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Publications

2019

Alpha rhythm collapse predicts iso-electric suppressions during anesthesia.
Cartailler J, Parutto P, Touchard C, Vallée F, Holcman D
Commun Biol. 2019 Sep 2. 2(1):327.

Inhibitory Receptor Diffusion Dynamics.
Maynard SA, Triller A
Front Mol Neurosci. 2019. 12:313.

Activity-dependent death of transient Cajal-Retzius neurons is required for functional cortical wiring.
Riva M, Genescu I, Habermacher C, Orduz D, Ledonne F, Rijli FM, López‑Bendito G, Coppola E, Garel S, Angulo MC, Pierani A
Elife. 2019 Dec 31. 8.

PySpacell : A Python Package for Spatial Analysis of Cell Images.
Rose F, Rappez L, Triana SH, Alexandrov T, Genovesio A
Cytometry A. 2019 Dec 24.

RSAT variation-tools : An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.
Santana‑Garcia W, Rocha‑Acevedo M, Ramirez‑Navarro L, Mbouamboua Y, Thieffry D, Thomas‑Chollier M, Contreras‑Moreira B, van Helden J, Medina‑Rivera A
Comput Struct Biotechnol J. 2019. 17:1415-1428.

A measure of force.
Strick TR, Yan J
Curr Opin Chem Biol. 2019 Dec. 53:A4-A6.

Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation.
Baduel P, Quadrana L, Hunter B, Bomblies K, Colot V
Nat Commun. 2019 Dec 20. 10(1):5818.

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus.
Pargana A, Musacchia F, Sanges R, Russo MT, Ferrante MI, Bowler C, Zingone A
Genes (Basel). 2019 Dec 20. 11(1).

Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions.
Quintero I, Landis MJ
Syst Biol. 2019 Dec 20.

GC content shapes mRNA storage and decay in human cells.
Courel M, Clément Y, Bossevain C, Foretek D, Vidal Cruchez O, Yi Z, Bénard M, Benassy MN, Kress M, Vindry C, Ernoult‑Lange M, Antoniewski C, Morillon A, Brest P, Hubstenberger A, Roest Crollius H, Standart N, Weil D
Elife. 2019 Dec 19. 8.

Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation.
Sánchez‑Villanueva JA, Rodríguez‑Jorge O, Ramírez‑Pliego O, Rosas Salgado G, Abou‑Jaoudé W, Hernandez C, Naldi A, Thieffry D, Santana MA
PLoS One. 2019. 14(12):e0226388.

cAMP-EPAC-Dependent Regulation of Gephyrin Phosphorylation and GABAAR Trapping at Inhibitory Synapses.
Niwa F, Patrizio A, Triller A, Specht CG
iScience. 2019 Dec 20. 22:453-465.

Ultrafast Two-Photon Imaging of a High-Gain Voltage Indicator in Awake Behaving Mice.
Villette V, Chavarha M, Dimov IK, Bradley J, Pradhan L, Mathieu B, Evans SW, Chamberland S, Shi D, Yang R, Kim BB, Ayon A, Jalil A, St‑Pierre F, Schnitzer MJ, Bi G, Toth K, Ding J, Dieudonné S, Lin MZ
Cell. 2019 Dec 12. 179(7):1590-1608.e23.

Massive centriole production can occur in the absence of deuterosomes in multiciliated cells.
Mercey O, Levine MS, LoMastro GM, Rostaing P, Brotslaw E, Gomez V, Kumar A, Spassky N, Mitchell BJ, Meunier A, Holland AJ
Nat Cell Biol. 2019 Dec. 21(12):1544-1552.

An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling.
Pagliuso A, Tham TN, Allemand E, Robertin S, Dupuy B, Bertrand Q, Bécavin C, Koutero M, Najburg V, Nahori MA, Tangy F, Stavru F, Bessonov S, Dessen A, Muchardt C, Lebreton A, Komarova AV, Cossart P
Cell Host Microbe. 2019 Dec 11. 26(6):823-835.e11.

Molecular scaffolds : when DNA becomes the hardware for single-molecule investigations.
Gosse C, Strick TR, Kostrz D
Curr Opin Chem Biol. 2019 Dec. 53:192-203.

Global Trends in Marine Plankton Diversity across Kingdoms of Life.
Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo‑Llonch M, Salazar G, Sanz‑Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp‑Boss L, Wincker P, Lombard F, Bowler C, Zinger L
Cell. 2019 Nov 14. 179(5):1084-1097.e21.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.
Salazar G, Paoli L, Alberti A, Huerta‑Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo‑Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp‑Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S
Cell. 2019 Nov 14. 179(5):1068-1083.e21.

The Crohn’s disease-associated Escherichia coli strain LF82 relies on SOS and stringent responses to survive, multiply and tolerate antibiotics within macrophages.
Demarre G, Prudent V, Schenk H, Rousseau E, Bringer MA, Barnich N, Tran Van Nhieu G, Rimsky S, De Monte S, Espéli O
PLoS Pathog. 2019 Nov. 15(11):e1008123.

