Summary
Papers
You'll find an informal, popular, discussion of our published work on our blog. Our published papers generally have a corresponding blog article.
The link for Publications above and here is autogenerated, and so more up to date, but not linked to blog/extras.
When we can we post preprints to either arXiv or bioRxiv
2023:
Cell lineage-specific mitochondrial resilience during mammalian organogenesis
Cell
Stephen P. Burr, Florian Klimm, Angelos Glynos, Malwina Prater, Pamella Sendon, Pavel Nash, Christopher A. Powell, Marie-Lune Simard, Nina A. Bonekamp, Julia Charl Hector Diaz, Lyuba V. Bozhilova, Yu Nie, Haixin Zhang, Michele Frison, Maria Falkenberg, Nick Jones, Michal Minczuk, James B. Stewart, Patrick F. Chinnery
2022:
Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.
PNAS, BLOG article
Insalata F, Hoitzing H, Aryaman J,
2021:
Science Advances,
Zhang H, Esposito M, Pezet MG,
Influencing dynamics on social networks without knowledge of network microstructure,
Journal of the Royal Society Interface,
Garrod M, Jones N
Nature Metabolism,
Lima A, Lubatti G, Burgstaller J,
Biology,
Marshall A, Jones N
Inference and influence of network structure using snapshot social behavior without network data,
Science Advances, BLOG article
Godoy-Lorite A, Jones N
2020:
A mechanistic explanation of the transition to simple multicellularity in fungi.,
Nature Communications, BLOG article
Heaton LLM, Jones NS, Fricker MD
Community detection in networks without observing edges,
Science Advances, BLOG articles
Hoffmann T, Peel L, Lambiotte R,
Visualizing, quantifying and manipulating mitochondrial DNA in vivo.,
Journal of Biological Chemistry
Prole DL, Chinnery PF, Jones NS
Inference of a universal social scale and segregation measures using social connectivity kernels,
Journal of the Royal Society Interface, BLOG article
Hoffmann T, Jones NS
Methods in Ecology and Evolution
Science Advances
Lechuga-Vieco AV, Latorre-Pellicer A, Johnston IG,
2019:
The homeostatic dynamics of feeding behaviour identify novel mechanisms of anorectic agents,
PLoS Biology, BLOG article
McGrath T, Spreckley E, Rodriguez A,
Data Mining and Knowledge Discovery, BLOG article
Lubba CH, Sethi SS, Knaute P,
Regulation of mother-to-offspring transmission of mtDNA heteroplasmy
Frontiers in Genetics BLOG article
Aryaman J, Johnston I, Jones N
Mitochondrial network state scales mtDNA genetic dynamics
Genetics BLOG article
Aryaman J, Bowles C, Jones* NS,
Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations
PLoS Computational Biology BLOG article
Hoitzing H, Gammage PA, Haute LV,
2018:
Nature Communications BLOG article
Burgstaller* JP, Kolbe T, Havlicek V,
Nature Communications BLOG article
Royal Society Interface
Tom McGrath, Kevin Murphy, Nick S. Jones
2017:
Looplessness in networks is linked to trophic coherence
PNAS preprint BLOG article
Samuel Johnson, Nick S. Jones
Biochemical Journal BLOG article
Juvid Aryaman, Iain Johnston, Nick S. Jones
Cell Systems
Ben Fulcher, Nick S. Jones
What we learn from the learning rate
Journal of Statistical Mechanics BLOG article
Rory A Brittain, Nick S Jones and Tom E Ouldridge
A biochemical machine for the interconversion of mutual information and work,
Physical Review Letters BLOG article
Tom McGrath, Nick S Jones, Peter Rein ten Wolde, Tom Ouldridge
Mitochondrial heterogeneity, metabolic scaling and cell death
BioEssays BLOG article
Juvid Aryaman, Hanne Hoitzing, Joerg Burgstaller, Iain J
Designing the optimal bit: balancing energetic cost, speed and reliability
Proceedings of the Royal Society A
Abhishek Deshpande, Manoj Gopalkrishnan, Tom Ouldridge, Nick S Jones
DNA23
William Poole, Andrés Ortiz-Muñoz, Abhishek Behera, Nick S. Jones, Thomas E. Ouldridge, Erik Winfree, Manoj Gopalkrishnan
2016:
Towards Precision Healthcare: Context and Mathematical Challenges
Frontiers in Physiology
Caroline Colijn, Nick S. Jones, Iain G. Johnston, Sophia Yaliraki, Mauicio Barahona
Evolution of Cell-to-Cell Variability in Stochastic, Controlled, Heteroplasmic mtDNA Populations,
American Journal of Human Genetics BLOG article
Iain G. Johnston, Nick S. Jones
The State of Vaccine Confidence 2016: Global Insights Through a 67-Country Survey,
