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Publications

2020

Active flow network generates molecular transport by packets : case of the endoplasmic reticulum.
Dora M, Holcman D
Proc Biol Sci. 2020 Jul 8. 287(1930):20200493.

Coordination of transcriptional and translational regulations in human epithelial cells infected by Listeria monocytogenes.
Besic V, Habibolahi F, Noël B, Rupp S, Genovesio A, Lebreton A
RNA Biol. 2020 Jun 25:1-16.

IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells.
Gutiérrez‑Reyna DY, Cedillo‑Baños A, Kempis‑Calanis LA, Ramírez‑Pliego O, Bargier L, Puthier D, Abad‑Flores JD, Thomas‑Chollier M, Thieffry D, Medina‑Rivera A, Spicuglia S, Santana MA
Front Immunol. 2020. 11:1089.

Conserved Small Nucleotidic Elements at the Origin of Concerted piRNA Biogenesis from Genes and lncRNAs.
Jensen S, Brasset E, Parey E, Roest Crollius H, Sharakhov IV, Vaury C
Cells. 2020 Jun 18. 9(6).

Direct Readout of Neural Stem Cell Transgenesis with an Integration-Coupled Gene Expression Switch.
Kumamoto T, Maurinot F, Barry‑Martinet R, Vaslin C, Vandormael‑Pournin S, Le M, Lerat M, Niculescu D, Cohen‑Tannoudji M, Rebsam A, Loulier K, Nedelec S, Tozer S, Livet J
Neuron. 2020 Jun 17.

A kinetic analysis of mouse rod and cone photoreceptor responses.
Reingruber J, Ingram NT, Griffis KG, Fain GL
J Physiol. 2020 Jun 17.

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications.
Parey E, Louis A, Cabau C, Guiguen Y, Crollius HR, Berthelot C
Mol Biol Evol. 2020 Jun 18.

Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal.
Sato S, Nanjappa D, Dorrell RG, Vieira FRJ, Kazamia E, Tirichine L, Veluchamy A, Heilig R, Aury JM, Jaillon O, Wincker P, Fussy Z, Obornik M, Muñoz‑Gómez SA, Mann DG, Bowler C, Zingone A
Sci Rep. 2020 Jun 10. 10(1):9449.

Model-based inference of punctuated molecular evolution.
Manceau M, Marin J, Morlon H, Lambert A
Mol Biol Evol. 2020 Jun 10.

Interactions among interactions : The dynamical consequences of antagonism between mutualists.
Yule KM, Johnson CA, Bronstein JL, Ferrière R
J Theor Biol. 2020 May 31. 501:110334.

Characterizing amplitude and frequency modulation cues in natural soundscapes : A pilot study on four habitats of a biosphere reserve.
Thoret E, Varnet L, Boubenec Y, Férriere R, Le Tourneau FM, Krause B, Lorenzi C
J Acoust Soc Am. 2020 May. 147(5):3260.

Co-evolution of primitive methane-cycling ecosystems and early Earth’s atmosphere and climate.
Sauterey B, Charnay B, Affholder A, Mazevet S, Ferrière R
Nat Commun. 2020 Jun 1. 11(1):2705.

Blind deconvolution for spike inference from fluorescence recordings.
Tubiana J, Wolf S, Panier T, Debregeas G
J Neurosci Methods. 2020 May 30. 342:108763.

FORK-seq : replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing.
Hennion M, Arbona JM, Lacroix L, Cruaud C, Theulot B, Tallec BL, Proux F, Wu X, Novikova E, Engelen S, Lemainque A, Audit B, Hyrien O
Genome Biol. 2020 May 26. 21(1):125.

Logical modeling of cell fate specification-Application to T cell commitment.
Cacace E, Collombet S, Thieffry D
Curr Top Dev Biol. 2020. 139:205-238.

Modular Organization of cis-Regulatory Control Information of Neurotransmitter Pathway Genes in Caenorhabditis elegans.
Serrano‑Saiz E, Gulez B, Pereira L, Gendrel M, Kerk SY, Vidal B, Feng W, Wang C, Kratsios P, Rand JB, Hobert O
Genetics. 2020 May 22.

Coevolutionary patterns caused by prey selection.
B L Araujo S, Borges ME, W von Hartenthal F, R Jorge L, M Lewinsohn T, Guimarães PR Jr, van Baalen M
J Theor Biol. 2020 May 15. 501:110327.

Response to technical comment ’A cautionary note for users of linear diversification dependencies’.
Morlon H, Rolland J, Condamine FL
Ecol Lett. 2020 Jul. 23(7):1172-1174.

Coherence of dengue incidence and climate in the wet and dry zones of Sri Lanka.
Prabodanie RAR, Schreider S, Cazelles B, Stone L
Sci Total Environ. 2020 Jul 1. 724:138269.

