From 1963 to Present (sans meeting abstracts)
Chemistry
1. Gordon, M., M.L. DePamphilis, and C.E. Griffin, (1963) Anion Exchange Resins in the Synthesis of Nitriles, J. Organic Chem. 28:698-700.
(see also references 10, 25)
Bacterial Structure and Physiology
2. DePamphilis, M.L. and J. Adler. (1971) Purification of Intact Flagella from E. coli and B. subtilis, J. Bacteriology 105:376-383.
3. DePamphilis, M.L. and J. Adler. (1971) Fine Structure and Isolation of the Hook-Basal Body Complex from E. coli and B. subtilis, J. Bacteriology 105:384-395.
4. DePamphilis, M.L. and J. Adler. (1971) Attachment of Flagellar Basal Bodies to the Cell Envelope: Specific Attachment to the Outer, Lipopolysaccharide, Membrane and the Cytoplasmic Membrane, J. Bacteriology 105:396-407.
5. DePamphilis, M.L. (1971) Dissociation and Reassembly of E. coli Outer Membrane and of Lipopolysaccharide, and their Reassembly onto Flagellar Basal Bodies, J. Bacteriology 105:1184-1199.
6. DePamphilis, M.L. (1971) Isolation of Bacteriophage T2 and T4 Attached to the Outer Membrane of E. coli, J. Virology 7:683-686.
7. DePamphilis, M.L. (1973) The Basal Body of Bacterial Flagella, pp. 182-194 In Behavior of Microrganisms (A. Perez-Miravete, ed.), Plenum Press.
8.
DePamphilis, M.L. (1974) Purification of Intact Bacterial Flagella and their Components, pp. 25-55 In Methods in Molecular Biology (A.I. Laskin and J.A. Last, eds.), Marcel Dekker, Inc.
9.
DePamphilis, M.L. (1974) Negative Staining for Electron Microscopy. pp. 265-288, In Methods in Molecular Biology (A.I. Laskin and J.A. Last, eds.), Marcel Dekker, Inc.
Enzymology
10.
DePamphilis, M.L. and W.W. Cleland. (1973) Preparation and properties of Chromatin (III) nucleotide complexes for use in the study of enzyme mechanisms, Biochemistry 12:3714-3724.
11.
Edenberg, H.J., S. Anderson and M.L. DePamphilis. (1978) Involvement of DNA Polymerase-a in Simian Virus 40 DNA Replication, J. Biol. Chem. 253:3273-3280.
12. Krokan, H., P. Schaffer and M.L. DePamphilis. (1979) Involvement of Eucaryotic DNA Polymerases-a and -g in the Replication of Cellular and Viral DNA, Biochemistry 18:4431-4443.
13. Weaver, D.T. and M.L. DePamphilis. (1982) Specific Sequences in Native DNA that Arrest Synthesis of DNA Polymerase-a , J. Biol. Chem. 257:2075-2086.
14. Pritchard, C.G. and M.L. DePamphilis. (1983) Preparation of DNA Polymerase-a[C1C2] by Reconstituting DNA Polymerase-a with its Specific Stimulatory Cofactors, C1C2, J. Biol. Chem. 258:9801-9809.
15. Pritchard, C.G., D.T. Weaver, E.F. Baril and M.L. DePamphilis. (1983) DNA Polymerase-a Cofactors C1C2 Function as Primer Recognition Proteins, J. Biol. Chem. 258:9810-9819.
16. Weaver, D.T. and M.L. DePamphilis. (1984) The Role of Palindromic and Nonpalindromic Sequences in Arresting DNA Synthesis In Vitro and In Vivo, J. Mol. Biol. 180:961-986.
17. Yamaguchi, M., E.A. Hendrickson, and M.L. DePamphilis. (1985) DNA primase-DNA Polymerase-a from Simian cells: Modulation of RNA Primer Synthesis by Ribonucleoside Triphosphates, J. Biol. Chem. 260:6254-6263.
18. Yamaguchi, M., E.A. Hendrickson and M.L. DePamphilis. (1985) DNA Primase-DNA Polymerase-a from Simian cells: Sequence Specificity of Initiation Sites on Simian Virus 40 DNA, Mol. Cell. Biol. 5:1170-1183.
19. Charette, M.F., D.T. Weaver, and M.L. DePamphilis. (1986) Persistence of DNA synthesis arrest sites in the presence of T4 DNA polymerase and T4 gene 32, 44, 45 and 62 DNA polymerase accessory proteins, Nucl. Acids Res. 14:3343-3362.
20. Vishwanatha, J.K., M. Yamaguchi, M.L. DePamphilis, and E.F. Baril. (1986) Selection of Template Initiation Sites and Lengths of RNA Primers Synthesized by DNA Primase are Strongly Affected by its Organization in a Multiprotein DNA Polymerase-a Complex, Nucl. Acids Res. 14:7305-7323.
DNA Replication and Animal Viruses
21. DePamphilis, M.L., P. Beard and P. Berg. (1975) Synthesis of Superhelical Simian Virus 40 DNA in Cell Lysates, J. Biol. Chem. 250:4340-4347.
22. DePamphilis, M.L. and P. Berg. (1975) Requirement of a Cytoplasmic Fraction for Synthesis of SV40 DNA in Isolated Nuclei, J. Biol. Chem. 250:4348-4354.
23. Wilson, J.H., M. DePamphilis and P. Berg. (1976) Simian Virus 40 - Permissive Cell Interactions: Selection and Characterization of Spontaneously Arising Monkey Cells that are Resistant to SV40 Infection, J. Virol. 20:391-399.
