Papers Citing Our Services

Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome. Cohen, A. J. et al., Nature Communications 2017

A stable but reversible integrated surrogate reporter for assaying CRISPR/Cas9-stimulated homology-directed repair. Wen, Y. et al., JBC 2017

Noroviruses Co-opt the Function of Host Proteins VAPA and VAPB for Replication via a Phenylalanine–Phenylalanine-Acidic-Tract-Motif Mimic in Nonstructural Viral Protein NS1/2. McCune B. T. et al., mBio 2017

Human iPS-derived endothelial cells for 3D microphysiological systems. Kurokawa et al., Tissue Engineering Part C: Methods 2017

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. Sundaram, V. et al., Nature Communications 2017

Discovery of a proteinaceous cellular receptor for a norovirus. Orchard et al., Science 2016

Blood Group O–Dependent Cellular Responses to Cholera Toxin: Parallel Clinical and Epidemiological Links to Severe Cholera. Kuhlmann et al., Am J Trop Med Hyg 2016

Clec16a is Critical for Autolysosome Function and Purkinje Cell Survival. Redmann et al., Sci Rep 2016

Multiple Domains of GlcNAc-1-Phosphotransferase Mediate Recognition of Lysosomal Enzymes. Van Meel et al., JBC 2016

A Puromycin Selectable Cell Line for the Enrichment of Mouse Embryonic Stem Cell-Derived V3 Interneurons. Xu et al., Stem Cell Research & Therapy 2015

A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-γ-Activated Human Cells. Selleck et al., MBio 2015

A calcium-dependent protease as a potential therapeutic target for Wolfram syndrome. Lu et al., PNAS 2014

Genome Engineering and Stem Cell Technology Papers by Our Scientists

 CRISPR/Cas9 Mediated Insertion of loxP Sites in the Mouse Dock7 Gene Provides an Effective Alternative to Use of Targeted Embryonic Stem Cells. Bishop, K.A., Harrington, A., Kouranova, E., Weinstein, E.J., Rosen, C.J., Cui, X., Liaw, L. G3: Genes, Genomes, Genetics. 2016

CRISPRs for optimal targeting: Delivery of CRISPR components as DNA, RNA and protein into cultured cells and single-cell embryos. Kouranova, E., Forbes, K., Zhao, G., Warren, J., Bartels, A., Wu, Y., Cui, XHum Gene Ther. 2016

Tissue Specific Expression of Cre in Rat Tyrosine Hydroxylase and Dopamine Active Transporter-Positive Neurons. Liu, Z., Brown, A., Fisher, D., Wu, Y., Warren, J., Cui, XPLoS One. 2016

Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation. Troung, D.M., Hewitt, F.C., Hanson, J. H. Cui, X., Lambowitz, A.M. PLoS Genet. 2015

Donor plasmid design for codon and single base genome editing using zinc finger nucleases. Pruett-Miller, et al., Methods Mol Biol 2015

Gene editing using ssODNs with engineered endonucleases. Chen F, Pruett-Miller SM, Davis GD., Methods Mol Biol 2015

Preface. Chromosomal mutagenesis. Pruett-Miller, Methods Mol Biol 2015

Efficient creation of an APOE knockout rabbit. Ji, D., Zhao, G., Songstad, A., Cui, X., Weinstein, E.J.Transgenic Res. 2014

Fmr1 and Nlgn3 knockout rats: novel tools for investigating autism spectrum disorders. Hamilton, S. M., Green, J. R., Veeraragavan, S., Yuva, L., McCoy, A., Wu, Y., Warren, J., Little, L., Ji, D., Cui, X., Weinstein, E. & Paylor, R. Behav. Neurosci. 2014

Characterization of Defects in Ion Transport and Tissue Development in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)-Knockout Rats. Tuggle, K.L., Birket, S.E., Cui, X., Hong, J., Warren, J., Reid, L., Chambers, A., Ji, D., Gamber, K., Chu, K.K., Tearney, G., Tang, L.P., Fortenberry, J.A., Du, M., Cadillac, J.M., Bedwell, D.M., Rowe, S.M., Sorscher, E.J. & Fanucchi, M.V., PLoS One. 2014

Phenotypic characterization of recessive gene knockout rat models of Parkinson’s disease. Dave, K. D., De Silva, S., Sheth, N.P., Ramboz, S., Beck, M.J., Quang, C., Switzer, R.C. 3rd, Ahmad, S.O., Sunkin, S.M., Walker, D., Cui, X., Fisher, D.A., McCoy, A.M., Gamber, K., Ding, X., Goldberg, M.S., Benkovic, S.A., Haupt, M., Baptista, M.A., Fiske, B.K., Sherer, T.B. & Frasier, M.A.  Neurobiol Dis. 2014

High-efficiency genome editing via 2A-coupled co-expression of fluorescent proteins and zinc finger nucleases or CRISPR/Cas9 nickase pairs. Duda  et al., Nucleic Acids Res 2014

Nuclease-mediated gene editing by homologous recombination of the human globin locus. Voit RA, Hendel A, Pruett-Miller SM, Porteus MH., Nucleic Acids Res 2014

Genome editing in mouse spermatogonial stem/progenitor cells using engineered nucleases. Fanslow DA, Wirt SE, Barker JC, Connelly JP, Porteus MH, Dann CT., PLoS One 2014

Targeted correction of RUNX1 mutation in FPD patient-specific induced pluripotent stem cells rescues megakaryopoietic defects. Connelly et al., Blood 2014

