Statistical Physics and Neuroscience
The Center for Polymer Studies at Boston University


[Citation counts listed when above 50.]

  1. 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]
  2. 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]
  3. 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
  4. 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]
  5. 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
  6. 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
  7. 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]
  8. 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
  9. 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]
  10. 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.
  11. 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
  12. 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]
  13. 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
  14. 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]
  15. 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]
  16. 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]
  17. 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
  18. 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]
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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]
  24. 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
  25. 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]
  26. 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
  27. 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]
  28. 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]
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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