Publications

For a full list see below or go to Google Scholar, Research Gate, Orcid
Pre-prints are here or on Arxiv and Biorxiv

Highlights

Environmental fluctuations explain the universal decay of species-abundance correlations with phylogenetic distance

We identify a novel macroecological law relating mean pairwise correlation with genetic similarity and show that fluctuations of shared environmental factors are responsible for such a universal pattern.

M. Sireci, M.A. Muñoz, and J. Grilli
PNAS. 120 (37) e2217144120. 2023

A macroecological description of alternative stable states reproduces intra-and inter-host variability of gut microbiome

A model with environmental stochasticity and alternative stable states reproduces variability in the human gut microbiome.

S. Zaoli, J. Grilli
SciAdv. 7 (43), eabj2882. 2021

News: ICTP: news highlights

Threshold accumulation of a constitutive protein explains E. coli cell division behavior in nutrient upshifts

We monitor single-cell growth division upon nutrient changes and we discriminate among fundamentally different mechanisms of cell-division control.

M. Panlilio, J. Grilli, G. Tallarico, I. Iuliani, B. Sclavi, P. Cicuta, M. Cosentino Lagomarsino
PNAS. 118 (18) e2016391118. 2021

Macroecological laws describe variation and diversity in microbial communities

Three macroecological laws quantitatively characterize the fluctuation of species presence and abundance across microbial communities and over time.

J. Grilli
NatComm. 11, 4743. 2020

News: ICTP: news highlights.

Higher-order interactions stabilize dynamics in competitive network models

Although higher-order interactions have been studied for decades, their role in shaping ecological communities is still unclear. The inclusion of higher-order interactions stabilizes dynamics, making species coexistence robust to the perturbation of both population abundance and parameter values.

J. Grilli, G. Barabás, M.J. Michalska-Smith, and S. Allesina
Nature. 548, 210–213. 2017

News: Nature: News&Views, Nature Eco&Evo: Behind the paper, Computation institute, Science Life, Phys.org.

Statistical mechanics of ecological systems: neutral theory and beyond

The simplest theories often have much merit and many limitations, and, in this vein, the value of neutral theory (NT) of biodiversity has been the subject of much debate over the past 15 years. Here we review the quantitative aspects of NT, its extensions, what its successes are, and what important problems remain unresolved

S. Azaele, S. Suweis, J. Grilli, I. Volkov, J.R. Banavar, and A. Maritan
RMP. 88, 035003. 2016

Preprints

W.R. Shoemaker, A. Sanchez, J. Grilli
Macroecological laws in experimental microbial systems
2023 - bioRxiv

W.R. Shoemaker, J. Grilli
Macroecological patterns in coarse-grained microbial communities
2023 - bioRxiv

S. Pompei, E. Bella, J.S. Weitz, J. Grilli, M. Cosentino Lagomarsino
Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps
2023 - bioRxiv

L. Fant, I. Macocco, J. Grilli
Eco-evolutionary dynamics lead to functionally robust and redundant communities
2021 - bioRxiv

M. Adorisio, J. Grilli, S. Suweis, S. Azaele, J.R. Banavar, and A. Maritan
Spatial maximum entropy modeling from presence/absence tropical forest data
2014 - arXiv

Full List

[47] M. Sireci, M.A. Muñoz, and J. Grilli
Environmental fluctuations explain the universal decay of species-abundance correlations with phylogenetic distance
Proceedings of the National Academy of Sciences, 120 (37) e2217144120. 2023
bioRxiv - - -

[46] A. Mazzolini, J. Grilli
Universality of evolutionary trajectories under arbitrary forms of self-limitation and competition
Physical Review E, 108, 034406. 2023
bioRxiv - -

[45] L. Fant, O. Mazzarisi, E. Panizon, J. Grilli
Stable cooperation emerges in stochastic multiplicative growth
Physical Review E, 108, L012401. 2023
arXiv - - -

[44] J. Grilli
Keystone intransitive loops
Proceedings of the National Academy of Sciences, 120 (17) e2304170120 [commentary]. 2023
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[43] I. Macocco, A. Glielmo, J. Grilli, A. Laio
Intrinsic dimension estimation for discrete metrics
Physical Review Letters, 130, 067401. 2023
arXiv - - -

[42] R.E. Szabo, S. Pontrelli, J. Grilli, J.A. Schwartzman, S. Pollak, U. Sauer, O.X. Cordero
Historical contingencies and phage induction diversify bacterioplankton communities at the microscale
Proceedings of the National Academy of Sciences, 119 (30) e2117748119. 2022
bioRxiv - - -

[41] M. Cosentino Lagomarsino, G. Pacifico, V. Firmano, E. Bella, P. Benzoni, J. Grilli, F. Bassetti, F. Capuani, P. Cicuta, and M. Gherardi
Remote teaching data-driven physical modeling through a COVID-19 data challenge
European Journal of Physics, . 2022
arXiv - -

