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Ben Hall

AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC, Shorthouse D, Durrani A, Fife K, Rytina E, Milne D, Roshan A, Mahububani K, Saeb-Parsy K, Hall BA, Gerstung M, Jones PH. Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site. Cancer Discov. 2020 Oct 21. PMID: 33087317.
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    2. Colom B, Alcolea MP, Piedrafita G, Hall MWJ, Wabik A, Dentro SC, Fowler JC, Herms A, King C, Ong SH, Sood RK, Gerstung M, Martincorena I, Hall BA, Jones PH. Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium. Nat Genet. 2020 06; 52(6):604-614. PMID: 32424351.
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    3. Piedrafita G, Kostiou V, Wabik A, Colom B, Fernandez-Antoran D, Herms A, Murai K, Hall BA, Jones PH. A single-progenitor model as the unifying paradigm of epidermal and esophageal epithelial maintenance in mice. Nat Commun. 2020 03 18; 11(1):1429. PMID: 32188860.
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    4. Hall BA, Fisher J. Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer. Curr Protoc Bioinformatics. 2020 03; 69(1):e95. PMID: 32078258.
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    5. Nik-Zainal S, Hall BA. Cellular survival over genomic perfection. Science. 2019 11 15; 366(6467):802-803. PMID: 31727818.
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    6. Hall MWJ, Jones PH, Hall BA. Relating evolutionary selection and mutant clonal dynamics in normal epithelia. J R Soc Interface. 2019 07 26; 16(156):20190230. PMID: 31362624.
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    7. Murai K, Skrupskelyte G, Piedrafita G, Hall M, Kostiou V, Ong SH, Nagy T, Cagan A, Goulding D, Klein AM, Hall BA, Jones PH. Epidermal Tissue Adapts to Restrain Progenitors Carrying Clonal p53 Mutations. Cell Stem Cell. 2018 11 01; 23(5):687-699.e8. PMID: 30269904.
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    8. Shorthouse D, Riedel A, Kerr E, Pedro L, Bihary D, Samarajiwa S, Martins CP, Shields J, Hall BA. Exploring the role of stromal osmoregulation in cancer and disease using executable modelling. Nat Commun. 2018 08 01; 9(1):3011. PMID: 30069015.
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    9. Paterson YZ, Shorthouse D, Pleijzier MW, Piterman N, Bendtsen C, Hall BA, Fisher J. A toolbox for discrete modelling of cell signalling dynamics. Integr Biol (Camb). 2018 06 18; 10(6):370-382. PMID: 29855020.
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    10. Coats BR, Schoenfelt KQ, Barbosa-Lorenzi VC, Peris E, Cui C, Hoffman A, Zhou G, Fernandez S, Zhai L, Hall BA, Haka AS, Shah AM, Reardon CA, Brady MJ, Rhodes CJ, Maxfield FR, Becker L. Metabolically Activated Adipose Tissue Macrophages Perform Detrimental and Beneficial Functions during Diet-Induced Obesity. Cell Rep. 2017 Sep 26; 20(13):3149-3161. PMID: 28954231.
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    11. Turrell FK, Kerr EM, Gao M, Thorpe H, Doherty GJ, Cridge J, Shorthouse D, Speed A, Samarajiwa S, Hall BA, Griffiths M, Martins CP. Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity. Genes Dev. 2017 07 01; 31(13):1339-1353. PMID: 28790158.
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    12. Riedel A, Shorthouse D, Haas L, Hall BA, Shields J. Tumor-induced stromal reprogramming drives lymph node transformation. Nat Immunol. 2016 09; 17(9):1118-27. PMID: 27400148.
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    13. Bagnéris C, Rogala KB, Baratchian M, Zamfir V, Kunze MB, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CW. Probing the solution structure of I?B kinase (IKK) subunit ? and its interaction with Kaposi sarcoma-associated herpes virus Flice-interacting protein and IKK subunit ß by EPR spectroscopy. J Biol Chem. 2015 Sep 18; 290(38):23024. PMID: 26386046.
