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Swygert, S.G., Senapati, S., Bolukbasi, M.F., Wolfe, S.A., Lindsay, S., Peterson, C.L. SIR proteins create compact heterochromatin fibers. Proc Natl Acad Sci U S A. 2018 Nov 19. pii: 201810647. doi: 10.1073/pnas.1810647115. PMID30455303

Bolukbasi, M.F., Liu, P., Luk, K., Kwok, S.F., Gupta, A., Amrani, N., Sontheimer, E.J., Zhu, L.J., Wolfe, S.A.*. Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nature Communications 2018 Nov 19;9(1):4856. PMID30451839 

Pulikkan, J.A., Hegde, M., Ahmad, H.M., Belaghzal, H., Illendula, A., Yu, J., O'Hagan, K., Ou, J., Muller-Tidow, C., Wolfe, S.A., Zhu, L.J., Dekker, J., Bushweller, J.H., Castilla, L.H. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. 2018, Cell. Jun 28;174(1):172-186 PMID29958106 

Gao, X. D., Tu, L.-C., Mir, A., Rodriguez, T., Ding, Y., Leszyk, J., Dekker, J., Shaffer, S. A., Zhu, L. J., Wolfe, S. A., and Sontheimer, E. J. C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. 2018, Nature Methods, 15(6):433-436. PMC6202229

Ou, J., Wolfe, S.A., Brodsky, M.H., Zhu, L.J. motifStack for the analysis of transcription factor binding site evolution. 2018 Nat Methods. 15(1):8-9. PMID29298290

Yin H, Song CQ, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W, Langer R, Anderson DG. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat Chem Biol. 2018, 14(3):311-316. PMC5902734

Yin, H., Song, C.Q., Suresh, S., Wu, Q., Walsh, S., Rhym, L.H., Mintzer, E., Bolukbasi, M.F., Zhu, L.J., Kauffman, K., Mou, H., Oberholzer, A., Ding, J., Kwan, S.Y., Bogorad, R.L., Zatsepin, T., Koteliansky, V., Wolfe, S.A., Xue, W., Langer, R., Anderson, D.G.”Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing” Nat Biotechnol. 2017, 35(12):1179-1187  PMID29131148

Ma, L., Boucher, J.I., Paulsen, J., Matuszewski, S., Eide, C.A., Ou, J., Eickelberg, G., Press, R.D., Zhu, L.J., Druker, B.J., Branford, S., Wolfe, S.A., Jensen, J.D., Schiffer, C.A., Green, M.R., Bolon, D.N. “CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy” Proc Natl Acad Sci U S A. 2017, 114(44):11751-11756. PMC5676903

Leonard, J.L., Leonard, D.M., Wolfe, S.A., Liu, J., Rivera, J., Yang, M., Leonard, R.T., Johnson, J.P.S., Kumar, P., Liebmann, K.L., Tutto, A.A., Mou, Z., Simin, K.J. “The Dkk3 gene encodes a vital intracellular regulator of cell proliferation” PLoS One. 2017;12(7):e0181724. PMC5524345

Zhu, L.J., Lawrence, M., Gupta, A., Pagès, H., Kucukural, A., Garber, M., Wolfe, S.A. “GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases” BMC Genomics. 2017, 18(1):379. PMC5433024

Markert, M.J., Zhang, Y., Enuameh, M.S., Reppert, S.M., Wolfe, S.A., Merlin, C. “Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis” G3 (Bethesda). 2016, 6(4), 905-15. PMC4825660

Yin, H., Song, C., Dorkin, J.R., Zhu, L.J., Li, Y., Wu, Q., Park, A., Yang. J., Suresh, S., Bizhanova, A., Gupta, A., Bolukbasi, M.F. Walsh, S., Bogorad, R., Gao, G., Weng, Z., Dong, Y., Koteliansky, V., Wolfe, S.A., Langer, R. Xue, W., Anderson, D.G., “Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo” Nat. Biotechnology 2016, 34(3), 328-33. PMC5423356

Bolukbasi, M.F., Gupta, A., Oikemus, S., Derr, A.G., Garber, M., Brodsky, M.H., Zhu, L.J., Wolfe, S.A.. "DNA-binding-domain fusions enhance the targeting range and precision of Cas9". Nature Methods , 12:1150-1156 (2015). PMC4679368

Ma, H., Naseri, A., Reyes-Gutierrez, P., Wolfe, S.A., Zhang, S. and Pederson, T.  “Multicolor CRISPR Labeling of Chromosomal Loci in Human Cells” PNAS 2015, 112(10), 3002-3007. PMC4364232

Kok, F. O., Shin, M., Ni, C-W., Gupta, A., Grosse, A. S., van Impel, A., Kirchmaier, B., Peterson-Meduro, J., Kourkoulis, G., Male, I., DeSantis, D.F., Sheppard-Tindell, S., Ebarasi, L., Betsholtz, C., Schulte-Merker, S., Wolfe, S.A., Lawson, N.D. “Reverse genetic screening reveals poor correlation between Morpholino-induced and mutant phenotypes in zebrafish” Dev Cell 2015, 32(1), 97-108. PMC4487878

