Sofja Kovalevskaja Research Group: Structure of Evolution

Matteo Smerlak (Email)

+49 (0) 341 - 9959 - 546

+49 (0) 341 - 9959 - 658

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.2211098120

Fant, Lorenzo ; Mazzarisi, Onofrio ; Panizon, Emanuele and Jacopo Grilli: Stable cooperation emerges in stochastic multiplicative growth
In: Physical review / E, 108 (2023) 1, L012401
Bibtex DOI: 10.1103/PhysRevE.108.L012401 ARXIV:
OA: gruen

Ippolito, 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, 35 (2023) 15, 221157
Bibtex DOI: 10.1002/adma.202211157
OA: hybrid

Ramirez, 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:
OA: gold

Salahshour, Mohammad: Interaction between games give rise to the evolution of moral norms of cooperation
In: PLoS computational biology, 18 (2023) 9, e1010429
Bibtex DOI: 10.1371/journal.pcbi.1010429
OA: gold

Bräutigam, Camila and Matteo Smerlak: Diffusion approximations in population genetics and the rate of Muller's ratchet
OA: gruen

Burger, Joseph R. ; Okie, Jordan G. ; Hatton, Ian A. ; Weinberger, Vanessa P. ; Shrestha, Munik ; Liedtke, Kyra J. ; Be, Tam ; Cruz, Austin R. ; Feng, Xiao ; Hinojo-Hinojo, Cesar ; Kibria, Abu S. M. G. ; Ernst, Kacey C. and Brian J. Enquist: Global city densities : re-examining urban scaling theory
In: Frontiers in conservation science, 3 (2022), 879934
Bibtex DOI: 10.3389/fcosc.2022.879934
OA: gold

Corberi, 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:
OA: gruen

Kenmoe, 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:
OA: gruen

Nono, 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-w
OA: gold

Opuu, Vaitea ; Nono, Cyrille Merleau ; Messow, Vincent and Matteo Smerlak: RAFFT : Efficient prediction of RNA folding pathways using the fast Fourier transform
OA: gold

Perkins, 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/s41467-022-32578-5
OA: gold

Salahshour, 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:
OA: gold

Smerlak, 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:
OA: gruen

Smerlak, Matteo and Carlo Rovelli: Put defence money into planetary emergencies, urge Nobel winners
In: Nature, 601 (2022), p. 318-318
Bibtex DOI: 10.1038/d41586-022-00096-5

Zadorin, 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:
OA: gruen

Biswas, 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:
OA: green

Charlat, 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:
OA: gold

Hatton, Ian A. ; Heneghan, Ryan F. ; Bar-On, Yinon M. and Eric D. Galbraith: The global ocean size spectrum from bacteria to whales
OA: gold

Mazzarisi, 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:
OA: hybrid

Nono, 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:
OA: gold

Salahshour, 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:
OA: gold

Salahshour, Mohammad: Freedom to choose between public resources promotes cooperation
OA: gold

Salahshour, 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:
OA: gold

Salahshour, 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.0254860
OA: gold

Salahshour, 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:
OA: gold

Schulz, Steven ; Boyer, Sébastien ; Smerlak, Matteo ; Cocco, Simona ; Monasson, Remi ; Nizak, Clément and Olivier Rivoire: Parameters and determinants of responses to selection in antibody libraries
OA: gold

Smerlak, Matteo: Intermittency as metastability : a predictive approach to evolution in disordered environments
OA: gruen

Smerlak, 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:
OA: gruen

Smerlak, Matteo: Neutral quasispecies evolution and the maximal entropy random walk
In: Science advances, 7 (2021) 16, eabb2376
Bibtex DOI: 10.1126/sciadv.abb2376
OA: gold

Zadorin, 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:
OA: gruen

Hatton, 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: 10.21685/2500-0578-2020-2-5
OA: green

Salahshour, Mohammad: Coevolution of cooperation and language
In: Physical review / E, 102 (2020) 4, 042409
Bibtex DOI: 10.1103/PhysRevE.102.042409
OA: hybrid

Tal, 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:
OA: hybrid

Tchappi, 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-y

Smerlak, 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:
OA: gruen

Tal, 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:
OA: gruen

Tal, 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:
OA: gruen

Granot, 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:
OA: gold

Tal, Omri: From typical sequences to typical genotype
In: Human heredity, 80 (2015) 3, p. 122-122
Bibtex DOI: 10.1159/000445228 ARXIV:
OA: gruen

Publications 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.)
New York : ACM, 2021. - P. 1027-1034
Bibtex DOI: 10.1145/3449639.3459280
OA: green

Hatton, Ian A.: What regulates growth across levels of organization?
In: Unsolved problems in ecology / Andrew Dobson... (eds.)
Princeton : Princeton University Press, 2020. - P. 203-217
Bibtex DOI: 10.1515/9780691195322

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.)
Setúbal (Portugal) : SCITEPRESS, 2020. - P. 143-148
Bibtex MIS-Preprint: 36/2020 DOI: 10.5220/0009582801430148 ARXIV:
OA: gruen

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: 10.1159/000360587

Pasemann, Frank ; Dieckmann, Ulf and Ulrich Steinmetz: Evolving structure and function of neurocontrollers
In: Proceedings of the 1999 Congress on Evolutionary Computation / CEC 99, July 6 - 9, 1999
Piscataway, NJ : IEEE Service Center, 1999
Bibtex MIS-Preprint: 27/1999

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/BFb0032588
OA: gruen


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:
OA: RepGruen
22.09.2023, 05:47