sebastian ahnert
I am a Gatsby Career Development Fellow at the Sainsbury Laboratory, and a Royal Society University Research Fellow at the Cavendish Laboratory, which are both part of the University of Cambridge. I am also a Fellow of King's College, Cambridge.

research | publications | lectures | people | links |

My research interests lie mainly in two areas: The first is the study of biological evolution and development from the perspective of algorithmic information. The second is network analysis, where I am interested in both method development and in interdisciplinary applications of network analysis to biology, the humanities, and social sciences.

Some recent results are outlined below.

A periodic table of protein complexes
(Science 2015)
Biological evolution has produced an enormous variety of protein complexes, which arise when several proteins bind together to form larger structures. We show that the vast majority of protein complexes can be broken down in terms of three different fundamental steps of protein evolution. These steps can combine in many different ways, giving rise to the observed variety of protein complexes. What this reveals is that heteromeric protein complexes, which are complexes that consist of more than one type of protein, can be represented as homomeric complexes of repeated multi-protein units. This approach also allows us to classify protein complexes in a periodic table, and to predict topologies of complexes that have not been observed yet.

The periodic table of protein complexes can be browsed here.

Universal properties of genotype-phenotype maps
(PLOS Computational Biology 2016; Royal Society Interface 2015; Royal Society Interface 2014)
We introduce a simple genotype-phenotype (GP) map for biological self-assembly on a lattice, and show that it shares many properties with the well-established GP maps of both RNA secondary structure and the HP model. These properties include a heavily skewed distribution of the number of genotypes per phenotype, shape space covering, and positively correlated phenotypic evolvability and robustness. The fact that these important properties emerge in three very different GP maps underline their fundamental importance for biological evolution. It also means that the lattice model, which is highly simplified and therefore tractable, can be used to study a wide variety of evolutionary phenomena.

In further work (2015) we show that all of the properties described above also arise in a much simpler GP map. The defining characteristic of this simple map is the presence of 'coding' and 'non-coding' sequence regions. The boundary between these two regions is itself defined in the sequence, much like start and stop codons in DNA. The fact that the properties of biologically realistic GP maps emerge in this extremely simple model suggests that the fundamental organisation of biological sequences into constrained and unconstrained regions has a profound impact on the structure of GP maps, and therefore on biological evolution.

In this context I co-organised the ESFCB 2012 conference on the evolution of structural and functional complexity in biology, and the IWGPM 2016 workshop on genotype-phenotype maps.

Network analysis identifies the sustainers of historical underground communities
(English Literary History 2015; Leonardo 2014)
We apply network analysis to a curated social network of the Protestant underground community during the reign of Mary I of England (1553-1558), derived from the contents of several hundred letters sent by members of this community. This quantitative approach identifies individuals in the network who did not necessarily have many connections to others, but who nevertheless occupied strategically important positions in the network. The importance of these individuals is confirmed by historical evidence of their role as sustainers who passed messages, provided shelter and financial support, and who continued to hold the network together after most of the leading figures had been executed by Mary I.

This work was also covered in the New Scientist.

Self-assembly, modularity and physical complexity
(Physical Review E 2016; Physical Review E 2016 (2); Physical Review E 2011; Physical Review E 2010; see also Royal Society Interface 2014)
Self-assembly is not just a ubiquitous phenomenon in biology and physics, it is also a language that can be used to describe a physical structure, and measure its complexity and modularity. To illustrate this, we introduce a versatile lattice model of self-assembly, before applying our approach to more general structures such as molecules and protein complexes. In further work we show that genetic algorithms can be used in conjunction with our lattice model to answer questions about the emergence of symmetry and modularity in biological evolution.

In our most recent contributions on this topic we also study non-deterministic self-assembly in this lattice model. We show that even very simple non-deterministic two-tile sets can exhibit a wide variety of concentration-dependent growth behaviours. Furthermore we also demonstrate, both computationally and experimentally, that asymmetric interactions can limit the growth of such non-deterministic tile sets.

Network analysis of chemical flavour compounds
(Flavour 2013; Scientific Reports 2011)
Using network analysis we investigate the widespread hypothesis that foods with compatible flavours share chemical flavour compounds. Until now this hypothesis has relied on anecdotal rather than quantitative evidence. We construct a bipartite network of flavour compounds and ingredients, and compare it to large recipe data sets. This reveals that the shared compound hypothesis holds in some regional cuisines but not in others. More generally our analysis demonstrates how the type of large-scale data analysis that has transformed biology in recent years can lead to new results in other fields, such as food science.

