Dr. Mark N. Read

I innovate in data science and its application to medical and biological domains. Algorithms, simulations, machine learning, gut microbial ecology, immunology and healthcare. Research is endless exciting possibilities.

2022

JP Molina Ortiz, MN Read, DD McClure, A Holmes, F Dehghani, ER Shanahan. (2022). High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure. Gut Microbes 14(1):2118831. [URL at journal]

Rebecca C Simpson, Erin R Shanahan, Marcel Batten, Irene LM Reijers, Mark Read, Ines P Silva, Judith M Versluis, Rosilene Ribeiro, Alexandra S Angelatos, Jian Tan, Chandra Adhikari, Alexander M Menzies, Robyn PM Saw, Maria Gonzalez, Kerwin F Shannon, Andrew J Spillane, Rebecca Velickovic, Alexander J Lazar, Ashish V Damania, Aditya K Mishra, Manoj Chelvanambi, Anik Banerjee, Nadim J Ajami, Jennifer A Wargo, Laurence Macia, Andrew J Holmes, James S Wilmott, Christian U Blank, Richard A Scolyer, Georgina V Long. (2022). Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome. Nature Medicine 28(11):2344-2352 [URL at journal]

Jian Tan, Duan Ni, Jemma Taitz, Gabriela Veronica Pinget, Mark Read, Alistair Senior, Jibran Abdul Wali, Reem Elnour, Erin Shanahan, Huiling Wu, Steven J Chadban, Ralph Nanan, Nicholas Jonathan Cole King, Georges Emile Grau, Stephen J Simpson, Laurence Macia. (2022). Dietary protein increases T-cell-independent sIgA production through changes in gut microbiota-derived extracellular vesicles. Nature Communications 13(1):4336. [URL at journal]

Givanna H Putri, Jonathan Chung, Davis N Edwards, Felix Marsh‐Wakefield, Irena Koprinska, Suat Dervish, Nicholas JC King, Thomas M Ashhurst, Mark N Read. (2022). TrackSOM: Mapping immune response dynamics through clustering of time‐course cytometry data Cytometry Part A 103(1):54-70 [URL at journal]

Felix Marsh‐Wakefield, Pierre Juillard, Thomas M Ashhurst, Annette Juillard, Diana Shinko, Givanna H Putri, Mark N Read, Helen M McGuire, Scott N Byrne, Simon Hawke, Georges E Grau. (2022). Peripheral B‐cell dysregulation is associated with relapse after long‐term quiescence in patients with multiple sclerosis. Immunology and Cell Biology 100(6):543-467. [URL at journal]

2021

GH Putri, I Koprinska, TM Ashhurst, NJC King, MN Read. (2021). Using single-cell cytometry to illustrate integrated multi-perspective evaluation of clustering algorithms using Pareto fronts. Bioinformatics :btab038. [URL at journal]

JD Hywood, G Rice, SV Pageon, MN Read, M Biro. (2021). Detection and characterisation of chemotactic swarming without cell tracking. Journal of the Royal Society Interface 18(176):20200879. [URL at journal]

T Ashhurst+, F Marsh-Wakefield+, G Putri+, A Spiteri, D Shinko, MN Read, A Smith, NJC King. (2022). Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre. Cytometry: Part A, 101(3):237-253. + equal contribution. [URL at journal]

J Tan+, D Ni+, JA Wali, DA Cox, GV Pinget, J Taitz, CI Daien, A Senior, MN Read, SJ Simpson, NJC King+, and L Macia+. (2021). Dietary carbohydrate, particularly glucose, drives B cell lymphopoiesis and function. iScience, 24(8):102835. + equal first/senior contributions.

