Primary Research Publications
113. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, Zhang Y. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nature Biotechnology 30, 440–446 (2012)
112. Wojtasz L, Cloutier JM, Baumann M, Daniel K, Varga J, Fu J, Anastassiadis K, Stewart AF, Reményi A, Turner JM, Tóth A. Meiotic DNA double-strand breaks and chromosome asynapsis in mice are monitored by distinct HORMAD2-independent and -dependent mechanisms. Genes & Dev. 2012
111. Austenaa L, Barozzi I, Chronowska A, Termanini A, Ostuni R, Prosperini E, Stewart AF, Testa G, Natoli G. The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. Cell Press
110. Sarov, M., Murray, J., Schanze, K., Pozniakovski, A., Angermann, K., Preston, E., Zinke, A., Enst, S., Niu, W., Janette, J., Reis, K., Hasse, S., Schloissnig, S., Ejsmont, R. K., Slightam, C., Xu, X., Kim, S. K., Reinke, V., Stewart, A. F., Snyder, M., R., W. and Hyman, A. A. (2011). "The TransgeneOme of C. elegans: a platform for in vivo analysis of protein function." (in revision).
109. Nedelkova, M., Maresca, M., Fu, J., Rostovskaya, M., Chenna, R., Thiede, C., Anastassiadis, K., Sarov, M. and Stewart, A. F. (2011). "Targeted isolation of cloned genomic regions by recombineering for haplotype phasing and isogenic targeting." Nucleic Acids Res.
108. Bird, A. W., Erler, A., Fu, J., Hériché, J. K., Maresca, M., Zhang, Y., Hyman, A. A. and Stewart, A. F. (2011). "High efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes." Nat Methods.
107. Daniel, K., Lange, J., Hached, K., Fu, J., Anastassiadis, K., Roig, I., Cooke, H. J., Stewart, A. F., Wassmann, K., Jasin, M., Keeney, S. and Toth, A. (2011). "Meiotic homologue alignment and its quality surveillance are controlled by mouse HORMAD1." Nat Cell Biol 13:599-610.
106. Suckale, J., Wendling, O., Masjkur, J., Jager, M., Munster, C., Anastassiadis, K., Stewart, A. F. and Solimena, M. (2011). "PTBP1 Is Required for Embryonic Development before Gastrulation." PLoS One 6: e16992.
105. Marks, H., Denissov, S., Menafra, R., Kalkan, T., Jones, K., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A. F., Smith, A. and Stunnenberg, H. G. (2011). "The permissive epigenomic landscape of naïve pluripotency." (submitted).
104. Royer, L., Stewart, A. F. and Schroeder, M. (2011). "Evaluating coverage and accuracy of protein interaction datasets with network compression." (submitted).
103. Skarnes, W. C., Rosen, B., West, A. P., Koutsourakis, M., Bushell, W., Iyer, V., Cox, R., Jackson, D., Severin, J., Biggs, P., Thomas, M., Mujica, A., Harrow, J., Fu, J., Nefedov, M., de Jong, P., Stewart, A. F. and Bradley, A. (2011). "A conditional knockout resource for genome-wide analysis of mouse gene function." Nature 474: 62-263.
102. Tuukkanen, A., Huang, B., Henschel, A., Stewart, F. and Schroeder, M. (2010). "Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint-based docking." Proteomics.
101. Sinha, I., Buchanan, L., Rönnerblad, M., Bonilla, C., Durand-Dubief, M. l., Shevchenko, A., Grunstein, M., Stewart, A. F. and Ekwall, K. (2010). "Genome-wide mapping of histone modifications and mass spectrometry reveal H4 acetylation bias and H3K36 methylation at gene promoters in fission yeast." Epigenomics 2: 377-393.
100. Tang, Z., Zhang, Y., Stewart, A. F., Geng, M., Tang, X., Tu, Q. and Yin, Y. (2010). "High-level expression, purification and antibacterial activity of bovine lactoferricin and lactoferrampin in Photorhabdus luminescens." Protein Expr Purif 73: 132-9.
99. Andreu-Vieyra, C. V., Chen, R., Agno, J. E., Glaser, S., Anastassiadis, K., Stewart, A. F. and Matzuk, M. M. (2010). "MLL2 Is Required in Oocytes for Bulk Histone 3 Lysine 4 Trimethylation and Transcriptional Silencing." PLoS Biol 8.
98. Kranz, A., Fu, J., Duerschke, K., Weidlich, S., Naumann, R., Stewart, A. F. and Anastassiadis, K. (2010). "An improved Flp deleter mouse in C57Bl/6 based on Flpo recombinase." Genesis.
96. Maresca, M., Erler, A., Fu, J., Friedrich, A., Zhang, Y. and Stewart, A. F. (2010). "Single-stranded heteroduplex intermediates in lambda Red homologous recombination." BMC Mol Biol 11: 54.
