Publications
Pre-prints
Matthews E, Lanham S, Kyriazi ME, Alexaki K, El-Sagheer A, Brown T, Kanaras A, West J, MacArthur BD, Stumpf PS*, Oreffo RO*.
Single cell RNA sequence analysis of human bone marrow samples reveals new targets for isolation of skeletal stem cells using DNA-coated gold nanoparticles.
bioRxiv 2020.
Articles
2021
Stumpf PS, Arai F, MacArthur, BD.
Modeling Stem Cell Fates using Non-Markov Processes
Cell Stem Cell. 2021; 28 (2): 187-190
https://doi.org/10.1016/j.stem.2021.01.009
Bell S, McCarty V, Peng H, Jefri M, Hettige N, Antonyan L, Crapper L, O'Leary LA, Zhang X, Zhang Y, Wu, H, Sutcliffe D, Kolobova I, Rosenberger TA, Moquin L, Gratton A, Popic J, Gantois I, Stumpf PS, Schuppert AS, Mechawar N, Sonenberg N, Tremblay ML, Jinnah HA, Ernst C.
Lesch-Nyhan disease causes impaired energy metabolism and reduced developmental potential in midbrain dopaminergic cells.
Stem Cell Reports. 2021; 16(7): 1749-1762.
https://doi.org/10.1016/j.stemcr.2021.06.003
Davies J, Vallejo AF, Sirvent S, Porter G, Clayton K, Qumbelo Y, Stumpf PS, West JJ, Gray CM, Chigorimbo-Murefu NTL, MacArthur BD, Polak ME.
An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells
Frontiers in Immunology. 2021; 12: 665312
https://doi.org/10.3389/fimmu.2021.665312
Harrington J, Esteban LB, Butement J, Vallejo AF, Lane SIR, Sheth B, Jongen MSA, Parker R, Stumpf PS, Smith RSG, MacArthur BDM, Rose-Zerilli MJ, Polak ME, Underwood TH, West JJ
Dual dean entrainment with volume ratio modulation for efficient droplet co-encapsulation: extreme single-cell indexing.
Lab Chip. 2021; 21, 3378-3386
https://doi.org/10.1039/D1LC00292A
2020
Stumpf PS, Du X, Imanishi H, Kunisaki Y, Semba Y, Noble T, Smith RC, Rose-Zerili M, West JJ, Oreffo RO, Niranjan M, Akashi K, Arai F, MacArthur, BD.
Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing
Communications Biology 2020; 3: 736
https://doi.org/10.1038/s42003-020-01463-6
Arai F*, Stumpf PS*, Ikushima YM*, Hosokawa K, Roch A, Lutolf MP, Suda T, MacArthur BD.
Machine Learning of Hematopoietic Stem Cell Divisions from Paired Daughter Cell Expression Profiles Reveals Effects of Aging on Self-Renewal
Cell Systems. 2020; 11 (6): 640-652.e5
https://doi.org/10.1016/j.cels.2020.11.004
Stumpf PS, Arai F, MacArthur, BD.
Heterogeneity and ‘memory’ in stem cell populations
Physical Biology. 2020; 16 (6): 065013
https://doi.org/10.1088/1478-3975/abba85
Stumpf PS, Schätzle LK, Schuppert A.
Transfer-lernen in der Biomedizin
Biospektrum 6/2020; 26: 682–684.
https://doi.org/10.1007/s12268-020-1459-2
Fidanza A, Stumpf PS, Ramachandran P, Tamagno S, Babtie A, Lopez-Yrigoyen M, Taylor AH, Easterbrook J, Henderson B, Axton R, Henderson NC, Medvinsky A, Ottersbach K, Romanò N, Forrester LM.
Single cell analyses and machine learning define hematopoietic progenitor and HSC-like cells derived from human PSCs.
Blood. 2020; 136 (25): 2893–2904.
https://doi.org/10.1182/blood.2020006229
Casey MJ, Stumpf PS, MacArthur BD.
Theory of cell fate.
Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2020; 12 (2): e1471.
https://doi.org/10.1002/wsbm.1471
Sirvent S, Vallejo AF, Davies J, Clayton K, Wu Z, Woo J, Riddell J, Chaudhri VK, Stumpf P, Nazlamova LA, Wheway G, Rose-Zerilli M, West J, Pujato M, Chen X, Woelk CH, MacArthur B, Ardern-Jones M, Friedmann PS, Weirauch MT, Singh H, Polak ME.