24. Su, R.T. and M.L. DePamphilis. (1976) In Vitro Replication of Simian Virus 40 DNA in a Nucleoprotein Complex, Proc. Nat. Acad. Sci. U.S.A. 73:3466-3470.
25. Anderson, S., G. Kaufmann and M.L. DePamphilis. (1977) RNA Primers in Simian Virus 40 DNA Replication: Identification of Transient RNA-DNA Covalent Linkages in Replicating DNA, Biochemistry 16:4990-4998.
26. Kaufmann, G., S. Anderson and M.L. DePamphilis. (1977) RNA Primers in Simian Virus 40 DNA Replication: Distribution of 5'-Terminal Oligoribonucleotides in Nascent DNA, J. Mol. Biol. 116:549-567.
27.
Tapper, D.P. and M.L. DePamphilis. (1978) Discontinous DNA Replication: Accumulation of Simian Virus 40 DNA at Specific Stages in its Replication, J. Mol. Biol. 120:401-422.
28.
Kaufmann, G., R.Bar-Shavit and M.L. DePamphilis. (1978) Okazaki Pieces Grow Opposite to the Replication Fork Direction During Simian Virus 40 Replication, Nucl. Acids Res. 5:2535-2545.
29.
Su, R.T. and M.L. DePamphilis. (1978) Simian Virus 40 DNA Replication in Isolated Replicating Viral Chromosomes, J. Virol. 28:53-65.
30. DePamphilis, M.L., S. Anderson, R. Bar-Shavit, E. Collins, H. Edenberg, T. Herman, B. Karas, G. Kaufmann, H. Krokan, E. Shelton, R. Su, D. Tapper and P.M. Wassarman. (1979) Replication and Structure of Simian Virus 40 Chromosomes, Cold Spring Harbor Symp. Quant. Biol. 43:679-692.
31.
Tapper, D.P., S. Anderson and M.L. DePamphilis. (1979) Maturation of Replicating Simian Virus 40 DNA Molecules in Isolated Nuclei by Continued Bidirectional Replication to the Normal Termination Region, Biochem. Biophys. Acta 565:84-97.
32.
Anderson, S. and M.L. DePamphilis. (1979) Metabolism of Okazaki Fragments During Simian Virus 40 DNA Replication, J. Biol. Chem. 254:11495-11504.
33.
DePamphilis, M.L., S. Anderson, M. Cusick, R. Hay, T. Herman, H. Krokan, E. Shelton, L. Tack, D Tapper, D. Weaver, and P.M. Wassarman. (1980) The Interdependence of DNA Replication, DNA Sequence and Chromatin Structure in Simian Virus 40 Chromosomes", pp. 55-78 In Mechanistic Studies of DNA Replication and Genetic Recombination (B. Alberts, ed.) ICN-UCLA Symp. Mol. Cell. Biol., Vol. 19, Academic Press.
34.
Tapper, D.P. and M.L. DePamphilis. (1980) Preferred DNA Sites are Involved in the Arrest and Initiation of DNA Synthesis During Replication of Simian Virus 40 DNA, Cell 22:97-108.
35.
Hay, R.T. and M.L. DePamphilis. (1981) Locations of 5'-Ends of Nascent DNA at the Origin of Simian Virus 40 DNA Replication", pp. 567-580, In The Initiation of DNA Replication (D.S. Ray, ed.), ICN-UCLA Symp. Mol. Cell. Biol., Vol. 22, Academic Press.
36. Tapper, D.P., S. Anderson and M.L. DePamphilis. (1982) Distribution of Replicating Simian Virus 40 DNA in Intact Cells and its Maturation in Isolated Nuclei, J. Virology 41:877-892.
37. Hay, R.T. and M.L. DePamphilis. (1982) Initiation of Simian Virus 40 DNA Replication in Vivo: Location and Structure of 5'-Ends of DNA Synthesized in the Ori Region, Cell 28:767-779.
38. DePamphilis, M.L., M.E. Cusick, R.T. Hay, C.G. Pritchard, L.C. Tack, P.M. Wassarman and D.T. Weaver. (1983) Chromatin Structure, DNA Sequences and Replication Proteins: Searching for the Principles of Eukaryotic Chromosome Replication, pp. 203-233 In New Approaches in Eukaryotic DNA Replication (A.M. de Recondo, ed.), Plenum Press.
39. Tack, L.C. and M.L. DePamphilis. (1983) Analysis of SV40 Chromosome-T-Antigen Complexes: T-Antigen is Preferentially Associated with Early Replicating DNA Intermediates, J. Virology 48:281-295.
40. DePamphilis, M.L., L.E. Chalifour, M.F. Charette, M.E. Cusick, R.T. Hay, E.A. Hendrickson, C.G. Pritchard, L.C. Tack, P.M. Wassarman, D.T. Weaver, and D.O. Wirak. (1983) Papovavirus Chromosomes as a Model for Mammalian DNA Replication, pp. 423-447 In Mechanisms of DNA Replication and Recombination, UCLA Symp. Mol. Cell. Biol., New Series, Vol. 10 (N.R. Cozarelli, ed.) Alan Liss, N.Y.
41. Hay, R.T., E.A. Hendrickson and M.L. DePamphilis. (1984) Sequence Specificity for the Initiation of RNA Primed-SV40 DNA Synthesis in Vivo, J. Mol. Biol. 175:131-157.
42. DePamphilis, M.L. (1984) Papovavirus Chromosomes as a Model for the Replication of Mammalian Chromosomes, pp. 369-384 In Genetics, New Frontiers, Proceedings of the XV International Congress of Genetics, Oxford and IBH Publishing Co., New Delhi, India.
