Publications
2023
Theory of the asynchronous state of structured rotator networks and its application to recurrent networks of excitatory and inhibitory units.
Ranft J, Lindner B
Phys Rev E. 2023 Apr. 107(4-1):044306.
Wavelet clustering analysis as a tool for characterizing community structure in the human microbiome.
Benincà E, Pinto S, Cazelles B, Fuentes S, Shetty S, Bogaards JA
Sci Rep. 2023 May 17. 13(1):8042.
Y-complex nucleoporins independently contribute to nuclear pore assembly and gene regulation in neuronal progenitors.
Orniacki C, Verrico A, Pelletier S, Souquet B, Coulpier F, Jourdren L, Benetti S, Doye V
J Cell Sci. 2023 May 17.
Prox2 and Runx3 vagal sensory neurons regulate esophageal motility.
Lowenstein ED, Ruffault PL, Misios A, Osman KL, Li H, Greenberg RS, Thompson R, Song K, Dietrich S, Li X, Vladimirov N, Woehler A, Brunet JF, Zampieri N, Kühn R, Liberles SD, Jia S, Lewin GR, Rajewsky N, Lever TE, Birchmeier C
Neuron. 2023 May 10.
Protein Biomarkers of New-Onset Heart Failure : Insights From the Heart Omics and Ageing Cohort, the Atherosclerosis Risk in Communities Study, and the Framingham Heart Study.
Girerd N, Levy D, Duarte K, Ferreira JP, Ballantyne C, Collier T, Pizard A, Björkman J, Butler J, Clark A, Cleland JG, Delles C, Diez J, González A, Hazebroek M, Ho J, Huby AC, Hwang SJ, Latini R, Mariottoni B, Mebazaa A, Pellicori P, Sattar N, Sever P, Staessen JA, Verdonschot J, Heymans S, Rossignol P, Zannad F
Circ Heart Fail. 2023 May. 16(5):e009694.
The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2.
Barido‑Sottani J, Morlon H
Syst Biol. 2023 May 10.
The build-up of the present-day tropical diversity of tetrapods.
Quintero I, Landis MJ, Jetz W, Morlon H
Proc Natl Acad Sci U S A. 2023 May 16. 120(20):e2220672120.
Dynamics of gene loss following ancient whole-genome duplication in the cryptic Paramecium complex.
Gout JF, Hao Y, Johri P, Arnaiz O, Doak TG, Bhullar S, Couloux A, Guérin F, Malinsky S, Potekhin A, Sawka N, Sperling L, Labadie K, Meyer E, Duharcourt S, Lynch M
Mol Biol Evol. 2023 May 8. 40(5).
The MIR34B/C genomic region contains multiple potential regulators of multiciliogenesis.
Cavard A, Redman E, Mercey O, Abelanet S, Plaisant M, Arguel MJ, Magnone V, Ruiz García S, Rios G, Deprez M, Lebrigand K, Ponzio G, Caballero I, Barbry P, Zaragosi LE, Marcet B
FEBS Lett. 2023 Apr 27.
Boundary vector cells in the goldfish central telencephalon encode spatial information.
Cohen L, Vinepinsky E, Donchin O, Segev R
PLoS Biol. 2023 Apr. 21(4):e3001747.
Regulation of cold-inducible RNA-binding protein (CIRBP) in response to cellular stresses.
Corre M, Lebreton A
Biochimie. 2023 Apr 8.
Multifaceted microglia during brain development : Models and tools.
Bridlance C, Thion MS
Front Neurosci. 2023. 17:1125729.
High Growth Rate of Diatoms Explained by Reduced Carbon Requirement and Low Energy Cost of Silica Deposition.
Inomura K, Pierella Karlusich JJ, Dutkiewicz S, Deutsch C, Harrison PJ, Bowler C
Microbiol Spectr. 2023 Apr 3:e0331122.
Interpreting the pervasive observation of U-shaped Site Frequency Spectra.
