Publications

Medina-Ruiz, L., Bartolini, R., Wilson, G.J., Dyer, D.P., Vidler, F., Hughes, C.E., Schuette, F., Love, S., Pingen, M., Hayes, A.J., Fu, J., Stewart, A.F. and Graham, G.J. (2022), "Analysis of combinatorial chemokine receptor expression dynamics using multi-receptor reporter mice" Elife, 11: e72418

Hanna, C.W., Huang, J., Belton, C., Reinhardt, S., Dahl, A., Andrews, S., Stewart, A.F., Kranz, A. and Kelsey. G. (2022), "Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation" Nucleic Acdis Res., 50(4), 1993 - 2004; doi: 10.1093/nar/gkac051

Grinat, J., Kosel, F., Goveas, N., Kranz, A., Alexopoulou, D., Rajewsky, K., Sigal, M., Stewart, A.F. and Heuberger J. (2022), "Epigenetic modifier balances MapK and Wnt signalling in differentiation of goblet and paneth cells" Life Sci. Alliance, 5(4): e202101187

Lackner, A., Sehlke, R., Garmhausen, M., Giuseppe Stirparo, G., Huth, M., Titz-Teixeira, F., van der Lelij, P., Ramesmayer, J., Thomas, H.F., Ralser, M., Santini, L., Galimberti, E., Sarov, M., Stewart, A.F., Smith, A., Beyer, A., and Leeb, M. (2021) "Coperative genetic network drive embryonic stem cell transition from naïve to formative pluripotency" EMBO J. 40(8), e105776; doi: 10.15252/embj.2020105776

Wang, X., Zheng, W., Zhou, H., Tu, Q., Tang, Y.J., Stewart, A.F., Zhang, Y. and Bian, X. (2021) "Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria" Nucleic Acids Res. (50(3), e15; doi: 10.1093/nar/gkab1076

Michurina, A., Sakib, M.S., Kerimoglu, C., Krüger, D.M., Kaurani, L., Islam, M.R., Joshi, P.D., Schröder, S., Centeno, T.P., Zhou, J., Pradhan, R., Cha, J., Xu, X., Eichele, G., Zeisberg, E.M., Kranz, A., Stewart, A.F. and Fischer A (2021) "Postnatal expression of the methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes" EMBO J. 41(1), e106459; doi: 10.15252/embj.2020106459

Goveas, N., Waskow, C., Arndt, K., Heuberger, J., Zhang, Q., Alexopoulou, D., Dahl, A., Birchmeier, W., Anastassiadis, K., Stewart, A.F. and Kranz, A (2021) "MLL1 is required for maintenance of intestinal stem cells" PLoS Genet. 17(12), e1009250

Ramakrishnan, S., Subramaniam, S., Kielar, C., Grundmeier, G., Stewart, A.F. and Keller, A. (2020) "Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and hierarchical DNA Nanostructures" Molecules 25(11), E5099

Song, C., Luan, J., Li, R., Jiang, C., Hou, Y., Cui, Q., Cui, T., Tan, L., Ma, Z., Tang, Y.J., Stewart, A.F., Fu, J., Zhang, Y. and Wang, H. (2020) "RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide gene clusters" Nucleic Acids Res., 48(22), e130; doi: 10.1093/nar/gkaa956

Ashokkumar, D., Zhang, Q., Much, C., Bledau, A.S., Naumann, R., Alexopoulou, D., Dahl, A., Goveas, N., Fu, J., Anastassiadis, K., Stewart, A.F. and Kranz, A. (2020) "MLL4 is required after implantation whereas MLL3 becomes essential during late gestation" Development, 147(12): dev186999; doi: 10.1242/dev.186999

Addicks, G.C., Brun, C.E., Sincennes, M.C., Saber, J., Porter, C.J., Stewart, A.F., Ernst, P. and Rudnicki, M.A. (2019) "MLL1 is required for PAX7 expression and satellite cell self-renewal in mice" Nat. Commun., 10(1), 4256

Bereshchenko, O., Lo Re, O., Nikulenkov, F., Flamini, S., Kotaskova, J., Mazza, T., Le Pannérer, M.M., Buschbeck, M., Giallongo, C., Palumbo, G., Li Volti, G., Pazienza, V., Cervinek, L., Riccardi, C., Krejci, L., Pospisilova, S., Stewart, A.F. and Vinciguerra, M. (2019) "Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome" Clin. Epigentics, 11(1): 121

Gentzel, M., Pardo, M., Subramaniam, S., Stewart, A.F. and Choudhary, J.S. (2019) "Proteomic navigation using proximity-labeling" Methods, 164-165, 67 - 72 doi: 10.1016/j.ymeth.2019.03.028