43. Weaver, D.T., Fields-Berry, S.C. and M.L. DePamphilis. (1985) The Termination Region for SV40 DNA Replication Directs the Mode of Separation for the Two Sibling Molecules, Cell 41:565-575.
44. Yamaguchi, M. and M.L. DePamphilis. (1986) DNA Binding Site for a Factor(s) Required to Initiate Simian Virus 40 DNA Replication, Proc. Natl. Acad. Sci. USA 83:1646-1650.
45. Decker, R.S, M. Yamaguchi, R. Possenti, and M.L. DePamphilis. (1986) Initiation of SV40 DNA Replication in vitro: Aphidicolin Causes Accumulation of Early Replicating Intermediates and Allows Determination of the Initial Direction of DNA Synthesis, Mol. Cell. Biol. 6:3815-3825.
46. DePamphilis, M.L., R.S. Decker, M. Yamaguchi, R. Possenti, D.O. Wirak, R. Perona, and J.A. Hassell. (1987) Transcriptional Elements and their Role in Activation of Simian Virus 40 and Polyoma Virus Origins of Replication: In DNA Replication and Recombination, UCLA Symp. Mol. Cell. Biol., Vol. 47 (T. Kelly and R. McMacken, eds.) Alan R. Liss, Inc., NY.
47. Decker, R.S., M. Yamaguchi, R. Possenti, M.L. Bradley, and M.L. DePamphilis. (1987) In Vitro Initiation of DNA Replication in Simian Virus 40 Chromosomes, J. Biol. Chem. 262:10863-10872.
48. Hendrickson, E.A., C.E. Fritze, W.R. Folk, and M.L. DePamphilis. (1987) The Origin of Bidirectional DNA Replication in Polyoma Virus, EMBO J. 6:2011-2018.
49. Hendrickson, E.A., C.E.Fritze, W.R. Folk, and M.L. DePamphilis. (1987) Polyoma Virus DNA Replication is Semi-Discontinuous, Nucl. Acids. Res. 15:6369-6385.
50. Taljanidisz, J., R.S. Decker, Z.-S. Guo, M.L. DePamphilis, and N. Sarkar. (1987) Initiation of Simian Virus 40 DNA Replication in vitro: Identification of RNA-Primed Nascent DNA Chains, Nucl. Acids Res. 15:7877-7888.
51. DePamphilis, M.L., Martínez-Salas, E., Cupo, D.Y., Hendrickson, E.A., Fritze, C.E., Folk, W.R. and U. Heine. (1988) Initiation of Polyomavirus and SV40 DNA Replication, and the Requirements for DNA Replication During Mammalian Development, pp. 165-175 In Eukaryotic DNA Replication (B. Stillman and T. Kelly, eds), Cancer Cells, Vol. 6, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
52.
Gutierrez, C., Guo, Z-S., Farell-Towt, J., Ju, G. and M.L. DePamphilis. (1987) C‑myc Protein and DNA Replication: Separation of c-Myc Antibodies from an Inhibitor of DNA Synthesis, Mol. Cell. Biol. 7:4594-4598.
53.
Gutierrez, C., Guo, Z-S., Burhans, W.C., DePamphilis, M.L., Farrell-Towt, J. and G. Ju. (1988) Is c-Myc Protein Directly Involved in DNA Replication? Science 240:1202.
54.
Fields-Berry, S.C. and M.L. DePamphilis. (1989) Sequences that Promote Formation of Catenated Intertwines During Termination of DNA Replication, Nucl. Acids Res. 17:3261-3273.
55.
Guo, Z-S., C. Gutierrez, U. Heine, J.M. Sogo, M.L. DePamphilis. (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.
56.
Gutierrez, C., Z-S. Guo, J. Roberts, M.L. DePamphilis. (1990) Simian Virus Origin Auxiliary Sequences Weakly Facilitate Binding of T-antigen, But Strongly Facilitate Initiation of DNA Unwinding, Mol. Cell. Biol. 10:1719-1728.
57.
Guo, Z-S., M. Wiekowski, S. Majumder, M. Miranda and M.L. DePamphilis. (1992) Role of Transcriptional Elements in Activating Origins of Replication, pp. 129 - 138 In DNA Replication: The Regulatory Mechanisms, (P. Hughes, E. Fanning and M. Kohiyama, eds.), Springer-Verlag.
58.
Guo, Z.-S., U. Heine, and M.L. DePamphilis. (1991) T-antigen binding to site I facilitates initiation of SV40 DNA replication but does not affect bidirectionality, Nucl. Acids Res. 19:7081-7088.
59.
Guo, Z.-S. and M.L. DePamphilis. (1992) Specific Transcription Factors Stimulate both Simian Virus 40 and Polyomavirus Origins of DNA Replication, Mol. Cell. Biol., 12:2514-2524.
60.
Nallaseth, F.S. and DePamphilis, M.L. (1994) Papillomavirus Contains Cis-Acting Sequences That Can Suppress But Not Regulate Origins of DNA Replication, J. Virology 68:3051-3064.
Chromatin Structure
61. Shelton, E.R., J. Kang, P.M. Wassarman and M.L. DePamphilis. (1978) Chromatin Assembly in Isolated Mammalian Nuclei, Nucl. Acids Res. 5:349-362.
62. Shelton, E.R., P.M. Wassarman and M.L. DePamphilis. (1978) Structure of Simian Virus 40 Chromosomes in Nuclei from Infected Monkey Cells, J. Mol. Biol. 125:491-514.