M Koutsakos, LC Rowntree, L Hensen, BY Chua, CE van de Sandt, JR Habel, W Zhang, X Jia, L Kedzierski, TM Ashhurst, GH Putri, F Marsh-Wakefield, MN Read, DN Edwards, EB Clemens, C Yi Wong, FL Mordant, JA Juno, F Amanat, J Audsley, NE Holmes, CL Gordon, OC Smibert, JA Trubiano, CM Hughes, M Catton, JT Denholm, SYC Tong, DL Doolan, TC Kotsimbos, DC Jackson, F Krammer, DI Godfrey, AW Chung, NJC King, SR Lewin, AK Wheatley, SJ Kent, K Subbarao, J McMahon, I Thevarajan, THO Nguyen, AC Cheng, and K Kedzierska. (2021). Integrated immune dynamics define correlates of COVID-19 severity and antibody responses. Cell Reports Medicine 2:100208. [URL at journal]

2020

MN Read, K Alden, J Timmis, and PS Andrews. (2020). Strategies for Calibrating Models of Biology. Briefings in Bioinformatics 21(1):24–35. [URL to paper at journal]

N Lamm, MN Read, M Nobis, D Van Ly, SG Page, VP Masamsetti, P Timpson, M Biro, and AJ Cesare. (2020). Nuclear F-actin counteracts nuclear deformation and promotes fork repair during replication stress. Nature Cell Biology 22(12):1460-1470. [URL at journal]

JLG Nino, SV Pageon, SS Tay, F Colakoglu, D Kempe, J Hywood, JK Mazalo, J Cremasco, M Govendir, LF Dagley, K Hsu, S Rizzetto, J Zieba, G Rice, V Prior, G O’Neill, RJ Williams, DR Nisbet, B Kramer, AI Webb, F Luciani, MN Read, and M Biro. (2020). Cytotoxic T Cells Swarm by Homotypic Chemokine Signalling. eLife 9:e56554. [URL at journal]

GK Rangan , A Raghubanshi , A Chaitarvornkit , AN Chandra , R Gardos , A Munt , MN Read , S Saravanabavan , JQJ Zhang, and ATY Wong (2020). Current and emerging treatment options to prevent renal failure due to autosomal dominant polycystic kidney disease. Expert Opinion on Orphan Drugs 8(8):285-302. [URL at journal]

J Zoll+, MN Read+, S Heywood, E Estevez, J Marshall, H Kammoun, T Allen, A Holmes, M Febbraio, and D Henstridge (2020). Fecal microbiota transplantation from high caloric-fed donors alters glucose metabolism in recipient mice, independently of adiposity or exercise status. American Journal of Physiology-Endocrinology and Metabolism 319(1):E203-216. + equal-first authors. [URL at journal]

2019

CAM Fois, TYL Le, A Schindeler, S Naficy, DD McClure, MN Read, P Valtchev, A Khademhosseini and F Dehghani. (2019). Models of the Gut for Analyzing the Impact of Food and Drugs. Advanced Healthcare Materials 8(21):1900968. [URL at journal].

GH Putri, MN Read, I Koprinska, TM Ashhurst and NJC King. (2019). Dimensionality reduction for clustering and cluster tracking of cytometry data. International Conference on Artificial Neural Networks pp 624-640. [URL at conference proceedings]

GH Putri, MN Read, I Koprinska, D Singh, U Rohm, TM Ashhurst, NJC King. (2019). ChronoClust: Density-based clustering and cluster tracking in high-dimensional time-series data. Knowledge-Based Systems 174:9-26. [URL to paper at the journal]

2018

S Stepney, FAC Polack, K Alden, PS Andrews, JL Bown, A Droop, MN Read, AT Sampson, J Timmis, AFT Winfield. (2018). Engineering Simulations as Scientific Instruments: A Pattern Language. Springer International Publishing. [URL to book at publisher]

I Moran, A Nguyen, W Khoo, D Butt, K Bourne, C Young, J Hermes, M Biro, G Gracie, C Ma, C Munier, F Luciani, J Zaunders, A Parker, A Kelleher, S Tangye, P Croucher, R Brink, MN Read, T Phan. (2018). Memory B Cells Are Reactivated in Subcapsular Proliferative Foci of Lymph Nodes. Nature Communications 9:3372. [URL to paper at journal]