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    14. Hall BA, Piterman N, Hajnal A, Fisher J. Emergent stem cell homeostasis in the C. elegans germline is revealed by hybrid modeling. Biophys J. 2015 Jul 21; 109(2):428-38. PMID: 26200879.
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    15. Bagnéris C, Rogala KB, Baratchian M, Zamfir V, Kunze MB, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CW. Probing the Solution Structure of I?B Kinase (IKK) Subunit ? and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit ß by EPR Spectroscopy. J Biol Chem. 2015 Jul 03; 290(27):16539-49. PMID: 25979343.
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    16. Chuang R, Hall BA, Benque D, Cook B, Ishtiaq S, Piterman N, Taylor A, Vardi M, Koschmieder S, Gottgens B, Fisher J. Drug target optimization in chronic myeloid leukemia using innovative computational platform. Sci Rep. 2015 Feb 03; 5:8190. PMID: 25644994.
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    17. Hall BA, Jackson E, Hajnal A, Fisher J. Logic programming to predict cell fate patterns and retrodict genotypes in organogenesis. J R Soc Interface. 2014 Sep 06; 11(98):20140245. PMID: 24966232.
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    18. Hall BA, Halim KB, Buyan A, Emmanouil B, Sansom MS. Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices. J Chem Theory Comput. 2014 May 13; 10(5):2165-75. PMID: 26580541.
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    19. Wright DW, Hall BA, Kenway OA, Jha S, Coveney PV. Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors. J Chem Theory Comput. 2014 Mar 11; 10(3):1228-1241. PMID: 24683369.
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    20. Reddy T, Manrique S, Buyan A, Hall BA, Chetwynd A, Sansom MS. Primary and secondary dimer interfaces of the fibroblast growth factor receptor 3 transmembrane domain: characterization via multiscale molecular dynamics simulations. Biochemistry. 2014 Jan 21; 53(2):323-32. PMID: 24397339.
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    21. Brickley DR, Agyeman AS, Kopp RF, Hall BA, Harbeck MC, Belova L, Volden PA, Wu W, Roe MW, Conzen SD. Serum- and glucocorticoid-induced protein kinase 1 (SGK1) is regulated by store-operated Ca2+ entry and mediates cytoprotection against necrotic cell death. J Biol Chem. 2013 Nov 08; 288(45):32708-19. PMID: 24043625.
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    22. Skor MN, Wonder EL, Kocherginsky M, Goyal A, Hall BA, Cai Y, Conzen SD. Glucocorticoid receptor antagonism as a novel therapy for triple-negative breast cancer. Clin Cancer Res. 2013 Nov 15; 19(22):6163-72. PMID: 24016618.
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    23. Bagnéris C, Decaen PG, Hall BA, Naylor CE, Clapham DE, Kay CW, Wallace BA. Role of the C-terminal domain in the structure and function of tetrameric sodium channels. Nat Commun. 2013; 4:2465. PMID: 24051986.
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    24. Crowet JM, Parton DL, Hall BA, Steinhauer S, Brasseur R, Lins L, Sansom MS. Multi-scale simulation of the simian immunodeficiency virus fusion peptide. J Phys Chem B. 2012 Nov 26; 116(46):13713-21. PMID: 23094791.
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    25. Vostrikov VV, Hall BA, Sansom MS, Koeppe RE. Accommodation of a central arginine in a transmembrane peptide by changing the placement of anchor residues. J Phys Chem B. 2012 Nov 01; 116(43):12980-90. PMID: 23030363.
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    26. Hall BA, Armitage JP, Sansom MS. Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles. PLoS Comput Biol. 2012; 8(9):e1002685. PMID: 23028283.
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    27. Doux JP, Hall BA, Killian JA. How lipid headgroups sense the membrane environment: an application of ¹4N NMR. Biophys J. 2012 Sep 19; 103(6):1245-53. PMID: 22995497.
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    28. Lindau M, Hall BA, Chetwynd A, Beckstein O, Sansom MS. Coarse-grain simulations reveal movement of the synaptobrevin C-terminus in response to piconewton forces. Biophys J. 2012 Sep 05; 103(5):959-69. PMID: 23009845.