Yin, J., Zheng, W., Gao, Y., Jiang, C., Shi, H., Diao, X., Li, S., Chen, H., Wang, H., Li, R., Li, A., Xia, L., Yin, Y., Stewart, A.F., Zhang, Y. and Fu, J. (2019) "Single-stranded DNA-binding protein and exogenous RecBCD inhibitors enhance phage-derived homologous recombination in Pseudomonas" iScience 14:1 - 14; doi: 10.1016/j.isci.2019.03.007

Choudhury, R., Singh, S., Arumugam, S., Roguev, A. and Stewart, A.F. (2019) "The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation" Genes Dev., 33(9 - 10), 550 - 564; doi: 10.1101/gad.322222.118

Korecki, A.J., Hickmott, J.W., Lam, S.L., Dreolini, L., Mathelier, A., Baker, O., Kuehne, C., Bonaguro, R.J., Smith, J., Tan, C.V., Zhou, M., Goldowitz, D., Deussing , J.M., Stewart, A.F., Wasserman, W.W., Holt, R.A. and Simpson E.M. (2019) "Twenty-seven tamoxifen-inducible iCre-driver mouse strains for eye and brain; including seventeen carrying a new inducible-first constitutive-ready allele" Genetics, 211(4), 1155 - 1177

Song, C., Luan, J., Cui, Q., Duan, Q., Li, Z., Gao, Y., Li, R., Li, A., Shen, Y., Li, Y., Stewart, A.F., Zhang, Y., Fu, J. and Wang, H. (2019) "Enhanced Heterologous Spinosad Production from a 79-kb Synthetic Multioperon Assembly", ACS Synth. Biol., 8(1), 137-147

Chen, Y., Jones, K.L., Anastassiadis, K., Kranz, A., Stewart, A.F., Grembecka, J., Meyerson, M. and Ernst, P. (2019) "Distinct pathways affected by Menin versus MLL1/MLL2 in MLL-rearranged Acute Myeloid Leukemia" Exp. Hematol. 69, 37 - 42; doi: 10.1016/j.exphem.2018.10.001

Tomizawa, S.I., Kobayashi, Y., Shirakawa, T., Watanabe, K., Mizoguchi, K., Hoshi, I., Nakajima, K., Nakabayashi, J., Singh, S., Dahl, A., Alexopoulou, D., Seki, M., Suzuki, Y., Royo, H., Peters, A.H.F.M., Anastassiadis, K., Stewart, A.F. and Ohbo, K. (2018) "Kmt2b conveys monovalent and bivalent H3K4me3 in mouse spermatogonial stem cells at germline and embryonic promoters" Development, 145(23), pii: dev169102

Barbagiovanni, G., Germain, P.L., Zech, M., Atashpaz, S., Lo Riso, P., D'Antonio-Chronowska, A., Tenderini, E., Caiazzo, M., Boesch, S., Jech, R., Haslinger, B., Broccoli, V., Stewart, A.F., Winkelmann, J. and Testa, G. (2018) "KMT2B is selectivly required for neironal transdifferentiation, and its loss exposes Dystonia candidate genes" Cell Reports, 25(4), 988-1001

Li, R., Helbig, L., Fu, J., Bian, X., Herrmann, J., Baumann, M., Stewart, A.F., Müller, R., Li, A., Zips, D. and Zhang, Y. (2018) "Expressing cytotoxic compounds in Escherichia coli Nissle 1917 for tumor-targeting therapy" Res. Microbiol. 170(2), 74 - 79

Liu, J., Boehme, P., Zhang, W., Fu, J., Yumul, R., Mese, K., Tsoukas, R., Solanki, M., Kaufmann, M., Lu, R., Schmidtko, A., Stewart, A.F., Lieber, A. and Ehrhardt, A. (2018) "Human adenovirus type 17 from species D transduces endothelial cells and human CD46 is involved in cell entry" Sci. Rep. 8(1): 13422

Schmidt, K., Zhang, Q., Tasdogan, A., Petzold, A., Dahl, A., Arneth, B.M., Slany, R., Fehling, H.J., Kranz, A., Stewart, A.F. and Anastassiadis, K. (2018) "The H3K4 methyltransferase Setd1b is essential for hematopoietic stem cell and progenitor cell homeostasis in mice" ELife, 7; doi: 10.7554/eLife.27157

Arndt, K., Kranz, A., Fohgrub, J., Jolly, A., Bledau, A.S., Di Virgilio, M., Lesche, M., Dahl, A., Höfer, T., Stewart, A.F. and Waskow, C. (2018) "SETD1A protects HSCs from activation-induced functional decline in vivo" Blood, 131(12), 1311 - 1324; doi: 10.1182/blood-2017-09-806844

Hanna, C.W., Taudt, A., Huang, J., Gahurova, L., Kranz, A., Andrews, S., Dean, W., Stewart, A.F., Colomé-Tatché, M. and Kelsey, G. (2018) "MLL2 conveys transcription-independent H3K4 trimethylation in oocytes" Nat. Struct. Mol. Biol. 25(1), 73 - 82; doi: 10.1038/s41594-017-0013-5

