Books

Avi Ma'ayan and Ben D. MacArthur, New Frontiers of Network analysis in systems biology, Springer New York (2012)


Papers

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)

Enrico Mossotto, James J. Ashton, Reuben J. Pengelly, Mark R. Beatie, Ben D. MacArthur and Sarah Ennis, GenePy - a tool for estimating gene pathogenicity in individuals using next-generation sequencing data, submitted (2018), bioRxiv preprint

Patrick S. Stumpf and Ben D. MacArthur, Machine learning of stem cell identities from single-cell expression data via regulatory network archetypes, submitted (2018), bioRxiv preprint

Brian Bonney, Ben D. MacArthur and Tim Sluckin, Turning old facts into new knowledge: D’Arcy Thompson’s “On Growth and Form” a century on, submitted (2017), preprint

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. MacArthurQuantifying 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. MacArthurVisualisation and clustering of high-dimensional transcriptome data using GATE, Stem Cell Transcriptional Networks, Springer New York, 131-139 (2014)

Ben D. MacArthurCollective 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. MacArthurCell 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 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)