97. Anastassiadis, K., Rostovskaya, M., Lubitz, S., Weidlich, S. and Stewart, A. F. (2010). "Precise conditional immortalization of mouse cells using tetracycline-regulated SV40 large T-antigen." Genesis
95. Schulz, H., Kolde, R., Adler, P., Aksoy, I., Anastassiadis, K., Bader, M., Billon, N., Boeuf, H., Bourillot, P. Y., Buchholz, F., Dani, C., Doss, M. X., Forrester, L., Gitton, M., Henrique, D., Hescheler, J., Himmelbauer, H., Hubner, N., Karantzali, E., Kretsovali, A., Lubitz, S., Pradier, L., Rai, M., Reimand, J., Rolletschek, A., Sachinidis, A., Savatier, P., Stewart, F., Storm, M. P., Trouillas, M., Vilo, J., Welham, M. J., Winkler, J., Wobus, A. M. and Hatzopoulos, A. K. (2009). "The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation." PLoS One 4: e6804.
94. Buchanan, L., Durand-Dubief, B., Roguev, A., Sakalar, C., Wilhelm, B., Stralfors, A., Shevchenko, A., Aasland, R., Shevchenko, A., Ekwall, K. and Stewart, A. F. (2009). "The S.pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains." PLoS Genetics 5: e1000726.
93. Anastassiadis, K., Fu, J., Patsch, C., Hu, S., Weidlich, S., Duerschke, K., Buchholz, F., Edenhofer, F. and Stewart, A. F. (2009). "Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice." Dis Model Mech 2: 508-15.
92. Cambridge, S. B., Geissler, D., Calegari, F., Anastassiadis, K., Hasan, M. T., Stewart, A. F. , Huttner, W. B., Hagen, V. and Bonhoeffer, T. (2009). "Doxycycline-dependent photoactivated gene expression in eukaryotic systems." Nat Methods 6: 527-31.
91. Erler, A., Wegmann, S., Elie-Caille, C., Bradshaw, C. R., Maresca, M., Seidel, R., Habermann, B., Muller, D. J. and Stewart, A. F. (2009). "Conformational adaptability of Redbeta during DNA annealing and implications for its structural relationship with Rad52." J Mol Biol 391: 586-98.
90. Ding, L., Paszkowski-Rogacz, M., Nitzsche, A., Slabicki, M. M., Heninger, A. K., de Vries, I., Kittler, R., Junqueira, M., Shevchenko, A., Schulz, H., Hubner, N., Doss, M. X., Sachinidis, A., Hescheler, J., Iacone, R., Anastassiadis, K., Stewart, A. F. , Pisabarro, M. T., Caldarelli, A., Poser, I., Theis, M. and Buchholz, F. (2009). "A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity." Cell Stem Cell 4: 403-15.
89. Glaser, S., Lubitz, S., Loveland, K. L., Ohbo, K., Robb, L., Schwenk, F., Seibler, J., Roellig, D., Kranz, A., Anastassiadis, K. and Stewart, A. F. (2009). "The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis." Epigenetics Chromatin 2: 5.
88. Shevchenko, A., Roguev, A., Schaft, D., Buchanan, L., Habermann, B., Sakalar, C., Thomas, H., Krogan, N. J. and Stewart, A. F. (2008). "Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment." Genome Biol 9: R167.
87. Fu, J., Wenzel, S. C., Perlova, O., Wang, J., Gross, F., Tang, Z., Yin, Y., Stewart, A. F. , Muller, R. and Zhang, Y. (2008). "Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition." Nucleic Acids Res 36: e113.
86. Poser, I., Sarov, M., Hutchins, J. R., Heriche, J. K., Toyoda, Y., Pozniakovsky, A., Weigl, D., Nitzsche, A., Hegemann, B., Bird, A. W., Pelletier, L., Kittler, R., Hua, S., Naumann, R., Augsburg, M., Sykora, M. M., Hofemeister, H., Zhang, Y., Nasmyth, K., White, K. P., Dietzel, S., Mechtler, K., Durbin, R., Stewart, A. F. , Peters, J. M., Buchholz, F. and Hyman, A. A. (2008). "BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals." Nat Methods 5: 409-15.
85. Augui, S., Filion, G. J., Huart, S., Nora, E., Guggiari, M., Maresca, M., Stewart, A. F. and Heard, E. (2007). "Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic." Science 318: 1632-6.
84. Lubitz, S., Glaser, S., Schaft, J., Stewart, A. F. and Anastassiadis, K. (2007). "Increased apoptosis and skewed differentiation in mouse embryonic stem cells lacking the histone methyltransferase Mll2." Mol Biol Cell 18: 2356-66.