63. Herman, T.M., M.L. DePamphilis and P.M. Wassarman. (1979) Structure of Chromatin at DNA Replication Forks: Okazaki Fragments Released from Replicating Simian Virus 40 Chromosomes by Single-Strand Specific Endonucleases are not in Nucleosomes, Biochemistry 18:4563-4571.
64. Shelton, E.R., P.M. Wassarman and M.L. DePamphilis. (1980) Structure, Spacing and Phasing of Nucleosomes on Isolated Forms of Mature Simian Virus 40 Chromosomes, J. Biol. Chem. 255:771-782.
65. Herman, T.M., M.L. DePamphilis and P.M. Wassarman. (1981) Structure of Chromatin at DNA Replication Forks: Location of the First Nucleosomes on Newly Synthesized Simian Virus 40 DNA, Biochemistry 20:621-630.
66. Tack, L.C., P.M. Wassarman and M.L. DePamphilis. (1981) Chromatin Assembly: Relationship of Chromatin Structure to DNA Sequence During SV40 Replication, J. Biol. Chem. 256:8821-8828.
67. Cusick, M.E., T.M. Herman, M.L. DePamphilis and P.M. Wassarman. (1981) Structure of Chromatin at DNA Replication Forks: Prenucleosomal DNA is Rapidly Excised from Replicating Simian Virus 40 Chromosomes by Micrococcal Nuclease, Biochemistry 20:6648-6658.
68. Cusick, M.E., K-S. Lee, M.L. DePamphilis and P.M. Wassarman. (1983) Structure of Chromatin at DNA Replication Forks: Nuclease Hypersensitivity Results from Both Prenucleosomal-DNA and an Immature Chromatin Structure, Biochemistry 22:3873-3884.
69. Cusick, M.E., M.L. DePamphilis and P.M. Wassarman. (1984) Dispersive Segregation of Nucleosomes During Replication of SV40 Chromosomes, J. Mol. Biol. 178:249-271.
70. Cusick, M.E., P.M. Wassarman and M.L. DePamphilis. (1989) Application of Nucleases to Visualizing Chromatin Organization at Replication Forks, pp. 290-316 In Methods in Enzymology - Nucleosomes, (P.M. Wassarman and R.D. Kornberg, eds) vol. 170, Academic Press, NY.
71. Gruss, C., C. Gutierrez, W.C. Burhans, M.L. DePamphilis, Th. Koller, J.M. Sogo. (1990) Nucleosome Ssembly in Mammalian Cell Extracts Before And After DNA Replication, EMBO J. 9:2911-2922.
(see also reference 103)
DNA Replication and Gene Expression in Mammalian Embryos
72. Wirak, D.O., L.E. Chalifour, P.M. Wassarman, W.J. Muller, J.A. Hassell, and M.L. DePamphilis. (1985) Sequence-Dependent DNA Replication in Preimplantation Mouse Embryos, Mol. Cell. Biol. 5:2924-2935.
73. Chalifour, L.E., D.O. Wirak, P.M. Wassarman, and M.L DePamphilis. (1986) Expression of Simian Virus 40 Early and Late Genes in Mouse Oocytes and Embryos, J. Virol. 59:619-627.
74. Chalifour, L.E., Wirak, D.O., Wassarman, P.M., Hansen, U. and M.L DePamphilis. (1987) Cis- and Trans-acting Sequences Required for Expression of Simian Virus 40 Genes in Mouse Oocytes, Genes & Devel. 1:1096-1106.
75. DePamphilis, M.L., Herman, S.A., Martínez-Salas, E., Chalifour, L.E., Wirak, D.O., Cupo, D.Y. and M. Miranda. (1988) Microinjecting DNA into Mouse Ova to Study DNA Replication and Gene Expression and to Produce Transgenic Animals, BioTechniques 6:662-680.
76. Martínez-Salas, E., D.Y. Cupo and M.L. DePamphilis. (1988) The Need For Enhancers Is Acquired Upon Formation of a Diploid Nucleus During Early Mouse Development, Genes & Devel. 2:1115-1126.
77. Martínez-Salas, E., E. Linney, J. Hassell and M.L. DePamphilis. (1989) The Need For Enhancers In Gene Expression First Appears During Mouse Development With Formation Of A Zygotic Nucleus, Genes & Devel. 3:1493-1506.
78. Dooley, T., M. Miranda, N.C. Jones and M.L. DePamphilis. (1989) Transactivation Of The Adenovirus EIIa Promoter in the Absence of Adenovirus E1a Protein Is Restricted to Mouse Oocytes and Preimplantation Embryos, Development 107:945-956.
79. Wiekowski, M., M. Miranda and M. L. DePamphilis. (1991) Regulation of Gene Expression in Preimplantation Mouse Embryos: Effects Of The Zygotic Clock And the First Mitosis on Promoter and Enhancer Activities, Devel. Biol. 147:403-414.
80. Wiekowski, M., M. Miranda and M. L. DePamphilis. (1993) Requirements For Promoter Activity In Mouse Oocytes And Embryos Distinguish Paternal Pronuclei From Maternal And Zygotic Nuclei, Devel. Biol. 159:366-378.
81. Miranda, M., Majumder, S., Wiekowski, M. and DePamphilis, M.L. (1993) Application of Firefly Luciferase to Preimplantation Development, pp. 412-433 In A Guide to Mouse Development, Meth. Enzymology, vol. 225 (P.M. Wassarman and M.L. DePamphilis, eds) Academic Press.
82. Wiekowski, M. and DePamphilis, M.L. ( 1993) One-Dimensional Gel Analysis of Histone Synthesis, pp. 489-501 In A Guide to Mouse Development, Meth. Enzymology, vol. 225 (P.M. Wassarman and M.L. DePamphilis, eds) Academic Press.
