Publications and Pre-prints

2024
Age-related dysregulation of the retinal transcriptome in African turquoise killifish.

Bergmans S, Noel NCL, Harding EG, Krzywanska AM, De Schutter JD, Ayana R, Hu CK, Arckens L, Ruzycki PA, MacDonald RB#, Clark BS#, Moons L#. 2024 bioRxiv. doi: https://doi.org/10.1101/2024.02.21.581372

# Co-corresponding Authors
Cellular heterogeneity in the developing forebrain masks transcriptional outcomes and principles of Evf2 enhancer lncRNA-Dlx5/6UCE-gene guidance.

Li E, Chakraborty A, Kohtz SJ, Cajigas I, Shiau F, Vassar R, Clark BS#, Kohtz JD#. 2024 bioRxiv. doi: https://doi.org/10.1101/2024.02.20.581236

# Co-corresponding Authors
2023
Dry eye disease in mice activates adaptive corneal epithelial regeneration distinct from constitutive renewal in homeostasis.

Lin JB, Shen X, Pfeifer CW, Shiau F, Santeford A, Ruzycki PA, Clark BS, Liu Q, Huang AJW, Apte RS. PNAS. 2023 Jan 10; 120(2):e2204134120. doi: 10.1073/pnas.2204134120. PMID: 36595669



2021
Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina

Lyu P, Hoang T, Santiago CP, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza DF, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, Blackshaw S. Cell Rep. 2021 Nov 16;37(7):109994. doi: 10.1016/j.celrep.2021.109994. PMID: 34788628
A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

Shiau F, Ruzycki PA, Clark BS. Dev Biol. 2021 doi: 10.1016/j.ydbio.2021.06.005. PMID: 34146533
Atoh7-independent specification of retinal ganglion cell identity.

Brodie-Kommit J*, Clark BS*, Shi Q, Shiau F, Kim DW, Langel J, Sheely C, Ruzycki PA, Fries M, Javed A, Cayouette M, Schmidt T, Badea T, Glaser T, Zhao H, Singer J, Blackshaw S, Hattar S. Science Advances. 2021 Mar 12;7(11). doi: 10.1126/sciadv.abe4983. PMID: 33712461
*Co-first authors
Dynamic Polarization of Rab11a Modulates Crb2a Localization and Impacts Signaling to Regulate Retinal Neurogenesis.

Clark BS, Miesfeld JB, Flinn MA, Collery RF, Link BA. Front Cell Dev Biol. 2021 Feb9;8:608112. doi: 10.3389/fcell.2020.608122. PMID: 33634099
A Casz1-NuRD complex regulates temporal identity transitions in neural progenitors

Mattar P, Jolicoeur C, Dang T, Shah S, Clark BS, Cayouette M. Sci Rep. 2021 Feb16; 11(1):3858. doi: 10.1038/s41598-021-83395-7. PMID: 33594190
2020
Zeb2 regulates the balance between retinal interneurons and muller glia by inhibition of BMP-Smad signaling

Menuchin-Lasowski Y, Dagan B, Conidi A, Cohen-Gulkar M, David A, Ehrlich M, Giladi PO, Clark BS, Blackshaw S, Shapira K, Huylebroeck D, Henis Y, Ashery-Padan R. Dev Biol. 2020 Sep 17:S0012-1606(20)30255-4. doi: 10.1016/j.ydbio.2020.09.006. PMID: 32950463
Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease.

Ray TA, Cochran K, Kozlowski C, Wang J, Alexander G, Cady MA, Spencer WJ,  Ruzycki PA, Clark BS, Laeremans A, He MX, Wang X, Park E, Hao Y, Iannaccone A, Hu G, Fedrigo O, Skiba NP, Arshavsky VY, Kay JN.Nat Commun. 2020 Jul 3;11(1):3328. doi: 10.1038/s41467-020-17009-7.PMID: 32620864
Single-cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development.

Lu Y*, Shiau F*, Yi W*, Lu S, Wu Q, Pearson JD, Kallman A, Zhong S, Hoang T, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O’Brien GL, Sherman TD, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T, Bremner R, Blackshaw S, Wang X, Clark BS#. Dev Cell. 2020 May 18:53(4):473-491.e9. doi: 10.1016/j.devcel.2020.04.009. Epub 2020 May 7.PMID: 32386599 * – Co-first Authors; # – Corresponding Author
ASCOT identifies key regulators of neuronal subtype-specific splicing.

Ling JP, Wilks C, Charles R, Leavey PJ, Ghosh D, Jiang L, Santiago CP, Pang B, Venkataraman A, Clark BS, Nellore A, Langmead B, Blackshaw S. Nat Commun. 2020 Jan 9;11(1):137. doi:10.1038/s41467-019-14020-5.PMID: 31919425
2019

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.

Clark BS*, Stein-O’Brien GL*, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S.Neuron. 2019 Jun 19;102(6):1111-1126.e5. doi: 10.1016/j.neuron.2019.04.010. Epub 2019 May 22.PMID: 31128945
Neuron Cover
*Co-first authors

Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.

