Publications
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2025
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Hamraoui A, Jourdren L, Thomas-Chollier M
Journal : Bioinformatics
2024
A low-level Cdkn1c/p57kip2 expression in spinal progenitors drives the transition from proliferative to neurogenic modes of division
Mida B, View Lehman N, Coulpier F, Bouhali K, Goiame R, Thomas-Chollier M, Fischer E, Morin X
Journal : biorxiv
An AluYa5 Insertion in the 3'UTR of COL4A1 and Cerebral Small Vessel Disease
Aloui C, Neumann L, Bergametti F, Sartori E, Herbreteau M, Maillard A, Coste T, Morel H, Hervé D, Chabriat H, Timsit S, Viakhireva I, Denoyer Y, Allibert R, Demurger F, Gollion C, Vermersch P, Marchelli F, Blugeon C, Lemoine S, Tourtier-Bellosta C, Brouazin A, Leutenegger AL, Pipiras E, Tournier-Lasserve E
Journal : JAMA Netw Open
Vascular dysfunction is at the onset of oxaliplatin-induced peripheral neuropathy symptoms in mice
Taïb S, Durand J, Dehais V, Boulay AC, Martin S, Blugeon C, Jourdren L, Freydier R, Cohen-Salmon M, Hazan J, Brunet I
Journal : Life Sci Alliance
Cell-cycle-dependent mRNA localization in P-bodies
Safieddine A, Benassy MN, Bonte T, Slimani F, Pourcelot O, Kress M, Ernoult-Lange M, Courel M, Coleno E, Imbert A, Laine A, Godebert AM, Vinit A, Blugeon C, Chevreux G, Gautheret D, Walter T, Bertrand E, Bénard M, Weil D
Journal : Mol Cell.
Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq
Rufflé F, Reboul J, Boureux A, Guibert B, Bessière C, Silva R, Jourdan E, Gaillard JB, Boland A, Deleuze JF, Sénamaud-Beaufort C, Selimoglu-Buet D, Solary E, Gilbert N, Commes T
Journal : NAR Genom Bioinform.
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Hamraoui A, Jourdren L, Thomas-Chollier M
Journal : biorxiv
Comparative transcriptomics reveal a novel tardigrade-specific DNA-binding protein induced in response to ionizing radiation
Anoud M, Delagoutte E, Helleu Q, Brion A, Duvernois-Berthet E, As M, Marques X, Lamribet K, Senamaud-Beaufort C, Jourdren L, Adrait A, Heinrich S, Toutirais G, Hamlaoui S, Gropplero G, Giovannini I, Ponger L, Geze M, Blugeon C, Couté Y, Guidetti R, Rebecchi L, Giovannangeli C, De Cian A, Concordet JP
Journal : Elife
A Screening Study Identified Decitabine as an Inhibitor of Equid Herpesvirus 4 That Enhances the Innate Antiviral Response
Normand C, Thieulent CJ, Fortier C, Sutton G, Senamaud-Beaufort C, Jourdren L, Blugeon C, Vidalain PO, Pronost S, Hue ES
Journal : Viruses
Deleterious effect of sustained neuroinflammation in pediatric traumatic brain injury
Jacquens A, Csaba Z, Soleimanzad H, Bokobza C, Delmotte PR, Userovici C, Boussemart P, Chhor V, Bouvier D, van de Looij Y, Diao S, Lemoine S, Blugeon C, Schwendimann L, Young-Ten P, Naffaa V, Laprevote O, Tanter M, Dournaud P, Van Steenwinckel J, Degos V, Gressens P
Journal : Brain Behav Immun.
Fasting upregulates the monocarboxylate transporter MCT1 at the rat blood-brain barrier through PPAR δ activation
Chasseigneaux S, Cochois-Guégan V, Lecorgne L, Lochus M, Nicolic S, Blugeon C, Jourdren L, Gomez-Zepeda D, Tenzer S, Sanquer S, Nivet-Antoine V, Menet MC, Laplanche JL, Declèves X, Cisternino S, Saubaméa B
Journal : Fluids Barriers CNS
Overlapping action of T3 and T4 during Xenopus laevis development
Tribondeau A, Du Pasquier D, Benchouaia M, Blugeon C, Buisine N, Sachs LM
Journal : Front Endocrinol
The pelvic organs receive no parasympathetic innervation
Sivori M, Dempsey B, Chettouh Z, Boismoreau F, Ayerdi M, Eymael A, Baulande S, Lameiras S, Coulpier F, Delattre O, Rohrer H, Mirabeau O, Brunet JF
Journal : Elife
2023
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
Journal : Elife
Blood Monocyte Phenotype Is A Marker of Cardiovascular Risk in Type 2 Diabetes
Julla JB, Girard D, Diedisheim M, Saulnier PJ, Tran Vuong B, Blériot C, Carcarino E, De Keizer J, Orliaguet L, Nemazanyy I, Potier C, Khider K, Tonui DC, Ejlalmanesh T, Ballaire R, Mambu Mambueni H, Germain S, Gaborit B, Vidal-Trécan T, Riveline JP, Garchon HJ, Fenaille F, Lemoine S, Potier L, Castelli F, Carlier A, Masson D, Roussel R, Vandiedonck C, Hadjadj S, Alzaid F, Gautier JF, Venteclef N
Journal : Circ Res.
