated lost during the course of evolution?  Front Insight (2022) 6:831062.

Hoang T, Kim DW, Appel H, Panullo N, Leavey P, Ozawa M, Zheng S, Yu M, Peachey P, Kim J, and Blackshaw S.  Ptbp1 deletion does not induce glia-to-neuron conversion in adult mouse retina.  Cell Reports (2022) 11:110849.

Kim DW, Liu K, Wang ZQ, Zhang YS, Bathini A, Brown MP, Lin SH, Washington PW, Sun C, Lindtner S, Lee B, Wang H, Shimogori T, Rubenstein JLR, and Blackshaw S. Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6 neurons. Comm Bio (2021) 4:95.

Brodie-Kommit J, Brian S. Clark BS, Shi Q, Shiau F, Kim DW, Langel J, Sheely C, Schmidt T, Badea T, Glaser T, Zhao H, Singer J, Blackshaw S*, and Hattar S* (*indicates corresponding author). Atoh7-independent specification of retinal ganglion cell identity. Sci Advances (2021)7:eabe4983.

Lyu P, Hoang T, Santiago CP, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza D, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, and Blackshaw S.  Integrated multiomic analysis identifies gene regulatory networks controlling temporal patterning, neurogenesis and cell fate specification in the mammalian retina. Cell Reports (2021) 37:109994.

Yoo S,  Kim J, Lyu P, Hoang TV, Ma A, Trinh V, Dai W, Jiang L, Leavy P, Won JK, Park SH, Qian J, Brown SP, and Blackshaw S. Control of neurogenic competence in mammalian hypothalamic tanycytes. Science Advances (2021) 7:eabg3777.

Hoang T, Wang J, Boyd P, Wang F, Santiago C, Jiang L, Lahne M, Todd LJ, Saez C, Yoo S, Keuthan C, Palazzo I, Squires N, Campbell WA , Jia M, Rajaii F, Payail T, Wang G , Ash J, Fischer AJ, Hyde DR, Qian J, and Blackshaw S. Cross-species transcriptomic and epigenomic analysis reveals key regulators of injury response and neuronal regeneration in vertebrate retinas.  Science (2020) 370(6519):eabb8598.

Kim DW, Washington PW, Wang ZQ, Lin S, Sun C, Jiang L, and Blackshaw S.  The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development.  Nat Comm (2020) 11:4360.

Ling JP, WilksC, CharlesR, GhoshD, JiangL, SantiagoCP, PangB, VenkataramanA, ClarkBS, NelloreA, LangmeadB, and Blackshaw S. ASCOT identifies key regulators of neuronal subtype-specific RNA splicing.  Nat Comm (2020) 11:37.

Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson J, Kallman A, Hoang T, Zhong S, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O’Brien GL, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T*, Bremner R*, Blackshaw S*, Wang X* and Clark BS* (* indicates corresponding author).  Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development.  Dev Cell (2020) 53:473-491. 

Clark BS, Stein-O’Brien GL, Shiau F, Cannon GH, Davis E, Sherman T, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, and Blackshaw S.   Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells.  Neuron (2019) 102:1111-1126.

Zibetti C, Liu S, Wan J, Qian J, and Blackshaw S.  Lhx2 regulates temporal changes in chromatin accessibility and transcription factor binding in retinal progenitor cells.  Comm Biology (2019) 2:142.

Yoo S, Cha D, Kim DW, Hoang T, and Blackshaw S.  Tanycyte-independent regulation of leptin signaling. Frontiers in Neuroscience (2019) https ://doi.org/10.3389/fnins.2019.00240

Newman EA, Wan J, Wang J, Jiang, Qian J, and Blackshaw S. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. Dev Biol (2018) 439:102-111.

Newman EA, Wu D, Makoto MM, Zhang J, and Blackshaw S.  Canonical Wnt signaling regulates patterning, differentiation and nucleogenesis in mouse hypothalamus and prethalamus. Dev Biol (2018) 442:236-248.

Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Ji H, Merbs SL, Zack DJ, Handa J, Sinha D, Blackshaw S* and Qian J*.  A widespread decrease in chromatin accessibility in age-related macular degeneration.  Nat Comm (2018) 9:1364 (* indicates co-corresponding author).

de Melo J, Venkataraman A, Clark BS, Shiau F, Zibetti C, and Blackshaw S.  Ldb1 and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in retina.  Development (2018) 145. pii: dev159970. doi: 10.1242/dev.159970

Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang K Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Seva G. Khambadkone5, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Anderson S, Myers RM, Boeke JD, Fenyo D,  Whiteley G, Bader JS, Pino  I, Eichinger  DJ, Zhu H, and Blackshaw S.  A toolbox of immunoprecipitation-grade monoclonal antibodies against human transcription factors.  Nat Methods (2018)  doi: 10.1038/nmeth.4632.

Liu K, Kim J, Kim DW, Zhang S, Denaxa M, Bao H, Lim SA, Kim E, Liu C, Wickersham IR, Pachinis V, Hattar S, Song J, Brown SR, and Blackshaw S. Lhx6-positive GABAergic neurons of the zona incerta promote sleep.  Nature (2017) 548:582-587.

Bedont JL, LeGates TA, Buhr E, Bathini A, Ling J, Wong P, van Gelder R, Mongrain V, Hattar  S, and Blackshaw S, An Lhx1-Regulated Transcriptional Network Controls Sleep-Wake Coupling and Thermal Resistance of the Central Circadian Clockworks.  Curr Biol (2017) 27:128-136.

De Melo J, Zibetti C, Clark BS, Hwang W, Miranda-Angulo AL, Qian J, Blackshaw S. Lhx2 Is an Essential Factor for Retinal Gliogenesis and Notch Signaling.  J Neurosci (2016) 36:2391-405.

Thein T, de Melo J, Zibetti C, Clark BS, Juarez F, and Blackshaw S.  Control of lens development by Lhx2-regulated neuroretinal FGFs.   Development (2016) 143: 3994-4002

Bedont JL, LeGates TA, Slat EA , Byerly MS, Wang H, Hu J, Rupp AC, Qian J, Wong GW, Herzog ED, Hattar S, and Blackshaw S.  Lhx1 controls terminal differentiation and circadian function of the suprachiasmatic nucleus. Cell Reports (2014) 7:609-22.

De Melo J, Miki K, Rattner A, Smallwood P, Hirokawa K, Monuki ES, Campochario P, and Blackshaw S.  Injury-independent induction of reactive gliosis in retinal Muller glia by loss of function of the LIM homeodomain transcription factor Lhx2.  Proc Natl Acad Sci USA (2012) 109:4657-62.

Lee DA, Pak T, Bedont JL, Wang H, Miranda-Angulo A, Takiar V, Charubhumi V, Balordi F, Takebayashi H, Fishell G, Ford E and Blackshaw S.  Tanycytes of the median eminence form a dietary-responsive neurogenic niche.  Nat Neurosci (2012) 15:700-2.

Shimogori T, Lee D A, Miranda-Angulo A, Yang Y, Yoshida A, Jiang L, Kataoka A, Wang H, Mashiko H,  Avetisyan M A, Qi L, Qian J, and Blackshaw S.  A genomic atlas of mouse hypothalamic development. Nat Neurosci (2010) 13:767-75.