/ Home / Communications / Publications

Transcriptome platform associated publications

• 2012
• 2011
• 2010
• 2009
• 2008
• 2007
• 2006
• 2005
• 2004
• 2003
• 2002
• 2001

2012

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 Antimicrobial Agents and Chemotherapy. (2012) 56 (1): 495-506. Research article.

2011

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 The Journal of Biological Chemistry. (2011) 286 (35): 30994-31002. Research article.
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. BMC Genomics. (2011) 12 (1): 331. Research article.
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 Proceedings of The National Academy of Sciences of the United States of America. (2011) 108 (26): 10714-10719. Research article.
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 BMC Genomics. (2011) 12 (1): 269. Research article.
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 Genome Biology. (2011) 18 (4): R40. Research article.
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 Eukaryot Cell. (2011) 10 (2): 262-271. Research article.
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 Glia. (2011) 59 (3): 351-362. Research article.
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 Rev Neurol (Paris). (2011) 167 (1): 51-56. Research article.
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 PLoS One. (2011) 6 (1): e16301. Research article.

2010

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. EMBO J. (2010) 29 (18): 3082-3093. Research article.
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 RNA. (2010) 16 (7): 1301-1307. Research article.
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 The Journal of Neuroscience. (2010) 30 (17): 5958-5967. Research article.
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 Nucleic Acids Res.. (2010) 38 (10): e117. Research article.
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 Stem Cells. (2010) 28 (3): 470-479. Research article.

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 PLoS ONE. (2009) 4 (10): e7458. Research article.
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 Proceedings of The National Academy of Sciences of the United States of America. (2009) 106 (38): 16151-16156. Research article.
Phenotypic Consequences of Purine Nucleotide Imbalance in Saccharomyces cerevisiae. Saint-Marc C, Pinson B, Coulpier F, Jourdren L, Lisova O, Daignan-Fornier B. Genetics. (2009) 183 (2): 529-538. Research article.
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 Glia. (2009) 57 (13): 1450-1457. Research article.
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 Genes and development. (2009) 23 (12): 1399-1407. Research article.
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 Bioinformatics. (2009) 25 (1): 128-129. Research article.
An evaluation of custom microarray applications: the oligonucleotide design challenge. Lemoine S, Combes F, Le Crom S Nucleic Acids Research. (2009) 37 (6): 1726–1739. Research article.

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. Neural development. (2008) 3 (14): 1-16. Research article.
Lethal accumulation of guanylic nucleotides in Saccharomyces cerevisiae HPT1-deregulated mutants. Breton A, Pinson B, Coulpier F, Giraud MF, Dautant A, Daignan-Fornier B Genetics. (2008) 178 (2): 815-824. Research article.
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 Genome Biology. (2008) 9 (11): R164. Research article.
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 Cell. (2008) 135 (2): 308-321. Research article.
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 BMC Genomics. (2008) 9 (Jul 15): 333. Research article.
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 PLoS ONE. (2008) 3 (6): e2293. Research article.
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 Molecular Microbiology. (2008) 68 (6): 1583-1594. Research article.

2007

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 J Biol Chem. (2007) 282 (7): 5063-5074. Research article.
Mitochondria-associated Yeast mRNAs and the Biogenesis of Molecular Complexes. Garcia M, Darzacq X, Delaveau T, Jourdren L, Singer RH, Jacq C Molecular Biology of the Cell. (2007) 18 (2): 362-368. Research article.

2006

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 Genes & Development. (2006) 20 (7): 836-847. Research article.
Goulphar: rapid access and expertise for standard two-color microarray normalization methods. Lemoine S, Combes F, Servant N, Le Crom S BMC Bioinformatics. (2006) 7 (): 467. Research article.

2005

Doelan: a solution for quality control monitoring of microarray production. Jourdren L, Le Crom S Bioinformatics. (2005) 21 (22): 4194-495. Research article.
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. J Biol Chem. (2005) 280 (4): 2759-70. Research article.
Early expression of yeast genes affected by chemical stress. Lucau-Danila A, Lelandais G, Kozovska Z, Tanty V, Delaveau T, Devaux F, Jacq C. Mol Cell Biol.. (2005) 25 (5): 1860-8. Research article.

2004

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. J Biol Chem.. (2004) 279 (36): 37973-81. Research article.
Ady2p is essential for the acetate permease activity in the yeast Saccharomyces cerevisiae. Paiva S, Devaux F, Barbosa S, Jacq C, Casal M Yeast. (2004) 21 (Issue 3 (Feb)): 201-210. Research article.
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states Lelandais G, Marc P, Vincens P, Jacq C, Vialette S BMC Bioinformatics. (2004) 5 (1): 20. Research article.
yMGV: a cross-species expression data mining tool Lelandais G, Le Crom S, Devaux F, Vialette S, Church GM, Jacq C, Marc P Nucleic Acids Research. (2004) 32 (Database issue): D323-325. Research article.

2003

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 EMBO Journal. (2003) 22 (issue 7 (Apr 1)): 1588-1598. Research article.
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 of Biological Chemistry. (2003) 278 (52): 52641-52650. Research article.
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 Molecular Microbiology. (2003) 47 (3): 745-754. Research article.
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 of Biological Chemistry. (2003) 278 (13): 11427-11432. Research article.

2002

Ammonia pulses and metabolic oscillations guide yeast colony development Palkova Z, Devaux F, Icicova M, Minarikova L, Le Crom S, Jacq C Molecular Biology of the Cell. (2002) 13 (11): 3901-3914. Research article.
Arrayplot for visualization and normalization of cDNA microarray data Marc P, Jacq C Bioinformatics. (2002) 18 (6): 888-889. Research article.
Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast Devaux F, Carvajal E, Moye-Rowley S, Jacq C FEBS Letters. (2002) 515 (1-3): 25-28. Research article.
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 Molecular and Cellular Biology. (2002) 22 (8): 2642-2649. Research article.
Genome-wide analysis of mRNAs targeted to yeast mitochondria Marc P, Margeot A, Devaux F, Blugeon C, Corral-Debrinski M, Jacq C EMBO Reports. (2002) 3 (2): 159-164. Research article.
yMGV: helping biologists with yeast microarray data mining Le Crom S, Devaux F, Jacq C, Marc P Nucleic Acids Research. (2002) 30 (1): 76-79. Research article.

2001

yMGV: a database for visualization and data mining of published genome-wide yeast expression data Marc P, Devaux F, Jacq C Nucleic Acids Research. (2001) 29 (13): E63. Research article.
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 EMBO Reports. (2001) 2 (6): 493-498. Research article.
Transcriptomes, transcription activators and microarrays Devaux F, Marc P, Jacq C FEBS Letter. (2001) 498 (2-3): 140-144. Review.