All Publications


A multimodal cell census and atlas of the mammalian primary motor cortex. BRAIN Initiative Cell Census Network (BICCN). Nature. 2021

Generation of a DAT-P2A-Flpo mouse line for intersectional genetic targeting of dopamine neuron subpopulations. Kramer DJ, Aisenberg EE, Kosillo P, Friedmann D, Stafford DA, Lee AY, Luo L, Hockemeyer D, Ngai J, Bateup HS. Cell Rep. 2021.

Cancer-associated POT1 mutations lead to telomere elongation without induction of a DNA damage response. Kim WT, Hennick K, Johnson J, Finnerty B, Choo S, Short SB, Drubin C, Forster R, McMaster ML, Hockemeyer D. The Embo Journal. 2021.


TINF2 is a haploinsufficient tumor suppressor that limits telomere length. Schmutz I, Mensenkamp AR, Takai KK, Haadsma M, Spruijt L, de Voer RM, Choo SS, Lorbeer FK, van Grinsven EJ, Hockemeyer D, Jongmans MC, de Lange T. Elife. 2020.  

Telomere length set point regulation in human pluripotent stem cells critically depends on the shelterin protein TPP1. Boyle JM, Hennick KM, Regalado SG, Vogan JM, Zhang X, Collins K, Hockemeyer D. Mol Biol Cell. 2020.

Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells. Shin JJ, Schröder MS, Caiado F, Wyman SK, Bray NL, Bordi M, Dewitt MA, Vu JT, Kim WT, Hockemeyer D, Manz MG, Corn JE. Cell Rep. 2020. 

TERT promoter mutations and telomeres during tumorigenesis. Lorbeer FK, Hockemeyer D. Curr Opin Genet Dev. 60:56-62. 2020.

Blueprint for a pop-up SARS-CoV-2 testing lab. IGI Testing Consortium:Alexandra M Amen, Kerrie W Barry,John M Boyle, Cara E Brook, Seunga Choo, L T Cornmesser, David J Dilworth, Jennifer A Doudna, Alexander J Ehrenberg, Indro Fedrigo, Skyler E Friedline, Thomas G W Graham, Ralph Green, Jennifer R Hamilton, Ariana Hirsh, Megan L Hochstrasser, Dirk Hockemeyer, Netravathi Krishnappa, Azra Lari, Hanqin Li, Enrique Lin-Shiao, Tianlin Lu, Elijah F Lyons, Kevin G Mark, Lisa Argento Martell, A Raquel O Martins, Shana L McDevitt, Patrick S Mitchell, Erica A Moehle, Christine Naca, Divya Nandakumar, Elizabeth O’Brien, Derek J Pappas, Kathleen Pestal, Diana L Quach, Benjamin E Rubin, Rohan Sachdeva, Elizabeth C Stahl, Abdullah Muhammad Syed, I-Li Tan, Amy L Tollner, Connor A Tsuchida, C Kimberly Tsui, Timothy K Turkalo, Fyodor D Urnov, M Bryan Warf, Oscar N, Whitney, Lea B Witkowsky (2020)  Nat Biotechnol. 38(7):791-797. 2020.

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS. Commun Biol. 3(1):480. 2020.


Transient activation of  the UPRER is an essential step in the acquisition of pluripotency during reprogramming. Milos S. Simic, Erica A. Moehle, Robert T. Schinzel, Franziska K. Lorbeer, Jonathan J. Halloran, Kartoosh Heydari, Melissa Sanchez, Damien Jullié, Dirk Hockemeyer, and Andrew Dillin. Sci Adv. 5(4). 2019


Genetically engineered human cortical spheroid models of tuberous sclerosis. John D. Blair, Dirk Hockemeyer, and Helen S. Bateup. Nature Medicine. 2018

Genome-edited human stem cells expressing fluorescently labeled endocytic markers allow quantitative analysis of clathrin-mediated endocytosis during differentiationDaphné Dambournet, Kem A. Sochacki, Aaron T. Cheng, Matthew Akamatsu, Justin W. Taraska, Dirk Hockemeyer, and David G. Drubin. JCB 217(9). 2018

Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Mustafa Mir, Armando Reimer, Michael Stadler, Astou Tangara, Anders S. Hansen, Dirk Hockemeyer, Michael B. Eisen, Hernan Garcia, and Xavier Darzacq. Nanoscale Imaging: Methods and Protocols, Methods in Molecular Biology (1814). 2018

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Tsung-Li Liu1, Srigokul Upadhyayula, Daniel E. Milkie, Ved Singh, Kai Wang, Ian A. Swinburne, Kishore R. Mosaliganti, Zach M. Collins, Tom W. Hiscock, Jamien Shea, Abraham Q. Kohrman, Taylor N. Medwig, Daphne Dambournet, Ryan Forster, Brian Cunniff, Yuan Ruan, Hanako Yashiro, Steffen Scholpp, Elliot M. Meyerowitz, Dirk Hockemeyer, David G. Drubin, Benjamin L. Martin, David Q. Matus, Minoru Koyama, Sean G. Megason, Tom Kirchhausen, Eric Betzig. Science 360(284). 2018


Widespread Translational Remodeling during Human Neuronal Differentiation. Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN. Cell Reports 21(7):2005-2016. 2017.