Ebiomedicine BLOG article, Commentary, Science article
Heidi Larson, Alex de Figueiredo, Xiahong Z, Will Schulz, Pierre Verger, Iain G. Johnston, Alex Cook, Nick S. Jones
Lancet Global Health BLOG article, Commentary
Alex de Figueiredo, Iain G. Johnston, David M.D. Smith, Sumeet
Energetic constraints on fungal growth
American Naturalist BLOG artcile
Luke L.M. Heaton, Nick S Jones, Mark Fricker
2015:
eLife BLOG article
Iain G Johnston, Joerg P Burgstaller, Vitezslav Havlicek, Thomas Kolbe, Thomas Rulicke, Gottfried Brem, Jo Poulton, Nick S Jones
Proceedings of the Royal Society A BLOG article
Iain G. Johnston, Nick S. Jones
What is the function of mitochondrial networks? (supplement)
BioEssays BLOG article
Hanne Hoitzing, Iain G. Johnston, Nick S. Jones
2014:
The mitoflash probe cpYFP does not respond to superoxide - Brief Communication Arising
Nature BLOG article
Markus Schwarzlander, S.Wagner, Y.Ermakova, V.V.Belousov, R.Radi, J.S.Beckman, G.R.Buettner, N.Demaurex, M.R.Duchen, H.J.Forman, M.D.Fricker, D.Gems, A.P. Halestrap, B.Halliwell, U.Jakob, Iain G. Johnston, Nick S. Jones, D.C. Logan, B.Morgan, F.L.Muller, D.G.Nicholls, S.James Remington, P.T.Schumacker, C.C.Winterbourn, L.J.Sweetlove, A.J.Meyer, T.P.Dick and Michael P. Murphy
Explicit tracking of uncertainty increases the power of quantitative rule-of-thumb reasoning in cell biology (CaladisWebsite, Nature Toolbox examples)
Biophysical Journal BLOG article
Iain G. Johnston, Ben Rickett, Nick S. Jones
FRIENDLY regulates mitochondrial distribution, fusion, and quality control in Arabidopsis
Plant Physiology BLOG article
Amr El Zawily, Markus Schwarzlsnder, Iris Finkemeier, Iain G Johnston, Abdelilah Benamar,Yongguo Cao, Clemence Gissot, Andreas Meyer, Ken Wilson, Raju Datla, David Macherel, Nick S. Jones and David Logan
Proceedings of the Royal Society A
Binh-Minh Bui-Xuan, Nick S. Jones
mtDNA Segregation in Heteroplasmic Tissues Is Common In Vivo and Modulated by Haplotype Differences and Developmental Stage (supplement)
Cell Reports BLOG article
Joerg Patrick Burgstaller, Iain G. Johnston, Nick S. Jones, J. Albrechtova, T. Kolbe, C. Vogl, A. Futschik, C. Mayrhofer, D. Klein, S. Sabitzer, M. Blattner, C. Gully, J. Poulton, T. Rulicke, J. Pialek, R. Steinborn, G. Brem
Highly comparative, feature-based, time-series classification (supplement)
IEEE Transactions in KDE BLOG article
Ben Fulcher, Nick S. Jones
2013:
Highly Comparative Time-Series Analysis: the empirical structure of time series and their methods (super supplement, rest of supplement)
Journal of the Royal Society Interface BLOG article
Ben Fulcher, Max Little, Nick S. Jones
Signal Processing and Inference for the Physical Sciences (volume)
Philosophical Transactions of the Royal Society A BLOG article
Editors Nick S. Jones and Thomas J. Maccarone
Inference for the Physical Sciences (introduction)
Phil. Trans. R. Soc. A. 371 20120493 BLOG article
Nick S. Jones and Thomas J. Maccarone
Signal processing for molecular and cellular biological physics
Phil. Trans. R. Soc. A. 371 20110546
Max Little and Nick S. Jones
Function-valued traits in evolution (supplement)
Journal of the Royal Society Interface BLOG article
Pantelis Z. Hadjipantelis, Nick S. Jones, John Moriarty, David Springate, Christopher G. Knight.
Evolutionary Inference for Functional Data: Using Gaussian Processes on Phylogenies to Study Shape Evolution (journal version, supplement)
Journal of the Royal Society Interface, 10, 20120616 BLOG article
Nick S. Jones, John Moriarty
2012:
Highly Comparative Fetal Heart Rate Analysis
(conference paper) Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE
Ben Fulcher, Alexandra Georgieva, Chris Redman and Nick S. Jones
What Evidence is There for the Homology of Protein-Protein Interactions? (supplement)
PLoS Computational Biology 8(9): e1002645 BLOG article
Anna Lewis, Nick S Jones, Mason Porter, Charlotte Deane
Advection, diffusion and delivery over a network (supplement)
Phys. Rev. E 86, 021905 BLOG article
Luke L. M. Heaton, Eduardo Lopez, Philip K. Maini, Mark D. Fricker, Nick S. Jones
Analysis of fungal networks
Fungal Biology Reviews doi:10.1016/j.fbr.2012.02.001.