Sensorimotor Transformations in the Zebrafish Auditory System.
Privat M, Romano SA, Pietri T, Jouary A, Boulanger‑Weill J, Elbaz N, Duchemin A, Soares D, Sumbre G
Curr Biol. 2019 Dec 2. 29(23):4010-4023.e4.

Trans-Synaptic Signaling through the Glutamate Receptor Delta-1 Mediates Inhibitory Synapse Formation in Cortical Pyramidal Neurons.
Fossati M, Assendorp N, Gemin O, Colasse S, Dingli F, Arras G, Loew D, Charrier C
Neuron. 2019 Dec 18. 104(6):1081-1094.e7.

Electrodiffusion Theory to Map the Voltage Distribution in Dendritic Spines at a Nanometer Scale.
Cartailler J, Holcman D
Neuron. 2019 Nov 6. 104(3):440-441.

No Extraction of Spine Neck Resistance from Underdetermined Equations.
Barbour B
Neuron. 2019 Nov 6. 104(3):438-439.

Investigating the epi-miRNome : identification of epi-miRNAs using transfection experiments.
Reale E, Taverna D, Cantini L, Martignetti L, Osella M, De Pittà C, Virga F, Orso F, Caselle M
Epigenomics. 2019 Nov. 11(14):1581-1599.

Electrical Stimulation in the Claustrum Area Induces a Deepening of Isoflurane Anesthesia in Rat.
Pavel B, Menardy F, Rotaru D, Paslaru AC, Acatrinei C, Zagrean L, Popa D, Zagrean AM
Brain Sci. 2019 Nov 1. 9(11).

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. 2019 Sep 6.

Sparse force-bearing bridges between neighboring synaptic vesicles.
Wesseling JF, Phan S, Bushong EA, Siksou L, Marty S, Pérez‑Otaño I, Ellisman M
Brain Struct Funct. 2019 Dec. 224(9):3263-3276.

Altered trophic interactions in warming climates : consequences for predator diet breadth and fitness.
Bestion E, Soriano‑Redondo A, Cucherousset J, Jacob S, White J, Zinger L, Fourtune L, Di Gesu L, Teyssier A, Cote J
Proc Biol Sci. 2019 Nov 6. 286(1914):20192227.

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. 2019 Oct 24.

Access to RNA-sequencing data from 1,173 plant species : The 1000 Plant transcriptomes initiative (1KP).
Carpenter EJ, Matasci N, Ayyampalayam S, Wu S, Sun J, Yu J, Jimenez Vieira FR, Bowler C, Dorrell RG, Gitzendanner MA, Li L, Du W, K Ullrich K, Wickett NJ, Barkmann TJ, Barker MS, Leebens‑Mack JH, Wong GK
Gigascience. 2019 Oct 1. 8(10).

Active Fluctuations of the Nuclear Envelope Shape the Transcriptional Dynamics in Oocytes.
Almonacid M, Al Jord A, El‑Hayek S, Othmani A, Coulpier F, Lemoine S, Miyamoto K, Grosse R, Klein C, Piolot T, Mailly P, Voituriez R, Genovesio A, Verlhac MH
Dev Cell. 2019 Oct 21. 51(2):145-157.e10.

Control of aversion by glycine-gated GluN1/GluN3A NMDA receptors in the adult medial habenula.
Otsu Y, Darcq E, Pietrajtis K, Mátyás F, Schwartz E, Bessaih T, Abi Gerges S, Rousseau CV, Grand T, Dieudonné S, Paoletti P, Acsády L, Agulhon C, Kieffer BL, Diana MA
Science. 2019 Oct 11. 366(6462):250-254.

The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair.
Mardenborough YSN, Nitsenko K, Laffeber C, Duboc C, Sahin E, Quessada‑Vial A, Winterwerp HHK, Sixma TK, Kanaar R, Friedhoff P, Strick TR, Lebbink JHG
Nucleic Acids Res. 2019 Dec 16. 47(22):11667-11680.

HEXIM1 Diffusion in the Nucleus Is Regulated by Its Interactions with Both 7SK and P-TEFb.
Furlan A, Gonzalez‑Pisfil M, Leray A, Champelovier D, Henry M, Le Nézet C, Bensaude O, Lefranc M, Wohland T, Vandenbunder B, Bidaux G, Héliot L
Biophys J. 2019 Nov 5. 117(9):1615-1625.

A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication.
Grandclaudon M, Perrot‑Dockès M, Trichot C, Karpf L, Abouzid O, Chauvin C, Sirven P, Abou‑Jaoudé W, Berger F, Hupé P, Thieffry D, Sansonnet L, Chiquet J, Lévy‑Leduc C, Soumelis V
Cell. 2019 Oct 3. 179(2):432-447.e21.

Does toe clipping for genotyping interfere with later-in-life nociception in mice ?
Frezel N, Kratzer G, Verzar P, Bürki J, Weber FA, Zeilhofer HU
Pain Rep. 2019 May-Jun. 4(3):e740.

