Romero M and Pyle AD. “Enhancing” Skeletal Muscle and Stem Cells in 3D: Genome regulation of skeletal muscle in development and disease. Current Opinion in Genetics & Development 2023, 83:102133

Hicks MR #, Saleh KK, Clock B, Gibbs DE, Yang M, Younesi S, Gane L, Guiterez-Garcia V, Xi H, Pyle AD #. Regenerating Human Skeletal Muscle Forms an Emerging Niche In Vivo to Support PAX7 cells. Nature Cell Biology. November 2 2023. # co-corresponding

Hicks MR#, Liu X#, Young CS, Saleh K, Ji Y, Jiang, J, Emami MR, Mokhonova E, Spencer MJ*, Meng H*, Pyle AD*. Nanoparticles systemically biodistribute to regenerating skeletal muscle in DMD. Journal of Nanobiotechnology volume 21, Article number: 303 (2023). #co-first, * co-corresponding

Emami MR, Espinoza, Young CS, Ma F, Farahat PK, Felgner PL, Chamberlain JS, Xu X, Pyle AD, Pellegrini M, Villalta A and Spencer MJ. Innate and adaptive AAV-mediated immune responses in a mouse model of Duchenne muscular dystrophy. Molecular Therapy, Methods and Clinical Development, Jun 8, 2023.

Jaime OG, Arias J, Pavani S, Pyle AD, Hicks MR. SIX1+PAX3+ identify a progenitor for myogenic lineage commitment from hPSCs. Development. 2023 Jun 27:dev.201509. doi: 10.1242/dev.201509. Online ahead of print.

Stearns-Reider KM, Hicks MR, Hammond KG, Reynolds JC, Maity A, Kurmangaliyev YZ, Chin J, Stieg AZ, Geisse NA, Hohlbauch S, Kaemmer S, Schmitt LR, Pham TT, Yamauchi K, Novitch BG, Wollman R, Hansen KC, Pyle AD, Crosbie RH. Myoscaffolds reveal laminin scarring is detrimental for stem cell function while sarcospan induces compensatory fibrosis.  NPJ Regen Med. 2023 Mar 15;8(1):16. doi: 10.1038/s41536-023-00287-2.

Gibbs DE, Pyle AD. Muscle fusogens go viral for gene delivery to skeletal muscle. Cell. 2023 May 11;186(10):2041-2043. doi: 10.1016/j.cell.2023.04.021.

Saleh KK, Switzler C, Hicks MR, Gane L, Gibbs DE, Pyle AD. Duchenne muscular dystrophy disease severity impacts skeletal muscle progenitor cells systemic delivery. Front Physiol. 2023 May 9;14:1190524. doi: 10.3389/fphys.2023.1190524. eCollection 2023.


Saleh KK, Xi H, Switzler C, Skuratovsky E, Romero MA, Chien P, Gibbs D, Gane L, Hicks MR, Spencer MJ, Pyle AD. Single cell sequencing maps skeletal muscle cellular diversity as disease severity increases in dystrophic mouse models.  iScience. 2022 Oct 21;25(11):105415. doi: 10.1016/j.isci.2022.105415. eCollection 2022 Nov 18.

Wei Y, Qin Q, Yan C, Hayes MN, Garcia SP, Xi H, Do D, Jin AH, Eng TC, McCarthy KM, Adhikari A, Onozato ML, Spentzos D, Neilsen GP, Iafrate AJ, Wexler LH, Pyle AD, Suvà ML, Dela Cruz F, Pinello L, Langenau DM. Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma. Nat Cancer. 2022 Aug;3(8):961-975. doi: 10.1038/s43018-022-00414-w. Epub 2022 Aug 18.

Hicks MR and Pyle AD. The emergence of the stem cell niche. Trends in Cell Biology. 2022 Aug 4;S0962-8924(22)00173-8. doi: 10.1016/j.tcb.2022.07.003.


Chien P, Xi H, Pyle AD. Recapitulating human myogenesis ex vivo using human pluripotent stem cells. Exp Cell Res. 2021 Dec 29:112990. doi: 10.1016/j.yexcr.2021.112990.

Petrigliano FA, Liu NQ, Lee S, Tassey J, Sarkar A, Lin Y, Li L, Yu Y, Geng D, Zhang J, Shkhyan R, Bogdanov J, Van Handel B, Ferguson GB, Lee Y, Hinderer S, Tseng KC, Kavanaugh A, Crump JG, Pyle AD, Schenke-Layland K, Billi F, Wang L, Lieberman J, Hurtig M, Evseenko D. Long-term repair of porcine articular cartilage using cryopreservable, clinically compatible human embryonic stem cell-derived chondrocytes. NPJ Regen Med 2021 Nov 23;6(1):77. doi: 10.1038/s41536-021-00187-3.