83.Perlova, O., Fu, J., Kuhlmann, S., Krug, D., Stewart, A. F., Zhang, Y. and Muller, R. (2006). "Reconstitution of the myxothiazol biosynthetic gene cluster by Red/ET recombination and heterologous expression in Myxococcus xanthus." Appl Environ Microbiol 72: 7485-94.
82. Gross, F., Ring, M. W., Perlova, O., Fu, J., Schneider, S., Gerth, K., Kuhlmann, S., Stewart, A. F. , Zhang, Y. and Muller, R. (2006). "Metabolic engineering of Pseudomonas putida for methylmalonyl-CoA biosynthesis to enable complex heterologous secondary metabolite formation." Chem Biol 13: 1253-64.
81. Sarov, M., Schneider, S., Pozniakovski, A., Roguev, A., Ernst, S., Zhang, Y., Hyman, A. A. and Stewart, A. F. (2006). "A recombineering pipeline for functional genomics applied to Caenorhabditis elegans." Nat Methods 3: 839-44.
80. Dehe, P. M., Dichtl, B., Schaft, D., Roguev, A., Pamblanco, M., Lebrun, R., Rodriguez-Gil, A., Mkandawire, M., Landsberg, K., Shevchenko, A., Rosaleny, L. E., Tordera, V., Chavez, S., Stewart, A. F. and Geli, V. (2006). "Protein interactions within the Set1 complex and their roles in the regulation of histone 3 lysine 4 methylation." J Biol Chem 281: 35404-12.
79. Glaser, S., Schaft, J., Lubitz, S., Vintersten, K., van der Hoeven, F., Tufteland, K. R., Aasland, R., Anastassiadis, K., Ang, S. L. and Stewart, A. F. (2006). "Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development." Development 133: 1423-32.
78. Erler, A., Maresca, M., Fu, J. and Stewart, A. F. (2006). "Recombineering reagents for improved inducible expression and selection marker re-use in Schizosaccharomyces pombe." Yeast 23: 813-23.
77. Wang, J., Sarov, M., Rientjes, J., Fu, J., Hollak, H., Kranz, H., Xie, W., Stewart, A. F. and Zhang, Y. (2006). "An improved recombineering approach by adding RecA to lambda Red recombination." Mol Biotechnol 32: 43-53.
75. Herrmann, T., Grone, H. J., Langbein, L., Kaiser, I., Gosch, I., Bennemann, U., Metzger, D., Chambon, P., Stewart, A. F. and Stremmel, W. (2005). "Disturbed epidermal structure in mice with temporally controlled fatp4 deficiency." J Invest Dermatol 125: 1228-35.
73. Nedelcheva, M. N., Roguev, A., Dolapchiev, L. B., Shevchenko, A., Taskov, H. B., Stewart, A. F. and Stoynov, S. S. (2005). "Uncoupling of unwinding from DNA synthesis implies regulation of MCM helicase by Tof1/Mrc1/Csm3 checkpoint complex." J Mol Biol 347: 509-21.
74. Wenzel, S. C., Gross, F., Zhang, Y., Fu, J., Stewart, A. F. and Muller, R. (2005). "Heterologous expression of a myxobacterial natural products assembly line in pseudomonads via red/ET recombineering." Chem Biol 12: 349-56.
76. Zhang, D. J., Wang, Q., Wei, J., Baimukanova, G., Buchholz, F., Stewart, A. F. , Mao, X. and Killeen, N. (2005). "Selective expression of the Cre recombinase in late-stage thymocytes using the distal promoter of the Lck gene." J Immunol 174: 6725-31.
72. Roguev, A., Shevchenko, A., Schaft, D., Thomas, H. and Stewart, A. F. (2004). "A comparative analysis of an orthologous proteomic environment in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe." Mol Cell Proteomics 3: 125-32.
71. Testa, G., Schaft, J., van der Hoeven, F., Glaser, S., Anastassiadis, K., Zhang, Y., Hermann, T., Stremmel, W. and Stewart, A. F. (2004). "A reliable lacZ expression reporter cassette for multipurpose, knockout-first alleles." Genesis 38: 151-8.
70. Herrmann, T., Muckenthaler, M., van der Hoeven, F., Brennan, K., Gehrke, S. G., Hubert, N., Sergi, C., Grone, H. J., Kaiser, I., Gosch, I., Volkmann, M., Riedel, H. D., Hentze, M. W., Stewart, A. F. and Stremmel, W. (2004). "Iron overload in adult Hfe-deficient mice independent of changes in the steady-state expression of the duodenal iron transporters DMT1 and Ireg1/ferroportin." J Mol Med 82: 39-48.
69. Ennifar, E., Meyer, J. E., Buchholz, F., Stewart, A. F. and Suck, D. (2003). "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res 31: 5449-60.
