Genomes and Genes
Affiliation: University of Lausanne
- Impact of normalization on miRNA microarray expression profilingSylvain Pradervand
Lausanne DNA Array Facility, Center for Integrative Genomics, University of Lausanne, CH 1015 Lausanne, Switzerland
RNA 15:493-501. 2009....
- Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arraysSylvain Pradervand
DNA Array Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
Biotechniques 44:759-62. 2008..This may reflect the impact of the target type. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array...
- Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAsSylvain Pradervand
Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, Switzerland
Biotechniques 48:219-22. 2010....
- Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signalingPatricia Hornitschek
Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH 1015 Lausanne, Switzerland
Plant J 71:699-711. 2012..Moreover our study suggests that PIF4 and PIF5 regulate elongation growth by controlling directly the expression of genes that code for auxin biosynthesis and auxin signaling components...
- Copy number variation modifies expression time coursesEvelyne Chaignat
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
Genome Res 21:106-13. 2011..Thus, modifying the copy number of a gene may potentially alter not only its expression level, but also the timing of its expression...
- Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnoverEavan Dorcey
Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
PLoS Genet 8:e1002652. 2012..Surprisingly then, transgenic ScSKI8 rescued all aspects of the vip3 phenotype, suggesting that the dual role of SKI8 depends on species-specific cellular context...
- The circadian clock modulates renal sodium handlingSvetlana Nikolaeva
Department of Pharmacology and Toxicology, University of Lausanne, 27 rue du Bugnon, Lausanne, Switzerland
J Am Soc Nephrol 23:1019-26. 2012..It also suggests that the circadian clock affects BP, at least in part, by exerting dynamic control over renal sodium handling...
- A comprehensive analysis of gene expression profiles in distal parts of the mouse renal tubuleSylvain Pradervand
Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
Pflugers Arch 460:925-52. 2010..Collectively, this in silico analysis provides comprehensive information about relative abundance and tissue specificity of the DCT/CNT and the CCD expressed transcripts and identifies new candidate genes for renal homeostasis...
- Sumoylated PPARalpha mediates sex-specific gene repression and protects the liver from estrogen-induced toxicity in miceNicolas Leuenberger
Center for Integrative Genomics, National Research Center Frontiers in Genetics, Switzerland
J Clin Invest 119:3138-48. 2009..Physiologically, this repression conferred on female mice protection against estrogen-induced intrahepatic cholestasis, the most common hepatic disease during pregnancy, suggesting a therapeutic target for prevention of this disease...
- Key electrophysiological, molecular, and metabolic signatures of sleep and wakefulness revealed in primary cortical culturesValérie Hinard
Center for Integrative Genomics, University of Lausanne, CH 1015 Lausanne, Switzerland
J Neurosci 32:12506-17. 2012..With our in vitro model, the cellular and molecular consequences of sleep and wakefulness can now be investigated in a dish...
- Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signaturesPratyaksha Wirapati
Swiss Institute of Bioinformatics, Batiment Genopode, University of Lausanne, 1015 Lausanne, Switzerland
Breast Cancer Res 10:R65. 2008....
- Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse modelsGuenola Ricard
Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
PLoS Biol 8:e1000543. 2010..Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype...
- Molecular clock is involved in predictive circadian adjustment of renal functionAnnie Mercier Zuber
Department of Pharmacology and Toxicology, University of Lausanne, 1005 Lausanne, Switzerland
Proc Natl Acad Sci U S A 106:16523-8. 2009..Collectively, this study uncovers a major role of molecular clock in renal function...
- Epithelial sodium channel and the control of sodium balance: interaction between genetic and environmental factorsBernard C Rossier
Institute of Pharmacology and Toxicology, University of Lausanne, Rue du Bugnon 27, Lausanne, CH 1005 Switzerland
Annu Rev Physiol 64:877-97. 2002..The role of single-nucleotide polymorphisms (SNPs) in determining salt sensitivity or salt resistance in general populations is one of the main challenges of the post-genomic era...
- Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arraysLuca Santuari
Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH 1015 Lausanne, Switzerland
Genome Biol 11:R4. 2010..Interestingly, individual deletions were frequently observed in two or more of the accessions examined, suggesting that variation in gene content partly reflects a common history of deletion events...
- Drosophila intestinal response to bacterial infection: activation of host defense and stem cell proliferationNicolas Buchon
Global Health Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
Cell Host Microbe 5:200-11. 2009..The Drosophila gut provides a powerful model to study the integration of stress and immunity with pathways associated with stem cell control, and this study should prove to be a useful resource for such further studies...
- Segmental copy number variation shapes tissue transcriptomesCharlotte N Henrichsen
The Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
Nat Genet 41:424-9. 2009..Dosage alterations of brain-expressed genes are less frequent than those of other genes and are buffered by tighter transcriptional regulation. Our study provides initial evidence that CNVs shape tissue transcriptomes on a global scale...
- Identification and functional characterization of Rca1, a transcription factor involved in both antifungal susceptibility and host response in Candida albicansPatrick Vandeputte
Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
Eukaryot Cell 11:916-31. 2012....
