-
2018checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes, Bioinformatics, 2018.
-
2018Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica, Sci Rep 2018 Jun;8(1):9042.
-
2018Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation, BMC Genomics 2018 May;19(1):373.
-
2017Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut., PLoS Negl Trop Dis 2017 12; 11(12): e0006152.
-
2017In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells, Cell Reports , Volume 21 , Issue 7 , 1982 - 1993.
-
2017An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum, Sci Rep 2017 Oct;7(1):14042.
-
2017Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis, EMBO J. 2017 May;36(9):1167-1181.
-
2017Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite, Microb Biotechnol. 2017 Feb 7. doi: 10.1111/1751-7915.12556.
-
2016Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network, Nat. Cell Biol. 2016 Oct;.
-
2016GH16 and GH81 family β-(1,3)-glucanases in Aspergillus fumigatus are essential for conidial cell wall morphogenesis, Cell Microbiol. 2016 Jun 15. doi: 10.1111/cmi.12630.
-
2016SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One. 2016 Jun 9;11(6):e0157022. doi: 10.1371/journal.pone.0157022. eCollection 2016.
-
2016RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori., RNA Biol. 2016;13(2):243-53. doi: 10.1080/15476286.2015.1132141..
-
2015Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress, Carcinogenesis 2016 Jan;37(1):39-48.
-
2015The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages, Genome Biol. 2015;16:212.
-
2015Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae, BMC Genomics 2015 May;16:419.
-
2015Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58, Mol. Plant Microbe Interact. 2015 May;28(5):580-9.
-
2015Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding, Nucleic Acids Res. 2015 Feb;43(3):1456-68.
-
2014Differences in gene transcriptomic pattern of Plasmodium falciparum in children with cerebral malaria and asymptomatic carriers, PLoS ONE 2014;9(12):e114401.
-
2014DYRK1A phoshorylates histone H3 to differentially regulate the binding of HP1 isoforms and antagonize HP1-mediated transcriptional repression, EMBO Rep. 2014 Jun;15(6):686-94.
-
2014Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella, PLoS ONE 2014;9(5):e96918.
-
2014Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism, BMC Microbiol. 2014;14:81.
-
2014Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation., PLoS Genet 2014 Apr; 10(4): e1004261.
-
2014A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans, Infect. Immun. 2014 Jun;82(6):2542-52.
-
2014Extracellular adenosine triphosphate affects the response of human macrophages infected with Mycobacterium tuberculosis, J. Infect. Dis. 2014 Sep;210(5):824-33.
-
2014Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum, BMC Genomics 2014;15:150.
-
2014The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing, Mol. Cell 2014 Jan;53(2):277-89.
-
2013The intestinal microbiota interferes with the microRNA response upon oral Listeria infection, MBio 2013;4(6):e00707-13.
-
2013Induction of the Cpx envelope stress pathway contributes to Escherichia coli tolerance to antimicrobial peptides, Appl. Environ. Microbiol. 2013 Dec;79(24):7770-9.
-
2013Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus, Mol. Microbiol. 2013 Nov;90(3):612-29.
-
2013Massive activation of archaeal defense genes during viral infection, J. Virol. 2013 Aug;87(15):8419-28.
-
2013Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile, PLoS Genet. 2013 May;9(5):e1003493.
-
2013Identification of RNA partners of viral proteins in infected cells, RNA Biol 2013 Jun;10(6):944-56.
-
2013Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin, PLoS Genet. 2013;9(1):e1003144.
-
2013Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26, Genome Biol Evol 2013;5(5):934-53.
-
2012Distinct transcriptional signatures of bone marrow-derived C57BL/6 and DBA/2 dendritic leucocytes hosting live Leishmania amazonensis amastigotes, PLoS Negl Trop Dis 2012;6(12):e1980.
-
2012Dicer-2- and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells, J. Virol. 2013 Feb;87(3):1631-48.
-
2012RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans, BMC Genomics 2012;13:396.
-
2012Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence, RNA Biol 2012 Apr;9(4):503-19.
-
2012Human cryptochrome-1 confers light independent biological activity in transgenic Drosophila correlated with flavin radical stability, PLoS ONE 2012;7(3):e31867.
-
2012Myf5 haploinsufficiency reveals distinct cell fate potentials for adult skeletal muscle stem cells, J. Cell. Sci. 2012 Apr;125(Pt 7):1738-49.
-
2011Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles, RNA 2012 Feb;18(2):253-64.
-
2011Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways, PLoS Genet. 2011 Sep;7(9):e1002305.
-
2011Extending KNIME for next-generation sequencing data analysis, Bioinformatics 2011 Oct;27(20):2907-9.
-
2011Artesunate tolerance in transgenic Plasmodium falciparum parasites overexpressing a tryptophan-rich protein, Antimicrob. Agents Chemother. 2011 Jun;55(6):2576-84.
-
2011Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae), BMC Mol. Biol. 2011;12:2.