68. Valenzuela, D. M., Murphy, A. J., Frendewey, D., Gale, N. W., Economides, A. N., Auerbach, W., Poueymirou, W. T., Adams, N. C., Rojas, J., Yasenchak, J., Chernomorsky, R., Boucher, M., Elsasser, A. L., Esau, L., Zheng, J., Griffiths, J. A., Wang, X., Su, H., Xue, Y., Dominguez, M. G., Noguera, I., Torres, R., Macdonald, L. E., Stewart, A. F. , DeChiara, T. M. and Yancopoulos, G. D. (2003). "High-throughput engineering of the mouse genome coupled with high-resolution expression analysis." Nat Biotechnol 21: 652-9.
67. Herrmann, T., van der Hoeven, F., Grone, H. J., Stewart, A. F. , Langbein, L., Kaiser, I., Liebisch, G., Gosch, I., Buchkremer, F., Drobnik, W., Schmitz, G. and Stremmel, W. (2003). "Mice with targeted disruption of the fatty acid transport protein 4 (Fatp 4, Slc27a4) gene show features of lethal restrictive dermopathy." J Cell Biol 161: 1105-15.
66. Schaft, D., Roguev, A., Kotovic, K. M., Shevchenko, A., Sarov, M., Neugebauer, K. M. and Stewart, A. F. (2003). "The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation." Nucleic Acids Res 31: 2475-82.
65. Testa, G., Zhang, Y., Vintersten, K., Benes, V., Pijnappel, W. W., Chambers, I., Smith, A. J., Smith, A. G. and Stewart, A. F. (2003). "Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles." Nat Biotechnol 21: 443-7.
64. Zhang, Y., Muyrers, J. P., Rientjes, J. and Stewart, A. F. (2003). "Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells." BMC Mol Biol 4: 1.
63. Voziyanov, Y., Konieczka, J. H., Stewart, A. F. and Jayaram, M. (2003). "Stepwise manipulation of DNA specificity in Flp recombinase: progressively adapting Flp to individual and combinatorial mutations in its target site." J Mol Biol 326: 65-76.
62. Roguev, A., Schaft, D., Shevchenko, A., Aasland, R. and Stewart, A. F. (2003). "High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in budding and fission yeasts." J Biol Chem 278: 8487-93.
61. Anastassiadis, K., Kim, J., Daigle, N., Sprengel, R., Scholer, H. R. and Stewart, A. F. (2002). "A predictable ligand regulated expression strategy for stably integrated transgenes in mammalian cells in culture." Gene 298: 159-72.
60. Shevchenko, A., Schaft, D., Roguev, A., Pijnappel, W. W. and Stewart, A. F. (2002). "Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry: analytical perspective." Mol Cell Proteomics 1: 204-12.
59. Casanova, E., Fehsenfeld, S., Greiner, E., Stewart, A. F. and Schutz, G. (2002). "Construction of a conditional allele of RSK-B/MSK2 in the mouse." Genesis 32: 158-60.
58. Casanova, E., Lemberger, T., Fehsenfeld, S., Greiner, E., Stewart, A. F. and Schutz, G. (2002). "Rapid localization of a gene within BACs and PACs." Biotechniques 32: 240-2.
57. Casanova, E., Fehsenfeld, S., Greiner, E., Stewart, A. F. and Schutz, G. (2002). "Conditional mutagenesis of CamKIV." Genesis 32: 161-4.
56. Voziyanov, Y., Stewart, A. F. and Jayaram, M. (2002). "A dual reporter screening system identifies the amino acid at position 82 in Flp site-specific recombinase as a determinant for target specificity." Nucleic Acids Res 30: 1656-63.
55. Shimshek, D. R., Kim, J., Hubner, M. R., Spergel, D. J., Buchholz, F., Casanova, E., Stewart, A. F. , Seeburg, P. H. and Sprengel, R. (2002). "Codon-improved Cre recombinase (iCre) expression in the mouse." Genesis 32: 19-26.
54. Andreu, T., Ebensperger, C., Westphal, E. M., Klenner, T., Stewart, A. F. , Westhof, A., Muller, P., Knaus, R. and von Melchner, H. (2001). "Self-deleting suicide vectors (SDSV): selective killing of p53-deficient cancer cells." Cancer Res 61: 6925-30.
53. Casanova, E., Fehsenfeld, S., Mantamadiotis, T., Lemberger, T., Greiner, E., Stewart, A. F. and Schutz, G. (2001). "A CamKIIalpha iCre BAC allows brain-specific gene inactivation." Genesis 31: 37-42.
52. Roguev, A., Schaft, D., Shevchenko, A., Pijnappel, W. W., Wilm, M., Aasland, R. and Stewart, A. F. (2001). "The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4." EMBO J 20: 7137-48.
