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Bradley Dickson, Ph.D.

Staff Scientist
Bradley Dickson, Ph.D.
Staff scientist
 

Biography

Dr. Brad Dickson received his Ph.D. in chemistry from Clemson University, where he studied enhanced sampling algorithms for molecular dynamics simulations. After studying path sampling techniques at UT Austin, in 2009 Brad began working with adaptive bias methods as a postdoctoral researcher at École Normale Supérieure de Lyon. Brad has deployed these adaptive schemes to probe kinase dynamics while at Purdue University, and to inform drug discovery efforts against epigenetic targets while working in the Center for Integrative Chemical Biology and Drug Discovery at University of North Carolina Chapel Hill. In 2015, Dr. Dickson joined the Rothbart Laboratory at Van Andel Research Institute (VARI), where he used computational biophysics to inform on the complex mechanics underlying chromatin accessibility, interaction and function. He is now a staff scientist at VARI.

Research focus

Improving the efficiency and applicability of adaptive biasing for free energy computation, and deploying such technologies in the study of chromatin biology and drug discovery.

Education

Ph.D. in chemistry, Clemson University (Steven Stuart’s Lab)
Postdoc: with Graeme Henkelman and Dmitrii Makarov, University of Texas at Austin
Postdoc: with Paul Fleurat-Lessard, École Normale Supérieure de Lyon
Postdoc: with Carol Post, Purdue University
Postdoc: with Stephen Frye, University of North Carolina at Chapel Hill

Selected publications

Dickson BM. 2019. Erroneous rates and false statistical confirmations from infrequent metadynamics and other equivalent violations of the hyperdynamics paradigm. J Chem Theory Comp 15(1):78–83.

Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB. 2018. Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1Proc Natl Acad Sci U S A.

Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB. 2018. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenanceNuc Acids Res

Cornett EM, Dickson BM, Krajewski K, Spellmon N, Umstead A, Vaughan RM, Shaw KM, Versluis PP, Cowles MW, Brunzelle J, Yang Z, Vega IE, Sun ZW, Rothbart SB. 2018. A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity. Sci Adv.

Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC, Ruthenberg AJ. 2018. Examining the roles of H3K4 methylation states with systematically characterized antibodiesMol Cell. 
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Video abstract

Dickson BM. 2017. Overfill protection and hyperdynamics in adaptively biased simulations.  J Chem Theory Comp 13(12):5925–5932.

Cornett EM, Dickson BM, Rothbart SB. 2017. Analysis of histone antibody specificity with peptide microarrays. JoVE (126):doi: 10.3791/55912.  

Dickson BM, de Waal P, Ramjan Z, Xu HE, Rothbart SB. 2016. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4J Chem Phys 145:154113.

Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, Bedford MT, Min J, Arrowsmith CH, James LI, Frye SV. 2016. A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1Nat Chem Biol 12:180–187. 

Dickson BM. 2016. Survey of adaptive biasing potentials: comparisons and outlook. Curr Opin Struct Biol 43:63–67.

Harrison J, Cornett E, Goldfarb D, DaRosa P, Li Z, Yan F, Dickson BM, Guo A, Cantu D, Kaustov L, Brown P, Arrowsmith C, Klevit R, Erie D, Major B, Krajewski K, Kulhman B, Strahl B, Rothbart SB. 2016. Hemi-methylated DNA regulates DN methylation inheritance through allosteric activation of H3 ubiquitylation for UHRF1eLife.  

Cornett EM, Dickson BM, Vaughan RM, Krishnan S, Trievel RC, Strahl BD, Rothbart SB. 2016. Substrate specificity profiling of histone-modifying enzymes by peptide microarrayMethods Enzymol 574:31–52.  

Dickson BM, Cornett EM, Ramjan Z, Rothbart SB. 2016. ArrayNinja: An open source platform for unified planning and analysis of microarray experimentsMethods Enzymol 574:53–57. 

Perfetti MT, Baughman BM, Dickson BM, Mu Y, Cui G, Mader P, Dong A, Norris JL, Rothbart SB, Strahl BD, Brown PJ, Janzen WP, Arrowsmith CH, Mer G, McBride KM, James LI, Frye SV. 2015. Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1. ACS Chem Biol 10(4):1072—1081.  

Dickson BM. 2015. μ-tempered metadynamics: Artifact independent convergence times for wide hillsJ Chem Phys 143.     

Rothbart SB, Dickson BM, and Strahl BD. 2015. From histones to ribosomes: A chromatin regulator tangoes with translationCancer Discov 5(3):228–230. 

Rothbart SB, Dickson BM, Raab JR, Gryzbowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenberg AJ, Strahl BD. 2015. An interactive database for the assessment of histone antibody specificityMol Cell 59(3):502–511. 

Rothbart SB, Dickson BM, Ong MS, Krajewski K, Houliston S, Kireev DB, Arrowsmith CH, Strahl BD. 2013. Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylationGenes Dev27(11):1288–1298. 

Dickson BM. 2011. Approaching a parameter-free metadynamicsPhys Rev E 84. http://dx.doi.org/10.1103/PhysRevE.84.037701