Parisi, Fabio, Sonderegger, Bernhard, Wirapati, Pratyaksha, Delorenzi, Mauro, Naef, Felix
Abstract Background To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression...
Selecting control genes for RT-QPCR using public microarray data (2009)
Popovici, Vlad, Goldstein, Darlene R, Antonov, Janine, Jaggi, Rolf, Delorenzi, Mauro, Wirapati, Pratyaksha
Abstract Background Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely...
Wirapati, Pratyaksha, Sotiriou, Christos, Kunkel, Susanne, Farmer, Pierre, Pradervand, Sylvain, Haibe-Kains, Benjamin, ...
Abstract Introduction Breast cancer subtyping and prognosis have been studied extensively by gene expression profiling, resulting in disparate signatures with little overlap in their constituent...
Loi, Sherene, Haibe-Kains, Benjamin, Desmedt, Christine, Wirapati, Pratyaksha, Lallemand, Françoise, Tutt, Andrew M, ...
Abstract Background Estrogen receptor positive (ER+) breast cancers (BC) are heterogeneous with regard to their clinical behavior and response to therapies. The ER is currently the best predictor of...
Expression profiling with RNA from formalin-fixed, paraffin-embedded material (2008)
Oberli, Andrea, Popovici, Vlad, Delorenzi, Mauro, Baltzer, Anna, Antonov, Janine, Matthey, Sybille, ...
Abstract Background Molecular characterization of breast and other cancers by gene expression profiling has corroborated existing classifications and revealed novel subtypes. Most profiling studies...
MAMOT: hidden Markov modeling tool (2008)
Schütz, Frédéric, Delorenzi, Mauro
Summary: Hidden Markov models (HMMs) are probabilistic models that are well adapted to many tasks in bioinformatics, for example, for predicting the occurrence of specific motifs in biological...
Bioconductor-compliant R package 'annotationTools' (2008)
Bmc Bioinformatics, Re Kuhn, Ruth Luthi-carter, Mauro Delorenzi, Open Access, Mauro Delorenzi
Software
Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaida Perier
Collections of precisely mapped eukaryotic transcription start sites (TSS) are important resources for studying gene control elements and for developing promoter prediction algorithms. The present...
Kuhn, Alexandre, Goldstein, Darlene R., Hodges, Angela, Strand, Andrew D., Sengstag, Thierry, Kooperberg, Charles, ...
To test the hypotheses that mutant huntingtin protein length and wild-type huntingtin dosage have important effects on disease-related transcriptional dysfunction, we compared the changes in mRNA in...
Schmid, Christoph D., Sengstag, Thierry, Bucher, Philipp, Delorenzi, Mauro
A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications...
Nucleic Acids Research, 2007, 1–4 (2007)
Christoph D. Schmid, Thierry Sengstag, Mauro Delorenzi
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data
Regional and cellular gene expression changes in human Huntington's disease brain (2006)
Hodges, Angela Kaye, Strand, Andrew D., Aragaki, Aaron K., Kuhn, Alexandre, Sengstag, Thierry, Hughes , Gareth, ...
Regional and cellular gene expression changes in human Huntington's disease brain (2006)
Hodges, Angela Kaye, Strand, Andrew D., Aragaki, Aaron K., Kuhn, Alexandre, Sengstag, Thierry, Hughes , Gareth, ...
Regional and cellular gene expression changes in human Huntington's disease brain (2006)
Hodges, Angela, Strand, Andrew D., Aragaki, Aaron K., Kuhn, Alexandre, Sengstag, Thierry, Hughes, Gareth, ...
Huntington's disease (HD) pathology is well understood at a histological level but a comprehensive molecular analysis of the effect of the disease in the human brain has not previously been...
Sotiriou, Christos, Wirapati, Pratyaksha, Loi, Sherene, Harris, Adrian, Fox, Steve, Smeds, Johanna, ...
Background: Histologic grade in breast cancer provides clinically important prognostic information. However, 30%–60% of tumors are classified as histologic grade 2. This grade is associated with an...