Stein-O’Brien GL*, Clark BS*, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ.Cell Syst. 2019 May 22;8(5):395-411.e8. doi: 10.1016/j.cels.2019.04.004.PMID: 31121116
*Co-first authors
2006-2018

Ldb1- and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in the retina.

de Melo J, Clark BS, Venkataraman A, Shiau F, Zibetti C, Blackshaw S.Development. 2018 Apr 30;145(9):dev159970. doi: 10.1242/dev.159970.PMID: 29650591.

A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors.

Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain 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, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S.Nat Methods. 2018 May;15(5):330-338. doi: 10.1038/nmeth.4632. Epub 2018 Mar 19.PMID: 29638227.

Understanding the Role of lncRNAs in Nervous System Development.

Clark BS, Blackshaw S.Adv Exp Med Biol. 2017;1008:253-282. doi: 10.1007/978-981-10-5203-3_9.PMID: 28815543.Review.

SHH E176/E177-Zn2+ conformation is required for signaling at endogenous sites.

Himmelstein DS, Cajigas I, Bi C, Clark BS, Van Der Voort G, Kohtz JD.Dev Biol. 2017 Apr 15;424(2):221-235. doi: 10.1016/j.ydbio.2017.02.006. Epub 2017 Mar 2.PMID: 28263766.

Control of lens development by Lhx2-regulated neuroretinal FGFs.

Thein T, de Melo J, Zibetti C, Clark BS, Juarez F, Blackshaw S.Development. 2016 Nov 1;143(21):3994-4002. doi: 10.1242/dev.137760. Epub 2016 Sep 15.PMID: 27633990.

Multiple intrinsic factors act in concert with Lhx2 to direct retinal gliogenesis.

de Melo J, Clark BS, Blackshaw S.Sci Rep. 2016 Sep 8;6:32757. doi: 10.1038/srep32757.PMID: 27605455.

Lhx2 Is an Essential Factor for Retinal Gliogenesis and Notch Signaling.

de Melo J, Zibetti C, Clark BS, Hwang W, Miranda-Angulo AL, Qian J, Blackshaw S.J Neurosci. 2016 Feb 24;36(8):2391-405. doi: 10.1523/JNEUROSCI.3145-15.2016.PMID: 26911688.

Yap and Taz regulate retinal pigment epithelial cell fate.

Miesfeld JB, Gestri G, Clark BS, Flinn MA, Poole RJ, Bader JR, Besharse JC, Wilson SW, Link BA.Development. 2015 Sep 1;142(17):3021-32. doi: 10.1242/dev.119008. Epub 2015 Jul 24.PMID: 26209646.

Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling.

Cajigas I, Leib DE, Cochrane J, Luo H, Swyter KR, Chen S, Clark BS, Thompson J, Yates JR 3rd, Kingston RE, Kohtz JD.Development. 2015 Aug 1;142(15):2641-52. doi: 10.1242/dev.126318. Epub 2015 Jul 2.PMID: 26138476.

Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease.

Clark BS, Blackshaw S.Front Genet. 2014 Jun 6;5:164. doi: 10.3389/fgene.2014.00164. eCollection 2014.PMID: 24936207.Review.

Mirror-symmetric microtubule assembly and cell interactions drive lumen formation in the zebrafish neural rod.

Buckley CE, Ren X, Ward LC, Girdler GC, Araya C, Green MJ, Clark BS, Link BA, Clarke JD.EMBO J. 2013 Jan 9;32(1):30-44. doi: 10.1038/emboj.2012.305. Epub 2012 Nov 30.PMID: 23202854.

Integrin α5/fibronectin1 and focal adhesion kinase are required for lens fiber morphogenesis in zebrafish.

Hayes JM, Hartsock A, Clark BS, Napier HR, Link BA, Gross JM.Mol Biol Cell. 2012 Dec;23(24):4725-38. doi: 10.1091/mbc.E12-09-0672. Epub 2012 Oct 24.PMID: 23097490.

JD induced pluripotent stem cell-derived hepatocytes faithfully recapitulate the pathophysiology of familial hypercholesterolemia.

Cayo MA, Cai J, DeLaForest A, Noto FK, Nagaoka M, Clark BS, Collery RF, Si-Tayeb K, Duncan SA.Hepatology. 2012 Dec;56(6):2163-71. doi: 10.1002/hep.25871. Epub 2012 Sep 17.PMID: 22653811.

Loss of Llgl1 in retinal neuroepithelia reveals links between apical domain size, Notch activity and neurogenesis.

Clark BS, Cui S, Miesfeld JB, Klezovitch O, Vasioukhin V, Link BA.Development. 2012 May;139(9):1599-610. doi: 10.1242/dev.078097.PMID: 22492354.

Generation of Rab-based transgenic lines for in vivo studies of endosome biology in zebrafish.

Clark BS, Winter M, Cohen AR, Link BA.Dev Dyn. 2011 Nov;240(11):2452-65. doi: 10.1002/dvdy.22758. Epub 2011 Oct 4.PMID: 21976318.

Balanced Shh signaling is required for proper formation and maintenance of dorsal telencephalic midline structures.

Himmelstein DS, Bi C, Clark BS, Bai B, Kohtz JD.BMC Dev Biol. 2010 Nov 29;10:118. doi: 10.1186/1471-213X-10-118.PMID: 21114856.

The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator.

Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD.Genes Dev. 2006 Jun 1;20(11):1470-84. doi: 10.1101/gad.1416106. Epub 2006 May 16.PMID: 16705037.