Garcia, H.G., Grayson, P., Han, L., Inamdar, M., Kondev, J., Nelson, P.C., Phillips, R., Widom, J., Wiggins, P.A. (2006), “Biological Consequences of Tightly Bent
DNA”, Biopolymers, in press.
Wiggins, P.A., van der Heijden, T., Moreno-Herrero, F., Spakowitz, A., Phillips, R.,
Widom, J., Dekker, C., and Nelson, P.C. (2006), “Beyond the wormlike chain: High
flexibility of DNA on short lengthscales probed by atomic force microscopy,” Nature Nanotechnology 1: 137–141. Featured in News & Views.
Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I.K., Wang, J.Z., and Widom, J. (2006), “A Genomic Code for Nucleosome Positioning”, Nature 442: 772–778 (full Article). Featured on cover of Nature, in Nature News & Views, and Nature Reviews Genetics, and highlighted on front page and summarized in Science section of The New York Times, 25 July 2006, and in numerous other popular-press articles internationally. Top-most downloaded research paper from Nature for two-month period; Highlighted again in Nature News Feature, (2006) 244: 259–261.
Pyle, A.M. and Widom, J. (2006), “Nucleic Acids”, Curr. Opin. Struct. Biol. 16: 267-269.
Wang, J.Z. and Widom, J. (2005), “Improved Alignment of Nucleosome DNA Sequences Using a Mixture Model”, Nucleic Acids Res. 33: 6743–6755.
Widom , J. (2005), “Target site localization by site-specific DNA binding proteins”, Proc. Natl. Acad. Sci. (USA) 102: 16909–16910.
Meyer, B.J. and Widom, J. (2005), “Chromosomes and gene expression mechanisms:
Theory and experiment”, Curr. Opin. Genet. Dev. 15: 113–115.
Sales-Pardo, M., Guimera, R., Moreira, A.A., Widom, J. and Amaral, L.A.N (2005),
“Mesoscopic modeling for nucleic acid chain dynamics”, Phys. Rev. E. 71: art. no.
051902 (13 pages).
Li, G., Levitus, M., Bustamante, C., and Widom, J. (2005), “Rapid Spontaneous Accessibility of Nucleosomal DNA.”, Nat. Struct. Mol. Biol., 12: 46-53.
Chen, L. and Widom, J. (2005), “Mechanism of transcriptional silencing in yeast. ”, Cell., 120(1):37-48.
Cloutier, T.E. and Widom, J. (2005), “DNA twisting fexibility and the formation of sharply looped protein-DNA complexes.”, Proc Natl Acad Sci U S A, 102(10):3645-50.
Li, G. and Widom, J. (2004), “Nucleosomes Facilitate Their Own Invasion”, Nat. Struct. Mol. Biol., 11: 763-769.
Chen, L. and Widom, J. (2004), “Molecular Basis of Transcriptional Silencing in Budding Yeast”, Biochem. Cell. Biol., in press.
Cloutier, T.E. and Widom, J. (2004), “Spontaneous Sharp Bending of Double Stranded DNA”, Mol. Cell, 14: 355-362.
Thåström, A., Bingham, L.M., and Widom, J. (2004), “Nucleosomal Locations of Dominant DNA Sequence Motifs for Histone-DNA Interactions and Nucleosome Positioning”, J. Mol. Biol., 338: 695-709.
Thåström, A., Lowary, P.T., and Widom, J. (2004), “Measurement of Histone-DNA Interaction Free Energy in Nucleosomes”, Methods, 33: 33-44.
Chin, J., Längst, G., Becker, P.B., and Widom, J. (2004), “Fluorescence Anisotropy Assays for Analysis of ISWI-DNA and ISWI-Nucleosome Interactions”, Meth. Enzymol., 376: 3-16.
Thåström, A., Gottesfeld, J.M., Luger, K., and Widom, J. (2004), “Histone-DNA Binding Free Energy Cannot be Measured in Dilution-Driven Dissociation Experiments”, Biochemistry, 43: 736-741.
Miller, J.A. and Widom, J. (2003), “Collaborative Competition Mechanism for Gene Activation in vivo”, Mol. Cell. Biol., 23: 1623-1632.
Anderson, J.D., Thåström, A., and Widom, J. (2002), “Spontaneous Access of Proteins to Buried Nucleosomal DNA Target Sites Occurs via a Mechanism that is Distinct from Nucleosome Translocation”, Mol. Cell. Biol., 22: 7147-7157. Featured in Journal Highlights, ASM News, 68: 619, 2002.