Our article in Scientific Reports was the most downloaded article across all Nature Publishing Group journals in December 2011, exceeding 100,000 PDF downloads and HTML page views in the first four weeks following publication. It also received attention from the Scientific American, Nature News, New Scientist, The Huffington Post, The Technology Review, BioTechniques, and Ingeniøren, among others. A poster of the network between food ingredients can be downloaded here.

In the context of this work I also organised a Royal Society International Scientific Seminar in 2014, bringing together a wide range of experts including computational scientists, food scientists, neuroscientists, and chefs to discuss the impact of data science on food consumption and culinary culture.

Power graph compression of networks reveals dominant relationships
(Scientific Reports 2014; Molecular BioSystems 2013; see also Nature 2015)
We show that compression of complex networks into power graphs with freely overlapping power nodes allows us to detect dominant connectivity patterns in a wide range of different networks. This approach can be applied to undirected, directed and bipartite networks such as social networks, food webs and recipe-ingredient networks. When applied to genetic transcription networks we can assign meaning to power nodes by using GO term enrichment, which reveals that functional modules in genetic transcription networks are highly overlapping.

This method has also been used to map the functional organisation of the gene regulatory network in Arabidopsis responsible for xylem specification and secondary wall biosynthesis (Nature 2015).

Pattern detection in microarray data
(Science 2010; PLOS One 2008; Bioinformatics 2006)
Over the last decade, microarrays have generated an unprecedented amount of genetic expression data. Here we introduce an approach for detecting statistically significant patterns in these datasets without making prior assumptions about the nature of the pattern. This method is based on concepts from Algorithmic Information Theory.

I am also interested in genome statistics, Boolean networks, natural language processing, and Gaussian processes, among other things, and am co-organiser of the Cambridge Networks Network meetings. Past research interests of mine include quantum measurement and molecular dynamics.


research | publications | lectures | people | links |


A. S. Fokas, D. J. Cole, S. E. Ahnert, A. W. Chin
Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis
Scientific Reports 6, 33213 (2016)

S. Tesoro, K. Göpfrich, T. Kartanas, U. F. Keyser, S. E. Ahnert
Nondeterministic self-assembly with asymmetric interactions
Physical Review E 94, 022404 (2016)

S. E. Ahnert, T. M. A. Fink
Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
Journal of the Royal Society Interface 13, 20160179 (2016)

S. Tesoro, S. E. Ahnert
Nondeterministic self-assembly of two tile types on a lattice
Physical Review E 93, 042412 (2016) - selected as Editors' Suggestion

S. F. Greenbury, S. Schaper, S. E. Ahnert, A. A. Louis
Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability
PLOS Computational Biology 12(3): e1004773 (2016)

S. E. Ahnert, J. A. Marsh, H. Hernandez, C. V. Robinson, S. A. Teichmann
Principles of assembly reveal a periodic table of protein complexes
Science 350, 1331 (2015)

S. F. Greenbury, S. E. Ahnert
The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps
Journal of The Royal Society Interface 12, 20150724 (2015)

R. Ahnert, S. E. Ahnert
Protestant letter networks in the reign of Mary I: A quantitative approach
English Literary History 82, 1 (2015)

J. Marsh, H. Rees, S. E. Ahnert, S. A. Teichmann
Structural and evolutionary versatility in protein complexes with uneven stoichiometry
Nature Communications 6, 6394 (2015)

M. Taylor-Teeples, L. Lin, M. de Lucas M, G. Turco, T. W. Toal, A. Gaudinier, N. F. Young, G. M. Trabucco, M. T. Veling, R. Lamothe, P. P. Handakumbura, G. Xiong, C. Wang, J. Corwin, N. Tsoukalas, L. Zhang, D. Ware, M. Pauly, D. J. Kliebenstein, K. Dehesh, I. Tagkopoulos, G. Breton, J. Pruneda-Paz, S. E. Ahnert, S. A. Kay, S. P. Hazen, S. M. Brady
An Arabidopsis Gene Regulatory Network for Xylem Specification and Secondary Wall Biosynthesis
Nature 517, 571 (2015)

S. Shin, S. E. Ahnert, J. Park
Ranking Competitors Using Degree-Neutralized Random Walks
PLOS ONE 9(12): e113685 (2014)

G. F. Chami, S. E. Ahnert, M. J. Voors, A. A. Kontoleon
Social Network Analysis Predicts Health Behaviours and Self-Reported Health in African Villages
PLOS ONE 9(7): e103500 (2014)

