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Avemann, K., Knippers, R., Koller, Th. and Sogo, J.M. (1988). Camptothecin, a specific inhibitor of type I DNA topoisomerase, induces DNA breakage at replication forks. Mol. Cell. Biol. 8, 3026-3034.

Avila, J., Montejo de Garcini, E., Wandosell, F., Villasante, A., Sogo, J.M. and Villanueva, N. (1983). Microtubule-associated protein MAP2 preferentially binds to a dA/dT sequence present in mouse satellite DNA. The EMBO J. 2, 1229-1234.

Banditt, M., Koller, T. and Sogo, J.M. (1999). Transcriptional activity and chromatin structure of enhancer-deleted rRNA genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 19. 4953-4960.

Barrera, I., Schuppli, D., Sogo, J.M. and Weber, H. (1993). Different mechanisms of recognition of bacteriophage Q beta plus and minus strand RNAs by Q beta replicase. J. Mol. Biol. 232. 512-521.

Burhans, W.C., Vassilev, L.T., Wu, J.-R., Sogo, J.M., Nallaseth, F. and DePamphilis, M.L. (1991). Emetine allows identification of origins of mammalian DNA replication by imbalanced DNA synthesis, not through conservative nucleosome segregation. EMBO J. 10, 4351-4360.

Burkhalter, M.D. and Sogo, J.M. (2004). rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication. Mol. Cell 15, 409-421.

Conconi, A., Losa, R., Koller, T. and Sogo, J.M. (1984). Psoralen-crosslinking of soluble and of H1-depleted soluble rat liver chromatin. J. Mol. Biol. 178. 920-928.

Conconi, A., Widmer, R.M., Koller, T. and Sogo, J.M. (1989). Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57. 753-761.

Conconi, A. Sogo, J.M. and Ryan, C.A. (1992). Ribosomal gene clusters are uniquely proportionated between open and closed chromatin structures in both tomato leaf cells and exponentially growing suspension cultures. Proc. Natl. Acad. Sci. USA 89, 5256-5260.

Cotta-Ramusino, C, Fachinetti, D., Lucca, C, Doksani, Y., Lopes, M., Sogo, J., and Foiani, M. (2005). Exol processes stalled replication forks and counteracts fork reversal in checkpoint-defective cells. Mol. Cell 17, 153-159.

Dammann, R., Lucchini, R., Koller, T. and Sogo, J.M. (1993). Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 21. 2331-2338.

Dammann, R., Lucchini, R., Koller, T. and Sogo, J.M. (1995). Transcription in the yeast rRNA gene locus: distribution of the active gene copies and chromatin structure of their flanking regulatory sequences. Mol. Cell. Biol. 15. 5294-5303.

De Bernardin, W., Koller, Th. and Sogo, J.M. (1986). Structure of in vivo transcribing chromatin as studied in simian virus 40 minichromosomes. J. Mol. Biol. 191, 469-482.

Del Olmo M., Sogo, J.M., Franco, L. and Pérez-Ortín J.E. (1993). Chromatin structure of the yeast FBP1 gene: Transcription-dependent changes in the regulatory and coding regions. Yeast 9, 1229-1240.

Dörig, C., Master, Mc., Sogo, J.M., Bruggmann, H. and Beard, P. (1986). Nucleoprotein complexes of minute virus of mice have a distinct structure different from that of chromatin. J. Virol. 58, 817-824.

Droge, P., Sogo, J.M. and Stahl, H. (1985). Inhibition of DNA synthesis by aphidicolin induces supercoiling in simian virus 40 replicative intermediates. EMBO J. 4. 3241-3246.

Escarmis, C., Sogo, J.M., Garcia, J.A. and Salas, M. (1984). Structure of bacteriophage phi 29 DNA. Folia Biol. (Praha) 45-51.

Fritsch, O., Burkhalter, M.D., Kais, S., Sogo, J.M. and Schär, P. (2010). DNA ligase 4 stabilizes the ribosomal DNA array upon fork collapse at the replication fork barrier. DNA Repair 9, 879-888.

Gasser, R., Koller, T. and Sogo, J.M. (1996). The stability of nucleosomes at the replication fork. J. Mol. Biol. 258, 224-239.

