Affiliation: Swiss Institute of Bioinformatics
- Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactorsFabio Parisi
School of Life Sciences, Swiss Institute for Experimental Cancer Research ISREC, Ecole Polytechnique Federale de Lausanne EPFL, CH 1015 Lausanne, Switzerland
BMC Genomics 10:381. 2009..In particular, we study the influence of patterns of DNA occupancy by hERalpha on expression phenotypes...
- Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissueJanine Antonov
Department of Clinical Research, University of Bern, Bern, Switzerland
BMC Cancer 10:37. 2010..The purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE) tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months...
- 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....
- Detecting epistasis with restricted response patterns in pairs of biallelic lociPratyaksha Wirapati
Swiss Institute of Bioinformatics, Lausanne, Switzerland
Ann Hum Genet 75:133-45. 2011..Interaction-only tests are the least powerful; while pattern search approach is the most powerful if the range of possibilities is restricted, but still includes the true pattern...
- Selecting control genes for RT-QPCR using public microarray dataVlad Popovici
Bioinformatics Core Facility, Swiss Institute of Bioinformatics, CH 1015 Lausanne, Switzerland
BMC Bioinformatics 10:42. 2009..Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones...
- Chromosomal number aberrations and transformation in adult mouse retinal stem cells in vitroMeta Djojosubroto
Unit of Gene Therapy and Stem Cell Biology, Department of Ophthalmology, Jules Gonin Eye Hospital, Lausanne, Switzerland
Invest Ophthalmol Vis Sci 50:5975-87. 2009..However, as cells in prolonged cultivation may be unstable and thus have a risk of transformation, it is important to assess the stability of these cells...
- 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....
- Identifying synergistic regulation involving c-Myc and sp1 in human tissuesFabio Parisi
Swiss Institute for Experimental Cancer Research ISREC and NCCR Molecular Oncology, Lausanne, Switzerland
Nucleic Acids Res 35:1098-107. 2007..Our approach shows how integrated functional analyses can uncover tissue-specific and combinatorial regulatory dependencies in mammals...
- 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...