Freund F, Kerdoncuff E, Matuszewski S, Lapierre M, Hildebrandt M, Jensen JD, Ferretti L, Lambert A, Sackton TB, Achaz G
PLoS Genet. 2023 Mar. 19(3):e1010677.
Spectral EEG correlations from the different phases of general anesthesia.
Sun C, Longrois D, Holcman D
Front Med (Lausanne). 2023. 10:1009434.
Filopodia-like protrusions of adjacent somatic cells shape the developmental potential of oocytes.
Crozet F, Letort G, Bulteau R, Da Silva C, Eichmuller A, Tortorelli AF, Blévinal J, Belle M, Dumont J, Piolot T, Dauphin A, Coulpier F, Chédotal A, Maître JL, Verlhac MH, Clarke HJ, Terret ME
Life Sci Alliance. 2023 Jun. 6(6).
The cerebellum regulates fear extinction through thalamo-prefrontal cortex interactions in male mice.
Frontera JL, Sala RW, Georgescu IA, Baba Aissa H, d’Almeida MN, Popa D, Léna C
Nat Commun. 2023 Mar 17. 14(1):1508.
At the crossroads of epidemiology and biology : Bridging the gap between SARS-CoV-2 viral strain properties and epidemic wave characteristics.
Poydenot F, Lebreton A, Haiech J, Andreotti B
Biochimie. 2023 Mar 15.
Direct whole-cell patch-clamp recordings from small boutons in rodent primary neocortical neuron cultures.
Ritzau‑Jost A, Nerlich J, Kaas T, Krueger M, Tsintsadze T, Eilers J, Barbour B, Smith SM, Hallermann S
STAR Protoc. 2023 Mar 14. 4(2):102168.
Beta oscillations and waves in motor cortex can be accounted for by the interplay of spatially structured connectivity and fluctuating inputs.
Kang L, Ranft J, Hakim V
Elife. 2023 Mar 14. 12.
Light-dependent signal transduction in the marine diatom Phaeodactylum tricornutum.
Agarwal A, Levitan O, Cruz de Carvalho H, Falkowski PG
Proc Natl Acad Sci U S A. 2023 Mar 14. 120(11):e2216286120.
The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases.
Hoguin A, Yang F, Groisillier A, Bowler C, Genovesio A, Ait‑Mohamed O, Vieira FRJ, Tirichine L
Commun Biol. 2023 Mar 9. 6(1):253.
Evolution is not Uniform Along Coding Sequences.
Bricout R, Weil D, Stroebel D, Genovesio A, Roest Crollius H
Mol Biol Evol. 2023 Mar 4. 40(3).
Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists.
Rius M, Rest JS, Filloramo GV, Novák Vanclová AMG, Archibald JM, Collier JL
Genome Biol Evol. 2023 Mar 3. 15(3).
Interactive nanocluster compaction of the ELKS scaffold and Cacophony Ca(2+) channels drives sustained active zone potentiation.
Ghelani T, Escher M, Thomas U, Esch K, Lützkendorf J, Depner H, Maglione M, Parutto P, Gratz S, Matkovic‑Rachid T, Ryglewski S, Walter AM, Holcman D, O’Connor Giles K, Heine M, Sigrist SJ
Sci Adv. 2023 Feb 17. 9(7):eade7804.
Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches.
Shao Z, Ampomah O, Vieira FRJ, Dorrell RG, Li S, Tirichine L, Bulone V, Duan D, Bowler C
mSystems. 2023 Apr 27. 8(2):e0113122.
Single-cytosine methylation at W-boxes repels binding of WRKY transcription factors through steric hindrance.
Charvin M, Halter T, Blanc‑Mathieu R, Barraud P, Aumont‑Nicaise M, Parcy F, Navarro L
Plant Physiol. 2023 May 2. 192(1):77-84.
Differential expression patterns of long noncoding RNAs in a pleiomorphic diatom and relation to hyposalinity.