Gilson, E., Müller, T., Sogo, J.M., Laroche, T. and Gasser, S.M. (1994). RAP1 stimulates single- to double-strand association of yeast telomeric DNA: implications for telomere-telomere interactions. Nucleic Acids Res. 22, 5310-5320.

Giménez-Martín, G., Risueño, M.C., and Sogo, J.M. (1970). Development of the vegetative cell in the pollen grain. Cytologia 35, 77-90.

Giménez-Martín, G., Sogo J.M., Esponda, P. and Stockert, J.C. (1971). Morphology of the nucleolus and transverse expression of the organizing area. Cytobiologie 3, 343-350.

Gruber, M., Wellinger, R. E. and Sogo, J.M. (2000). Architecture of the replication fork stalled at the 3' end of the yeast ribosomal genes. Mol. Cell. Biol. 20, 5777-5787.

Gruss, C., Gutierrez, C., Burhans, W.C., DePamphilis, M.L., Koller, T. and Sogo, J.M. (1990). Nucleosome assembly in mammalian cell extracts before and after DNA replication. EMBO J. 9. 2911-2922.

Gruss, C. and Sogo, J.M. (1992). Chromatin replication. Bioessays 14, 1-8.

Gruss, C., Wu, J., Koller, T. and Sogo, J.M. (1993). Disruption of the nucleosomes at the replication fork. EMBO J. 12, 4533-4545.

Guo, Z.S., Gutierrez, C., Heine, U., Sogo, J.M. and Depamphilis, M.L. (1989). Origin auxiliary sequences can facilitate initiation of simian virus 40 DNA replication in vitro as they do in vivo. Mol. Cell. Biol. 9, 3593-3602.

Gutierrez, C., Martin, G., Sogo, J.M. and Salas, M. (1991a). Mechanism of stimulation of DNA replication by bacteriophage phi 29 single-stranded DNA-binding protein p5. J. Biol. Chem. 266, 2104-2111.

Gutierrez, C., Sogo, J.M. and Salas, M. (1991b). Analysis of replicative intermediates produced during bacteriophage phi 29 DNA replication in vitro. J. Mol. Biol. 222, 983-994.

Hertner, T., Hertner-Meyer, B., Sogo, J.M., Schläpfer, G., Jäckle, H., Edström, J.-E. and Lezzi, M. (1986). Microcloning of a long segment of a gene from the primary ecdysterone-controlled puff region I-18C of Chironomus tentans: Molecular characterization and effect of hormone on its transcription. Dev. Biol. 113, 29-39.

Hübscher, U. and Sogo, J.M. (1997). The eukaryotic DNA replication fork. News Physiol. Sci. 12. 125-131.

Inciarte, M.R., Salas, M. and Sogo, J.M. (1980). Structure of replicating DNA molecules of Bacillus subtilis bacteriophage f29. J. Virol. 34, 187-199.

Keller, R. C., Mossi, R., Maga, G., Wellinger, R. E., Hübscher, U. and Sogo, J.M. (1999). Electron microscopic analysis reveals that replication factor C is sequestered by single-stranded DNA. Nucleic Acids Res. 27(17), 3433-3437.

Koller, Th. and Sogo, J.M. (1974). An electron microscopic method for studying nucleic acid-protein complexes. Visualization of RNA polymerase bound to the DNA of bacteriophages T7 and T3. Biopolymers 13, 995-1009.

Koller, Th., Kübler, O., Portmann R. and Sogo, J.M. (1978). High resolution physical mapping of specific binding sites of Escherichia coli RNA polymerase on the DNA of bacteriophage T7. J. Mol. Biol. 120, 121-131.

Krawiec, S., Jiménez, F., García, J.A., Villanueva, N., Sogo, J.M. and Salas M. (1981). The orderly, in vitro emergence of DNA from bacteriophage f29 particles. Virology 111, 440-454.

Laurie, B., Katritch, V., Sogo, J.M., Koller, Th., Dubochet, J. and Stasiak, A. (1998). Geometry and physics of catenanes applied to the study of DNA replication. Biophysical J. 74, 2815-2822.