Chakraborty, D., Paszkowski-Rogacz, M., Berger, N., Ding, L., Mircetic, J., Fu, J., Iesmantavicius, V., Choudhary, C., Anastassiadis, K., Stewart, A.F. and Buchholz, F. (2017) "IncRNA Panct1 Maintains Mouse Embryonic Stem Cell Identity by Regulating TOBF1 Recruitment to Oct-Sox Sequences in Early G1" Cell Rep. 21(11), 3012 - 3021, doi: 10.1016/j.celrep.2017.11.045

Wang, H., Li, Z., Jia, R., Yin ,J., Li, A., Xia, L., Yin, Y., Müller, R., Fu, J., Stewart, A.F. and Zhang, Y. (2017) "ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes" Nucl. Acids Res. 46(5), e28; doi: 10.1093/nar/gkx1249

Kerimoglu, C., Sakib, M.S., Jain, G., Benito, E., Burkhardt, S., Capece, V., Kaurani, L., Halder, R., Agís-Balboa, R.C., Stilling, R., Urbanke, H., Kranz, A., Stewart, A.F. and Fischer, A. (2017) "KMT2A and KMT2B mediate memory function by affecting distinct genomic regions" Cell Rep., 20(3), 538 - 548

Chen, Y., Anastassiadis, K., Kranz, A., Stewart, A.F., Arndt, K., Waskow, C., Yokoyama, A., Jones, K., Neff, T., Lee, Y. and Ernst P. (2017) "MLL2, not MLL1, plays a major role in sustaining MLL-rearranged accute myeloid leukemia" Cancer Cell, 31(6), 755 - 770

Brici, D., Zhang, Q., Reinhardt, S., Dahl, A., Hartmann, H., Schmidt, K., Goveas, N., Huang, J., Gahurova, L., Kelsey, G., Anastassiadis, K., Stewart, A.F. and Kranz, A. (2017) "Set1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program" Development, 144(14), 2606 - 2617; doi: 10.1242/dev..143347

Baker, O., Tsurkan, S., Fu, J., Klink, B., Rump, A., Obst, M., Kranz, A., Schröck, E., Anastassiadis, K. and Stewart, A.F. (2017) "The contribution of homology arms to nuclease-assisted genome engineering" Nucl. Acids Res., 45(13), 8105 - 8115; doi: 10.1093/nar/gkx497

Zhang, W., Fu, J., Liu, J., Wang, H., Schiwon, M., Janz, S., Schaffarczyk, L., von der Goltz, L., Ehrke-Schulz, E., Dörner, J., Solanki, M,. Boehme, P., Bergmann, T., Lieber, A., Lauber, C., Dahl, A., Petzold, A., Zhang, Y., Stewart, A.F. and Ehrhardt, A. (2017) "An Engineered Virus Library as a Resource for the Spectrum-wide Exploration of Virus and Vector Diversity" Cell Rep., 19(8), 1698 - 1709

Bian, X., Tang, B., Yu, Y., Tu, Q., Gross, F., Wang, H., Li, A., Fu, J., Shen, Y., Li, Y.Z., Stewart, A.F., Zhao, G., Ding, X., Müller, R. and Zhang, Y. (2017) "Heterologous production and yield improvement of epothilones in Burkholderiales strain DSM 7029" ACS Chem. Biol., 12(7), 1805 - 1812

Papanikos, F., Daniel, K., Goercharn-Ramlal, A., Fei, J.F., Kurth, T., Wojtasz, L., Dereli, I., Fu, J., Penninger, J., Habermann, B., Surani, A., Stewart, A.F. and Toth, A. (2017) "The enigmatic meiotic dense body and its newly discovered component, SCML1, are dispensable for fertility and gametogenesis in mice" Chromosoma, 126(3), 399 - 415; doi: 10.1007/s00412-016-0598-1

Ramakrishnan, S., Subramaniam, S., Stewart, A.F., Grundmeier, G. and Keller, A. (2016) "Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks", ACS Appl. Mater. Interfaces, 8(45), 31239 - 31247

Subramaniam, S., Erler, A., Fu, J., Kranz, A., Tang, J., Gopalswamy, M., Ramakrishnan, S., Keller, A., Grundmeier, G., Müller, D. Sattler, M. and Stewart, A.F. (2016) "DNA Annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter-molecular interactions" Sci. Rep. 6: 34525

Tasdogan, A., Kumar, S., Allies, G., Bausinger, J. Beckel, F., Hofemeister, H., Mulaw, M., Madan, V. Scharfetter-Kochanek, K., Feuring-Buske, M., Doehner, K. Speit, G., Stewart, A.F. and Fehling, H.J. (2016) "DNA Damage-Induced HSPC Malfunction Depends on ROS Accumulation Downstream of IFN-1 Signaling and Bid Mobilization" Cell Stem Cell, 19(6), 752 - 767