Taste bud formation depends on taste nerves.
Fan D, Chettouh Z, Consalez GG, Brunet JF
Elife. 2019 Oct 1. 8.

A modular DNA scaffold to study protein-protein interactions at single-molecule resolution.
Kostrz D, Wayment‑Steele HK, Wang JL, Follenfant M, Pande VS, Strick TR, Gosse C
Nat Nanotechnol. 2019 Oct. 14(10):988-993.

Selection and gene flow shape niche-associated variation in pheromone response.
Lee D, Zdraljevic S, Cook DE, Frézal L, Hsu JC, Sterken MG, Riksen JAG, Wang J, Kammenga JE, Braendle C, Félix MA, Schroeder FC, Andersen EC
Nat Ecol Evol. 2019 Oct. 3(10):1455-1463.

Intrinsic and extrinsic drivers of transmission dynamics of hemorrhagic fever with renal syndrome caused by Seoul hantavirus.
Li Y, Cazelles B, Yang G, Laine M, Huang ZXY, Cai J, Tan H, Stenseth NC, Tian H
PLoS Negl Trop Dis. 2019 Sep. 13(9):e0007757.

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.
Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D
PLoS Biol. 2019 Sep. 17(9):e3000483.

Characterizing and comparing phylogenetic trait data from their normalized Laplacian spectrum.
Lewitus E, Aristide L, Morlon H
Syst Biol. 2019 Sep 16.

Molecular characterisation of a cellular conveyor belt in Clytia medusae.
Condamine T, Jager M, Leclère L, Blugeon C, Lemoine S, Copley RR, Manuel M
Dev Biol. 2019 Dec 15. 456(2):212-225.

Alpha rhythm collapse predicts iso-electric suppressions during anesthesia.
Cartailler J, Parutto P, Touchard C, Vallée F, Holcman D
Commun Biol. 2019. 2:327.

Understanding the effect of competition during evolutionary radiations : an integrated model of phenotypic and species diversification.
Aristide L, Morlon H
Ecol Lett. 2019 Dec. 22(12):2006-2017.

Dynamics of centriole amplification in centrosome-depleted brain multiciliated progenitors.
Mercey O, Al Jord A, Rostaing P, Mahuzier A, Fortoul A, Boudjema AR, Faucourt M, Spassky N, Meunier A
Sci Rep. 2019 Sep 10. 9(1):13060.

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets.
Sompairac N, Nazarov PV, Czerwinska U, Cantini L, Biton A, Molkenov A, Zhumadilov Z, Barillot E, Radvanyi F, Gorban A, Kairov U, Zinovyev A
Int J Mol Sci. 2019 Sep 7. 20(18).

Competition for resources may reinforce the evolution of altruism in spatially structured populations.
Baalen MV, Yamauchi A
Math Biosci Eng. 2019 Apr 26. 16(5):3694-3717.

Assessing the causes of diversification slowdowns : temperature-dependent and diversity-dependent models receive equivalent support.
Condamine FL, Rolland J, Morlon H
Ecol Lett. 2019 Nov. 22(11):1900-1912.

Network Reconstruction and Significant Pathway Extraction Using Phosphoproteomic Data from Cancer Cells.
Buffard M, Naldi A, Radulescu O, Coopman PJ, Larive RM, Freiss G
Proteomics. 2019 Nov. 19(21-22):e1800450.

How differing modes of non-genetic inheritance affect population viability in fluctuating environments.
Proulx SR, Dey S, Guzella T, Teotónio H
Ecol Lett. 2019 Nov. 22(11):1767-1775.

Noda-Like RNA Viruses Infecting Caenorhabditis Nematodes : Sympatry, Diversity, and Reassortment.
Frézal L, Jung H, Tahan S, Wang D, Félix MA
J Virol. 2019 Nov 1. 93(21).

Natural Viruses of Caenorhabditis Nematodes.
Félix MA, Wang D
Annu Rev Genet. 2019 Dec 3. 53:313-326.

Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly Heliconius numata.
Saenko SV, Chouteau M, Piron‑Prunier F, Blugeon C, Joron M, Llaurens V
Evodevo. 2019. 10:16.

MicroRNA gene regulation in extremely young and parallel adaptive radiations of crater lake cichlid fish.
Franchini P, Xiong P, Fruciano C, Schneider RF, Woltering JM, Hulsey CD, Meyer A
Mol Biol Evol. 2019 Aug 9.

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis.
Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C
Genome Biol. 2019 Aug 7. 20(1):157.

Optical control of protein activity and gene expression by photoactivation of caged cyclofen.
Hamouri F, Zhang W, Aujard I, Le Saux T, Ducos B, Vriz S, Jullien L, Bensimon D
Methods Enzymol. 2019. 624:1-23.

Transposition favors the generation of large effect mutations that may facilitate rapid adaption.
Quadrana L, Etcheverry M, Gilly A, Caillieux E, Madoui MA, Guy J, Bortolini Silveira A, Engelen S, Baillet V, Wincker P, Aury JM, Colot V
Nat Commun. 2019 Jul 31. 10(1):3421.

