ESPCI web site
Publications
Google scholar listing of publications
Publications
Pavlinova, P., Lambert, C.N., Malaterre, C. and Nghe, P. (2023), Abiogenesis through gradual evolution of autocatalysis into template-based replication. FEBS Lett, 597: 344-379. https://doi.org/10.1002/1873-3468.14507
Leo, S.D., Marni, S., Plata, C.A., Fraccia, T.P., Smith, G.P., Maritan, A., et al. (2022) Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments PLOS Computational Biology. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010051
Tony Z. Jia, Tommaso Bellini, Noel Clark, Tommaso P. Fraccia; A liquid crystal world for the origins of life. (2022). Emerg Top Life Sci 6 (6): 557–569. doi: https://doi.org/10.1042/ETLS20220081
Soysal, U., Azevedo, P.N., Bureau, F., Aubry, A., Carvalho, M.S., Pessoa, A.C.S.N., et al. (2022) Freeze-Dried Microfluidic Monodisperse Microbubbles as a New Generation of Ultrasound Contrast Agents. Ultrasound in Medicine and Biology. https://www.umbjournal.org/article/S0301-5629(22)00120-X/abstract.
Ripoll, M., Martin, E., Enot, M., Robbe, O., Rapisarda, C., Nicolai, M.-C., et al. (2022) Optimal self-assembly of lipid nanoparticles (LNP) in a ring micromixer - Scientific Reports. Nature. https://www.nature.com/articles/s41598-022-13112-5
Ardré M, Doulcier G, Brenner N, Rainey PB. (2022). leader cell triggers end of lag phase in populations of Pseudomonas fluorescens. MicroLife FEMS doi:https://10.1093/femsml/uqac022.
Unterberger J, Nghe P. (2022). Stoechiometric and dynamical autocatalysis for diluted chemical reaction networks. Journal of Mathematical Biology. doi:https://10.1007/s00285-022-01798-0.
Malaterre, C., Jeancolas, C., & Nghe, P. (2022). The Origin of Life: What Is the Question?. Astrobiology.
Sakhawoth, Y., Dupire, J., Leonforte, F., Chardon, M., Monti, F., Tabeling, P., et al. (2021) Real time observation of the interaction between aluminium salts and sweat under microfluidic conditions - Scientific Reports. Nature. https://www.nature.com/articles/s41598-021-85691-8
Charlat, S., Ariew, A., Bourrat, P., Ferreira Ruiz, M., Heams, T., Huneman, P., Krishna S., Lachmann M., Lartillot N., Le Sergeant d’Hendecourt L., Malaterre C., Nghe P., Rajon E., Rivoire O., Smerlak M., Zeravcic Z., (2021). Natural Selection beyond Life? A Workshop Report, Life 11 (10), 1051
Jeancolas, C., Matsubara, Y. J., Vybornyi, M., Lambert, C. N., Blokhuis, A., Alline, T., Griffiths, A. D., Ameta S., Krishna S., Nghe P. (2021). RNA diversification by a self-reproducing ribozyme revealed by deep sequencing and kinetic modelling. Chemical Communications
DOI:doi:10.1039/d1cc02290c
Ameta, S., Arsène, S., Foulon, S., Saudemont, B., Clifton, B. E., Griffiths, A. D., & Nghe, P. (2021). Darwinian properties and their trade-offs in autocatalytic RNA reaction networks. Nature Communications, 12, 842
DOI:10.1101/726497
Garneret, P., Coz, E., Martin, E., Manuguerra, J.-C., Brient-Litzler, E., Enouf, V., … Tabeling, P. (2021). Performing point-of-care molecular testing for SARS-CoV-2 with RNA extraction and isothermal amplification. PLOS ONE, 16(1), e0243712. doi:10.1371/journal.pone.0243712
Sakhawoth, Y., Dupire, J., Leonforte, F., Chardon, M., Monti, F., Tabeling, P., … Galey, J.-B. (2021). Real time observation of the interaction between aluminium salts and sweat under microfluidic conditions. Scientific Reports, 11(1). doi:10.1038/s41598-021-85691-8
Porto Santos, T., Cejas, C. M., Cunha, R. L., & Tabeling, P. (2021). Unraveling driving regimes for destabilizing concentrated emulsions within microchannels. Soft Matter, 17(7), 1821–1833. doi:10.1039/d0sm01674h
