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Publications

2017

Cerebellar re-encoding of self-generated head movements.
Dugué GP, Tihy M, Gourévitch B, Léna C
Elife. 2017 Jun 13. 6.

Co-agonists differentially tune GluN2B-NMDA receptor trafficking at hippocampal synapses.
Ferreira JS, Papouin T, Ladépêche L, Yao A, Langlais VC, Bouchet D, Dulong J, Mothet JP, Sacchi S, Pollegioni L, Paoletti P, Oliet SHR, Groc L
Elife. 2017 Jun 9. 6.

Experimental Evolution with Caenorhabditis Nematodes.
Teotónio H, Estes S, Phillips PC, Baer CF
Genetics. 2017 Jun. 206(2):691-716.

RSAT matrix-clustering : dynamic exploration and redundancy reduction of transcription factor binding motif collections.
Castro‑Mondragon JA, Jaeger S, Thieffry D, Thomas‑Chollier M, van Helden J
Nucleic Acids Res. 2017 Jun 7.

Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells.
Santos R, Vadodaria KC, Jaeger BN, Mei A, Lefcochilos‑Fogelquist S, Mendes APD, Erikson G, Shokhirev M, Randolph‑Moore L, Fredlender C, Dave S, Oefner R, Fitzpatrick C, Pena M, Barron JJ, Ku M, Denli AM, Kerman BE, Charnay P, Kelsoe JR, Marchetto MC, Gage FH
Stem Cell Reports. 2017 Jun 6. 8(6):1757-1769.

An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics.
Romano SA, Pérez‑Schuster V, Jouary A, Boulanger‑Weill J, Candeo A, Pietri T, Sumbre G
PLoS Comput Biol. 2017 Jun 7. 13(6):e1005526.

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.
Collombet S, van Oevelen C, Sardina Ortega JL, Abou‑Jaoudé W, Di Stefano B, Thomas‑Chollier M, Graf T, Thieffry D
Proc Natl Acad Sci U S A. 2017 Jun 6. 114(23):5792-5799.

Functional Interactions between Newborn and Mature Neurons Leading to Integration into Established Neuronal Circuits.
Boulanger‑Weill J, Candat V, Jouary A, Romano S, Pérez‑Schuster V, Sumbre G
Curr Biol. 2017 May 26.

Smooth 2D manifold extraction from 3D image stack.
Shihavuddin A, Basu S, Rexhepaj E, Delestro F, Menezes N, Sigoillot SM, Del Nery E, Selimi F, Spassky N, Genovesio A
Nat Commun. 2017 May 31. 8:15554.

Epithelial cell behaviours during neurosensory organ formation.
Kapsimali M
Development. 2017 Jun 1. 144(11):1926-1936.

Heterozygous Gnal mice are a novel animal model to study dystonia pathophysiology.
Pelosi A, Menardy F, Popa D, Girault JA, Hervé D
J Neurosci. 2017 May 25.

Neuroglobin Can Prevent or Reverse Glaucomatous Progression in DBA/2J Mice.
Cwerman‑Thibault H, Lechauve C, Augustin S, Roussel D, Reboussin É, Mohammad A, Degardin‑Chicaud J, Simonutti M, Liang H, Brignole‑Baudouin F, Maron A, Debeir T, Corral‑Debrinski M
Mol Ther Methods Clin Dev. 2017 Jun 16. 5:200-220.

Unreeling the chromatin thread : a genomic perspective on organization around the periphery of the Arabidopsis nucleus.
Barneche F, Baroux C
Genome Biol. 2017 May 23. 18(1):97.

Optocontrol of glutamate receptor activity by single side-chain photoisomerization.
Klippenstein V, Hoppmann C, Ye S, Wang L, Paoletti P
Elife. 2017 May 23. 6.