2017

MN Read, A Holmes. (2017). Towards an integrative understanding of diet-host-gut microbiome interactions. Frontiers in Immunology 8:538. [URL to paper at journal]

AJ Holmes, YV Chew, F Colakoglu, JB. Cliff, E Klaassens, MN Read, SM Solon-Biet, AC McMahon, VC Cogger, K Ruohonen, D Raubenheimer, DG Le Couteur, SJ Simpson. (2017). Diet-microbiome interactions in health are controlled by intestinal nitrogen source constraints. Cell Metabolism 25(1):140–151. [URL to paper at journal]

2016

MN Read, K Alden, LM Rose, J Timmis. (2016). Automated Multi-Objective Calibration of Biological Agent-Based Simulations. Journal of the Royal Society Interface 13(122):20160543. [URL to paper at journal]

MN Read, J Bailey, J Timmis and T Chtanova. (2016). Leukocyte Motility Models Assessed through Simulation and Multi-Objective Optimization-Based Model Selection. PLOS Computational Biology 12(9):e1005082. doi:10.1371/journl.pcbi.1005082. [URL to paper at journal]

J Hywood, MN Read and G Rice. (2016). Statistical analysis of spatially homogeneous dynamic agent-based processes using functional time series analysis. Spatial Statistics 17:199-219. [URL to paper at journal]

2015

J Cosgrove, JA Butler, K Alden, M Read, V Kumar, J Timmis and M Coles. (2015). Agent-based modelling in systems pharmacology. CPT: Pharmacometrics & Systems Pharmacology 4(11):615–629. [URL to paper at journal]

M Read, J Timmis and T Chtanova. (2015). Simulation-based analysis of in situ cellular motility. Abstract, Proceedings of the European Conference on Artificial Life, page 637, 2015.

M Read, AJ Holmes, M Hartill-Law, S Solon-Biet, D Raubenheimer and SJ Simpson. (2015). Simulating the influence of diet on the intestinal microbiome composition. Abstract, Proceedings of the European Conference on Artificial Life, page 638, 2015.

2014

K Alden, M Read, P Andrews, J Timmis and M Coles. (2014). Applying spartan to understanding uncertainty in simulations. The R Journal 6(2):1-10. [URL to paper]

M Read, PS Andrews, J Timmis, V Kumar. (2014). Modelling biological behaviours with the unified modelling language: an immunological case study and critique. Journal of the Royal Society Interface 11(9):20140704. [URL to paper]

B Naylor, M Read, A Turner, J Timmis, A Tyrrell. (2014). The Relay Chain: A Scalable Dynamic Communication link between an Exploratory Underwater Shoal and a Surface Vehicle. Proceedings of Artificial Life (ALife), pages 290-297.

2013

K Alden, M Read. (2013). Scientific software needs quality control. Nature 502:448. This is an editor-reviewed correspondence, not a peer-reviewed article.

M Read, PS Andrews, J Timmis, RA Williams, RB Greaves, H Sheng, M Coles, V Kumar. (2013). Determining disease intervention strategies using spatially resolved simulations. PLOS ONE 8(11):e80506. [URL to paper]

M Read, M Tripp, H Leonova, L Rose, J Timmis. (2013). Automated calibration of agent-based immunological simulations. Abstract, published in ICARIS track at ECAL, MIT press, pages 874-875.

E Hart, M Read, C McEwan, J Greensmith, U Aickelin. (2013). On the Role of the AIS Practitioner. Abstract, published in ICARIS track at ECAL, MIT press, pages 891-892.

M Read, C Moeslinger, T Dipper, D Kengyel, J Hilder, R Thenius, A Tyrrell, J Timmis, T Schmickl. (2013). Profiling underwater swarm robotic shoaling performance using simulation. Proceedings of Towards Autonomous Robotic Systems (TAROS), pages 404 – 416.

