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Related publications (23)
ASAP: 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 Press2017Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals
Mitochondrial stress activates a mitonuclear response to safeguard and repair mitochondrial function and to adapt cellular metabolism to stress. Using a multiomics approach in mammalian cells treated with four types of mitochondrial stressors, we identify ...
Rockefeller Univ Press2017Systems Biology Approaches for Inflammatory Bowel Disease: Emphasis on Gut Microbial Metabolism
Although the prevalence of main idiopathic forms of inflammatory bowel disease (IBD) has risen considerably over the last decades, their clinical features do not allow accurate prediction of prognosis, likelihood of disease progression, or response to spec ...
Lippincott Williams & Wilkins2014Nuclear 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 Central2013PyroTRF-ID: a novel bioinformatics approach for the identification of terminal-restriction fragments using microbiome pyrosequencing data
Christof Holliger, Julien Maillard, Pierre Rossi, Jacques Rougemont, David Gregory Weissbrodt, Noam Shani, Lucas Sinclair
Aim: In molecular microbial ecology, pyrosequencing is gradually supplanting classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for enhanced characterization of microbiome ...
2012Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell
Jacques Rougemont, Amalio Telenti
Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G env ...
2011Prediction of Survival and Risk Assessment Using Joint Analysis of Microarray Gene Expression Data
Gene expression profiles have been widely used in molecular classification, diagnosis and prediction, particularly in the area of oncology where accurate and early diagnosis is needed for appropriate treatment. Avoiding under-/over-treatment when it is not ...
EPFL2010Two-Dimensional Statistical Recoup ling for the Identification of Perturbed Metabolic Networks from NMR Spectroscopy
The development of Statistical Total Correlation Spectroscopy (STOCSY), a representation of the autocorrelation matrix of a spectral data set as a 2D pseudospectrum, has allowed more reliable assignment of one- and two-dimensional NMR spectra acquired from ...
AMER CHEMICAL SOC2010Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals
Jacques Fellay, Patrick Descombes, Amalio Telenti
There is great interindividual variability in HIV-1 viral setpoint after seroconversion, some of which is known to be due to genetic differences among infected individuals. Here, our focus is on determining, genome-wide, the contribution of variable gene e ...
2010CleanEx: new data extraction and merging tools based on MeSH term annotation
The CleanEx expression database (http://www.cleanex.isb-sib.ch) provides access to public gene expression data via unique gene names as well as via experiments biomedical characteristics. To reach this, a dual annotation of both sequences and experiments h ...
Oxford University Press2009