Evolutionary forces affecting synonymous variations in plant genomes.
Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, Bacilieri R, Besnard G, Berger A, Cardi C, De Bellis F, Fouet O, Jourda C, Khadari B, Lanaud C, Leroy T, Pot D, Sauvage C, Scarcelli N, Tregear J, Vigouroux Y, Yahiaoui N, Ruiz M, Santoni S, Labouisse JP, Pham JL, David J, Glémin S
PLoS Genet. 2017 May. 13(5):e1006799.

Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome.
Dorrell RG, Gile G, McCallum G, Méheust R, Bapteste EP, Klinger CM, Brillet‑Guéguen L, Freeman KD, Richter DJ, Bowler C
Elife. 2017 May 12. 6.

vConTACT : an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.
Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB
PeerJ. 2017. 5:e3243.

Comparative analysis of DNA extraction methods to study the body surface microbiota of insects : a case study with ant cuticular bacteria.
Birer C, Tysklind N, Zinger L, Duplais C
Mol Ecol Resour. 2017 May 6.

The Natural Biotic Environment of Caenorhabditis elegans.
Schulenburg H, Félix MA
Genetics. 2017 May. 206(1):55-86.

The genealogical decomposition of a matrix population model with applications to the aggregation of stages.
Bienvenu F, Akçay E, Legendre S, McCandlish DM
Theor Popul Biol. 2017 Jun. 115:69-80.

A mechanistic study of helicases with magnetic traps.
Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Fiorini F, Kanaan J, Le Hir H, Allemand JF, Bensimon D, Croquette V
Protein Sci. 2017 May 5.

The Emergence of the Spatial Structure of Tectal Spontaneous Activity Is Independent of Visual Inputs.
Pietri T, Romano SA, Pérez‑Schuster V, Boulanger‑Weill J, Candat V, Sumbre G
Cell Rep. 2017 May 2. 19(5):939-948.

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.
Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J
Cell Rep. 2017 May 2. 19(5):1056-1067.

Crop fertilisation impacts epidemics and optimal latent period of biotrophic fungal pathogens.
Précigout PA, Claessen D, Robert C
Phytopathology. 2017 Apr 28.

Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements.
Guérin F, Arnaiz O, Boggetto N, Denby Wilkes C, Meyer E, Sperling L, Duharcourt S
BMC Genomics. 2017 Apr 26. 18(1):327.

An aggregation-removal model for the formation and size determination of post-synaptic scaffold domains.
Ranft J, Almeida LG, Rodriguez PC, Triller A, Hakim V
PLoS Comput Biol. 2017 Apr. 13(4):e1005516.

Study of gene expression alteration in male androgenetic alopecia : evidence of predominant molecular signaling pathways.
Michel L, Reygagne P, Benech P, Jean‑Louis F, Scalvino S, Ly Ka So S, Hamidou Z, Bianovici S, Pouch J, Ducos B, Bonnet M, Bensussan A, Patatian A, Lati E, Wdzieczak‑Bakala J, Choulot JC, Loing E, Hocquaux M
Br J Dermatol. 2017 Apr 12.

The development and functions of multiciliated epithelia.
Spassky N, Meunier A
Nat Rev Mol Cell Biol. 2017 Apr 12.

Caenorhabditis elegans as a Model for Microbiome Research.
Zhang F, Berg M, Dierking K, Félix MA, Shapira M, Samuel BS, Schulenburg H
Front Microbiol. 2017. 8:485.

Translation in astrocyte distal processes sets molecular heterogeneity at the gliovascular interface.
Boulay AC, Saubaméa B, Adam N, Chasseigneaux S, Mazaré N, Gilbert A, Bahin M, Bastianelli L, Blugeon C, Perrin S, Pouch J, Ducos B, Le Crom S, Genovesio A, Chrétien F, Declèves X, Laplanche JL, Cohen‑Salmon M
Cell Discov. 2017. 3:17005.

Accelerated body size evolution during cold climatic periods in the Cenozoic.
Clavel J, Morlon H
Proc Natl Acad Sci U S A. 2017 Apr 18. 114(16):4183-4188.

Aozan : an automated post-sequencing data-processing pipeline.
Perrin S, Firmo C, Lemoine S, Le Crom S, Jourdren L
Bioinformatics. 2017 Mar 24.