Francia, T. P., Zanchetta, G. (2021). Liquid–liquid crystalline phase separation in biomolecular solutions. Current Opinion in Colloid & Interface Science https://www.sciencedirect.com/science/article/pii/S1359029421000844
Jia, T. Z., & Fraccia, T. P. (2020). Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution. Crystals, 10(11), 964. DOI:10.3390/cryst10110964
Fraccia, T. P., & Jia, T. Z. (2020). Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides. ACS Nano, 14(11), 15071–15082. doi:10.1021/acsnano.0c05083
Lucchetti, L., Fraccia, T. P., Nava, G., Turiv, T., Ciciulla, F., Bethge, L., Klussmann, S., Lavrentovich, O. D., & Bellini, T. (2020). Elasticity and Viscosity of DNA Liquid Crystals. ACS Macro Letters, 9(7), 1034–1039. DOI:10.1021/acsmacrolett.0c00394
Jeancolas, C., Malaterre, C., & Nghe, P. (2020). Thresholds in origin of life scenarios. Iscience, 23(11), 101756.
doi:10.1016/j.isci.2020.101756
Kogenaru, M.*, Nghe, P.*, Poelwijk, F. J., & Tans, S. J. (2020). Predicting Evolutionary Constraints by Identifying Conflicting Demands in Regulatory Networks. Cell Systems, 10(6), 526–534.e3.
DOI:10.1016/j.cels.2020.05.004
Blokhuis, A., Lacoste, D., & Nghe, P. (2020). Universal motifs and the diversity of autocatalytic systems. Proceedings of the National Academy of Sciences, 117(41), 25230-25236.
DOI:10.1073/pnas.2013527117
Kemble, H., Eisenhauer, C., Couce, A., Chapron, A., Magnan, M., Gautier, G., Le Nagard H., Nghe, P.* & Tenaillon, O.* (2020). Flux, toxicity and protein expression costs shape genetic interaction in a metabolic pathway. Science Advances 6 (23), eabb2236
DOI:10.1126/sciadv.abb2236
Woronoff, G.*, Nghe, P.*, Baudry, J., Boitard, L., Braun, E., Griffiths, A. D., & Bibette, J. (2020). Metabolic cost of rapid adaptation of single yeast cells. Proceedings of the National Academy of Sciences, 117(20), 10660-10666.
DOI:10.1101/564419
Nghe, P., de Vos, M. G., Kingma, E., Kogenaru, M., Poelwijk, F. J., Laan, L., & Tans, S. J. (2020). Predicting Evolution Using Regulatory Architecture. Annual review of biophysics, 49, 181-197.
DOI:10.1146/annurev-biophys-070317-032939
Blokhuis, A., Nghe, P., Peliti, L., & Lacoste, D. (2020). The generality of transient compartmentalization and its associated error thresholds. Journal of theoretical biology, 487, 110110.
DOI:10.1016/j.jtbi.2019.110110
Porto Santos, T., Cunha, R. L., Tabeling, P., & Cejas, C. M. (2020). Colloidal particle deposition on microchannel walls, for attractive and repulsive surface potentials. Physical Chemistry Chemical Physics, 22(30), 17236–17246. doi:10.1039/d0cp01999b
Russo, M., Amara, Z., Fenneteau, J., Chaumont-Olive, P., Maimouni, I., Tabeling, P., & Cossy, J. (2020). Stable liquid foams from a new polyfluorinated surfactant. Chemical Communications, 56(43), 5807–5810. doi:10.1039/d0cc02182b
https://doi.org/10.1039%2Fd0cc02182b
Maimouni, I., Cejas, C. M., Cossy, J., Tabeling, P., & Russo, M. (2020). Microfluidics Mediated Production of Foams for Biomedical Applications. Micromachines, 11(1), 83. doi:10.3390/mi11010083
Todisco, M., Smith, G. P., & Fraccia, T. P. (2019). Liquid Crystal ordering of DNA Dickerson Dodecamer duplexes with different 5’- Phosphate terminations. Molecular Crystals and Liquid Crystals, 683(1), 69–80. DOI:10.1080/15421406.2019.1581706
Ardré, M., Dufour, D., Rainey, P. B. (2019). Causes and consequences of cellulose production by Pseudomonas fluorescens SBW25 at the air-liquid interface. Journal of Bacteriology.
