Oxford University, Structural Bioinformatics & Computational Biochemistry Unit
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Tyler Reddy

Structural Bioinformatics and Computational Biochemistry Unit
Dept. of Biochemistry
University of Oxford
South Parks Road
Oxford
OX1 3QU
U.K.

Telephone: 01865 613304
Fax: 01865 613238

e-mail: tyler.reddy@bioch.ox.ac.uk
division line

Background
I completed my BSc Honours and PhD degrees in Biochemistry & Molecular Biology at Dalhousie University in Halifax, N.S., Canada. My undergraduate research interests spanned murine developmental biology and racemase enzymology. My graduate training was primarily focused on membrane protein NMR spectroscopy, NMR spin relaxation experiments, and coarse-grained molecular dynamics simulations of membrane proteins.

Research
My current focus is on the study of very large lipid envelope-based biomolecular systems, specifically the human influenza and dengue virions, by coarse-grained MD simulations. My work has been supported by the Canadian Institutes of Health Research and I held a post as a Fulford Junior Research Fellow (Medical) at Somerville College (October 2012-October 2014). I was co-PI on a successful PRACE grant application (2012-2013) for 22.2 million CPU hours to support the large computational demands of these projects. More recently, I was co-PI on another successful PRACE grant application (2014-2015) focused on curvature in large lipid bilayer systems (12.7 million CPU hours). We are now in the benchmarking phase of a US Department of Energy INCITE program for our most realistic virion simulations to date.

Online Videos of My Talks
  1. Veni, Vidi, Voronoi: Attacking Viruses using spherical Voronoi diagrams in Python [PyData London 2015]
  2. Computational Geometry in Python [PyCon 2016]

Programming and Open Source Tools
I have a proclivity for writing code and I'm the Leader of the Documentation Task Force / a core developer on the open source Python project MDAnalysis. My Open Source Projects:
  1. Analyze diffusion of particles in MD simulations
  2. Voronoi diagrams on the surface of a sphere (analysis of spherical virion simulations)
Here are my github and Stack Overflow profiles. My Twitter activity is primarily open source related.

Selected Press Releases
  1. Biomedical Computation Review, Stanford University (2015): Viral Physics Lessons: Simulations offer novel insights by Kristin Sainani
  2. American Insitutue of Physics (2015): "Virtual Virus" Unfolds the Flu on a CPU
  3. IFLS (2015): Outer Envelope of Flu Virus Simulated for the First Time [impact: > 11,000 social media responses]
  4. spectroscopyNOW (2015): Flu shot: NMR spectroscopy helps with model building

Proceedings Papers
  1. Gowers, R.J., Linke, M., Barnoud, J., Reddy, T., Melo, M.N., Seyler, S.L., Dotson, D.L., Domanski, J., Buchoux, S., Kenney, I.M., and Beckstein, O. (2016) MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX. SciPy.

Publications
Google Scholar Profile
h-index: 10
total citations: 278
(citation statistics: Google Scholar, November 24, 2016)
*Equal contributions
  1. Koldsø, H., Reddy, T., Fowler, P., Duncan, A., and Sansom, M.S.P. (2016) Membrane Compartmentalization Reduces the Mobility of Lipids and Proteins within a Model Plasma Membrane. The Journal of Physical Chemistry B. 120: 8873-8881. [DOI]
  2. Review Reddy, T. and Sansom, M.S.P. (2016) Computational Virology: from the Inside Out. BBA - Biomembranes 1858: 1610-1618. [DOI] [citations: 4]
  3. Reddy, T. and Sansom, M.S.P. (2016) The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope. Structure 24: 375-382. [DOI] [citations: 6]
  4. Editorial Reddy, T. (2015) Building a complete model of the outer envelope of an influenza A virion: how can this take us forward? Future Virology. Available Online [doi: 10.2217/fvl.15.44]
  5. Reddy, T., Shorthouse, D., Parton, D., Jefferys, E., Fowler, P.W., Chavent, M., Baaden, M., and Sansom, M.S.P. (2015) Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure 23: 584-597. [DOI] [citations: 21]
               Associated Comment Article: Risselada, H.J. (2015) Simulations Move Toward a Cure for Viral Diseases. Structure 23: 439-440. [DOI]
  6. Chavent, M.*, Reddy, T.*, Goose, J., Dahl, C.E., Stone, J.E., Jobard, B., and Sansom, M.S.P. (2014) Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems. Faraday Discussions 169: 1-18. [RSC] [citations: 12]
  7. Reddy, T., Manrique, S., Buyan, A., Hall, B., Chetwynd, A., and Sansom, M.S.P. (2014) Primary and Secondary Dimer Interfaces of the FGFR3 Transmembrane Domain: Characterization via Multiscale Molecular Dynamics Simulations. Biochemistry 53: 323-332. [Pubmed] [citations: 10]
  8. Langelaan, D.N., Reddy, T., Banks, A.W., Dellaire, G., Dupre, D.J., and Rainey, J.K. (2013) Structural features of the apelin receptor N-terminal tail and first transmembrane segment implicated in ligand binding and receptor trafficking. Biochim Biophys Acta: Biomembranes. 1828: 1471-1483. [Pubmed] [citations: 13]
  9. Reddy, T. and Rainey, J.K. (2012) Multifaceted Substrate Capture Scheme of a Rhomboid Protease. The Journal of Physical Chemistry B. 116: 8942-8954. [Pubmed] [citations: 16]
  10. Reddy, T., Li, X., Fliegel, L., Sykes, B.D., and Rainey, J.K. (2010) Correlating structure, dynamics, and function in transmembrane segment VII of the Na+/H+ exchanger isoform 1. Biochim Biophys Acta: Biomembranes. 1798: 94-104. [Pubmed] [citations: 9]
  11. Review Reddy, T. and Rainey, J.K. (2010) Interpretation of biomolecular NMR spin relaxation parameters. Biochemistry and Cell Biology. 88: 131-142. [Pubmed] [citations: 18]
  12. Langelaan, D.N., Bebbington, E.M., Reddy, T., and Rainey, J.K. (2009) Structural insight into G-protein coupled receptor binding by apelin. Biochemistry. 48: 537-548. [Pubmed] [citations: 48]
  13. Reddy, T.*, Ding, J.*, Li, X., Sykes, B.D., Rainey, J.K., and Fliegel, L. (2008) Structural and Functional Characterization of Transmembrane Segment IX of the NHE1 Isoform of the Na+/H+ Exchanger. Journal of Biological Chemistry. 283: 22018-22030. [Pubmed] [PDB entry (2K3C)] [BMRB entry (15747)] [citations: 32]
  14. Review Baguma-Nibasheka, M., Reddy, T., Abbas-Butt, A., and Kablar, B. (2006) Fetal ocular movements and retinal cell differentiation: analysis employing DNA microarrays. Histology and histopathology. 21: 1331-1337. [Pubmed] [citations: 7]
  15. Reddy, T.*, Rot-Nikcevic, I.*, Downing, K.J., Belliveau, A.C., Hallgrimsson, B., Hall, B.K., and Kablar, B. (2006) Myf5-/-: MyoD-/- amyogenic fetuses reveal the importance of early contraction and static loading by striated muscle in mouse skeletogenesis. Development genes and evolution. 216: 1-9. [Pubmed] [citations: 70]
  16. Reddy, T. and Kablar, B. (2004) Evidence for the involvement of neurotrophins in muscle transdifferentiation and acetylcholine receptor transformation in the esophagus of Myf5-/-:MyoD-/- and NT-3-/- embryos. Developmental Dynamics. 231: 683-692. [Pubmed] [citations: 11]
Last updated 24 November 2016