Genomic programming of IRF4-expressing human Langerhans cells.
Nature Communications. 2020; 11 (1): 1-2.
https://doi.org/10.1038/s41467-019-14125-x
2019
Stumpf PS, MacArthur BD.
Machine learning of stem cell identities from single-cell expression data via regulatory network archetypes.
Frontiers in Genetics. 2019; 10:2.
https://doi.org/10.3389/fgene.2019.00002
Nakamura-Ishizu A, Matsumura T, Stumpf PS, Umemoto T, Takizawa H, Takihara Y, O'Neil A, MacArthur BD, Suda T.
Thrombopoietin metabolically primes hematopoietic stem cells to megakaryocyte-lineage differentiation.
Cell Reports. 2018; 25 (7): 1772-85.
https://doi.org/10.1016/j.celrep.2018.10.059
2017
Stumpf PS, Smith RC, Lenz M, Schuppert A, Müller FJ, Babtie A, Chan TE, Stumpf MP, Please CP, Howison SD, Arai F, MacArthur BD.
Stem cell differentiation as a non-Markov stochastic process.
Cell Systems. 2017; 5 (3): 268-82.
https://doi.org/10.1016/j.cels.2017.08.009
Smith RC, Stumpf PS, Ridden SJ, Sim A, Filippi S, Harrington HA, MacArthur BD.
Nanog fluctuations in embryonic stem cells highlight the problem of measurement in cell biology.
Biophysical journal. 2017; 112 (12): 2641-52.
https://doi.org/10.1016/j.bpj.2017.05.005
2016
Stumpf PS, Ewing R, MacArthur BD.
Single‐cell pluripotency regulatory networks.
Proteomics. 2016; 16 (17): 2303-12.
https://doi.org/10.1002/pmic.201500528
Scarpa E, Bailey JL, Janeczek AA, Stumpf PS, Johnston AH, Oreffo RO, Woo YL, Cheong YC, Evans ND, Newman TA.
Quantification of intracellular payload release from polymersome nanoparticles.
Scientific Reports. 2016; 6: 29460.
https://doi.org/10.1038/srep29460
Earlier
Cheung KS, Sposito N, Stumpf PS, Wilson DI, Sanchez-Elsner T, Oreffo RO.
MicroRNA-146a regulates human foetal femur derived skeletal stem cell differentiation by down-regulating SMAD2 and SMAD3.
PloS one. 2014; 9 (6): e98063.
https://doi.org/10.1371/journal.pone.0098063
MacArthur BD, Sevilla A, Lenz M, Müller FJ, Schuldt BM, Schuppert AA, Ridden SJ, Stumpf PS, Fidalgo M, Ma’ayan A, Wang J, Lemischka IR.
Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity.
Nature Cell Biology. 2012; 14 (11): 1139-47.
https://doi.org/10.1038/ncb2603
Schulz JC, Stumpf PS, Katsen‐Globa A, Sachinidis A, Hescheler J, Zimmermann H.
First steps towards the successful surface‐based cultivation of human embryonic stem cells in hanging drop systems.
Engineering in life sciences. 2012; 12 (6): 584-7
https://doi.org/10.1002/elsc.201100213
Stierl M, Stumpf P, Udwari D, Gueta R, Hagedorn R, Losi A. Gärtner, Petereit L, efetova M, Schwarzel M, Oertner TG, Nagel G, Hegemann P.
Light modulation of cellular cAMP by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa.
Journal of Biological Chemistry. 2011; 286: 1181-8.
Book chapters
MacArthur BD, Stumpf PS, Oreffo RO.
From mathematical modeling and machine learning to clinical reality.
Principles of Tissue Engineering 2020 (pp. 37-51). Academic Press.
https://doi.org/10.1016/B978-0-12-818422-6.00001-0
Kanczler J, Tare RS, Stumpf P, Noble TJ, Black C, Oreffo RO.
Isolation, Differentiation, and Characterization of Human Bone Marrow Stem Cells In Vitro and In Vivo.
Bone Research Protocols 2019 (pp. 53-70). Humana Press, New York, NY.
https://doi.org/10.1007/978-1-4939-8997-3_4
Stumpf PS, MacArthur BD.
