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Publications

2023

Neonatal CD4+T cells have a characteristic transcriptome and epigenome and respond to TCR stimulation with proliferation and yet a limited immune response.
Kempis‑Calanis LA, Rodríguez‑Jorge O, Gutiérrez‑Reyna DY, Ventura‑Martínez CJ, Spicuglia S, Medina‑Rivera A, Thieffry D, González A, Santana MA
J Leukoc Biol. 2023 Dec 26.

KCNN4 links PIEZO-dependent mechanotransduction to NLRP3 inflammasome activation.
Ran L, Ye T, Erbs E, Ehl S, Spassky N, Sumara I, Zhang Z, Ricci R
Sci Immunol. 2023 Dec 22. 8(90):eadf4699.

Transfer learning for versatile and training free high content screening analyses.
Corbe M, Boncompain G, Perez F, Del Nery E, Genovesio A
Sci Rep. 2023 Dec 18. 13(1):22599.

Fast wavefront shaping for two-photon brain imaging with multipatch correction.
Blochet B, Akemann W, Gigan S, Bourdieu L
Proc Natl Acad Sci U S A. 2023 Dec 19. 120(51):e2305593120.

Neural tube-associated boundary caps are a major source of mural cells in the skin.
Gerschenfeld G, Coulpier F, Gresset A, Pulh P, Job B, Topilko T, Siegenthaler J, Kastriti ME, Brunet I, Charnay P, Topilko P
Elife. 2023 Dec 14. 12.

GluD1 binds GABA and controls inhibitory plasticity.
Piot L, Heroven C, Bossi S, Zamith J, Malinauskas T, Johnson C, Wennagel D, Stroebel D, Charrier C, Aricescu AR, Mony L, Paoletti P
Science. 2023 Dec 22. 382(6677):1389-1394.

Airway ciliated cells in adult lung homeostasis and COPD.
Petit LMG, Belgacemi R, Ancel J, Saber Cherif L, Polette M, Perotin JM, Spassky N, Pilette C, Al Alam D, Deslée G, Dormoy V
Eur Respir Rev. 2023 Dec 31. 32(170).

SCO-spondin knockout mice exhibit small brain ventricles and mild spine deformation.
Xu H, Dugué GP, Cantaut‑Belarif Y, Lejeune FX, Gupta S, Wyart C, Lehtinen MK
Fluids Barriers CNS. 2023 Dec 5. 20(1):89.

Effect of the res2 transcription factor gene deletion on protein secretion and stress response in the hyperproducer strain Trichoderma reesei Rut-C30.
Alharake J, Bidard F, Aouam T, Sénamaud‑Beaufort C, Margeot A, Heiss‑Blanquet S
BMC Microbiol. 2023 Nov 30. 23(1):374.

Prdm12 represses the expression of the visceral neuron determinants Phox2a/b in developing somatosensory ganglia.
Vermeiren S, Cabochette P, Dannawi M, Desiderio S, San José AS, Achouri Y, Kricha S, Sitte M, Salinas‑Riester G, Vanhollebeke B, Brunet JF, Bellefroid EJ
iScience. 2023 Dec 15. 26(12):108364.

Viral strain-dependent impact of plant developmental stages on the nestedness and modularity of plant-virus interaction matrices.
Melero I, Elena SF, González R
MicroPubl Biol. 2023. 2023.

rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers.
Parée T, Noble L, Gonçalves JF, Teotónio H
Genetics. 2023 Nov 24.

Paired single-cell multi-omics data integration with Mowgli.
Huizing GJ, Deutschmann IM, Peyré G, Cantini L
Nat Commun. 2023 Nov 24. 14(1):7711.

Fluorescence to measure light intensity.
Lahlou A, Tehrani HS, Coghill I, Shpinov Y, Mandal M, Plamont MA, Aujard I, Niu Y, Nedbal L, Lazár D, Mahou P, Supatto W, Beaurepaire E, Eisenmann I, Desprat N, Croquette V, Jeanneret R, Le Saux T, Jullien L
Nat Methods. 2023 Dec. 20(12):1930-1938.

