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 | Pages: e0273198 | Issue: 8 | Volume: 17 |

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 |


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. | Pages: 100956 | Volume: 41 |

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 | Pages: 11472 | Issue: 21 | Volume: 22 |

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 | Pages: 2375 | Issue: 9 | Volume: 10 |

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. | Pages: 1704-1721 | Issue: 11 | Volume: 34 |

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. | Pages: 8951 | Issue: 16 | Volume: 22 |

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. | Pages: 324–336 | Issue: 3 | Volume: 9 |

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) | Pages: 170-183 | Issue: 45 | Volume: 1 |


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. | Pages: 588411 | Volume: 11 |

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 | Pages: 855 | Issue: 21 | Volume: 1 |

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 | Pages: 381 | Issue: 1 | Volume: 10 |

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. | Pages: 4058 | Issue: 1 | Volume: 11 |

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. | Pages: 108141 | Issue: 11 | Volume: 32 |

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. | Pages: 108076 | Issue: 8 | Volume: 32 |

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 | Pages: 25 | Issue: 17 | Volume: 1 |

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 | Pages: 101066 | Volume: 13 |

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 | Issue: Apr 29 | Volume: 9 |


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 | Pages: 145-157 | Issue: 2 | Volume: 51 |

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 | Pages: 30409-30413 | Volume: 18 |

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 | Pages: 457-476 | Issue: 138 | Volume: 3 |

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 | Pages: 16 | Issue: 10 |

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 | Pages: 100 | Issue: 20 |

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 | Pages: 194 | Volume: 10 |

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 | Pages: 6928-6940 | Issue: 10 | Volume: 56 |

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 | Pages: 1759-1778 | Issue: 1 | Volume: 50 |

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 | Pages: 849 |


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. | Pages: 2689 | Volume: 9 |

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. | Pages: 3343-3360 | Issue: 141 | Volume: 12 |

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. | Pages: 4725 | Issue: 9 |

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 | Pages: 130-147 | Issue: 1 | Volume: 9 |

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. | Pages: 10157–10172 | Issue: 19 | Volume: 46 |

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 | Pages: 1749-1760 | Volume: 12 |

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 | Pages: 12272 | Volume: 8 |

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 | Issue: 14 | Volume: 7 |

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 | Pages: 2384–2395 | Issue: 6 | Volume: 29 |

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. | Issue: 4 | Volume: 8 |

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 | Pages: 500-516 | Issue: 3 | Volume: 172 |


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 | Pages: 16153 | Issue: 1 | Volume: 7 |

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 | Pages: 208 | Issue: 1 | Volume: 18 |

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 | Pages: 209 | Volume: 10 |

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 | Pages: 527–541 | Volume: 42 |

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 | Pages: e1006903 | Issue: 7 | Volume: 13 |

Aozan: an automated post-sequencing data-processing pipeline

Perrin S, Firmo C, Lemoine S, Le Crom S, Jourdren L
| Journal: Bioinformatics | Pages: 2212–2213 | Issue: 33 | Volume: 14 |

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 | Pages: 17005 | Volume: 3 |

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 | Pages: 909-925 | Issue: 3 | Volume: 19 |


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 | Pages: e88689 | Issue: 1 | Volume: 20 |

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 | Issue: 7 | Volume: 12238 |

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 | Issue: 7 | Volume: 645 |

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 | Pages: 185-202 | Volume: 1361 |


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 | Pages: e161 | Volume: 4 |

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 | Pages: 442-453 | Issue: 5 | Volume: 14 |

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 | Pages: 326 | Issue: 1 | Volume: 16 |

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 | Pages: 4427-4439 | Issue: 10 | Volume: 35 |

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 | Pages: 405-418 | Issue: 2 | Volume: 96 |

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 | Pages: 1-9 | Issue: 9 | Volume: 9 |

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 | Pages: 1818-1833 | Issue: 3 | Volume: 43 |

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 | Pages: 1-13 | Volume: 5 |


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 | Pages: e111589 | Issue: 11 | Volume: 9 |

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 | Pages: 443-455 | Issue: 3 | Volume: 104 |

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 | Pages: 375-391 | Issue: 10 | Volume: 31 |

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 | Pages: 173 | Issue: 1 | Volume: 7 |

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 | Pages: 447-452 | Issue: 7501 | Volume: 509 |


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 | Pages: 671-683 | Issue: 6 | Volume: 14 |

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 | Pages: 1082–1094 | Issue: 4 | Volume: 5 |

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 | Pages: 2091 | Issue: 0 | Volume: 4 |

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 | Pages: 121 | Issue: 1 | Volume: 14 |


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 | Pages: 5271-5282 | Issue: 12 | Volume: 40 |

Eoulsan: A Cloud Computing-Based Framework Facilitating High Throughput Sequencing Analyses

Jourdren L, Bernard M, Dillies MA, Le Crom S
| Journal: Bioinformatics | Pages: 1542-1543 | Issue: 11 | Volume: 28 |

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 | Pages: 393-403 | Issue: 3 | Volume: 60 |