51. Pijnappel, W. W., Schaft, D., Roguev, A., Shevchenko, A., Tekotte, H., Wilm, M., Rigaut, G., Seraphin, B., Aasland, R. and Stewart, A. F. (2001). "The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program." Genes Dev 15: 2991-3004.
50. Buchholz, F. and Stewart, A. F. (2001). "Alteration of Cre recombinase site specificity by substrate-linked protein evolution." Nat Biotechnol 19: 1047-52.
49. Schaft, J., Ashery-Padan, R., van der Hoeven, F., Gruss, P. and Stewart, A. F. (2001). "Efficient FLP recombination in mouse ES cells and oocytes." Genesis 31: 6-10.
48. Angrand, P. O., Apiou, F., Stewart, A. F. , Dutrillaux, B., Losson, R. and Chambon, P. (2001). "NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines." Genomics 74: 79-88.
47. Zhang, Y., Muyrers, J. P., Testa, G. and Stewart, A. F. (2000). "DNA cloning by homologous recombination in Escherichia coli." Nat Biotechnol 18: 1314-7.
46. Muyrers, J. P., Zhang, Y., Benes, V., Testa, G., Ansorge, W. and Stewart, A. F. (2000). "Point mutation of bacterial artificial chromosomes by ET recombination." EMBO Rep 1: 239-43.
45. Muyrers, J. P., Zhang, Y., Buchholz, F. and Stewart, A. F. (2000). "RecE/RecT and Redalpha/Redbeta initiate double-stranded break repair by specifically interacting with their respective partners." Genes Dev 14: 1971-82.
44. Rodriguez, C. I., Buchholz, F., Galloway, J., Sequerra, R., Kasper, J., Ayala, R., Stewart, A. F. and Dymecki, S. M. (2000). "High-efficiency deleter mice show that FLPe is an alternative to Cre-loxP." Nat Genet 25: 139-40.
43. Hill, F., Benes, V., Thomasova, D., Stewart, A. F. , Kafatos, F. C. and Ansorge, W. (2000). "BAC trimming: minimizing clone overlaps." Genomics 64: 111-3.
42. Ringrose, L., Chabanis, S., Angrand, P. O., Woodroofe, C. and Stewart, A. F. (1999). "Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances." EMBO J 18: 6630-41.
41. Angrand, P. O., Daigle, N., van der Hoeven, F., Scholer, H. R. and Stewart, A. F. (1999). "Simplified generation of targeting constructs using ET recombination." Nucleic Acids Res 27: e16.
40. Narayanan, K., Williamson, R., Zhang, Y., Stewart, A. F. and Ioannou, P. A. (1999). "Efficient and precise engineering of a 200 kb beta-globin human/bacterial artificial chromosome in E. coli DH10B using an inducible homologous recombination system." Gene Ther 6: 442-7.
39. Fukagawa, T., Hayward, N., Yang, J., Azzalin, C., Griffin, D., Stewart, A. F. and Brown, W. (1999). "The chicken HPRT gene: a counter selectable marker for the DT40 cell line." Nucleic Acids Res 27: 1966-9.
38. Muyrers, J. P., Zhang, Y., Testa, G. and Stewart, A. F. (1999). "Rapid modification of bacterial artificial chromosomes by ET-recombination." Nucleic Acids Res 27: 1555-7.
37. Zhang, Y., Buchholz, F., Muyrers, J. P. and Stewart, A. F. (1998). "A new logic for DNA engineering using recombination in Escherichia coli." Nat Genet 20: 123-8.
36. Ringrose, L., Lounnas, V., Ehrlich, L., Buchholz, F., Wade, R. and Stewart, A. F. (1998). "Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination." J Mol Biol 284: 363-84.
35. Angrand, P. O., Woodroofe, C. P., Buchholz, F. and Stewart, A. F. (1998). "Inducible expression based on regulated recombination: a single vector strategy for stable expression in cultured cells." Nucleic Acids Res 26: 3263-9.
34. Logie, C., Nichols, M., Myles, K., Funder, J. W. and Stewart, A. F. (1998). "Positive and negative discrimination of estrogen receptor agonists and antagonists using site-specific DNA recombinase fusion proteins." Mol Endocrinol 12: 1120-32.
33. Buchholz, F., Angrand, P. O. and Stewart, A. F. (1998). "Improved properties of FLP recombinase evolved by cycling mutagenesis." Nat Biotechnol 16: 657-62.
32. Nichols, M., Rientjes, J. M. and Stewart, A. F. (1998). "Different positioning of the ligand-binding domain helix 12 and the F domain of the estrogen receptor accounts for functional differences between agonists and antagonists." EMBO J 17: 765-73.
31. Schwenk, F., Kuhn, R., Angrand, P. O., Rajewsky, K. and Stewart, A. F. (1998). "Temporally and spatially regulated somatic mutagenesis in mice." Nucleic Acids Res 26: 1427-32.