Metabolic Innovations Underpinning the Origin and Diversification of the Diatom Chloroplast.
Nonoyama T, Kazamia E, Nawaly H, Gao X, Tsuji Y, Matsuda Y, Bowler C, Tanaka T, Dorrell RG
Biomolecules. 2019 Jul 30. 9(8).

Biphasic Impact of Prenatal Inflammation and Macrophage Depletion on the Wiring of Neocortical Inhibitory Circuits.
Thion MS, Mosser CA, Férézou I, Grisel P, Baptista S, Low D, Ginhoux F, Garel S, Audinat E
Cell Rep. 2019 Jul 30. 28(5):1119-1126.e4.

The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution.
Roy J, Mazel F, Sosa‑Hernández MA, Dueñas JF, Hempel S, Zinger L, Rillig MC
New Phytol. 2019 Oct. 224(2):936-948.

GemC1 is a critical switch for neural stem cell generation in the postnatal brain.
Lalioti ME, Kaplani K, Lokka G, Georgomanolis T, Kyrousi C, Dong W, Dunbar A, Parlapani E, Damianidou E, Spassky N, Kahle KT, Papantonis A, Lygerou Z, Taraviras S
Glia. 2019 Dec. 67(12):2360-2373.

m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants.
Yang L, Perrera V, Saplaoura E, Apelt F, Bahin M, Kramdi A, Olas J, Mueller‑Roeber B, Sokolowska E, Zhang W, Li R, Pitzalis N, Heinlein M, Zhang S, Genovesio A, Colot V, Kragler F
Curr Biol. 2019 Aug 5. 29(15):2465-2476.e5.

Characterizing symbiont inheritance during host-microbiota evolution : Application to the great apes gut microbiota.
Perez‑Lamarque B, Morlon H
Mol Ecol Resour. 2019 Nov. 19(6):1659-1671.

Phaeodactylum tricornutum.
Bowler C, Falciatore A
Trends Genet. 2019 Sep. 35(9):706-707.

Subsynaptic Domains in Super-Resolution Microscopy : The Treachery of Images.
Yang X, Specht CG
Front Mol Neurosci. 2019. 12:161.

Neural signatures of sleep in zebrafish.
Leung LC, Wang GX, Madelaine R, Skariah G, Kawakami K, Deisseroth K, Urban AE, Mourrain P
Nature. 2019 Jul. 571(7764):198-204.

Optical control of neuronal ion channels and receptors.
Paoletti P, Ellis‑Davies GCR, Mourot A
Nat Rev Neurosci. 2019 Sep. 20(9):514-532.

Loss of a Fragile Chromosome Region leads to the Screwy Phenotype in Paramecium tetraurelia.
Nekrasova I, Nikitashina V, Bhullar S, Arnaiz O, Singh DP, Meyer E, Potekhin A
Genes (Basel). 2019 Jul 6. 10(7).

Partial Selfing Can Reduce Genetic Loads While Maintaining Diversity During Experimental Evolution.
Chelo IM, Afonso B, Carvalho S, Theologidis I, Goy C, Pino‑Querido A, Proulx SR, Teotónio H
G3 (Bethesda). 2019 Sep 4. 9(9):2811-2821.

Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes.
Busseni G, Vieira FRJ, Amato A, Pelletier E, Pierella Karlusich JJ, Ferrante MI, Wincker P, Rogato A, Bowler C, Sanges R, Maiorano L, Chiurazzi M, d’Alcalà MR, Caputi L, Iudicone D
Mol Biol Evol. 2019 Jul 1.

Molecular Inverse Comorbidity between Alzheimer’s Disease and Lung Cancer : New Insights from Matrix Factorization.
Greco A, Sanchez Valle J, Pancaldi V, Baudot A, Barillot E, Caselle M, Valencia A, Zinovyev A, Cantini L
Int J Mol Sci. 2019 Jun 26. 20(13).

Where and what ? Frugivory is associated with more efficient foraging in three semi-free ranging primate species.
Trapanese C, Robira B, Tonachella G, di Gristina S, Meunier H, Masi S
R Soc Open Sci. 2019 May. 6(5):181722.

Poultry population dynamics and mortality risks in smallholder farms of the Mekong river delta region.
Delabouglise A, Nguyen‑Van‑Yen B, Thanh NTL, Xuyen HTA, Tuyet PN, Lam HM, Boni MF
BMC Vet Res. 2019 Jun 17. 15(1):205.

EEG power spectral density under Propofol and its association with burst suppression, a marker of cerebral fragility.
Touchard C, Cartailler J, Levé C, Parutto P, Buxin C, Garnot L, Matéo J, Kubis N, Mebazaa A, Gayat E, Vallée F
Clin Neurophysiol. 2019 Aug. 130(8):1311-1319.