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
Journal : BMC Microbiol.
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
Journal : Nucleic Acids Res.
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
Journal : BMC Genomics
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
Journal : J Cell Sci
Filopodia-like protrusions of adjacent somatic cells shape the developmental potential of oocytes
Crozet F, Letort G, Bulteau R, Da Silva C, Eichmuller A, Tortorelli AF, Blévinal J, Belle M, Dumont J, Piolot T, Dauphin A, Coulpier F, Chédotal A, Maître JL, Verlhac MH, Clarke HJ, Terret ME
Journal : Life Sci Alliance
2022
p53/p21 pathway activation contributes to the ependymal fate decision downstream of GemC1
Ortiz-Álvarez G, Fortoul A, Srivastava A, Moreau MX, Bouloudi B, Mailhes-Hamon C, Delgehyr N, Faucourt M, Bahin M, Blugeon C, Breau M, Géli V, Causeret F, Meunier A, Spassky N
Journal : Cell Rep.
In mice and humans, brain microvascular contractility matures postnatally
Slaoui L, Gilbert A, Rancillac A, Delaunay-Piednoir B, Chagnot A, Gerard Q, Letort G, Mailly P, Robil N, Gelot A, Lefebvre M, Favier M, Dias K, Jourdren L, Federici L, Auvity S, Cisternino S, Vivien D, Cohen-Salmon M, Boulay AC
Journal : Brain Struct Funct.
A conserved molecular template underlies color pattern diversity in estrildid finches
Hidalgo M, Curantz C, Quenech'Du N, Neguer J, Beck S, Mohammad A, Manceau M
Journal : Sci Adv.
Individual differences in cocaine-induced conditioned place preference in male rats: Behavioral and transcriptomic evidence
Atehortua Martinez LA, Curis E, Mekdad N, Larrieu C, Courtin C, Jourdren L, Blugeon C, Laplanche JL, Megarbane B, Marie-Claire C, Benturquia N
Journal : J Psychopharmacol
Early macrophage response to obesity encompasses Interferon Regulatory Factor 5 regulated mitochondrial architecture remodelling
Orliaguet L, Ejlalmanesh T, Humbert A, Ballaire R, Diedisheim M, Julla JB, Chokr D, Cuenco J, Michieletto J, Charbit J, Lindén D, Boucher J, Potier C, Hamimi A, Lemoine S, Blugeon C, Legoix P, Lameiras S, Baudrin LG, Baulande S, Soprani A, Castelli FA, Fenaille F, Riveline JP, Dalmas E, Rieusset J, Gautier JF, Venteclef N, Alzaid F
Journal : Nat Commun.
Single amino-acid mutation in a Drosoph ila melanogaster ribosomal protein: An insight in uL11 transcriptional activity
Grunchec H, Deraze J, Dardalhon-Cuménal D, Ribeiro V, Coléno-Costes A, Dias K, Bloyer S, Mouchel-Vielh E, Peronnet F, Thomassin H
Journal : PLoS One
A unique cerebellar pattern of microglia activation in a mouse model of encephalopathy of prematurity
Klein L, Van Steenwinckel J, Fleiss B, Scheuer T, Bührer C, Faivre V, Lemoine S, Blugeon C, Schwendimann L, Csaba Z, Bokobza C, Vousden DA, Lerch JP, Vernon AC, Gressens P, Schmitz T
Journal : Glia
2021
Comparative transcriptome analysis of goat (Capra hircus) adipose tissue reveals physiological regulation of body reserve recovery after the peak of lactation
Faulconnier Y, Boby C, Coulpier F, Lemoine S, Martin P, Leroux C
Journal : Comp Biochem Physiol Part D Genomics Proteomics.
