Invited Papers
  E. Emberly and G. Kirzenow, "Molecular Spintronics: Spin-Dependent Electron Transport in Molecular Wires", contributed to special issue of Chemical Physics on the topic of Molecular Electronics, edited by P. Haengeei, M. Ratner and S. Yaliraki. Chem. Phys. 281, 311 (2002).
   
 
Refereed Papers

Saberi S, Emberly E. "Chromosome driven spatial patterning of proteins in bacteria". PLoS Comput Biol. 6, e1000986 (2010).



Sadeghi S, Emberly E. "Length Dependent Force Response of Coiled-coil Proteins", Phys Rev E  80, 061909 (2009).



Jiang N, Emberly E, Cuvier O, Hart CM. Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription.  Mol Cell Biol. 29, 3556-68 (2009).



Emberly E, Blattes R, Schuettengruber B, Hennion M, Jiang N, Hart CM, Käs E, Cuvier O. "BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites.".PLoS Biol. 6, 2896-910 (2008).



E. Emberly. "Optimizing the Read-out of Morphogen Gradients". PRE 77, 041903 (2008).



E. Emberly and N. Wingreen. "Hourglass model for a protein-based circadian oscillator". Phys Rev Lett 96, 038303 (2006).


  M. Schroeder, M. Pearce, J. Fak, H.Q. Fan, U. Unnerstall, E. Emberly, N. Rajewsky, E.D. Siggia, U. Gaul, “Transcriptional Control in the Segmentation Network of Drosophila”, PLOS Biology 2, 1396-1410 (2004)
   
  S. Moelbert, E. Emberly, and C. Tang, “Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins”, Protein Sci. 13, 752-762 (2004).
   
  E. Emberly, R. Mukhopadhyay, C. Tang and N. Wingreen, “Flexibility of beta-sheets: Principal-component analysis of database protein structures”, Proteins 55, 91-98 (2004).
   
  E. Emberly and G. Kirczenow, "The Smallest Molecular Switch", Phys. Rev. Lett. 91, 188301 (2003).
   
  E. Emberly, N. Rajewsky, E. Siggia, “Conservation of regulatory elements between two species of Drosophila”, BMC Bioninformatics, 4, 57 (2003).
   
  R. Mukhopadhyay, E. Emberly, N. Wingreen and C. Tang, "Statistical Mechanics of RNA Folding: Effects of Alphabet Size", Phys. Rev. E. 68, 041904 (2003).
   
  E. Emberly, R. Mukhopadhyay, N. Wingreen and C. Tang, "Flexibility of alpha-helices: Results of a Statistical Analysis of Database Protein Structures", J. Mol. Bio. 327, 229 (2003).
   
  E. Emberly, N. Wingreen and C. Tang, "Designability of Alpha-helical Proteins". Proc. Natl. Acad. Sci. USA 99, 11163 (2002).
   
  E. Emberly, J. Miller, C. Zheng, N. Wingreen and C. Tang, "Identifying Proteins of High Designability via Surface Exposure Pattern", Proteins 47, 295 (2002).
   
  E. Emberly and G. Kirczenow, "Charging Effects, Forces and Conduction in Molecular Wire Systems", Ann. NY Acad. Sci. 960, 131 (2002).
   
  E. Emberly and G. Kirczenow, "Comment on "First-Principles Calculation of Transport Properties of a Molecular Wire Device'"", Phys. Rev. Lett. 87, 269701 (2001).
   
  E. Emberly and G. Kirczenow, "Models of Electron Transport through Organic Molecular Monolayers Self-Assembled on Nanoscale Metallic Contacts", Phys. Rev. B 64, 235412 (2001).
   
  E. Emberly and G. Kirczenow, "Current-Driven Conformational Changes, Charging and Negative Differential Resistance in Molecular Wires", Phys. Rev. B, 64, 125318 (2001).
   
  E. Emberly and G. Kirczenow, "Principles for the Design and Operation of a Molecular Wire Transistor", J. App. Phys., 88, 5280-5282 (2000).
   
  E. Emberly and G. Kirczenow, "Multi-terminal Molecular Wire Systems: A Self-consistent Theory and Computer Simulations of Charging and Transport", Phys. Rev. B, 62, 10451-10458 (2000).
   
  E. Emberly and G. Kirczenow, "Landauer Theory, Inelastic Scattering and Electron Transport in Molecular Wires", Phys. Rev. B, 61, 5740-5750 (2000).
   
  E. Emberly and G. Kirczenow, "Antiresonances in Molecular Wires", J. Phys. Cond. Matt., 11, 6911-6926 (1999).
   
  E. Emberly and G. Kirczenow, "Electrical Conductance of Molecular Wires", Nanotechnology, 10, 285-289 (1999).
   
  E. Emberly and G. Kirczenow, "Electron Standing-wave Formation in Atomic Wires", Phys. Rev. B, 60, 6028-6033 (1999).
   
  E. Emberly and G. Kirczenow, "State Orthogonalization by Building a Hilbert Space: A New Approach to Electronic Quantum Transport in Molecular Wires", Phys. Rev. Lett., 81, 5205-5208 (1998).
   
  E. Emberly and G. Kirczenow, "Theoretical Study of Electrical Conduction Through a Molecule Connected to Metallic Nanocontacts", Phys. Rev. B, 58, 10911-10920 (1998).
   
  E. Emberly and G. Kirczenow, "Theory of Electrical Conduction Through a Molecule", Ann. New York Acad. Sci., 852, 54-60(1998).
   
  J. M. Vail, E. Emberly, T. Lu, M. Gu and R. Pandey, "Simulation of Point Defects in High Density Luminescent Materials: Oxygen in Barium Fluoride", Phys. Rev. B, 57, 764-772 (1998).