Publications

Tapasin-mediated editing of the MHC I immunopeptidome is epitope specific and dependent on peptide off-rate, abundance, and level of tapasin expression

Boulanger DS, Douglas LR, Duriez PJ, Kang Y, Dalchau N, James E, Elliott T
October 2022 Frontiers in Immunology
DOI

Programming Molecular Systems To Emulate a Learning Spiking Neuron

Fil J, Dalchau N, Chu D
May 2022 ACS Synthetic Biology
DOI
Programming Molecular Systems To Emulate a Learning Spiking Neuron

Decentralizing Cell-Free RNA Sensing With the Use of Low-Cost Cell Extracts

Arce A, Guzman-Chavez F, Gandini C, Puig J, Matute T, Haseloff J, Dalchau N, Molloy J, Pardee K, Federici F
August 2021 Frontiers in Bioengineering and Biotechnology
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A Deep Learning Model for Predicting NGS Sequencing Depth from DNA Sequence

Zhang J, Yordanov B, Gaunt A, Wang M, Dai P, Chen Y-J, Zhang K, Fang J, Dalchau N, Li J, Phillips A, Zhang D
July 2021 Nature Communications
DOI

Parameter Inference with Bifurcation Diagrams

Szép G, Dalchau N, Csikász-Nagy A
June 2021 Neural Information Processing Systems (NeurIPS)
Preprint Github
Parameter Inference with Bifurcation Diagrams

Conditional sanctioning in a legume-rhizobium mutualism

Westhoek A, Clark LJ, Culbert M, Dalchau N, Griffiths M, Karunakaran R, Ledermann R, Tkacz A, Webb I, James EK, Poole PS, Turnbull LA
May 2021 Proc Natl Acad Sci U S A
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A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

Ho T, Shao A, Lu Z, Savilahti H, Menolascina F, Wang L, Dalchau N, Wang B
April 2021 Nature Communications
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Turing patterning in stratified domains

Krause AL, Klika V, Halatek J, Grant PK, Woolley TE, Dalchau N, Gaffney EA
October 2020 Bulletin of Mathematical Biology
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Interpretation of morphogen gradients by a synthetic bistable circuit

Grant PK, Szép G, Patange O, Halatek J, Coppard V, Csikász-Nagy A, Haseloff J, Locke JCW, Dalchau N, Phillips A
August 2020 Nature Communications
DOI Github
Interpretation of morphogen gradients by a synthetic bistable circuit

Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

Nadezhdin E, Murphy N, Dalchau N, Phillips A, Locke JCW
February 2020 Nature Communications
DOI Github

Fast enumeration of non-isomorphic chemical reaction networks

Spaccasassi C, Yordanov B, Phillips A, Dalchau N
September 2019 Computational Methods in Systems Biology (CMSB)
DOI Github

Scalable dynamic characterization of synthetic gene circuits

Dalchau N, Grant PK, Vaidyanathan P, Spaccasassi C, Gravill C, Phillips A
August 2019 bioRxiv
Preprint DOI

Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems

Roeder G, Grant PK, Phillips A, Dalchau N, Meeds E
June 2019 International Conference on Machine Learning (ICML)
Preprint Github
Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems

DNA-based communication in populations of synthetic protocells

Joesaar A, Yang S, Bögels B, van der Linden A, Pieters P, Pavan Kumar BVVS, Dalchau N, Phillips A, Mann S, de Greef TFA
April 2019 Nature Nanotechnology
DOI

Modelling ordinary differential equations using a variational auto encoder

Meeds E, Roeder G, Dalchau N
January 2019 US Patent
Justia

Dynamic Characterization of Synthetic Genetic Circuits in Living Cells

Dalchau N, Phillips A, Grant PK
January 2019 US Patent
Justia

A theory for how the antigen presentation profile influences the timing of T-cell detection

Carignano A, Dalchau N
November 2018 bioRxiv
Preprint

Scaling up genetic circuit design for cellular computing: advances and prospects

Xiang Y, Dalchau N, Wang B
October 2018 Natural Computing
DOI

Synthesizing and tuning stochastic chemical reaction networks with specified behaviours

Murphy N, Petersen R, Phillips A, Yordanov B, Dalchau N
August 2018 Journal of The Royal Society Interface
DOI Github

A mechanistic model for predicting cell surface presentation of competing peptides by MHC class I molecules

Boulanger DS, Eccleston RC, Phillips A, Coveney PV, Elliott T, Dalchau N
July 2018 Frontiers in Immunology
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Computing with biological switches and clocks

Dalchau N, Szép G, Hernansaiz-Ballesteros R, Barnes CP, Cardelli L, Phillips A, Csikász-Nagy A
June 2018 Natural Computing
DOI

Beyond activator-inhibitor networks: the generalised Turing mechanism

Smith S, Dalchau N
March 2018 arXiv
Preprint

Model reduction enables Turing instability analysis of large reaction–diffusion models

Smith S, Dalchau N
March 2018 Journal of The Royal Society Interface
DOI Github

Predicting DNA hybridization kinetics from sequence

Zhang JX, Fang JZ, Duan W, Wu LR, Zhang AW, Dalchau N, Yordanov B, Petersen R, Phillips A, Zhang DY
November 2017 Nature Chemistry
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Host genotype and time dependent antigen presentation of viral peptides: predictions from theory

Eccleston RC, Coveney PV, Dalchau N
October 2017 Scientific Reports
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A spatially localized architecture for fast and modular DNA computing

Chatterjee G, Dalchau N, Muscat RA, Phillips A, Seelig G
July 2017 Nature Nanotechnology
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The role of multiscale protein dynamics in antigen presentation and T lymphocyte recognition