83. Miranda, M. and DePamphilis, M.L. ( 1993) Preparation of injection pipettes, pp. 407-411 In A Guide to Mouse Development, Meth. Enzymology, vol. 225 (P.M. Wassarman and M.L. DePamphilis, eds) Academic Press.
84. Majumder, S., Miranda, M. and DePamphilis, M.L. (1993) Analysis of Gene Expression in Mouse Preimplantation Embryos Demonstrates that the Primary Role of Enhancers Is to Relieve Repression of Promoters, EMBO J. 12:1131-1140.
85. Blatt, C. and DePamphilis, M.L. (1993) Striking homology between Mouse and Human Transcription Enhancer Factor-1 (TEF-1), Nucl. Acids Res. 21:747-748.
86. Mélin, F., Miranda, M., Montreau, N., DePamphilis, M.L. and Blangy, D. (1993) Transcription enhancer factor-1 (TEF-1) DNA binding sites can specifically enhance gene expression at the beginning of mouse development, EMBO J., 12:4657-4666.
87. Majumder, S. and DePamphilis, M.L. (1994) TATA-Dependent Enhancer Stimulation of Promoter Activity In Mice Is Developmentally Acquired, Mol. Cell. Biol. 14:4258-4268.
88. Henery, C. C., M. Miranda, M., Wiekowski, I. Wilmut, and M.L. DePamphilis. (1995) Repression of Gene Expression At the Beginning of Mouse Development, Devel. Biol. 169:448-460.
89. Nothias, J.Y., M. Miranda and M.L. DePamphilis. (1996) Uncoupling Of Transcription And Translation During Zygotic Gene Activation In The Mouse, EMBO J. 15:5715-5725.
90. Wiekowski, M., M. Miranda, J-Y Nothias, and M. L. DePamphilis. (1997) Changes in Histone Synthesis And Modification at the Beginning of Mouse Development Correlate With the Establishment of Chromatin Mediated Repression of Transcription, J. Cell Science 110:1147-1158.
91. Majumder, S., Z. Zhao, K. Kaneko and M.L. DePamphilis. (1997) Developmental Acquisition of Enhancer Function Requires A Unique Co-Activator Activity, EMBO J. 16:1721-1731.
92. Kaneko, K.J., E.B. Cullinan, K. E. Latham and M.L. DePamphilis. (1997) Transcription Factor mTEAD-2 Is Selectively Expressed at the Beginning of Zygotic Gene Expression In the Mouse, Development 124:1963-1973.
93. Kaneko, K.J. and M.L. DePamphilis. (1998) Regulation Of Gene Expression At The Beginning Of Mammalian Development And The TEAD Family Of Transcription Factors, Devel. Genetics, 22:43-55.
94. Kaneko, K.J. and M.L. DePamphilis. (2000) Soggy, A Spermatocyte-Specific Gene, Lies 3.8 kb Upstream Of And Antipodal To TEAD-2, A Transcription Factor Expressed At The Beginning Of Mouse Development, Nucl. Acids Res. 28:3982-3990.
95. Vassilev, A., K.J. Kaneko, H. Shu, Y. Zhao and M.L. DePamphilis. (2001) TEAD(TEF) Transcription Factors Utilize The Activation Domain Of YAP65, A Src/Yes-Associated Protein Localized In The Cytoplasm, Genes & Devel. 15:1229-1241.
96. Kaneko, K.J., T. Rein, Z-S Guo, K. Latham and M.L. DePamphilis. (2004) DNA Methylation May Restrict But Does Not Determine Differential Gene Expression at the Sgy/Tead2 locus During Mouse Development, Mol. Cell. Biol. 24:1968-1982.
97. Intine, R. V., M. Dundr, A. Vassilev, E. Schwartz, Y. Zhou, Y. Zhao, M. L. DePamphilis, and R. J. Maraia. (2004) Nonphosphorylated Human La Antigen Interacts With Nucleolin At Nucleolar Sites Involved In rRNA Biogenesis, Mol. Cell. Biol. 24:10894-904.
98. Kohn, M.J., K.J. Kaneko and M.L. DePamphilis (2005) DkkL1(Soggy), A Dickkopf Family Member, Localizes To The Acrosome During Mammalian Spermatogenesis, Mol. Reprod. Dev. 71:516-522.
99. Park, J-M., M. J. Kohn, M. Bruinsma, C. Vech, R.V. Intine, S. Fuhrmann, A. Grinberg, I. Mukherjee, P.E. Love, M.S. Ko, M.L. DePamphilis and R.J. Maraia. (2006) The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells. , Mol. Cell. Biol. 26:1445-51.
DNA Replication in Mammalian Chromosomes
100. Vassilev, L.T., W.C. Burhans and M.L. DePamphilis. (1990) Mapping an origin of DNA replication at a single copy locus in exponentially proliferating mammalian cells, Mol. Cell. Biol., 10:4685-4689.
101.
Burhans, W.C., L.T. Vassilev, M.S. Caddle, N.H. Heintz, and M.L. DePamphilis. (1990) Identification of an origin of bidirectional DNA replication in mammalian chromosomes, Cell 62:955-965.
102. Burhans, W.C., L.T. Vassilev, J. Wu, J.M. Sogo, F. Nallaseth and M.L. DePamphilis. (1992) Origins of DNA Replication And Nucleosome Segregation In Mammalian Chromosomes, pp. 73-82 In DNA Replication: The Regulatory Mechanisms, (P. Hughes, E. Fanning and M. Kohiyama, eds.) Springer-Verlag.