Shen, E.Y., Jiang, Y., Javidfar, B., Kassim, B., Loh, Y.H., Ma, Q., Mitchell, A.C., Pothula, V., Stewart, A.F., Ernst, P., Yao, W.D., Martin, G., Shen, L., Jakovcevski, M. and Akbarian, S. (2016) "Neuronal Deletion of Kmt2a/Mll1 Histone Methyltransferase in Ventral Striatum is Associated with Defective Spike-Timing Dependent Striatal Synaptic Plasticity, Altered Response to Dopaminergic Drugs and Increased Anxiety" Neuropsychopharmacology, 41(13), 3103 - 3113

Singh, S., Hein, M.Y. and Stewart, A.F. (2016) "msVolcano: a flexible web application for visualizing quantitative proteomics data" Proteomics, 16(18), 2491 - 2494; doi: 10.1002/pmic.201600167

Hu, S., Liu, Z., Zhang, X., Zhang, G., Xie, Y., Ding, X., Mo, X., Stewart, A.F., Fu, J., Zhang, Y. and  Xia, L. (2016) "Cre/loxP plus BAC: a strategy for direct cloning of large DNA fragment and its applications in Photorhabdus luminescens and Agrobacterium tumefaciens." Sci Rep. 6:29087. doi: 10.1038/srep29087.

Wang, H., Li, Z., Jia, R., Hou, Y., Bian, X., Li, A., Müller, R., Stewart, A.F., Fu, J. and Zhang, Y. (2016) "RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression" Nat. Protoc., 11(7), 1175 - 1190

Baker, O., Gupta, A., Obst, M., Zhang, y., Anastassiadis, K., Fu, J. and Stewart, A.F. (2016) "RAC-tagging: Recombineering and Cas9-assisted targeting for protein tagging and conditional analyses" Sci. Rep., 6:25529 doi:10.1038/srep25529

Tu, Q., Yin, J., Fu, J., Herrmann, J., Li, Y., Yin, Y., Stewart, A.F., Müller, R. and Zhang, Y. (2016) "Room temperature electrocompetent bacterial cells improve DNA transformation and recombineering efficiency." Sci Rep. 6:24648

Kantidakis, T., Saponaro, M., Mitter, R., Horswell, S., Kranz, A., Boeing, S., Aygün, O., Kelly, G.P., Matthews, N., Stewart, A., Stewart, A.F. and Svejstrup, J.Q. (2016) "Mutation of cancer driver MLL2 results in transcription stress and genome instability" Genes Dev. 30, 408 - 20

Yin, J., Hoffmann, M., Bian, X., Tu, Q., Yan, F., Xia, L., Ding, X., Stewart, A.F., Müller, R., Fu, J. and Zhang, Y. (2015) "Direct cloning and heterologous expression of the salinomycin biosynthetic gene cluster from Streptomyces albus DSM41398 in Streptomyces coelicolor A3(2)" Sci Rep 5:15081.

Ding, L., Paszkowski-Rogacz, M., Winzi, M., Chakraborty, D., Theis, M., Singh, S., Giotta, G. Poser, I., Roguev, A., Chu, W.K., Choudhary, C., Mann, M., Stewart, A.F., Krogan, N. and Buchholz, F. (2015) "Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells" Cell Syst. 26(2), 141-51

Bögershausen, N., Tsai, I. C., Pohl, E., Kiper, P. O., Beleggia, F., Percin, E. F., Keupp, K., Matchan, A., Milz, E., Alanay, Y., Kayserili, H., Liu, Y., Banka, S., Kranz, A., Zenker, M., Wieczorek, D., Elcioglu, N., Prontera, P., Lyonnet, S., Meitinger, T., Stewart, A. F., Donnai, D., Strom, T. M., Boduroglu, K., Yigit, G., Li, Y., Katsanis, N. and Wollnik, B. (2015). "RAP1-mediated MEK/ERK pathway defects in Kabuki syndrome" J Clin Invest. 125(9): 3585 - 99.

Ander, M., Subramaniam, S., Fahmy, K., Stewart, A. F. and Schäffer, E. (2015). "A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology" PLoS Biol 13: e1002213.

Wong, F. K., Fei, J. F., Mora-Bermudez, F., Taverna, E., Haffner, C., Fu, J., Anastassiadis, K., Stewart, A. F. and Huttner, W. B. (2015). "Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex" PLoS Biol 13: e1002217.

Jakovcevski, M., Ruan, H., Shen, E. Y., Dincer, A., Javidfar, B., Ma, Q., Peter, C. J., Cheung, I., Mitchell, A. C., Jiang, Y., Lin, C. L., Pothula, V., Stewart, A. F., Ernst, P., Yao, W. D. and Akbarian, S. (2015). "Neuronal Kmt2a/Mll1 histone methyltransferase is essential for prefrontal synaptic plasticity and working memory" J Neurosci 35: 5097-108.

