Genomic Paris Centre

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

- https://doi.org/10.1038/s41398-020-01050-7

- http://www.ncbi.nlm.nih.gov/pubmed/33159041

The impact of transposable elements on tomato diversity

Domínguez M, Dugas E, Benchouaia M, Leduque B, Jiménez‑Gómez JM, Colot V, Quadrana L

- https://doi.org/10.1038/s41467-020-17874-2

- http://www.ncbi.nlm.nih.gov/pubmed/32792480

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 : | Issue : |

- https://doi.org/10.1038/s41366-020-00694-1

- http://www.ncbi.nlm.nih.gov/pubmed/33037328

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

- https://doi.org/10.1016/j.celrep.2020.108141

- http://www.ncbi.nlm.nih.gov/pubmed/32937117

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

- https://doi.org/10.1016/j.celrep.2020.108076

- http://www.ncbi.nlm.nih.gov/pubmed/32846133

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

- https://doi.org/10.1186/s12977-020-00533-1

- http://www.ncbi.nlm.nih.gov/pubmed/32807178

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

- https://doi.org/10.1016/j.molmet.2020.101066

- http://www.ncbi.nlm.nih.gov/pubmed/32807178

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

- https://doi.org/10.7554/elife.52985

- http://www.ncbi.nlm.nih.gov/pubmed/32338592

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.

- https://doi.org/10.3389/fimmu.2020.588411

- http://www.ncbi.nlm.nih.gov/pubmed/33365028

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

- https://doi.org/10.1186/s12864-020-07281-8

- http://www.ncbi.nlm.nih.gov/pubmed/33302864

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

- https://doi.org/10.1111/ejn.14375

- http://www.ncbi.nlm.nih.gov/pubmed/30767299

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 |

- https://doi.org/10.1186/s13227-019-0129-2

- http://www.ncbi.nlm.nih.gov/pubmed/31406559

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 |

- https://doi.org/10.1186/s13059-019-1705-4

- http://www.ncbi.nlm.nih.gov/pubmed/31113491

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

- https://doi.org/10.3389/fendo.2019.00194

- http://www.ncbi.nlm.nih.gov/pubmed/31001200

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 | Issue : |

- https://doi.org/10.1038/s41598-018-36785-3

- http://www.ncbi.nlm.nih.gov/pubmed/30696855

Molecular characterisation of a cellular conveyor belt in Clytia medusa

Condamine T, Jager M, Leclère L, Blugeon C, Lemoine S, Copley RR, Manuel M

- https://linkinghub.elsevier.com/retrieve/pii/S0012-1606(18)30409-3

- http://www.ncbi.nlm.nih.gov/pubmed/31509769

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

- https://doi.org/10.1007/s00401-019-02011-1

- http://www.ncbi.nlm.nih.gov/pubmed/31011859

Zinc Uptake and Storage During the Formation of the Cerebral Cortex in Mice

Hasna J, Bohic S, Lemoine S, Blugeon C, Bouron A

- https://link.springer.com/article/10.1007%2Fs12035-019-1581-7

- http://www.ncbi.nlm.nih.gov/pubmed/30941734

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

- https://www.sciencedirect.com/science/article/abs/pii/S1534580719307397

- http://www.ncbi.nlm.nih.gov/pubmed/31607652

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

- https://doi.org/10.1093/brain/awy276

- http://www.ncbi.nlm.nih.gov/pubmed/30462183

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

- http://doi.org/10.1158/2159-8290.CD-18-0156

- http://www.ncbi.nlm.nih.gov/pubmed/30348676

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

- https://academic.oup.com/cercor/advance-article-abstract/doi/10.1093/cercor/bhy108/4996557