Expression Pattern of Purinergic Signaling Components in Colorectal Cancer Cells and Differential Cellular Outcomes Induced by Extracellular ATP and Adenosine
Dillard C, Borde C, Mohammad A, Puchois V, Jourdren L, Larsen AK, Sabbah M, Maréchal V, Escargueil AE, Pramil E
Journal : Int J Mol Sci
Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses
Lehmann N, Perrin S, Wallon C, Bauquet X, Deshaies V, Firmo C, Du R, Berthelier C, Hernandez C, Michaud C, Thieffry D, Le Crom S, Thomas-Chollier M, Jourdren L
Journal : Biorxiv
Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis
Buisine N, Grimaldi A, Jonchere V, Rigolet M, Blugeon C, Hamroune J, Sachs LM
Journal : Cells
Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly, the Ithomiini Melinaea marsaeus
Piron-Prunier F, Persyn E, Legeai F, McClure M, Meslin C, Robin S, Alves-Carvalho S, Mohammad A, Blugeon C, Jacquin-Joly E, Montagné N, Elias M, Gauthier J
Journal : J Evol Biol.
OTX2 Homeoprotein Functions in Adult Choroid Plexus
Planques A, Oliveira Moreira V, Benacom D, Bernard C, Jourdren L, Blugeon C, Dingli F, Masson V, Loew D, Prochiantz A, Di Nardo AA
Journal : Int J Mol Sci.
The tumor microenvironment impairs Th1 IFNγ secretion through alternative splicing modifications of Irf1 pre-mRNA
Bernard A, Hibos C, Richard C, Viltard E, Chevrier S, Lemoine S, Melin J, Humblin E, Mary R, Accogli T, Chalmin F, Bruchard M, Peixoto P, Hervouet E, Apetoh L, Ghiringhelli F, Vegran F, Boidot R
Journal : Cancer Immunol Res.
Type 2 diabetes is associated with impaired jejunal enteroendocrine GLP-1 cell lineage in human obesity
Osinski C, Le Gléau L, Poitou C, de Toro-Martin J, Genser L, Fradet M, Soula HA, Leturque A, Blugeon C, Jourdren L, Hubert EL, Clément K, Serradas P, Ribeiro A
Journal : Int J Obes (Lond)
2020
Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains
Crisci E, Moroldo M, Vu Manh TP, Mohammad A, Jourdren L, Urien C, Bouguyon E, Bordet E, Bevilacqua C, Bourge M, Pezant J, Pléau A, Boulesteix O, Schwartz I, Bertho N, Giuffra E
Journal : Front Immunol.
Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30
Pirayre A, Duval L, Blugeon C, Firmo C, Perrin S, Jourdier E, Margeot A, Bidard F
Journal : BMC Genomics
Translational study of the whole transcriptome in rats and genetic polymorphisms in humans identifies LRP1B and VPS13A as key genes involved in tolerance to cocaine-induced motor disturbances
Vorspan F, Icick R, Mekdad N, Courtin C, Bloch V, Bellivier F, Laplanche JL, Prince N, Pishalin D, Firmo C, Blugeon C, Mégarbane B, Marie-Claire C, Benturquia N
Journal : Transl Psychiatry
The impact of transposable elements on tomato diversity
Domínguez M, Dugas E, Benchouaia M, Leduque B, Jiménez‑Gómez JM, Colot V, Quadrana L
Journal : Nat Commun.
Adipocyte Reprogramming by the Transcriptional Coregulator GPS2 Impacts Beta Cell Insulin Secretion.
Drareni K, Ballaire R, Alzaid F, Goncalves A, Chollet C, Barilla S, Nguewa JL, Dias K, Lemoine S, Riveline JP, Roussel R, Dalmas E, Velho G, Treuter E, Gautier JF, Venteclef N
Journal : Cell Rep.
Local Translation in Perisynaptic Astrocytic Processes Is Specific and Changes after Fear Conditioning.
Mazaré N, Oudart M, Moulard J, Cheung G, Tortuyaux R, Mailly P, Mazaud D, Bemelmans AP, Boulay AC, Blugeon C, Jourdren L, Le Crom S, Rouach N, Cohen‑Salmon M
Journal : Cell Rep.
Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection
Nguyen Quang N, Goudey S, Ségéral E, Mohammad A, Lemoine S, Blugeon C, Versapuech M, Paillart JC, Berlioz‑Torrent C, Emiliani S, Gallois‑Montbrun S
Journal : Retrovirology
Loss of G protein pathway suppressor 2 in human adipocytes triggers lipid remodeling through upregulation of ATP binding cassette subfamily G member 1
Barilla S, Liang N, Mileti E, Ballaire R, Lhomme M, Ponnaiah M, Lemoine S, Soprani A, Gautier JF, Amri EZ, Le Goff W, Venteclef N, Treuter E
Journal : Mol Metab
Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus
Guyon C, Jmari N, Padonou F, Li YC, Ucar O, Fujikado N, Coulpier F, Blanchet C, Root DE, Giraud M
Journal : Elife
2019
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
Journal : Developmental Cell
Molecular characterisation of a cellular conveyor belt in Clytia medusa
Condamine T, Jager M, Leclère L, Blugeon C, Lemoine S, Copley RR, Manuel M
Journal : Developmental Biology
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
Journal : Acta Neuropathologica
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
Journal : EvoDevo
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
Journal : Genome Biology
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
Journal : Frontiers in Endocrinology
Zinc Uptake and Storage During the Formation of the Cerebral Cortex in Mice
Hasna J, Bohic S, Lemoine S, Blugeon C, Bouron A
Journal : Molecular Neurobiology
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
Journal : European Journal of Neuroscience
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
Journal : Scientific Reports
2018
Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human Pathogen Candida glabrata
Benchouaia M, Ripoche H, Sissoko M, Thiébaut A, Merhej J, Delaveau T, Fasseu L, Benaissa S, Lorieux G, Jourdren L, Le Crom S, Lelandais G, Corel E, Devaux F
Journal : Front Microbiol.
