Accepted and/or published

18. Sarah M. Griffin and Florian Klimm. "Networks and Museum Collections." Oxford Handbook of Archaeological Network Research (Oxford University Press, in print)
19. 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, and Patrick F. Chinnery. "Cell lineage-specific mitochondrial resilience during mammalian organogenesis." Cell [Journal]
20. Florian Klimm. "Quantifying the ‘end of history’ through a Bayesian Markov-chain approach." Royal Society Open Science [Journal] [code] [arXiv]
21. Florian Klimm, Nick S. Jones, and Michael T. Schaub. "Modularity maximisation for graphons." SIAM Journal on Applied Mathematics [Journal] [code] [arXiv]
22. Florian Klimm. "Topological data analysis of truncated contagion maps." Chaos: An Interdisciplinary Journal of Nonlinear Science [Journal] [code] [arXiv]
23. Haixin Zhang, Marco Esposito, Mikael Pezet, Juvid Aryaman, Wei Wei, Florian Klimm, Claudia Calabrese, Stephen P. Burr, Carolina H. Macabelli, Carlo Viscomi, Mitinori Saitou, Marcos R. Chiaratti, James Stewart, Nick S. Jones, and Patrick F. Chinnery. "Mitochondrial DNA heteroplasmy is modulated during oocyte development propagating mutation transmission." Science Advances [Journal]
24. Mikael G. Pezet, Aurora Gomez-Duran*, Florian Klimm*, Juvid Aryaman, Stephen P. Burr, Wei Wei, Mitinori Saitou, Julien Prudent, and Patrick F. Chinnery. "Oxygen tension modulates the mitochondrial genetic bottleneck and influences the segregation of a heteroplasmic mtDNA variant." Communications Biology [Journal]
25. Florian Klimm. "Extracting biological context from cellular trajectories." Nature Computational Sciences (invited News & Views article) [Journal]
26. Florian Klimm, Enrique M. Toledo, Thomas Monfeuga, Fang Zhang, Charlotte M. Deane, and Gesine Reinert. "Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks." BMC Genomics [Journal] [bioRxiv] [code] [link to poster]

    • The poster received the Best Poster Award at the Cambridge Network Day 2019

27. Florian Klimm, Charlotte M. Deane, and Gesine Reinert. "Hypergraphs for predicting essential genes using multiprotein complex data." Journal of Complex Networks [Journal] [bioRxiv] [code]
28. Florian Klimm* and Benjamin F. Maier*. "Commentary: A network science summer course for high-school students." Network Science [link] [material] [arXiv] [poster] [slides]
29. Florian Klimm. "Minimal connections and what they reveal." Mathematics Today. Vol. 56 No. 4 August 2020.
30. Papadopoulos, Lia, Pablo Blinder, Henrik Ronellenfitsch, Florian Klimm, Eleni Katifori, David Kleinfeld, and Danielle S. Bassett. "Embedding of biological distribution networks with differing environmental constraints." PLoS Computational Biology, 14(9), e1006428. [link] [arXiv]
31. Megan Sperry, Qawi Telesford, Florian Klimm and Danielle S. Bassett. "Rentian scaling for the measurement of optimal embedding of complex networks into physical space." Journal of Complex Networks 5.2 (2016): 199-218. [link]
32. Dane Taylor, Florian Klimm, Heather A. Harrington, Miroslav Kramar, Konstantin Mischaikow, Mason A. Porter, and Peter J. Mucha. "Topological data analysis of contagion maps for examining spreading processes on networks." Nature Communications. [link] [arXiv]

    • Nature Physics is reporting on our work as Research Highlight: Bring the noise

33. Florian Klimm, Javier Borge-Holthoefer, Niels Wessel, Jürgen Kurths, and Gorka Zamora-López. "Individual node's contribution to the mesoscale of complex networks." New Journal of Physics. [link]
34. Florian Klimm, Danielle S. Bassett, Jean M. Carlson, and Peter J. Mucha. "Resolving structural variability in network models and the brain." PLoS Computational Biology 10, no. 3 (2014): e1003491. [link]

Peer-reviewed extended abstracts

1. Florian Klimm, Charlotte M. Deane, Jonny Wray and Mason A. Porter. "Reconfiguration of Protein Interaction Networks during Nematode Development." Complex Networks & Their Applications 2017. [link]

   • A version of this talk received the Best Talk Award at the Graduate Student Meeting of the London Mathematical Society in 2017

Theses

• Florian Klimm. "Generalised Networks for Protein Interaction Analysis." DPhil thesis, University of Oxford, 2018. [Link]

  • I received an EPSRC DPhil Prize to extend my doctoral research during a Postdoc at the University of Oxford.

• Florian Klimm. "Characterisation of Individual Nodes in the Mesoscale of Complex Networks." Master thesis, Humboldt-Universität Berlin, 2014. [pdf (21 MB)]
• Florian Klimm. "Charge transmission through single molecules – A density matrix approach." Bachelor thesis, Humboldt-Universität Berlin, 2011. [pdf]

SABS short project reports

As part of the Systems Approaches to Biomedical Sciences Doctoral Training Centre at the University of Oxford I wrote two reports on short projects. Each of these was an academic-industrial co-supervision.

• Florian Klimm. "Hadoop for large-scale eQTL Analysis." Project with Satu Nahkuri from Roche Basel, academic supervisors Chris Yau and Peter Humburg, Spring 2015.
• Florian Klimm. "Multilayer-Network Analysis of Protein Interaction Networks." Project with Jonny Wray from e-Therapeutics, academic supervisors Mason Porter and Charlotte Deane, Summer 2015.

Study Group Papers

• [AO:] Henry Allen, Laura Cooper, Gustav Delius, Meurig Gallagher, Tom Johnson, Florian Klimm, Ferdinando Randisi, Tom Shearer, and Clare Ziegler. "Root Segmentation Over Multiple Time Points." Multi-scale Biology Study Group University of Birmingham, December 2016. [link]
• [AO:] Gerold Baier, Teresa Collins, Joanne Dunster, Ciarán Fisher, Enuo He, Andrzej Kierzek, John King, Florian Klimm, Gary Mirams, Tom Snowden, and John Ward. "Abstract Modelling of Adverse Outcome Pathways." Quantitative Systems Pharmacology Study Group AstraZeneca, September 2015. [link]

Translations

• Andreas Joseph, Florian Klimm. "Netzwerke in der heutigen Welt." Translation of "Network Literacy." 2015. [link]

[AO:] notes papers with alphabetic ordering of authors, independent of their contribution.
* indicates equal contribution by the authors.