Eccleston RC, Wan S, Dalchau N, Coveney PV
July 2017 Frontiers in Immunology
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Efficient switches in biology and computer science

Cardelli L, Hernansaiz-Ballesteros RD, Dalchau N, Csikász-Nagy A
January 2017 PLoS Computational Biology
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Noise reduction in complex biological switches

Cardelli L, Csikász-Nagy A, Dalchau N, Tribastone M, Tschaikowski M
February 2016 Scientific Reports
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Orthogonal intercellular signaling for programmed spatial behavior

Grant PK, Dalchau N, Brown JR, Federici F, Rudge TJ, Yordanov B, Patange O, Phillips A, Haseloff J
January 2016 Molecular Systems Biology
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Selector function of MHC I molecules is determined by protein plasticity

Bailey A, Dalchau N, Carter R, Emmott S, Phillips A, Werner JM, Elliott T
October 2015 Scientific Reports
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Characterization of intrinsic properties of promoters

Rudge TJ, Brown JR, Federici F, Dalchau N, Phillips A, Ajioka JW, Haseloff J
October 2015 ACS Synthetic Biology
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Synthesizing and tuning chemical reaction networks with specified behaviours

Dalchau N, Murphy N, Petersen R, Yordanov B
July 2015 International Workshop on DNA-Based Computers
DOI

Probabilistic analysis of localized DNA hybridization circuits

Dalchau N, Chandran H, Gopalkrishnan N, Phillips A, Reif J
July 2015 ACS Synthetic Biology
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Is 'peak N' key to understanding the timing of flowering in annual plants?

Guilbaud CS, Dalchau N, Purves DW, Turnbull LA
October 2014 New Phytologist
DOI

What makes a biological clock efficient?

Csikász-Nagy A, Dalchau N
September 2014 Microsoft Research Cambridge
PDF

Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks

Dalchau N, Seelig G, Phillips A
September 2014 International Workshop on DNA-Based Computers
DOI

Understanding and predicting biological networks using linear system identification

Carignano A, Yuan Y, Dalchau N, Webb AAR, Gonçalves JM
July 2014 A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations
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Ten simple rules for effective computational research

Osborne JM, Bernabeu MO, Bruna M, Calderhead B, Cooper J, Dalchau N, Dunn SJ, Fletcher A, Groen D, Knapp B, Mirams G, Pitt-Francis J, Sengupta B, Wright D, Yates C, Gavaghan D, Emmott S, Deane C
March 2014 PLoS Computational Biology
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A computational method for automated characterization of genetic components

Yordanov B, Dalchau N, Grant PK, Pedersen M, Emmott S, Haseloff J, Phillips A
February 2014 ACS Synthetic Biology
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Programmable chemical controllers made from DNA

Chen YJ, Dalchau N, Srinivas N, Phillips A, Cardelli L, Soloveichik D, Seelig G
September 2013 Nature Nanotechnology
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The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis

Dodd AN, Dalchau N, Gardner MJ, Baek SJ, Webb AAR
September 2013 New Phytologist
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Towards the rational design of synthetic cells with prescribed population dynamics

Dalchau N, Smith MJ, Martin S, Brown JR, Emmott S, Phillips A
June 2012 Journal of the Royal Society Interface
DOI

Understanding biological timing using mechanistic and black-box models

Dalchau N
December 2011 New Phytologist
DOI

A peptide filtering relation quantifies MHC class I peptide optimization

Dalchau N, Phillips A, Goldstein LD, Howarth M, Cardelli L, Emmott S, Elliott T, Werner JM
October 2011 PLoS Computational Biology
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The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose

Dalchau N, Baek SJ, Briggs HM, Robertson FC, Dodd AN, Gardner MJ, Stancombe MA, Haydon MJ, Stan GB, Goncalves JM, Webb AAR
March 2011 Proceedings of the National Academy of Sciences
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Ticking over. Circadian systems across the kingdoms of life

Dalchau N, Webb AAR
February 2011 Biochemist
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The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding

Van Hateren A, James E, Bailey A, Phillips A, Dalchau N, Elliott T
September 2010 Tissue Antigens
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Correct biological timing in Arabidopsis requires multiple light-signaling pathways

Dalchau N, Hubbard KE, Robertson FC, Hotta CT, Briggs HM, Stan GB, Goncalves JM, Webb AAR
July 2010 Proceedings of the National Academy of Sciences
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Disruption of two defensive signaling pathways by a viral RNA silencing suppressor

Lewsey MG, Murphy AM, MacLean D, Dalchau N, Westwood JH, Macaulay K, Bennett MH, Moulin M, Hanke DE, Powell G, Smith AG
June 2010 Molecular plant-microbe interactions
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Systems analyses of circadian networks

Hubbard KE, Robertson FC, Dalchau N, Webb AA
August 2009 Molecular BioSystems
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Mathematical modelling of circadian signalling in Arabidopsis

Dalchau N
December 2008 Department of Plant Sciences
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The Arabidopsis circadian clock incorporates a cADPR-based feedback loop

Dodd AN, Gardner MJ, Hotta CT, Hubbard KE, Dalchau N, Love J, Assie J-M, Robertson FC, Jakobsen MK, Goncalves JM, Sanders D, Webb AAR
December 2007 Science
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Circadian Rhythms in Stomata: Physiological and Molecular Aspects

Hubbard KE, Hotta CT, Gardner MJ, Baek SJ, Dalchau N, Dontamala S, Webb AA
June 2007 Rhythms in Plants
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Modulation of environmental responses of plants by circadian clocks

Hotta CT, Gardner MJ, Hubbard KE, Baek SJ, Dalchau N, Suhita D, Dodd AN, Webb AAR
March 2007 Plant, Cell & Environment
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