Nitzahn M, Truong B, Khoja S, Vega-Crespo A, Le C, Eliav A, Makris G, Pyle AD, Häberle J, Lipshutz GS. CRISPR-Mediated Genomic Addition to CPS1 Deficient iPSCs is Insufficient to Restore Nitrogen Homeostasis. Yale J Biol Med. 2021 Dec 29;94(4):545-557. eCollection 2021 Dec.

Harn H I-C, Wang S-P, Lai Y-C, Handel BV, Liang Y-C, Tsai S, Schiessl IM, Sarkar A, Xi H,  Hughes M, Kaemmer S, Tang MJ, Peti-Peterdi J, Pyle AD, Woolley TE, Evseenko D, Jiang T-X& Chuong C-M. Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration of laboratory and spiny mice. Nat. Communications. 2021 May 10;12(1):2595.


Xi H, Young CS, Pyle AD. Generation of PAX7 Reporter Cells to Investigate Skeletal Myogenesis from Human Pluripotent Stem Cells. STAR Protocols 1, Cell Press, 100158, December 18, 2020.

Liu J, Campagna J, John V,  Damoiseaux R,  Mokhonova E,  Becerra D, Meng H, McNally EM, Pyle AD, Kramerova I, Spencer MJ. A Small-Molecule Approach to Restore a Slow-Oxidative Phenotype and Defective CaMKIIBeta Signaling in Limb Girdle Muscular Dystrophy. Cell Reports Medicine.  Volume 1, ISSUE 7, 100122, October 20, 2020

Sengupta K, Mishra MK, Loro E, Spencer MJ, Pyle AD, Khurana TS. Genome editing-mediated Utrophin upregulation in Duchenne Muscular Dystrophy stem cells. Molecular Therapy – Nucleic Acids. 2020 Aug 29;22:500-509.

Xi H, Langerman J, Sabri S, Chien P, Young CS, Hicks M, Gonzalez K, Fujiwara W, Marzi J, Liebscher S, Spencer M, Van Handel B, Evseenko D, Schenke-Layland K, Plath K, Pyle AD.  A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells. Cell Stem Cell, May 11, 2020.PMID:32396864


Mosich GM, Husman R, Shah P, Sharma A, Rezzadeh K, Aderibigbe T, Hu VJ, McClintick DJ, Wu G, Gatto JD, Xi H, Pyle AD, Péault B, Petrigliano FA, Dar A.Non-fibro-adipogenic pericytes from human embryonic stem cells attenuate degeneration of the chronically injured mouse muscle.JCI Insight. 2019 Dec 19;4(24). pii: 125334. doi: 10.1172/jci.insight.125334.

Xi H, Pyle A. Beyond the genome: RNA control of stem cells.
Science. 2019 Nov 8;366(6466):684-685. doi: 10.1126/science.aaz4859. No abstract available.

Young CS, Pyle AD, Spencer MJ. CRISPR for Neuromuscular Disorders: Gene Editing and Beyond.Physiology (Bethesda). 2019 Sep 1;34(5):341-353. doi: 10.1152/physiol.00012.2019. Review.

Bellmann J, Goswami RY, Girardo S, Rein N, Hosseinzadeh Z, Hicks MR, Busskamp V, Pyle AD, Werner C, Sterneckert J. A customizable microfluidic platform for medium-throughput modeling of neuromuscular circuits. Biomaterials. 2019 Dec;225:119537.

Emami ME#, Young CS#, Ji Y#, Liu X, Mokhonova E, Pyle AD*, Meng H*, Spencer MJ*. Polyrotaxane Nanocarriers Can Deliver CRISPR/Cas9 Plasmid to Dystrophic Muscle Cells to Successfully Edit the DMD Gene. Advanced Therapeutics. June 3, 2019. # co-first, *co-corresponding


Hicks MR, Hiserodt J, Paras K, Fujiwara W, Eskin A, Jan M, Xi H, Young C, Evseenko D, Nelson S, Spencer M, Van Handel B, Pyle AD.  ERBB3 and NGFR mark a distinct skeletal muscle progenitor cell in human development and hPSCs.  Nature Cell Biology, 20, 46–57. Jan 1, 2018.