R. Ahnert, S. E. Ahnert
A community under attack: Protestant letter networks in the reign of Mary I
Leonardo 47, 275 (2014)

S. E. Ahnert
Generalised power graph compression reveals dominant relationship patterns in complex networks
Scientific Reports 4, 4385 (2014)

S. F. Greenbury, I. G. Johnston, A. A. Louis, S. E. Ahnert
A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure
Journal of The Royal Society Interface 11, 20140249 (2014)

S. E. Ahnert
Power graph compression reveals dominant relationships in genetic transcription networks
Molecular BioSystems 9, 2681 (2013)

D. Garlaschelli, S. E. Ahnert, T. Fink, G. Caldarelli
Low-Temperature Behaviour of Social and Economic Networks
Entropy 15, 3148 (2013)

Y.-Y. Ahn, S. E. Ahnert
The Flavor Network
Leonardo 46, 272 (2013)

J. A. Marsh, H. Hernandez, Z. Hall, S. E. Ahnert, T. Perica, C. V. Robinson, S. A. Teichmann
Protein complexes are under evolutionary selection to assemble via ordered pathways
Cell 153, 461 (2013)

E. K. Towlson, P. Vertes, S. E. Ahnert, W. Schafer, E. Bullmore
The rich club of the C. elegans neuronal connectome
Journal of Neuroscience 33, 6380 (2013)

S. E. Ahnert
Network analysis and data mining in food science: the emergence of computational gastronomy
Flavour 2:4 (2013)

T. Perica, J. A. Marsh, F. L. Sousa, E. Natan, L. J. Colwell, S. E. Ahnert, S. A. Teichmann
The emergence of protein complexes: quaternary structure, dynamics and allostery
Biochem. Soc. Trans. 40, 475 (2012)

Y. Y. Ahn, S. E. Ahnert, J. P. Bagrow, A.-L. Barabasi
Flavor network and the principles of food pairing
Scientific Reports 1:196 (2011)

I. G. Johnston, S. E. Ahnert, J. P. K. Doye, A. A. Louis
Evolutionary dynamics in a simple model of self-assembly
Physical Review E 83, 066105 (2011)

S. M. Brady, L. Zhang, M. Megraw, N. J. Martinez, E. Jiang, C. S. Yi, W. Liu, A. Zeng, M. Taylor-Teeples, D. Kim, S. E. Ahnert, U. Ohler, D. Ware, A. J. M. Walhout, P. N. Benfey
A stele-enriched gene regulatory network in the Arabidopsis root
Molecular Systems Biology, 7:459 (2011)

M. A. Moreno-Risueno, J. M. Van Norman, A. Moreno, J. Zhang, S. E. Ahnert, P. N. Benfey
Oscillating Gene Expression Determines Competence for Periodic Arabidopsis Root Branching
Science 329, 1306 (2010)

S. E. Ahnert, I. G. Johnston, T. M. A. Fink, J. P. K. Doye, A. A. Louis
Self-assembly, modularity and physical complexity
Physical Review E 82, 026117 (2010)

D. A. Orlando, S. M. Brady, T. M. A. Fink, P. N. Benfey, S. E. Ahnert
Detecting separate time scales in genetic expression data
BMC Genomics 11:381 (2010)

S. E. Ahnert, B. A. N. Travencolo, L. da Costa Fontoura
Connectivity and dynamics of neuronal networks as defined by the shape of individual neurons
New Journal of Physics 11, 103053 (2009)

J. B. Coe, S. E. Ahnert, T. M. A. Fink
When are cellular automata random?
Europhysics Letters 84, 50005 (2008)

S. E. Ahnert, S. A. Teichmann
Networks for all
Genome Biology 9, 324 (2008)

S. E. Ahnert, T. M. A. Fink
Clustering signatures classify directed networks
Physical Review E 78, 036112 (2008)

T. M. A. Fink, J. B. Coe, S. E. Ahnert
Single-elimination competition
Europhysics Letters 83, 60010 (2008)

M.-L. Dequeant, S. E. Ahnert, H. Edelsbrunner, T. M. A. Fink, Y. Mileyko, J. Morton, A. R. Mushegian, L. Pachter, M. Rowicka, A. Shiu, B. Sturmfels, O. Pourquie
Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock
PLOS ONE 3(8): e2856 (2008)