Weicksel, S.E., Gupta, A., Zannino, D.A., Wolfe, S.A., Sagerström, C.G. “Targeted germ line disruptions reveal general and species-specific roles for paralog group 1 hox genes in zebrafish.” BMC Dev Biol. 2014 Jun 5;14(1):25. PMC4061917

Gupta, A., Christensen, R.G., Bell, H.A., Goodwin, M., Patel, R.Y., Pandey, M., Enuameh, M.S., Rayla, A.L., Zhu, C., Thibodeau-Beganny, S., Brodsky, M.H., Joung, J.K. Wolfe, S.A.*, Stormo, G.D.* “An improved predictive recognition model for Cys2-His2 zinc finger proteins” Nucleic Acids Res. 2014 42(8):4800-12. PMC4005693 *Co-corresponding author

Kearns, N.A., Genga, R.M.J, Enuameh, M.S., Garber, M., Wolfe, S.A.*, Maehr, R*. “Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells” Development 2014, 141(1):219-23. PMC3865759 *Co-corresponding author

Kazemian, M., Pham, H., Wolfe, S.A., Brodsky, M.H., Sinha, S., “Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.” Nucleic Acids Res 2013, 41(17):8237-52. PMC3783179

Cheng, Q., Kazemian, M., Pham, H., Blatti, C., Celniker, S.E., Wolfe, S.A., Brodsky, M.H., Sinha, S., “Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.” PLoS Genetics 2013, 9(8) e1003571. PMC3731213

Enuameh, M.S., Asriyan, Y., Richards, A., Christensen, R.G., Hall, V.L., Kazemian, M., Zhu, C., Pham, H., Cheng, Q., Blatti, C., Brasefield, J.A., Basciotta, M.D., Ou, J., McNulty, J.C., Zhu, L.J., Celniker, S.E., Sinha, S., Stormo, G.D., Brodsky, M.H., Wolfe, S.A., “Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.” Genome Research. 2013, 23(6), 928-40. PMC3668361.

Gupta, A., Hall, V.L., Kok, F.O., Shin, M., McNulty, J.C., Lawson, N.D., Wolfe, S.A., “Targeted Chromosomal Deletions and Inversions in Zebrafish.” Genome Research. 2013, 23(6),1008-17. PMC3668355.

Zhu, C., Gupta, A., Hall, V.L., Rayla, A.L., Christensen,  R.G., Dake, B., Lakshmanan, A., Kuperwasser, C., Stormo, G.D., Wolfe, S.A. “Using Defined Finger-Finger Interfaces as Units of Assembly for Constructing Zinc Finger Nucleases” Nucleic Acids Res. 2013, 41(4), 2455-65. PMC3575815

Merlin, C., Beaver, L.E., Taylor, O.R., Wolfe, S.A., Reppert, S.M. “Efficient targeted mutagenesis in the monarch butterfly using zinc finger nucleases.” Genome Res. 2013 23(1), 159-68. PMC3530676

Anderson, D.M., George, R., Noyes, M.B., Rowton, M., Liu, W., Jiang, R., Wolfe, S.A., Wilson-Rawls, J., Rawls, A. “Characterization of the DNA-Binding Properties of the Mohawk (Mkx) Homeobox Transcription Factor.” J Biol Chem, 2012, 287(42), 35351-9. PMC3471766

Shin, J., Padmanabhan, A., de Groh, E.D., Lee, J.S., Haidar, S., Dahlberg, S., Guo, F., He, S., Wolman, M.A., Granato, M., Lawson, N.D., Wolfe, S.A., Kim, S.H., Solnica-Krezel, L., Kanki, J.P., Ligon, K.L., Epstein, J.A., Look, A.T. “Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development.” Dis Model Mech, 2012, 5(6),881-94. PMC3484870

Chu, S.W., Noyes, M.B., Christensen, R.G., Pierce, B.G., Zhu, L.J., Weng, Z., Stormo, G.D., Wolfe, S.A. “Exploring the DNA-recognition potential of homeodomains” Genome Res. 2012, 22(10),1889-98. PMC3460184.

Gupta, A., Christensen, R.G., Rayla, A.L., Lakshmanan, A., Stormo, G.D., Wolfe, S.A. “An optimized two-finger archive for ZFN-mediated gene targeting” Nat Methods. 2012, 9, 588–590. PMC3443678

Christensen, R.G., Enuameh, M.S., Noyes, M.B., Brodsky, M.H., Wolfe, S.A., Stormo, G.D. “Recognition models to predict DNA-binding specificities of homeodomain proteins” Bioinformatics. 2012, 28(12), i84-i89. PMC3371834

Lawson, N.D. & Wolfe, S.A. “Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish.” Dev Cell. 2011, 21(1), 48-64.  (Review)

Zhu, C., Smith, T., McNulty, J., Rayla, A.L., Lakshmanan, A., Siekmann, A.F., Buffardi, M., Meng, X.; Shin, J., Padmadanhan, A., Cifuentes, D.,Giraldez, G.; Look, A.T., Epstein, J.A.; Lawson, N. D., Wolfe, S.A., “Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish.” Development, 2011,138, 4555-64. PMC3177320

