Books
Avi Ma’ayan and Ben D. MacArthur, New Frontiers of Network analysis in systems biology, Springer New York (2012)
Papers
Anthony Baptista, Marta Niedostatek, Jun Yamamoto, Ben D MacArthur, Jurgen Kurths, Ruben Sanchez Garcia, Ginestra Bianconi, Mining higher-order triadic interactions, arXiv preprint (2024)
Anthony Baptista, Alessandro Barp, Tapabrata Chakraborti, Chris Harbron, Ben D MacArthur and Christopher RS Banerji, Deep learning as Ricci flow, arXiv preprint (2024)
Anthony Baptista, Ben D MacArthur and Christopher RS Banerji, Charting cellular differentiation trajectories with Ricci flow, Nature Communications 15: 2258 (2024)
Christopher RS Banerji, Tapabrata Chakraborti, Chris Harbron and Ben D MacArthur, Clinical AI tools must convey predictive uncertainty for each individual patient, Nature Medicine (2023)
Kentaro Nakashima, Yuya Kunisaki, Kentaro Hosokawa, Kazuhito Gotoh, Hisayuki Yao, Ryosuke Yuta, Yuichiro Semba, Jumpei Nogami, Yoshikane Kikushige, Patrick S Stumpf, Ben D MacArthur, Dongchon Kang, Koichi Akashi, Shouichi Ohga, and Fumio Arai, POT1a deficiency in mesenchymal niches perturbs B-lymphopoiesis, Communications Biology 6: 996 (2023)
Michael J Casey, Jörg Fliege, Ruben J Sanchez-Garcia and Ben D MacArthur, An information-theoretic approach to single cell sequencing analysis, BMC Bioinformatics 24: 311 (2023)
Elloise Z Matthews, Stuart Lanham, Kate White, Maria-Eleni Kyriazi, KonstantinaAlexaki, Afaf H El-Sagheer, Tom Brown, Antonios G Kanaras, Jonathan J West, Ben D MacArthur, Patrick S Stumpf, and Richard OC Oreffo, Single-cell RNA-sequence analysis of human bone marrow reveals new targets for isolation of skeletal stem cells using spherical nucleic acids, Journal of Tissue Engineering, 10.1177/20417314231169375 (2023)
Robin Mitra, Sarah F. McGough, Tapabrata Chakraborti, Chris Holmes, Ryan Copping, Niels Hagenbuch, Stefanie Biedermann, Jack Noonan, Brieuc Lehmann, Aditi Shenvi, Xuan Vinh Doan, David Leslie, Ginestra Bianconi, Ruben Sanchez-Garcia, Alisha Davies, Maxine Mackintosh, Eleni-Rosalina Andrinopoulou, Anahid Basiri, Chris Harbron and Ben D. MacArthur, Learning from data with structured missingness, Nature Machine Intelligence, 5, 13–23 (2023)
Ben D MacArthur, Stem cell biology needs a theory, Stem Cell Reports 18 (1): 3-5 (2023)
James Davies, Sofia Sirvent, Andres F Vallejo, Kalum Clayton, Gemma Douihet, Patrick S Keeler, Jonathan West, Michael Ardern-Jones, Ben D MacArthur, Harinder Singh and Marta E Polak, Transcriptional programming of immunoregulatory responses in human Langerhans cells, Frontiers in Immunology (2022)
Ben D MacArthur, Cosmina L Dorobantu and Helen Z Margetts, Resilient government requires data science reform, Nature Human Behaviour (2022)
Joseph R Egan, Enas Abu-Shah, Omer Dushek, Tim Elliott and Ben D MacArthur, Fluctuations in T cell receptor and pMHC interactions regulate T cell activation, J. R. Soc. Interface. 19: 20210589 (2022)
Ben D MacArthur, The geometry of cell fate, Cell Systems (2022)
Raffaella Mulas, Ruben J Sanchez-Garcia and Ben D MacArthur, Geometry and symmetry in biochemical reaction systems, Theory in Biosciences (2021)
Ben Gaastra, Peter Barron, Laura Newitt, Simran Chhugani, Carole Turner, Peter Kirkpatrick, Ben D MacArthur, Ian Galea and Diederik Bulter, CRP (C-Reactive Protein) in outcome prediction after subarachnoid hemorrhage and the role of machine learning, Stroke (2021)
Jack Harrington, Luis Blay Esteban, Jonathan Butement, Andres F Vallejo, Simon I.R. Lane, Bhavwanti Sheth, Maaike S.A. Jongen, Rachel Parker, Patrick S Stumpf, Rosanna C G Smith, Ben D MacArthur, Matthew J Rose-Zerilli, Marta E Polak, Tim J Underwood, Jonathan West, Dual Dean entrainment with volume ratio modulation for efficient co-encapsulation: Extreme single-cell indexing, Lab on a Chip (2021)
Philip S Greulich, Ben D MacArthur, Cristina Parigini and Ruben J Sanchez-Garcia, Universal principles of lineage architecture and stem cell identity in renewing tissues, Development (2021) 148 (11): dev194399.