103. Burhans, W.C., L.T. Vassilev, J. Wu, J. M. Sogo, F. Nallaseth and M.L. DePamphilis. (1991) Emetine allows identification of origins of mammalian DNA replication by imbalanced DNA synthesis, not through conservative nucleosome segregation, EMBO J. 10:4351-4360.
104. DePamphilis, M.L., Burhans, W.C., Vassilev, L.T. and Guo, Z.-S. (1992) Eukaryotic Origins of DNA Replication, pp. In DNA Replication and the Cell Cycle, 43rd Mosbach Colloquium, Springer-Verlag Berlin Heidelberg.
105. DePamphilis, M.L. (1993) Eukaryotic Origins of DNA Replication, in The Chromosome, (Eds. J.S. Heslop-Harrison and R.B. Flavell) Oxford: BIOS Scientific.
106. Gilbert, D. M., Miyazawa, H., Nallaseth, F.S., Ortega, J.M., Blow, J.J. and DePamphilis, M.L. (1994) Site-Specific DNA Replication in Metazoan Chromosomes And the Role of Nuclear Organization, Cold Spring Harbor Symp. Quant. Biol. 58:475-485.
107. Gilbert, D.M., Neilson, A., Miyazawa, H., DePamphilis, M.L. and Burhans, W.C. (1995) Mimosine Arrests DNA Synthesis at Replication Forks by Inhibiting Deoxyribonucleotide Metabolism, J. Biol. Chem. 270:9597-9606.
108. Gilbert, D.M., H. Miyazawa, and M. L. DePamphilis. (1995) Site-Specific Initiation of Mammalian DNA Replication in Xenopus Egg Extract Requires Nuclear Structure, Mol. Cell. Biol. 15:2942-2954.
109. Rein, T., D. A. Natale, U. Gärtner, M. Niggemann, M. L. DePamphilis, and H. Zorbas. (1997) Absence Of An Unusual "Densely Methylated Island" At The Hamster DHFR Ori-b, J. Biol. Chem. 272:10021-10029.
110. Rein, T., H. Zorbas and M. L. DePamphilis. (1997) Active Mammalian Replication Origins Are Associated With A High Density Cluster Of mCpG Dinucleotides, Mol. Cell. Biol. 17:416-426.
111. Kobayashi, T., T. Rein and M. L. DePamphilis. (1998) Identification of Primary Initiation Sites for DNA Replication in the Hamster DHFR Gene Initiation Zone, Mol. Cell. Biol. 18:3266-3277.
112. Ortega, J. M. and M. L. DePamphilis. (1998) Nucleoskeleton and Initiation of DNA Replication in Metazoan Cells. J. Cell Sci. 111:3663-3673.
113. Rein, T., T. Kobayashi, M. Malott, M. Leffak and M.L. DePamphilis. (1999) DNA Methylation at Mammalian Replication Origins, J. Biol. Chem. 274:25792-25800.
114. Li, C-J., J.A. Bogan, D.A. Natale, and M.L. DePamphilis. (2000) Selective Activation of Pre-Replication Complexes In Vitro at Specific Sites In Mammalian Nuclei, J. Cell Sci. 113:887-898.
115. Natale, D.A., C-J. Li, W-H. Sun and M.L. DePamphilis. (2000) Selective Instability Of Orc1 Protein Accounts For The Absence Of Functional Origin Recognition Complexes During The M-G1 Transition In Mammals, EMBO J. 19:2728-2738.
116.
Kong, D. and M. L. DePamphilis. (2001) Site-Specific DNA Binding Of The Schizosaccharomyces Pombe Origin Recognition Complex Is Determined By The Orc4 Subunit, Mol. Cell. Biol. 21:8095-8103.
117.
Li, C-J. and M.L. DePamphilis. (2002) Mammalian Orc1 Protein Is Selectively Released From Chromatin and Ubiquitinated During the S To M Transition In The Cell Division Cycle, Mol. Cell. Biol. 22:105-116.
118. Sun, W-H, T.R. Coleman, and M.L. DePamphilis. (2002) Cell Cycle Dependent Regulation Of The Association Between Origin Recognition Proteins And Somatic Cell Chromatin, EMBO J. 21:1437-1446.
119. Kong, D. and M.L. DePamphilis. (2002) Site-Specific ORC Binding, Pre-Replication Complex Assembly, And DNA Synthesis At S. pombe Replication Origins, EMBO J. 21:5567-5576.
120. Kong, D., T.R. Coleman and M.L. DePamphilis. (2003) Xenopus Origin Recognition Complex (ORC) Initiates DNA Replication Preferentially At Sequences Targeted By Schizosaccharomyces pombe ORC, EMBO J. 22:3441-3450.
121. Li, C-J., A. Vassilev, and M.L. DePamphilis. (2004) A Role for Cdk1(Cdc2)/Cyclin A In Preventing The Mammalian Origin Recognition Complex’s Largest Subunit (Orc1) From Binding To Chromatin During Mitosis, Mol. Cell. Biol. 24:5875-5886.
122. Saha, T., S. Ghosh, A. Vassilev and M.L. DePamphilis. (2006) Ubiquitination, Phosphorylation And Orc2 Modulate The Subcellular Location Of Orc1 And Prevent It From Inducing Apoptosis, J. Cell Sci. 119:1371-1382.
123. Radichev, I., S.W. Kwon, Y. Zhao, M.L. DePamphilis, and A. Vassilev. (2006) Genetic analysis of human ORC2 reveals specific domains that are required in vivo for assembly and nuclear localization of the origin recognition complex, J. Biol. Chem. 281:23264-23273.