Debit A, Charton F, Pierre‑Elies P, Bowler C, Cruz de Carvalho H
Sci Rep. 2023 Feb 10. 13(1):2440.
Genome structures resolve the early diversification of teleost fishes.
Parey E, Louis A, Montfort J, Bouchez O, Roques C, Iampietro C, Lluch J, Castinel A, Donnadieu C, Desvignes T, Floi Bucao C, Jouanno E, Wen M, Mejri S, Dirks R, Jansen H, Henkel C, Chen WJ, Zahm M, Cabau C, Klopp C, Thompson AW, Robinson‑Rechavi M, Braasch I, Lecointre G, Bobe J, Postlethwait JH, Berthelot C, Roest Crollius H, Guiguen Y
Science. 2023 Feb 10. 379(6632):572-575.
PlantACT ! - how to tackle the climate crisis.
Hirt H, Al‑Babili S, Almeida‑Trapp M, Martin A, Aranda M, Bartels D, Bennett M, Blilou I, Boer D, Boulouis A, Bowler C, Brunel‑Muguet S, Chardon F, Colcombet J, Colot V, Daszkowska‑Golec A, Dinneny JR, Field B, Froehlich K, Gardener CH, Gojon A, Gomès E, Gomez‑Alvarez EM, Gutierrez C, Havaux M, Hayes S, Heard E, Hodges M, Alghamdi AK, Laplaze L, Lauersen KJ, Leonhardt N, Johnson X, Jones J, Kollist H, Kopriva S, Krapp A, Masson ML, McCabe MF, Merendino L, Molina A, Moreno Ramirez JL, Mueller‑Roeber B, Nicolas M, Nir I, Orduna IO, Pardo JM, Reichheld JP, Rodriguez PL, Rouached H, Saad MM, Schlögelhofer P, Singh KA, De Smet I, Stanschewski C, Stra A, Tester M, Walsh C, Weber APM, Weigel D, Wigge P, Wrzaczek M, Wulff BBH, Young IM
Trends Plant Sci. 2023 May. 28(5):537-543.
High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing.
Chen KY, Karuppusamy J, O’Neill MB, Opuu V, Bahin M, Foulon S, Ibanez P, Quintana‑Murci L, Ozawa T, van der Werf S, Nghe P, Naffakh N, Griffiths A, Isel C
Proc Natl Acad Sci U S A. 2023 Feb 7. 120(6):e2211098120.
Bottlenecks can constrain and channel evolutionary paths.
Gamblin J, Gandon S, Blanquart F, Lambert A
Genetics. 2023 Feb 2.
Author Correction : Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes.
Lehman NL, Spassky N, Sak M, Webb A, Zumbar CT, Usubalieva A, Alkhateeb KJ, McElroy JP, Maclean KH, Fadda P, Liu T, Gangalapudi V, Carver J, Abdullaev Z, Timmers C, Parker JR, Pierson CR, Mobley BC, Gokden M, Hattab EM, Parrett T, Cooke RX, Lehman TD, Costinean S, Parwani A, Williams BJ, Jensen RL, Aldape K, Mistry AM
Nat Commun. 2023 Jan 31. 14(1):507.
SCORPiOs, a Novel Method to Reconstruct Gene Phylogenies in the Context of a Known WGD Event.
Parey E, Roest Crollius H, Berthelot C
Methods Mol Biol. 2023. 2545:155-173.
Towards evolutionary predictions : Current promises and challenges.
Wortel MT, Agashe D, Bailey SF, Bank C, Bisschop K, Blankers T, Cairns J, Colizzi ES, Cusseddu D, Desai MM, van Dijk B, Egas M, Ellers J, Groot AT, Heckel DG, Johnson ML, Kraaijeveld K, Krug J, Laan L, Lässig M, Lind PA, Meijer J, Noble LM, Okasha S, Rainey PB, Rozen DE, Shitut S, Tans SJ, Tenaillon O, Teotónio H, de Visser JAGM, Visser ME, Vroomans RMA, Werner GDA, Wertheim B, Pennings PS
Evol Appl. 2023 Jan. 16(1):3-21.