James Davies, Andres F Vallejo, Sofia Sirvent, Gemma Porter, Kalum Clayton, Yamkela Qumbelo, Patrick Stumpf, Jonathan West, Clive M Gray, Nyaradzo T.L Chigorimbo-Murefu, Ben D MacArthur, Marta E Polak, An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells, Frontiers in Immunology 12:2249 (2021)
Nick Fuggle, Helen Harrison, and Ben D MacArthur, Will social media banish the bleep? An analysis of hospital pager activity and instant messaging patterns, BMJ Open Quality 10:e001100 (2021)
Ana Sevilla, Dimitri Papatsenko, Amin R. Mazloom, Huilei Xu, Ana Vasileva, Richard D. Unwin, Gary Leroy, Edward Y. Chen, Francine Garrett-Bakelman, Dung-Fang Lee, Benjamin Trinite, Ryan L. Webb, Zichen Wang, Jie Su, Julian Gingold, Ari Melnick, Benjamin A. Garcia, Anthony D. Whetton, Ben D MacArthur, Avi Ma’ayan and Ihor R. Lemischka, An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions, Frontiers in Cell and Molecular Biology 9:502 (2021)
Ben D. MacArthur, Truth and beauty in physics and biology, Nature Physics 17, 149–151 (2021)
Patrick S Stumpf, Fumio Arai and Ben D MacArthur, Modelling stem cell fates using non-Markov processes, Cell Stem Cell 28(2), 187-190 (2021)
Fumio Arai, Patrick S Stumpf, Yoshiko M Ikushima, Kentaro Hosokawa, Aline Roch, Matthias P Luttolf, Toshio Suda and Ben D MacArthur, Machine learning of hematopoietic stem cell divisions from paired daughter cell expression profiles reveals effects of aging on self-renewal, Cell Systems, 11:6, p640-652.E5 (2020)
Patrick S Stumpf, Xin Du, Haruka Imanishi, Yuya Kunisaki, Yuichiro Semba, Timothy Noble, Rosanna CG Smith, Matthew Rose-Zerili, Jonathan J West, Richard OC Oreffo, Katayoun Farrahi, Mahesan Niranjan, Koichi Akashi, Fumio Arai and Ben D MacArthur, Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing, Communications Biology, 3: 736 (2020)
Ashley I. Heinson, Jeongmin Woo, Amey Mukim, Cory H. White, Bastiaan Moesker, Alberto Bosque, Celsa A. Spina, Christopher H. Woelk, Ben D. MacArthur and Nadejda Beliakova-Bethell, Micro RNA targets in HIV latency: insights into novel layers of latency control, AIDS Research and Human Retroviruses (2020)
Patrick S. Stumpf, Fumio Arai and Ben D. MacArthur, Heterogeneity and ‘memory’ in stem cell populations, Physical Biology (2020)
Philip S. Greulich, Rosanna Smith and Ben D. MacArthur, The physics of cell fate, in Phenotypic Switching (Levine et al, Eds.), (2020)
Maaike S. A. Jongen, Ben D. MacArthur, Nicola A. Englyst and Jonathan West, Single platelet variability governs population sensitivity and initiates intrinsic heterotypic behaviours, Communications Biology 3: 281 (2020)
Ben D. MacArthur, Patrick S. Stumpf and Richard O. C. Oreffo, From mathematical models and machine learning to clinical reality, Principles of Tissue Engineering (5th Ed.), Robert Lanza, Robert Langer and Joseph Vacanti (Eds.), Academic Press (2020)