- http://www.ncbi.nlm.nih.gov/pubmed/29771284

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 |

- https://doi.org/10.1038/s41467-018-07171-4

- http://www.ncbi.nlm.nih.gov/pubmed/30413696

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

- http://rnajournal.cshlp.org/content/early/2018/09/14/rna.067173.118

- http://www.ncbi.nlm.nih.gov/pubmed/30217866

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

- https://doi.org/10.1093/nar/gky797

- http://www.ncbi.nlm.nih.gov/pubmed/30189101

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

- http://www.mdpi.com/2076-3425/8/4/50

- http://www.ncbi.nlm.nih.gov/pubmed/29565275

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

- https://www.sciencedirect.com/science/article/pii/S0092867417314320

- http://www.ncbi.nlm.nih.gov/pubmed/29275859

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

- https://doi.org/10.3389/fmicb.2018.02689

- http://www.ncbi.nlm.nih.gov/pubmed/30505294

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

- https://doi.org/10.1371/journal.pgen.1007498

- http://www.ncbi.nlm.nih.gov/pubmed/29995890

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

- https://www.nature.com/articles/s41598-018-30739-5

- http://www.ncbi.nlm.nih.gov/pubmed/30116021

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

- http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13398/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/27236063

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

- http://www.cell.com/developmental-cell/fulltext/S1534-5807(17)30632-9

- http://www.ncbi.nlm.nih.gov/pubmed/28867488

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

- http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006903

- http://www.ncbi.nlm.nih.gov/pubmed/28749941

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

- https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1344-6

- http://www.ncbi.nlm.nih.gov/pubmed/29084568

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

- https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-017-0897-7

- http://www.ncbi.nlm.nih.gov/pubmed/28912831

Aozan: an automated post-sequencing data-processing pipeline

Perrin S, Firmo C, Lemoine S, Le Crom S, Jourdren L

- https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx154/3089940/Aozan-an-automated-post-sequencing-data-processing

- http://www.ncbi.nlm.nih.gov/pubmed/28369225

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

- http://www.nature.com/articles/celldisc20175

- http://www.ncbi.nlm.nih.gov/pubmed/28377822

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

- https://www.nature.com/articles/s41598-017-16543-7

- http://www.ncbi.nlm.nih.gov/pubmed/29170465

ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses

Lelandais G, Blugeon C, Merhej J

- http://link.springer.com/protocol/10.1007%2F978-1-4939-3079-1_11

- http://www.ncbi.nlm.nih.gov/pubmed/26483023

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

- http://www.nature.com/ncomms/2016/160718/ncomms12238/full/ncomms12238.html

- http://www.ncbi.nlm.nih.gov/pubmed/27426965

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

- http://insight.jci.org/articles/view/88689

- http://www.ncbi.nlm.nih.gov/pubmed/27942586

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

- http://journal.frontiersin.org/article/10.3389/fmicb.2016.00645/full

- http://www.ncbi.nlm.nih.gov/pubmed/27242683

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

- http://www.sciencedirect.com/science/article/pii/S2213671115001861

- http://www.ncbi.nlm.nih.gov/pubmed/26212662

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

- http://journal.frontiersin.org/article/10.3389/fncel.2015.00009/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/25698924

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

- http://onlinelibrary.wiley.com/doi/10.1111/mmi.12944/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/25626518

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

- http://www.jneurosci.org/content/35/10/4427.long

- http://www.ncbi.nlm.nih.gov/pubmed/25762685

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

- http://www.biomedcentral.com/1471-2164/16/326

- http://www.ncbi.nlm.nih.gov/pubmed/25909478

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

- http://ec.asm.org/content/14/5/442

- http://www.ncbi.nlm.nih.gov/pubmed/25724885

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

- http://nar.oxfordjournals.org/content/43/3/1818.long

- http://www.ncbi.nlm.nih.gov/pubmed/25593325

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

- http://www.nature.com/oncsis/journal/v4/n7/full/oncsis201520a.html

- http://www.ncbi.nlm.nih.gov/pubmed/26214578

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

- http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0111589

- http://www.ncbi.nlm.nih.gov/pubmed/25365506

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

- http://www.biotechnologyforbiofuels.com/content/7/1/173

- http://www.ncbi.nlm.nih.gov/pubmed/25550711

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

- http://www.nature.com/nature/journal/v509/n7501/full/nature13318.html

- http://www.ncbi.nlm.nih.gov/pubmed/24805235

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

- http://onlinelibrary.wiley.com/doi/10.1002/yea.3031/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/25041923