DOI:10.1101/538561
Deyell, M., Ameta, S., & Nghe, P. (2019). Large scale control and programming of gene expression using CRISPR. Seminars in cell & developmental biology 96, 124-132. Academic Press.
DOI:10.1016/j.semcdb.2019.05.013
Kemble, H., Nghe, P., & Tenaillon, O. (2019). Recent insights into the genotype–phenotype relationship from massively parallel genetic assays. Evolutionary applications, 12(9), 1721-1742.
DOI:10.1111/eva.12846
Mizuuchi, R., Blokhuis, A., Vincent, L., Nghe, P., Lehman, N., & Baum, D. (2019). Mineral surfaces select for longer RNA molecules. Chemical communications, 55(14), 2090-2093.
DOI:10.1039/c8cc10319d
Arsène, S., Ameta, S., Lehman, N., Griffiths, A. D., & Nghe, P. (2018). Coupled catabolism and anabolism in autocatalytic RNA sets. Nucleic acids research, 46(18), 9660-9666.
DOI:[https://doi.org/10.1093/nar/gky598]
Nghe, P., Mulder, B. M., & Tans, S. J. (2018). A graph-based algorithm for the multi-objective optimization of gene regulatory networks. European Journal of Operational Research, 270(2), 784-793.
DOI:10.1016/j.ejor.2018.04.020
Nghe, P., Kogenaru, M., & Tans, S. J. (2018). Sign epistasis caused by hierarchy within signalling cascades. Nature communications, 9(1), 1-9.
DOI:10.1038/s41467-018-03644-8
Blokhuis, A., Lacoste, D., Nghe, P., & Peliti, L. (2018). Selection dynamics in transient compartmentalization. Physical review letters, 120(15), 158101.
DOI:10.1103/physrevlett.120.158101
Wehrens, M., Büke, F., Nghe, P., & Tans, S. J. (2018). Stochasticity in cellular metabolism and growth: approaches and consequences. Current Opinion in Systems Biology, 8, 131-136.
DOI:10.1016/j.coisb.2018.02.006
Pichugin, Y., Peña, J., Rainey, P. B. & Tralusen, A. (2017). Fragmentation modes and the evolution of life cycles. PLoS Computational Biology.
DOI: 10.1371/journal.pcbi.1005860
Rainey, P. B., Remigi, P., Farr, A. D. & Lind, P. A. (2017). Darwin was right: where now for experimental evolution? Current Opinion in Genetics and Development. 47, 102-109.
DOI: 10.1016/j.gde.2017.09.003
Farr, A. D., Remigi, P. & Rainey, P. B. (2017). Adaptive evolution by spontaneous domain fusion and protein re-localisation. Nature Ecology and Evolution 1, 1562-1568.
DOI: 10.1038/s41559-017-0283-7
Bertels, F., Gallie, J. & P. B. Rainey. (2017). Identification and characterisation of domesticated bacterial transposases. Genome Biology and Evolution 9, 2110-2121.
DOI: 10.1093/gbe/evx146
Liu, Y, Gokhale, C. S., Rainey, P. B. & Zhang, X.-X. (2017). Unravelling the complexity and redundancy of carbon catabolic repression in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. Molecular Microbiology 105, 589-605.
DOI: 10.1111/mmi.13720
McCann, H. C., Li, L., Liu, Y., Templeton, M., Colombi, E., Straub, C., Rainey, P. B*. & Huang, H.* (2017). Origin and evolution of the kiwifruit canker pandemic. *Joint senior authors. Genome Biology and Evolution 9, 932-944.