Microglial phenotypes in the human epileptic temporal lobe
Morin-Brureau M, Milior G, Royer J, Chali F, LeDuigou C, Savary E, Blugeon C, Jourdren L, Akbar D, Dupont S, Navarro V, Baulac M, Bielle F, Mathon B, Clemenceau S, Miles R
Journal : Brain.
Active intermixing of indirect and direct neurons builds the striatal mosaic
Tinterri A, Menardy F, Diana MA, Lokmane L, Keita M, Coulpier F, Lemoine S, Mailhes C, Mathieu B, Merchan-Sala P, Campbell K, Gyory I, Grosschedl R, Popa D, Garel S
Journal : Nat Commun.
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
Journal : Cancer Discoveery
Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions
Wu X, Kabalane H, Kahli M, Petryk N, Laperrousaz B, Jaszczyszyn Y, Drillon G, Nicolini FE, Perot G, Robert A, Fund C, Chibon F, Xia R, Wiels J, Argoul F, Maguer-Satta V, Arneodo A, Audit B, Hyrien O
Journal : Nucleic Acids Res.
Dual-layer transposon repression in heads of Drosophila melanogaster
van den Beek M, da Silva B, Pouch J, Ali Chaouche MEA, Carré C, Antoniewski C
Journal : RNA
Isolation and differential transcriptome of vascular smooth muscle cells and mid-capillary pericytes from the rat brain
Chasseigneaux S, Moraca Y, Cochois-Guégan V, Boulay AC, Gilbert A, Le Crom S, Blugeon C, Firmo C, Cisternino S, Laplanche JL, Curis E, Declèves X, Saubaméa B
Journal : Scientific Reports
Cyclin G and the Polycomb Repressive Complexes PRC1 and PR-DUB cooperate for developmental stability
Dardalhon-Cuménal D, Deraze J, Dupont CA, Ribeiro V, Coléno-Costes A, Pouch J, Le Crom S, Thomassin H, Debat V, Randsholt NB, Peronnet F
Journal : PLOS Genetics
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
Journal : Cereb Cortex
Connexin 43 Controls the Astrocyte Immunoregulatory Phenotype
Boulay AC, Gilbert A, Oliveira Moreira V, Blugeon C, Perrin S, Pouch J, Le Crom S, Ducos B, Cohen‑Salmon M
Journal : Brain Sci.
Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner
Thion MS, Low D, Silvin A, Chen J, Grisel P, Schulte-Schrepping J, Blecher R, Ulas T, Squarzoni P, Hoeffel G, Coulpier F, Siopi E, David FS, Scholz C, Shihui F, Lum J, Amoyo AA, Larbi A, Poidinger M, Buttgereit A, Lledo PM, Greter M, Chan JKY, Amit I, Beyer M, Schultze JL, Schlitzer A, Pettersson S, Ginhoux F, Garel S
Journal : Cell
2017
Egr1 deficiency induces browning of inguinal subcutaneous white adipose tissue in mice
Milet C, Bléher M, Allbright K, Orgeur M, Coulpier F, Duprez D, Havis E
Journal : Scientific Reports
The fitness cost of mis-splicing is the main determinant of alternative splicing patterns
Saudemont B, Popa A, Parmley JL, Rocher V, Blugeon C, Necsulea A, Meyer E, Duret L
Journal : Genome Biology
Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction
Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F
Journal : Biotechnology for Biofuels
Quaking RNA-Binding Proteins Control Early Myofibril Formation by Modulating Tropomyosin
Bonnet A, Lambert G, Ernest S, Dutrieux FX, Coulpier F, Lemoine S, Lobbardi R, Rosa FM
Journal : Developmental Cell
Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements
Thierion E, Le Men J, Collombet S, Hernandez C, Coulpier F, Torbey P, Thomas-Chollier M, Noordermeer D, Charnay P, Gilardi-Hebenstreit P
Journal : PLoS Genetics
Aozan: an automated post-sequencing data-processing pipeline
Perrin S, Firmo C, Lemoine S, Le Crom S, Jourdren L
Journal : Bioinformatics
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
Journal : Cell Discovery
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, Jean Lopez P
Journal : Environmental Microbiology
2016
IRF5 governs liver macrophage activation that promotes hepatic fibrosis in mice and humans
Alzaid F, Lagadec F, Albuquerque M, Ballaire R, Orliaguet L, Hainault I, Blugeon C, Lemoine S, Lehuen A, Saliba DG, Udalova IA, Paradis V, Foufelle F, Venteclef N
Journal : JCI Insight
Molecular signatures of neural connectivity in the olfactory cortex
Diodato A, Ruinart de Brimont M, Yim YS, Derian N, Perrin S, Pouch J, Klatzmann D, Garel S, Choi GB, Fleischmann A
