About Dr. Benham

Dr. Craig J. Benham
UC Davis Genome Center
University of California
One Shields Avenue
Davis, CA 95616

(530) 754-9647 (Office)
(530) 754-9658 (FAX)



  1. 2008 Mielke, S.P., Gronbach-Jensen, N. and Benham, C.J. Brownian Dynamics of Double Stranded DNA In Periodic Systems with Discrete Salt, Phys. Rev. E. 77, 031924 (11 pages).
  2. 2008 Wang, H.Q. and Benham, C.J. Superhelical Destabilization in Regulatory Regions of Stress Response Genes. PLoS Comp. Biol. 4, e17. doi:10.1371/journal.pcbi.0040017 (15 pages)
  3. 2007 Nieduszynski, C., Hiraga, S-I., AK, P., Benham, C. J. and Donaldson, A. OriDB: a DNA Replication Origin Database. Nucl. Acids Res. 35, D40-D46
  4. 2006 Kang, Y., Moressi, C., Scheetz, T., Xie, L., Tran, D., Casavant, T., AK, Prashanth, Benham, C.J., Davidson, B. and McCray, P.B. Integration Site Choice of a Feline Immunodeficiency Virus Vector in Somatic Cells In Vitro and In Vivo. J. Virol. 80, 8820-8823.
  5. 2006 Benham, C.J. and Singh, R. Comment on “Can One Predict DNA Transcription Start Sites by Studying Bubbles?” Phys. Rev. Lett. 97, 059801.
  6. 2006 Wang, H.Q. and Benham, C.J. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress, BMC Bioinformatics 7: 248-262.
  7. 2006 Bode, J., Winkelmann, S., Goetze, S., Spiker, S., Tsutsui, K., Bi, C., AK, Prashanth and Benham, C.J. Correlations between Scaffold/Matrix Attachment Region (S/MAR) Binding Activity and DNA Duplex Destabilization Energy, J. Mol. Biol. 358: 597-613.
  8. 2006 Wang, H., Kaloper, M and Benham, C.J. SIDDBASE: A Database Containing the Stress-Induced DNA Duplex Destabilization (SIDD) Profiles of Complete Microbial Genomes, Nucleic Acids Res., 34 (Database issue): D373-D378.
  9. 2005 Mielke, S.P., Gronbach-Jensen, N., Krishnan, V.V., Fink, W.H. and Benham, C.J. Brownian Dynamics Simulation of Sequence-dependent Duplex Denaturation in Dynamically Superhelical DNA, J. Chem. Phys., 123, 124911 (11 pages). (Refereed)
  10. 2005 Benham, C.J. and Mielke, S.P. DNA Mechanics, Ann. Rev. Biomed. Eng. 7: 21-53.
  11. 2005 AK, Prashanth, and C.J. Benham. Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins, PLoS – Comp Biol. 1:41-46.
  12. 2004 Polonskaya, Z., Benham, C.J., and J. Hearing. Role for a Region of Helically Unstable DNA within the Epstein-Barr Virus Latent Cycle Origin of DNA Replication oriP in Origin Function, Virology, 328: 282-291.
  13. 2004 Mielke, S.P., Fink, W.H., Krishnan, V.V., Gronbech-Jensen, N. and C.J. Benham. Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study, J. Chem. Phys., 121:8104-8112.
  14. 2004 Wang, H., Noordewier, M. and C.J Benham. Stress-Induced DNA Duplex Destabilization (SIDD) in the Escherichia coli Genome: SIDD Sites are Closely Associated with Promoters, Genome Research, 14:1575-1584.
  15. 2004 Bi, C.-P. and C.J. Benham. WebSIDD: Server for Predicting of the Stress-induced Duplex Destabilized (SIDD) Sites in Superhelical DNA, Bioinformatics, 20: 1477-1479.
  16. 2004 Benham, C.J. and C.-P Bi. The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences, J. Comp. Biol., 11:519-543.
  17. 2004 Opel, M. L., Aeling, K.A., Holmes, W.M., Johnson, R., Benham, C.J., and G.W. Hatfield. Activation of Transcription Initiation from a Stable RNA Promoter by a Fis Protein-mediated DNA Structural Transmission Mechanism, Molec. Microbiol., 53:665-674.