Loidl, P., Lucchini, R. and Sogo, J.M. (1992). Histone composition and core histone acetylation of transcriptional active ribisomal chromatin of Physarum polycephalum. Cell Biol. International reports 16, 1177-1183.

Lopes M., Foiani, M. and Sogo, J.M. (2006). Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol. Cell 21, 15-27.

Lucas, I., Chevrier-Miller, M., Sogo, J.M. and Hyrien, O. (2000). Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos. J. Mol. Biol. 296, 769- 786.

Lucchini, R., Pauli, U., Braun, R., Koller, T. and Sogo, J.M. (1987). Structure of the extrachromosomal ribosomal RNA chromatin of Physarum polycephalum. J. Mol. Biol. 196. 829-843.

Lucchini, R. and Sogo, J.M. (1992). Different chromatin structures along the spacers flanking active and inactive Xenopus rRNA genes. Mol. Cell. Biol. 12. 4288-4296.

Lucchini, R. and Sogo, J.M. (1994). Chromatin structure and transcriptional activity around the replication forks arrested at the 3' end of the yeast rRNA genes. Mol. Cell Biol. 14. 318-326.

Lucchini, R. and Sogo, J.M. (1995). Replication of transcriptionally active chromatin. Nature 374. 276-280.

Lucchini, R. and Sogo, J.M. (1998). The dynamic structure of ribosomal RNA gene chromatin. In: Transcription of ribosomal RNA genes by Eukaryotic RNA polymerase I. pp. 255-276. Landes Bioscience, Austin, TX USA,

Lucchini, R., Wellinger, R.E., and Sogo, J.M. (2001). Nucleosome positioning at the replication fork. EMBO J. 24. 7294-7302.

Miranda, G., Schuppli, D., Barrera, I., Hausherr, C., Sogo, J.M. and Weber, H. (1997). Recognition of bacteriophage Qbeta plus strand RNA as a template by Qbeta replicase: role of RNA interactions mediated by ribosomal proteins S1 and host factor. J. Mol. Biol. 267. 1089-1103.

Moreno, M. L., Sogo, J.M. and De la Torre, C. (1978). Higher plant nucleosomes. A miocromethod for isolating and dispersing chromatin fibres. New Phytol. 81, 681-683.

Muller, M., Lucchini, R. and Sogo, J.M. (2000). Replication of yeast rDNA initiates downstream of transcriptionally active genes. Molecular Cell 5, 767-77.

Müller, T., Gilson, E. Schmidt, R. Giraldo, R., Sogo, J.M., Gross, H. and Gasser, S. M. (1994). Imaging the asymmetrical DNA bend induced by repressor activator protein 1 with scanning tunneling microscopy. J. of Structural Biol. 113, 1-12.

Müller-Storm, H-P., Sogo, J.M., and Schaffner, W. (1989). An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge. Cell 58, 767-777.

Nightingale, K.P., Wellinger, R.E., Sogo, J.M. and Becker, P.B. (1998). Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin. EMBO J. 17, 2865-2876.

Olavarrieta, L., Martinez-Robles, M.L., Sogo, J.M., Stasiak, A., Hernandez, P., Krimer, D., and Schvartzman, J.B. (2002). Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucleic Acids Res. 30, 656-666.

Podust, L.M., Podust, V.N., Sogo, J.M. and Hübscher, U. (1995). Mammalian DNA polymerase auxiliary proteins: analysis of replication factor C-catalyzed proliferating cell nuclear antigen loading onto circular double-stranded DNA. Mol. Cell. Biol. 15, 3072-3081.

Portmann, R., Sogo, J.M., Koller, Th. and Zillig, W. (1974). Binding sites of E. coli polymerase on T7 DNA as determined by electron microscopy. FEBS Letters 45, 64-67.

Risueño, M.C., Sogo, J.M., Giménez-Martín, G. and R-García, M.I. (1970). Vacuolation in the cytoplasm of plant cells. Cytologia 35, 609-621.

Salas, M., Mellado, R.P., Viñuela, E. and Sogo, J.M. (1978). Characterization of a protein covalently linked to the 5' termini of the DNA of Bacillus subtilis phage f29. J. Mol. Biol. 119, 269-291.