Automated inference of Boolean models from molecular interaction maps using CaSQ.
Aghamiri SS, Singh V, Naldi A, Helikar T, Soliman S, Niarakis A
Bioinformatics. 2020 May 13.

Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo.
Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto R, Llano I
Elife. 2020 May 13. 9.

Tara Oceans : towards global ocean ecosystems biology.
Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C
Nat Rev Microbiol. 2020 May 12.

Direct observation of helicase-topoisomerase coupling within reverse gyrase.
Yang X, Garnier F, Débat H, Strick TR, Nadal M
Proc Natl Acad Sci U S A. 2020 May 19. 117(20):10856-10864.

Early correction of synaptic long-term depression improves abnormal anxiety-like behavior in adult GluN2B-C456Y-mutant mice.
Shin W, Kim K, Serraz B, Cho YS, Kim D, Kang M, Lee EJ, Lee H, Bae YC, Paoletti P, Kim E
PLoS Biol. 2020 Apr. 18(4):e3000717.

In vivo large-scale analysis of Drosophila neuronal calcium traces by automated tracking of single somata.
Delestro F, Scheunemann L, Pedrazzani M, Tchenio P, Preat T, Genovesio A
Sci Rep. 2020 Apr 28. 10(1):7153.

Aire-dependent genes undergo Clp1-mediated 3’UTR shortening associated with higher transcript stability in the thymus.
Guyon C, Jmari N, Padonou F, Li YC, Ucar O, Fujikado N, Coulpier F, Blanchet C, Root DE, Giraud M
Elife. 2020 Apr 29. 9.

Structural and functional insights into CWC27/CWC22 heterodimer linking the exon junction complex to spliceosomes.
Busetto V, Barbosa I, Basquin J, Marquenet É, Hocq R, Hennion M, Paternina JA, Namane A, Conti E, Bensaude O, Le Hir H
Nucleic Acids Res. 2020 Jun 4. 48(10):5670-5683.

Inhibitory synaptic transmission tuned by Ca2+ and glutamate through the control of GABAA R lateral diffusion dynamics.
Bannai H, Niwa F, Sakuragi S, Mikoshiba K
Dev Growth Differ. 2020 Apr 23.

Publisher Correction : Genetic tool development in marine protists : emerging model organisms for experimental cell biology.
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M Jr, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire‑Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro‑Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura‑Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz‑Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
Nat Methods. 2020 May. 17(5):551.

Extreme escape from a cusp : When does geometry matter for the fastest Brownian particles moving in crowded cellular environments ?
Basnayake K, Holcman D
J Chem Phys. 2020 Apr 7. 152(13):134104.

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development.
Utz SG, See P, Mildenberger W, Thion MS, Silvin A, Lutz M, Ingelfinger F, Rayan NA, Lelios I, Buttgereit A, Asano K, Prabhakar S, Garel S, Becher B, Ginhoux F, Greter M
Cell. 2020 Apr 30. 181(3):557-573.e18.

Genetic tool development in marine protists : emerging model organisms for experimental cell biology.
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M Jr, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire‑Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro‑Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura‑Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz‑Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
Nat Methods. 2020 May. 17(5):481-494.

Corrigendum : Synaptic Mechanisms Underlying the Network State-Dependent Recruitment of VIP-Expressing Interneurons in the CA1 Hippocampus.
Luo X, Guet‑McCreight A, Villette V, Francavilla R, Marino B, Chamberland S, Skinner FK, Topolnik L
Cereb Cortex. 2020 May 14. 30(5):3437.

Artificially decreasing cortical tension generates aneuploidy in mouse oocytes.
Bennabi I, Crozet F, Nikalayevich E, Chaigne A, Letort G, Manil‑Ségalen M, Campillo C, Cadart C, Othmani A, Attia R, Genovesio A, Verlhac MH, Terret ME
Nat Commun. 2020 Apr 3. 11(1):1649.

Entrainment of mammalian motile cilia in the brain with hydrodynamic forces.
Pellicciotta N, Hamilton E, Kotar J, Faucourt M, Delgehyr N, Spassky N, Cicuta P
Proc Natl Acad Sci U S A. 2020 Apr 14. 117(15):8315-8325.

Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects.
Van Dooren TJM, Silveira AB, Gilbault E, Jiménez‑Gómez JM, Martin A, Bach L, Tisné S, Quadrana L, Loudet O, Colot V
J Exp Bot. 2020 Jun 22. 71(12):3588-3602.

Dynamics and organization of proteins in the neuronal plasma membrane.
Triller A, Renner M, Choquet D
Neuropharmacology. 2020 Jun 1. 169:108043.

Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014.
Teissier Y, Paul R, Aubry M, Rodo X, Dommar C, Salje H, Sakuntabhai A, Cazelles B, Cao‑Lormeau VM
PLoS Negl Trop Dis. 2020 Mar. 14(3):e0008110.

Disentangling the assembly mechanisms of ant cuticular bacterial communities of two Amazonian ant species sharing a common arboreal nest.
Birer C, Moreau CS, Tysklind N, Zinger L, Duplais C
Mol Ecol. 2020 Apr. 29(7):1372-1385.

Synaptic Mechanisms Underlying the Network State-Dependent Recruitment of VIP-Expressing Interneurons in the CA1 Hippocampus.
Luo X, Guet‑McCreight A, Villette V, Francavilla R, Marino B, Chamberland S, Skinner FK, Topolnik L
Cereb Cortex. 2020 May 18. 30(6):3667-3685.

Author Correction : Biotic soil-plant interaction processes explain most of hysteretic soil CO2 efflux response to temperature in cross-factorial mesocosm experiment.
Dusza Y, Sanchez‑Cañete EP, Galliard JL, Ferrière R, Chollet S, Massol F, Hansart A, Juarez S, Dontsova K, Haren JV, Troch P, Pavao‑Zuckerman MA, Hamerlynck E, Barron‑Gafford GA
Sci Rep. 2020 Feb 20. 10(1):3070.

A review of pathogens in selected Baltic Sea indicator species.
Sonne C, Lakemeyer J, Desforges JP, Eulaers I, Persson S, Stokholm I, Galatius A, Gross S, Gonnsen K, Lehnert K, Andersen‑Ranberg EU, Tange Olsen M, Dietz R, Siebert U
Environ Int. 2020 Apr. 137:105565.

Lifetime of a structure evolving by cluster aggregation and particle loss, and application to postsynaptic scaffold domains.
Hakim V, Ranft J
Phys Rev E. 2020 Jan. 101(1-1):012411.

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.
Zinovyev A, Czerwinska U, Cantini L, Barillot E, Frahm KM, Shepelyansky DL
PLoS Comput Biol. 2020 Feb. 16(2):e1007652.

The signaling peptide PapR is required for the activity of the quorum-sensor PlcRa in Bacillus thuringiensis.
Huillet E, Bridoux L, Barboza I, Lemy C, André‑Leroux G, Lereclus D
Microbiology. 2020 Apr. 166(4):398-410.

Reliable Phylogenetic Regressions for Multivariate Comparative Data : Illustration with the MANOVA and Application to the Effect of Diet on Mandible Morphology in Phyllostomid Bats.
Clavel J, Morlon H
Syst Biol. 2020 Feb 15.

Differential Membrane Binding and Seeding of Distinct α-Synuclein Fibrillar Polymorphs.
Shrivastava AN, Bousset L, Renner M, Redeker V, Savistchenko J, Triller A, Melki R
Biophys J. 2020 Mar 24. 118(6):1301-1320.

Photocontrol of Metabotropic Glutamate Receptors : When One Agonist Is Not Enough, Make It Two.
Mony L, Paoletti P
Neuron. 2020 Feb 5. 105(3):395-397.

Cheating in arbuscular mycorrhizal mutualism : a network and phylogenetic analysis of mycoheterotrophy.
Perez‑Lamarque B, Selosse MA, Öpik M, Morlon H, Martos F
New Phytol. 2020 Jun. 226(6):1822-1835.

Biotic soil-plant interaction processes explain most of hysteric soil CO2 efflux response to temperature in cross-factorial mesocosm experiment.
Dusza Y, Sanchez‑Cañete EP, Galliard JL, Ferrière R, Chollet S, Massol F, Hansart A, Juarez S, Dontsova K, Haren JV, Troch P, Pavao‑Zuckerman MA, Hamerlynck E, Barron‑Gafford GA
Sci Rep. 2020 Jan 22. 10(1):905.

Spatiotemporal properties of whisker-evoked tactile responses in the mouse secondary somatosensory cortex.
Hubatz S, Hucher G, Shulz DE, Férézou I
Sci Rep. 2020 Jan 21. 10(1):763.

Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation.
Clément Y, Torbey P, Gilardi‑Hebenstreit P, Crollius HR
Nucleic Acids Res. 2020 Mar 18. 48(5):2357-2371.

Adaptation of Biotrophic Leaf Pathogens to Fertilization-Mediated Changes in Plant Traits : A Comparison of the Optimization Principle to Invasion Fitness.
Précigout PA, Robert C, Claessen D
Phytopathology. 2020 May. 110(5):1039-1048.

Naturalistic Behavior : The Zebrafish Larva Strikes Back.
Privat M, Sumbre G
Curr Biol. 2020 Jan 6. 30(1):R27-R29.