Visualization and Clustering of High-Dimensional Transcriptome Data Using GATE.
Stem Cell Transcriptional Networks 2014 (pp. 131-139). Humana Press, New York, NY.
Talks
2021-10-01 When AI meets Biology: a workshop. Lyon, France (virtual).
2021-06-01 Systems Biology Seminar, RWTH Aachen University, Germany.
2020-01-20 MPN seminar series, Uniklinik RWTH Aachen, Germany. Machine learning for translational medicine.
2019-06-14 Wessex Investigational Science Hub (WISH) seminar, Southampton, UK. Harnessing machine learning to bridge the gap between mouse and human cell biology.
2019-06-07 CHDSCR science meeting, Southampton, UK. Evolutionary physiology of bone marrow stem cell regulation using artificial neural networks.
2019-05-22 Broad Interest Omics annual conference, Southampton, UK. Machine learning of Stem Cell Identities from Single-Cell Data via Regulatory Network Archetypes.
2019-05-13 Symposium on Interdisciplinary Machine Learning, Southampton, UK: Mapping Cell Identities from Mouse to Man.
2018-06-08 Computational analysis of single-cell data and cell-type heterogeneity: the next frontier. CAS-MPG, Shanghai, China. Investigating stem-cell differentiation dynamics using single-cell profiling.
2017-09-07 Mathematics in Life Sciences (MILS), Southampton, UK. Single-cell gene regulatory networks uncover sub-states of pluripotency.
2017-06-14 Southampton Medical & Health Research Conference, Southampton, UK. Stem cell differentiation is a stochastic process with memory.
2016-09-08 The 13th Taiwan International Symposium on Statistical Physics and Complex Systems, Taipei, Taiwan. Toward a Theory of Cell-State changes.
2016-07-14 Broad Interest Omics annual conference, Southampton, UK. High-throughput single-cell sequencing with Drop-Seq: Dissecting tissue heterogeneity one cell at a time.
Posters
Davies J, Clayton K, Sirvent S, Stumpf P, West J, Ardern-Jones M, Parker R, Rose-Zerelli M, MacArthur B, Polak ME. Single-cell transcriptomic analysis reveals a spectrum of immune activation in human epidermal Langerhans cells. In: British Journal of Dermatology. 2018 Jun 1 (Vol. 178, No. 6, pp. E400-E401). Hoboken, NJ, USA: Wiley
Sirvent S, Davies J, Clayton K, Wu Z, Riddell J, Stumpf P, MacArthur B, Ardern-Jones M, Singh H, Polak ME. Genomic programming of human migratory LCs for efficient antigen presentation. In: European Journal of Immunology. 2018 May 1 (Vol. 48, pp. 191-192). Hoboken, NJ, USA: Wiley
Stumpf PS et al. Archetypes of stem cell regulatory network activity. Physics of living matter 12th edition. 14-15 September 2017. Cambridge, UK.
Stumpf PS et al. Lineage commitment of pluripotent stem cells as a phase transition. At: Single Cell Biology. 08 - 10 March 2016. Wellcome Genome Campus, Hinxton, UK
Stumpf PS et al. Lineage commitment of pluripotent stem cells as a phase transition. At: ISSCR Annual meeting. 24-27 June 2015. Stockholm, Sweden.
Stumpf PS et al. Lineage commitment of pluripotent stem cells as a phase transition. At: EMBL Symposium on Single-cell Biology: Role of Variability and Noise in Biological Decision-Making. 15 - 18 Apr 2015. EMBL Heidelberg.
Stumpf PS et al. Gene expression signature of individual skeletal stem cells. BORS/BRS annual meeting. 04-05 September 2013. Oxford, UK.
Ehrhart F, Stumpf P, Wiedemeier S, Weyand E, Danzebrink R, Weber MM, Metze J, Sukhorukov V, Zimmermann U, Zimmermann H. A Novel Microfluidic Based Technique for Encapsulation of Langerhans´ Islets Using High Viscosity Alginate and BaSO4 Nanoparticles. In: Dössel O., Schlegel W.C. (eds) World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany. IFMBE Proceedings, vol 25/8. Springer, Berlin, Heidelberg.
Thesis
Stumpf PS
Investigating the origins and consequences of cell-to-cell variability in stem cell populations
University of Southampton 2015, Doctoral Thesis, 282pp.