DOI: 10.1093/gbe/evx055
Gerth, M. L., Liu, Y., Jiao, W., Zhang, X.-X., Baker, E. N., Lott, J. S., Rainey, P. B. & Johnston, J. M. (2017). Crystal structure of a bicupin protein HutD involved in histidine utilisation in Pseudomonas 85, 1580-1588. Proteins: Structure, Function, and Bioinformatics.
DOI: 10.1002/prot.25303
Shewaramani, S., Finn, T. J., Leahy, S. C., Kassen, R., Rainey, P. B. & Moon, C. D. (2017). Anaerobically grown Escherichia coli has an enhanced mutation rate and distinct mutational spectra. PLoS Genetics.
DOI: 10.1371/journal.pgen.1006570
Colombi, E., Straub, C., Kunzel, S., Templeton, M. D., McCann, H. C. & Rainey, P. B. (2017). Evolution of copper resistance in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids. Environmental Microbiology 19, 819-832.
DOI: 10.1111/1462-2920.13662.
See also accompanying Research Highlight by Steve Lindow (2017) Horizontal gene transfer gone wild: promiscuity in a kiwifruit pathogen leads to resistance to chemical control. Environmental Microbiology 19, 1363-1365.
DOI: 10.1111/1462-2920.13717
Lind, P. A., Farr, A. D. & Rainey, P. B. (2017). Convergence in experimental Pseudomonas populations. ISME Journal 11, 589-600.
DOI: 10.1038/ismej.2016.157
Lahiri, S., Nghe, P., Tans, S. J., Rosinberg, M. L., & Lacoste, D. (2017). Information-theoretic analysis of the directional influence between cellular processes. Plos one, 12(11), e0187431.
DOI:10.1371/journal.pone.0187431
Yeates, J. A., Nghe, P., & Lehman, N. (2017). Topological and thermodynamic factors that influence the evolution of small networks of catalytic RNA species. RNA, 23(7), 1088-1096.
DOI:10.1261/rna.061093.117
Selected publications
Matsumura, S., Kun, A., Ryckelynck, M., Coldren, F., Szilagyi, A., Jossinet, F., Nghe P., Szathmary E., Griffiths, A. D. (2016). Transient compartmentalization of RNA replicators prevents extinction due to parasites. Science, 354(6317), 1293–1296.
doi:10.1126/science.aag1582
Nghe, P., Hordijk, W., Kauffman, S. A., Walker, S. I., Schmidt, F. J., Kemble, H., Yeates, J. A. M. Lehman, N. (2015). Prebiotic network evolution: six key parameters. Molecular BioSystems, 11(12), 3206–3217.
doi:10.1039/c5mb00593k
Lind, P. A., Farr, A.D. & Rainey, P. B. (2015). Experimental evolution reveals hidden diversity in evolutionary pathways. eLife 10.7554/eLife.07074.
DOI: 10.7554/eLife.07074
Gallie, J., Libby, E., Bertels, F., Remigi, P., Jendresen, C. B., Ferguson, G. C., Desprat, N., Buffing, M. F., Sauer, U., Beaumont, H. J. E., Martinussen, J., Kilstrup, M. & Rainey, P. B. (2015). Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biology 13(3): e1002109.
DOI: 10.1371/journal.pbio.1002109
Kiviet, D. J.*, Nghe, P.*, Walker, N., Boulineau, S., Sunderlikova, V., & Tans, S. J. (2014). Stochasticity of metabolism and growth at the single-cell level. Nature, 514(7522), 376–379.
doi:10.1038/nature13582
Hammerschmidt, K., Rose, C., Kerr, B. & Rainey, P. B. (2014). Life cycles, fitness decoupling and the evolution of multicellularity. Nature 515, 75-79.
DOI: 10.1038/nature13884
Rainey, P. B., Desprat, N., Driscoll, W. W. & Zhang, X.-X. (2014). Microbes are not bound by sociobiology. Evolution 68, 3344-3355.