124. Noguchi, K., A. Vassilev, S. Ghosh, J.L. Yates and M.L. DePamphilis. (2006) The BAH Domain Facilitates the Ability of Human Orc1 Protein To Activate Replication Origins In Vivo. EMBO J. 25: 5372-5382.
125.
Vassilev, A., S.W. Kwon, Y. Zhao and M.L. DePamphilis. (2006) S-Phase Dependent Degradation Of The Human Origin Recognition Complex Large Subunit (Orc1) Requires Binding Of Cyclin A. In preparation.
126. Yagi R, Kohn MJ, Karavanova I, Kaneko KJ, Vullhorst D, Depamphilis ML, Buonanno A. (2007) Transcription factor TEAD4 specifies the trophectoderm lineage at the beginning of mammalian development. Development 134:3827-3836.
127. Kaneko KJ, Kohn MJ, Liu C, DePamphilis ML. (2007) Transcription factor TEAD2 is involved in neural tube closure. Genesis 45:577-587.
Reviews
127. DePamphilis, M.L. (1980) Simian Virus 40 Chromosomes: A Model for the Replication of Mammalian Chromosomes, pp. 259-265 In Microbiology-1980 (D. Schlessinger, ed.), American. Society for Microbiology.
128. DePamphilis, M.L. and P.M. Wassarman. (1980) Replication of Eukaryotic Chromosomes: A Close-Up of the Replication Fork, Ann. Rev. Biochem. 49:627-666.
129. DePamphilis, M.L. and P.M. Wassarman. (1982) Organization and Replication of Papovavirus DNA, pp. 37-114 In Organization and Replication of Viral DNA (A.S. Kaplan, ed.), CRC Press.
130. DePamphilis, M.L. and M.K. Bradley. (1986) Replication of Simian Virus 40 and Polyoma Virus Chromosomes, In The Papovaviridae, Vol. 1 (N.P. Salzman, ed.), pp 99-246, Plenum Press, NY.
131.
DePamphilis, M.L. (1987) Replication of Simian Virus 40 and Polyoma Virus Chromosomes, pp. 1-40 In Molecular Aspects of Papovaviruses (Y. Aloni, ed.), Martinus Nijhoff, Boston.
132. DePamphilis, M.L. and P.M. Wassarman. (1987) Regulation of Chromosomal Replication and Transcription During Early Mammalian Development, BioEssays 7:265-271.
133. DePamphilis, M.L. (1988) Transcriptional Elements as Components of Origins of Eukaryotic DNA Replication, Cell 52:635-638.
134. DePamphilis, M.L. (1992) DNA Replication and the Role of Transcriptional Elements During Animal Development, pp. 31-83 In Advances in Developmental Biochemistry, vol. 1 (P.M. Wassarman, ed.), JAI Press, Greenwich Conn.
135. Vassilev, L.T. and M.L. DePamphilis. (1992) Guide to Identification of Origins of DNA Replication in Eukaryotic Cell Chromosomes, Critical Reviews in Biochemistry and Molecular Biology, 27:445-472.
136. DePamphilis, M.L. (1993) Origins of DNA Replication in Metazoan Chromosomes, J. Biol. Chem. 268:1-4.
137. DePamphilis, M.L. (1993) Eukaryotic DNA Replication: Anatomy of an Origin, Ann. Rev. Biochem. 62:29-63.
138. DePamphilis, M.L. (1993) How Transcription Factors Regulate Origins of DNA Replication in Eukaryotic Cells, Trends in Cell Biology, 3:161-167.
139. DePamphilis, M.L. (1993) Origins of DNA Replication that Function in Eukaryotic Cells, Curr. Opin. Cell Biol. 5:434-441.
140.
Majumder, S. and DePamphilis, M.L. (1994) Requirements for DNA Transcription and Replication at the Beginning of Mouse Development, J. Cell. Biochem. 55:59-68.
141. DePamphilis, M.L. (1995) Specific Labeling of Newly Replicated DNA, pp. 628-669 In Methods in Enzymology - DNA Replication, vol. 262 (J. Campbell, ed.), Academic Press, NY.
142. Nothias, J.-Y., S. Majumder, K.J. Kaneko and M.L. DePamphilis. (1995) Regulation of Gene Expression at the Beginning of Mammalian Development, J. Biol. Chem. 270:22077-22080.
143. Majumder, S. and M.L. DePamphilis. (1995) A Unique Role For Enhancers Is Revealed During Early Mouse Development, BioEssays 17:879-889.
144. DePamphilis, M.L. (1996) Replication Origins in Metazoan Chromosomes, pp. 96-123 In Eukaryotic DNA Replication - Frontiers in Molecular Biology (J. Blow, ed.), Oxford University Press, England.
145. DePamphilis, M.L. (1996) Origins of DNA Replication, pp. 45-86 In DNA Replication in Eukaryotic Cells, (M.L. DePamphilis, ed.) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
146. Salas , M., J.T. Miller, J. Leis and M.L. DePamphilis. (1996) Mechanisms for Priming DNA Synthesis, pp. 131-176 In DNA Replication in Eukaryotic Cells, (M.L. DePamphilis, ed) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
147. DePamphilis, M.L. (1997) The Search For Origins Of DNA Replication. In Identification and Analysis of Replication Origins in Eukaryotic Cells (M.L. DePamphilis, ed.) Methods 13:211 - 219.
148. Rein, T., M.L. DePamphilis, and H. Zorbas. (1998) Identifying 5-Methylcytosine and Related Modifications in DNA Genomes, Nucleic Acids Res. 26:2255-2264.