Reddy, T. R., Fevat, L. M., Munson, S. E., Stewart, A. F. and Cowley, S. M. (2015). "Lambda Red Mediated Gap Repair Utilizes a Novel Replicative Intermediate in Escherichia coli" PLoS One 10(3): e0120681.

Yin, J., Zhu, H., Xia, L., Ding, X., Hoffmann, T., Hoffmann, M., Bian, X., Müller, R., Fu, J., Stewart, A.F., Zhang, Y. (2015) “A new recombineering system for Photorhabdus and Xenorhabdus” Nucleic Acids Res 43(6): e36.

Xu, K., Stewart, A. F. and Porter, A. C. (2014) "Stimulation of Oligonucleotide-Directed Gene Correction by Redbeta Expression and MSH2 Depletion in Human HT1080 Cells" Mol Cells 38(1): 33 - 9

Wachter, E., Quante, T., Merusi, C., Arczewska, A., Stewart, F., Webb, S. and Bird, A. (2014). "Synthetic CpG islands reveal DNA sequence determinants of chromatin structure" Elife 3: e03397

Bledau, A. S., Schmidt, K., Neumann, K., Hill, U., Ciotta, G., Gupta, A., Torres, D. C., Fu, J., Kranz, A., Stewart, A. F. and Anastassiadis, K. (2014). "The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation" Development 141: 1022 - 1035

da Rocha, S. T., Boeva, V., Escamilla-Del-Arenal, M., Ancelin, K., Granier, C., Matias, N. R., Sanulli, S., Chow, J., Schulz, E., Picard, C., Kaneko, S., Helin, K., Reinberg, D., Stewart, A. F., Wutz, A., Margueron, R. and Heard, E. (2014). "Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome" Mol Cell 53: 301-16

Denissov, S., Hofemeister, H., Marks, H., Kranz, A., Ciotta, G., Singh, S., Anastassiadis, K., Stunnenberg, H. G. and Stewart, A. F. (2014). "Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant" Development 141(3): 526 - 37

Wang, H., Bian, X., Xia, L., Ding, X., Müller, R., Zhang, Y., Fu, J. and Stewart A.F. (2013) "Improved seamless mutagenesis by recombineering using ccdB for counterselection" Nucleic Acids Res 42(5): e37

Hu, S., Fu, J., Huang, F., Ding, X., Stewart, A.F., Xia, L. and Zhang, Y. (2013) "Genome engineering of Agrobacterium tumefaciens using the lambda Red recombination system" Appl Microbiol Biotechnol 98(5): 2165 - 21

Andreasson, C., Schick, A. J., Pfeiffer, S. M., Sarov, M., Stewart, F., Wurst, W. and Schick, J. A. (2013). "Direct cloning of isogenic murine DNA in yeast and relevance of isogenicity for targeting in embryonic stem cells" PLoS One 8: e74207

Kerimoglu, C., Agis-Balboa, R. C., Kranz, A., Stilling, R., Bahari-Javan, S., Benito-Garagorri, E., Halder, R., Burkhardt, S., Stewart, A. F. and Fischer, A. (2013). "Histone-methyltransferase MLL2 (KMT2B) is required for memory formation in mice" J Neurosci 33: 3452-3464

Bian, X., Fu, J., Plaza, A., Herrmann, J., Pistorius, D., Stewart, A. F., Zhang, Y. and Müller, R. (2013). "In Vivo Evidence for a Prodrug Activation Mechanism during Colibactin Maturation" Chembiochem 14: 1194-1197

Singh, R. P., Franke, K., Kalucka, J., Mamlouk, S., Muschter, A., Gembarska, A., Grinenko, T., Willam, C., Naumann, R., Anastassiadis, K., Stewart, A. F., Bornstein, S., Chavakis, T., Breier, G., Waskow, C. and Wielockx, B. (2013). "HIF-prolyl hydroxylase 2 (PHD2) is a critical regulator of hematopoietic stem cell maintenance during steady-state and stress" Blood 121: 5158-5166

Thieme, S., Gyarfas, T., Richter, C., Ozhan, G., Fu, J., Alexopoulou, D., Muders, M. H., Michalk, I., Jakob, C., Dahl, A., Klink, B., Bandola, J., Bachmann, M., Schrock, E., Buchholz, F., Stewart, A. F., Weidinger, G., Anastassiadis, K. and Brenner, S. (2013). "The histone demethylase UTX regulates stem cell migration and hematopoiesis" Blood 121: 2462-2473

Ladopoulos, V., Hofemeister, H., Hoogenkamp, M., Riggs, A. D., Stewart, A. F. and Bonifer, C. (2013). "The histone methyltransferase KMT2B is required for RNA polymerase II association and protection from DNA-methylation at the MagohB CpG island promoter" Mol Cell Biol 33: 1383-93