- Separating the contribution of glucocorticoids and wakefulness to the molecular and electrophysiological correlates of sleep homeostasisValérie Mongrain
Center for Integrative Genomics, University of Lausanne, CH 1015 Lausanne, Switzerland
Sleep 33:1147-57. 2010..Because sleep deprivation also induces stress, we here determined the contribution of the corticosterone component of the stress response to the electrophysiological and molecular markers of sleep need in mice...
- Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red lightSéverine Lorrain
Center for Integrative Genomics, University of Lausanne, Genopode Building, CH 1015 Lausanne, Switzerland
Plant J 60:449-61. 2009..Our genetic analysis suggests that this is achieved through sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long hypocotyl in FR light)...
- c-Cbl expression levels regulate the functional responses of human central and effector memory CD4 T cellsNicolò C Brembilla
Division of Experimental Oncology, Multidisciplinary Oncology Center, Department of Medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
Blood 112:652-60. 2008..Our study reports c-Cbl as a critical regulator of the functional responses of memory T cell subsets and identifies for the first time in humans a mechanism controlling the functional heterogeneity of memory CD4 cells...
- The genome of the fire ant Solenopsis invictaYannick Wurm
Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
Proc Natl Acad Sci U S A 108:5679-84. 2011..Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species...
- Dysfunction of the epithelial sodium channel expressed in the kidney of a mouse model for Liddle syndromeSylvain Pradervand
Institut de Pharmacologie et de Toxicologie de l Université, Lausanne, Switzerland
J Am Soc Nephrol 14:2219-28. 2003..Aldosterone (5 x 10(-7)M for 3 h) further increased I(eq) from cultured L/L CCD. Thus, this study brings three independent lines of evidence for the constitutive hyperactivity of ENaC in CCD from mice harboring the Liddle mutation...
- Mineralocorticoid regulation of epithelial Na+ channels is maintained in a mouse model of Liddle's syndromeAnke Dahlmann
Department of Physiology and Biophysics, Weill Medical College of Cornell Univ, 1300 York Ave, New York, NY 10021, USA
Am J Physiol Renal Physiol 285:F310-8. 2003..Analysis of spontaneous channel noise indicated that the open probability was similar in the two genotypes(WT: 0.77; L/L: 0.80). Thus the increase in whole cell current is attributed to a difference in the density of conducting channels...
- Nkx2-5 pathways and congenital heart disease; loss of ventricular myocyte lineage specification leads to progressive cardiomyopathy and complete heart blockMohammad Pashmforoush
UCSD Institute of Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
Cell 117:373-86. 2004..Accordingly, loss of ventricular muscle cell lineage specification into trabecular and conduction system myocytes is a new mechanistic pathway for progressive cardiomyopathy and conduction defects in congenital heart disease...
- Small proline-rich protein 1A is a gp130 pathway- and stress-inducible cardioprotective proteinSylvain Pradervand
UCSD Institute of Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
EMBO J 23:4517-25. 2004..Thus, this study identifies SPRR1A as a novel stress-inducible downstream mediator of gp130 cytokines in cardiomyocytes and documents its cardioprotective effect against ischemic stress...
- Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophagesSylvain Pradervand
Bioinformatics and Data Coordination Laboratory, Alliance for Cellular Signaling, San Diego Supercomputer Center, University of California at San Diego, Gilman Drive, La Jolla, CA 92093, USA
Genome Biol 7:R11. 2006....
- Identification of corticosteroid-regulated genes in cardiomyocytes by serial analysis of gene expressionOlivier Muller
Cardiology Service, University Hospital, CHUV, CH 1011 Lausanne, Switzerland
Genomics 89:370-7. 2007..Our study identifies a new set of corticosteroid-regulated genes in cardiomyocytes and demonstrates a new approach to studying the selectivity of MR- vs GR-dependent effects...
- Systems biology of macrophagesMano Ram Maurya
Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093 0412, USA
Adv Exp Med Biol 598:62-79. 2007..macrophages? (3) How can we combine proteomic and other cellular measurements to characterize the repertoire of upstream signaling networks invoked by macrophages? (4) How do designed knockdowns of proteins influence cellular phenotypes?..
- Aldosterone responsiveness of the epithelial sodium channel (ENaC) in colon is increased in a mouse model for Liddle's syndromeMarko Bertog
Institut fur Zellulare und Molekulare Physiologie, Waldstr 6, 91054 Erlangen, Germany
J Physiol 586:459-75. 2008..This may be pathophysiologically relevant in patients with Liddle's syndrome, in particular on a high salt diet, when suppression of P Aldo is likely to be insufficient to reduce Na+ absorption to an appropriate level...
- Low expression of the beta-ENaC subunit impairs lung fluid clearance in the mouseNadia Randrianarison
INSERM U773, CRB3, Universite Denis Diderot Paris 7, 16 rue Henri Huchard, 75018 Paris, France
Am J Physiol Lung Cell Mol Physiol 294:L409-16. 2008..Finally, adequate beta-ENaC expression appears to be required for AFC stimulation by beta2-agonists...