30. Nichols, M., Rientjes, J. M., Logie, C. and Stewart, A. F. (1997). "FLP recombinase/estrogen receptor fusion proteins require the receptor D domain for responsiveness to antagonists, but not agonists." Mol Endocrinol 11: 950-61.
29. Ringrose, L., Angrand, P. O. and Stewart, A. F. (1997). "The Kw recombinase, an integrase from Kluyveromyces waltii." Eur J Biochem 248: 903-12.
28. Herrera, R. E., Nordheim, A. and Stewart, A. F. (1997). "Chromatin structure analysis of the human c-fos promoter reveals a centrally positioned nucleosome." Chromosoma 106: 284-92.
27. Buchholz, F., Ringrose, L., Angrand, P. O., Rossi, F. and Stewart, A. F. (1996). "Different thermostabilities of FLP and Cre recombinases: implications for applied site-specific recombination." Nucleic Acids Res 24: 4256-62.
26. Buchholz, F., Angrand, P. O. and Stewart, A. F. (1996). "A simple assay to determine the functionality of Cre or FLP recombination targets in genomic manipulation constructs." Nucleic Acids Res 24: 3118-9.
25. Aasland, R., Stewart, A. F. and Gibson, T. (1996). "The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB." Trends Biochem Sci 21: 87-8.
24. Rossi, F., McNagny, K. M., Logie, C., Stewart, A. F. and Graf, T. (1996). "Excision of Ets by an inducible site-specific recombinase causes differentiation of Myb-Ets-transformed hematopoietic progenitors." Curr Biol 6: 866-72.
23. Kellendonk, C., Tronche, F., Monaghan, A. P., Angrand, P. O., Stewart, A. F. and Schutz, G. (1996). "Regulation of Cre recombinase activity by the synthetic steroid RU 486." Nucleic Acids Res 24: 1404-11.
22. Aasland, R. and Stewart, A. F. (1995). "The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1." Nucleic Acids Res 23: 3168-73.
21. Logie, C. and Stewart, A. F. (1995). "Ligand-regulated site-specific recombination." Proc Natl Acad Sci U S A 92: 5940-4.
20. Aasland, R., Gibson, T. J. and Stewart, A. F. (1995). "The PHD finger: implications for chromatin-mediated transcriptional regulation." Trends Biochem Sci 20: 56-9.
19. Reik, A., Stewart, A. F. and Schutz, G. (1994). "Cross-talk modulation of signal transduction pathways: two mechanisms are involved in the control of tyrosine aminotransferase gene expression by phorbol esters." Mol Endocrinol 8: 490-7.
18. Thomas, H. E., Stunnenberg, H. G. and Stewart, A. F. (1993). "Heterodimerization of the Drosophila ecdysone receptor with retinoid X receptor and ultraspiracle." Nature 362: 471-5.
17. Strähle, U., Schmidt, A., Kelsey, G., Stewart, A. F. , Cole, T. J., Schmid, W. and Schutz, G. (1992). "At least three promoters direct expression of the mouse glucocorticoid receptor gene." Proc Natl Acad Sci U S A 89: 6731-5.
16. Reik, A., Schutz, G. and Stewart, A. F. (1991). "Glucocorticoids are required for establishment and maintenance of an alteration in chromatin structure: induction leads to a reversible disruption of nucleosomes over an enhancer." EMBO J 10: 2569-76.
15. Stewart, A. F. , Reik, A. and Schutz, G. (1991). "A simpler and better method to cleave chromatin with DNase 1 for hypersensitive site analyses." Nucleic Acids Res 19: 3157.
14. Weih, F., Stewart, A. F. , Boshart, M., Nitsch, D. and Schutz, G. (1990). "In vivo monitoring of a cAMP-stimulated DNA-binding activity." Genes Dev 4: 1437-49.
13. Nitsch, D., Stewart, A. F. , Boshart, M., Mestril, R., Weih, F. and Schutz, G. (1990). "Chromatin structures of the rat tyrosine aminotransferase gene relate to the function of its cis-acting elements." Mol Cell Biol 10: 3334-42.
12. Stewart, A. F. , Herrera, R. E. and Nordheim, A. (1990). "Rapid induction of c-fos transcription reveals quantitative linkage of RNA polymerase II and DNA topoisomerase I enzyme activities." Cell 60: 141-9.
11. Alexander, L. J., Hayes, G., Pearse, M. J., Beattie, C. W., Stewart, A. F. , Willis, I. M. and Mackinlay, A. G. (1989). "Complete sequence of the bovine beta-lactoglobulin cDNA." Nucleic Acids Res 17: 6739.
