B. T. Hyman, H. L. West, G. W. Rebeck, S. V. Buldyrev,
R. N. Mantegna, M. Ukleja, S. Havlin, and H. E. Stanley, "Quantitative
Analysis of Senile Plaques in Alzheimer Disease: Observation of
Log-Normal Size Distribution and Molecular Epidemiology of Differences
Associated with Apolipoprotein E Genotype and Trisomy 21 (Down
Syndrome)," Proc. Natl. Acad. Sci. 92, 3586-3590 (1995). PDF[Citations: 170]
L. Cruz, B. Urbanc, S. V. Buldyrev, R. Christie, T. Gosmez-Isla,
S. Havlin, M. McNamara, H. E. Stanley, and B. T. Hyman, "Aggregation and
Disaggregation of Senile Plaques in Alzheimer Disease,"
Proc. Acad. Natl. Sci. 94, 7612-7616 (1997). PDF[Citations: 71]
H. E. Stanley, S. V. Buldyrev, L. Cruz, T. Gomez-Isla,
S. Havlin, B. T. Hyman, R. Knowles, B. Urbanc, and C. Wyart,
"Statistical Physics and Alzheimer's Disease," Physica A 249,
460-471 (1998). PDF
N. Dokholyan, S. V. Buldyrev, H. E. Stanley, and
E. I. Shakhnovich, "Discrete Molecular Dynamics Studies of the Folding
of a Protein-Like Model," Folding & Design 3, 577-587 (1998). PDF[Citations: 172]
B. Urbanc, L. Cruz, S. V. Buldyrev, S. Havlin, M. C. Irizarry,
H. E. Stanley, and B. T. Hyman, "Dynamics of Plaque Formation in
Alzheimer Disease," Biophys. J. 76, 1330-1334 (1999). PDF
B. Urbanc, L. Cruz, S. V. Buldyrev, S. Havlin, B. T. Hyman, and
H. E. Stanley, "Dynamic Feedback in an Aggregation-Disaggregation
Model," Phys. Rev. E 60, 2120-2126 (1999). PDF
R. B. Knowles, C. Wyart, S. V. Buldyrev, L. Cruz, B. Urbanc, M. E.
Hasselmo, H. E. Stanley, and B. T. Hyman, "Plaque-Induced Neurite
Abnormalities: Implications for Disruption of Neural Networks in
Alzheimer's Disease," Proc. Natl. Acad. Sci. 96, 5274-5279
(1999). PDF[Citations: 143]
S. V. Buldyrev, L. Cruz, T. Gomez-Isla, E. Gomez-Tortosa, S. Havlin,
R. Le, H. E. Stanley, B. Urbanc and B. T. Hyman, "Description of
Microcolumnar Ensembles in Association Cortex and their Disruption in
Alzheimer and Lewy Body Dementias," Proc. Natl. Acad. Sci. 97,
5039-5043 (2000). PDF[Citations: 63]
Invited commentary accompanying this article on pages 5019-5021:
E. G. Jones, "Microcolumns in the Cerebral Cortex." PDF
N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and
E. I. Shakhnovich, "Identifying the Protein Folding Nucleus Using
Molecular Dynamics," J. Mol. Biol. 296, 1183-1188 (2000). PDF[Citations: 116]
N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich,
"Kinetics of the Protein Folding Transition" in Statistical
Physics--3rd Tohwa University International Conference, edited by
Michio Tokuyama (AIP Conference Series, Volume 519, 2000), p. 419-425.
A. Scala, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and
E. I. Shakhnovich, "Thermodynamically Important Contacts in Folding of
Model Proteins," Phys. Rev. E 63, 032901 (2001). PDF
R. Le, L. Cruz, B. Urbanc, R. B. Knowles, K. Hsiao-Ashe, K. Duff,
M. Irizarry H. E. Stanley, and B. T. Hyman, "Plaque-Induced
Abnormalities in Neurite Geometry in Transgenic Models of Alzheimer's
Disease: Implications for Neural System Disruption," J. Neuropathology
and Experimental Neurolology 60, 753-758 (2001).
