Sofja Kovalevskaja Research Group: Structure of Evolution
Head:
Matteo Smerlak (Email)
Phone:
+49 (0) 341 - 9959 - 546
Fax:
+49 (0) 341 - 9959 - 658
Address:
Inselstr. 22
04103 Leipzig
Institute publications of the group
Journal Articles
Chen, Kuang-Yu ; Karuppusamy, Jayaprakash ; O'Neill, Mary B. ; Opuu, Vaitea ; Bahin, Mathieu ; Foulon, Sophie ; Ibanez, Pablo ; Ozawa, Tatsuhiko ; van der Werf, Sylvie ; Nghe, Philippe ; Naffakh, Nadia ; Griffiths, Andrew and Catherine Isel:
High-throughput droplet-based analysis of influenza A virus genetic reassortment by
single-virus RNA sequencing
In: Proceedings of the National Academy of Sciences of the United States of America,
120 (2023) 6, e2211098120
Bibtex DOI: 10.1073/pnas.2211098120Ippolito, Stefano ; Urban, Francesca ; Zheng, Wenhao ; Mazzarisi, Onofrio ; Valentini, Cataldo ; Kelly, Adam G. ; Gali, Sai Manoj ; Bonn, Mischa ; Beljonne, David ; Corberi, Federico ; Coleman, Jonathan N. and Paolo Samori:
Unveiling charge transport mechanisms in electronic devices based on defect-engineered
MoS\(_2\) covalent networks
In: Advanced materials,
Vol. not yet known, pp. not yet known
Bibtex DOI: 10.1002/adma.202211157Ramirez, Maria Alejandra ; Smerlak, Matteo ; Traulsen, Arne and Jürgen Jost:
Diversity enables the jump towards cooperation for the Traveler's Dilemma
In: Scientific reports,
13 (2023), 1441
Bibtex MIS-Preprint: 30/2022 DOI: 10.1038/s41598-023-28600-5 ARXIV: https://arxiv.org/abs/2210.15971Bräutigam, Camila and Matteo Smerlak:
Diffusion approximations in population genetics and the rate of Muller's ratchet
In: Journal of theoretical biology,
550 (2022), 111236
Bibtex DOI: 10.1016/j.jtbi.2022.111236 ARXIV: https://arxiv.org/abs/2111.13344 LINK: https://www.biorxiv.org/content/10.1101/2021.11.25.469985v2 CODE: https://github.com/msmerlak/mullers-ratchetCorberi, Federico ; Cugliandolo, Leticia F. ; Espositio, Marco ; Mazzarisi, Onofrio and Marco Picco:
How many phases nucleate in the bidimensional Potts model?
In: Journal of statistical mechanics,
2022 (2022) 7, 073204
Bibtex DOI: 10.1088/1742-5468/ac7aa9 ARXIV: https://arxiv.org/abs/2102.01003Kenmoe, Maseim ; Kriemann, Ronald ; Smerlak, Matteo and Anton Zadorin:
A fast iterative algorithm for near-diagonal eigenvalue problems
In: SIAM journal on matrix analysis and applications,
43 (2022) 4, p. 1573-1598
Bibtex DOI: 10.1137/21M1401474 ARXIV: https://arxiv.org/abs/2012.14702Nono, Cyrille Merleau and Matteo Smerlak:
aRNAque : an evolutionary algorithm for inverse pseudoknotted RNA folding inspired
by Lévy flights
In: BMC bioinformatics,
23 (2022), 335
Bibtex DOI: 10.1186/s12859-022-04866-wOpuu, Vaitea ; Nono, Cyrille Merleau ; Messow, Vincent and Matteo Smerlak:
RAFFT : Efficient prediction of RNA folding pathways using the fast Fourier transform
In: PLoS computational biology,
Vol. not yet known, pp. not yet known
Bibtex DOI: 10.1371/journal.pcbi.1010448 ARXIV: https://www.biorxiv.org/content/10.1101/2021.07.02.450908v2 CODE: https://github.com/strevol-mpi-mis/RAFFTPerkins, Daniel M. ; Hatton, Ian A. ; Gauzens, Benoit ; Barnes, Andrew D. ; Ott, David ; Rosenbaum, Benjamin ; Vinagre, Catarina and Ulrich Brose:
Consistent predator-prey biomass scaling in complex food webs
In: Nature communications,
13 (2022), 4990
Bibtex DOI: 10.1038/s41467-022-32578-5Salahshour, Mohammad:
Interaction between games give rise to the evolution of moral norms of cooperation
In: PLoS computational biology,
Vol. not yet known, pp. not yet known
Bibtex DOI: 10.1371/journal.pcbi.1010429Salahshour, Mohammad ; Oberhauser, Vincent and Matteo Smerlak:
The cost of noise : stochastic punishment falls short of sustaining cooperation in
