I am a Scientist in the Biological Computation research group (part of Computational Science Laboratory) at Microsoft Research, Cambridge. I also hold an Honorary Senior Research Associate position at the Department of Chemistry, UCL.
My overall research interests are in how biological systems process information, perform computations, and make life-preserving decisions. The immune system is a great example of biological information processing, that operates at multiple temporal and spatial scales; without it, we'd struggle to survive again the many opportunistic pathogens that we encounter on a daily basis.
In addition to taking inspiration from understanding complex natural systems, I'm interested in engineering complex systems, using the building blocks of nature. Our project on Synthetic Biology seeks to understand how we can utilise the machinery of cells to perform new functions. Endowing cells with additional functions and refining their mechanisms enables us to enhance production of biofuels and medicine.
In all of our research areas, we are developing software tools to enable other researchers to understand or create biological function.
I started life as a mathematician, studying Mathematics at the University of Oxford, UK (2001-2005). I then went to the University of Cambridge to do a Ph.D, the project being a collaboration between Alex Webb's group at the Department of Plant Sciences and Jorge Goncalves in the Control Group at the Department of Engineering. You can download my thesis here.
Following my PhD, I briefly held a research associate position in the Control Group, working with Glenn Vinnicombe on applications of stochastic control theory to gene networks.
I came to Microsoft Research as a postdoc in 2009, during which I worked with Andrew Phillips on modelling immune systems and synthetic gene networks. I became a permanent member of the Biological Computation group in 2012.
- DNA computing: Molecules reach consensus - Nature Nanotechnology, 4 October 2013.
- Neil wins 2011 Tansley Medal for Excellence in Plant Science - New Phytologist, December 2011
- Researchers Find Link Between Plant Metabolism and Biological Clock - Crop Biotech Update, 25th March 2011
- Coming Soon to a Lab Near You: Drag-and-Drop Virtual Worlds - Science, 11th February 2011
- Computational Modelling of Immune System Processes
Immunodominance lies at the heart of the immune system's ability to distinguish self from non-self. Understanding and possibly controlling the mechanisms that govern immunodominance will have profound consequences for the fight against several classes of diseases, including viral infections and cancer. In the first phase of this project, we focus on computational modelling of MHC class I peptide editing.
- Genetic Engineering of Living Cells
Synthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. An ultimate dream is to design these systems at a high level of abstraction using engineering-based tools and programming languages, press a button, and have the design translated to DNA sequences that can be synthesised and put to work in living cells.
- Modelling of Circadian Oscillator Networks
Circadian oscillators provide rhythmic temporal cues for a range of biological processes in animals and plants, enabling anticipation of the day/night cycle and enhancing fitness. Near 24 h oscillations are maintained at the gene transcription level, which integrate environmental cues such as light and temperature and internal cues such as metabolism and signalling. Characterising these interactions is vital for understanding how physiology is optimised with respect to the time of day.
- Open Solving Library for ODEs
OSLO is a .NET and Silverlight class library for the numerical solution of ordinary differential equations (ODEs). The library enables numerical integration to be performed in C#, F# and Silverlight applications. OSLO implements Runge-Kutta and back differentiation formulae (BDF) for non-stiff and stiff initial value problems.
- Programming DNA circuits
Molecular devices made of nucleic acids show great potential for applications ranging from bio-sensing to intelligent nanomedicine. They allow computation to be performed at the molecular scale, while also interfacing directly with the molecular components of living systems. They form structures that are stable inside cells, and their interactions can be precisely controlled by modifying their nucleotide sequences.
- Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, and John Reif, Probabilistic analysis of localized DNA hybridization circuits, in ACS Synthetic Biology, In press, June 2015.
- Camille Guilbaud, Neil Dalchau, Drew Purves, and Lindsay Turnbull, Is 'peak N' key to understanding the timing of flowering in annual plants?, in New Phytologist, vol. 205, no. 2, pp. 918-927, New Phytologist Trust, January 2015.
- Attila Csikász-Nagy and Neil Dalchau, What makes a biological clock efficient?, no. MSR-TR-2014-134, 8 September 2014.
- Neil Dalchau, Georg Seelig, and Andrew Phillips, Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks, in International Conference on DNA Computing and Molecular Programming, vol. 8727, pp. 84-99, Springer, September 2014.
- James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg McInerny, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, and Charlotte Deane, Ten simple rules for effective computational research, in PLoS Computational Biology, vol. 10, no. 3, pp. e1003506, PLoS Computational Biology (Public Library of Science Computational Biology), , March 2014.
- Boyan Yordanov, Neil Dalchau, Paul Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, and Andrew Phillips, A Computational Method for Automated Characterization of Genetic Components, in ACS Synthetic Biology, vol. 3, no. 8, pp. 578-588, American Chemical Society, February 2014.