Luke L. M. Heaton, Boguslaw Obara, Vincente Grau, Nick S. Jones, Toshi Nakagaki, Lynne Boddy, Mark D. Fricker
Taxonomies of Networks from Community Structure (supplement)
Phys. Rev. E 86, 036104 BLOG article
Jukka-Pekka Onnela, Daniel J. Fenn, Stephen Reid, Mason A. Porter, Peter J. Mucha, Mark D. Fricker, Nick S. Jones
Mitochondrial Variability as a Source of Extrinsic Cellular Noise (supplement)
PLoS Computational Biology 8(3): e1002416. doi:10.1371/journal.pcbi.1002416 BLOG article
Iain G. Johnston, Bernadett Gaal, Ricardo Pires das Neves, Tariq Enver, Francisco J. Iborra, Nick S. Jones
Pulsing of Membrane Potential in Individual Mitochondria: A Stress-Induced Mechanism to Regulate Respiratory Bioenergetics in Arabidopsis
Plant Cell 24, 1188-1201 BLOG article
M. Schwarzlander, D. C. Logan, I. G. Johnston, N. S. Jones, M. D. Fricker and L. J. Sweetlove
Dynamical Clustering of Exchange Rates
Quantitative Finance 12, 1493-1520
Daniel J. Fenn, Mason A. Porter, Peter J. Mucha, Mark McDonald, Stacy Williams, Neil F. Johnson, Nick S. Jones
2011:
Phylogenetic inference for function-valued traits: speech sound evolution
Trends in Evolution and Ecology (free version and non-free weblink) 27, 160-166 BLOG article
John Aston, Dorothy Buck, John Coleman, Colin Cotter, Nick S. Jones, Vincent Macaulay, Norman Macleod, John Moriarty, Andrew Nevins.
Biophysical Journal 2, 477 BLOG article
M.A. Little, B.C. Steel, F. Bai, Y. Sowa, T. Bilyard, D.M. Mueller, R.M. Berry, N.S. Jones
Proceedings of the Royal Society A, 467, 2088 BLOG article
M.A. Little N.S. Jones
Generalized methods and solvers for noise removal from piecewise constant signals. II. New Methods
Proceedings of the Royal Society A, 467, 3115 BLOG article
M.A. Little N.S. Jones
Temporal evolution of financial-market correlations
Phys. Rev. E 84, 026109 BLOG article
D.J. Fenn, M.A. Porter, S. Williams, M. McDonald, N.F. Johnson and N.S. Jones
2010:
Connecting Variability in Global Transcription Rate to Mitochondrial Variability
PLoS Biology 8(12): e1000560 doi:10.1371/journal.pbio.1000560 BLOG article
Ricardo Pires das Neves, Nick S. Jones, Lorena Andreu, Rajeev Gupta, Tariq Enver, Francisco J. Iborra
Growth-induced mass flows in fungal networks
Proceedings of the Royal Society B 277, 3265 BLOG article
Luke Heaton, Eduardo Lopez, Philip K. Maini, Mark D. Fricker, Nick S. Jones
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks
PLoS Computational Biology 6(6):e1000817 BLOG article
Sumeet Agarwal, Charlotte M. Deane, Mason A. Porter, Nick S. Jones
The Function of Communities in Protein Interaction Networks at Multiple Scales
BMC Systems Biology 4, 100 BLOG article
Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane
Structural dynamics and robustness of food webs.
Ecology Letters 13, 891 doi: 10.1111/j.1461-0248.2010.01485.x
Phillip P. A. Staniczenko, Owen T. Lewis, Nick S. Jones, Felix Reed-Tsochas
Sparse bayesian step-filtering for high-throughput analysis of molecular machine dynamics
(conference paper) Proceedings IEEE ICASP 2010 p4162
Max A. Little and Nick S. Jones
2009-2008:
Dynamic communities in multichannel data
Chaos 19, 033119 (2009) BLOG article
Daniel J. Fenn, Mason A. Porter, Mark McDonald, Stacy Williams, Neil F. Johnson, Nick S. Jones
Master-equation analysis of accelerating networks
Phys. Rev. E 79, 056101 (2009)
David M.D. Smith, Jukka-Pekka Onnela, Nick S. Jones
Phys. Rev. E 79, 011915 (2009)
Phillip P. A. Staniczenko, Chiu Fan Lee, Nick S. Jones
Using the Memories of Multiscale Machines to Characterize Complex Systems
Phys. Rev. Lett. 100, 208702 (2008)
Nick S. Jones
Key Distillation and the Secret-Bit Fraction
IEEE Transactions Information Theory, 54, 680 (2008)
Nick S. Jones and Lluis Masanes
Early work:
Photon Frequency Mode Matching using Acousto-Optic Frequency Beam Splitters
Phys. Rev. A 73, 033813 (2006)
Nick S. Jones and T.M. Stace
Interconversion of Nonlocal Correlations
Phys. Rev. A 72, 052312 (2005)
Nick S. Jones and Lluis Masanes
Mediated Digraphs and Quantum Nonlocality
Discrete Appl. Math. 150, 41 (2005)
Gregory Gutin, Nick S. Jones, Arash Rafiey, Simone Severini, Anders Yeo
The Extent of Multi-particle Quantum Non-locality
Physical Review A 71, 042329 (2005)
Nick S. Jones, Noah Linden, Serge Massar
Phys. Rev. A 71, 012324 (2005)
Nick S. Jones and Noah Linden