social dilemma experiments
In: PLOS ONE,
17 (2022) 3, e0263028
Bibtex DOI: 10.1371/journal.pone.0263028 ARXIV: https://arxiv.org/abs/2109.13547Smerlak, Matteo:
Perturbation theory without power series : iterative construction of non-analytic
operator spectra
In: epl,
140 (2022) 3, 32001
Bibtex DOI: 10.1209/0295-5075/ac9e72 ARXIV: http://arxiv.org/abs/2105.04972Smerlak, Matteo and Carlo Rovelli:
Put defence money into planetary emergencies, urge Nobel winners
In: Nature,
601 (2022), p. 318-318
Bibtex DOI: 10.1038/d41586-022-00096-5Zadorin, Anton:
Exact travelling solution for a reaction-diffusion system with a piecewise constant
production supported by a codimension-1 subspace
In: Communications on pure and applied analysis,
21 (2022) 5, p. 1567-1580
Bibtex DOI: 10.3934/cpaa.2022030 ARXIV: https://arxiv.org/abs/1906.00484Biswas, Niloy ; Etheridge, Alison and Aleksander Klimek:
The spatial Lambda-Fleming-Viot process with fluctuating selection
In: Electronic journal of probability,
26 (2021), 25
Bibtex DOI: 10.1214/21-EJP593 ARXIV: https://arxiv.org/abs/1802.08188Charlat, Sylvain ; Ariew, André ; Bourrat, Pierrick ; Ruiz, Maria Ferreira ; Heams, Thomas ; Huneman, Philippe ; Krishna, Sandeep ; Lachmann, Michael ; Lartillot, Nicolas ; Le Sergeant d'Hendecourt, Loius ; Malaterre, Christope ; Nghe, Philippe ; Rajon, Etienne ; Rivoire, Olivier ; Smerlak, Matteo and Zorana Zeravcic:
Natural selection beyond life? A workshop report
In: Life : open access journal,
11 (2021) 10, 1051
Bibtex DOI: 10.3390/life11101051 LINK: https://hal.inria.fr/hal-03418757/Hatton, Ian A. ; Heneghan, Ryan F. ; Bar-On, Yinon M. and Eric D. Galbraith:
The global ocean size spectrum from bacteria to whales
In: Science advances,
7 (2021) 46, eabh3732
Bibtex DOI: 10.1126/sciadv.abh3732 ARXIV: https://www.biorxiv.org/content/10.1101/2021.04.03.438320Mazzarisi, Onofrio ; Azevedo-Lopes, Amanda ; Arenzon, Jeferson J. and Federico Corberi:
Maximal diversity and Zipf's law
In: Physical review letters,
127 (2021) 12, 128301
Bibtex DOI: 10.1103/PhysRevLett.127.128301 ARXIV: https://arxiv.org/abs/2103.09143Nono, Cyrille Merleau ; Pénisson, Sophie ; Gerrish, Philip J. ; Elena, Santiago F. and Matteo Smerlak:
Why are viral genomes so fragile? The bottleneck hypothesis
In: PLoS computational biology,
17 (2021) 7, e1009128
Bibtex DOI: 10.1371/journal.pcbi.1009128 ARXIV: https://www.biorxiv.org/content/10.1101/2021.01.23.427881v1Salahshour, Mohammad:
Evolution of cooperation and consistent personalities in public goods games
In: Scientific reports,
11 (2021), 23708
Bibtex DOI: 10.1038/s41598-021-03045-w ARXIV: https://arxiv.org/abs/2010.05307Salahshour, Mohammad:
Freedom to choose between public resources promotes cooperation
In: PLoS computational biology,
17 (2021) 2, e1008703
Bibtex DOI: 10.1371/journal.pcbi.1008703 ARXIV: https://www.biorxiv.org/content/10.1101/2020.09.30.320382v1 CODE: https://zenodo.org/record/4294725Salahshour, Mohammad:
Evolution of cooperation in costly institutions exhibits Red Queen and Black Queen
dynamics in heterogeneous public goods
In: Communications biology,
4 (2021), 1340
Bibtex DOI: 10.1038/s42003-021-02865-w ARXIV: https://arxiv.org/abs/2102.11432Salahshour, Mohammad:
Evolution of prosocial punishment in unstructured and structured populations and in
the presence of antisocial punishment
In: PLOS ONE,
16 (2021) 8, e0254860
Bibtex DOI: 10.1371/journal.pone.0254860Salahshour, Mohammad and Shahin Rouhani:
Collective movement and collective information acquisition with signaling
In: Frontiers in physics,
9 (2021), 668283
Bibtex DOI: 10.3389/fphy.2021.668283 ARXIV: https://arxiv.org/abs/2010.14190Schulz, Steven ; Boyer, Sébastien ; Smerlak, Matteo ; Cocco, Simona ; Monasson, Remi ; Nizak, Clément and Olivier Rivoire:
Parameters and determinants of responses to selection in antibody libraries
In: PLoS computational biology,
17 (2021) 3, e1008751
Bibtex DOI: 10.1371/journal.pcbi.1008751 ARXIV: https://www.biorxiv.org/content/10.1101/712539v1 LINK: https://hal.archives-ouvertes.fr/hal-02322339Smerlak, Matteo:
Intermittency as metastability : a predictive approach to evolution in disordered
environments
In: epl,
134 (2021) 2, 28002
Bibtex DOI: 10.1209/0295-5075/134/28002 ARXIV: https://arxiv.org/abs/2009.03608Smerlak, Matteo:
Quasi-species evolution maximizes genotypic reproductive value (not fitness or flatness)
In: Journal of theoretical biology,
522 (2021), 110699
Bibtex DOI: 10.1016/j.jtbi.2021.110699 ARXIV: https://www.biorxiv.org/content/10.1101/2021.02.23.432496v1Smerlak, Matteo:
Neutral quasispecies evolution and the maximal entropy random walk
In: Science advances,
7 (2021) 16, eabb2376
Bibtex DOI: 10.1126/sciadv.abb2376Zadorin, Anton and Olivier Rivoire:
Sex as information processing : optimality and evolution
In: Physical review / E,
103 (2021) 6, 062413
Bibtex DOI: 10.1103/PhysRevE.103.062413 ARXIV: https://arxiv.org/abs/2102.05459Hatton, Ian A. and Eric D. Galbraith:
Commentary on ''Key ecological parameters of immotile versus locomotive life'' by
Gorshkov and Makarieva
In: Russian journal of ecosystem ecology,
5 (2020) 2, 5
Bibtex DOI: 10.21685/2500-0578-2020-2-5Salahshour, Mohammad:
Coevolution of cooperation and language
In: Physical review / E,
102 (2020) 4, 042409
Bibtex DOI: 10.1103/PhysRevE.102.042409Tal, Omri and Tat Dat Tran:
Adaptive bet-hedging revisited : considerations of risk and time horizon
In: Bulletin of mathematical biology,
82 (2020) 4, 50
Bibtex MIS-Preprint: 36/2019 DOI: 10.1007/s11538-020-00729-8 ARXIV: https://arxiv.org/abs/2003.06793Tchappi, Igor Haman ; Galland, Stéphane ; Kamla, Vivient Corneille ; Kamgang, Jean-Claude ; Nono, Cyrille Merleau and Hui Zhao:
Holonification model for a multilevel agent-based system : application to road traffic
In: Personal and ubiquitous computing,
23 (2019) 5/6, p. 633-651
Bibtex DOI: 10.1007/s00779-018-1181-ySmerlak, Matteo:
Natural selection as coarsening
In: Journal of statistical physics,
172 (2018) 1, p. 105-113
Bibtex DOI: 10.1007/s10955-017-1925-5 ARXIV: https://arxiv.org/abs/1707.05317Tal, Omri and Tat Dat Tran:
New perspectives on multilocus ancestry informativeness
In: Mathematical biosciences,
306 (2018), p. 60-81
Bibtex MIS-Preprint: 24/2018 DOI: 10.1016/j.mbs.2018.10.011 ARXIV: https://www.biorxiv.org/content/10.1101/273466v3Tal, Omri ; Tran, Tat Dat and Jacobus W. Portegies:
From typical sequences to typical genotypes
In: Journal of theoretical biology,
419 (2017), p. 159-183
Bibtex MIS-Preprint: 66/2016 DOI: 10.1016/j.jtbi.2017.02.010 ARXIV: https://www.biorxiv.org/content/10.1101/079491v2Granot, Yaron ; Tal, Omri ; Rosset, Saharon and Karl Skorecki:
On the apportionment of population structure
In: PLOS ONE,
11 (2016) 8, e0160413
Bibtex MIS-Preprint: 28/2016 DOI: 10.1371/journal.pone.0160413 ARXIV: https://www.biorxiv.org/content/10.1101/033852v4Tal, Omri:
From typical sequences to typical genotype
In: Human heredity,
80 (2015) 3, p. 122-122
Bibtex DOI: 10.1159/000445228 ARXIV: https://www.biorxiv.org/content/10.1101/079491v2Publications in Books and Conference Proceedings
Nono, Cyrille Merleau and Matteo Smerlak:
A simple evolutionary algorithm guided by local mutations for an efficient RNA design
In: GECCO '21 : proceedings of the genetic and evolutionary computation conference ; Lille
France 10 July, 2021- 14 July, 2021 / Francisco Chicano (ed.)
