Publication
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
Related publications (37)
Circadian dynamics of RNA localisation in the mammalian liver
Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modif ...
EPFL2021Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis
Kristin Schirmer, Anze Zupanic
The use of omics is gaining importance in the field of nanoecotoxicology; an increasing number of studies are aiming to investigate the effects and modes of action of engineered nanomaterials (ENMs) in this way. However, a systematic synthesis of the outco ...
AMER CHEMICAL SOC2020Transcriptomic analysis across liver diseases reveals disease-modulating activation of constitutive androstane receptor in cholestasis
Kristina Schoonjans, Jian Liu, Bhoomika Mathur
Background & Aims: Liver diseases are caused by many factors, such as genetics, nutrition, and viruses. Therefore, it is important to delineate transcriptomic changes that occur in various liver diseases. Methods: We performed high-throughput sequencing of ...
2020Development of topological tools for the analysis of biological data
There is a growing need for unbiased clustering algorithms, ideally automated to analyze complex data sets. Topological data analysis (TDA) has been used to approach this problem. This recent field of mathematics discerns characteristic features of a space ...
EPFL2018ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
Bart Deplancke, Vincent Roland Julien Gardeux, Adrian Shajkofci, Petra Catalina Schwalie
Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research gr ...
Oxford University Press2017Comparative study of joint analysis of microarray gene expression data in survival prediction and risk assessment of breast cancer patients
Microarray gene expression data sets are jointly analyzed to increase statistical power. They could either be merged together or analyzed by meta-analysis. For a given ensemble of data sets, it cannot be foreseen which of these paradigms, merging or meta-a ...
Oxford Univ Press2016Nuclear Factor I genomic binding associates with chromatin boundaries
Giovanni Dietler, Giovanna Ambrosini, Jan Kerschgens, Philipp Bucher, Nicolas Mermod, Petar Pjanic, Armelle Gaussin
Background: The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequenci ...
BioMed Central2013ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries
Bernard Moret, Philipp Bucher, Nishanth Ulhas Nair
The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit diff ...
Public Library of Science2012Spot Identification and Quality Control in Cell-Based Microarrays
Cell-based microarrays are being increasingly used as a tool for combinatorial and high throughput screening of cellular microenvironments. Analysis of microarrays requires several steps, including microarray imaging, identification of cell spots, quality ...
Amer Chemical Soc2012Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the ...
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