Craig J. Benham - Publications

Affiliations: 
Applied Mathematics University of California, Davis, Davis, CA 
Area:
Bioinformatics Biology, General Biophysics

93 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Zhabinskaya D, Madden S, Benham CJ. SIST: stress-induced structural transitions in superhelical DNA. Bioinformatics (Oxford, England). 31: 421-2. PMID 25282644 DOI: 10.1093/bioinformatics/btu657  0.44
2014 Du X, Gertz EM, Wojtowicz D, Zhabinskaya D, Levens D, Benham CJ, Schäffer AA, Przytycka TM. Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation. Nucleic Acids Research. 42: 12367-79. PMID 25336616 DOI: 10.1093/nar/gku921  0.44
2014 Turan S, Qiao J, Madden S, Benham C, Kotz M, Schambach A, Bode J. Expanding Flp-RMCE options: the potential of Recombinase Mediated Twin-Site Targeting (RMTT). Gene. 546: 135-44. PMID 24905650 DOI: 10.1016/j.gene.2014.06.002  0.44
2013 Zhabinskaya D, Benham CJ. Competitive superhelical transitions involving cruciform extrusion. Nucleic Acids Research. 41: 9610-21. PMID 23969416 DOI: 10.1093/nar/gkt733  0.44
2013 Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM. The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli. Nucleic Acids Research. 41: 5965-77. PMID 23620297 DOI: 10.1093/nar/gkt308  0.44
2012 Zhabinskaya D, Benham CJ. Theoretical analysis of competing conformational transitions in superhelical DNA. Plos Computational Biology. 8: e1002484. PMID 22570598 DOI: 10.1371/journal.pcbi.1002484  0.44
2011 Sershen CL, Mell JC, Madden SM, Benham CJ. Superhelical duplex destabilization and the recombination position effect. Plos One. 6: e20798. PMID 21695263 DOI: 10.1371/journal.pone.0020798  0.44
2011 Levens D, Benham CJ. DNA stress and strain, in silico, in vitro and in vivo. Physical Biology. 8: 035011. PMID 21572180 DOI: 10.1088/1478-3975/8/3/035011  0.44
2011 Zhabinskaya D, Benham CJ. Theoretical analysis of the stress induced B-Z transition in superhelical DNA. Plos Computational Biology. 7: e1001051. PMID 21283778 DOI: 10.1371/journal.pcbi.1001051  0.44
2010 Strawbridge EM, Benson G, Gelfand Y, Benham CJ. The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome. Current Genetics. 56: 321-40. PMID 20446088 DOI: 10.1007/s00294-010-0302-6  0.44
2009 Hallin PF, Stærfeldt HH, Rotenberg E, Binnewies TT, Benham CJ, Ussery DW. GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes. Standards in Genomic Sciences. 1: 204-15. PMID 21304658 DOI: 10.4056/sigs.28177  0.44
2009 Mielke SP, Benham CJ, Grønbech-Jensen N. Persistence lengths of DNA obtained from Brownian dynamics simulations. The Journal of Physical Chemistry. A. 113: 4213-6. PMID 19371114 DOI: 10.1021/jp8107599  0.44
2008 Tanaka H, Mielke SP, Benham CJ, Kawai T. Visualization of the detailed structure of plasmid DNA. The Journal of Physical Chemistry. B. 112: 16788-92. PMID 19368012 DOI: 10.1021/jp804634s  0.44
2008 Mielke SP, Grønbech-Jensen N, Benham CJ. Brownian dynamics of double-stranded DNA in periodic systems with discrete salt. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 031924. PMID 18517439 DOI: 10.1103/PhysRevE.77.031924  0.44
2008 Wang H, Benham CJ. Superhelical destabilization in regulatory regions of stress response genes. Plos Computational Biology. 4: e17. PMID 18208321 DOI: 10.1371/journal.pcbi.0040017  0.44
2007 Nieduszynski CA, Hiraga S, Ak P, Benham CJ, Donaldson AD. OriDB: a DNA replication origin database. Nucleic Acids Research. 35: D40-6. PMID 17065467 DOI: 10.1093/nar/gkl758  0.44
2007 Wang H, Benham CJ. Annotation of promoter regions in microbial genomes based on DNA structural and sequence properties Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4023: 212-224.  0.44
2006 Benham CJ, Singh RR. Comment on "Can one predict DNA transcription start sites by studying bubbles?". Physical Review Letters. 97: 059801; discussion 0. PMID 17026148 DOI: 10.1103/PhysRevLett.97.059801  0.44