Spatiotemporal structure of cell fate decisions in murine neural crest.
Soldatov R, Kaucka M, Kastriti ME, Petersen J, Chontorotzea T, Englmaier L, Akkuratova N, Yang Y, Häring M, Dyachuk V, Bock C, Farlik M, Piacentino ML, Boismoreau F, Hilscher MM, Yokota C, Qian X, Nilsson M, Bronner ME, Croci L, Hsiao WY, Guertin DA, Brunet JF, Consalez GG, Ernfors P, Fried K, Kharchenko PV, Adameyko I
Science. 2019 Jun 7. 364(6444).

Fast calcium transients in dendritic spines driven by extreme statistics.
Basnayake K, Mazaud D, Bemelmans A, Rouach N, Korkotian E, Holcman D
PLoS Biol. 2019 Jun. 17(6):e2006202.

A model with many small shifts for estimating species-specific diversification rates.
Maliet O, Hartig F, Morlon H
Nat Ecol Evol. 2019 Jul. 3(7):1086-1092.

Accounting for ocean connectivity and hydroclimate in fish recruitment fluctuations within transboundary metapopulations.
Hidalgo M, Rossi V, Monroy P, Ser‑Giacomi E, Hernández‑García E, Guijarro B, Massutí E, Alemany F, Jadaud A, Perez JL, Reglero P
Ecol Appl. 2019 Jul. 29(5):e01913.

Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish.
Fruciano C, Meyer A, Franchini P
Genome Biol Evol. 2019 Jun 1. 11(6):1644-1657.

Author Correction : The new nanophysiology : regulation of ionic flow in neuronal subcompartments.
Holcman D, Yuste R
Nat Rev Neurosci. 2019 Aug. 20(8):509.

Publisher Correction : The new nanophysiology : regulation of ionic flow in neuronal subcompartments.
Holcman D, Yuste R
Nat Rev Neurosci. 2019 Aug. 20(8):510.

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination.
Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton‑Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F
Genome Biol. 2019 May 21. 20(1):100.

Transient Confinement of CaV2.1 Ca2+-Channel Splice Variants Shapes Synaptic Short-Term Plasticity.
Heck J, Parutto P, Ciuraszkiewicz A, Bikbaev A, Freund R, Mitlöhner J, Andres‑Alonso M, Fejtova A, Holcman D, Heine M
Neuron. 2019 Jul 3. 103(1):66-79.e12.

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.
Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka‑Katayama T, Nakano H, Rowe ML, Elphick MR, Thomas‑Chollier M, Hankeln T, Mertes F, Wallberg A, Rast JP, Copley RR, Martinez P, Telford MJ
Curr Biol. 2019 Jun 3. 29(11):1818-1826.e6.

Proteomic Bioprofiles and Mechanistic Pathways of Progression to Heart Failure.
Ferreira JP, Verdonschot J, Collier T, Wang P, Pizard A, Bär C, Björkman J, Boccanelli A, Butler J, Clark A, Cleland JG, Delles C, Diez J, Girerd N, González A, Hazebroek M, Huby AC, Jukema W, Latini R, Leenders J, Levy D, Mebazaa A, Mischak H, Pinet F, Rossignol P, Sattar N, Sever P, Staessen JA, Thum T, Vodovar N, Zhang ZY, Heymans S, Zannad F
Circ Heart Fail. 2019 May. 12(5):e005897.

Detecting dynamic spatial correlation patterns with generalized wavelet coherence and non-stationary surrogate data.
Chavez M, Cazelles B
Sci Rep. 2019 May 14. 9(1):7389.

Tridimensional mapping of Phox2b expressing neurons in the brainstem of adult Macaca fascicularis and identification of the retrotrapezoid nucleus.
Levy J, Facchinetti P, Jan C, Achour M, Bouvier C, Brunet JF, Delzescaux T, Giuliano F
J Comp Neurol. 2019 Dec 1. 527(17):2875-2884.

Functional Integration of Newborn Neurons in the Zebrafish Optic Tectum.
Boulanger‑Weill J, Sumbre G
Front Cell Dev Biol. 2019. 7:57.

Barhl2 maintains T cell factors as repressors and thereby switches off the Wnt/β-Catenin response driving Spemann organizer formation.
Sena E, Rocques N, Borday C, Muhamad Amin HS, Parain K, Sitbon D, Chesneau A, Durand BC
Development. 2019 May 22. 146(10).

DNA metabarcoding-Need for robust experimental designs to draw sound ecological conclusions.
Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, De Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen PF, Willerslev E, Taberlet P
Mol Ecol. 2019 Apr. 28(8):1857-1862.

One-locus-several-primers : A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies.
Corse E, Tougard C, Archambaud‑Suard G, Agnèse JF, Messu Mandeng FD, Bilong Bilong CF, Duneau D, Zinger L, Chappaz R, Xu CCY, Meglécz E, Dubut V
Ecol Evol. 2019 Apr. 9(8):4603-4620.

Marine DNA Viral Macro- and Microdiversity from Pole to Pole.
Gregory AC, Zayed AA, Conceição‑Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez‑Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp‑Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB
Cell. 2019 May 16. 177(5):1109-1123.e14.