DOI: 10.1111/evo.12508
Rainey, P. B. & De Monte, S. (2014). Resolving conflicts during the transition to multicellular life. Annual Review of Ecology Evolution and Systematics 45, 599-620.
DOI: 10.1146/annurev-ecolsys-120213-091740
Taute, K. M., Gude, S., Nghe, P., & Tans, S. J. (2014). Evolutionary constraints in variable environments, from proteins to networks. Trends in Genetics, 30(5), 192–198. doi:10.1016/j.tig.2014.04.003
Nghe, P., Boulineau, S., Gude, S., Recouvreux, P., van Zon, J. S., & Tans, S. J. (2013). Microfabricated Polyacrylamide Devices for the Controlled Culture of Growing Cells and Developing Organisms. PLoS ONE, 8(9), e75537.
doi:10.1371/journal.pone.0075537
Boulineau, S., Tostevin, F., Kiviet, D. J., ten Wolde, P. R., Nghe, P., & Tans, S. J. (2013). Single-Cell Dynamics Reveals Sustained Growth during Diauxic Shifts. PLoS ONE, 8(4), e61686.
doi:10.1371/journal.pone.0061686
Zhang, X.-X. & Rainey, P. B. (2013). Exploring the social biology of pyoverdin-producing Pseudomonas. Evolution 67, 3161-3174. DOI: 10.1111/evo.12183
McCann, H., Rikkerink, E. H., Bertels, F. Fiers, M., Lu, A., Rees-George, J., Andersen, M. T., Gleave, A. P., Haubold, B., Wohlers, Guttman, D. S., Wang, P., Vanneste, J., Rainey, P. B*. & Templeton, M. D*. (2013). Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insights into the origins of an emergent plant disease. PLoS Pathogens 9(7): e1003503. *Joint senior authors. DOI: 10.1371/journal.ppat.1003503
Libby, E. & Rainey, P. B. (2013). A conceptual framework for the evolutionary origins of multicellularity. Physical Biology 10, 035001. DOI: 10.1088/1478-3975/10/3/035001.
Bertels, F. & Rainey, P. B. (2011). Within genome evolution of REPINs: A new family of miniature mobile DNA in bacteria. PLoS Genetics, 7(6): e1002132.
Libby, E. & Rainey, P. B. (2011). Exclusion rules, population bottlenecks, and the evolution of stochastic switching. Proceedings of the Royal Society (London) B 278, 3574-3583. DOI:10.1098/rspb.2011.0146.
Refardt, D. & Rainey, P. B. (2010). Tuning a genetic switch: experimental evolution and natural variation of prophage induction. Evolution 64, 1086-1097.
Beaumont, H. J. E., Gallie, J., Kost, C., Ferguson, G. C. & Rainey, P. B. (2009). Experimental evolution of bet-hedging. Nature 462, 90-93.
McDonald, M. J., Gehrig, S. M., Meintjes, P. L., Zhang, X.-X. & Rainey, P. B. (2009). Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 183, 1041-1053.
Silby, M. W., Cerdeno-Tarranga, A. M., Vernikos, G., Giddens, S. R., Jackson, R. W., Preston, G. M., Zhang, X.-X., Moon, C. D., Gehrig, S. M., Godfrey, S. A. C., Knight, C. G., Malone, J. G., Robinson, Z., Spiers, A. J., Harris, S., Challis, G. L., Yaxley, A. M., Harris, D., Seeger, K., Murphy, L., Rutter, S., Squares, R., Quail, M. A., Saunders, E., Anderson, I., Mavromat, K., Brettin, T. S., Bentley, S., Hothersall, J., Stephens, E., Thomas, C. M., Parkhill, J., Levy, S. B., Rainey, P. B. & Thomson, N. R. (2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10, R51.
Giddens, S. R., Jackson, R. W., Moon, C. D., Jacobs, M. A., Zhang, X.-X., Gehrig, S. M. & Rainey, P. B. (2007). Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. Proceedings of the National Academy of Sciences, USA 104, 18247-18252.
Rainey, P. B. (2007). Unity from conflict. Nature 446, 616.
