Team:Penn/References

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             <b><center><h1>
             <b><center><h1>
References
References
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<p>
<p>
Baylin, S. B., Herman, J. G., Graff, J. R., Vertino, P. M., & Issa, J. P. (1998). Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res, 72, 141-196.
Baylin, S. B., Herman, J. G., Graff, J. R., Vertino, P. M., & Issa, J. P. (1998). Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res, 72, 141-196.
-
 
+
<br>
  <br>
  <br>
Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., & Marraffini, L. A. (2013). Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res, 41(15), 7429-7437.
Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., & Marraffini, L. A. (2013). Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res, 41(15), 7429-7437.
-
  <br>
+
  <br> <br>
Cong, L., Zhou, R., Kuo, Y. C., Cunniff, M., & Zhang, F. (2012). Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun, 3, 968.
Cong, L., Zhou, R., Kuo, Y. C., Cunniff, M., & Zhang, F. (2012). Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun, 3, 968.
-
 
+
<br>
   <br>
   <br>
Cooper, D. N., & Youssoufian, H. (1988). The CpG dinucleotide and human genetic disease. Hum Genet, 78(2), 151-155.
Cooper, D. N., & Youssoufian, H. (1988). The CpG dinucleotide and human genetic disease. Hum Genet, 78(2), 151-155.
-
 
+
<br>
   
   
  <br>
  <br>
Darst, R. P., Pardo, C. E., Ai, L., Brown, K. D., & Kladde, M. P. (2010). Bisulfite sequencing of DNA. Curr Protoc Mol Biol, Chapter 7, Unit 7 9 1-17.
Darst, R. P., Pardo, C. E., Ai, L., Brown, K. D., & Kladde, M. P. (2010). Bisulfite sequencing of DNA. Curr Protoc Mol Biol, Chapter 7, Unit 7 9 1-17.
-
+
  <br>
  <br>
  <br>
 +
Protein structure prediction on the web: a case study using the Phyre server
 +
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009)
 +
</br></br>
Daya, S., & Berns, K. I. (2008). Gene therapy using adeno-associated virus vectors. Clin Microbiol Rev, 21(4), 583-593.
Daya, S., & Berns, K. I. (2008). Gene therapy using adeno-associated virus vectors. Clin Microbiol Rev, 21(4), 583-593.
-
   <br>
+
   <br> <br>
Desjarlais, J. R., & Berg, J. M. (1992). Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc Natl Acad Sci U S A, 89(16), 7345-7349.
Desjarlais, J. R., & Berg, J. M. (1992). Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc Natl Acad Sci U S A, 89(16), 7345-7349.
   
   
-
  <br>
+
  <br> <br>
Ellis, B. L., Hirsch, M. L., Barker, J. C., Connelly, J. P., Steininger, R. J., 3rd, & Porteus, M. H. (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. Virol J, 10, 74.
Ellis, B. L., Hirsch, M. L., Barker, J. C., Connelly, J. P., Steininger, R. J., 3rd, & Porteus, M. H. (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. Virol J, 10, 74.
-
+
  <br>
  <br>
  <br>
Gaj, T., Gersbach, C. A., & Barbas, C. F., 3rd. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 31(7), 397-405.
Gaj, T., Gersbach, C. A., & Barbas, C. F., 3rd. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 31(7), 397-405.
-
+
  <br>
  <br>
  <br>
Jones, P. A. (1999). DNA methylation in development of bladder cancer. Adv Exp Med Biol, 462, 419-423.
Jones, P. A. (1999). DNA methylation in development of bladder cancer. Adv Exp Med Biol, 462, 419-423.
-
+
  <br>
  <br>
  <br>
Jones, P. L., Veenstra, G. J., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., et al. (1998). Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet, 19(2), 187-191.
Jones, P. L., Veenstra, G. J., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., et al. (1998). Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet, 19(2), 187-191.
-
   <br>
+
   <br> <br>
Klose, R. J., & Bird, A. P. (2006). Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci, 31(2), 89-97.
Klose, R. J., & Bird, A. P. (2006). Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci, 31(2), 89-97.
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+
<br>
   <br>
   <br>
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  <br> <br>
Li, F., Papworth, M., Minczuk, M., Rohde, C., Zhang, Y., Ragozin, S., et al. (2007). Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes. Nucleic Acids Res, 35(1), 100-112.
Li, F., Papworth, M., Minczuk, M., Rohde, C., Zhang, Y., Ragozin, S., et al. (2007). Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes. Nucleic Acids Res, 35(1), 100-112.
-
   <br>
+
   <br> <br>
Li, L. C., & Dahiya, R. (2002). MethPrimer: designing primers for methylation PCRs. Bioinformatics, 18(11), 1427-1431.
Li, L. C., & Dahiya, R. (2002). MethPrimer: designing primers for methylation PCRs. Bioinformatics, 18(11), 1427-1431.
   <br>
   <br>
-
 