Rostovskaya, M., Naumann, R., Fu, J., Obst, M., Mueller, D., Stewart, A. F. and Anastassiadis, K. (2013). "Transposon mediated BAC transgenesis via pronuclear injection of mouse zygotes" Genesis 51: 135-41

Bian, X., Huang, F., Stewart, F. A., Xia, L., Zhang, Y. and Müller, R. (2012). "Direct Cloning, Genetic Engineering, and Heterologous Expression of the Syringolin Biosynthetic Gene Cluster in E. coli through Red/ET Recombineering." Chembiochem 13: 1946 - 1952

Rostovskaya, M., Fu, J., Obst, M., Baer, I., Weidlich, S., Wang, H., Smith, A., Anastassiadis, K. and Stewart, A. F. (2012) “Transposon Mediated BAC Transgenesis in Human ES Cells” Nucleic Acids Res 40: e150

Fu, J., Bian, X., Hu, S., Wang, H., Huang, F., Seibert, P., Plaza, A., Xia, L., Müller, R., Stewart, A. F. and Zhang, Y. (2012) "Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting” Nat Biotechnol 30: 440-446

Wojtasz, L., Cloutier, J. M., Baumann, M., Daniel, K., Varga, J., Fu, J., Anastassiadis, K., Stewart, A. F., Remenyi, A., Turner, J. M. and Toth, A. (2012). "Meiotic DNA double-strand breaks and chromosome asynapsis in mice are monitored by distinct HORMAD2-independent and -dependent mechanisms" Genes Dev 26: 958 - 973

Austenaa, L., Barozzi, I., Chronowska, A., Termanini, A., Ostuni, R., Prosperini, E., Stewart, A. F., Testa, G. and Natoli, G. (2012). "The histone methyltransferase Wbp7 controls macrophage function through GPI glycolipid anchor synthesis" Immunity 36: 572 - 585

Sarov, M., Murray, J. I., Schanze, K., Pozniakovski, A., Niu, W., Angermann, K., Hasse, S., Rupprecht, M., Vinis, E., Tinney, M., Preston, E., Zinke, A., Enst, S., Teichgraber, T., Janette, J., Reis, K., Janosch, S., Schloissnig, S., Ejsmont, R. K., Slightam, C., Xu, X., Kim, S. K., Reinke, V., Stewart, A. F., Snyder, M., Waterston, R. H. and Hyman, A. A. (2012). "A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans" Cell 150: 855 - 866

Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A. F., Smith, A. and Stunnenberg, H. G. (2012). "The transcriptional and epigenomic foundations of ground state pluripotency" Cell 149: 590 - 604

Royer, L., Reimann, M., Stewart, A. F. and Schroeder, M. (2012). "Network compression as a quality measure for protein interaction networks" PLoS One 7: e35729

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 39: e137

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 9: 103 - 109

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

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

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(7351): 337 - 342

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 10: 4186 - 4195

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

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: 132-139

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(8): e1000453

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 48: 512 - 520

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 48: 220 - 232

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

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

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

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 - 515

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 - 531

Erler, A., Wegmann, S., Elie-Caille, C., Bradshaw, C. R., Maresca, M., Seidel, R., Habermann, B., Müller, D. J. and Stewart, A. F. (2009). "Conformational adaptability of Redβ during DNA annealing and implications for its structural relationship with Rad52." J Mol Biol 391: 586 - 598

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 - 415

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

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

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

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 - 415

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 - 1636

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 - 2366

Perlova, O., Fu, J., Kuhlmann, S., Krug, D., Stewart, A. F., Zhang, Y. and Müller, R. (2006) "Reconstitution of the myxothiazol biosynthetic gene cluster by Red/ET recombination and heterologous expression in Myxococcus xanthus" Appl Environ Microbiol 72: 7485 - 7494

Gross, F., Ring, M. W., Perlova, O., Fu, J., Schneider, S., Gerth, K., Kuhlmann, S., Stewart, A. F. , Zhang, Y. and Müller, R. (2006) "Metabolic engineering of Pseudomonas putida for methylmalonyl-CoA biosynthesis to enable complex heterologous secondary metabolite formation." Chem Biol 13: 1253 - 1264

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 - 844

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 - 35412

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 - 1432

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 - 823

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

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 - 6731

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 - 1235

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 - 521

Wenzel, S. C., Gross, F., Zhang, Y., Fu, J., Stewart, A. F. and Müller, R. (2005) "Heterologous expression of a myxobacterial natural products assembly line in pseudomonads via red/ET recombineering." Chem Biol 12: 349 - 356

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 - 132

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 - 815

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

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 - 5460

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 - 659

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 - 1115

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 - 2482

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 - 447

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

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

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 - 8493

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 - 172

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 - 212

Casanova, E., Fehsenfeld, S., Greiner, E., Stewart, A. F. and Schütz, G. (2002) "Construction of a conditional allele of RSK-B/MSK2 in the mouse" Genesis 32: 158 - 160