Journal : Nature Communications
A Network of Paralogous Stress Response Transcription Factors in the Human Pathogen Candida glabrata
Merhej J, Thiebaut A, Blugeon C, Pouch J, Ali Chaouche Mel A, Camadro JM, Le
Crom S, Lelandais G, Devaux F
Journal : Frontiers in Microbiology
ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses
Lelandais G, Blugeon C, Merhej J
Journal : Methods in Molecular Biology
2015
Combined transcriptome studies identify AFF3 as a mediator of the oncogenic effects of β-catenin in adrenocortical carcinoma
Lefèvre L, Omeiri H, Drougat L, Hantel C, Giraud M, Val P, Rodriguez S, Perlemoine K, Blugeon C, Beuschlein F, de Reyniès A, Rizk-Rabin M, Bertherat J, Ragazzon B
Journal : Oncogenesis
Control of plasma membrane permeability by ABC transporters
Khakhina S, Johnson SS, Manoharlal R, Russo SB, Blugeon C, Lemoine S, Sunshine AB, Dunham M, Cowart LA, Devaux F, Moye-Rowley WS
Journal : Eukaryotic Cell
Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype
Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP
Journal : BMC Genomics
Immune quiescence of the brain is set by astroglial connexin 43
Boulay AC, Mazeraud A, Cisternino S, Saubaméa B, Mailly P, Jourdren L, Blugeon C, Mignon V, Smirnova M, Cavallo A, Ezan P, Avé P, Dingli F, Loew D, Vieira P, Chrétien F, Cohen-Salmon M
Journal : Journal of Neurosciences
The ß-importin KAP8 (Pse1/Kap121) is required for nuclear import of the cellulase transcriptional regulator XYR1, asexual sporulation and stress resistance in Trichoderma reesei
Ghassemi S, Lichius A, Bidard F, Lemoine S, Rossignol MN, Herold S, Seidl-Seiboth V, Seiboth B, Espeso EA, Margeot A, Kubicek CP
Journal : Molecular Microbiology
The Sarcoglycan complex is expressed in the cerebrovascular system and is specifically regulated by astroglial Cx30 channels
Boulay AC, Saubaméa B, Cisternino S, Mignon V, Mazeraud A, Jourdren L, Blugeon C, Cohen-Salmon M
Journal : Frontiers in Cellular Neuroscience
Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia
Carradec Q, Götz U, Arnaiz O, Pouch J, Simon M, Meyer E, Marker S
Journal : Nucleic Acids Research
Boundary Caps Give Rise to Neurogenic Stem Cells and Terminal Glia in the Skin
Gresset A, Coulpier F, Gerschenfeld G, Jourdon A, Matesic G, Richard L, Vallat JM, Charnay P, Topilko P
Journal : Stem Cell Reports
2014
Role of the DHH1 Gene in the Regulation of Monocarboxylic Acids Transporters Expression in Saccharomyces cerevisiae
Mota S, Vieira N, Barbosa S, Delaveau T, Torchet C, Le Saux A, Garcia M, Pereira A, Lemoine S, Coulpier F, Darzacq X, Benard L, Casal M, Devaux F, Paiva S
Journal : PLoS One
Loss of Krox20 results in aortic valve regurgitation and impaired transcriptional activation of fibrillar collagen genes
Odelin G, Faure E, Kober F, Maurel-Zaffran C, Théron A, Coulpier F, Guillet B, Bernard M, Avierinos JF, Charnay P, Topilko P, Zaffran S
Journal : Cardiovasular research
bPeaks: a bioinformatics tool to detect transcription factor binding sites from ChIPseq data in yeasts and other organisms with small genomes
Merhej J, Frigo A, Le Crom S, Camadro JM, Devaux F, Lelandais G
Journal : Yeast
Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain
Poggi-Parodi D, Bidard F, Pirayre A, Portnoy T, Blugeon C, Seiboth B, Kubicek CP, Le Crom S, Margeot A
Journal : Biotechnology for Biofuels
Genome-defence small RNAs exalted for epigenetic mating-type inheritance
Singh DP, Saudemont B, Guglielmi G, Arnaiz O, Goût JF, Prajer M, Potekhin A, Przybòs E, Aubusson-Fleury A, Bhullar S, Bouhouche K, Lhuillier-Akakpo M, Tanty V, Blugeon C, Alberti A, Labadie K, Aury JM, Sperling L, Duharcourt S, Meyer E
Journal : Nature
2013
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Le Crom S, Guedj M, Jaffrézic F; French StatOmique Consortium
Journal : Briefings in Bioinformatics
High-frequency promoter firing links THO complex function to heavy chromatin formation
Mouaikel J, Causse SZ, Rougemaille M, Daubenton-Carafa Y, Blugeon C, Lemoine S, Devaux F, Darzacq X, Libri D