Mutations in the promoter of the telomerase gene TERT contribute to tumorigenesis by a two-step mechanism. Chiba K, Lorbeer F, Shain A, McSwiggen D, Schruf E, Oh A, Ryu J, Darzacq X, Bastain B, Hockemeyer D. Science, 357: 1416-1420. 2017.

Defined and Scalable Differentiation of Human Oligodendrocyte Precursors from Pluripotent Stem Cells in a 3D Culture System. GMC, Gaj T, Adil MM, Wahba J, Rao AT, Lorbeer FK, Kulkarni RU, Diogo MM, Cabral JMS, Miller EW, Hockemeyer D, and Schaffer DV. Stem Cell Reports 8(6):1770-1783. 2017.


Endogenous TERT N-terminal tagging affects human telomerase function at telomeres in vivoChiba K, Vogan JM, Wu RA, Gill MS, Zhang X, Collins K, Hockemeyer D. Molecular and Cell Biology 37:e00541-16. 2016.

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Minimized human telomerase maintains telomeres and resolves endogenous roles of H/ACA proteins, TCAB1, and Cajal bodies. Vogan JM, Zhang X, Youmans DT, Regalado SGJohnson JZHockemeyer D, Collins K. eLife 5: e18221. 2016.

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Induced Pluripotent Stem Cells Meet Genome Editing. Hockemeyer D, Jaenisch R. Cell Stem Cell 18(5) 573-586. 2016.

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Establishment of Genome-edited Human Pluripotent Stem Cell Lines: From Targeting to Isolation. Blair JD, Bateup H, Hockemeyer D. J VisExp. 2016; (108): 53583. 2016.


Human stem cell-based disease modeling: prospects and challenges. Johnson JZHockemeyer D. Curr. Opin. Cell. Biol. 37: 84-90. 2015.

Control of telomerase action at human telomeres. Hockemeyer D, Collins, K. Nat. Struct. Mol. Biol. 22(11) 848-852. 2015.

Chiba KJohnson JZ, Vogan JM, Wagner TBoyle JMHockemeyer D. (2015) Cancer-associated TERT promoter mutations abrogate telomerase silencing. Chiba KJohnson JZ, Vogan JM, Wagner TBoyle JMHockemeyer D. eLIFE 4:e07918. 2015.

Genome Editing in Human Pluripotent Stem Cells Using Site-Specific Nucleases. Chiba KHockemeyer D. Methods Mol. Biol. 1239:267-280. 2015.


Genetic and molecular identification of three human TPP1 functions in telomerase action: recruitment, activation, and homeostasis set point regulation. Sexton AN, Regalado SG, Lai CS, Cost GJ, O’Neil CM, Urnov FD, Gregory PD, Jaenisch R, Collins K, Hockemeyer D. Genes and Development 28(17). 2014.

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Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells. Forster RChiba K, Schaeffer L, Regalado SG, Lai C, Gao Qing, Kiana S, Farin HF, Clevers H, Cost GJ, Chan A, Rebar EJ, Urnov FD, Gregory PD, Pachter L, Jaenisch R, Hockemeyer D. Cell Stem Cell Reports 2(6):838-52. 2014.

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Forster RHockemeyer D (2014) Genome editing 101: Let’s go digital. Nature methods 11, 248-249. 2014.


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Global transciptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons. Li Y, Wang H, Muffat J, Cheng AW, Orlando DA, Lovén J, Kwok SM, Feldman DA, Bateup HS, Gao Q, Hockemeyer D, Mitalipova M, Lewis CA, Vander Heiden MG, Sur M, Young RA, Jaenisch R. Cell Stem Cell 13(4):446-58. 2013


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Deletion of the de novo methyltransferase Dnmt3a promotes lung tumor progression. Gao Q, Steine E, Barrasa M, Hockemeyer D, Pawlak M, Fu D, Reddy S, Bell G, Jaenisch R. Proceedings of the National Academy of Sciences of the United States of America. 2011.

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Transgene Excision Has No Impact on In Vivo Integration of Human iPS Derived Neural Precursors. Major T, Menon J, Auyeung G, Soldner F, Hockemeyer D, Jaenisch R, Tabar V. PLoS ONE 6: e24687. 2011.

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Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Soldner F, Laganiere J, Cheng AW, Hockemeyer D, Gao Q, Alagappan R, Khurana V, Golbe LI, Myers RH, Lindquist S, Zhang L, Guschin D, Fong LK, Vu BJ, Meng X, Urnov FD, Rebar EJ, Gregory PD, Zhang HS, Jaenisch R. Cell 146: 318-31. 2011.

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Genetic engineering of human pluripotent cells using TALE nucleases. Hockemeyer D, Wang H, Kiani S, Lai CS, Gao Q, Cassady JP, Cost GJ, Zhang L, Santiago Y, Miller JC, Zeitler B, Cherone JM, Meng X, Hinkley SJ, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R. Nature biotechnology 29: 731-4 *equal contribution. 2011.


