Formal models in systems biology
My research focuses on applying formal methods to prove properties of biological networks, and to generate predictions which can be tested experimentally. Specifically, working under Dr Jasmin Fisher, I'm building models of cell fate specification in C. elegans vulval development and developing tools to make the underlying formal methods more accessible to the wider biological community.
Benjamin A. Hall, Ethan Jackson, Alex Hajnal, Jasmin Fisher. Logic programming to predict cell fate patterns and retrodict genotypes in organogenesis Accepted by Journal of the Royal Society: Interface
Benjamin A. Hall, Khairul Abd Halim, Amanda Buyan, Beatrice Emmanouil, Mark S. P. Sansom. A Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices in JCTC 10 p 2165-2175
David W. Wright, Benjamin A Hall, Owain A. Kenway, Shantenu Jha, Peter V. Coveney. Computing clinically relevant binding free energies of HIV-1 protease inhibitors in JCTC 10 p 1228-1241
Tyler Reddy, Santiago Manrique, Amanda Buyan, Benjamin A. Hall, Alan Chetwynd, Mark S P Sansom (2014) Primary and secondary dimer interfaces of the fibroblast growth factor receptor 3 transmembrane domain: Characterization via multiscale molecular dynamics simulations. In Biochemistry 53, p 323-332
Claire Bagneris, Paul G DeCaen, Benjamin A Hall, Claire E Naylor, David E Clapham, Christopher W M Kay, Bonnie Wallace (2013) Role of the C-terminal domain in the structure and function of tetrameric sodium channels. In Nature Communications 4, p 2465
Vitaly V Vostrikov, Benjamin A Hall, Mark S P Sansom, Roger E Koeppe (2012) Accommodation of a Central Arginine in a Transmembrane Peptide by Changing the Placement of Anchor Residues.. In The journal of physical chemistry. B.
Manfred Lindau, Benjamin A. Hall, Alan Chetwynd, Oliver Beckstein, Mark S.P. Sansom (2012) Coarse-Grain Simulations Reveal Movement of the Synaptobrevin C-Terminus in Response to Piconewton Forces, 959-969. In Biophysical Journal 103 (5).
David W. Wright, Benjamin A. Hall, Paul Kellam, Peter V. Coveney (2012) Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors, 222-244. In Biology 1 (2).
Jacques P.F. Doux, Benjamin A. Hall, J. Antoinette Killian (2012) How Lipid Headgroups Sense the Membrane Environment: An Application of 14N NMR, 1245-1253. In Biophysical Journal 103 (6).
Benjamin A. Hall, Judith P. Armitage, Mark S. P. Sansom (2012) Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles, e1002685. In PLoS Computational Biology 8 (9).
Jean-Marc Crowet, Daniel L Parton, Benjamin A Hall, Sven Steinhauer, Robert Brasseur, Laurence Lins, Mark S P Sansom (2012) Multi-Scale Simulation of the Simian Immunodeficiency Virus Fusion Peptide.. In The journal of physical chemistry. B.
Benjamin A Hall, David W Wright, Shantenu Jha, Peter Vivian Coveney (2012) Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity.. In Biochemistry.
Antreas C Kalli; Benjamin A Hall; Iain D Campbell; Mark SP Sansom (2011) A Helix Heterodimer in a Lipid Bilayer: Prediction of the Structure of an Integrin Transmembrane Domain via Multiscale Simulations, 1477-1484. In Structure 19 (10).
Benjamin A Hall, Alan P Chetwynd, Mark S P Sansom (2011) Exploring Peptide-Membrane Interactions with Coarse-Grained MD Simulations., 1940-1948. In Biophysical journal 100 (8).
Aleksandra A Watson, Andrey A Lebedev, Benjamin A Hall, Angharad E Fenton-May, Alexei A Vagin, Wanwisa Dejnirattisai, James Felce, Juthathip Mongkolsapaya, Angelina S Palma, Yan Liu, Ten Feizi, Gavin R Screaton, Garib N Murshudov, Christopher A O'Callaghan (2011) Structural flexibility of the macrophage dengue virus receptor CLEC5A: Implications for ligand binding and signaling.. In The Journal of biological chemistry.
Benjamin A. Hall, Judith P. Armitage, Mark S. P. Sansom (2011) Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling, e1002204. In PLoS Computational Biology 7 (10).
Shabana Vohra, Benjamin A Hall, Daniel A Holdbrook, Syma Khalid, Philip C Biggin (2010) Bookshelf: a simple curation system for the storage of biomolecular simulation data., baq033. In Database : the journal of biological databases and curation.
Vitaly V Vostrikov, Benjamin A Hall, Denise V Greathouse, Roger E Koeppe, Mark S P Sansom (2010) Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations, 5803-5811. In Journal of the American Chemical Society 132 (16).
Alan Chetwynd, Chze Ling Wee, Benjamin A. Hall, Mark S.P. Sansom (2010) The Energetics of Transmembrane Helix Insertion into a Lipid Bilayer, 2534-2540. In Biophysical Journal 99 (8).
Benjamin A Hall, Mark S P Sansom (2009) Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System, 1-7. In JCTC.
Benjamin A Hall, Samantha L Kaye, Andy Pang, Rafael Perera, Philip C Biggin (2007) Characterization of protein conformational States by normal-mode frequencies., 11394-11401. In J Am Chem Soc 129 (37).
Shozeb Haider, Benjamin A Hall, Mark S P Sansom (2006) Simulations of a protein translocation pore: SecY, 13018-13024. In Biochemistry 45 (43).
Alessandro Grottesi, Carmen Domene, Benjamin A Hall, Mark S P Sansom (2005) Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations, 14586-14594. In Biochemistry 44 (44).
Shozeb Haider, Alessandro Grottesi, Benjamin A Hall, Frances M Ashcroft, Mark S P Sansom (2005) 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, 3310-3320. In Biophysical Journal 88 (5).
C Paul Barrett, Benjamin A Hall, Martin E M Noble (2004) Dynamite: a simple way to gain insight into protein motions, 2280-2287. In Acta Crystallogr D Biol Crystallogr 60 (Pt 12 Pt 1).
Kathryn A Scott, Elizabeth E Jefferys, Benjamin A Hall, Mark AJ Roberts, Judith P Armitage (2012) Bacterial Chemotaxis, 223-260. In Bacterial Regulatory Networks.
- Tom Crick, Benjamin A. Hall, and Samin Ishtiaq, “Can I Implement Your Algorithm?”: A Model for Reproducible Research Software, in 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2), WSSSPE, November 2014
- Byron Cook, Jasmin Fisher, Benjamin Hall, Samin Ishtiaq, Garvit Juniwal, and Nir Piterman, Finding instability in biological models, in Computer Aided Verification (CAV), 2014
Present and former interns
Ismail Kuru (PhD student, Koc University)
Caroline Dahl (DPhil student, University of Oxford)
Garvit Juniwal (PhD student, UC Berkeley)
Modelling C. elegans germ line development using F# and the BioModelAnalyzer
Bio Model Analyzer
High Throughput, multiscale modelling approaches for understanding bacterial signalling