S. E. Ahnert, D. Garlaschelli, T. M. A. Fink, G. Caldarelli
Applying weighted network measures to microarray distance matrices
Journal of Physics A 41, 224011 (2008)

S. E. Ahnert, T. M. A. Fink, A. Zinovyev
How much non-coding DNA do eukaryotes require?
Journal of Theoretical Biology 252, 587 (2008)

S. E. Ahnert, D. Garlaschelli, T. M. A. Fink, G. Caldarelli
An ensemble approach to the analysis of weighted networks
Physical Review E 76, 016101 (2007)

S. E. Ahnert, K. Willbrand, F. C. S. Brown, T. M. A. Fink
Unbiased pattern detection in microarray data series
Bioinformatics 22, 1471 (2006)

S. E. Ahnert, M. C. Payne
All possible bipartite positive-operator-value measurements of two-photon polarization states
Physical Review A 73, 022333 (2006)

S. E. Ahnert, M. C. Payne
General implementation of all possible positive-operator-value measures of single photon polarization states
Physical Review A 71, 012330 (2005)

S. E. Ahnert, M. C. Payne
Linear optics implementation of weak values in Hardy's paradox
Physical Review A 70, 042102 (2004)

S. E. Ahnert, M. C. Payne
Weak measurement of the arrival times of single photons and pairs of entangled photons
Physical Review A 69, 042103 (2004)

S. E. Ahnert, M. C. Payne
Nonorthogonal projective positive-operator-value measurement of photon polarization states with unit probability of success
Physical Review A 69, 012312 (2004)


research | publications | lectures | people | links |


I have given two graduate lecture courses on the following topics:

Complex Networks - Slides can be found here.

Quantum Information Theory - Lecture notes can be found here.


research | publications | lectures | people | links |

Current students:

Will Grant (MPhil 2015-16, PhD)
Alexander Leonard (PhD)
Salvatore Tesoro (PhD)
Pascal Grobecker (Part III)

Former students:

Emma Towlson (PhD 2011-15)
Sam Greenbury (PhD 2010-14)
Giles Barton-Owen (summer student, 2014)
Laura Imperatori (summer student, 2013)
Robert Baldock (summer student, 2010)

Some of my collaborators, past and present:

Yong-Yeol Ahn
Albert-Laszlo Barabasi
Siobhan Brady
Ed Bullmore
Guido Caldarelli
Gabor Csanyi
Thomas Fink
Iain Johnston
Ard Louis
Mike Payne
Sarah Teichmann
Andrei Zinovyev


research | publications | lectures | people | links |

Links to pages on various scientific and non-scientific topics.

Imbrella - A free and invisible umbrella
How to play Go on a Hypercube
John Baez's Homepage
The Chocolate Revolution
The biggest number
The Clay Millenium Prize
The Klein Bottle Shop
The Complexity Zoo
Non-Transitive Dice
Non-Transitive Lizards
'Math In LaTeX'
The CSS Zen Garden
The Simulation Argument
Minds, Machines and Gödel by John Lucas
Robert J. Lang's Origami Designs
The elgooG Google mirror
Iocaine Powder
57 Optical Illusions
Puzzles


contact

TCM Group
Cavendish Laboratory
JJ Thomson Avenue
Cambridge CB3 0HE
United Kingdom

email: sea31@cam.ac.uk
phone: +44 (0)1223 331137

recent publications

Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis
Scientific Reports 6, 33213 (2016)

Nondeterministic self-assembly with asymmetric interactions
Physical Review E 94, 022404 (2016)

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
Journal of the Royal Society Interface 13, 20160179 (2016)

Nondeterministic self-assembly of two tile types on a lattice
Physical Review E 93, 042412 (2016)

Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability
PLOS Computational Biology 12(3): e1004773 (2016)

Principles of assembly reveal a periodic table of protein complexes
Science 350, 1331 (2015)

The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps
Journal of The Royal Society Interface 12, 20150724 (2015)

Protestant letter networks in the reign of Mary I:
A quantitative approach

English Literary History 82, 1 (2015)

Structural and evolutionary versatility in protein complexes with uneven stoichiometry
Nature Communications 6, 6394 (2015)

An Arabidopsis Gene Regulatory Network for Xylem Specification and Secondary Wall Biosynthesis
Nature 517, 571 (2015)

[full publications list]