Ferguson GB, Van Handel B, Bay M, Fiziev P, Org T, Lee S, Shkhyan R, Banks NW, Scheinberg M, Wu L, Saitta B, Elphingstone J, Larson AN, Riester SM, Pyle AD, Bernthal NM, Mikkola HK, Ernst J, van Wijnen AJ, Bonaguidi M, Evseenko D. Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes. Nat Commun. 2018 Sep 7;9(1):3634.


Young CS, Mokhonova E, Quinonez M, Pyle AD, Spencer MJ. Creation of a Novel Humanized Dystrophic Mouse Model of Duchenne Muscular Dystrophy and Application of a CRISPR/Cas9 Gene Editing TherapyJ Neuromuscul Dis, 2017; 4(2):139-145.

Hazima RA, Karumbayaramb S, Dimashkiee A, Jianga M, Lopesa VS, Lia D, Burgessa BL, Vijayara P, Alva-Ornelas JA, Zack JA, Kohn DB, Gomperts BN, Pyle AD, Lowry WE, Williams D.  Differentiation of RPE cells from integration-free iPS cells and their cell biological characterization. Stem Cell Research & Therapy, 8:217, 2017.

Xi H, Fujiwara W, Gonzalez K, Jan M, Liebscher S, Van Handel B, Schenke-Layland K, Pyle AD.  In Vivo Human Somitogenesis Guides Somite Development from hPSCs.  Cell Reports.  18, 1-13. Feb 7, 2017.


Young CS, Hicks MR, Ermolova NV, Nakano H, Jan M, Younesi S, Karumbayaram S, Kumagai-Cresse C, Wang D, Zack JA, Kohn DB, Nakano A, Nelson SF, Miceli MC, Spencer MJ*, Pyle AD*. A Single CRISPR-Cas9 Deletion Strategy that Targets the Majority of DMD Patients Restores Dystrophin Function in hiPSC-Derived Muscle Cells, Cell Stem Cell, 2016; 18: 1-8. * co-corresponding

Lee PC, Truong B, Vega-Crespo A, Gilmore WB, Hermann K, Angarita SA, Tang JK, Chang KM, Wininger AE, Lam AK, Schoenberg BE, Cederbaum SD, Pyle AD, Byrne JA, Lipshutz GS.  Restoring Ureagenesis in Hepatocytes by CRISPR/Cas9-mediated Genomic Addition to Arginase-deficient Induced Pluripotent Stem Cells.  Mol Ther Nucleic Acids. 2016 Nov 29;5(11).

Young CS, Pyle AD.  Exon Skipping Therapy.  Cell. 2016 Nov 17;167(5):1144.


Thakore-Shah K, Koleilat T, Jan M, John A, Pyle AD. REST/NRSF Knockdown Alters Survival, Lineage Differentiation and Signaling in Human Embryonic Stem Cells, Plos One, 2015; 10(12). (link)

Hicks M, Pyle A. The Path from Pluripotency to Skeletal Muscle: Developmental Myogenesis Guides the Way, Cell Stem Cell, 2015; 17(3): 255-7. (link)


Peng J, Garcia MA, Choi J, Zhao L, Chen K, Bernstein JR, Peyda P, Hsiao Y, Liu KW, Lin W, Pyle AD, Wang H, Hou S, Tseng H. Molecular recognition enables nanosubstrate-mediated delivery of gene-encapsulated nanoparticles with high efficiency, ACS nano, 2014; 8(5): 4621-9. (link)


Awe JP, Lee PC, Ramathal C, Vega-Crespo A, Durruthy-Durruthy J, Cooper A, Karumbayaram S, Lowry WE, Clark AT, Zack JA, Sebastiano V, Kohn DB, Pyle AD, Martin MG, Lipshutz GS, Phelps PE, Pera RA, Byrne JA. Generation and characterization of transgene-free human induced pluripotent stem cells and conversion to putative clinical-grade status, Stem cell research & therapy, 2013; 4(4): 87. (link)

Yanes RE, Tarn D, Hwang AA, Ferris DP, Sherman SP, Thomas CR, Lu J, Pyle AD, Zink JI, Tamanoi F. Involvement of lysosomal exocytosis in the excretion of mesoporous silica nanoparticles and enhancement of the drug delivery effect by exocytosis inhibition Small (Weinheim an der Bergstrasse, Germany), 2013; 9(5): 697-704. (link)