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

- http://cardiovascres.oxfordjournals.org/content/104/3/443.long

- http://www.ncbi.nlm.nih.gov/pubmed/25344368

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

- http://linkinghub.elsevier.com/retrieve/pii/S2211-1247(13)00582-2

- http://www.ncbi.nlm.nih.gov/pubmed/24210826

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

- http://www.nature.com/ncomms/2013/130702/ncomms3091/full/ncomms3091.html

- http://www.ncbi.nlm.nih.gov/pubmed/23820484

Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism

Atanasova L, Le Crom S, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, Druzhinina IS

- http://www.biomedcentral.com/1471-2164/14/121/

- http://www.ncbi.nlm.nih.gov/pubmed/23432824

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

- http://bib.oxfordjournals.org/content/14/6/671.long

- http://www.ncbi.nlm.nih.gov/pubmed/22988256

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

- http://www.biomedcentral.com/1471-2164/13/396/

- http://www.ncbi.nlm.nih.gov/pubmed/22897889

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

- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505855/

- http://www.ncbi.nlm.nih.gov/pubmed/22379615

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

- http://nar.oxfordjournals.org/content/40/12/5271.long

- http://www.ncbi.nlm.nih.gov/pubmed/22379133

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

- http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003006

- http://www.ncbi.nlm.nih.gov/pubmed/23071455

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

Jourdren L, Bernard M, Dillies MA, Le Crom S

- http://bioinformatics.oxfordjournals.org/content/28/11/1542

- http://www.ncbi.nlm.nih.gov/pubmed/22492314

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

- http://aac.asm.org/content/56/1/495

- http://www.ncbi.nlm.nih.gov/pubmed/22006003

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

- http://www.jbc.org/content/286/35/30994.abstract

- http://www.ncbi.nlm.nih.gov/pubmed/21757731

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

- http://ec.asm.org/cgi/pmidlookup?view=long&pmid=21169417

- http://www.ncbi.nlm.nih.gov/pubmed/21169417

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

- http://genomebiology.com/2011/12/4/R40/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/21501500

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

- http://www.biomedcentral.com/1471-2164/12/269

- http://www.ncbi.nlm.nih.gov/pubmed/21619626

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

- http://www.pnas.org/content/108/26/10714

- http://www.ncbi.nlm.nih.gov/pubmed/21670295

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

- http://www.biomedcentral.com/1471-2164/12/331

- http://www.ncbi.nlm.nih.gov/pubmed/21711526

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

- http://dx.doi.org/10.1002/glia.21106

- http://www.ncbi.nlm.nih.gov/pubmed/21264944

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

- http://www.masson.fr/masson/S0035-3787(10)00472-8

- http://www.ncbi.nlm.nih.gov/pubmed/21193208

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

- http://dx.plos.org/10.1371/journal.pone.0016301

- http://www.ncbi.nlm.nih.gov/pubmed/21298006

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

- http://www.jneurosci.org/cgi/content/short/30/17/5958

- http://www.ncbi.nlm.nih.gov/pubmed/20427655

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

- http://nar.oxfordjournals.org/cgi/content/abstract/gkq110?ijkey=XbGwzIKPrHAyFqz&keytype=ref

- http://www.ncbi.nlm.nih.gov/pubmed/20176570

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

- http://www3.interscience.wiley.com/journal/123227095/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/20039366

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

- http://www.nature.com/emboj/journal/vaop/ncurrent/abs/emboj2010199a.html

- http://www.ncbi.nlm.nih.gov/pubmed/20729808

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

- http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=20494971

- http://www.ncbi.nlm.nih.gov/pubmed/20494971

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

- http://www3.interscience.wiley.com/journal/122219371/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/19243017