[Citations: 63]
J. M. Borreguero, N. V. Dokholyan, S. V. Buldyrev,
H. E. Stanley, and E. I. Shakhnovich, "Thermodynamics and Folding
Kinetics Analysis of the SH3 Domain from Discrete Molecular Dynamics,"
J. Mol. Biol. 318, 863-876 (2002). PDF
B. Urbanc, L. Cruz, R. Le, K. Hsiao-Ashe, K. Duff, H. E. Stanley,
M. C. Irizarry, and B. T. Hyman, "Neurotoxic Effects of Thioflavin
S-Positive Amyloid Deposits in Transgenic Mice and Alzheimer's Disease,"
Proc. Natl. Acad. Sci. 99, 13990-13995 (2002). PDF[Citations: 136]
F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and
E. I. Shakhnovich, "Direct Molecular Dynamics Observation of Protein
Folding Transition State Ensemble," Biophys. J. 83, 3525-3532
(2002). PDF[Citations: 93]
F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and
E. I. Shakhnovich, "Molecular Dynamics Simulation of the SH3 Domain
Aggregation Suggests a Generic Amyloidogenesis Mechanism,"
J. Mol. Biol. 324, 851-857 (2002). PDF[Citations: 119]
N. V. Dokholyan, J. M. Borreguero, S. V. Buldyrev, F. Ding,
H. E. Stanley, and E. I. Shakhnovich, "Identifying the Importance of
Amino Acids for Protein Folding from Crystal Structures,"
in Macromolecular crystallography, Part D, Editors: C. W. Carter
Jr. and R. M. Sweet [Volume 374 of Methods in Enzymology] (Elsevier,
Amsterdam,
2003). PDF
F. Ding, J. M. Borreguero, S. V. Buldyrev, H. E. Stanley, and
N. V. Dokholyan, "Mechanism for the α-Helix to &beta-Hairpin
Transition," Proteins: Structure, Function, and Genetics 53,
220-228 (2003). PDF[Citations: 131]
S. Peng, B. Urbanc, L. Cruz, B. T. Hyman, and H. E. Stanley,
"Neuron Recognition by Parallel Potts Segmentation,"
Proc. Natl. Acad. Sci. 100, 3847-3852 (2003). PDF
M. I. Marques, J. M. Borreguero, H. E. Stanley, and
N. V. Dokholyan, "A Possible Mechanism for Cold Denaturation of Proteins
at High Pressure," Phys. Rev. Lett. 91, 138103 (2003). PDF
S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. C. Cruz,
H. E. Stanley, and N. V. Dokholyan, "Discrete Molecular Dynamics
Simulations of Peptide Aggregation," Phys. Rev. E 69, 041908
(2004). PDF
J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and
N. V. Dokholyan, "Multiple Folding Pathways of the SH3 Domain,"
Biophys. J. 87, 521-533 (2004). PDF
B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev,
H. E. Stanley, and N. V. Dokholyan, "Molecular Dynamics Simulation of
Amyloid Beta Dimer Formation," Biophys. J. 87, 2310-2321 (2004).
PDF[Citations: 127]
L. Cruz, D. L. Roe, B. Urbanc, H. Cabral, H. E. Stanley, and
D. L. Rosene, "Age-Related Reduction in Microcolumnar Structure in Area
46 of the Rhesus Monkey Correlates with Behavioral Decline,"
Proc. Natl. Acad. Sci. 101, 15846-15851 (2004). PDF
B. Urbanc, L. Cruz, S. Yun, S. V. Buldyrev G. Bitan, D. B. Teplow,
and H. E. Stanley, "In Silico Study of Amyloid Beta Protein
Folding and Oligomerization," Proc. Natl. Acad. Sci. 101,
17345-17350 (2004). PDF[Citations: 213]
L. Cruz, S. V. Buldyrev, S. Peng, D. L. Roe, B. Urbanc,
H. E. Stanley, and D. L. Rosene, "A Statistically-Based Density
Map Method for Identification and Quantification of Regional Differences
in Microcolumnarity in the Monkey Brain," J. Neurosci. Methods
141, 321-332 (2005). PDF
J. M. Borreguero, B. Urbanc, N. D. Lazo, S. V. Buldyrev,
D. B. Teplow, and H. E. Stanley, "Folding Events in the 21-30 Region of
Amyloid Beta-Protein (ABeta) Studied in silico,"
Proc. Natl. Acad. Sci. 102, 6015-6020
(2005). PDF[Citations: 93]
L. Cruz, B. Urbanc, J. M. Borreguero, N. D. Lazo, D. B. Teplow, and
H. E. Stanley, "Solvent and Mutation Effects on the Nucleation of
Amyloid Beta-Protein Folding," Proc. Natl. Acad. Sci. 102,
18258-18263 (2005). PDF of Paper[Supporting
Information]
S. Peng, B. Urbanc, S. V. Buldyrev, L. Cruz, S. Yun, D. B. Teplow,
and H. E. Stanley, "Discrete Molecular Dynamics Study of ABeta16-22
Folding and Aggregation," Biophys. J. (under review). PDF
B. Urbanc, J. M. Borreguero, L. Cruz, and H. E. Stanley, "Amyloid
Beta-Protein Aggregation: Ab initio Discrete Molecular
Dynamics Approach" [invited review paper], Methods in Enzymology
412, Chapter 19, 314-338 (2006). PDF
A. Lam, B. Urbanc, J. M. Borreguero, N. D. Lazo, D. B. Teplow, and
H. E. Stanley, "Discrete Molecular Dynamics Study of Alzheimer
Amyloid Beta-Protein (ABeta) Folding," Proceedings of The 2006
International Conference on Bioinformatics & Computational Biology.