Fukami, T, Beaumont, H. J. E. & Zhang, X.-X. Rainey, P. B. Immigration history controls diversification in experimental adaptive radiation. Nature 446, 436-439.
Kirkelund Hansen, S., Rainey, P. B*., Haagensen, J. A. J & Molin, S. (2007). Evolution of species interactions in a biofilm community. Nature 445, 533-536. *Corresponding author.
Knight, C. G., Zitzmann, N, Prabhakar, S, Antrobus, R, Dwek, R, Hebestreit, H., & Rainey, P. B. (2006). Unravelling adaptive evolution: how a single point mutation affects the protein co-regulation network. Nature Genetics 38, 1015-1022.
Knight, C. G., Kassen, R, Hebestreit, H. & Rainey, P. B. (2004) Global analysis of predicted proteomes: functional adaptation and physical properties. Proceedings of the National Academy of Sciences, USA 101, 8390-8395.
MacLean, C. Bell, G. & Rainey, P. B. (2004) The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proceedings of the National Academy of Sciences, USA 101, 8072-8077.
Kassen, R & Rainey, P. B. (2004). The ecology and genetics of microbial diversity. Annual Review of Microbiology 58, 207-231.
Jessup, C. M., Kassen, R., Forde, S. E., Kerr, B., Buckling, A., Rainey, P. B. & Bohannan, B. J. M. (2004) Big questions, small worlds: Microbial model systems in ecology. Trends in Ecology and Evolution 19, 189-197.
Gal, M., Preston, G. M., Massey, R. M., Spiers, A. J. & Rainey, P. B. (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Molecular Ecology 12, 3109-3121.
Rainey, P. B. & Rainey. K. (2003). Evolution of co-operation and conflict in experimental bacterial populations. Nature 425, 72-74.
Buckling, A. & Rainey, P. B. (2002). The role of parasites on sympatric and allopatric diversification of hosts. Nature 420, 496-499.
D’Argenio, D. A., Calfee, M. W., Rainey, P. B. & Pesci, E. C. (2002) Autolysis and autoaggregation in Pseudomonas aeruginosa colony morphology mutants. Journal of Bacteriology 184, 6481-6489.
Buckling, A & Rainey, P. B. (2002). Antagonistic coevolution between a bacterium and a bacteriophage. Proceedings of the Royal Society (London) B 269, 931-936.
Spiers, A. J., Kahn, S. G., Bohannon, J., Travisano, M. & Rainey, P. B. (2002). Adaptive divergence in experimental populations of Pseudomonas fluorescens. 1. Genetic and phenotypic bases of wrinkly spreader fitness. Genetics 161, 33-46.
Preston, G. M. Bertrand, N. & Rainey, P. B. (2001). Type III (Hrp) secretion in plant growth-promoting Pseudomonas fluorescens SBW25. Molecular Microbiology 41, 999-1014.
Buckling, A. Kassen, R. Bell, G. & Rainey, P. B. (2000). Diversity and disturbance in experimental microcosms. Nature 408, 961-964.
Kassen, R. Buckling, A. Bell, G. & Rainey, P. B. (2000) Diversity peaks at intermediate productivity in a laboratory microcosm. Nature 406, 508-512.
Spiers, A. J., Buckling, A. & Rainey, P. B. (2000). The causes of Pseudomonas diversity. Microbiology 146, 2345-2350.
Rainey, P. B. (1999). Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environmental Microbiology 1, 243-258.
Rainey, P. B. & Travisano, M. (1998) Adaptive radiation in a heterogeneous environment. Nature 394, 69-72.
Haubold, B. & Rainey, P. B. (1996). Genetic and ecotypic structure of a fluorescent Pseudomonas population. Molecular Ecology 5, 747-761.
Moxon, E. R., Rainey, P. B., Nowak, M. & Lenski, R. E (1994). Adaptive evolution of highly mutable loci in pathogenic bacteria. Current Biology 4, 24-33.
Rainey, P. B. & Moxon, E. R. (1993). Unusual mutational mechanisms and evolution. Science 260, 1958.