Journal : Cell Reports
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum
Veluchamy A, Lin X, Maumus F, Rivarola M, Bhavsar J, Creasy T, O\\'Brien K, Sengamalay NA, Tallon LJ, Smith AD, Rayko E, Ahmed I, Le Crom S, Farrant GK, Sgro JY, Olson SA, Bondurant SS, Allen A, Rabinowicz PD, Sussman MR, Bowler C, Tirichine L
Journal : Nature Communications
Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism
Atanasova L, Le Crom S, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, Druzhinina IS
Journal : BMC Genomics
2012
Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress
Servant G, Pinson B, Tchalikian-Cosson A, Coulpier F, Lemoine S, Pennetier C, Bridier-Nahmias A, Todeschini AL, Fayol H, Daignan-Fornier B, Lesage P
Journal : Nucleic Acids Res
New partners in regulation of gene expression: the enhancer of trithorax and polycomb corto interacts with methylated ribosomal protein l12 via its chromodomain
Coléno-Costes A, Jang SM, de Vanssay A, Rougeot J, Bouceba T, Randsholt NB, Gibert JM, Le Crom S, Mouchel-Vielh E, Bloyer S, Peronnet F
Journal : PLoS Genetics
Cthrc1 is a negative regulator of myelination in Schwann cells
Apra C, Richard L, Coulpier F, Blugeon C, Gilardi-Hebenstreit P, Vallat JM, Lindner V, Charnay P, Decker L
Journal : Glia
In Vitro Effect of Malachite Green on Candida albicans Involves Multiple Pathways and Transcriptional Regulators UPC2 and STP2
Dhamgaye S, Devaux F, Manoharlal R, Vandeputte P, Shah AH, Singh A, Blugeon C, Sanglard D, Prasad R
Journal : Antimicrobial Agents and Chemotherapy
Eoulsan: A Cloud Computing-Based Framework Facilitating High Throughput Sequencing Analyses
Jourdren L, Bernard M, Dillies MA, Le Crom S
Journal : Bioinformatics
RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans
Dhamgaye S, Bernard M, Lelandais G, Sismeiro O, Lemoine S, Coppée JY, Le Crom S, Prasad R, Devaux F
Journal : BMC Genomics
2011
Boundary cap cells are peripheral nervous system stem cells that can be redirected into central nervous system lineages
Zujovic V, Thibaud J, Bachelin C, Vidal M, Deboux C, Coulpier F, Stadler N, Charnay P, Topilko P, Baron-Van Evercooren A
Journal : Proceedings of The National Academy of Sciences of the United States of America
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Doehren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gomez-Rodriguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernandez-Onate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lubeck M, Lubeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV
Journal : Genome Biology
Secreted amyloid precursor protein β and secreted amyloid precursor protein α induce axon outgrowth in vitro through Egr1 signaling pathway
Chasseigneaux S, Dinc L, Rose C, Chabret C, Coulpier F, Topilko P, Mauger G, Allinquant B
Journal : PLoS One
Krox20 inactivation in the PNS leads to CNS/PNS boundary transgression by central glia
Coulpier F, Decker L, Funalot B, Vallat JM, Garcia-Bragado F, Charnay P, Topilko P
Journal : Rev Neurol (Paris)
Differential regulation of the cellulase transcription factors XYR1, ACE2, and ACE1 in Trichoderma reesei strains producing high and low levels of cellulase
Portnoy T, Margeot A, Seidl-Seiboth V, Le Crom S, Ben Chaabane F, Linke R, Seiboth B, Kubicek CP
Journal : Eukaryot Cell
The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation
Portnoy T, Margeot A, Linke R, Atanasova L, Fekete E, Sandor E, Hartl L, Karaffa L, Druzhinina IS, Seiboth B, Le Crom S, Kubicek CP
Journal : BMC Genomics
Physiological and Toxic Effects of Purine Intermediate 5-Amino-4-imidazolecarboxamide Ribonucleotide (AICAR) in Yeast
Hürlimann HC, Laloo B, Simon-Kayser B, Saint-Marc C, Coulpier F, Lemoine S, Daignan-Fornier B, Pinson B
Journal : The Journal of Biological Chemistry
Dok4 is involved in Schwann cell myelination and axonal interaction in vitro
Blugeon C, Le Crom S, Richard L, Vallat JM, Charnay P, Decker L
Journal : Glia
Ploidy influences cellular responses to gross chromosomal rearrangements in Saccharomyces cerevisiae