Mechanisms of NMDA receptor regulation.
Mony L, Paoletti P
Curr Opin Neurobiol. 2023 Dec. 83:102815.

Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans.
Frézal L, Saglio M, Zhang G, Noble L, Richaud A, Félix MA
EMBO Rep. 2023 Dec 6. 24(12):e58116.

Convergent adaptation of true crabs (Decapoda : Brachyura) to a gradient of terrestrial environments.
Wolfe JM, Ballou L, Luque J, Watson‑Zink VM, Ahyong ST, Barido‑Sottani J, Chan TY, Chu KH, Crandall KA, Daniels SR, Felder DL, Mancke H, Martin JW, Ng PKL, Ortega‑Hernández J, Palacios Theil E, Pentcheff ND, Robles R, Thoma BP, Tsang LM, Wetzer R, Windsor AM, Bracken‑Grissom HD
Syst Biol. 2023 Nov 6.

Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection.
Corre M, Boehm V, Besic V, Kurowska A, Viry A, Mohammad A, Sénamaud‑Beaufort C, Thomas‑Chollier M, Lebreton A
Nucleic Acids Res. 2023 Dec 11. 51(22):12459-12475.

Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila.
Morillo L, Paternina T, Alasseur Q, Genovesio A, Schwartz S, Le Hir H
BMC Biol. 2023 Nov 7. 21(1):246.

iPS-cell-derived microglia promote brain organoid maturation via cholesterol transfer.
Park DS, Kozaki T, Tiwari SK, Moreira M, Khalilnezhad A, Torta F, Olivié N, Thiam CH, Liani O, Silvin A, Phoo WW, Gao L, Triebl A, Tham WK, Gonçalves L, Kong WT, Raman S, Zhang XM, Dunsmore G, Dutertre CA, Lee S, Ong JM, Balachander A, Khalilnezhad S, Lum J, Duan K, Lim ZM, Tan L, Low I, Utami KH, Yeo XY, Di Tommaso S, Dupuy JW, Varga B, Karadottir RT, Madathummal MC, Bonne I, Malleret B, Binte ZY, Wei Da N, Tan Y, Wong WJ, Zhang J, Chen J, Sobota RM, Howland SW, Ng LG, Saltel F, Castel D, Grill J, Minard V, Albani S, Chan JKY, Thion MS, Jung SY, Wenk MR, Pouladi MA, Pasqualini C, Angeli V, Cexus ONF, Ginhoux F
Nature. 2023 Nov. 623(7986):397-405.

Local glycolysis fuels actomyosin contraction during axonal retraction.
Santos R, Lokmane L, Ozdemir D, Traoré C, Agesilas A, Hakibilen C, Lenkei Z, Zala D
J Cell Biol. 2023 Dec 4. 222(12).

Choroid plexuses carry nodal-like cilia that undergo axoneme regression from early adult stage.
Ho KH, Candat A, Scarpetta V, Faucourt M, Weill S, Salio C, D’Este E, Meschkat M, Wurm CA, Kneussel M, Janke C, Magiera MM, Genovesio A, Meunier A, Sassoè‑Pognetto M, Brill MS, Spassky N, Patrizi A
Dev Cell. 2023 Dec 4. 58(23):2641-2651.e6.

Radial astrocyte synchronization modulates the visual system during behavioral-state transitions.
Uribe‑Arias A, Rozenblat R, Vinepinsky E, Marachlian E, Kulkarni A, Zada D, Privat M, Topsakalian D, Charpy S, Candat V, Nourin S, Appelbaum L, Sumbre G
Neuron. 2023 Dec 20. 111(24):4040-4057.e6.

Revealing invisible cell phenotypes with conditional generative modeling.
Lamiable A, Champetier T, Leonardi F, Cohen E, Sommer P, Hardy D, Argy N, Massougbodji A, Del Nery E, Cottrell G, Kwon YJ, Genovesio A
Nat Commun. 2023 Oct 11. 14(1):6386.

Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii.
Paré L, Bideau L, Baduel L, Dalle C, Benchouaia M, Schneider SQ, Laplane L, Clément Y, Vervoort M, Gazave E
BMC Genomics. 2023 Oct 2. 24(1):583.

Gains and losses of the epiphytic lifestyle in epidendroid orchids : review and new analyses of succulence traits.
Collobert G, Perez‑Lamarque B, Dubuisson JY, Martos F
Ann Bot. 2023 Nov 25. 132(4):787-800.

Disentangling local and global climate drivers in the population dynamics of mosquito-borne infections.
Cazelles B, Cazelles K, Tian H, Chavez M, Pascual M
Sci Adv. 2023 Sep 29. 9(39):eadf7202.

A protocol for whole-brain Ca(2+) imaging in Astyanax mexicanus, a model of comparative evolution.
Lloyd E, Privat M, Sumbre G, Duboué ER, Keene AC
STAR Protoc. 2023 Sep 23. 4(4):102517.

Predicting global distributions of eukaryotic plankton communities from satellite data.
Kaneko H, Endo H, Henry N, Berney C, Mahé F, Poulain J, Labadie K, Beluche O, El Hourany R, Chaffron S, Wincker P, Nakamura R, Karp‑Boss L, Boss E, Bowler C, de Vargas C, Tomii K, Ogata H
ISME Commun. 2023 Sep 22. 3(1):101.

Human-environment feedback and the consistency of proenvironmental behavior.
Ecotière C, Billiard S, André JB, Collet P, Ferrière R, Méléard S
PLoS Comput Biol. 2023 Sep. 19(9):e1011429.

Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis.
Gribaudo S, Robert R, van Sambeek B, Mirdass C, Lyubimova A, Bouhali K, Ferent J, Morin X, van Oudenaarden A, Nedelec S
Nat Biotechnol. 2023 Sep 14.

Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.
Chang LH, Ghosh S, Papale A, Luppino JM, Miranda M, Piras V, Degrouard J, Edouard J, Poncelet M, Lecouvreur N, Bloyer S, Leforestier A, Joyce EF, Holcman D, Noordermeer D
Nat Commun. 2023 Sep 12. 14(1):5615.

Real-time detection of virus antibody interaction by label-free common-path interferometry.
Alhaddad S, Bey H, Thouvenin O, Boulanger P, Boccara C, Boccara M, Izeddin I
Biophys Rep (N Y). 2023 Sep 13. 3(3):100119.

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation.
Sanz‑Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós‑Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG
ISME Commun. 2023 Sep 2. 3(1):92.

Selection and the direction of phenotypic evolution.
Mallard F, Afonso B, Teotónio H
Elife. 2023 Aug 31. 12.

Global determinants of insect mitochondrial genetic diversity.
French CM, Bertola LD, Carnaval AC, Economo EP, Kass JM, Lohman DJ, Marske KA, Meier R, Overcast I, Rominger AJ, Staniczenko PPA, Hickerson MJ
Nat Commun. 2023 Aug 29. 14(1):5276.

Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits.
Parey E, Fernandez‑Aroca D, Frost S, Uribarren A, Park TJ, Zöttl M, St John Smith E, Berthelot C, Villar D
Genome Res. 2023 Sep. 33(9):1513-1526.

Ocean-wide comparisons of mesopelagic planktonic community structures.
Rigonato J, Budinich M, Murillo AA, Brandão MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Frémont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E, Bork P, Bowler C, de Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O
ISME Commun. 2023 Aug 18. 3(1):83.

Model of membrane deformations driven by a surface pH gradient.
Mendes TV, Ranft J, Berthoumieux H
Phys Rev E. 2023 Jul. 108(1-1):014113.

Special issue : Synaptic logistics - Maintenance of synaptic composition, properties and function.
Ziv NE, Triller A
Mol Cell Neurosci. 2023 Dec. 127:103885.

Deep Learning from Phylogenies for Diversification Analyses.
Lambert S, Voznica J, Morlon H
Syst Biol. 2023 Aug 9.