Christensen, R.G., Gupta, A., Zuo, Z., Schriefer, L.A., Wolfe, S.A., Stormo, G.D. “A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity”  Nucleic Acids Res. 2011, 39(12),e83. PMC3130293

Bussmann, J., Wolfe, S.A., Siekmann, A.F., “Arterial-venous network formation during brain vascularization involves hemodynamic regulation of chemokine signaling” Development 2011, 138, 1717-26. PMC3074448

Zhu, L.J., Christensen, R.G., Kazemian, M., Hull, C.J., Enuameh, M.S., Basciotta, M.D., Brasefield, J.A., Zhu, C., Asriyan, Y., Lapointe, D.S., Sinha, S., Wolfe, S.A.*, Brodsky, M.H.*, “FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.” Nucleic Acids Res. 2011, 39, D111-7. PMC3013762 *Co-corresponding author

Gupta, A., Meng, X., Zhu, L.J., Lawson, N.D., Wolfe, S.A., ”Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases.” Nucleic Acids Res. 2011, 39, 381-92. PMC3017618

Kazemian, M., Blatti, C., Richards, A., McCutchan, M., Wakabayashi-Ito, N., Hammonds, A.S., Celniker, S.E., Kumar, S., Wolfe, S.A., Brodsky, M.H., Sinha, S., “Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials.” PLoS Biol. 2010 8(8) e1000456. PMC2923081

Cifuentes, D., Xue, H., Taylor, D.W., Patnode, H., Mishima, Y., Cheloufi, S., Ma, E., Mane, S., Hannon, G.J., Lawson, N.D., Wolfe, S.A., Giraldez, A.J., “A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity” Science, 2010, 328,1694-8.  PMC3093307

Siekmann, A.F., Standley, C., Fogarty, K.E., Wolfe, S.A., Lawson, N.D. “Chemokine signaling guides regional patterning of the first embryonic artery” Genes Dev, 2009, 23, 2272-2277. Pubmed

Noyes, M.B., Christensen, R.G., Wakabayashi, A., Stormo, G.D., Brodsky, M.H.; Wolfe, S.A. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289. (Preview Cell, 2008, 133, 1133 & Editor’s Choice Science 2008, 321, 16.) PubMed

Meng, X., Noyes, M.B., Zhu, L.J., Lawson, N.D., Wolfe, S.A. (2008) Targeted gene inactivation in zebrafish using engineered zinc finger nucleases. Nat Biotechnol, 26, 695-701. (Research Highlight in Nature 2008, 453, 700 & Nat. Methods 2008, 5, 579.) PubMed

Noyes, M.B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M.H.; Wolfe, S.A. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Research, 36, 2547-2560. PubMed

Meng, X., Thibodeau-Beganny, S., Jiang, T., Joung, J. K., and Wolfe, S. A. (2007) Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Research, 35(11), e81.

Meng, X., Wolfe, S.A. (2006) Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nature Protocols 1, 30.

Meng, X., Brodsky, M.H., and Wolfe, S.A. (2005) A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol., 23: 988-994.

Wolfe, S.A., Grant, R.A., and Pabo, C.O. (2003) Structure of a designed dimeric zinc finger protein bound to DNA. Biochemistry, 42: 13401-13409.

Wolfe, S.A., Grant, R.A., Elrod-Erickson, M., and Pabo, C.O. (2001) Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure, 9: 717-723.

Wolfe, S.A, Ramm, E.I., and Pabo, C.O. (2000) Combining structure-based design with phage display to create new Cys2His2 zinc finger dimers. Structure, 8: 739-750.

Wolfe, S.A., Nekludova, L., and Pabo, C.O. (2000) DNA recognition by Cys2His2 zinc finger proteins. Ann. Rev. Biophys. Biomol. Struct., 29: 183-212.

Wolfe, S.A., Greisman, H.A., Ramm, E.I., and Pabo, C. O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol., 285: 1917-1934.

Pomerantz, J.P., Wolfe, S.A., and Pabo, C.O. (1998) Structure-based design of a dimeric zinc finger protein. Biochemistry, 37: 965-970.

Erlanson, D.A., Wolfe, S.A., Chen, L., and Verdine, G.L. (1997) Selective base-pair destabilization enhances binding of a DNA methyltransferase. Tetrahedron, 53: 12041-12056.

Wolfe, S.A., Zhou, P., Dtsch, V., Chen, L., You, A., Ho, S.H., Crabtree, G.R., Wagner, G., and Verdine, G.L. (1997) Unusual Rel-like architecture in the DNA-binding domain of the transcription factor NFATc. Nature, 385: 172-176.

Wolfe, S.A., Ferentz, A.E., Grantcharova, V., Churchill, M.E.A.,and Verdine, G.L. (1995) Modifying the helical structure of DNA by design: recruitment of an architecture-specific protein to an enforced DNA bend. Chem. Biol., 2: 213-221.

Wolfe, S.A. and Verdine, G.L. (1993) Ratcheting torsional stress in duplex DNA. J. Am. Chem. Soc., 115: 12585-12586.

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