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

- http://genesdev.cshlp.org/content/23/12/1399.abstract

- http://www.ncbi.nlm.nih.gov/pubmed/19528318

Phenotypic Consequences of Purine Nucleotide Imbalance in Saccharomyces cerevisiae

Saint-Marc C, Pinson B, Coulpier F, Jourdren L, Lisova O, Daignan-Fornier B

- http://www.genetics.org/cgi/content/abstract/genetics.109.105858v1

- http://www.ncbi.nlm.nih.gov/pubmed/19635936

An evaluation of custom microarray applications: the oligonucleotide design challenge

Lemoine S, Combes F, Le Crom S

- http://nar.oxfordjournals.org/cgi/content/abstract/37/6/1726

- http://www.ncbi.nlm.nih.gov/pubmed/19208645

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

- http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007458

- http://www.ncbi.nlm.nih.gov/pubmed/19829693

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

- http://bioinformatics.oxfordjournals.org/cgi/content/full/25/1/128

- http://www.ncbi.nlm.nih.gov/pubmed/19015129

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

- http://www.pnas.org/content/106/38/16151.abstract

- http://www.ncbi.nlm.nih.gov/pubmed/19805272

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

- http://genomebiology.com/2008/9/11/R164/abstract

- http://www.ncbi.nlm.nih.gov/pubmed/19025642

Lethal accumulation of guanylic nucleotides in Saccharomyces cerevisiae HPT1-deregulated mutants

Breton A, Pinson B, Coulpier F, Giraud MF, Dautant A, Daignan-Fornier B

- http://www.genetics.org/cgi/content/full/178/2/815

- http://www.ncbi.nlm.nih.gov/pubmed/18245832

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

- http://www.neuraldevelopment.com/content/4/1/6

- http://www.ncbi.nlm.nih.gov/pubmed/18565209

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

- http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002293

- http://www.ncbi.nlm.nih.gov/pubmed/18523582

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

- http://www.biomedcentral.com/1471-2164/9/333

- http://www.ncbi.nlm.nih.gov/pubmed/18627600

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

- http://linkinghub.elsevier.com/retrieve/pii/S0092-8674

- http://www.ncbi.nlm.nih.gov/pubmed/18957205

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

- http://www.blackwell-synergy.com/openurl?genre=article&sid=nlm:pubmed&issn=0950-382X&date=2008&volume=68&issue=6&spage=1583

- http://www.ncbi.nlm.nih.gov/pubmed/18433446

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

- http://www.jbc.org/cgi/content/abstract/282/7/5063

- http://www.ncbi.nlm.nih.gov/pubmed/17158869

Mitochondria-associated Yeast mRNAs and the Biogenesis of Molecular Complexes

Garcia M, Darzacq X, Delaveau T, Jourdren L, Singer RH, Jacq C

- http://www.molbiolcell.org/cgi/reprint/18/2/362

- http://www.ncbi.nlm.nih.gov/pubmed/17108321

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

- http://genesdev.cshlp.org/content/20/7/836.long

- http://www.ncbi.nlm.nih.gov/pubmed/16600913

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

Lemoine S, Combes F, Servant N, Le Crom S

- http://www.biomedcentral.com/1471-2105/7/467

- http://www.ncbi.nlm.nih.gov/pubmed/17059595

Doelan: a solution for quality control monitoring of microarray production

Jourdren L, Le Crom S

- http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/22/4194

- http://www.ncbi.nlm.nih.gov/pubmed/16179358

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

- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15528187

- http://www.ncbi.nlm.nih.gov/pubmed/15528187

Early expression of yeast genes affected by chemical stress

Lucau-Danila A, Lelandais G, Kozovska Z, Tanty V, Delaveau T, Devaux F, Jacq C

- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15713640

- http://www.ncbi.nlm.nih.gov/pubmed/15713640

Ady2p is essential for the acetate permease activity in the yeast Saccharomyces cerevisiae