-
2011Overexpression of proinflammatory TLR-2-signalling lipoproteins in hypervirulent mycobacterial variants, Cell. Microbiol. 2011 May;13(5):692-704.
-
2010Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans, BMC Genomics 2010;11:709.
-
2010Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum, Appl. Environ. Microbiol. 2011 Feb;77(4):1449-59.
-
2010From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma, BMC Genomics 2010;11:368.
-
2010From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma., BMC Genomics. 2010 Jun 10;11:368. doi: 10.1186/1471-2164-11-368..
-
2010Decreased in vitro susceptibility of Plasmodium falciparum isolates to artesunate, mefloquine, chloroquine, and quinine in Cambodia from 2001 to 2007, Antimicrob. Agents Chemother. 2010 May;54(5):2135-42.
-
2010Structure, function, and evolution of the Thiomonas spp. genome, PLoS Genet. 2010 Feb;6(2):e1000859.
-
2010Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans, BMC Microbiol. 2010;10:53.
-
2009The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila, Proc. Natl. Acad. Sci. U.S.A. 2009 Dec;106(50):21258-63.
-
2009FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance, Malar. J. 2009;8:229.
-
2009The global regulator CodY regulates toxin gene expression in Bacillus anthracis and is required for full virulence, Infect. Immun. 2009 Oct;77(10):4437-45.
-
2009Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses, Appl. Environ. Microbiol. 2009 Oct;75(19):6406-9.
-
2009Urinary NGAL marks cystic disease in HIV-associated nephropathy, J. Am. Soc. Nephrol. 2009 Aug;20(8):1687-92.
-
2009Unusual composition of a yeast chromosome arm is associated with its delayed replication, Genome Res. 2009 Oct;19(10):1710-21.
-
2009The Listeria transcriptional landscape from saprophytism to virulence., Nature 2009 Jun; 459(7249): 950-6.
-
2009CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation, Mol. Microbiol. 2009 Jul;73(2):194-211.
-
2009Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes, BMC Genomics 2009;10:119.
-
2009Field-based evidence of fast and global increase of Plasmodium falciparum drug-resistance by DNA-microarrays and PCR/RFLP in Niger, Malar. J. 2009;8:32.
-
2008Genomic polymorphism in the population of Candida glabrata: gene copy-number variation and chromosomal translocations, Fungal Genet. Biol. 2009 Mar;46(3):264-76.
-
2008Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data, Biochimie 2009 Feb;91(2):192-203.
-
2008Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia, BMC Genomics 2008;9:417.
-
2008Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate, BMC Genomics 2008;9:388.
-
2008Do DNA microarrays have their future behind them?, Microbes Infect. 2008 Jul;10(9):1067-71.
-
2008AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests, J Bioinform Comput Biol 2008 Apr;6(2):317-34.
-
2008Plasmodium falciparum transcriptome analysis reveals pregnancy malaria associated gene expression, PLoS ONE 2008;3(3):e1855.
-
2007Whole-transcriptome analysis of Plasmodium falciparum field isolates: identification of new pathogenicity factors, J. Infect. Dis. 2007 Dec;196(11):1603-12.
-
2007Long oligonucleotide microarrays for African green monkey gene expression profile analysis., FASEB J 2007 Oct; 21(12): 3262-71.
-
2007Rapid microarray-based method for monitoring of all currently known single-nucleotide polymorphisms associated with parasite resistance to antimalaria drugs, J. Clin. Microbiol. 2007 Nov;45(11):3685-91.
-
2007Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague., Microbiology (Reading, Engl.) 2007 Sep; 153(Pt 9): 3112-3124.
-
2007beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors, Development 2007 Sep;134(17):3177-90.
-
2007Histone modifications induced by a family of bacterial toxins, Proc. Natl. Acad. Sci. U.S.A. 2007 Aug;104(33):13467-72.
-
2006Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila, Cell. Microbiol. 2006 Aug;8(8):1228-40.
-
2006Anti-inflammatory effect of Lactobacillus casei on Shigella-infected human intestinal epithelial cells, J. Immunol. 2006 Jan;176(2):1228-37.
-
2006Cell-based assays using primary endothelial cells to study multiple steps in inflammation, Meth. Enzymol. 2006;414:266-83.
-
2005Transcriptome analysis of antigenic variation in Plasmodium falciparum–var silencing is not dependent on antisense RNA, Genome Biol. 2005;6(11):R93.
-
2005Sequence characteristics of functional siRNAs, RNA 2005 Jun;11(6):864-72.
-
2005On the origin of leprosy, Science 2005 May;308(5724):1040-2.
-
2005Adherence modifies the regulation of gene expression induced by interleukin-10, Cytokine 2005 Jan;29(1):1-12.
-
2004GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli, Microbiology (Reading, Engl.) 2004 Jan;150(Pt 1):61-72.
-
2003Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA, Mol. Microbiol. 2003 Mar;47(6):1613-25.
-
2000Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites, Bioinformatics 2000 Mar;16(3):245-50.