[40] L. Calabrese, J. Grilli, M. Osella, C.P. Kempes, M. Cosentino Lagomarsino, L. Ciandrini
Protein degradation sets the fraction of active ribosomes at vanishing growth
Plos Computational Biology, 18(5): e1010059. 2022
bioRxiv - - -

[39] S. Zaoli, J. Grilli
The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities
Plos Computational Biology, 18(4):e1010043. 2022
bioRxiv - - -

[38] F. Buke, J. Grilli, M. Cosentino Lagomarsino, G. Bokinsky, S.J. Tans
ppGpp is a bacterial cell size regulator
Current Biology, 32(4):870-877. 2022
bioRxiv - - -

[37] F. de Castro, S.M. Adl, S. Allesina, R.D. Bardgett, T. Bolger, J.J. Dalzell, M. Emmerson, T. Fleming, D. Garlaschelli, J. Grilli, S.E. Hannula, F. de Vries, Z. Lindo, A.G. Maule, M. Öpik, M.C. Rillig, S.D. Veresoglou, D.H. Wall, T. Caruso
Local stability properties of complex, species-rich soil food webs with functional block structure
Ecology and Evolution, 00:1–12 (2021). 2021
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[36] S. Zaoli, J. Grilli
A macroecological description of alternative stable states reproduces intra-and inter-host variability of gut microbiome
Science Advances, 7 (43), eabj2882. 2021
bioRxiv - - -

[35] L. Descheemaeker, J. Grilli, S. de Buyl
Heavy-tailed abundance distributions from stochastic Lotka-Volterra models
Physical Review E, 104, 034404. 2021
bioRxiv - - -

[34] M. Panlilio, J. Grilli, G. Tallarico, I. Iuliani, B. Sclavi, P. Cicuta, M. Cosentino Lagomarsino
Threshold accumulation of a constitutive protein explains E. coli cell division behavior in nutrient upshifts
Proceedings of the National Academy of Sciences, 118 (18) e2016391118. 2021
bioRxiv - - -

[33] J. Grilli
Macroecological laws describe variation and diversity in microbial communities
Nature Communications, 11, 4743. 2020
bioRxiv - - -

[32] K. Jovic, J. Grilli, M.G. Sterken, J.A.G. Riksen, B.L. Snoek, S. Allesina, J.E. Kammenga
Transcriptome dynamics predict thermotolerance in Caenorhabditis elegans
BMC Biology, 17, 102. 2019
bioRxiv - - -

[31] C. Tu, S. Suweis, J. Grilli, M. Formentin, and A. Maritan
Reconciling cooperation, biodiversity and stability in complex ecological communities
Scientific Reports, 9, 5580. 2019
arXiv - - -

[30] G. Micali, J. Grilli, M. Osella, and M. Cosentino Lagomarsino
Concurrent processes set E. coli cell division
Science Advances, 4, eaau3324. 2018
bioRxiv - - -

[29] G. Micali, J. Grilli, J. Marchi, M. Osella, and M. Cosentino Lagomarsino
Dissecting the control mechanisms for DNA replication and cell division in E. coli
Cell Reports, 25,3:761-771.E4. 2018
bioRxiv - - - -

[28] J.N. Pruitt, A. Berdahl, C. Riehl, N. Pinter-Wollman, H.V. Moeller, E.G. Pringle, L.M. Aplin, E.J.H. Robinson, J. Grilli, P. Yeh, V.M. Savage, M.H. Price, J. Garland, I.C. Gilby, M. C. Crofoot, G.N. Doering, and E.A. Hobson
Social tipping points in animal societies
Proceedings of the Royal Society B, 285:20181282. 2018
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[27] T. Gibbs, J. Grilli, T. Rogers, and S. Allesina
The effect of population abundances on the stability of large random ecosystems
Physical Review E, 98, 022410. 2018
arXiv - - - -

[26] C. Cadart, S. Monnier, J. Grilli, P.J. Sáez, N. Srivastava, R. Attia, E. Terriac, B. Baum, M. Cosentino Lagomarsino, and M. Piel
Size control in mammalian cells involves modulation of both growth rate and cell cycle duration
Nature Communications, 9:3275. 2018
bioRxiv - - -

[25] J. Grilli, C. Cadart, G. Micali, M. Osella, and M. Cosentino Lagomarsino
The empirical fluctuation pattern of E. coli division control
Frontiers in Microbiology, 9, 1541. 2018
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[24] A. Mazzolini, J. Grilli, E. De Lazzari, M. Osella, M. Cosentino Lagomarsino, and M. Gherardi
Zipf and Heaps laws from dependency structures in component systems
Physical Review E, 98, 012315. 2018
arXiv - - - -

[23] C.A. Serván, J.A. Capitán, J. Grilli, K.E. Morrison, and S. Allesina
Coexistence of many species in random ecosystems
Nature Ecology & Evolution, 2, 1237–1242. 2018
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[22] K. Jovic, M.G. Sterken, J. Grilli, R.P.J. Bevers, M. Rodriguez, J.A.G. Riksen, S. Allesina, J.E. Kammenga, and B.L. Snoek
Temporal dynamics of gene expression in heat-stressed Caenorhabditis elegans
Plos One, 2(12), e0189445. 2017
bioRxiv - - - -

