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Items: 50

1.

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.

Front Microbiol. 2018 Nov 16;9:2689. doi: 10.3389/fmicb.2018.02689. eCollection 2018.

2.

How do Nucleotides Adsorb Onto Clays?

Pedreira-Segade U, Hao J, Razafitianamaharavo A, Pelletier M, Marry V, Le Crom S, Michot LJ, Daniel I.

Life (Basel). 2018 Nov 27;8(4). pii: E59. doi: 10.3390/life8040059.

3.

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.

Sci Rep. 2018 Aug 16;8(1):12272. doi: 10.1038/s41598-018-30739-5.

4.

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.

PLoS Genet. 2018 Jul 11;14(7):e1007498. doi: 10.1371/journal.pgen.1007498. eCollection 2018 Jul.

5.

Increased Fatty Acid Oxidation in Differentiated Proximal Tubular Cells Surviving a Reversible Episode of Acute Kidney Injury.

Bataille A, Galichon P, Chelghoum N, Oumoussa BM, Ziliotis MJ, Sadia I, Vandermeersch S, Simon-Tillaux N, Legouis D, Cohen R, Xu-Dubois YC, Commereuc M, Rondeau E, Le Crom S, Hertig A.

Cell Physiol Biochem. 2018;47(4):1338-1351. doi: 10.1159/000490819. Epub 2018 Jun 19.

6.

A de novo approach to disentangle partner identity and function in holobiont systems.

Meng A, Marchet C, Corre E, Peterlongo P, Alberti A, Da Silva C, Wincker P, Pelletier E, Probert I, Decelle J, Le Crom S, Not F, Bittner L.

Microbiome. 2018 Jun 9;6(1):105. doi: 10.1186/s40168-018-0481-9.

7.

Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network.

Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A, Alberti A, Da Silva C, Wincker P, Le Crom S, Not F, Bittner L.

Mol Ecol. 2018 May;27(10):2365-2380. doi: 10.1111/mec.14579. Epub 2018 May 3.

PMID:
29624751
8.

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.

Brain Sci. 2018 Mar 22;8(4). pii: E50. doi: 10.3390/brainsci8040050.

9.

Meet-U: Educating through research immersion.

Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes J, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes A.

PLoS Comput Biol. 2018 Mar 15;14(3):e1005992. doi: 10.1371/journal.pcbi.1005992. eCollection 2018 Mar.

10.

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.

Biotechnol Biofuels. 2017 Sep 7;10:209. doi: 10.1186/s13068-017-0897-7. eCollection 2017.

11.

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.

Cell Discov. 2017 Mar 28;3:17005. doi: 10.1038/celldisc.2017.5. eCollection 2017.

12.

Aozan: an automated post-sequencing data-processing pipeline.

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

Bioinformatics. 2017 Jul 15;33(14):2212-2213. doi: 10.1093/bioinformatics/btx154.

PMID:
28369225
13.

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.

Front Microbiol. 2016 May 9;7:645. doi: 10.3389/fmicb.2016.00645. eCollection 2016.

14.

Erratum to: 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.

BMC Genomics. 2015 Sep 22;16(1):725. doi: 10.1186/s12864-015-1917-2. No abstract available.

15.

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.

BMC Genomics. 2015 Apr 20;16:326. doi: 10.1186/s12864-015-1526-0. Erratum in: BMC Genomics. 2015;16(1):725.

16.

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.

Biotechnol Biofuels. 2014 Dec 12;7(1):173. doi: 10.1186/s13068-014-0173-z. eCollection 2014.

17.

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.

Yeast. 2014 Oct;31(10):375-91. doi: 10.1002/yea.3031. Epub 2014 Jul 28.

18.

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 AE, Rabinowicz PD, Sussman MR, Bowler C, Tirichine L.

Nat Commun. 2013;4:2091. doi: 10.1038/ncomms3091. Erratum in: Nat Commun. 2014;5:3028. Allen, Andrew [corrected to Allen, Andrew E].

PMID:
23820484
19.

Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism.

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

BMC Genomics. 2013 Feb 22;14:121. doi: 10.1186/1471-2164-14-121.

20.

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.

PLoS Genet. 2012;8(10):e1003006. doi: 10.1371/journal.pgen.1003006. Epub 2012 Oct 11.

21.

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.

Brief Bioinform. 2013 Nov;14(6):671-83. doi: 10.1093/bib/bbs046. Epub 2012 Sep 17.

PMID:
22988256
22.

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.

BMC Genomics. 2012 Aug 16;13:396.

23.

Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses.