Palomares K, Vigant F, Van Handel B, Pernet O, Chikere K, Hong P, Sherman SP, Patterson M, An Dong S, Lowry WE, Mikkola HK, Morizono K, Pyle AD, Lee B. Nipah virus envelope-pseudotyped lentiviruses efficiently target ephrinB2-positive stem cell populations in vitro and bypass the liver sink when administered in vivo, Journal of virology, 2013; 87(4): 2094-108. (link)

Sherman SP, Pyle AD. Small molecule screening with laser cytometry can be used to identify pro-survival molecules in human embryonic stem cells, PloS one, 2013; 8(1): e54948. (link)


Karumbayaram S, Lee P, Azghadi SF, Cooper AR, Patterson M, Kohn DB, Pyle A, Clark A, Byrne J, Zack JA, Plath K, Lowry WE. From skin biopsy to neurons through a pluripotent intermediate under Good Manufacturing Practice protocols Stem cells translational medicine, 2012; 1(1): 36-43. (link)


Alva JA, Lee GE, Escobar EE, Pyle AD. Phosphatase and tensin homolog regulates the pluripotent state and lineage fate choice in human embryonic stem cells, Stem cells (Dayton, Ohio), 2011; 29(12): 1952-62. (link)

Sherman SP, Alva JA, Thakore-Shah K, Pyle AD. Human pluripotent stem cells: the development of high-content screening strategies Methods in molecular biology (Clifton, N.J.), 2011; 767(1): 283-95. (link)

Le Belle JE, Orozco NM, Paucar AA, Saxe JP, Mottahedeh J, Pyle AD, Wu H, Kornblum HI. Proliferative neural stem cells have high endogenous ROS levels that regulate self-renewal and neurogenesis in a PI3K/Akt-dependent manner Cell stem cell, 2011; 8(1): 59-71. (link)


Tchieu J, Kuoy E, Chin MH, Trinh H, Patterson M, Sherman SP, Aimiuwu O, Lindgren A, Hakimian S, Zack JA, Clark AT, Pyle AD, Lowry WE, Plath K. Female human iPSCs retain an inactive X chromosome Cell stem cell, 2010; 7(3): 329-42. (link)

Tseng H, Arasteh A, Paranjpe A, Teruel A, Yang W, Behel A, Alva JA, Walter G, Head C, Ishikawa T, Herschman HR, Cacalano N, Pyle AD, Park N, Jewett A. Increased lysis of stem cells but not their differentiated cells by natural killer cells; de-differentiation or reprogramming activates NK cells, PloS one, 2010; 5(7): e11590. (link)

Kamei K, Ohashi M, Gschweng E, Ho Q, Suh J, Tang J, For Yu ZT, Clark AT, Pyle AD, Teitell MA, Lee K, Witte ON, Tseng H. Microfluidic image cytometry for quantitative single-cell profiling of human pluripotent stem cells in chemically defined conditions, Lab on a chip, 2010; 10(9): 1113-9. (link)


Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pellegrini M, Plath K, Lowry WE. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures, Cell stem cell, 2009; 5(1): 111-23. (link)

Zeng W, de Greef JC, Chen Y, Chien R, Kong X, Gregson HC, Winokur ST, Pyle A, Robertson KD, Schmiesing JA, Kimonis VE, Balog J, Frants RR, Ball AR, Lock LF, Donovan PJ, van der Maarel SM, Yokomori K. Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD), PLoS genetics, 2009; 5(7): e1000559. (link)

Damoiseaux R, Sherman SP, Alva JA, Peterson C, Pyle AD. Integrated chemical genomics reveals modifiers of survival in human embryonic stem cells, Stem cells (Dayton, Ohio), 2009; 27(3): 533-42. (link)

Conway AE, Lindgren A, Galic Z, Pyle AD, Wu H, Zack JA, Pelligrini M, Teitell M, Clark AT. A self-renewal program controls the expansion of genetically unstable cancer stem cells in pluripotent stem cell-derived tumors, Stem cells (Dayton, Ohio), 2009; 27(1): 18-28. (link)


Wu H, Kim KJ, Mehta K, Paxia S, Sundstrom A, Anantharaman T, Kuraishy AI, Doan T, Ghosh J, Pyle AD, Clark A, Lowry W, Fan G, Baxter T, Mishra B, Sun Y, Teitell MA. Copy number variant analysis of human embryonic stem cells, Stem cells (Dayton, Ohio), 2008; 26(6): 1484-9. (link)