Anderson, J.D. and Widom, J. (2001), "Poly(dA:dT) Promoter Elements Increase the Equilibrium Accessibility of Nucleosomal DNA Target Sites", Mol. Cell. Biol., 21: 3830-3839.
Anderson, J.D., Lowary, P.T. and Widom, J. (2001), "Effects of Histone Acetylation on the Dynamic Equilibrium Accessibility of Nucleosomal DNA Target Sites", J. Mol. Biol., 307: 977-985.
Schiessel, H., Widom, J., Bruinsma, R.F. and Gelbart, W.M. (2001), "Polymer Reptation and Nucleosome Repositioning", Phys. Rev. Let., 86: 4414-4417.
Richmond, T.J. and Widom, J. (2000), "Nucleosome and Chromatin Structure", Chapter 1 in Chromatin Structure and Gene Expression, Second edition, Workman, J.L. and Elgin, S.C., eds., Oxford University Press, Oxford, UK, 328pp.
Protacio, R.U., Li, G., Lowary, P.T. and Widom, J. (2000), "Effects of the Histone Tail Domains on the Rate of Transcriptional Elongation Through a Nucleosome", Mol. Cell. Biol., 20: 8866-8878.
Bailey, K.A., Pereira, S.L., Widom, J. and Reeve, J.N. (2000), "Archaeal Histone Selection of Nucleosome Positioning Sequences and the Procaryotic Origin of Histone-dependent Genome Evolution", J. Mol. Biol., 303: 25-34.
Polach, K.J., Lowary, P.T. & Widom, J. (2000), "Effects of Core Histone Tail Domains on the Equilibrium Constants for Dynamic DNA Site Accessibility in Nucleosomes", J. Mol. Biol., 298: 211-223.
Anderson, J.D. & Widom, J. (2000), "Sequence- and Position-dependence of the Equilibrium Accessibility of Nucleosomal DNA Target Sites", J. Mol. Biol., 296: 979-987.
Widom, J. (1999), "Chromatin Structure and Function"-Review of Chromatin Structure and Function, 3rd ed. by A. Wolffe, Academic Press, 1999, Cell 98: 701-702.
Thåström, A., Lowary, P.T., Widlund, H., Cao, H., Kubista, M., and Widom, J. (1999), "Sequence Motifs and Free Energies of Selected Natural and Non-Natural Nucleosome Positioning DNA Sequences", J. Mol. Biol., 288: 213-229.
Polach, K.J. and Widom, J. (1999), "Restriction Enzymes as Probes of Nucleosome Stability", Methods in Enzymology, 304: 278-298.
Widom, J. (1999), "Equilibrium and Dynamic Nucleosome Stability", Methods in Molecular Biology, 119: 61-77.
Widom, J. (1998), "Chromatin Structure: Linking Structure to Function with Histone H1", Current Biology, 8: R788-791.
Widom, J. (1998), "Structure, Dynamics, and Function of Chromatin in vitro", Ann. Rev. Biophys., 27: 285-327.
Lowary, P.T. and Widom, J. (1998), "New DNA Sequence Rules for High Affinity Binding to Histone Octamer and Sequence-Directed Nucleosome Positioning", J. Mol. Biol., 276: 19-42.
Protacio, R.U., Polach, K.J., and Widom, J. (1997), "Coupled Enzymatic Assays for the Rate and Mechanism of DNA Site Exposure in a Nucleosome", J. Mol. Biol., 274: 708-721.
Widom, J. (1997), "Getting Around the Nucleosomes", Science, 278: 1899-1901.
Widom, J. (1997), "Chromatin: The Nucleosome Unwrapped", Curr. Biol., 7: R653-655.
Widom, J. (1997), "Chromosome Structure and Gene Regulation", Physica A, 244: 497-509.
Lowary, P.T. and Widom, J. (1997), "Nucleosome-Packaging and Nucleosome-Positioning of Genomic DNA", Proc. Natl. Acad. Sci. (USA), 94: 1183-1188.
Parthun, M.R., Widom, J., and Gottschling, D.E. (1996), "The Major Cytoplasmic Histone Acetyl-transferase in Yeast: Links to Chromatin Replication and Histone Metabolism", Cell, 87: 85-94.
Widom, J. (1996), "Short-range Order in Two Eukaryotic Genomes: Relation to Chromosome Structure", J. Mol. Biol., 259: 579-588.
Polach, K.J. and Widom, J. (1996), "A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites", J. Mol. Biol., 258: 800-812.
Protacio, R.U. and Widom, J. (1996) "Nucleosome Transcription Studied in a Real-time Synchronous System: Test of the Lexosome Model, and Direct Determination of Effects Due to Histone Octamer", J. Mol. Biol., 256: 458-472.