Plasticity of thalamocortical axons is regulated by serotonin levels modulated by preterm birth.
Sinclair‑Wilson A, Lawrence A, Ferezou I, Cartonnet H, Mailhes C, Garel S, Lokmane L
Proc Natl Acad Sci U S A. 2023 Aug 15. 120(33):e2301644120.

Rif1 restrains the rate of replication origin firing in Xenopus laevis.
Haccard O, Ciardo D, Narrissamprakash H, Bronchain O, Kumagai A, Dunphy WG, Goldar A, Marheineke K
Commun Biol. 2023 Jul 29. 6(1):788.

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis.
Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV, Schrumpfová PP, Fajkus J, Amiard S, Grob S, Bourbousse C, Barneche F
Cell Rep. 2023 Aug 29. 42(8):112894.

A genome-wide screen reveals new regulators of the 2-cell-like cell state.
Gupta N, Yakhou L, Albert JR, Azogui A, Ferry L, Kirsh O, Miura F, Battault S, Yamaguchi K, Laisné M, Domrane C, Bonhomme F, Sarkar A, Delagrange M, Ducos B, Cristofari G, Ito T, Greenberg MVC, Defossez PA
Nat Struct Mol Biol. 2023 Aug. 30(8):1105-1118.

Evolutionary modifications of Astyanax larval prey capture (LPC) in a dark environment.
Espinasa L, Diamant R, Vinepinsky E, Espinasa M
Zool Res. 2023 Jul 18. 44(4):750-760.

Differences in carbonate chemistry up-regulation of long-lived reef-building corals.
Canesi M, Douville E, Montagna P, Taviani M, Stolarski J, Bordier L, Dapoigny A, Coulibaly GEH, Simon AC, Agelou M, Fin J, Metzl N, Iwankow G, Allemand D, Planes S, Moulin C, Lombard F, Bourdin G, Troublé R, Agostini S, Banaigs B, Boissin E, Boss E, Bowler C, de Vargas C, Flores M, Forcioli D, Furla P, Gilson E, Galand PE, Pesant S, Sunagawa S, Thomas OP, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, Reynaud S
Sci Rep. 2023 Jul 18. 13(1):11589.

Diversity of dynamic voltage patterns in neuronal dendrites revealed by nanopipette electrophysiology.
Mc Hugh J, Makarchuk S, Mozheiko D, Fernandez‑Villegas A, Kaminski Schierle GS, Kaminski CF, Keyser UF, Holcman D, Rouach N
Nanoscale. 2023 Jul 27. 15(29):12245-12254.

The genetic basis of epigenetic variation and its consequences for adaptation.
Baduel P, Sasaki E
Curr Opin Plant Biol. 2023 Oct. 75:102409.

G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions.
Esnault C, Magat T, Zine El Aabidine A, Garcia‑Oliver E, Cucchiarini A, Bouchouika S, Lleres D, Goerke L, Luo Y, Verga D, Lacroix L, Feil R, Spicuglia S, Mergny JL, Andrau JC
Nat Genet. 2023 Aug. 55(8):1359-1369.

Editorial : Neurobiology of Drosophila : the 19th NeuroFly-2022 meeting.
Martin JR, Chatterjee A, Salecker I
Front Physiol. 2023. 14:1237065.

Natural antisense transcription of presenilin in sea urchin reveals a possible role for natural antisense transcription in the general control of gene expression during development.
Bronchain O, Ducos B, Putzer H, Delagrange M, Laalami S, Philippe‑Caraty L, Saroul K, Ciapa B
J Cell Sci. 2023 Jul 15. 136(14).

Diverse eukaryotic phytoplankton from around the Marquesas Islands documented by combined microscopy and molecular techniques.
Veselá‑Strejcová J, Scalco E, Zingone A, Colin S, Caputi L, Sarno D, Nebesářová J, Bowler C, Lukeš J
Protist. 2023 Aug. 174(4):125965.