Neuronal Dynamics Regulating Brain and Behavioral State Transitions.
Andalman AS, Burns VM, Lovett‑Barron M, Broxton M, Poole B, Yang SJ, Grosenick L, Lerner TN, Chen R, Benster T, Mourrain P, Levoy M, Rajan K, Deisseroth K
Cell. 2019 May 2. 177(4):970-985.e20.

Prologue to the special issue of JTB dedicated to the memory of René Thomas (1928-2017) : A journey through biological circuits, logical puzzles and complex dynamics.
Thieffry D, Kaufman M
J Theor Biol. 2019 Aug 7. 474:42-47.

Blood vessels guide Schwann cell migration in the adult demyelinated CNS through Eph/ephrin signaling.
Garcia‑Diaz B, Bachelin C, Coulpier F, Gerschenfeld G, Deboux C, Zujovic V, Charnay P, Topilko P, Baron‑Van Evercooren A
Acta Neuropathol. 2019 Sep. 138(3):457-476.

Comparative genomics of 10 new Caenorhabditis species.
Stevens L, Félix MA, Beltran T, Braendle C, Caurcel C, Fausett S, Fitch D, Frézal L, Gosse C, Kaur T, Kiontke K, Newton MD, Noble LM, Richaud A, Rockman MV, Sudhaus W, Blaxter M
Evol Lett. 2019 Apr. 3(2):217-236.

Opposite T3 Response of ACTG1-FOS Subnetwork Differentiate Tailfin Fate in Xenopus Tadpole and Post-hatching Axolotl.
Kerdivel G, Blugeon C, Fund C, Rigolet M, Sachs LM, Buisine N
Front Endocrinol (Lausanne). 2019. 10:194.

Mechanistic characterization of the DEAD-box RNA helicase Ded1 from yeast as revealed by a novel technique using single-molecule magnetic tweezers.
Raj S, Bagchi D, Orero JV, Banroques J, Tanner NK, Croquette V
Nucleic Acids Res. 2019 Apr 23. 47(7):3699-3710.

Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation.
Rodríguez‑Jorge O, Kempis‑Calanis LA, Abou‑Jaoudé W, Gutiérrez‑Reyna DY, Hernandez C, Ramirez‑Pliego O, Thomas‑Chollier M, Spicuglia S, Santana MA, Thieffry D
Sci Signal. 2019 Apr 16. 12(577).

Cranial and endocranial diversity in extant and fossil atelids (Platyrrhini : Atelidae) : A geometric morphometric study.
Aristide L, Strauss A, Halenar‑Price LB, Gilissen E, Cruz FW, Cartelle C, Rosenberger AL, Lopes RT, Dos Reis SF, Perez SI
Am J Phys Anthropol. 2019 Jun. 169(2):322-331.

Dissection of Local Ca2+ Signals in Cultured Cells by Membrane-targeted Ca2+ Indicators.
Bannai H, Hirose M, Niwa F, Mikoshiba K
J Vis Exp. 2019 Mar 22. (145).

Asymmetric ephaptic inhibition between compartmentalized olfactory receptor neurons.
Zhang Y, Tsang TK, Bushong EA, Chu LA, Chiang AS, Ellisman MH, Reingruber J, Su CY
Nat Commun. 2019 Apr 5. 10(1):1560.

Single-molecule characterization of extrinsic transcription termination by Sen1 helicase.
Wang S, Han Z, Libri D, Porrua O, Strick TR
Nat Commun. 2019 Apr 4. 10(1):1545.

Zinc Uptake and Storage During the Formation of the Cerebral Cortex in Mice.
Hasna J, Bohic S, Lemoine S, Blugeon C, Bouron A
Mol Neurobiol. 2019 Oct. 56(10):6928-6940.

Assessing reproducibility of matrix factorization methods in independent transcriptomes.
Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A
Bioinformatics. 2019 Nov 1. 35(21):4307-4313.

PICH and TOP3A cooperate to induce positive DNA supercoiling.
Bizard AH, Allemand JF, Hassenkam T, Paramasivam M, Sarlós K, Singh MI, Hickson ID
Nat Struct Mol Biol. 2019 Apr. 26(4):267-274.

Mapping and characterization of G-quadruplexes in the genome of the social amoeba Dictyostelium discoideum.
Saad M, Guédin A, Amor S, Bedrat A, Tourasse NJ, Fayyad‑Kazan H, Pratviel G, Lacroix L, Mergny JL
Nucleic Acids Res. 2019 May 21. 47(9):4363-4374.

ALFA : annotation landscape for aligned reads.
Bahin M, Noël BF, Murigneux V, Bernard C, Bastianelli L, Le Hir H, Lebreton A, Genovesio A
BMC Genomics. 2019 Mar 29. 20(1):250.

Motile ciliogenesis and the mitotic prism.
Al Jord A, Spassky N, Meunier A
Biol Cell. 2019 Aug. 111(8):199-212.

Aedes mosquitoes acquire and transmit Zika virus by breeding in contaminated aquatic environments.
Du S, Liu Y, Liu J, Zhao J, Champagne C, Tong L, Zhang R, Zhang F, Qin CF, Ma P, Chen CH, Liang G, Liu Q, Shi PY, Cazelles B, Wang P, Tian H, Cheng G
Nat Commun. 2019 Mar 22. 10(1):1324.