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

Bioinformatics. 2012 Jun 1;28(11):1542-3. doi: 10.1093/bioinformatics/bts165. Epub 2012 Apr 5.

PMID:
22492314
24.

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, Sándor E, Hartl L, Karaffa L, Druzhinina IS, Seiboth B, Le Crom S, Kubicek CP.

BMC Genomics. 2011 May 27;12:269. doi: 10.1186/1471-2164-12-269.

25.

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 Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck 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 Biol. 2011;12(4):R40. doi: 10.1186/gb-2011-12-4-r40. Epub 2011 Apr 18.

26.

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 Mar;59(3):351-62. doi: 10.1002/glia.21106. Epub 2010 Dec 1.

PMID:
21264944
27.

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 Feb;10(2):262-71. doi: 10.1128/EC.00208-10. Epub 2010 Dec 17.

28.

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 Jun;38(10):e117. doi: 10.1093/nar/gkq110. Epub 2010 Feb 21.

29.

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 Oct 14;4(10):e7458. doi: 10.1371/journal.pone.0007458.

30.

Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing.

Le Crom S, Schackwitz W, Pennacchio L, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16151-6. doi: 10.1073/pnas.0905848106. Epub 2009 Sep 2.

31.

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 Oct;57(13):1450-7. doi: 10.1002/glia.20862.

PMID:
19243017
32.

An evaluation of custom microarray applications: the oligonucleotide design challenge.

Lemoine S, Combes F, Le Crom S.

Nucleic Acids Res. 2009 Apr;37(6):1726-39. doi: 10.1093/nar/gkp053. Epub 2009 Feb 10.

33.

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 Jan 1;25(1):128-9. doi: 10.1093/bioinformatics/btn573. Epub 2008 Nov 10.

34.

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 Dev. 2008 Jun 19;3:14. doi: 10.1186/1749-8104-3-14.

35.

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 Jun 4;3(6):e2293. doi: 10.1371/journal.pone.0002293.

36.

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 Feb 16;282(7):5063-74. Epub 2006 Dec 11.

37.

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

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

BMC Bioinformatics. 2006 Oct 23;7:467.

38.

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 Dev. 2006 Apr 1;20(7):836-47.

39.

Doelan: a solution for quality control monitoring of microarray production.

Jourdren L, Le Crom S.

Bioinformatics. 2005 Nov 15;21(22):4194-5. Epub 2005 Sep 22.

PMID:
16179358
40.

Delineation of the conserved functional properties of D1A, D1B and D1C dopamine receptor subtypes in vertebrates.

Le Crom S, Sugamori KS, Sidhu A, Niznik HB, Vernier P.

Biol Cell. 2004 Jun;96(5):383-94.

PMID:
15207908
41.

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 Res. 2004 Jan 1;32(Database issue):D323-5.

42.

Evolution and cell biology of dopamine receptors in vertebrates.

Callier S, Snapyan M, Le Crom S, Prou D, Vincent JD, Vernier P.

Biol Cell. 2003 Oct;95(7):489-502. Review.

PMID:
14597267
43.

Dopamine receptors for every species: gene duplications and functional diversification in Craniates.

Le Crom S, Kapsimali M, Barôme PO, Vernier P.

J Struct Funct Genomics. 2003;3(1-4):161-76. Review.

PMID:
12836695
44.

Ammonia pulses and metabolic oscillations guide yeast colony development.

Palková Z, Devaux F, Icicová M, Mináriková L, Le Crom S, Jacq C.

Mol Biol Cell. 2002 Nov;13(11):3901-14.

45.
46.
47.

yMGV: helping biologists with yeast microarray data mining.

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

Nucleic Acids Res. 2002 Jan 1;30(1):76-9.

48.

Intracellular retention of the two isoforms of the D(2) dopamine receptor promotes endoplasmic reticulum disruption.

Prou D, Gu WJ, Le Crom S, Vincent JD, Salamero J, Vernier P.

J Cell Sci. 2001 Oct;114(Pt 19):3517-27.

49.

[Evolution and development of dopaminergic neurotransmitter systems in vertebrates].

Kapsimali M, Dumond H, Le Crom S, Coudouel S, Vincent JD, Vernier P.

J Soc Biol. 2000;194(2):87-93. Review. French.

PMID:
11098433
50.

Dopamine D1 and adenosine A1 receptors form functionally interacting heteromeric complexes.

Ginés S, Hillion J, Torvinen M, Le Crom S, Casadó V, Canela EI, Rondin S, Lew JY, Watson S, Zoli M, Agnati LF, Verniera P, Lluis C, Ferré S, Fuxe K, Franco R.

Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8606-11.

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