Phylogenetic Comparative Approach Reveals Evolutionary Conservatism, Ancestral Composition, and Integration of Vertebrate Gut Microbiota.
Perez‑Lamarque B, Sommeria‑Klein G, Duret L, Morlon H
Mol Biol Evol. 2023 Jul 5. 40(7).

Repurposing of the multiciliation gene regulatory network in fate specification of Cajal-Retzius neurons.
Moreau MX, Saillour Y, Elorriaga V, Bouloudi B, Delberghe E, Deutsch Guerrero T, Ochandorena‑Saa A, Maeso‑Alonso L, Marques MM, Marin MC, Spassky N, Pierani A, Causeret F
Dev Cell. 2023 Aug 7. 58(15):1365-1382.e6.

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 Jun 1. 136(11).

Artificial selection of communities drives the emergence of structured interactions.
Fraboul J, Biroli G, De Monte S
J Theor Biol. 2023 Aug 21. 571:111557.

Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds.
Wang YJ, Valotteau C, Aimard A, Villanueva L, Kostrz D, Follenfant M, Strick T, Chames P, Rico F, Gosse C, Limozin L
Biophys J. 2023 Jun 20. 122(12):2518-2530.

Magnetic actuation of otoliths allows behavioral and brain-wide neuronal exploration of vestibulo-motor processing in larval zebrafish.
Beiza‑Canelo N, Moulle H, Pujol T, Panier T, Migault G, Le Goc G, Tapie P, Desprat N, Straka H, Debrégeas G, Bormuth V
Curr Biol. 2023 Jun 19. 33(12):2438-2448.e6.

A QTL on chromosome IV explains a natural variation of QR.pap final position in Caenorhabditis elegans.
Dubois C, Félix MA
MicroPubl Biol. 2023. 2023.

Pervasive tandem duplications and convergent evolution shape coral genomes.
Noel B, Denoeud F, Rouan A, Buitrago‑López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê‑Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM
Genome Biol. 2023 Jun 1. 24(1):123.

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.
Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL
Commun Biol. 2023 Jun 1. 6(1):566.

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.
Belser C, Poulain J, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S, Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, Wincker P
Sci Data. 2023 Jun 1. 10(1):326.

Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean.
Armstrong EJ, Lê‑Hoang J, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz‑García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, Wincker P
Nat Commun. 2023 Jun 1. 14(1):3056.

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems.
Lombard F, Bourdin G, Pesant S, Agostini S, Baudena A, Boissin E, Cassar N, Clampitt M, Conan P, Da Silva O, Dimier C, Douville E, Elineau A, Fin J, Flores JM, Ghiglione JF, Hume BCC, Jalabert L, John SG, Kelly RL, Koren I, Lin Y, Marie D, McMinds R, Mériguet Z, Metzl N, Paz‑García DA, Pedrotti ML, Poulain J, Pujo‑Pay M, Ras J, Reverdin G, Romac S, Rouan A, Röttinger E, Vardi A, Voolstra CR, Moulin C, Iwankow G, Banaigs B, Bowler C, de Vargas C, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Sullivan MB, Thomas OP, Troublé R, Thurber RV, Wincker P, Zoccola D, Allemand D, Planes S, Boss E, Gorsky G
Sci Data. 2023 Jun 1. 10(1):324.

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.
Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz‑García DA, Nugues MM, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE
Nat Commun. 2023 Jun 1. 14(1):3037.

Diversity of the Pacific Ocean coral reef microbiome.
Galand PE, Ruscheweyh HJ, Salazar G, Hochart C, Henry N, Hume BCC, Oliveira PH, Perdereau A, Labadie K, Belser C, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Armstrong EJ, Paz‑García DA, Ziegler M, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Zoccola D, Voolstra CR, Thurber RV, Sunagawa S, Wincker P, Allemand D, Planes S
Nat Commun. 2023 Jun 1. 14(1):3039.

Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals.
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Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.
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PLoS Comput Biol. 2023 May. 19(5):e1011138.

Excitatory GluN1/GluN3A glycine receptors (eGlyRs) in brain signaling.
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Trends Neurosci. 2023 Aug. 46(8):667-681.