149. DePamphilis, M.L. (1998) Structural and Functional Organization of DNA Replication Origins, In DNA Replication and Repair, Experimental Medicine (Japanese) 16 (8):41-52.
150. DePamphilis, M.L. (1998) Initiation of DNA Replication In Eukaryotic Chromosomes, J. Cell. Biochem. suppls 30/31:8-17.
151. DePamphilis, M.L. (1999) DNA Replication in Eukaryotic Cells: 1996 - 1998, pp. 461-507 In Concepts in Eukaryotic DNA Replication, (M.L. DePamphilis, ed) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
152. DePamphilis, M.L. (1999) Replication Origins In Metazoan Chromosomes: Fact or Fiction? BioEssays 21:5-16.
153. DePamphilis, M.L. (2000) Review: Nuclear Structure and DNA Replication, J. Struct. Biol. 129:186-197.
154. Bogan, J.A., D.A. Natale, and M.L. DePamphilis. (2000) Initiation Of Eukaryotic DNA Replication: Conservative or Liberal?, J. Cell. Physiol. 184:139-150.
155. DePamphilis, M.L. (2001) “Eukaryotic Replication Origins and Initiation of DNA Replication”, Encyclopedia of Life Sciences, Macmillan Reference Ltd, London, www.els.net.
156. DePamphilis, M.L. (2002) “DNA Replication In Humans”,pp. 1080 – 1086, In Wiley Encyclopedia Of Molecular Medicine, John Wiley and Sons, NY.
157. DePamphilis, M.L., K.J. Kaneko, and A. Vassilev (2002) “Activation Of Zygotic Gene Expression In Mammals”, pp. 55-84 In Gene Expression At The Beginning Of Animal Development (M.L. DePamphilis, ed.), Advances in Developmental Biology and Biochemistry series, vol. 12 (P.M. Wassarman, series ed.), Elsevier Science, Netherlands.
158. DePamphilis, M.L. (2002) “Eukaryotic DNA Replication Forks”, ChemTracts – Biochemistry & Molecular Biology, 15(9):313-325, Data Trace Publishing.
159. Sun, W-H. and M.L. DePamphilis (2003) “Methods for Detecting Cells In S-Phase”, pp. 37-54 in Cell Cycle Checkpoint Control Protocols (H.B. Lieberman, ed.), vol. 241, Methods in Molecular Biology, Humana Press, Inc., Totowa, NJ.
160. DePamphilis, M.L. (2003) Eukaryotic DNA Replication Origins: Reconciling Disparate Data, Cell 114:274-275.
161. DePamphilis, M.L. (2003) The “ORC Cycle”: A Novel Pathway For Regulating Eukaryotic DNA Replication, Gene 310:1-15.
162. DePamphilis, M.L. (2004) Preimplantation Mammalian Development, Regulation of Gene Expression in, in Meyers, R.A. (Ed.): Encyclopedia of Molecular Cell Biology and Molecular Medicine, vol. 10, pp. 483-505, WILEY-VCH Verlag, Weinheim, Germany.
163. DePamphilis, M.L. and Cong-jun Li (2004) DNA Replication: Eukaryotic Origins and the Origin Recognition Complex, in Encyclopedia of Biological Chemistry, (W.J. Lennarz & M.D. Lane, eds), Elsevier, Oxford, Vol. 1, pp. 753-760.
164. DePamphilis, M.L. (2004) “Eukaryotic DNA Replication Origins And The Proteins That Recognize Them”, ChemTracts – Biochemistry & Molecular Biology, 17(3): 115-126, Data Trace Publishing.
165. DePamphilis, M.L. (2005) Cell Cycle Dependent Regulation of the Origin Recognition Complex, Cell Cycle 4(1):70-79.
166. DePamphilis, M.L. and J.J. Blow (2006) Regulating Initiation of DNA Replication In the Metazoa, in DNA Replication and Human Disease, (M.L. DePamphilis, ed.), pp. 313-334, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
167. DePamphilis, M.L., J.J. Blow, S. Ghosh, T. Saha, K. Noguchi, and A. Vassilev. (2006) Regulating the Licensing of DNA Replication Origins in Metazoa, Curr. Opin. Cell Biol. 18:231-239.
168. Kohn, M.J., Kaneko, K.J., Yagi, R., Litscher, E.S., Wassarman, P.M., DePamphilis, M.L. (2007) Dickkopf-like 1- a Protein Unique to Mammals that is Associated Both With Formation of Trophoblast Stem Cells and With Spermatogenesis. In "The Y Chromosome and Male Germ Cell Biology in Health and Disease" (Lau, Y.-F.C. and Chan, W.Y., eds), pp. 185-199, World Scientific Publishers, Hackensack, NJ.
Books
169. Wassarman, P.M. and M.L. DePamphilis (editors), Guide to Techniques in Mouse Development, Methods in Enzymology, vol 225, Academic Press, NY, 1993.
170. DePamphilis, M.L. (editor), DNA Replication in Eukaryotic Cells, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1996.
171. DePamphilis, M.L. (editor), Identification and Analysis of Replication Origins in Eukaryotic Cells, Methods 13:209–324, 1997.
172. DePamphilis, M.L. (editor), Concepts in Eukaryotic DNA Replication, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1999.
173. DePamphilis, M.L. (editor), Gene Expression At The Beginning Of Animal Development, Advances in Developmental Biology and Biochemistry series, vol. 12 (P.M. Wassarman, series ed), Elsevier Science, Netherlands, 2002.
174. DePamphilis, M.L. (editor), Eukaryotic DNA Replication, ChemTracts – Biochemistry & Molecular Biology, Data Trace Publishing, vol. 15(6), 2002.