Casanova, E., Lemberger, T., Fehsenfeld, S., Greiner, E., Stewart, A. F. and Schütz, G. (2002) "Rapid localization of a gene within BACs and PACs" Biotechniques 32: 240 - 242

Casanova, E., Fehsenfeld, S., Greiner, E., Stewart, A. F. and Schütz, G. (2002) "Conditional mutagenesis of CamKIV." Genesis 32: 161 - 164

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 - 1663

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

Andreu, T., Ebensperger, C., Westphal, E. M., Klenner, T., Stewart, A. F. , Westhof, A., Müller, P., Knaus, R. and von Melchner, H. (2001) "Self-deleting suicide vectors (SDSV): selective killing of p53-deficient cancer cells" Cancer Res 61: 6925 - 6930

Casanova, E., Fehsenfeld, S., Mantamadiotis, T., Lemberger, T., Greiner, E., Stewart, A. F. and Schütz, G. (2001) "A CamKIIα iCre BAC allows brain-specific gene inactivation" Genesis 31: 37 - 42

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 - 7148

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

Buchholz, F. and Stewart, A. F. (2001) "Alteration of Cre recombinase site specificity by substrate-linked protein evolution" Nat Biotechnol 19: 1047 - 1052

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

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

Zhang, Y., Muyrers, J. P., Testa, G. and Stewart, A. F. (2000) "DNA cloning by homologous recombination in Escherichia coli" Nat Biotechnol 18: 1314 - 1317

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 - 243

Muyrers, J. P., Zhang, Y., Buchholz, F. and Stewart, A. F. (2000) "RecE/RecT and Redα/Redβ initiate double-stranded break repair by specifically interacting with their respective partners" Genes Dev 14: 1971 - 1982

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 - 140

Hill, F., Benes, V., Thomasova, D., Stewart, A. F. , Kafatos, F. C. and Ansorge, W. (2000) "BAC trimming: minimizing clone overlaps" Genomics 64: 111 - 113

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 - 6641

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

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 - 447

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 - 1969

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 - 1557

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 - 128

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 - 384

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 - 3269

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 - 1132

Buchholz, F., Angrand, P. O. and Stewart, A. F. (1998) "Improved properties of FLP recombinase evolved by cycling mutagenesis" Nat Biotechnol 16: 657 - 662

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 - 773

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 - 1432

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 - 961

Ringrose, L., Angrand, P. O. and Stewart, A. F. (1997) "The Kw recombinase, an integrase from Kluyveromyces waltii" Eur J Biochem 248: 903 - 912

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 - 292

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 - 4262

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 - 3119

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 - 88

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 - 872

Kellendonk, C., Tronche, F., Monaghan, A. P., Angrand, P. O., Stewart, A. F. and Schütz, G. (1996) "Regulation of Cre recombinase activity by the synthetic steroid RU 486" Nucleic Acids Res 24: 1404 - 1411

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 - 3173

Logie, C. and Stewart, A. F. (1995) "Ligand-regulated site-specific recombination" Proc Natl Acad Sci U S A 92: 5940 - 5944.

Aasland, R., Gibson, T. J. and Stewart, A. F. (1995) "The PHD finger: implications for chromatin-mediated transcriptional regulation" Trends Biochem Sci 20: 56 - 59

Reik, A., Stewart, A. F. and Schütz, 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 - 497

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 - 475.

Strähle, U., Schmidt, A., Kelsey, G., Stewart, A. F. , Cole, T. J., Schmid, W. and Schütz, G. (1992) "At least three promoters direct expression of the mouse glucocorticoid receptor gene" Proc Natl Acad Sci U S A 89: 6731 - 6735

Reik, A., Schütz, 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 - 2576

Stewart, A. F. , Reik, A. and Schütz, G. (1991) "A simpler and better method to cleave chromatin with DNase 1 for hypersensitive site analyses" Nucleic Acids Res 19: 3157

Weih, F., Stewart, A. F. , Boshart, M., Nitsch, D. and Schütz, G. (1990) "In vivo monitoring of a cAMP-stimulated DNA-binding activity" Genes Dev 4: 1437 - 1449

Nitsch, D., Stewart, A. F. , Boshart, M., Mestril, R., Weih, F. and Schütz, G. (1990) "Chromatin structures of the rat tyrosine aminotransferase gene relate to the function of its cis-acting elements" Mol Cell Biol 10: 3334 - 3342

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 - 149

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

Strähle, U., Boshart, M., Klock, G., Stewart, A. F. and Schütz, G. (1989) "Glucocorticoid- and progesterone-specific effects are determined by differential expression of the respective hormone receptors" Nature 339: 629 - 632

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 - 537

Weih, F., Stewart, A. F. and Schütz, G. (1988) "A novel and rapid method to generate single stranded DNA probes for genomic footprinting" Nucleic Acids Res 16: 1628

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.