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    29. Hall BA, Wright DW, Jha S, Coveney PV. Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity. Biochemistry. 2012 Aug 21; 51(33):6487-9. PMID: 22866962.
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    30. Hall BA, Kim TY, Skor MN, Conzen SD. Serum and glucocorticoid-regulated kinase 1 (SGK1) activation in breast cancer: requirement for mTORC1 activity associates with ER-alpha expression. Breast Cancer Res Treat. 2012 Sep; 135(2):469-79. PMID: 22842983.
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    31. Wright DW, Hall BA, Kellam P, Coveney PV. Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors. Biology (Basel). 2012 Jul 26; 1(2):222-44. PMID: 24832224.
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    32. Gregg BE, Moore PC, Demozay D, Hall BA, Li M, Husain A, Wright AJ, Atkinson MA, Rhodes CJ. Formation of a human ß-cell population within pancreatic islets is set early in life. J Clin Endocrinol Metab. 2012 Sep; 97(9):3197-206. PMID: 22745242.
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    33. Hall BA, Armitage JP, Sansom MS. Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling. PLoS Comput Biol. 2011 Oct; 7(10):e1002204. PMID: 22028633.
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    34. Kalli AC, Hall BA, Campbell ID, Sansom MS. A helix heterodimer in a lipid bilayer: prediction of the structure of an integrin transmembrane domain via multiscale simulations. Structure. 2011 Oct 12; 19(10):1477-84. PMID: 22000516.
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    35. Watson AA, Lebedev AA, Hall BA, Fenton-May AE, Vagin AA, Dejnirattisai W, Felce J, Mongkolsapaya J, Palma AS, Liu Y, Feizi T, Screaton GR, Murshudov GN, O'Callaghan CA. Structural flexibility of the macrophage dengue virus receptor CLEC5A: implications for ligand binding and signaling. J Biol Chem. 2011 Jul 08; 286(27):24208-18. PMID: 21566123.
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    36. Hall BA, Chetwynd AP, Sansom MS. Exploring peptide-membrane interactions with coarse-grained MD simulations. Biophys J. 2011 Apr 20; 100(8):1940-8. PMID: 21504730.
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    37. Vohra S, Hall BA, Holdbrook DA, Khalid S, Biggin PC. Bookshelf: a simple curation system for the storage of biomolecular simulation data. Database (Oxford). 2010; 2010:baq033. PMID: 21169341.
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    38. Chetwynd A, Wee CL, Hall BA, Sansom MS. The energetics of transmembrane helix insertion into a lipid bilayer. Biophys J. 2010 Oct 20; 99(8):2534-40. PMID: 20959094.
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    39. Vostrikov VV, Hall BA, Greathouse DV, Koeppe RE, Sansom MS. Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations. J Am Chem Soc. 2010 Apr 28; 132(16):5803-11. PMID: 20373735.
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    40. Hall BA, Sansom MS. Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System. J Chem Theory Comput. 2009 Sep 08; 5(9):2465-71. PMID: 26616626.
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    41. Hall BA, Kaye SL, Pang A, Perera R, Biggin PC. Characterization of protein conformational states by normal-mode frequencies. J Am Chem Soc. 2007 Sep 19; 129(37):11394-401. PMID: 17715919.
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    42. Haider S, Hall BA, Sansom MS. Simulations of a protein translocation pore: SecY. Biochemistry. 2006 Oct 31; 45(43):13018-24. PMID: 17059218.
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    43. Haider S, Grottesi A, Hall BA, Ashcroft FM, Sansom MS. Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating. Biophys J. 2005 May; 88(5):3310-20. PMID: 15749783.
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    44. Barrett CP, Hall BA, Noble ME. Dynamite: a simple way to gain insight into protein motions. Acta Crystallogr D Biol Crystallogr. 2004 Dec; 60(Pt 12 Pt 1):2280-7. PMID: 15572782.
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