Imogen. S. Stafford, Melina Kellermann, Enrico Mossotto, R. Mark Beattie, Ben. D. MacArthur and Sarah Ennis, A systematic review of the applications of artificial intelligence and machine learning in autoimmune diseases, npj Digital Medicine 3: 30 (2020)
Sofia Sirvent, Andres F. Vallejo, James Davies, Kalum Clayton, Zhiguo Wu, Jeongmin Woo, Jeremy Riddell, Virendra K. Chaudhri, Patrick Stumpf, Liliya Angelova Nazlamova, Gabrielle Wheway, Matthew Rose-Zerilli, Jonathan West, Mario Pujato, Xiaoting Chen, Christopher H. Woelk, Ben D. MacArthur, Michael Ardern-Jones, Peter S. Friedmann, Matthew T. Weirauch, Harinder Singh and Marta E. Polak, Genomic programming of IRF4-expressing human Langerhans cells, Nature Communications, 11: 313 (2020)
Michael J. Casey, Patrick S. Stumpf and Ben D. MacArthur, Theory of cell fate, WIREs Systems Biology & Medicine e1471 (2019)
Philip Greulich, Ben D. MacArthur, Cristina Parigini, and Rubén J. Sánchez García, Stability and steady state of complex cooperative systems: a diakoptic approach, Royal Society Open Science 6(12): 191090 (2019)
Ben D. MacArthur, Book review: Does science undermine faith? by Roger Trigg, Science & Christian Belief, 31:2, 219-220 (2019)
Ayako Nakamura-Ishizu, Ben D. MacArthur and Toshio Suda, Beginning of a New Era: Mapping the Bone Marrow Niche, Cell 177 (7), 1679-1681 (2019)
Enrico Mossotto, James J. Ashton, Reuben J. Pengelly, Mark R. Beatie, Ben D. MacArthur and Sarah Ennis, GenePy – a score for estimating gene pathogenicity in individuals using next-generation sequencing data, BMC Bioinformatics 20:254 (2019)
Patrick S. Stumpf and Ben D. MacArthur, Machine learning of stem cell identities from single-cell expression data via regulatory network archetypes, Frontiers in Genetics, 10:2 (2019)
Ayako Nakamura-Ishizu, Takayoshi Matsumura, Patrick S. Stumpf, Terumasa Umemoto, Hitoshi Takizawa, Yuji Takihara, Aled O’Neil, A’Qilah Banu Bte Abdul Majeed, Ben D. MacArthur and Toshio Suda, Thrombopoietin metabolically primes hematopoietic stem cells to megakaryocyte-lineage differentiation, Cell Reports 25(7), 1772-1785.e6 (2018)
Ben D. MacArthur, Connected development, Nature Physics, 14: 975–976 (2018)
Kentaro Hosokawa, Ben D. MacArthur, Yoshiko Ikushima, Hirofumi Toyama, Yoshikazu Masuhiro, Shigemasa Hanazawa, Toshio Suda, Fumio Arai, Functional analysis of Protection of Telomeres 1a (Pot1a) in regulation of hematopoietic stem cell aging, Rinsho Ketsueki (The Japanese Journal of Clinical Hematology), 58(8): 942-949 (2017)
Philip Greulich and Ben D. MacArthur, Systems biology of development and differentiation, Current Opinion in Systems Biology 5, vi–viii (2017)
Patrick S. Stumpf, Rosanna C. G. Smith, Michael Lenz, Andreas Schuppert, Franz-Josef Müller, Ann Babtie, Thalia E. Chan, Michael P. H. Stumpf, Colin P. Please, Sam D. Howison, Fumio Arai, and Ben D. MacArthur, Stem cell differentiation as a non-Markov stochastic process, Cell Systems 5(3): 268–282.e7 (2017)