Stewart, A. F. and Schütz, G. (1987) "Camptothecin-induced in vivo topoisomerase I cleavages in the transcriptionally active tyrosine aminotransferase gene" Cell 50: 1109 - 1117

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 - 241

Jantzen, H. M., Strahle, U., Gloss, B., Stewart, A. F. , Schmid, W., Boshart, M., Miksicek, R. and Schütz, G. (1987) "Cooperativity of glucocorticoid response elements located far upstream of the tyrosine aminotransferase gene" Cell 49: 29 - 38

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 - 1902

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 - 3907

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 - 386

Anastassiadis, K., Schnütgen, F., von Melchner, H. and Stewart, A. F. (2013). "Gene Targeting and Site-Specific Recombination in Mouse ES Cells." Methods Enzymol. 533: 133 - 155.

Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Kent Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Francis Stewart A, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura KI, Yoshinaga Y, Wurst W. (2012) The mammalian gene function resource: the international knockout mouse consortium. Mamm. Genome, 23 (9-10), SI: Mouse Genomic Programs and Resources, 580 - 586

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: Molecular Methods for Evolutionary Genetics, 445 - 458.

Justice, M. J., Siracusa, L. D. and Stewart, A. F. (2011). "Technical approaches for mouse models of human disease." Dis. Model Mech., 4, 305 - 310.

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, 53 (4), 437 - 452.

von Melchner, H. and Stewart, A. F. (2011). "Methods for Extracting Function from the Mammalian Genome." Methods, 53 (4), 329 - 330.

Ciotta, G., Hofemeister, H., Maresca, M., Fu, J., Sarov, M., Anastassiadis, K. and Stewart, A. F. (2011). "Recombineering BAC transgenes for protein tagging." Methods, 53 (2), 113 - 116.

Fu, J., Teucher, M., Anastassiadis, K., Skarnes, W. and Stewart, A. F. (2010). "A Recombineering Pipeline to Make Conditional Targeting Constructs." Methods Enzymol., 477, 125-144.

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., 477, 109-123.

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: Innate Immuinity, 83-100.

Schnütgen, F., Stewart, A. F., von Melchner, H. and Anastassiadis, K. (2006). "Engineering embryonic stem cells with recombinase systems." Methods Enzymol., 420, 100 - 136.

Glaser, S., Anastassiadis, K. and Stewart, A. F. (2005). "Current issues in mouse genome engineering." Nat. Genet., 37, 1187 - 1193.

Sarov, M. and Stewart, A. F. (2005). "The best control for the specificity of RNAi." Trends Biotechnol. 23(9), 446 - 448.

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 -927.

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 - 924.

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, 1. ed., Burlington, Academic Press: 609 - 622.

Vintersten, K., Testa, G. and Stewart, A. F. (2004). "Microinjection of BAC DNA into the pronuclei of fertilized mouse oocytes." Methods Mol. Biol., 256: Bacterial Artificial Chromosomes, Vol. 2, Functional Studies, 141 - 158.

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: Bacterial Artificial Chromosomes, Vol. 2, Functional Studies, 123 - 139.

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: Bacterial Artificial Chromosomes, Vol. 2, Functional Studies, 107 - 121.

Muyrers, J. P., Zhang, Y. and Stewart, A. F. (2001). "Techniques: Recombinogenic engineering--new options for cloning and manipulating DNA." Trends Biochem. Sci., 26(5), 325 - 331.

Muyrers, J. P., Zhang, Y. and Stewart, A. F. (2000). "ET-cloning: think recombination first." Genet. Eng.(NY), 22, 77 - 98.

Testa, G. and Stewart, A. F. (2000). "Creating a transloxation. Engineering interchromosomal translocations in the mouse." EMBO Rep., 1(2), 120 - 121.

Aasland, R. and Stewart, A. F. (1999). "Analysis of DNaseI hypersensitive sites in chromatin by cleavage in permeabilized cells." Methods Mol. Biol., 119: Chromatin Protocols, 355 - 362.

Gasser, S. M., Paro, R., Stewart, A. F. and Aasland, R. (1998). "The genetics of epigenetics." Cell Mol. Life Sci., 54(1), 1 - 5.

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. eds.: A. Cid-Arregui and A. Garcia-Carrancá. Heidelberg, New York, Tokyo, Springer: 225-274.

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: In Vivo Footprinting, 159 - 180.

Stewart, A. F., Logie, C. and Nichols, M. (1996). "Regulation of nuclear receptors by agonists and antagonists." Curr. Opin. in Endocrin., Diabetes and Obesity ,3, 397 - 402.

Shaw, P. E. and Stewart, A. F. (1994). "Identification of protein-DNA contacts with dimethyl sulfate. Methylation protection and methylation interference." Methods Mol. Biol., 30: DNA-Protein Interactions, Principles and Protocols, 79 - 87.