+
<br>
Nan, X., Cross, S., & Bird, A. (1998). Gene silencing by methyl-CpG-binding proteins. Novartis Found Symp, 214, 6-16; discussion 16-21, 46-50.
Nan, X., Cross, S., & Bird, A. (1998). Gene silencing by methyl-CpG-binding proteins. Novartis Found Symp, 214, 6-16; discussion 16-21, 46-50.
  <br>
  <br>
-
+
  <br>
Papworth, M., Kolasinska, P., & Minczuk, M. (2006). Designer zinc-finger proteins and their applications. Gene, 366(1), 27-38.
Papworth, M., Kolasinska, P., & Minczuk, M. (2006). Designer zinc-finger proteins and their applications. Gene, 366(1), 27-38.
-
   <br>
+
   <br> <br>
Rideout, W. M., 3rd, Coetzee, G. A., Olumi, A. F., & Jones, P. A. (1990). 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science, 249(4974), 1288-1290.
Rideout, W. M., 3rd, Coetzee, G. A., Olumi, A. F., & Jones, P. A. (1990). 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science, 249(4974), 1288-1290.
-
   <br>
+
   <br> <br>
Sanjana, N. E., Cong, L., Zhou, Y., Cunniff, M. M., Feng, G., & Zhang, F. (2012). A transcription activator-like effector toolbox for genome engineering. Nat Protoc, 7(1), 171-192.
Sanjana, N. E., Cong, L., Zhou, Y., Cunniff, M. M., Feng, G., & Zhang, F. (2012). A transcription activator-like effector toolbox for genome engineering. Nat Protoc, 7(1), 171-192.
-
   <br>
+
   <br> <br>
van Steensel, B., & Henikoff, S. (2000). Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol, 18(4), 424-428.
van Steensel, B., & Henikoff, S. (2000). Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol, 18(4), 424-428.
   <br>
   <br>
-
 
+
<br>
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., et al. (2001). The sequence of the human genome. Science, 291(5507), 1304-1351.
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., et al. (2001). The sequence of the human genome. Science, 291(5507), 1304-1351.
-
   <br>
+
   <br> <br>
Wan, M., Lee, S. S., Zhang, X., Houwink-Manville, I., Song, H. R., Amir, R. E., et al. (1999). Rett syndrome and beyond: recurrent spontaneous and familial MECP2 mutations at CpG hotspots. Am J Hum Genet, 65(6), 1520-1529.
Wan, M., Lee, S. S., Zhang, X., Houwink-Manville, I., Song, H. R., Amir, R. E., et al. (1999). Rett syndrome and beyond: recurrent spontaneous and familial MECP2 mutations at CpG hotspots. Am J Hum Genet, 65(6), 1520-1529.
   <br>
   <br>
-
 
+
<br>
Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., et al. (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell, 153(4), 910-918.
Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., et al. (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell, 153(4), 910-918.
   <br>
   <br>
-
 
+
<br>
Wang, H. H., & Church, G. M. (2011). Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol, 498, 409-426.
Wang, H. H., & Church, G. M. (2011). Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol, 498, 409-426.
   <br>
   <br>
-
 
+
<br>
Xiong, Z., & Laird, P. W. (1997). COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res, 25(12), 2532-2534.
Xiong, Z., & Laird, P. W. (1997). COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res, 25(12), 2532-2534.
   <br>
   <br>
-
 
+
<br>
Xu, G. L., & Bestor, T. H. (1997). Cytosine methylation targetted to pre-determined sequences. Nat Genet, 17(4), 376-378. </p></div>
Xu, G. L., & Bestor, T. H. (1997). Cytosine methylation targetted to pre-determined sequences. Nat Genet, 17(4), 376-378. </p></div>
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References


Baylin, S. B., Herman, J. G., Graff, J. R., Vertino, P. M., & Issa, J. P. (1998). Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res, 72, 141-196.

Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., & Marraffini, L. A. (2013). Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res, 41(15), 7429-7437.

Cong, L., Zhou, R., Kuo, Y. C., Cunniff, M., & Zhang, F. (2012). Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun, 3, 968.

Cooper, D. N., & Youssoufian, H. (1988). The CpG dinucleotide and human genetic disease. Hum Genet, 78(2), 151-155.

Darst, R. P., Pardo, C. E., Ai, L., Brown, K. D., & Kladde, M. P. (2010). Bisulfite sequencing of DNA. Curr Protoc Mol Biol, Chapter 7, Unit 7 9 1-17.

Protein structure prediction on the web: a case study using the Phyre server Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009)

Daya, S., & Berns, K. I. (2008). Gene therapy using adeno-associated virus vectors. Clin Microbiol Rev, 21(4), 583-593.

Desjarlais, J. R., & Berg, J. M. (1992). Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc Natl Acad Sci U S A, 89(16), 7345-7349.

Ellis, B. L., Hirsch, M. L., Barker, J. C., Connelly, J. P., Steininger, R. J., 3rd, & Porteus, M. H. (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. Virol J, 10, 74.

Gaj, T., Gersbach, C. A., & Barbas, C. F., 3rd. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 31(7), 397-405.

Jones, P. A. (1999). DNA methylation in development of bladder cancer. Adv Exp Med Biol, 462, 419-423.

Jones, P. L., Veenstra, G. J., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., et al. (1998). Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet, 19(2), 187-191.

Klose, R. J., & Bird, A. P. (2006). Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci, 31(2), 89-97.

Konermann, S., Brigham, M. D., Trevino, A. E., Hsu, P. D., Heidenreich, M., Cong, L., et al. (2013). Optical control of mammalian endogenous transcription and epigenetic states. Nature, 500(7463), 472-476.

Li, F., Papworth, M., Minczuk, M., Rohde, C., Zhang, Y., Ragozin, S., et al. (2007). Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes. Nucleic Acids Res, 35(1), 100-112.

Li, L. C., & Dahiya, R. (2002). MethPrimer: designing primers for methylation PCRs. Bioinformatics, 18(11), 1427-1431.

Nan, X., Cross, S., & Bird, A. (1998). Gene silencing by methyl-CpG-binding proteins. Novartis Found Symp, 214, 6-16; discussion 16-21, 46-50.

Papworth, M., Kolasinska, P., & Minczuk, M. (2006). Designer zinc-finger proteins and their applications. Gene, 366(1), 27-38.

Rideout, W. M., 3rd, Coetzee, G. A., Olumi, A. F., & Jones, P. A. (1990). 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science, 249(4974), 1288-1290.

Sanjana, N. E., Cong, L., Zhou, Y., Cunniff, M. M., Feng, G., & Zhang, F. (2012). A transcription activator-like effector toolbox for genome engineering. Nat Protoc, 7(1), 171-192.

van Steensel, B., & Henikoff, S. (2000). Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol, 18(4), 424-428.

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., et al. (2001). The sequence of the human genome. Science, 291(5507), 1304-1351.

Wan, M., Lee, S. S., Zhang, X., Houwink-Manville, I., Song, H. R., Amir, R. E., et al. (1999). Rett syndrome and beyond: recurrent spontaneous and familial MECP2 mutations at CpG hotspots. Am J Hum Genet, 65(6), 1520-1529.

Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., et al. (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell, 153(4), 910-918.

Wang, H. H., & Church, G. M. (2011). Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol, 498, 409-426.

Xiong, Z., & Laird, P. W. (1997). COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res, 25(12), 2532-2534.

Xu, G. L., & Bestor, T. H. (1997). Cytosine methylation targetted to pre-determined sequences. Nat Genet, 17(4), 376-378.



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