Sanz, C., Gorab, E., Ruiz, M.F., Sogo, J.S. and Díez, J.L. (2007). Chromatin structure of ribosomal genes in Chironomus thummi (Diptera: Chironomidae): tissue specificity and behaviour under drug treatment. Chromosome Res. 15, 429-438.

Schuppli, D., Miranda, G., Tsui, H.C., Winkler, M.E., Sogo, J.M. and Weber, H. (1997). Altered 3'-terminal RNA structure in phage Qbeta adapted to host factor- less Escherichia coli. Proc. Natl. Acad. Sci. U S A 94, 10239-42.

Sogo, J.M., Koller, Th. and Diener, T.O. (1973). Potato spindle tuber viroid. X. Visualization and size determination by electron microscopy. Virology 55, 70-80.

Sogo, J.M., Schneider, I.R. and Koller, Th. (1974). Size determination by electron microscopy of the RNA of tobacco ringspot satellite virus. Virology 57, 459-466.

Sogo, J.M., Portmann, R., Kaufmann, P. and Koller, Th. (1975). Adsorption of DNA molecules to different support films. J. Microscopy 104, 187-198.

Sogo, J.M., Greenstein, M. and Skalka, A. (1976). The circle mode of replication of bacteriophage Lambda: The role of covalently closed templates and the formation of mixed catenated dimers. J. Mol. Biol. 103, 537-562.

Sogo, J.M., Inciarte, M.R., Corral, J., Viñuela, E. and Salas. M. (1979). RNA polymerase binding sites and transcription map of the DNA of Bacillus subtilis phage f29. J. Mol. Biol. 127, 411-436.

Sogo, J.M., Rodeño, P., Koller, Th., Viñuela E. and Salas, M. (1979). Comparison of the A-T rich regions and the Bacillus subtilis RNA polymerase binding sites in phage f29 DNA. Nucl. Acids Res. 7, 107-120.

Sogo, J.M. and Schneider, I.R. (1982). Electron microscopy of double-stranded nucleic acids found in tissue infected with the satellite of tobacco ringspot virus. Virology 117, 401-415.

Sogo, J.M., García, J.A., Peñalva, M.A. and Salas, M. (1982). Structure of protein-containing replicative intermediates of Bacillus subtilis phage f29 DNA. Virology 116, 1-18.

Sogo, J.M., Almendral, J.M., Talavera, A. and Viñuela, E. (1984a). Terminal and internal inverted repetitions in African swine fever virus DNA. Virology 133, 271-275.

Sogo, J.M., Lozano, M. and Salas, M. (1984b). In vitro transcription of the Bacillus subtilis phage phi 29 DNA by Bacillus subtilis and Escherichia coli RNA polymerases. Nucleic Acids Res. 12. 1943-1960.

Sogo, J.M., Ness, P.J., Widmer, R.M., Parish, R.W. and Koller, T. (1984c). Psoralen-crosslinking of DNA as a probe for the structure of active nucleolar chromatin. J. Mol. Biol. 178. 897-919.

Sogo, J.M., Stahl, H., Koller, T. and Knippers, R. (1986). Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures. J. Mol. Biol. 189. 189-204.

Sogo, J. M., Stasiak, A., De Bernardin, W., Losa, R. and Koller, Th. (1987). Binding of protein to nucleic acids. In Electron microscopy in molecular biology. Ed. By Somerville, J. and Scheer, U. pp. 61-79. IRL Press, Oxford.

Sogo, J.M. and Thoma, F. (1989). Electron microscopy of chromatin. Methods Enzymol. 170, 142-165.

Sogo, J. M. Conconi, A. and Widmer, R.M. (1989). The use of psoralen-photocrosslinking for the analysis of the chromatin structure during transcription. Ed. By Nielsen P.E. Photochemical probes in biochemistry. 179-194.

Sogo, J.M. and Laskey, R. A. (1995). Chromatin replication and assembly. In: Chromatin structure and gene expression. Ed. By S. Elgin. Oxford University Press 49-70.

Sogo, J. M., Stasiak, A. Martinez-Robles, M-l., Krimer, D.B., Hernandez, P. and Schvartzman J.B. (1999). “Formation of knots in partially replicated DNA molecules.” J. Mol. Biol. 286, 637-643.