  18. 2003 Bode, J., Goetze, S., Heng, H., Krawetz, S.A. and C.J. Benham. From DNA Structure to Gene Expression: Mediators of Nuclear Compartmentalization and Dynamics, Chromosome Research, 11:435-445
  19. 2003 Potaman, V., Bissler, J., Hashem, V., Oussatcheva, E., Lu, L., Shlyakhtenko, L., Lyubchenko, Y., Matsuura, T., Ashizawa, T., Leffak, M, Benham, C.J., and R.R. Sinden. Unwound Structures in SCA10 (ATTCT)n (AGAAT)n Repeats, J. Mol. Biol., 326:1095-1111.
  20. 2003 Goetze, S., Gluch, A., Benham, C.J., and J. Bode. Computational and in vitro Analysis of Destabilized DNA Regions in the Interferon Gene Cluster: The Potential of Predicting Functional Gene Domains, Biochemistry, 42:154-166.
  21. 2002 Hatfield, G.W. and C.J. Benham. DNA Topology-Mediated Control of Global Gene Expression in Escherichia coli, Ann. Rev. Genetics, 36:175-203.
  22. 2002 Benham, C.J., Savitt, A. and W.R.Bauer. Extrusion of an Imperfect Palindrome to a Cruciform in Superhelical DNA: Complete Determination of Energetics Using a Statistical Mechanical Model, J. Mol. Biol., 316:563-580.
  23. 2002 Mielke, C., Christensen, M., Westergaard, O., Bode, J., Benham, C.J. and M. Breindl. Multiple Collagen I Gene Regulatory Elements Have Sites of Stress-Induced DNA Duplex Destabilization and Nuclear Scaffold/Matrix Association Potential, J. Cell. Biochem., 84:484-496.
  24. 2001 Woynarowski, J.M., Trevino, A., Rodriguez, K., Hardies, S.C. and C.J. Benham. AT-rich Islands in Genomic DNA – A Novel Target for AT-specific DNA-reactive Antitumor Drugs, J. Biol. Chem., 276:40555-40566.
  25. 2001 Bode, J., Fetzer, C., Nehlsen, K., Scinteie, M., Hinrichs, B.-H., Baiker, A., Piechaczek, C., Benham, C.J. and H.J. Lipps. The Hitchhiking Principle: Optimizing Episomal Vectors for Use in Gene Therapy and Biotechnology, Gene Ther. Mol. Biol., 6:33-46.
  26. 2001 Engel, H., Ruehl, H., Benham, C.J., Bode, J., and S. Weiss. Germ-line Transcripts of the Immunoglobulin _ J-C Clusters in the Mouse: Characterization of the Initiation Sites and Regulatory Elements, Mol. Immunol. 38:289-302. (Was Submitted #2 at Appointment, 3-1-01)
  27. 2000 Baiker, A., C. Maercker, C. Piechaczek, S. Schmidt, J. Bode, C.J. Benham, and H.L. Lipps. Mitotic Stability of an Episomal Vector Containing a Human Scaffold/Matrix-Attached Region is Provided by Nuclear Matrix Association, Nature Cell Biol., 2: 182-184.
  28. 2000 He, L., J. Liu, I. Collins, S. Sanford, B. O’Connell, C.J. Benham, and D. Levens. Loss of FBP Function Arrests Cellular Proliferation and Extinguishes c- myc Expression, EMBO J., 19(5): 1034-1044.
  29. Messmer, B., C.J. Benham, and D. Thaler. Sequential Determination of Ligands Binding to Discrete Components in Heterogeneous Mixtures by Iterative Panning and Blocking (IPAB), J. Mol. Biol., 296(3): 821-832.
  30. 1999 Sheridan, S., C.J. Benham, and G.W. Hatfield. Inhibition of DNA Supercoiling- Dependent Transcriptional Activation by a Distant B-DNA to Z-DNA Transition, J. Biol. Chem., 274(13): 8169-8174.
  31. 1999 Fye, R.M., and C.J. Benham. Exact Method for Numerically Analyzing a Model of Local Denaturation in Superhelically Stressed DNA, Phys. Rev. E, 59(3): 3408-3426.
  32. 1998 Sheridan, S., C.J. Benham, and G.W. Hatfield. Activation of Gene Expression by a Novel DNA Structural Transmission Mechanism that Requires Supercoiling-Induced DNA Duplex Destabilization in an Upstream Activating Sequence, J. Biol. Chem. 273(33): 21298-21308.