10. Strähle, U., Boshart, M., Klock, G., Stewart, A. F. and Schutz, G. (1989). "Glucocorticoid- and progesterone-specific effects are determined by differential expression of the respective hormone receptors." Nature 339: 629-32.
9. Bonsing, J., Ring, J. M., Stewart, A. F. and Mackinlay, A. G. (1988). "Complete nucleotide sequence of the bovine beta-casein gene." Aust J Biol Sci 41: 527-37.
8. Weih, F., Stewart, A. F. and Schutz, G. (1988). "A novel and rapid method to generate single stranded DNA probes for genomic footprinting." Nucleic Acids Res 16: 1628.
7. Alexander, L. J., Stewart, A. F. , Mackinlay, A. G., Kapelinskaya, T. V., Tkach, T. M. and Gorodetsky, S. I. (1988). "Isolation and characterization of the bovine kappa-casein gene." Eur J Biochem 178: 395-401.
6. Stewart, A. F. and Schutz, G. (1987). "Camptothecin-induced in vivo topoisomerase I cleavages in the transcriptionally active tyrosine aminotransferase gene." Cell 50: 1109-17.
5. Stewart, A. F. , Bonsing, J., Beattie, C. W., Shah, F., Willis, I. M. and Mackinlay, A. G. (1987). "Complete nucleotide sequences of bovine alpha S2- and beta-casein cDNAs: comparisons with related sequences in other species." Mol Biol Evol 4: 231-41.
4. Jantzen, H. M., Strahle, U., Gloss, B., Stewart, A. F. , Schmid, W., Boshart, M., Miksicek, R. and Schutz, G. (1987). "Cooperativity of glucocorticoid response elements located far upstream of the tyrosine aminotransferase gene." Cell 49: 29-38.
3. Yu-Lee, L. Y., Richter-Mann, L., Couch, C. H., Stewart, A. F. , Mackinlay, A. G. and Rosen, J. M. (1986). "Evolution of the casein multigene family: conserved sequences in the 5' flanking and exon regions." Nucleic Acids Res 14: 1883-902.
2. Stewart, A. F. , Willis, I. M. and Mackinlay, A. G. (1984). "Nucleotide sequences of bovine alpha S1- and kappa-casein cDNAs." Nucleic Acids Res 12: 3895-907.
1. Willis, I. M., Stewart, A. F. , Caputo, A., Thompson, A. R. and Mackinlay, A. G. (1982). "Construction and identification by partial nucleotide sequence analysis of bovine casein and beta-lactoglobulin cDNA clones." DNA 1: 375-86.
Reviewed Book Chapters, Commentaries and Reviews (Selected)
26. Ejsmont, R. K., Ahlfeld, P., Pozniakovsky, A., Stewart, A. F., Tomancak, P. and Sarov, M. (2011). "Recombination-mediated genetic engineering of large genomic DNA transgenes." Methods Mol Biol 772: 445-58.
25. Justice, M. J., Siracusa, L. D. and Stewart, A. F. (2011). "Technical approaches for mouse models of human disease." Dis Model Mech 4: 305-10.
24. Hofemeister, H., Ciotta, G., Fu, J., Seibert, P. M., Schulz, A., Maresca, M., Sarov, M., Anastassiadis, K. and Stewart, A. F. (2011). "Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis." Methods.
23. von Melchner, H. and Stewart, A. F. (2011). "Methods for Extracting Function from the Mammalian Genome." Methods.
22. Ciotta, G., Hofemeister, H., Maresca, M., Fu, J., Sarov, M., Anastassiadis, K. and Stewart, A. F. (2010). "Recombineering BAC transgenes for protein tagging." Methods.
21. Fu, J., Teucher, M., Anastassiadis, K., Skarnes, W. and Stewart, A. F. (2010). "A Recombineering Pipeline to Make Conditional Targeting Constructs." Methods Enzymol 477C: 125-144.
20. Anastassiadis, K., Glaser, S., Kranz, A., Bernhardt, K. and Stewart, A. F. (2010). "A Practical Summary of Site-Specific Recombination, Conditional Mutagenesis, and Tamoxifen Induction of CreERT2." Methods Enzymol 477C: 109-123.
19. Vintersten, K., Testa, G., Naumann, R., Anastassiadis, K. and Stewart, A. F. (2008). "Bacterial artificial chromosome transgenesis through pronuclear injection of fertilized mouse oocytes." Methods Mol Biol 415: 83-100.
18. Schnütgen, F., Stewart, A. F., von Melchner, H. and Anastassiadis, K. (2006). "Engineering embryonic stem cells with recombinase systems." Methods Enzymol 420: 100-36.
17. Glaser, S., Anastassiadis, K. and Stewart, A. F. (2005). "Current issues in mouse genome engineering." Nat Genet 37: 1187-93.
