Patrick NITSCHKE
Bioinformatics
Published on 31.08.2026
Presentation
Fondation Imagine, as a partner of the Paris-Descartes University and of the Faculty of Medicine, benefits from the support of the Paris-Descartes Bioinformatics Platform to come-along with the scientists throughout their Imagine labeled projects (support for the experimental design planning, data handling and analysis, biological tools for data integration and interpretation).
The bioinformatics Platform collaborated with the Imagine scientists and genomic platform to develop an original pipeline for genetic linkage studies (from raw SNP microarray data to visualisation and annotation of the candidate genomic regions via an interactive web interface). This pipeline allowed the analysis of 50 linkage projects by year.
Since 2009, the Fondation Imagine followed the “next” generation sequencer evolution and acquired severall machines more and more powerful. The increasing amount of data generated by these technologies created new challenging issues to store, analyze, integrate and visualize pertinent information. To reach this goal, we have developed a new original pipeline to analyze resequencing projects. Our pipeline, Polypipeline is based on public tools (alignment, variation finding) as well as an original database design PolyDB (storage and minning data) and finally a new graphical interface Polyweb (interpretation and visualization). Our tool is completely generic and is independant from the sequencing technology used.
Our team participates also to various projects, either relating to sequencing like chip/seq, rna/seq… or more broadly to biostatistics like transcriptomic, pathway analysis… We can also help the researcher during the design step of her/his experiment to optimize the odds of positive findings.
The bioinformatics Platform collaborated with the Imagine scientists and genomic platform to develop an original pipeline for genetic linkage studies (from raw SNP microarray data to visualisation and annotation of the candidate genomic regions via an interactive web interface). This pipeline allowed the analysis of 50 linkage projects by year.
Since 2009, the Fondation Imagine followed the “next” generation sequencer evolution and acquired severall machines more and more powerful. The increasing amount of data generated by these technologies created new challenging issues to store, analyze, integrate and visualize pertinent information. To reach this goal, we have developed a new original pipeline to analyze resequencing projects. Our pipeline, Polypipeline is based on public tools (alignment, variation finding) as well as an original database design PolyDB (storage and minning data) and finally a new graphical interface Polyweb (interpretation and visualization). Our tool is completely generic and is independant from the sequencing technology used.
Our team participates also to various projects, either relating to sequencing like chip/seq, rna/seq… or more broadly to biostatistics like transcriptomic, pathway analysis… We can also help the researcher during the design step of her/his experiment to optimize the odds of positive findings.
Team
Scientific Publications
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2020
IL-15 superagonist RLI has potent immunostimulatory properties on NK cells: i..., J Immunother Cancer
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2020
MeCP2 is involved in random mono-allelic expression for a subset of human aut..., Biochim Biophys Acta Mol Basis Dis
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2019
A TP63 Mutation Causes Prominent Alopecia with Mild Ectodermal Dysplasia., J Invest Dermatol
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2019
A variant erythroferrone disrupts iron homeostasis in -mutated myelodysplasti..., Sci Transl Med
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2018
Mutations in PERP Cause Dominant and Recessive Keratoderma., J Invest Dermatol
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2018
NDUFB8 Mutations Cause Mitochondrial Complex I Deficiency in Individuals with..., Am J Hum Genet
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2017
FDXR Mutations Cause Sensorial Neuropathies and Expand the Spectrum of Mitoch..., Am J Hum Genet
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2017
Neutropenia in Patients with Common Variable Immunodeficiency: a Rare Event A..., J Clin Immunol
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2016
Early born neurons are abnormally positioned in the doublecortin knockout hip..., Hum Mol Genet
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2015
TCL1 expression patterns in Waldenström macroglobulinemia., Mod Pathol
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2015
Mutations in the endothelin receptor type A cause mandibulofacial dysostosis ..., Am J Hum Genet
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2015
Synergy of chemotherapy and immunotherapy revealed by a genome-scale analysis..., J Antimicrob Chemother
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2014
Metabolic and adipose tissue signatures in adults with Prader-Willi syndrome:..., J Clin Endocrinol Metab
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2014
Reverse interferon signature is characteristic of antigen-presenting cells in..., Arthritis Rheumatol
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2013
Mutations in endothelin 1 cause recessive auriculocondylar syndrome and domin..., Am J Hum Genet
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2013
Lung tumor microenvironment induces specific gene expression signature in int..., Front Immunol
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2012
Translation termination efficiency modulates ATF4 response by regulating ATF4..., Nucleic Acids Res
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2012
Functional intestinal stem cells after Paneth cell ablation induced by the lo..., Proc Natl Acad Sci U S A
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2011
Implication of clusterin in TNF-α response of rheumatoid synovitis: lesson fr..., Physiol Genomics
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2011
Combined transcriptomic-(1)H NMR metabonomic study reveals that monoethylhexy..., J Proteome Res
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2011
Insights into the pathogenesis of systemic sclerosis based on the gene expres..., Arthritis Rheum
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2011
Systematic candidate gene investigations in the SPA2 locus (9q32) show an ass..., Arthritis Rheum
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2010
Cell cloning-based transcriptome analysis in cyclin-dependent kinase-like 5 m..., J Mol Med (Berl)
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2010
Gene expression profile in the salivary glands of primary Sjögren's syndrome ..., Arthritis Rheum
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2009
The OTT-MAL fusion oncogene activates RBPJ-mediated transcription and induces..., J Clin Invest
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2006
Failure to confirm coxsackievirus infection in primary Sjögren's syndrome., Arthritis Rheum
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2006
Activation of IFN pathways and plasmacytoid dendritic cell recruitment in tar..., Proc Natl Acad Sci U S A
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2006
Interleukin-32, CCL2, PF4F1 and GFD10 are the only cytokine/chemokine genes d..., Eur Cytokine Netw