Paiva S, Devaux F, Barbosa S, Jacq C, Casal M

- http://www3.interscience.wiley.com/cgi-bin/abstract/107612571/ABSTRACT

- http://www.ncbi.nlm.nih.gov/pubmed/14968426

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

- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15229222

- http://www.ncbi.nlm.nih.gov/pubmed/15229222

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states

Lelandais G, Marc P, Vincens P, Jacq C, Vialette S

- http://www.biomedcentral.com/1471-2105/5/20

- http://www.ncbi.nlm.nih.gov/pubmed/15053844

yMGV: a cross-species expression data mining tool

Lelandais G, Le Crom S, Devaux F, Vialette S, Church GM, Jacq C, Marc P

- http://nar.oupjournals.org/cgi/pmidlookup?view=full&pmid=14681424

- http://www.ncbi.nlm.nih.gov/pubmed/14681424

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

- http://www.jbc.org/cgi/pmidlookup?view=full&pmid=14512416

- http://www.ncbi.nlm.nih.gov/pubmed/14512416

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

- http://www.blackwell-synergy.com/openurl?genre=article&sid=nlm:pubmed&issn=0950-382X&date=2003&volume=47&issue=3&spage=745

- http://www.ncbi.nlm.nih.gov/pubmed/12535073

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

- http://www.jbc.org/cgi/pmidlookup?view=full&pmid=12529331

- http://www.ncbi.nlm.nih.gov/pubmed/12529331

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

- http://www.nature.com/cgi-taf/DynaPage.taf?file=/emboj/journal/v22/n7/abs/7595052a.html&dynoptions=doi1092130913

- http://www.ncbi.nlm.nih.gov/pubmed/12660165

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

- http://mcb.asm.org/cgi/pmidlookup?view=full&pmid=11909958

- http://www.ncbi.nlm.nih.gov/pubmed/11909958

yMGV: helping biologists with yeast microarray data mining

Le Crom S, Devaux F, Jacq C, Marc P

- http://nar.oupjournals.org/cgi/pmidlookup?view=full&pmid=11752259

- http://www.ncbi.nlm.nih.gov/pubmed/11752259

Genome-wide analysis of mRNAs targeted to yeast mitochondria

Marc P, Margeot A, Devaux F, Blugeon C, Corral-Debrinski M, Jacq C

- http://dx.doi.org/10.1093/embo-reports/kvf025

- http://www.ncbi.nlm.nih.gov/pubmed/11818335

Ammonia pulses and metabolic oscillations guide yeast colony development

Palkova Z, Devaux F, Icicova M, Minarikova L, Le Crom S, Jacq C

- http://www.molbiolcell.org/cgi/pmidlookup?view=full&pmid=12429834

- http://www.ncbi.nlm.nih.gov/pubmed/12429834

Arrayplot for visualization and normalization of cDNA microarray data

Marc P, Jacq C

- http://bioinformatics.oupjournals.org/cgi/pmidlookup?view=reprint&pmid=12075027

- http://www.ncbi.nlm.nih.gov/pubmed/12075027

Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast

Devaux F, Carvajal E, Moye-Rowley S, Jacq C

- http://linkinghub.elsevier.com/retrieve/pii/S0014579302023876

- http://www.ncbi.nlm.nih.gov/pubmed/11943188

yMGV: a database for visualization and data mining of published genome-wide yeast expression data

Marc P, Devaux F, Jacq C

- http://nar.oupjournals.org/cgi/pmidlookup?view=full&pmid=11433039

- http://www.ncbi.nlm.nih.gov/pubmed/11433039

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

- http://dx.doi.org/10.1093/embo-reports/kve114

- http://www.ncbi.nlm.nih.gov/pubmed/11415981

Transcriptomes, transcription activators and microarrays

Devaux F, Marc P, Jacq C

- http://linkinghub.elsevier.com/retrieve/pii/S0014579301024784

- http://www.ncbi.nlm.nih.gov/pubmed/11412845

Publications

2020