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Gene targeting in human pluripotent cells. Hockemeyer D, Jaenisch R. Cold Spring Harbor symposia on quantitative biology 75: 201-9. 2010.

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Differentiated Parkinson patient-derived induced pluripotent stem cells grow in the adult rodent brain and reduce motor asymmetry in Parkinsonian rats. Hargus G, Cooper O, Deleidi M, Levy A, Lee K, Marlow E, Yow A, Soldner F, Hockemeyer D, Hallett PJ, Osborn T, Jaenisch R, Isacson O. Proceedings of the National Academy of Sciences of the United States of America 107: 15921-6. 2010.

Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, Jaenisch R, Young RA. (2010) Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 7: 249-57. 2010.

Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. DeKelver RC, Choi VM, Moehle EA, Paschon DE, Hockemeyer D, Meijsing SH, Sancak Y, Cui X, Steine EJ, Miller JC, Tam P, Bartsevich VV, Meng X, Rupniewski I, Gopalan SM, Sun HC, Pitz KJ, Rock JM, Zhang L, Davis GD, Rebar EJ, Cheeseman IM, Yamamoto KR, Sabatini DM, Jaenisch R, Gregory PD, Urnov FD. Genome Research 20: 1133-42. 2010.


Parkinson’s disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Soldner F, Hockemeyer D, Beard C, Gao Q, Bell GW, Cook EG, Hargus G, Blak A, Cooper O, Mitalipova M, Isacson O, Jaenisch R. Cell 136: 964-77 *equal contribution. 2009.

Mammalian telomeres resemble fragile sites and require TRF1 for efficient replication. Sfeir A, Kosiyatrakul ST, Hockemeyer D, MacRae SL, Karlseder J, Schildkraut CL, de Lange T. Cell 138: 90-103. 2009.

Functional dissection of human and mouse POT1 proteins. Palm W, Hockemeyer D, Kibe T, de Lange T. Molecular and Cellular Biology 29: 471-82. 2009.

 Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Hockemeyer D, Soldner F, Beard C, Gao Q, Mitalipova M, DeKelver RC, Katibah GE, Amora R, Boydston EA, Zeitler B, Meng X, Miller JC, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R. Nature Biotechnology 27: 851-7 *equal contribution. 2009.

Direct reprogramming of somatic cells to a pluripotent state. Hockemeyer D, Soldner, F., Jaenisch, R. Essentials of Stem Cell Biology, Second edition, pp. pp. 29-32. (San Diego, USA, Academic Press, Elsevier): Robert Lanza, John Gearhart, Brigid Hogan, Douglas Melton, Roger Pederson, E. Donnall Thomas, James Thomson, and Sir Ian Wilmut. 2009.


A drug-inducible system for direct reprogramming of human somatic cells to pluripotency. Hockemeyer D, Soldner F, Cook EG, Gao Q, Mitalipova M, Jaenisch R. Cell Stem Cell 3: 346-53 *equal contribution. 2008

Engineered telomere degradation models dyskeratosis congenita. Hockemeyer D, Palm W, Wang RC, Couto SS, de Lange T. Genes & Development 22: 1773-85. 2008.


Telomere protection by mammalian Pot1 requires interaction with Tpp1. Hockemeyer D, Palm W, Else T, Daniels JP, Takai KK, Ye JZ, Keegan CE, de Lange T, Hammer GD. Nature Structural & Molecular Biology 14: 754-61. 2007.


Recent expansion of the telomeric complex in rodents: Two distinct POT1 proteins protect mouse telomeres. Hockemeyer D, Daniels JP, Takai H, de Lange T. Cell 126: 63-77. 2006


POT1 protects telomeres from a transient DNA damage response and determines how human chromosomes end. Hockemeyer D, Sfeir AJ, Shay JW, Wright WE, de Lange T. The EMBO journal 24: 2667-78. 2005.


POT1-interacting protein PIP1: a telomere length regulator that recruits POT1 to the TIN2/TRF1 complex. Ye JZ, Hockemeyer D, Krutchinsky AN, Loayza D, Hooper SM, Chait BT, de Lange T. Genes & Development 18: 1649-54. 2004.

Myocardin and ternary complex factors compete for SRF to control smooth muscle gene expression. Wang Z, Wang DZ, Hockemeyer D, McAnally J, Nordheim A, Olson EN. Nature 428: 185-9. 2004

SRF regulates Bcl-2 expression and promotes cell survival during murine embryonic development. Schratt G, Philippar U, Hockemeyer D, Schwarz H, Alberti S, Nordheim A. The EMBO Journal 23: 1834-44. 2004.


Potentiation of serum response factor activity by a family of myocardin-related transcription factors. Wang DZ, Li S, Hockemeyer D, Sutherland L, Wang Z, Schratt G, Richardson JA, Nordheim A, Olson EN. Proceedings of the National Academy of Sciences of the United States of America 99: 14855-60. 2002.