2006 Kang Y, Moressi CJ, Scheetz TE, Xie L, Tran DT, Casavant TL, Ak P, Benham CJ, Davidson BL, McCray PB. Integration site choice of a feline immunodeficiency virus vector. Journal of Virology. 80: 8820-3. PMID 16912328 DOI: 10.1128/JVI.00719-06  0.44
2006 Winkelmann S, Klar M, Benham C, Prashanth A, Goetze S, Gluch A, Bode J. The positive aspects of stress: strain initiates domain decondensation (SIDD). Briefings in Functional Genomics & Proteomics. 5: 24-31. PMID 16769674 DOI: 10.1093/bfgp/ell003  0.44
2006 Wang H, Benham CJ. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. Bmc Bioinformatics. 7: 248. PMID 16677393 DOI: 10.1186/1471-2105-7-248  0.44
2006 Wang H, Kaloper M, Benham CJ. SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes. Nucleic Acids Research. 34: D373-8. PMID 16381890 DOI: 10.1093/nar/gkj007  0.44
2005 Mielke SP, Grønbech-Jensen N, Krishnan VV, Fink WH, Benham CJ. Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA. The Journal of Chemical Physics. 123: 124911. PMID 16392531 DOI: 10.1063/1.2038767  0.44
2005 Benham CJ, Mielke SP. DNA mechanics. Annual Review of Biomedical Engineering. 7: 21-53. PMID 16004565 DOI: 10.1146/annurev.bioeng.6.062403.132016  0.44
2004 Benham CJ, Bi C. The analysis of stress-induced duplex destabilization in long genomic DNA sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 519-43. PMID 15579230 DOI: 10.1089/1066527041887311  0.44
2004 Mielke SP, Fink WH, Krishnan VV, Grønbech-Jensen N, Benham CJ. Transcription-driven twin supercoiling of a DNA loop: a Brownian dynamics study. The Journal of Chemical Physics. 121: 8104-12. PMID 15485274 DOI: 10.1063/1.1799613  0.44
2004 Polonskaya Z, Benham CJ, Hearing J. 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: 282-91. PMID 15464848 DOI: 10.1016/j.virol.2004.07.023  0.44
2004 Wang H, Noordewier M, Benham CJ. Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. Genome Research. 14: 1575-84. PMID 15289476 DOI: 10.1101/gr.2080004  0.44
2004 Opel ML, Aeling KA, Holmes WM, Johnson RC, Benham CJ, Hatfield GW. Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism. Molecular Microbiology. 53: 665-74. PMID 15228542 DOI: 10.1111/j.1365-2958.2004.04147.x  0.44
2004 Bi C, Benham CJ. WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA. Bioinformatics (Oxford, England). 20: 1477-9. PMID 15130924 DOI: 10.1093/bioinformatics/bth304  0.44
2003 Bode J, Goetze S, Heng H, Krawetz SA, Benham C. From DNA structure to gene expression: Mediators of nuclear compartmentalization and dynamics Chromosome Research. 11: 435-445. PMID 12971720 DOI: 10.1023/A:1024918525818  0.44
2003 Potaman VN, Bissler JJ, Hashem VI, Oussatcheva EA, Lu L, Shlyakhtenko LS, Lyubchenko YL, Matsuura T, Ashizawa T, Leffak M, Benham CJ, Sinden RR. Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats. Journal of Molecular Biology. 326: 1095-111. PMID 12589756 DOI: 10.1016/S0022-2836(03)00037-8  0.44
2003 Goetze S, Gluch A, Benham C, Bode J. Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: Potential of predicting functional gene domains Biochemistry. 42: 154-166. PMID 12515550 DOI: 10.1021/bi026496  0.44
2003 Bi C, Benham CJ. The approximate algorithm for analysis of the strand separation transition in superhelical DNA using nearest neighbor energetics Proceedings of the 2003 Ieee Bioinformatics Conference, Csb 2003. 460-461. DOI: 10.1109/CSB.2003.1227372  0.44
2002 Hatfield GW, Benham CJ. DNA topology-mediated control of global gene expression in Escherichia coli. Annual Review of Genetics. 36: 175-203. PMID 12429691 DOI: 10.1146/annurev.genet.36.032902.111815  0.44