PDF
D. B. Teplow, N. D. Lazo, G. Bitan, S. Bernstein, T. Wyttenbach,
M. T. Bowers, A. Baumketner, J. E. Shea, B. Urbanc, L. Cruz,
J. M. Borreguero, and H. E. Stanley, "Elucidating Amyloid
Beta-Protein Folding and Assembly: A multidisciplinary Approach,"
Accounts of Chemical Research 39, 635-645 (2006). PDF
B. Urbanc, L. Cruz, D. B. Teplow, and H. E. Stanley,
"Computer Simulations of Alzheimer's Amyloid Beta-Protein Folding
and Assembly," Current Alzheimer Research 3, 493-504 (2006). PDF
S. Yun, B. Urbanc, G. Bitan, D. B. Teplow, and H. E. Stanley,
"Role of Electrostatic Interactions in Amyloid Beta-Protein (ABeta)
Oligomer Formation: A Discrete Molecular Dynamics Study,"
Biophys. J. 92, 4064-4077 (2007). PDF
A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan,
S. V. Buldyrev, H. E. Stanley, and E. Shakhnovich, "Parallel Folding
Pathways in the SH3 Domain Protein," J. Mol. Bio. 373, 1348-1360
(2007). PDF
L. Cruz, B. Urbanc, A. Inglis, D. L. Rosene, and
H. E. Stanley, "Generating a Model of the Three-dimensional
Spatial Distribution of Neurons Using Density Maps," Neuroimage
40, 1105-1115 (2008). PDF
S. Yun, S. Peng, L. Cruz, S. V. Buldyrev, D. B. Teplow,
H. E. Stanley, and B. Urbanc, "Discrete Molecular Dynamics Observation
of ABeta16-22 Folding and Aggregation" (preprint). PDF
A. Inglis, B. Urbanc, L. Cruz, D. Roe, H. E. Stanley, and D. Rosene,
"Automated Identification of Neurons and Their Locations," Journal of
Microscopy 230, 339-352
(2008). PDF
A. Lam, D. Teplow, H. E. Stanley, and B. Urbanc, "Effects of the
Arctic (Glu^22--->Gly) Mutation on Amyloid Beta-Protein Folding:
Discrete Molecular Dynamics Study," J. Amer. Chem. Soc. 130[51],
17413-17422 (2008).
PDF
S. V. Buldyrev, "Application of Discrete Molecular Dynamics to
Protein Folding and Aggregation," in Aspects of Physical Biology:
Biological Water, Protein Solutions, Transport, and Replication
[Proceedings of the 2006 Sitges Conference], edited by G. Franzese and
M. Rubi (Springer, Berlin, 2008), pp. 97-131.
PDF
L. Cruz, D. L. Roe, B. Urbanc, A. Inglis, H. E. Stanley,
D. L. Rosene, "Age-Related Reduction in Microcolumnar Structure
Correlates with Cognitive Decline in Ventral but Not Dorsal Area 46 of
the Rhesus Monkey," Neuroscience 158, 1509-1520 (2009).
PDF
C. H. Comin, J. R. Santos, D. Corradini, W. Morrison, C. Curme,
D. L. Rosene, A. Gabrielli, L. de F. Costa, and H. E. Stanley,
"Statistical Physics Approach to Quantifying Differences in Myelinated
Nerve Fibers," Nature Scientific Reports 4, 4511 (2014).
PDF
E. Galea, W. Morrison, E. Hudry, M. Arbel-Ornath, B. J. Bacskai,
T. Gómez-Isla, H. E. Stanley, and B. T. Hyman, "Topological
Analyses in APP/PS1 Mice Reveal that Astrocytes Do Not Migrate to
Amyloid-aL Plaques," Proc. Natl. Acad. Sci. USA 112, 15556-15561
(2015).
PDF