Clustering coefficient and periodic orbits in flow networks.
Rodríguez‑Méndez V, Ser‑Giacomi E, Hernández‑García E
Chaos. 2017 Mar. 27(3):035803.

Introduction to Focus Issue : Complex network perspectives on flow systems.
Donner RV, Hernández‑García E, Ser‑Giacomi E
Chaos. 2017 Mar. 27(3):035601.

On the evolutionary origins of equity.
Debove S, Baumard N, André JB
PLoS One. 2017. 12(3):e0173636.

Activity patterns of serotonin neurons underlying cognitive flexibility.
Matias S, Lottem E, Dugué GP, Mainen ZF
Elife. 2017 Mar 21. 6.

The retinoblastoma homolog RBR1 mediates localization of the repair protein RAD51 to DNA lesions in Arabidopsis.
Biedermann S, Harashima H, Chen P, Heese M, Bouyer D, Sofroni K, Schnittger A
EMBO J. 2017 May 2. 36(9):1279-1297.

Epigenetic memory and cell fate reprogramming in plants.
Birnbaum KD, Roudier F
Regeneration (Oxf). 2017 Feb. 4(1):15-20.

Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies.
Xu M, Xie YA, Abouzeid H, Gordon CT, Fiorentino A, Sun Z, Lehman A, Osman IS, Dharmat R, Riveiro‑Alvarez R, Bapst‑Wicht L, Babino D, Arno G, Busetto V, Zhao L, Li H, Lopez‑Martinez MA, Azevedo LF, Hubert L, Pontikos N, Eblimit A, Lorda‑Sanchez I, Kheir V, Plagnol V, Oufadem M, Soens ZT, Yang L, Bole‑Feysot C, Pfundt R, Allaman‑Pillet N, Nitschké P, Cheetham ME, Lyonnet S, Agrawal SA, Li H, Pinton G, Michaelides M, Besmond C, Li Y, Yuan Z, von Lintig J, Webster AR, Le Hir H, Stoilov P, Amiel J, Hardcastle AJ, Ayuso C, Sui R, Chen R, Allikmets R, Schorderet DF
Am J Hum Genet. 2017 Apr 6. 100(4):592-604.

Modelling plankton ecosystems in the meta-omics era. Are we ready ?
Stec KF, Caputi L, Buttigieg PL, D’Alelio D, Ibarbalz FM, Sullivan MB, Chaffron S, Bowler C, Ribera d’Alcalà M, Iudicone D
Mar Genomics. 2017 Apr. 32:1-17.

Understanding bias in DNA repair.
Strick TR, Savery NJ
Proc Natl Acad Sci U S A. 2017 Mar 14. 114(11):2791-2793.

Structural Alteration of OmpR as a Source of Ertapenem Resistance in a CTX-M-15-Producing Escherichia coli O25b:H4 Sequence Type 131 Clinical Isolate.
Dupont H, Choinier P, Roche D, Adiba S, Sookdeb M, Branger C, Denamur E, Mammeri H
Antimicrob Agents Chemother. 2017 May. 61(5).

Utilization of interferometric light microscopy for the rapid analysis of virus abundance in a river.
Roose‑Amsaleg C, Fedala Y, Vénien‑Bryan C, Garnier J, Boccara AC, Boccara M
Res Microbiol. 2017 Jun. 168(5):413-418.

Molecular Mechanisms of Bipolar Disorder : Progress Made and Future Challenges.
Kim Y, Santos R, Gage FH, Marchetto MC
Front Cell Neurosci. 2017. 11:30.

Neurons derived from patients with bipolar disorder divide into intrinsically different sub-populations of neurons, predicting the patients’ responsiveness to lithium.
Stern S, Santos R, Marchetto MC, Mendes AP, Rouleau GA, Biesmans S, Wang QW, Yao J, Charnay P, Bang AG, Alda M, Gage FH
Mol Psychiatry. 2017 Feb 28.