Single-cell phenotypic plasticity modulates social behavior in Dictyostelium discoideum.
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iScience. 2023 Jun 16. 26(6):106783.

Cerebellar control of fear learning via the cerebellar nuclei-Multiple pathways, multiple mechanisms ?
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Front Syst Neurosci. 2023. 17:1176668.

Inferring the ecological and evolutionary determinants of community genetic diversity.
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Upregulation of breathing rate during running exercise by central locomotor circuits in mice.
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Theory of the asynchronous state of structured rotator networks and its application to recurrent networks of excitatory and inhibitory units.
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Phys Rev E. 2023 Apr. 107(4-1):044306.

Wavelet clustering analysis as a tool for characterizing community structure in the human microbiome.
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Sci Rep. 2023 May 17. 13(1):8042.

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
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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.
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Precise temporal control of neuroblast migration through combined regulation and feedback of a Wnt receptor.
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Elife. 2023 May 15. 12.

The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2.
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The build-up of the present-day tropical diversity of tetrapods.
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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.
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Mol Biol Evol. 2023 May 2. 40(5).

The MIR34B/C genomic region contains multiple potential regulators of multiciliogenesis.
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Boundary vector cells in the goldfish central telencephalon encode spatial information.
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PLoS Biol. 2023 Apr. 21(4):e3001747.

Multifaceted microglia during brain development : Models and tools.
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Front Neurosci. 2023. 17:1125729.

High Growth Rate of Diatoms Explained by Reduced Carbon Requirement and Low Energy Cost of Silica Deposition.
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Microbiol Spectr. 2023 Jun 15. 11(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.
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Filopodia-like protrusions of adjacent somatic cells shape the developmental potential of oocytes.
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The cerebellum regulates fear extinction through thalamo-prefrontal cortex interactions in male mice.
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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.
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Biochimie. 2023 Oct. 213:54-65.

Direct whole-cell patch-clamp recordings from small boutons in rodent primary neocortical neuron cultures.
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Beta oscillations and waves in motor cortex can be accounted for by the interplay of spatially structured connectivity and fluctuating inputs.
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Elife. 2023 Mar 14. 12.

Light-dependent signal transduction in the marine diatom Phaeodactylum tricornutum.
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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.
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Mol Biol Evol. 2023 Mar 4. 40(3).

Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists.
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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.
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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.
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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
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PlantACT ! - how to tackle the climate crisis.
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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
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Bottlenecks can constrain and channel evolutionary paths.
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Genetics. 2023 May 26. 224(2).

Author Correction : Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes.
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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.
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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.
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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.
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Nat Protoc. 2023 Apr. 18(4):1260-1295.

Data-driven multiscale dynamical framework to control a pandemic evolution with non-pharmaceutical interventions.
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PLoS One. 2023. 18(1):e0278882.

Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.
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Nat Ecol Evol. 2023 Mar. 7(3):355-366.

Annexin A1 is a polarity cue that directs mitotic spindle orientation during mammalian epithelial morphogenesis.
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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.

Guidelines for G-quadruplexes : I. In vitro characterization.
Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL
Biochimie. 2023 Nov. 214(Pt A):5-23.

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.
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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.

Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process.
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Syst Biol. 2023 Jun 16. 72(2):466-475.

In mice and humans, brain microvascular contractility matures postnatally.
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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.

Collective and harmonized high throughput barcoding of insular arthropod biodiversity : Toward a Genomic Observatories Network for islands.
Emerson BC, Borges PAV, Cardoso P, Convey P, deWaard JR, Economo EP, Gillespie RG, Kennedy S, Krehenwinkel H, Meier R, Roderick GK, Strasberg D, Thébaud C, Traveset A, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Arribas P, Andújar C
Mol Ecol. 2023 Dec. 32(23):6161-6176.

Comparing different computational approaches for detecting long-term vertical transmission in host-associated microbiota.
Perez‑Lamarque B, Morlon H
Mol Ecol. 2023 Dec. 32(23):6671-6685.

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.

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests.
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Mol Ecol. 2023 Dec. 32(23):6110-6128.