Jung PP, Fritsch ES, Blugeon C, Souciet JL, Potier S, Lemoine S, Schacherer J, de Montigny J
Journal : BMC Genomics
2010
CNS/PNS Boundary Transgression by Central Glia in the Absence of Schwann Cells or Krox20/Egr2 Function
Coulpier F, Decker F, Funalot B, Vallat JM, Garcia-Bragado F, Charnay P, Topilko P
Journal : The Journal of Neuroscience
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression
Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Jourdren L, Coulpier F, Triller A, Spector DL, Bessis A
Journal : EMBO J
CORSEN, a new software dedicated to microscope-based 3D distance measurements: mRNA-mitochondria distance, from single-cell to population analyses
Jourdren L, Delaveau T, Marquenet E, Jacq C, Garcia M
Journal : RNA
Boundary Cap Cells are Highly Competitive for CNS Remyelination: Fast Migration and Efficient Differentiation in PNS and CNS Myelin-Forming Cells
Zujovic V, Thibaud J, Bachelin C, Vidal M, Coulpier F, Charnay P, Topilko P, Baron-Van Evercooren A
Journal : Stem Cells
Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments
Jourdren L, Duclos A, Brion C, Portnoy T, Mathis H, Margeot A, Le Crom S
Journal : Nucleic Acids Res.
2009
Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters
Sapriel G, Quinet M, Heijde M, Jourdren L, Tanty V, Luo G, Le Crom S, Lopez PJ
Journal : PLoS ONE
Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing
Le Crom S, Schackwitz W, Pennacchio P, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis S, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A
Journal : Proceedings of The National Academy of Sciences of the United States of America
An evaluation of custom microarray applications: the oligonucleotide design challenge
Lemoine S, Combes F, Le Crom S
Journal : Nucleic Acids Research
Selection of oligonucleotides for whole-genome microarrays with semi-automatic update
Golfier G, Lemoine S, van Miltenberg A, Bendjoudi A, Rossier J, Le Crom S, Potier MC
Journal : Bioinformatics
Phenotypic Consequences of Purine Nucleotide Imbalance in Saccharomyces cerevisiae
Saint-Marc C, Pinson B, Coulpier F, Jourdren L, Lisova O, Daignan-Fornier B
Journal : Genetics
Novel features of boundary cap cells revealed by the analysis of newly identified molecular markers
Coulpier F, Le Crom S, Maro GS, Manent J, Giovannini M, Maciorowski Z, Fischer A, Gessler M, Charnay P, Topilko P
Journal : Glia
Metabolic intermediates selectively stimulate transcription factor interaction and modulate phosphate and purine pathways
Pinson B, Vaur S, Sagot I, Coulpier F, Lemoine S, Daignan-Fornier B
Journal : Genes and development
2008
Identification of Phox2b-regulated genes by expression profiling of cranial motoneuron precursors
Pla P, Hirsch MR, Le Crom S, Reiprich S, Harley VR, Goridis C
Journal : Neural development
THO/Sub2p functions to coordinate 3\\'-end processing with gene-nuclear pore association
Rougemaille M, Dieppois G, Kisseleva-Romanova E, Gudipati RK, Lemoine S, Blugeon C, Boulay J, Jensen TH, Stutz F, Devaux F, Libri D
Journal : Cell
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata
Lelandais G, Tanty V, Geneix C, Etchebest C, Jacq C, Devaux F
Journal : Genome Biology
Lethal accumulation of guanylic nucleotides in Saccharomyces cerevisiae HPT1-deregulated mutants
Breton A, Pinson B, Coulpier F, Giraud MF, Dautant A, Daignan-Fornier B
Journal : Genetics
Yeast Mitochondrial Biogenesis: A Role for the PUF RNA-Binding Protein Puf3p in mRNA Localization
Saint-Georges Y, Garcia M, Delaveau T, Jourdren L, Le Crom S, Lemoine S, Tanty V, Devaux F, Jacq C
Journal : PLoS ONE
Structure and properties of transcriptional networks driving selenite stress response in yeasts
Salin H, Fardeau V, Piccini E, Lelandais G, Tanty V, Lemoine S, Jacq C, Devaux F
Journal : BMC Genomics
Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations
Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B
Journal : Molecular Microbiology
2007
Mitochondria-associated Yeast mRNAs and the Biogenesis of Molecular Complexes