Oxidation of F-actin controls the terminal steps of cytokinesis.
Frémont S, Hammich H, Bai J, Wioland H, Klinkert K, Rocancourt M, Kikuti C, Stroebel D, Romet‑Lemonne G, Pylypenko O, Houdusse A, Echard A
Nat Commun. 2017 Feb 23. 8:14528.

Recent progress in diatom genomics and epigenomics.
Tirichine L, Rastogi A, Bowler C
Curr Opin Plant Biol. 2017 Apr. 36:46-55.

Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development.
Rosspopoff O, Chelysheva L, Saffar J, Lecorgne L, Gey D, Caillieux E, Colot V, Roudier F, Hilson P, Berthomé R, Da Costa M, Rech P
Development. 2017 Apr 1. 144(7):1187-1200.

Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories.
Amitai A, Seeber A, Gasser SM, Holcman D
Cell Rep. 2017 Jan 31. 18(5):1200-1214.

A noninvasive optical approach for assessing chloride extrusion activity of the K-Cl cotransporter KCC2 in neuronal cells.
Ludwig A, Rivera C, Uvarov P
BMC Neurosci. 2017 Jan 31. 18(1):23.

The hypothalamic NPVF circuit modulates ventral raphe activity during nociception.
Madelaine R, Lovett‑Barron M, Halluin C, Andalman AS, Liang J, Skariah GM, Leung LC, Burns VM, Mourrain P
Sci Rep. 2017 Jan 31. 7:41528.

Differential Routing of Mindbomb1 via Centriolar Satellites Regulates Asymmetric Divisions of Neural Progenitors.
Tozer S, Baek C, Fischer E, Goiame R, Morin X
Neuron. 2017 Feb 8. 93(3):542-551.e4.

Insights into the design and interpretation of iCLIP experiments.
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J
Genome Biol. 2017 Jan 16. 18(1):7.

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.
Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV
Nature. 2017 Jan 26. 541(7638):536-540.

The crystal structure of the 5΄ functional domain of the transcription riboregulator 7SK.
Martinez‑Zapien D, Legrand P, McEwen AG, Proux F, Cragnolini T, Pasquali S, Dock‑Bregeon AC
Nucleic Acids Res. 2017 Apr 7. 45(6):3568-3579.

IGF-1 Induces GHRH Neuronal Axon Elongation during Early Postnatal Life in Mice.
Decourtye L, Mire E, Clemessy M, Heurtier V, Ledent T, Robinson IC, Mollard P, Epelbaum J, Meaney MJ, Garel S, Le Bouc Y, Kappeler L
PLoS One. 2017. 12(1):e0170083.

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates.
Hauer MH, Seeber A, Singh V, Thierry R, Sack R, Amitai A, Kryzhanovska M, Eglinger J, Holcman D, Owen‑Hughes T, Gasser SM
Nat Struct Mol Biol. 2017 Feb. 24(2):99-107.

Early Commissural Diencephalic Neurons Control Habenular Axon Extension and Targeting.
Beretta CA, Dross N, Guglielmi L, Bankhead P, Soulika M, Gutierrez‑Triana JA, Paolini A, Poggi L, Falk J, Ryu S, Kapsimali M, Engel U, Carl M
Curr Biol. 2017 Jan 23. 27(2):270-278.

Proteomic analysis of the Rett syndrome experimental model mecp2Q63X mutant zebrafish.
Cortelazzo A, Pietri T, De Felice C, Leoncini S, Guerranti R, Signorini C, Timperio AM, Zolla L, Ciccoli L, Hayek J
J Proteomics. 2017 Feb 10. 154:128-133.

Preparation of DNA Substrates and Functionalized Glass Surfaces for Correlative Nanomanipulation and Colocalization (NanoCOSM) of Single Molecules.
Duboc C, Fan J, Graves ET, Strick TR
Methods Enzymol. 2017. 582:275-296.