  33. 1997 Benham, C.J., T. Kohwi-Shigematsu, and J. Bode. Stress-Induced Duplex Destabilization in Chromosomal Scaffold/Matrix Attachment Regions, J. Mol. Biol., 274(2): 181-196.
  34. 1996 Benham, C.J. Theoretical Analysis of the Helix-Coil Transition in Positively Superhelical DNA at High Temperatures, Phys. Rev. E, 53(3): 2984-2987.
  35. 1996 Benham, C.J. Duplex Destabilization in Superhelical DNA is Predicted to Occur at Specific Transcriptional Regulatory Regions, J. Mol. Biol., 255(3): 425-434.
  36. 1995 Sun, H., M. Mezei, R. Fye, and C.J. Benham. Monte Carlo Analysis of Conformational Transitions in Superhelical DNA, J. Chem. Phys., 103: 8653- 8665.
  37. 1995 Bauer, W.R., H. Ohtsubo, E. Ohtsubo, and C.J. Benham. Energetics of Coupled Twist and Writhe Changes in Closed Circular pSM1 DNA, J. Mol. Bio., 253: 438-452.
  38. 1993 Bauer, W.R. and C.J. Benham. The Free Energy, Enthalpy and Entropy of Native and of Partially Denatured Closed Circular DNA, J. Mol. Biol., 234(4): 1184-1196.
  39. 1993 Benham, C.J. Sites of Predicted Stress-Induced DNA Duplex Destabilization Occur Preferentially at Regulatory Loci, Proc. Natl. Acad. Sci. USA., 90(7): 2999-3003.
  40. 1993 Benham, C.J., and M.S. Jafri. Disulfide Bonding Patterns and Protein Topologies, Protein Science, 2: 41-54.
  41. 1990 Benham, C.J. Theoretical Analysis of Heteropolymeric Transitions in Superhelical DNA Molecules of Specified Sequence, Journal of Chemical Physics, 92: 6294-6305.
  42. 1989 Benham, C.J. Onset of Writhing in Circular Elastic Polymers, Phys. Rev. A., 39: 2582-2586.
  43. 1987 Benham, C.J. The Influence of Tertiary Structural Restraints on Conformational transitions in Superhelical DNA, Nuc. Acids Res., 15: 9985-9995.
  44. 1987 Benham, C.J. The Role of the Stress Resultant in Determining Mechanical Equilibria of Superhelical DNA, Biopolymers, 28: 9-15.
  45. 1983 Benham, C. Geometry and Mechanics of DNA Superhelicity, Biopolymers, 22: 2477-2495.
  46. 1983 Benham, C. The Cylindrical Poisson-Boltzmann Equation I: Transformations and General Solutions, J. Chem. Phys., 79: 1969-1973.
  47. 1983 Brady, G., D. Fein, H. Lambertson, V. Grassian, D. Foos, and C. Benham. X-rayScattering from the Superhelix in Circular DNA, Proc. Nat’l. Acad. Sci. USA , 80: 741-744.
  48. 1983 Grassian, V, G. Brady, and C. Benham. X-ray Conformational Study of the DNA Duplex in Solution, Biopolymers, 22: 1523-1543.
  49. 1982 Benham, C. Stable Cruciform Formation at Inverted Repeat Sequences in Supercoiled DNA, Biopolymers, 21: 679-693.
  50. 1980 Benham, C. Theoretical Analysis of Transitions between B- and Z- Conformations in Torsionally Stressed DNA, Nature, 288: 637-638.
  51. 1980 Benham, C. The Equilibrium Statistical Mechanics of the Helix-Coil Transition in Torsionally Stressed DNA, J. Chem. Phys., 72: 3633-3639.
  52. 1979 Benham, C. Torsional Stress and Local Denaturation in Supercoiled DNA, Proc, Nat’l. Acad. Sci. USA, 76: 3870-3874.
  53. 1979 Benham, C. An Elastic Model of the Large-Scale Structure of Duplex DNA, Biopolymers, 18: 609-623.
  54. 1977 Benham, C. Elastic Model of Supercoiling, Proc. Nat’l. Acad. Sci. USA, 74: 2397-2401.

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