Sogo, J. M., Lopes, M. and Foiani, M. (2002). Science 297, 599-602.

Sogo, J.M. and Thoma, F. (2003). In: The Nucleolus, M.O.J., Olson, Ed., and Kluwer Academic/Plenum Publishers.

Stancheva, I., Lucchini, R., Koller, T. and Sogo, J.M. (1997). Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking. Nucleic Acids Res. 25. 1727-1735.

Stancheva, I., Koller, Th. and Sogo, J.M. (1999). Asymmetry of Dam remethylation on the leading and lagging arms of plasmid replicative intermediates. EMBO J. 18. 6542-6551.

Stockert, J.C., Sogo, J.M., Díez, J.L. and Giménez-Martín, G. (1969). Alteration in the SATZ-chromosome of Allium cepa affecting the size of the nucleolus. Experientia 25, 773-774.

Stockert, J.C., Giménez-Martín, G. and Sogo, J.M. (1970). Nucleolus and synaptonemal complexes in pachytene meiocytes of Allium cepa. Cytobiologie 2, 235-250.

Stockert, J.C., Fernández-Gómez, Sogo, J.M. and López-Sáez, J.F. (1970). Nucleolar segregation by adenosine 3'-deoxyriboside (cordycepin) in root-tip cells of Allium cepa. Exp. Cell Res. 59, 85-89.

Travaglini, G., Rohrer, H., Stoll, E., Amrein, M., Stasiak, A. Sogo, J.M. and Heinz, H. (1988). Scanning tunneling microscopy of recA-DNA complexes. Physica Scripta. 38, 309-314.

Thoma, F. and Sogo, J.M. (1988). Structures of bulk and transcriptionally active chromatin revealed by electron microscopy. In: Chromosomes and Chromatin, pp. 85-108, Ed. By Adolph. K.W.

Vergeer, W.P., Sogo, J.M., Petrorius, P.J. and de Vries, W.N. (2000). Interaction of Ap1, Ap2 and Sp1 with the regulatory regions of the human Pro-a1(I) collagen gene. Archives of Biochem. and Biophysics, 377, 69-79.

Vollenweider, H.J., Sogo, J.M. and Koller, Th. (1975). A routine method for protein-free spreading of double and single-stranded nucleic acid molecules. Proc. Natl. Acad. Sci. USA 72, 83-87.

Vollenweider, H.J., Koller, Th., Parello, J. and Sogo J.M. (1976). Superstructure of linear duplex DNA. Proc. Natl. Acad. Sci. USA 73, 4125-4129.

Wellinger, R.E. and Sogo, J.M. (1998). In vivo mapping of nucleosomes using psoralen-DNA crosslinking and primer extension. Nucleic Acids Res. 26, 1544-1545.

Wellinger, R.E., Lucchini, R., Dammann, R. and Sogo, J.M. (1999). In vivo mapping of nucleosomes using psoralen-DNA crosslinking and primer extension. Methods in Molecular Biology: Chromatin Protocols. Edited by: P. Becker. Humana Press Inc., Totowa, N.J. 119, 161-173.

Wellinger, R.E., Schär, P. and Sogo, J.M. (2003). Rad52-independent accumulation of joint circular minichromosomes during S phase in Saccharomyces cerevisiae. Mol. Cell. Biol. 23, 6363-6372.

Widmer, R.M., Lucchini, R., Lezzi, M., Meyer, B., Sogo, J.M., Edstrom, J.E. and Koller, T. (1984). Chromatin structure of a hyperactive secretory protein gene (in Balbiani ring 2) of Chironomus. EMBO J. 3, S 1635-1641.

Widmer, R.M., Koller, T. and Sogo, J.M. (1988). Analysis of the psoralen-crosslinking pattern in chromatin DNA by exonuclease digestion. Nucleic Acids Res. 16. 7013-7024.

Wiesendanger, B., Lucchini, R., Koller, T. and Sogo, J.M. (1994). Replication fork barriers in the Xenopus rDNA. Nucleic Acids Res. 22. 5038-5046.

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