D Sutantyo, P Levi, C Moeslinger, M Read. (2013). Collective-Adaptive Levy Flight for Underwater Multi-Robot Exploration. Proceedings of IEEE Conference of Mechatronics and Automation, pages 456-462.

RA Williams, R Greaves, M Read, J Timmis, PS Andrews, V Kumar. (2013). In silico investigation into dendritic cell regulation of CD8Treg mediated killing of Th1 cells within murine experimental autoimmune encephalomyelitis. BMC Bioinformatics 14(Suppl 6):S9. [URL to paper]

RB Greaves, M Read, J Timmis, PS Andrews, J Butler, B Gerckens, V Kumar. (2013). In silico investigation of novel biological pathways: the role of CD200 in regulation of T cell priming in Experimental Autoimmune Encephalomyelitis. Biosystems 112(2):107-121. [URL at Biosystems]

K Alden, M Read, J Timmis, PS Andrews, H Veiga-Fernandes, M Coles. (2013). Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems. PLoS Computational Biology 9(2). [URL to paper]

2012

M Read, J Butler, BO Gerckens, J Timmis, V Kumar. (2012). CD200 Regulation can Promote Recovery from Autoimmunity in Experimental Autoimmune Encephalomyelitis. Abstract presented at ICARIS 2012.

RB Greaves, M Read, J Timmis, PS Andrews, V Kumar. (2012). Extending an established simulation: exploration of the possible effects using a case study in experimental autoimmune encephalomyelitis. Proceedings of the 9th International Conference on Information Processing in Cells and Tissues (IPCAT), LNCS 7223, pages 150-161.

M Read, P Andrews, J Timmis, V Kumar. (2012). Techniques for Grounding Agent-Based Simulations in the Real Domain: a case study in Experimental Autoimmune Encephalomyelitis. Mathematical and Computer Modelling of Dynamical Systems (MCMDS), 18(1):67-86.

M Read. (2012). Statistical and Modelling Techniques to Build Confidence in the Investigation of Immunology through Agent-Based Simulation. PhD Thesis, University of York, 2012. [Available here]

2011

T Schmickl, R Thenius, C Moslinger, J Timmis, A Tyrrell, M Read, J Hilder, J Halloy, C Stefanini, L Manfredi, A Campo, T Dipper, D Sutantyo, S Kernbach. (2011). CoCoRo – The Self-aware Underwater Swarm.
Proceedings of the Fifth IEEE Conference on Self-Adaptive and Self-Organizing Systems.

M Read, P Andrews, J Timmis. (2011). An Introduction to Artificial Immune Systems. The Handbook of Natural Computing, edited by Grzegorz Rozenberg, Thomas Bäck and Joost Kok. Published by Springer.

R Williams, M Read, J Timmis, P Andrews, V Kumar. (2011). In Silico Investigation into CD8Treg Mediated Recovery in Murine Experimental Autoimmune Encephalomyelitis. Proceedings of ICARIS, LNCS volume 6825, pp 51-54.

2010

FAC Polack, P Andrews, T Ghetiu, M Read, S Stepney, J Timmis, A Sampson. (2010). Reflections on the Simulation of Complex Systems for Science. IEEE ICECCS, pp:276-285.

2009

M Read, J Timmis, P Andrews, V Kumar. (2009). A Domain Model of Experimental Autoimmune Encephalomyelitis. 2nd Workshop on Complex Systems Modelling and Simulation, pp:9-44.

M Read, J Timmis, P Andrews, V Kumar. (2009) Using UML to Model EAE and its Regulatory Network. Proceedings of 8th International Conference on Artificial Immune Systems, LNCS 5666, pp:4-6.

2008

M Read, J Timmis and P Andrews. (2008). Empirical Investigation of an Artificial Cytokine Network. Proc. 7th International Conference on Artificial Immune Systems (ICARIS), LNCS 5132. pp. 340-351, 2008. [URL at Springer]

2007

M Read. (2007). Explicable Boolean Functions. Masters degree dissertation, University of York, under the supervision of Prof. John Clark.