Garcia M, Darzacq X, Delaveau T, Jourdren L, Singer RH, Jacq C
Journal : Molecular Biology of the Cell
The Central Role of PDR1 in the Foundation of Yeast Drug Resistance
Fardeau V, Lelandais G, Oldfield A, Salin H, Lemoine S, Garcia M, Tanty V, Le Crom S, Jacq C, Devaux F
Journal : J Biol Chem
2006
Goulphar: rapid access and expertise for standard two-color microarray normalization methods
Lemoine S, Combes F, Servant N, Le Crom S
Journal : BMC Bioinformatics
Role of heat-shock factor 2 in cerebral cortex formation and as a regulator of p35 expression
Chang Y, Ostling P, Akerfelt M, Trouillet D, Rallu M, Gitton Y, El Fatimy R, Fardeau V, Le Crom S, Morange M, Sistonen L, Mezger V
Journal : Genes & Development
2005
Transcriptional regulation by Lge1p requires a function independent of its role in histone H2B ubiquitination
Zhang X, Kolaczkowska A, Devaux F, Panwar SL, Hallstrom TC, Jacq C, Moye-Rowley WS
Journal : J Biol Chem
Doelan: a solution for quality control monitoring of microarray production
Jourdren L, Le Crom S
Journal : Bioinformatics
Early expression of yeast genes affected by chemical stress
Lucau-Danila A, Lelandais G, Kozovska Z, Tanty V, Delaveau T, Devaux F, Jacq C
Journal : Mol Cell Biol.
2004
yMGV: a cross-species expression data mining tool
Lelandais G, Le Crom S, Devaux F, Vialette S, Church GM, Jacq C, Marc P
Journal : Nucleic Acids Research
Sok2p transcription factor is involved in adaptive program relevant for long term survival of Saccharomyces cerevisiae colonies
Vachova L, Devaux F, Kucerova H, Ricicova M, Jacq C, Palkova Z
Journal : J Biol Chem.
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states
Lelandais G, Marc P, Vincens P, Jacq C, Vialette S
Journal : BMC Bioinformatics
Ady2p is essential for the acetate permease activity in the yeast Saccharomyces cerevisiae
Paiva S, Devaux F, Barbosa S, Jacq C, Casal M
Journal : Yeast
2003
A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast
Hikkel I, Lucau-Danila A, Delaveau T, Marc P, Devaux F, Jacq C
Journal : Journal of Biological Chemistry
Competitive promoter occupancy by two yeast paralogous transcription factors controlling the multidrug resistance phenomenon
Lucau-Danila A, Delaveau T, Lelandais G, Devaux F, Jacq C
Journal : Journal of Biological Chemistry
Domestication of wild Saccharomyces cerevisiae is accompanied by changes in gene expression and colony morphology
Kuthan M, Devaux F, Janderova B, Slaninova I, Jacq C, Palkova Z
Journal : Molecular Microbiology
Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeast
Ganem C, Devaux F, Torchet C, Jacq C, Quevillon-Cheruel S, Labesse G, Facca C, Faye G
Journal : EMBO Journal
2002
Ammonia pulses and metabolic oscillations guide yeast colony development
Palkova Z, Devaux F, Icicova M, Minarikova L, Le Crom S, Jacq C
Journal : Molecular Biology of the Cell
Arrayplot for visualization and normalization of cDNA microarray data
Marc P, Jacq C
Journal : Bioinformatics
yMGV: helping biologists with yeast microarray data mining
Le Crom S, Devaux F, Jacq C, Marc P
Journal : Nucleic Acids Research
Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast
Devaux F, Carvajal E, Moye-Rowley S, Jacq C
Journal : FEBS Letters
New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system
Le Crom S, Devaux F, Marc P, Zhang X, Moye-Rowley WS, Jacq C
Journal : Molecular and Cellular Biology
Genome-wide analysis of mRNAs targeted to yeast mitochondria
Marc P, Margeot A, Devaux F, Blugeon C, Corral-Debrinski M, Jacq C
Journal : EMBO Reports
2001
yMGV: a database for visualization and data mining of published genome-wide yeast expression data
Marc P, Devaux F, Jacq C
Journal : Nucleic Acids Research
An artificial transcription activator mimics the genome-wide properties of the yeast Pdr1 transcription factor
Devaux F, Marc P, Bouchoux C, Delaveau T, Hikkel I, Potier MC, Jacq C
Journal : EMBO Reports
Transcriptomes, transcription activators and microarrays
Devaux F, Marc P, Jacq C
Journal : FEBS Letter