Kentaro Hosokawa, Ben D. MacArthur, Yoshiko Ikushima, Hirofumi Toyama, Yoshikazu Masuhiro, Shigemasa Hanazawa, Toshio Suda, and Fumio Arai, The telomere binding protein Pot1 maintains haematopoietic stem cell activity with age, Nature Communications, 8: 804 (2017)
Rosanna C. G. Smith and Ben D. MacArthur, Information theoretic approaches to understanding stem cell variability, Current Stem Cell Reports, 3(3): 225–231 (2017)
Rosanna C. G. Smith, Patrick S. Stumpf, Sonya Ridden, Aaron Sim, Sarah Filippi, Heather A. Harrington and Ben D. MacArthur, Nanog fluctuations in embryonic stem cells highlight the problem of measurement in cell biology, Biophysical Journal 112 (12): 2641-2652 (2017)
Enrico Mossotto, Tracy Coelho, R Mark Beattie, Ben D. MacArthur and Sarah Ennis, Classification of paediatric inflammatory bowel disease using machine learning, Scientific Reports 7:2427 (2017)
Styliani Kontogeorgaki, Ruben Sanchez-Garcia, Rob Ewing, Konstantinos Zygalakis and Ben D. MacArthur, Noise-processing by signaling networks, Scientific Reports, 532 (2017)
Jeffrey M. Bernitz, Huen Suk Kim, Ben D. MacArthur, Hans Sieburg, Kateri Moore, Hematopoietic stem cells count and remember self-renewal divisions, Cell 167 (5): 1296–1309.e10 (2016)
Kimiyo N. Yamamoto, Masatsugu Ishii, Yoshihiro Inoue, Fumitoshi Hirokawa, Ben D. MacArthur, Akira Nakamura, Hiroshi Haeno and Kazuhisa Uchiyama, Prediction of postoperative liver regeneration from clinical information using a data-led mathematical model, Scientific Reports 6:34214 (2016)
Patrick S. Stumpf, Rob Ewing and Ben D. MacArthur, Single cell pluripotency regulatory networks, Proteomics, 16(17): 2303–2312 (2016)
Miranda C. Lewis, Ben D. MacArthur, Rahul S. Tare, Richard O.C. Oreffo and Colin P. Please, Extracellular matrix deposition in engineered micromass pellet cultures: measurements and modelling, PLOS ONE, 11(2): e0147302 (2016)
Sonya J. Ridden, Hannah H. Chang, Konstantinos Zygalakis and Ben D. MacArthur, Entropy, ergodicity and stem cell multipotency, Physical Review Letters, 115, 208103 (2015)
Dmitri Papatsenko, Henia Darr, Ivan V. Kulakovskiy, Avinash Waghray, Vsevolod J. Makeev, Ben D. MacArthur and Ihor R. Lemischka, Single-cell analyses of ESCs reveal alternative pluripotent cell states and molecular mechanisms that control self-renewal, Stem Cell Reports, 5(2):207–220 (2015)
Conor Smyth, Iva Špakulová, Owen Cotton-Barratt, Sajjad Rafiq, William Tapper, Rosanna Upstill-Goddard, John L. Hopper, Enes Makalic, Daniel F. Schmidt, Miroslav Kapuscinski, Jörg Fliege, Andrew Collins, Jacek Brodzki, Diana M. Eccles and Ben D. MacArthur, Quantifying the cumulative effect of low-penetrance genetic variants on breast cancer risk, Molecular Genetics & Genomic Medicine, DOI: 10.1002/mgg3.129 (2015)
Patrick S. Stumpf and Ben D. MacArthur, Visualisation and clustering of high-dimensional transcriptome data using GATE, Stem Cell Transcriptional Networks, Springer New York, 131-139 (2014)
Ben D. MacArthur, Collective dynamics of stem cell populations, Proc. Natl. Acad. Sci. U.S.A. 1401030111 (2014).