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 | Pages: e1003006 | Issue: 10 | Volume: 8 |

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 | Pages: 396 | Issue: 1 | Volume: 13 |

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 | Pages: 495-506 | Issue: 1 | Volume: 56 |


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) | Pages: 51-56 | Issue: 1 | Volume: 167 |

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 | Pages: 351-362 | Issue: 3 | Volume: 59 |

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 | Pages: 10714-10719 | Issue: 26 | Volume: 108 |

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 | Pages: 269 | Issue: 1 | Volume: 12 |

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 | Pages: R40 | Issue: 4 | Volume: 18 |

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 | Pages: 331 | Issue: 1 | Volume: 12 |

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 | Pages: 30994-31002 | Issue: 35 | Volume: 286 |

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 | Pages: 262-271 | Issue: 2 | Volume: 10 |

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 | Pages: e16301 | Issue: 1 | Volume: 6 |


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 | Pages: 470-479 | Issue: 3 | Volume: 28 |

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 | Pages: 3082-3093 | Issue: 18 | Volume: 29 |

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 | Pages: 1301-1307 | Issue: 7 | Volume: 16 |

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 | Pages: 5958-5967 | Issue: 17 | Volume: 30 |

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. | Pages: e117 | Issue: 10 | Volume: 38 |


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 | Pages: e7458 | Issue: 4 | Volume: 10 |

An evaluation of custom microarray applications: the oligonucleotide design challenge

Lemoine S, Combes F, Le Crom S
| Journal: Nucleic Acids Research | Pages: 1726–1739 | Issue: 6 | Volume: 37 |

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 | Pages: 16151-16156 | Issue: 38 | Volume: 106 |

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 | Pages: 128-129 | Issue: 1 | Volume: 25 |

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 | Pages: 1399-1407 | Issue: 12 | Volume: 23 |

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 | Pages: 1450-1457 | Issue: 13 | Volume: 57 |

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 | Pages: 529-538 | Issue: 2 | Volume: 183 |


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 | Pages: 815-824 | Issue: 2 | Volume: 178 |

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 | Pages: 1-16 | Issue: 14 | Volume: 3 |

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 | Pages: e2293 | Issue: 6 | Volume: 3 |

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 | Pages: 333 | Issue: Jul 15 | Volume: 9 |

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 | Pages: R164 | Issue: 11 | Volume: 9 |

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 | Pages: 1583-1594 | Issue: 6 | Volume: 68 |

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 | Pages: 308-321 | Issue: 2 | Volume: 135 |


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 | Pages: 5063-5074 | Issue: 7 | Volume: 282 |

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 | Pages: 362-368 | Issue: 2 | Volume: 18 |


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 | Pages: 836-847 | Issue: 7 | Volume: 20 |

Goulphar: rapid access and expertise for standard two-color microarray normalization methods

Lemoine S, Combes F, Servant N, Le Crom S
| Journal: BMC Bioinformatics | Pages: 467 | Volume: 7 |


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. | Pages: 1860-8 | Issue: 5 | Volume: 25 |

Doelan: a solution for quality control monitoring of microarray production

Jourdren L, Le Crom S
| Journal: Bioinformatics | Pages: 4194-495 | Issue: 22 | Volume: 21 |

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 | Pages: 2759-70 | Issue: 4 | Volume: 280 |


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 | Pages: D323-325 | Issue: Database issue | Volume: 32 |

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 | Pages: 201-210 | Issue: Issue 3 (Feb) | Volume: 21 |

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. | Pages: 37973-81 | Issue: 36 | Volume: 279 |

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 | Pages: 20 | Issue: 1 | Volume: 5 |


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 | Pages: 52641-52650 | Issue: 52 | Volume: 278 |

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 | Pages: 745-754 | Issue: 3 | Volume: 47 |

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 | Pages: 11427-11432 | Issue: 13 | Volume: 278 |

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 | Pages: 1588-1598 | Issue: issue 7 (Apr 1) | Volume: 22 |


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 | Pages: 2642-2649 | Issue: 8 | Volume: 22 |

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 | Pages: 159-164 | Issue: 2 | Volume: 3 |

Arrayplot for visualization and normalization of cDNA microarray data

Marc P, Jacq C
| Journal: Bioinformatics | Pages: 888-889 | Issue: 6 | Volume: 18 |

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 | Pages: 3901-3914 | Issue: 11 | Volume: 13 |

yMGV: helping biologists with yeast microarray data mining

Le Crom S, Devaux F, Jacq C, Marc P
| Journal: Nucleic Acids Research | Pages: 76-79 | Issue: 1 | Volume: 30 |

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 | Pages: 25-28 | Issue: 1-3 | Volume: 515 |


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 | Pages: E63 | Issue: 13 | Volume: 29 |

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 | Pages: 493-498 | Issue: 6 | Volume: 2 |

Transcriptomes, transcription activators and microarrays

Devaux F, Marc P, Jacq C
| Journal: FEBS Letter | Pages: 140-144 | Issue: 2-3 | Volume: 498 |