Local adaptation, dispersal evolution, and the spatial eco-evolutionary dynamics of invasion.
Andrade‑Restrepo M, Champagnat N, Ferrière R
Ecol Lett. 2019 May. 22(5):767-777.

Males as somatic investment in a parthenogenetic nematode.
Grosmaire M, Launay C, Siegwald M, Brugière T, Estrada‑Virrueta L, Berger D, Burny C, Modolo L, Blaxter M, Meister P, Félix MA, Gouyon PH, Delattre M
Science. 2019 Mar 15. 363(6432):1210-1213.

Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes.
Dorrell RG, Azuma T, Nomura M, Audren de Kerdrel G, Paoli L, Yang S, Bowler C, Ishii KI, Miyashita H, Gile GH, Kamikawa R
Proc Natl Acad Sci U S A. 2019 Apr 2. 116(14):6914-6923.

Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase.
Remigi P, Ferguson GC, McConnell E, De Monte S, Rogers DW, Rainey PB
Mol Biol Evol. 2019 May 1. 36(5):1056-1070.

Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.
Ortiz‑Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti ME, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N
Neuron. 2019 Apr 3. 102(1):159-172.e7.

The golden death bacillus Chryseobacterium nematophagum is a novel matrix digesting pathogen of nematodes.
Page AP, Roberts M, Félix MA, Pickard D, Page A, Weir W
BMC Biol. 2019 Feb 28. 17(1):10.

Teleconnection between phytoplankton dynamics in north temperate lakes and global climatic oscillation by time-frequency analysis.
Xiao X, He J, Yu Y, Cazelles B, Li M, Jiang Q, Xu C
Water Res. 2019 May 1. 154:267-276.

Corrigendum : A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO2 in the Model Diatom Phaeodactylum tricornutum.
Huang R, Ding J, Gao K, Cruz de Carvalho MH, Tirichine L, Bowler C, Lin X
Front Microbiol. 2019. 10:158.

Lipid markers and related transcripts during excitotoxic neurodegeneration in kainate-treated mice.
Chali F, Milior G, Marty S, Morin‑Brureau M, Le Duigou C, Savary E, Blugeon C, Jourdren L, Miles R
Eur J Neurosci. 2019 Jul. 50(1):1759-1778.

A Dynamic Signaling Path to Chromatin-Level Control of Plant Drought Response.
Bourbousse C, Barneche F
Mol Plant. 2019 Mar 4. 12(3):292-294.

Comparison of stochastic and deterministic frameworks in dengue modelling.
Champagne C, Cazelles B
Math Biosci. 2019 Apr. 310:1-12.

Functional Alteration of Cerebello-Cerebral Coupling in an Experimental Mouse Model of Parkinson’s Disease.
Menardy F, Varani AP, Combes A, Léna C, Popa D
Cereb Cortex. 2019 Apr 1. 29(4):1752-1766.

Necessity and Contingency in Developmental Genetic Screens : EGF, Wnt, and Semaphorin Pathways in Vulval Induction of the Nematode Oscheius tipulae.
Vargas‑Velazquez AM, Besnard F, Félix MA
Genetics. 2019 Apr. 211(4):1315-1330.

Exon junction complex components Y14 and Mago still play a role in budding yeast.
Boisramé A, Devillers H, Onésime D, Brunel F, Pouch J, Piot M, Neuvéglise C
Sci Rep. 2019 Jan 29. 9(1):849.

Atoh1 Controls Primary Cilia Formation to Allow for SHH-Triggered Granule Neuron Progenitor Proliferation.
Chang CH, Zanini M, Shirvani H, Cheng JS, Yu H, Feng CH, Mercier AL, Hung SY, Forget A, Wang CH, Cigna SM, Lu IL, Chen WY, Leboucher S, Wang WJ, Ruat M, Spassky N, Tsai JW, Ayrault O
Dev Cell. 2019 Jan 28. 48(2):184-199.e5.

Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins.
Parey E, Crombach A
Genome Biol Evol. 2019 Mar 1. 11(3):660-677.

Hope4Genes : a Hopfield-like class prediction algorithm for transcriptomic data.
Cantini L, Caselle M
Sci Rep. 2019 Jan 23. 9(1):337.

Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.
Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A
Sci Rep. 2019 Jan 18. 9(1):213.

On logical bifurcation diagrams.
Abou‑Jaoudé W, Monteiro PT
J Theor Biol. 2019 Apr 7. 466:39-63.

Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer.
Cantini L, Bertoli G, Cava C, Dubois T, Zinovyev A, Caselle M, Castiglioni I, Barillot E, Martignetti L
Nucleic Acids Res. 2019 Mar 18. 47(5):2205-2215.

Genome sequencing of strains of the most prevalent clonal group of O1:K1:H7 Escherichia coli that causes neonatal meningitis in France.
Geslain G, Birgy A, Adiba S, Magnan M, Courroux C, Levy C, Cohen R, Bidet P, Bonacorsi S
BMC Microbiol. 2019 Jan 17. 19(1):17.