Ben D. MacArthur and Richard O.C. Oreffo, From mathematical models to clinical reality, Principles of Tissue Engineering (4th Ed.), Robert Lanza, Robert Langer and Joseph Vacanti (Eds.), Academic Press (2013)
Ben D. MacArthur and Ihor R. Lemischka, Statistical mechanics of pluripotency, Cell 154(3), 484-489 (2013)
Bernhard M. Schuldt, Anke Guhr, Michael Lenz, Sabine Kobold, Ben D. MacArthur, Andreas Schuppert, Peter Löser, Franz-Josef Müller, Power-laws and the use of pluripotent stem cell lines, PLOS ONE 8(1): e52068 (2013)
Ben D. MacArthur, Ana Sevilla, Michel Lenz, Franz-Josef Müller, Berhard M. Schuldt, Andreas A. Schuppert, Sonya J. Ridden, Patrick S. Stumpf, Miguel Fidalgo, Avi Ma’ayan, Jianlong Wang and Ihor R. Lemischka, Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity, Nature Cell Biology 14, 1139-1147 (2012)
Sonya J. Ridden and Ben D. MacArthur, Cell fate regulatory networks, New Frontiers of Network Analysis in Systems Biology, 15-29 (2012)
Simón Méndez-Ferrer,Tatyana V. Michurina, Francesca Ferraro, Amin R. Mazloom, Ben D. MacArthur, Sergio A. Lira, David T. Scadden, Avi Ma’ayan, Grigori N. Enikolopov and Paul S. Frenette, Mesenchymal and haematopoietic stem cells form a unique bone marrow niche, Nature 466, 829–834 (2010)
Ben D. MacArthur, Rubén J. Sánchez-García and Avi Ma’ayan, Microdynamics and criticality of adaptive regulatory networks, Physical Review Letters, 104(16):168701 (2010), arXiv preprint
Ben D. MacArthur, Alexander Lachmann and Avi Ma’ayan, GATE: software for the analysis and visualization of high-dimensional time-series expression data, Bioinformatics 26, 143–144 (2010)
Rong Lu, Florian Markowetz, Richard D. Unwin, Jeffrey T. Leek, Edoardo M. Airoldi, Ben D. MacArthur, Alexander Lachmann, Roye Rozov, Avi Ma’ayan, Laurie A. Boyer, Olga G. Troyanskaya, Anthony D. Whetton and Ihor R. Lemischka, Systems-level dynamic analyses of fate change in murine embryonic stem cells, Nature 462, 358–362 (2009)
Ben D. MacArthur, Avi Ma’ayan and Ihor R. Lemischka, Systems biology of stem cell fate and cellular reprogramming, Nature Reviews Molecular Cell Biology, 10, 672–681 (2009)
Ben D. MacArthur and Rubén J. Sánchez-García, Spectral characteristics of network redundancy, Physical Review E 80:026117 (2009), arXiv preprint
Ben D. MacArthur, Avi Ma’ayan and Ihor R. Lemischka, Toward stem cell systems biology: from molecules to networks and landscapes, Cold Spring Harbor Symposia on Quantitative Biology 73, 211–215 (2008)
Ben D. MacArthur, Rahul S. Tare, Kate Murawski and Richard O. C. Oreffo, Identification of candidate regulators of multipotency in human skeletal progenitor cells, Biochemical and Biophysical Research Communications, 377(1):68–72 (2008)
Ben D. MacArthur, Colin P. Please and Richard O. C. Oreffo, Stochasticity and the molecular mechanisms of induced pluripotency, PLOS ONE 3(8):e3086 (2008)
Yanghua Xiao, Ben D. MacArthur, Hui Wang, Momiao Xiong and Wei Wang, Network quotients: structural skeletons of complex systems, Physical Review E 78:046102 (2008), arXiv preprint
Ben D. MacArthur, Rubén J. Sánchez-García and James W. Anderson, Symmetry in complex networks, Discrete Applied Mathematics 156(18):3525–3531 (2008), arXiv preprint
Ben D. MacArthur, Rahul S. Tare, Colin P. Please, Phil Prescott and Richard O. C. Oreffo, A non-invasive method for in situ quantification of subpopulation behaviour in mixed cell culture, Journal of the Royal Society Interface, 3(6):63–69 (2006)
Ben D. MacArthur and Richard O. C. Oreffo, Bridging the gap, Nature 433(7021):19 (2005)
Miranda C. Lewis, Ben D. MacArthur, Jos Malda, Graeme Pettet and Colin P. Please, Heterogeneous proliferation within engineered cartilaginous tissue: the role of oxygen tension, Biotechnology and Bioengineering, 91(5):607–615 (2005)
Ben D. MacArthur, Colin P. Please and Graeme J. Pettet, A mathematical model for dynamic glioma-host interactions: receptor mediated invasion and local proteolysis, Mathematical Medicine and Biology 22(3):247–264 (2005)
Ben D. MacArthur, A right to voice dissent against the establishment, Nature, 433, 355 (2005)
Ben D. MacArthur and Colin P. Please, Residual stress generation and necrosis formation in multi-cell tumour spheroids, Journal of Mathematical Biology 49(6):537–552 (2004)
Ben D. MacArthur, Mark Taylor, Colin P. Please and Richard O. C. Oreffo, Mathematical modelling of skeletal repair, Biochemical and Biophysical Research Communications 313(4):825–833 (2004)
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