Polach, K.J. and Widom, J. (1995), "Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation", J. Mol. Biol. 254: 130-149.
Feng, H.-P. and Widom, J. (1994) "Kinetics of compaction during lysozyme refolding studied by continuous-flow quasielaastic light scattering", Biochemistry, 33: 13382-13390.
Feng, E., Scherl, D.S., and Widom, J. (1993) "Lifetime of the Histone Octamer Studied by Continuous-Flow Quasielastic Light Scattering: Test of a Model for Nucleosome Transcription", Biochemistry, 32: 7824-7831.
Yao, J., Lowary, P.T., and Widom, J. (1993) "Twist constraints on linker DNA in the 30nm chromatin fiber: Implications for nucleosome phasing", Proc. Natl. Acad. Sci. (USA), 90: 9364-9368.
Widom, J. (1993) "DNA Structure", invited chapter for textbook Genetics: From Genes to Genomes by Hood, L. et al., McGraw-Hill, 1999.
Draves, P.H., Lowary, P.T., and Widom, J. (1992), "Cooperative Binding of the Globular Domain of Histone H5 to DNA", J. Mol. Biol., 225: 1105-1121.
Godde, J.S. and Widom, J. (1992) "Chromatin Structure of Schizosaccharomyces pombe: a Nucleosome Repeat Length that is Shorter than the Chromatosomal DNA Length", J. Mol. Biol., 226: 1009-1025.
Widom, J. (1992) "A Relationship Between the Helical Twist of DNA and the Ordered Positioning of Nucleosomes in all Eukaryotic Cells", Proc. Natl. Acad. Sci. (USA), 89: 1095-1099.
Widom, J. (1991) "Nucleosomes and Chromatin", Current Opinion in Structural Biology 1: 245-250.
Yao, J., Lowary, P.T., and Widom, J. (1991) "Linker DNA Bending Induced by the Core Histones of Chromatin", Biochemistry 30: 8408-8414.
Widom, J. (1991), "Chromatin Folding", in Encyclopedia of Human Biology, Academic Press.
Yao, J., Lowary, P.T., and Widom, J. (1990), "Direct Detection of Linker DNA Bending in Defined Length Oligomers of Chromatin", Proc.Natl. Acad. Sci. (USA) 87: 7603-7607.
Lowary, P.T. and Widom, J. (1989), "Higher Order Structure of Saccharomyces cerevisiae Chromatin", Proc. Natl. Acad. Sci. (USA) 86: 8266-8270.
Widom, J. and Feng, H.-P. (1989), "High Performance X-ray Area Detector Suitable for Small-angle Scattering, Crystallographic, and Kinetic Studies", Rev. Sci. Inst. 60: 3231-3238.
Widom, J. (1989), "Toward a Unified Model of Chromatin Folding", Annual Review of Biophysics and Biophysical Chemistry 18: 365-395.
Widom, J. (1989), "Structure of the 300Å Chromatin Filament", in Chromosomes: Eukaryotic, Prokaryotic, and Viral, Adolph, K.W., ed., CRC Press, 127-147.
Widom, J. (1986), "Physicochemical Studies of the Folding of the 100Å Nucleosome Filament into the 300A Filament", J. Mol. Biol. 190: 411-424.
Widom, J., Finch, J.T., and Thomas, J.O. (1985), "Higher-order Folding of Long Repeat Chromatin", EMBO J. 4: 3189-3194.
Widom, J. and Klug, A. (1985), "Structure of the 300A Chromatin Filament: X-ray Diffraction from Oriented Samples", Cell 43: 207-213.
Widom, J. (1985), "Bent DNA for Gene Regulation and DNA Packaging", BioEssays (review article) 2: 11-14.
Widom, J. (1984), "DNA Bending and Kinking", Nature (News and Views) 309: 312-313.
Widom, J. and Baldwin, R.L. (1983), "Tests of Spool Models for DNA Packaging in Phage Lambda", J. Mol. Biol. 171: 419-437.
Widom, J. and Baldwin, R.L. (1983), "Inhibition of Cation-induced DNA Condensation by Intercalating Dyes", Biopolymers 22: 1621-1632.
Widom, J. and Baldwin, R.L. (1983), "Monomolecular Condensation of Lambda DNA Induced by Cobalt Hexammine", Biopolymers 22: 1595-1620.
Widom, J. and Baldwin, R.L. (1980), "Cation-induced Toroidal Condensation of DNA", J. Mol. Biol. 144: 431-453
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