Bibtex DOI: 10.1145/3449639.3459280New York : ACM, 2021. - P. 1027-1034
Hatton, Ian A.:
What regulates growth across levels of organization?
In: Unsolved problems in ecology / Andrew Dobson... (eds.)
Bibtex DOI: 10.1515/9780691195322Princeton : Princeton University Press, 2020. - P. 203-217
Yamshchikov, Ivan P. ; Nono, Cyrille Merleau ; Samenko, Igor and Jürgen Jost:
It means more if it sounds good : yet another hypothesis concerning the evolution
of polysemous words
In: Proceedings of the 5th international conference on complexity, future information
systems and risk : COMPLEXIS 2020 ; May 8-9, 2020 ; Volume 1 / Reinhold Behringer... (eds.)
Bibtex MIS-Preprint: 36/2020 DOI: 10.5220/0009582801430148 ARXIV: https://arxiv.org/abs/2003.05758Setúbal (Portugal) : SCITEPRESS, 2020. - P. 143-148
Tal, Omri:
Quantifying the high-dimensional information of population structure
In: 42nd European Mathematical Genetics Meeting (EMGM) 2014, April 1-2, 2014, Cologne,
Germany : Abstracts
Basel : Karger, 2014
(Human Heredity ; 76 (2013) 2)
Bibtex DOI: 10.1159/000360587Pasemann, Frank ; Dieckmann, Ulf and Ulrich Steinmetz:
Evolving structure and function of neurocontrollers
Pasemann, Frank and Ulf Dieckmann:
Evolved neurocontrollers for pole-balancing
In: Biological and artificial computation : from neuroscience to technology ; International
Work-Conference on Artificial and Natural Neural Networks, IWANN'97 Lanzarote, Canary
Islands, Spain, June 4-6, 1997 proceedings / José Mira (ed.)
Berlin : Springer, 1997. - P. 1279-1287
(Lecture notes in computer science ; 1240)
Bibtex MIS-Preprint: 37/1997 DOI: 10.1007/BFb0032588Preprints
Fant, Lorenzo ; Mazzarisi, Onofrio ; Panizon, Emanuele and Jacopo Grilli:
Stable cooperation emerges in stochastic multiplicative growth
Nono, Cyrille Merleau and Matteo Smerlak:
An evolutionary algorithm for inverse RNA folding inspired by Levy flights
Opuu, Vaitea and Hélène Bret:
Investigating graph neural network for RNA structural embedding
Salahshour, Mohammad:
Predator-prey interactions give rise to scale-invariant ecosystems
Salahshour, Mohammad:
Playing soft with cooperators emerges as a moral norm and promotes cooperation in
evolutionary games
Kenmoe, Maseim ; Smerlak, Matteo and Anton Zadorin:
Dynamical perturbation theory for eigenvalue problems
Klimek, Aleksander and Tommaso Cornelis Rosati:
The spatial \(\lambda\)-Fleming-Viot process in a random environment
Salahshour, Mohammad:
The evolution of punishing institutions
Smerlak, Matteo:
Localization of neutral evolution : selection for mutational robustness and the maximal
entropy random walk
Chetwynd-Diggle, Jonathan and Aleksander Klimek:
Rare mutations in the spatial Lambda-Fleming-Viot model in a fluctuating environment
and SuperBrownian Motion
Smerlak, Matteo:
Effective potential reveals evolutionary trajectories in complex fitness landscapes
Academic Theses
Nono, Cyrille Merleau:
From RNA folding to inverse folding : a computational study
Dissertation, Universität Leipzig, 2023
Bibtex LINK: https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa2-834884