Early born neurons are abnormally positioned in the doublecortin knockout hippocampus.
Khalaf‑Nazzal R, Stouffer MA, Olaso R, Muresan L, Roumegous A, Lavilla V, Carpentier W, Moutkine I, Dumont S, Albaud B, Cagnard N, Roest Crollius H, Francis F
Hum Mol Genet. 2017 Jan 1. 26(1):90-108.

Uncovering Higher-Taxon Diversification Dynamics from Clade Age and Species-Richness Data.
Sánchez‑Reyes LL, Morlon H, Magallón S
Syst Biol. 2017 May 1. 66(3):367-378.

Whole-GUV patch-clamping.
Garten M, Mosgaard LD, Bornschlögl T, Dieudonné S, Bassereau P, Toombes GE
Proc Natl Acad Sci U S A. 2017 Jan 10. 114(2):328-333.

Physiology : Mechanosensor of lung inflation identified.
Goridis C
Nature. 2017 Jan 12. 541(7636):165-166.

mTORC1 signaling and primary cilia are required for brain ventricle morphogenesis.
Foerster P, Daclin M, Asm S, Faucourt M, Boletta A, Genovesio A, Spassky N
Development. 2017 Jan 15. 144(2):201-210.

Heritable expansion of the genetic code in mouse and zebrafish.
Chen Y, Ma J, Lu W, Tian M, Thauvin M, Yuan C, Volovitch M, Wang Q, Holst J, Liu M, Vriz S, Ye S, Wang L, Li D
Cell Res. 2017 Feb. 27(2):294-297.

Strain-specific impact of the high-pathogenicity island on virulence in extra-intestinal pathogenic Escherichia coli.
Smati M, Magistro G, Adiba S, Wieser A, Picard B, Schubert S, Denamur E
Int J Med Microbiol. 2017 Jan. 307(1):44-56.

A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory.
Iberg‑Badeaux A, Collombet S, Laurent B, van Oevelen C, Chin KK, Thieffry D, Graf T, Shi Y
Mol Cell Biol. 2017 Feb 15. 37(4).

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.
Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas‑Chollier M, Vingron M, Meijsing SH
Nucleic Acids Res. 2017 Feb 28. 45(4):1805-1819.

Whole genome DNA methylation : beyond genes silencing.
Tirado‑Magallanes R, Rebbani K, Lim R, Pradhan S, Benoukraf T
Oncotarget. 2017 Jan 17. 8(3):5629-5637.

Progressive and Biased Divergent Evolution Underpins the Origin and Diversification of Peridinin Dinoflagellate Plastids.
Dorrell RG, Klinger CM, Newby RJ, Butterfield ER, Richardson E, Dacks JB, Howe CJ, Nisbet ER, Bowler C
Mol Biol Evol. 2017 Feb 1. 34(2):361-379.

Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays.
Boccara M, Sarazin A, Billoud B, Bulski A, Chapell L, Baulcombe D, Colot V
Methods Mol Biol. 2017. 1456:127-139.

BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire.
Najafova Z, Tirado‑Magallanes R, Subramaniam M, Hossan T, Schmidt G, Nagarajan S, Baumgart SJ, Mishra VK, Bedi U, Hesse E, Knapp S, Hawse JR, Johnsen SA
Nucleic Acids Res. 2017 Jan 9. 45(1):127-141.

GABAergic Microcircuits in Alzheimer’s Disease Models.
Villette V, Dutar P
Curr Alzheimer Res. 2017. 14(1):30-39.

Mammalian microRNAs and long noncoding RNAs in the host-bacterial pathogen crosstalk.
Duval M, Cossart P, Lebreton A
Semin Cell Dev Biol. 2017 May. 65:11-19.

Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms.
Bussard A, Corre E, Hubas C, Duvernois‑Berthet E, Le Corguillé G, Jourdren L, Coulpier F, Claquin P, Lopez PJ
Environ Microbiol. 2017 Mar. 19(3):909-925.

RNA- and protein-mediated control of Listeria monocytogenes virulence gene expression.
Lebreton A, Cossart P
RNA Biol. 2017 May 4. 14(5):460-470.