[21] J. Grilli, G. Barabás, M.J. Michalska-Smith, and S. Allesina
Higher-order interactions stabilize dynamics in competitive network models
Nature, 548, 210–213. 2017
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[20] J. Grilli and S. Allesina
Last name analysis of mobility, gender imbalance, and nepotism across academic systems
Proceedings of the National Academy of Sciences, 114(29):7600-7605. 2017
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[19] C. Tu, J. Grilli, F. Schuessler, and S. Suweis
Collapse of resilience patterns in generalized Lotka-Volterra dynamics and beyond
Physical Review E, 95, 062307. 2017
arXiv - - - -

[18] E. De Lazzari, J. Grilli, S. Maslov, and M. Cosentino Lagomarsino
Family-specific scaling laws in bacterial genomes
Nucleic Acids Research, 45(13):7615-7622. 2017
arXiv - - - -

[17] J. Grilli, M. Osella, A.S. Kennard, and M. Cosentino Lagomarsino
Relevant parameters in models of cell division control
Physical Review E, 95, 032411. 2017
arXiv - - - -

[16] J. Grilli, M. Adorisio, S. Suweis, G. Barabás, J.R. Banavar, S. Allesina, and A. Maritan
Feasibility and coexistence of large ecological communities
Nature Communications, 8:14389. 2017
arXiv - - - -

[15] S. Azaele, S. Suweis, J. Grilli, I. Volkov, J.R. Banavar, and A. Maritan
Statistical mechanics of ecological systems: neutral theory and beyond
Review of Modern Physics, 88, 035003. 2016
arXiv - - -

[14] J. Grilli, T. Rogers, and S. Allesina
Modularity and stability in ecological communities
Nature Communications, 7:12031. 2016
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[13] J. Hidalgo, J. Grilli, S. Suweis, A. Maritan, and M.A. Muñoz
Cooperation, competition and the emergence of criticality in communities of adaptive systems
Journal of Statistical Mechanics: Theory and Experiment, 2016(3):033203. 2016
arXiv - - -

[12] A.S. Kennard, M. Osella, A. Javer, J. Grilli, P. Nghe, S. Tans, P. Cicuta, and M. Cosentino Lagomarsino
Individuality and universality in the growth-division laws of single E. coli cells
Physical Review E, 93, 012408. 2016
arXiv - - - -

[11] S. Suweis, J. Grilli, J.R. Banavar, S. Allesina, and A. Maritan
Effect of localization on the stability of mutualistic ecological networks
Nature Communications, 6:10179. 2015
bioRxiv - - - -

[10] S. Allesina, J. Grilli, G. Barabás, S. Tang, J. Aljadeff, and A. Maritan
Predicting the stability of large structured food webs
Nature Communications, 6:7842. 2015
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[9] J. Grilli, G. Barabás, and S. Allesina
Metapopulation persistence in random fragmented landscapes
Plos Computational Biology, 11(5):e1004251. 2015
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[8] J. Hidalgo, J. Grilli, S. Suweis, M.A. Muñoz, J.R. Banavar, and A. Maritan
Information-based fitness and the emergence of criticality in living systems
Proceedings of the National Academy of Sciences, 111(28):10095-10100. 2014
arXiv - - - -

[7] J. Grilli, M. Romano, F. Bassetti, and M. Cosentino Lagomarsino
Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers
Nucleic Acids Research, 42(11):6850-6860. 2014
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[6] S. Suweis, J. Grilli, and A. Maritan
Disentangling the effect of hybrid interactions and of the constant effort hypothesis on ecological community stability
Oikos, 123(5):525-532. 2014
arXiv - - -

[5] J. Grilli, S. Suweis, and A. Maritan
Growth or reproduction: emergence of an evolutionary optimal strategy
Journal of Statistical Mechanics: Theory and Experiment, 2013(10):P10020. 2013
arXiv - - -

[4] J. Grilli, S. Azaele, J.R. Banavar, and A. Maritan
Absence of detailed balance in ecology
Europhysics Letters, 100:38002. 2012
arXiv - - -

[3] J. Grilli, S. Azaele, J.R. Banavar, and A. Maritan
Spatial aggregation and the species-area relationship across scales
Journal of Theoretical Biology, 313:87-97. 2012
arXiv - - - -

[2] L. Grassi, J. Grilli, and M. Cosentino Lagomarsino
Large-scale dynamics of horizontal transfers
Mobile Genetics Elements, 2(3):163-167. 2012
arXiv - - - -

[1] J. Grilli, B. Bassetti, S. Maslov, and M. Cosentino Lagomarsino
Joint scaling laws in functional and evolutionary categories in prokaryotic genomes
Nucleic Acids Research, 40(2):530-540. 2012
arXiv - - - -