Jagannathan, Vidhya, Roulet, Emmanuelle, Delorenzi, Mauro, Bucher, Philipp
HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The...
Regional and cellular gene expression changes in human Huntington's disease brain (2006)
Hodges, Angela, Strand, Andrew D., Aragaki, Aaron K., Kuhn, Alexandre, Sengstag, Thierry, Hughes, Gareth, ...
Huntington's disease (HD) pathology is well understood at a histological level but a comprehensive molecular analysis of the effect of the disease in the human brain has not previously been...
Buyse, Marc, Loi, Sherene, Van't Veer, Laura, Viale, Giuseppe, Delorenzi, Mauro, Glas, Annuska M., ...
Background: A 70-gene signature was previously shown to have prognostic value in patients with node-negative breast cancer. Our goal was to validate the signature in an independent group of patients....
Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi
for transcription factor binding sites
An atlas of human gene expression from massively parallel signature sequencing (MPSS) (2005)
Jongeneel, C. Victor, Delorenzi, Mauro, Iseli, Christian, Zhou, Daixing, Haudenschild, Christian D., Khrebtukova, Irina, ...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost...
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension (2004)
Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaõèda Peârier
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally de®ned by a transcription start site (TSS). There may be multiple...
Bourgon, Richard, Delorenzi, Mauro, Sargeant, Tobias, Hodder, Anthony N., Crabb, Brendan S., Speed, Terence P.
Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential...
Bourgon, Richard, Delorenzi, Mauro, Sargeant, Tobias, Hodder, Anthony N., Crabb, Brendan S., Speed, Terence P.
Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential...
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension (2004)
Schmid, Christoph D., Praz, Viviane, Delorenzi, Mauro, Périer, Rouaïda, Bucher, Philipp
The Eukaryotic Promoter Database (EPD) is an annotated non‐redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple...
Bourgon, Richard, Delorenzi, Mauro, Sargeant, Tobias, Hodder, Anthony N., Crabb, Brendan S., Speed, Terence P.
Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential...
Expression profiling with RNA from formalin-fixed, paraffin-embedded material
Oberli, Andrea, Popovici, Vlad, Delorenzi, Mauro, Baltzer, Anna, Antonov, Janine, Matthey, Sybille, ...
Loi, Sherene, Haibe-Kains, Benjamin, Desmedt, Christine, Wirapati, Pratyaksha, Lallemand, Françoise, Tutt, Andrew M, ...
Wirapati, Pratyaksha, Sotiriou, Christos, Kunkel, Susanne, Farmer, Pierre, Pradervand, Sylvain, Haibe-Kains, Benjamin, ...
Selecting control genes for RT-QPCR using public microarray data
Popovici, Vlad, Goldstein, Darlene R, Antonov, Janine, Jaggi, Rolf, Delorenzi, Mauro, Wirapati, Pratyaksha
Modulation of Angiogenic and Inflammatory Response in Glioblastoma by Hypoxia
Murat, Anastasia, Migliavacca, Eugenia, Hussain, S. Farzana, Heimberger, Amy B., Desbaillets, Isabelle, Hamou, Marie-France, ...
Glioblastoma are rapidly proliferating brain tumors in which hypoxia is readily recognizable, as indicated by focal or extensive necrosis and vascular proliferation, two independent diagnostic...
Vlassenbroeck, Ilse, Califice, Stéphane, Diserens, Annie-Claire, Migliavacca, Eugenia, Straub, Josef, Di Stefano, Ivano, ...
Epigenetic silencing of the DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) by promoter methylation predicts successful alkylating agent therapy, such as with temozolomide, in...
Norrmén, Camilla, Ivanov, Konstantin I., Cheng, Jianpin, Zangger, Nadine, Delorenzi, Mauro, Jaquet, Muriel, ...
The mechanisms of blood vessel maturation into distinct parts of the blood vasculature such as arteries, veins, and capillaries have been the subject of intense investigation over recent years. In...