Guidelines for DNA recombination and repair studies : Mechanistic assays of DNA repair processes.
Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira‑da‑Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E
Microb Cell. 2019 Jan 7. 6(1):65-101.

Fractional occupancy of synaptic binding sites and the molecular plasticity of inhibitory synapses.
Specht CG
Neuropharmacology. 2019 Jan 12:107493.

Clustering of Tau fibrils impairs the synaptic composition of α3-Na+/K+-ATPase and AMPA receptors.
Shrivastava AN, Redeker V, Pieri L, Bousset L, Renner M, Madiona K, Mailhes‑Hamon C, Coens A, Buée L, Hantraye P, Triller A, Melki R
EMBO J. 2019 Feb 1. 38(3).

Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis.
Furci L, Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F, Ton J
Elife. 2019 Jan 4. 8.

Transcription-dependent regulation of replication dynamics modulates genome stability.
Blin M, Le Tallec B, Nähse V, Schmidt M, Brossas C, Millot GA, Prioleau MN, Debatisse M
Nat Struct Mol Biol. 2019 Jan. 26(1):58-66.

Ca2+-activated Cl- current ensures robust and reliable signal amplification in vertebrate olfactory receptor neurons.
Reisert J, Reingruber J
Proc Natl Acad Sci U S A. 2019 Jan 15. 116(3):1053-1058.

The Latitudinal Diversity Gradient : Novel Understanding through Mechanistic Eco-evolutionary Models.
Pontarp M, Bunnefeld L, Cabral JS, Etienne RS, Fritz SA, Gillespie R, Graham CH, Hagen O, Hartig F, Huang S, Jansson R, Maliet O, Münkemüller T, Pellissier L, Rangel TF, Storch D, Wiegand T, Hurlbert AH
Trends Ecol Evol. 2019 Mar. 34(3):211-223.

The Species Problem from the Modeler’s Point of View.
Manceau M, Lambert A
Bull Math Biol. 2019 Mar. 81(3):878-898.

Adaptation of Proteins to the Cold in Antarctic Fish : A Role for Methionine ?
Berthelot C, Clarke J, Desvignes T, William Detrich H ?III, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS
Genome Biol Evol. 2019 Jan 1. 11(1):220-231.

G4HunterApps.
Lacroix L
Bioinformatics. 2019 Jul 1. 35(13):2311-2312.

An inter-dimer allosteric switch controls NMDA receptor activity.
Esmenjaud JB, Stroebel D, Chan K, Grand T, David M, Wollmuth LP, Taly A, Paoletti P
EMBO J. 2019 Jan 15. 38(2).

Quantitative resistance to clubroot infection mediated by transgenerational epigenetic variation in Arabidopsis.
Liégard B, Baillet V, Etcheverry M, Joseph E, Lariagon C, Lemoine J, Evrard A, Colot V, Gravot A, Manzanares‑Dauleux MJ, Jubault M
New Phytol. 2019 Apr. 222(1):468-479.

MethMotif : an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T
Nucleic Acids Res. 2019 Jan 8. 47(D1):D145-D154.

Cellular Origin, Tumor Progression, and Pathogenic Mechanisms of Cutaneous Neurofibromas Revealed by Mice with Nf1 Knockout in Boundary Cap Cells.
Radomska KJ, Coulpier F, Gresset A, Schmitt A, Debbiche A, Lemoine S, Wolkenstein P, Vallat JM, Charnay P, Topilko P
Cancer Discov. 2019 Jan. 9(1):130-147.

Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms.
Shao Z, Thomas Y, Hembach L, Xing X, Duan D, Moerschbacher BM, Bulone V, Tirichine L, Bowler C
New Phytol. 2019 Mar. 221(4):1890-1905.

Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae.
Cooper MB, Kazamia E, Helliwell KE, Kudahl UJ, Sayer A, Wheeler GL, Smith AG
ISME J. 2019 Feb. 13(2):334-345.

Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom.
Murik O, Tirichine L, Prihoda J, Thomas Y, Araújo WL, Allen AE, Fernie AR, Bowler C
New Phytol. 2019 Feb. 221(3):1303-1316.

Dengue modeling in rural Cambodia : Statistical performance versus epidemiological relevance.
Champagne C, Paul R, Ly S, Duong V, Leang R, Cazelles B
Epidemics. 2019 Mar. 26:43-57.

A Penalized Likelihood Framework for High-Dimensional Phylogenetic Comparative Methods and an Application to New-World Monkeys Brain Evolution.
Clavel J, Aristide L, Morlon H
Syst Biol. 2019 Jan 1. 68(1):93-116.

Non-cell Autonomous OTX2 Homeoprotein Regulates Visual Cortex Plasticity Through Gadd45b/g.
Apulei J, Kim N, Testa D, Ribot J, Morizet D, Bernard C, Jourdren L, Blugeon C, Di Nardo AA, Prochiantz A
Cereb Cortex. 2019 Jun 1. 29(6):2384-2395.