- Alberto Carignano, Ye Yuan, Neil Dalchau, Alex AR Webb, and Jorge M Goncalves, Understanding and predicting biological networks using linear system identification, in A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, Springer, 1 January 2014.
- Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, and Georg Seelig, Programmable chemical controllers made from DNA, in Nature Nanotechnology, vol. 8, no. 10, pp. 755-762, Nature Publishing Group, 29 September 2013.
- Antony N Dodd, Neil Dalchau, Michael J Gardner, Seong Jin Baek, and Alex AR Webb, The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis, in New Phytologist, vol. 201, no. 1, pp. 168-179, 24 September 2013.
- Boyan Yordanov, Neil Dalchau, Paul Grant, Jim Haseloff, Stephen Emmott, and Andrew Phillips, Automated Ratiometric Characterization using GEC, in International Workshop on Biodesign Automation, July 2013.
- Neil Dalchau, Matthew Smith, Samuel Martin, James R Brown, Stephen Emmott, and Andrew Phillips, Towards the rational design of synthetic cells with prescribed population dynamics, in Journal of the Royal Society Interface, vol. 9, pp. 2883-2898, The Royal Society, May 2012.
- Neil Dalchau, Understanding biological timing using mechanistic and black-box models, in New Phytologist, vol. 193, no. 4, pp. 852-858, March 2012.
- Neil Dalchau, Andrew Phillips, Leonard D Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott, and Joern M Werner, A peptide filtering relation quantifies MHC class I peptide optimization, in PLoS Computational Biology, vol. 7, no. 10, pp. e1002144, PLoS, 13 October 2011.
- Neil Dalchau, Seong Jin Baek, Helen M Briggs, Fiona C Robertson, Antony N Dodd, Michael J Gardner, Matthew A Stancombe, Michael J Haydon, Guy-Bart Stan, Jorge M Goncalves, and Alex AR Webb, The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose, in PNAS, vol. 108, no. 12, pp. 5104-5109, Proceedings of the National Academy of Sciences, 22 March 2011.
- Neil Dalchau and Alex AR Webb, Ticking over - Circadian systems across the kingdoms of life, in Biochemist, vol. 33, no. 1, 1 February 2011.
- Andy van Hateren, Ed James, Alistair Bailey, Andrew Phillips, Neil Dalchau, and Tim Elliott, The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding, in Tissue Antigens, vol. 76, no. 4, pp. 259 - 275, Wiley, October 2010.
- Neil Dalchau, Katharine E Hubbard, Fiona C Robertson, Carlos T Hotta, Helen M Briggs, Guy-Bart Stan, Jorge M Goncalves, and Alex A R Webb, Correct biological timing in Arabidopsis requires multiple light signaling pathways, in PNAS, vol. 107, no. 29, pp. 13171-13176, Proceedings of the National Academy of Sciences, 1 July 2010.
- Mathew G Lewsey, Alex M Murphy, Daniel MacLean, Neil Dalchau, Jack H Westwood, Keith Macaulay, Mark H Bennett, Michael Moulin, David E Hanke, Glen Powell, Alison G Smith, and John P Carr, Disruption of two defensive signaling pathways by a viral RNA silencing suppressor, in Molecular Plant-Microbe Interations, vol. 23, no. 7, pp. 835-845, 2010.
- Katharine E Hubbard, Fiona C Robertson, Neil Dalchau, and Alex A R Webb, Systems analyses of circadian networks., in Molecular Biosystems, vol. 5, pp. 1502-1511, 3 August 2009.
- Neil Dalchau, Mathematical modelling of circadian signalling in Arabidopsis, December 2008.
- Antony N Dodd, Michael J Gardner, Carlos T Hotta, Katharine E Hubbard, Neil Dalchau, John Love, Jean-Maurice Assie, Fiona C Robertson, Mia Kyed Jakobsen, Jorge Gonçalves, Dale Sanders, and Alex A R Webb, The Arabidopsis circadian clock incorporates a cADPR-based feedback loop., in Science, vol. 318, no. 5857, pp. 1789–1792, American Association for the Advancement of Science, 14 December 2007.
- Carlos T Hotta, Michael J Gardner, Katharine E Hubbard, Seong Jin Baek, Neil Dalchau, Dontamala Suhita, Antony N Dodd, and Alex A R Webb, Modulation of environmental responses of plants by circadian clocks., in Plant Cell Environ, vol. 30, no. 3, pp. 333–349, March 2007.
- Katharine E Hubbard, Carlos T Hotta, Michael J Gardner, Seong Jin Baek, Neil Dalchau, Suhita Dontamala, Antony N. Dodd, and Alex AR Webb, Circadian Rhythms in Stomata: Physiological and Molecular Aspects, pp. 157–177, Springer-Verlag, 2007.
- Joseph Eugene, Clive Lewis, Chris Riley, Neil Dalchau, and Alex Michaelides, FEA Modelling of a Novel Tubular Linear Generator, in Linear Drives for Industrial Applications, 2007.