Plastic responses lead to increased neurotoxin production in the diatom Pseudo-nitzschia under ocean warming and acidification.
Xu D, Zheng G, Brennan G, Wang Z, Jiang T, Sun K, Fan X, Bowler C, Zhang X, Zhang Y, Wang W, Wang Y, Li Y, Wu H, Li Y, Fu FX, Hutchins DA, Tan Z, Ye N
ISME J. 2023 Apr. 17(4):525-536.
Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.
Wu X, Liu Y, d’Aubenton‑Carafa Y, Thermes C, Hyrien O, Chen CL, Petryk N
Nat Protoc. 2023 Apr. 18(4):1260-1295.
Data-driven multiscale dynamical framework to control a pandemic evolution with non-pharmaceutical interventions.
Reingruber J, Papale A, Ruckly S, Timsit JF, Holcman D
PLoS One. 2023. 18(1):e0278882.
Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.
Muffato M, Louis A, Nguyen NTT, Lucas J, Berthelot C, Roest Crollius H
Nat Ecol Evol. 2023 Mar. 7(3):355-366.
Annexin A1 is a polarity cue that directs mitotic spindle orientation during mammalian epithelial morphogenesis.
Fankhaenel M, Hashemi FSG, Mourao L, Lucas E, Hosawi MM, Skipp P, Morin X, Scheele CLGJ, Elias S
Nat Commun. 2023 Jan 11. 14(1):151.
Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability.
Uzonyi A, Dierks D, Nir R, Kwon OS, Toth U, Barbosa I, Burel C, Brandis A, Rossmanith W, Le Hir H, Slobodin B, Schwartz S
Mol Cell. 2023 Jan 19. 83(2):237-251.e7.
Variation in mutational (co)variances.
Mallard F, Noble L, Baer CF, Teotónio H
G3 (Bethesda). 2023 Feb 9. 13(2).
Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.
Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C
Life Sci Alliance. 2023 Mar. 6(3).
Microglial TNFα orchestrates protein phosphorylation in the cortex during the sleep period and controls homeostatic sleep.
Pinto MJ, Cottin L, Dingli F, Laigle V, Ribeiro LF, Triller A, Henderson F, Loew D, Fabre V, Bessis A
EMBO J. 2023 Jan 4. 42(1):e111485.
In mice and humans, brain microvascular contractility matures postnatally.
Slaoui L, Gilbert A, Rancillac A, Delaunay‑Piednoir B, Chagnot A, Gerard Q, Letort G, Mailly P, Robil N, Gelot A, Lefebvre M, Favier M, Dias K, Jourdren L, Federici L, Auvity S, Cisternino S, Vivien D, Cohen‑Salmon M, Boulay AC
Brain Struct Funct. 2023 Mar. 228(2):475-492.
Quantifying postsynaptic receptor dynamics : insights into synaptic function.
Maynard SA, Ranft J, Triller A
Nat Rev Neurosci. 2023 Jan. 24(1):4-22.
KCa1.1 channels contribute to optogenetically driven post-stimulation silencing in cerebellar molecular layer interneurons.
Kassa M, Bradley J, Jalil A, Llano I
J Gen Physiol. 2023 Jan 2. 155(1).
Fungal microbiomes associated with Lycopodiaceae during ecological succession.
Perez‑Lamarque B, Laurent‑Webb L, Bourceret A, Maillet L, Bik F, Cartier D, Labolle F, Holveck P, Epp D, Selosse MA
Environ Microbiol Rep. 2023 Apr. 15(2):109-118.
A robust approach to estimate relative phytoplankton cell abundances from metagenomes.
Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C
Mol Ecol Resour. 2023 Jan. 23(1):16-40.