2002 Benham CJ, Savitt AG, Bauer WR. Extrusion of an imperfect palindrome to a cruciform in superhelical DNA: complete determination of energetics using a statistical mechanical model. Journal of Molecular Biology. 316: 563-81. PMID 11866518 DOI: 10.1006/jmbi.2001.5361  0.44
2002 Mielke C, Christensen MO, Westergaard O, Bode J, Benham CJ, Breindl M. Multiple collagen I gene regulatory elements have sites of stress-induced DNA duplex destabilization and nuclear scaffold/matrix association potential. Journal of Cellular Biochemistry. 84: 484-96. PMID 11813254 DOI: 10.1002/jcb.10034  0.44
2001 Engel H, Rühl H, Benham CJ, Bode J, Weiss S. Germ-line transcripts of the immunoglobulin λ J-C clusters in the mouse: Characterization of the initiation sites and regulatory elements Molecular Immunology. 38: 289-302. PMID 11566322 DOI: 10.1016/S0161-5890(01)00056-6  0.44
2001 Woynarowski JM, Trevino AV, Rodriguez KA, Hardies SC, Benham CJ. AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs Journal of Biological Chemistry. 276: 40555-40566. PMID 11487576 DOI: 10.1074/jbc.M103390200  0.44
2001 Benham CJ. Stress-induced DNA duplex destabilization in transcriptional initiation Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 103-114. PMID 11262932  0.44
2001 Mistry SJ, Benham CJ, Atweh GF. Development of ribozymes that target stathmin, a major regulator of the mitotic spindle Antisense and Nucleic Acid Drug Development. 11: 41-49. PMID 11258620  0.44
2000 Bode J, Benham C, Ernst E, Knopp A, Marschalek R, Strick R, Strissel P. Fatal connections: when DNA ends meet on the nuclear matrix. Journal of Cellular Biochemistry. Supplement. 3-22. PMID 11389527 DOI: 10.1002/1097-4644(2000)79:35+<3::AID-JCB1121>3.0.CO;2-9  0.44
2000 Leblanc BP, Benham CJ, Clark DJ. An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled. Proceedings of the National Academy of Sciences of the United States of America. 97: 10745-50. PMID 10984524 DOI: 10.1073/pnas.200365097  0.44
2000 Baiker A, Maercker C, Piechaczek C, Schmidt SB, Bode J, Benham C, Lipps HJ. Mitotic stability of an episomal vector containing a human scaffold/matrix-attached region is provided by association with nuclear matrix. Nature Cell Biology. 2: 182-4. PMID 10707091 DOI: 10.1038/35004061  0.44
2000 He L, Liu J, Collins I, Sanford S, O'Connell B, Benham CJ, Levens D. Loss of FBP function arrests cellular proliferation and extinguishes c-myc expression Embo Journal. 19: 1034-1044. PMID 10698944  0.44
2000 Messmer BT, Benham CJ, Thaler DS. Sequential determination of ligands binding to discrete components in heterogeneous mixtures by iterative panning and blocking (IPAB) Journal of Molecular Biology. 296: 821-832. PMID 10677284 DOI: 10.1006/jmbi.1999.3487  0.44
2000 Mistry SJ, Benham CJ, Atweh GF. Novel strategies for anti-leukemia therapy: development of ribozymes that target stathmin, a major regulator of the mitotic spindle Blood. 96: 382b.  0.44
1999 Sheridan SD, Benham CJ, Hatfield GW. Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition. The Journal of Biological Chemistry. 274: 8169-74. PMID 10075720 DOI: 10.1074/jbc.274.12.8169  0.44
1999 Fye RM, Benham CJ. Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 3408-3426.  0.44
1998 Sheridan SD, Benham CJ, Hatfield GW. Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence. The Journal of Biological Chemistry. 273: 21298-308. PMID 9694890 DOI: 10.1074/jbc.273.33.21298  0.44
1997 Aranda A, Pérez-Ortín JE, Benham CJ, Lí Del Olmo M. Analysis of the structure of a natural alternating d(TA)(n) sequence in yeast chromatin Yeast. 13: 313-326. PMID 9133735 DOI: 10.1002/(SICI)1097-0061(19970330)13:4<313::AID-YEA93>3.0.CO;2-8  0.44
1996 Benham CJ. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions Journal of Molecular Biology. 255: 425-434. PMID 8568887 DOI: 10.1006/jmbi.1996.0035  0.44
1996 Benham CJ. Theoretical analysis of the helix-coil transition in positively superhelical DNA at high temperatures Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 53: 2984-2987.  0.44