A calcium-dependent protease as a potential therapeutic target for Wolfram syndrome. Lu S, Kanekura K, Hara T, Mahadevan J, Spears LD, Oslowski CM, Martinez R, Yamazaki-Inoue M, Toyoda M, Neilson A, Blanner P, Brown CM, Semenkovich CF, Marshall BA, Hershey T, Umezawa A, Greer PA, Urano F., PNAS 2014

 Regulation of dopamine presynaptic markers and receptors in the striatum of DJ-1 and Pink1 knockout rats. Sun, J., Kouranova, E., Cui, X., Mach, R. H. & Xu, J. Neurosci. Lett. 2013

Whole rat conditional knockout via genome editing. Brown, A., Fisher, D., Kouranova, J., McCoy, A., Forbes, K., Wu, Y., Ji, D., Henry, R., Chambers, A., Shu, W., Weinstein, E. J., Cui, XNature Meth. 2013

A survey of ex vivo/in vitro transduction efficiency of mammalian primary cells and cell lines with Nine natural adeno-associated virus (AAV1-9) and one engineered adeno-associated virus serotype. Ellis BL, Hirsch ML, Barker JC, Connelly JP, Steininger RJ 3rd, Porteus MH., Virol J 2013

Expanding the Repertoire of Target Sites for Zinc Finger Nuclease-mediated Genome Modification. Wilson KA, McEwen AE, Pruett-Miller SM, Zhang J, Kildebeck EJ, Porteus MH., Mol Ther Nucleic Acids 2013

Zinc-finger nuclease mediated disruption of Rag1 in the LEW/Ztm rat.  Zschemisch, N. H., Glage, S., Wedekind, D., Weinstein, E. J., Cui, X., Dorsch, M., Hedrich, H. J.  BMC Immunol. 2012

 Creation and preliminary characterization of a Tp53 knockout rat. McCoy, A., Besch-Williford, C. L., Franklin, C. L., Weinstein, E. J. & Cui, XDisease Models & Mechanisms. 2012

Creation and preliminary characterization of a Leptin Knockout rat. Vaira, S., Yang, C., McCoy, A., Keys, K., Xue, S., Weinstein, E. J., Novack, D. & Cui, XEndocrinology 2012

 Targeted integration in rat and mouse embryos with zinc-finger nucleasesCui, X., Ji, D., Fisher, D., Wu, Y., Briner, D. & Weinstein, E. J. Nat. Biotechnol. 2011

High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, Collingwood TN, Frodin M, Davis GD, Nat Methods 2011

Targeted genome modification in mice using zinc-finger nucleases. Carbery, I. D., Ji, D., Harrington, A., Weinstein, E. J., Liaw, L. & Cui, X. Genetics 2010

A universal zinc finger nuclease for targeted gene addition to human cells. DeKelver, R. C., Choi, V.M., Moehle, E.A., Paschon, D.E., Hockemeyer, D., Meijsing, S.H., Sancak, Y., Cui, X., Miller, J.C., Tam, P., Bartsevich, V., Rupniewski, I., Meng, X., Gopalan, S.M., Rock, J.M., Zhang, L., Davis, G.D., Rebar, E.J., Jaenisch, R., Cheeseman, I.M., Yamamoto, K.R., Sabatini, D.M., Gregory, P.D., and Urnov, F.D.,  Genome Res. 2010

Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase. Gu, S. Q., Cui, X., Mou, S., Mohr, S., Yao, J., & Lambowitz, A. M., RNA 2010

Generation of gene-specific mutated rats using zinc-finger nucleases. Geurts, A. M., Cost, G. J., Remy, S., Cui, X., Tesson, L., Usal, C., Menoret, S., Jacob, H. J., Anegon, I., & Buelow, R., Methods in Molecular Biology 2010

Gene correction by homologous recombination with zinc finger nucleases in primary cells from a mouse model of a generic recessive genetic disease. Connelly et al., Mol Ther 2010

Knockout rats via embryo microinjection of zinc-finger nucleases. Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, Jenkins SS, Wood A, Cui X, Meng X, Vincent A, Lam S, Michalkiewicz M, Schilling R, Foeckler J, Kalloway S, Weiler H, Ménoret S, Anegon I, Davis GD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Jacob HJ, Buelow R., Science 2009

Attenuation of zinc finger nuclease toxicity by small-molecule regulation of protein levels. Pruett-Miller et al., PLoS Genet 2009

Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Jizhong Zou, Morgan L. Maeder, Prashant Mali, Shondra M Pruett-Miller, Stacey Thibodeau-Beganny, Bin-Kuan Chou, Guibin Chen, Zhaohui Ye, In-Hyun Park, George Q. Daley, Matthew H. Porteus, J. Keith Joung, Linzhao Cheng, Cell Stem Cell 2009

Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Pruett-Miller et al., Mol Ther 2008

Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification.Morgan L. Maeder, Stacey Thibodeau-Beganny, Anna Osiak, David A. Wright, Reshma M. Anthony, Magdalena Eichtinger, Tao Jiang, Jonathan E. Foley, Ronnie J. Winfrey, Jeffrey A. Townsend, Erica Unger-Wallace, Jeffry D. Sander, Felix Müller-Lerch, Fengli Fu, Joseph Pearlberg, Carl Göbel, Justin P. Dassie, Shondra M. Pruett-Miller, Matthew H. Porteus, Dennis C. Sgroi, A. John Iafrate, Drena Dobbs, Paul B. McCray, Jr., Toni Cathomen, Daniel F. Voytas, J. Keith Joung, Mol Cell 2008

 Mobile group II intron targeting: applications in prokaryotes and perspectives in eukaryotes (Invited review).  Cui, X. & Davis, G. Frontiers in Bioscience 2007

A look to future directions in gene therapy research for monogenic diseases. Matthew H Porteus, Jon P Connelly, and Shondra M Pruett PLoS Genet 2006