[Corrigendum to "EEG power spectral density under Propofol and its association with burst suppression, a marker of cerebral fragility" [Clin. Neurophysiol. 130 (2019) 1311-1319].->https://doi.org/10.1016/j.clinph.2019.12.001]
Touchard C, Cartailler J, Levé C, Parutto P, Buxin C, Garnot L, Matéo J, Kubis N, Mebazaa A, Gayat E, Vallée F
Clin Neurophysiol. 2020 Mar. 131(3):781.

Interpreting pathways to discover cancer driver genes with Moonlight.
Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, Chen XS, Papaleo E
Nat Commun. 2020 Jan 3. 11(1):69.

Phytoplankton in the Tara Ocean.
Pierella Karlusich JJ, Ibarbalz FM, Bowler C
Ann Rev Mar Sci. 2020 Jan 3. 12:233-265.

From behavior to circuit modeling of light-seeking navigation in zebrafish larvae.
Karpenko S, Wolf S, Lafaye J, Le Goc G, Panier T, Bormuth V, Candelier R, Debrégeas G
Elife. 2020 Jan 2. 9.

PySpacell : A Python Package for Spatial Analysis of Cell Images.
Rose F, Rappez L, Triana SH, Alexandrov T, Genovesio A
Cytometry A. 2020 Mar. 97(3):288-295.

Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions.
Quintero I, Landis MJ
Syst Biol. 2020 Jul 1. 69(4):739-755.

Increased Confinement and Polydispersity of STIM1 and Orai1 after Ca2+ Store Depletion.
Qin X, Liu L, Lee SK, Alsina A, Liu T, Wu C, Park H, Yu C, Kim H, Chu J, Triller A, Tang BZ, Hyeon C, Park CY, Park H
Biophys J. 2020 Jan 7. 118(1):70-84.

Synaptic zinc contributes to motor and cognitive deficits in 6-hydroxydopamine mouse models of Parkinson’s disease.
Sikora J, Kieffer BL, Paoletti P, Ouagazzal AM
Neurobiol Dis. 2020 Feb. 134:104681.

Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.
Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix MA, de Bono M
Neuron. 2020 Jan 8. 105(1):106-121.e10.

TFregulomeR reveals transcription factors’ context-specific features and functions.
Lin QXX, Thieffry D, Jha S, Benoukraf T
Nucleic Acids Res. 2020 Jan 24. 48(2):e10.

ParameciumDB 2019 : integrating genomic data across the genus for functional and evolutionary biology.
Arnaiz O, Meyer E, Sperling L
Nucleic Acids Res. 2020 Jan 8. 48(D1):D599-D605.

JASPAR 2020 : update of the open-access database of transcription factor binding profiles.
Fornes O, Castro‑Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana‑Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A
Nucleic Acids Res. 2020 Jan 8. 48(D1):D87-D92.

Only negligible deviations from electroneutrality are expected in dendritic spines.
Barbour B
Nat Rev Neurosci. 2020 Jan. 21(1):53.

Estimating Diversity Through Time Using Molecular Phylogenies : Old and Species-Poor Frog Families are the Remnants of a Diverse Past.
Billaud O, Moen DS, Parsons TL, Morlon H
Syst Biol. 2020 Mar 1. 69(2):363-383.

ANISEED 2019 : 4D exploration of genetic data for an extended range of tunicates.
Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse MB, Louis A, Nitta KR, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult‑Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan JF, Davidson B, Nishida H, Dantec C, Lemaire P
Nucleic Acids Res. 2020 Jan 8. 48(D1):D668-D675.

Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest.
Sommeria‑Klein G, Zinger L, Coissac E, Iribar A, Schimann H, Taberlet P, Chave J
Mol Ecol Resour. 2020 Mar. 20(2):371-386.

A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum.
Rastogi A, Vieira FRJ, Deton‑Cabanillas AF, Veluchamy A, Cantrel C, Wang G, Vanormelingen P, Bowler C, Piganeau G, Hu H, Tirichine L
ISME J. 2020 Feb. 14(2):347-363.

Does the Latent Period of Leaf Fungal Pathogens Reflect Their Trophic Type ? A Meta-Analysis of Biotrophs, Hemibiotrophs, and Necrotrophs.
Précigout PA, Claessen D, Makowski D, Robert C
Phytopathology. 2020 Feb. 110(2):345-361.

Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum.
Lewitus E, Aristide L, Morlon H
Syst Biol. 2020 Mar 1. 69(2):234-248.

Fractional occupancy of synaptic binding sites and the molecular plasticity of inhibitory synapses.
Specht CG
Neuropharmacology. 2020 Jun 1. 169:107493.

Cell biology and dynamics of Neuronal Na+/K+-ATPase in health and diseases.
Shrivastava AN, Triller A, Melki R
Neuropharmacology. 2020 Jun 1. 169:107461.