1996 Miller JH, Nelson JM, Fleck EW, Benham CJ. Effects of torsional stress on the interaction of DNA with radiation and chemicals Applied Occupational and Environmental Hygiene. 11: 417-420.  0.44
1995 Benham C, Kannan S, Paterson M, Warnow T. Hen's teeth and whale's feet: generalized characters and their compatibility Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 2: 515-525. PMID 8634903 DOI: 10.1089/cmb.1995.2.515  0.44
1995 Bauer WR, Ohtsubo H, Ohtsubo E, Benham CJ. Energetics of coupled twist and writhe changes in closed circular pSM1 DNA. Journal of Molecular Biology. 253: 438-52. PMID 7473726 DOI: 10.1006/jmbi.1995.0565  0.44
1995 Sun H, Mezei M, Fye R, Benham CJ. Monte Carlo analysis of conformational transitions in superhelical DNA The Journal of Chemical Physics. 103: 8653-8665.  0.44
1994 Sioud M, Opstad A, Zhao Jq, Levitz R, Benham C, Drlica K. In vivo decay kinetic parameters of hammerhead ribozymes Nucleic Acids Research. 22: 5571-5575. PMID 7838709 DOI: 10.1093/nar/22.25.5571  0.44
1993 Benham CJ, Jafri MS. Disulfide bonding patterns and protein topologies. Protein Science : a Publication of the Protein Society. 2: 41-54. PMID 8443589 DOI: 10.1002/pro.5560020105  0.44
1993 Benham CJ. Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci Proceedings of the National Academy of Sciences of the United States of America. 90: 2999-3003. PMID 8385354  0.44
1993 Bauer WR, Benham CJ. The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA. Journal of Molecular Biology. 234: 1184-96. PMID 8263920 DOI: 10.1006/jmbi.1993.1669  0.44
1992 Benham CJ. Energetics of the strand separation transition in superhelical DNA Journal of Molecular Biology. 225: 835-847. PMID 1602485 DOI: 10.1016/0022-2836(92)90404-8  0.44
1992 Magarshak Y, Benham CJ. An algebraic representation of rna secondary structures Journal of Biomolecular Structure and Dynamics. 10: 465-488. PMID 1283516 DOI: 10.1080/07391102.1992.10508663  0.44
1991 Enami M, Sharma G, Benham C, Palese P. An influenza virus containing nine different RNA segments Virology. 185: 291-298. PMID 1833874 DOI: 10.1016/0042-6822(91)90776-8  0.44
1991 Miller JH, Nelson JM, Ye M, Swenberg CE, Speicher JM, Benham CJ. Negative supercoiling increases the sensitivity of plasmid DNA to single-Strand break induction by x-rays International Journal of Radiation Biology. 59: 941-949. PMID 1674278 DOI: 10.1080/09553009114550831  0.44
1990 Benham CJ. Theoretical analysis of heteropolymeric transitions in superhelical DNA molecules of specified sequence The Journal of Chemical Physics. 92: 6294-6305.  0.44
1989 Benham CJ. Onset of writhing in circular elastic polymers Physical Review A. 39: 2582-2586. DOI: 10.1103/PhysRevA.39.2582  0.44
1987 Benham CJ. The role of the stress resultant in determining mechanical equilibria of superhelical DNA Biopolymers - Peptide Science Section. 26: 9-15. PMID 3801598  0.44
1987 Brady GW, Satkowski M, Foos D, Benham CJ. Environmental influences on DNA superhelicity. The effect of ionic strength on superhelix conformation in solution. Journal of Molecular Biology. 195: 185-91. PMID 3656409 DOI: 10.1016/0022-2836(87)90335-4  0.44
1987 Benham CJ. The influence of tertiary structural restraints on conformational transitions in superhelical DNA Nucleic Acids Research. 15: 9985-9995. PMID 3320960 DOI: 10.1093/nar/15.23.9985  0.44
1987 Benham CJ. Energetics of superhelicity and of B-Z transitions in superhelical DNA Cell Biophysics. 10: 193-204. PMID 2446766 DOI: 10.1007/BF02797340  0.44
1985 Benham CJ. Theoretical analysis of conformational equilibria in superhelical DNA Annual Review of Biophysics and Biophysical Chemistry. 14: 23-45. PMID 3890881  0.44