16. Sarov, M. and Stewart, A. F. (2005). "The best control for the specificity of RNAi." Trends Biotechnol 23: 446-8.
15. Auwerx, J., Avner, P., Baldock, R., Ballabio, A., Balling, R., Barbacid, M., Berns, A., Bradley, A., Brown, S., Carmeliet, P., Chambon, P., Cox, R., Davidson, D., Davies, K., Duboule, D., Forejt, J., Granucci, F., Hastie, N., de Angelis, M. H., Jackson, I., Kioussis, D., Kollias, G., Lathrop, M., Lendahl, U., Malumbres, M., von Melchner, H., Muller, W., Partanen, J., Ricciardi-Castagnoli, P., Rigby, P., Rosen, B., Rosenthal, N., Skarnes, B., Stewart, A. F., Thornton, J., Tocchini-Valentini, G., Wagner, E., Wahli, W. and Wurst, W. (2004). "The European dimension for the mouse genome mutagenesis program." Nat Genet 36: 925-7.
14. Austin, C. P., Battey, J. F., Bradley, A., Bucan, M., Capecchi, M., Collins, F. S., Dove, W. F., Duyk, G., Dymecki, S., Eppig, J. T., Grieder, F. B., Heintz, N., Hicks, G., Insel, T. R., Joyner, A., Koller, B. H., Lloyd, K. C., Magnuson, T., Moore, M. W., Nagy, A., Pollock, J. D., Roses, A. D., Sands, A. T., Seed, B., Skarnes, W. C., Snoddy, J., Soriano, P., Stewart, D. J., Stewart, A. F., Stillman, B., Varmus, H., Varticovski, L., Verma, I. M., Vogt, T. F., von Melchner, H., Witkowski, J., Woychik, R. P., Wurst, W., Yancopoulos, G. D., Young, S. G. and Zambrowicz, B. (2004). "The knockout mouse project." Nat Genet 36: 921-4.
13. von Melchner, H., Stewart, A. F., Robert, L., John, G., Brigid, H., Douglas, M., Roger, P., James, T. and Michael, W. (2004). "Engineering of ES Cell Genomes with Recombinase Systems." In Handbook of Stem Cells. Burlington, Academic Press: 609-622.
12. Vintersten, K., Testa, G. and Stewart, A. F. (2004). "Microinjection of BAC DNA into the pronuclei of fertilized mouse oocytes." Methods Mol Biol 256: 141-58.
11. Testa, G., Vintersten, K., Zhang, Y., Benes, V., Muyrers, J. P. and Stewart, A. F. (2004). "BAC engineering for the generation of ES cell-targeting constructs and mouse transgenes." Methods Mol Biol 256: 123-39.
10. Muyrers, J. P., Zhang, Y., Benes, V., Testa, G., Rientjes, J. M. and Stewart, A. F. (2004). "ET recombination: DNA engineering using homologous recombination in E. coli." Methods Mol Biol 256: 107-21.
9. Muyrers, J. P., Zhang, Y. and Stewart, A. F. (2001). "Techniques: Recombinogenic engineering--new options for cloning and manipulating DNA." Trends Biochem Sci 26: 325-31.
8. Muyrers, J. P., Zhang, Y. and Stewart, A. F. (2000). "ET-cloning: think recombination first." Genet Eng (N Y) 22: 77-98.
7. Testa, G. and Stewart, A. F. (2000). "Creating a transloxation. Engineering interchromosomal translocations in the mouse." EMBO Rep 1: 120-1.
6. Aasland, R. and Stewart, A. F. (1999). "Analysis of DNaseI hypersensitive sites in chromatin by cleavage in permeabilized cells." Methods Mol Biol 119: 355-62.
5. Gasser, S. M., Paro, R., Stewart, A. F. and Aasland, R. (1998). "The genetics of epigenetics." Cell Mol Life Sci 54: 1-5.
4. Angrand, P. O., Woodroofe, C. P. and Stewart, A. F. (1997). "Application of ligand-dependent site-specific recombination in ES cells." In Microinjection and transgenesis : strategies and protocols. A. Cid - Arregui and A. Garcia - Carranca. Heidelberg, New York, Tokyo, Springer: 225-274.
3. Reik, A., Schütz, G., Stewart, A. F. and Bittar, E. E. (1997). "Analyzing Hormone Regulation of Transcription by Genomic Footprinting." In Advances in Molecular and Cell Biology, Elsevier. Volume 21: 159-180.
2. Stewart, A. F., Logie, C. and Nichols, M. (1996). "Regulation of nuclear receptors by agonists and antagonists." Current Opinion in Endocrinology, Diabetes and Obesity 3: 397-402.
1. Shaw, P. E. and Stewart, A. F. (1994/2001). "Identification of protein-DNA contacts with dimethyl sulfate. Methylation protection and methylation interference." Methods Mol Biol 30: 79-87.
