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Publications

2019

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 Apr 10.

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 Apr 2.

Assessing reproducibility of matrix factorization methods in independent transcriptomes.
Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A
Bioinformatics. 2019 Apr 2.

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 Mar 29.

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 Mar 24.

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 Mar 5.

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 Feb 11. 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 Feb 14.

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.

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.

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.