1984 Brady GW, Foos D, Benham CJ. Evidence for an interwound form for the superhelix in circular DNA. Biopolymers. 23: 2963-6. PMID 6525411 DOI: 10.1002/bip.360231219  0.44
1983 Grassian V, Brady GW, Benham CJ. X-ray conformational study of the DNA duplex in solution. Biopolymers. 22: 1523-43. PMID 6871379 DOI: 10.1002/bip.360220608  0.44
1983 Benham CJ. Geometry and mechanics of DNA superhelicity Biopolymers - Peptide Science Section. 22: 2477-2495. PMID 6652227  0.44
1983 Brady GW, Fein DB, Lambertson H, Grassian V, Foos D, Benham CJ. X-ray scattering from the superhelix in circular DNA. Proceedings of the National Academy of Sciences of the United States of America. 80: 741-4. PMID 6572365  0.44
1983 Benham CJ. The cylindrical Poisson-Boltzmann equation. I. Transformations and general solutions The Journal of Chemical Physics. 79: 1969-1973.  0.44
1982 Benham CJ. Stable cruciform formation at inverted repeat sequences in supercoiled DNA Biopolymers - Peptide Science Section. 21: 679-696. PMID 7066478 DOI: 10.1002/bip.360210314  0.44
1982 Benham CJ. Statistical mechanical analysis of competing conformational transitions in superhelical DNA Cold Spring Harbor Symposia On Quantitative Biology. 47: 219-227. PMID 6574842  0.44
1981 Crowley PH, Benham CJ, Lenhart SM, Morgan JL. Peripheral doublet microtubules and wave generation in eukaryotic flagella. Journal of Theoretical Biology. 93: 769-84. PMID 7341877 DOI: 10.1016/0022-5193(81)90339-8  0.44
1981 Benham CJ. Theoretical analysis of competitive conformational transitions in torsionally stressed DNA Journal of Molecular Biology. 150: 43-68. PMID 7299820 DOI: 10.1016/0022-2836(81)90324-7  0.44
1980 Benham CJ. Kinetics of reactions involving DNA containing stress-induced single-stranded regions Biopolymers - Peptide Science Section. 19: 2143-2164. PMID 7459421 DOI: 10.1002/bip.1980.360191202  0.44
1980 Benham CJ. Theoretical analysis of transitions between B- and Z- Conformations in torsionally stressed DNA Nature. 286: 637-638. PMID 7402345 DOI: 10.1038/286637a0  0.44
1980 Benham CJ, Brady GW, Fein DB. X-ray scattering from randomly oriented superhelices. Circular superhelical DNA. Biophysical Journal. 29: 351-66. PMID 7028148 DOI: 10.1016/S0006-3495(80)85139-3  0.44
1980 Benham CJ. The equilibrium statistical mechanics of the helix-coil transition in torsionally stressed DNA The Journal of Chemical Physics. 72: 3633-3639.  0.44
1979 Benham CJ. An elastic model of the large-scale structure of duplex DNA Biopolymers - Peptide Science Section. 18: 609-623. PMID 444635 DOI: 10.1002/bip.1979.360180310  0.44
1979 Benham CJ. Torsional stress and local denaturation in supercoiled DNA Proceedings of the National Academy of Sciences of the United States of America. 76: 3870-3874. PMID 226985  0.44
1978 Benham CJ. The statistics of superhelicity Journal of Molecular Biology. 123: 361-370. PMID 691052 DOI: 10.1016/0022-2836(78)90084-0  0.44
1978 Benham CJ, Kozak JJ. Catastrophes in statistical biophysics Behavioral Science. 23: 355-359. DOI: 10.1002/bs.3830230406  0.44
1977 Benham CJ, Kozak JJ. Denaturation: an example of a catastrophe. III. Phase diagrams for multistate transformations. Journal of Theoretical Biology. 66: 679-93. PMID 881852 DOI: 10.1016/0022-5193(77)90238-7  0.44
1977 Benham CJ. Elastic model of supercoiling Proceedings of the National Academy of Sciences of the United States of America. 74: 2397-2401. PMID 267934  0.44
1976 Benham CJ, Kozak JJ. Denaturation: an example of a catastrophe II. Two-state transitions Journal of Theoretical Biology. 63: 125-149. PMID 12407 DOI: 10.1016/0022-5193(76)90089-8  0.44
1974 Kozak JJ, Benham CJ. Denaturation: an example of a catastrophe. Proceedings of the National Academy of Sciences of the United States of America. 71: 1977-81. PMID 4525309  0.44
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