Publications



Jack Smith, Melissa Romanus, Pradeep Kumar Mantha, Yaakoub El Khamra, T.C. Bishop, Shantenu Jha. Scalable Online Comparative Genomics of Mononucleosomes: A BigJob. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), ACM, New York, NY, USA, Article 23, 8 pages. DOI: 10.1145/2484762.2484819

Mithun Biswas, Jörg Langowski, T. C. Bishop. Atomistic simulations of nucleosomes. Wiley Interdisciplinary Reviews: Computational Molecular Science, DOI: 10.1002/wcms.1139.


Rajib Mukherjee, Abhinav Thota, Hideki Fujioka, T.C. Bishop , Shantenu Jha. Running many molecular dynamics simulations on many supercomputers. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond (XSEDE '12 ), ACM, New York, NY, USA, , Article 2, 9 pages, DOI: 10.1145/2335755.2335787 .


Melissa Romanus, Pradeep Kumar Mantha, Matt McKenzie, T.C. Bishop, Emilio Gallichio, Andre Merzky, Yaakoub El Khamra, and Shantenu Jha. The anatomy of successful ECSS projects: lessons of supporting high-throughput high-performance ensembles on XSEDE. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond (XSEDE '12). ACM, New York, NY, USA, Article 46 , 9 pages. DOI: 10.1145/2335755.2335843 .


Rajib Mukherjee and T.C. Bishop. Nucleosomal DNA: Kinked, Not Kinked, or Self-Healing Material? Frontiers in Nucleic Acids Chapter 5, pp 69–92. ACS Symposium Series, Vol. 1082 ISBN13: 9780841226234 eISBN: 9780841226289 DOI: 10.1021/bk-2011-1082.ch005


T.C. Bishop. Chromatin in 1, 2 and 3 dimensions: comment on "Cracking the chromatin code: Precise rule of nucleosome positioning." by E.N. Trifonov. Phys Life Rev. 2011 Mar;8(1):56-8; discussion 69-72. PMID: 21295530

R. Stolz and T.C. Bishop. ICM Web: the interactive chromatin modeling web server. Nucleic Acids Research 38, W254-261, 2010; DOI:10.1093/nar/gkq496 . PMID: 20542915 ICM homepage
*chosen by the Editors as a Featured Article, representing the top 5% of NAR papers in terms of originality, significance and scientific excellence.

Sereda and T.C. Bishop. Evaluation of Elastic Rod Models with Long Range Interactions for Predicting Nucleosome Stability. J. Biol. Struc. Dyn. 27(6):713-894, 2010. PMID: 20232939. DOI: 10.1080/073911010010524948

T.C. Bishop. VDNA: The Virtual DNA plug-in for VMD. Bioinformatics, 25(23):3187-3188, 2009; DOI:10.1093/bioinformatics/btp566. PMID: 19789266 VDNA homepage

R. Lavery, K. Zakrzewska, D. Beveridge, T.C. Bishop, D. Case, T. Cheatham III, S. Dixit, B.Jayaram, F. Lankas, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, N. Spackova, J. Sponar. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Research, 2009.
*chosen as a “Must Read” by Faculty of 1000 in Biology.
Trajectories available: http://holmes.cancres.nottingham.ac.uk/~charlie/ABC2


S. Y. Ponomarev, Vakhtang Putkaradze, T.C. Bishop. Relaxation dynamics of nucleosomal DNA. Physical Chemistry Chemical Physics, 2009.

J. Zlatanova, T.C. Bishop. J-M. Victor, J. Vaughn, K. van Holde. The nucleosome family: dynamic and growing. Structure 17(2):160-71, 2009. Suboctasome Image Files (12Mb zip)

T.C. Bishop. Geometry of the Nucleosomal DNA Superhelix. Biophysical J. 95:1007-1017,2008.

T.C. Bishop. Conformation and Dynamics of Nucleosomal and Free DNA. J. Biol. Struc. Dyn. 22(6): 673-686, 2005.

T.C. Bishop, R. Cortez, and O. O. Zhmudsky. Investigation of Bend and Shear Waves in a Geometrically Exact Model of an Elastic Rod. J. Comp. Phys. 193(2): 642-665, 2004.

J. B. Delehanty, R. M. Jones, T.C. Bishop, and D.A. Blake. Identification of Important Residues in Metal-Chelate Recognition by Monoclonal Antibodies. Biochemistry 42(48):14173-14183, 2003.

A. K. Mohanty, C. M. Bishop, T.C. Bishop, W. C. Wimley, and M. C. Wiener. Enzymatic E-colicins bind to their target receptor BtuB by presentation of a small binding epitope on a coiled-coil scaffold. J. Biol. Chem., 278(42):40953-40958, 2003.

T.C. Bishop and O. Zhmudsky. Mechanical Model of Nucleosome and Chromatin Dynamics. J. Biol. Struc. Dyn., 19(5):877-887, 2002.

C. A. Marhefka, B.M. Moore II, T.C. Bishop, L. Kirkovsky, A. Mukherjee, J.T. Dalton, and D. D. Miller. Homology Modeling Using Multiple Molecular Dynamics Simulations and Docking Studies of the Human Androgen Receptor Ligand Binding Domain Bound to Testosterone and Nonsteroidal Ligands. J. Med. Chem., 44:1729-1740, 2001.

T.C. Bishop and O.O. Zhmudsky. Information Transmission Along DNA, in Currents in Computational Molecular Biology 2001, N. El-Mabrouk, T. Lengauer, and D. Sankoff, Editors, Les Publications CRM: Montreal. p. 105-106, 2001.

T.C. Bishop and J.E. Hearst. Potential Function Describing the Folding of the 30nm Fiber. J. Chem. Phys. B, 102(33):6433-6439, 1998.

Y. Shi, J.E.Hearst, T.C. Bishop and H.R. Halvorson. Erratum: "The Kirchhoff elastic rod, the nonlinear Schrödinger equation, and DNA supercoiling" [J. Chem. Phys. 101,5186 (1994)]. J. Chem. Phys., 109(7):2959-2961, 1998.

T.C. Bishop, R. Skeel and K. Schulten. Difficulties with multiple time stepping and the fast multipole algorithm in molecular dynamics. J. Comp. Chem., 18(14):1785-1791, 1997.

D. Kosztin, T. Bishop and K. Schulten. Binding of the estrogen receptor to DNA: The role of waters. Biophys. J. 73:557-570, 1997.

T. Bishop, D. Kosztin and K. Schulten. How hormone receptor-DNA binding affects nucleosomal DNA: The role of symmetry. Biophys. J., 72:2056-2067, 1997.

T.C. Bishop and K. Schulten. Molecular dynamics study of glucocorticoid receptor-DNA binding. Proteins Struct., Funct. and Genet., 24(1):115-133, 1996.