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  • center
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  • whocc
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  • Assistant Professor
  • Associate Professor
  • Clinical Research Assistant
  • Clinical Research Nurse
  • Clinician Researcher
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  • Dual-education Student
  • Full Professor
  • Honorary Professor
  • Lab assistant
  • Master Student
  • Non-permanent Researcher
  • Nursing Staff
  • Permanent Researcher
  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Prize
  • Project Manager
  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
  • Director of National Reference Center
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  • Head of Facility
  • Head of Operations
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Projects

Project
Ongoing
4 Members

DECIDER: artificial intelligence to improve diagnosis and treatment of ovarian cancer

Benno Schwikowski (PI)

The DECIDER project aims to develop diagnostic tools and treatments for high-grade serous ovarian cancer with the help of AI methods. The aim is to identify earlier those patients who do not respond well […]
Project
Ongoing
2 Members

Precision drugs Against Resistance In Subpopulations (PARIS)

Benno Schwikowski (PI)

The ERA PerMed PARIS project combines preclinical research with advanced bioinformatics and medical ethics research to evolve the state of the art in the personalised treatment of chemoresistant high-grade serous ovarian cancer.
Project
Ongoing
2 Members

SLE Map: a consensus map of SLE patients into a low dimensional space

Benno Schwikowski (PI)

Human transcriptome profiles typically contain gene expression values for many thousands of genes, thus representing points in a high-dimensional feature space. A principal technical challenge in understanding the pathways involved in the disease and […]
Project
Ongoing
2 Members

New clinical endpoints in primary Sjögren’s Syndrome: an interventional trial based on stratifying patients (NECESSITY)

Benno Schwikowski (PI)

Primary Sjögren’s syndrome is an autoimmune disease affecting exocrine glands resulting in dryness of the eyes and the mouth with multiple systemic complications in different organs. In 30% to 50% of the patients, systemic […]
Project
Completed
2 Members

Comprehensive characterization and effective combinatorial targeting of high-grade serous ovarian cancer via single-cell analysis (HERCULES)

Benno Schwikowski (PI)

In the HERCULES EU project, we are studying samples from high-grade serous ovarian cancer tumours. The samples are analysed using mass cytometry, DNA, RNA and ChIP (chromatin immunoprecipitation) sequencing; and computational tools to find […]
Project
Completed
3 Members

Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes

Javier Pizarro-Cerda (PI)

In the context of the Swiss consortium InfectX (www.infectx.ch), we have previously performed siRNA, microRNA and drug screens  to investigate signaling pathways modulating invasion of host cells by the bacterial pathogen Listeria monocytogenes. In […]

Software

A large set of colored circles, linked by gray segments.
Software
Ongoing
4 Members

OntoWeaver

Johann Dreo (PI)

OntoWeaver is a tool for importing table data in Semantic Knowledge Graphs (SKG) databases and ontologies. OntoWeaver allows writing a simple declarative mapping to express how columns from a Pandas table are to be […]
Software
Ongoing
8 Members

GRAVITY

Thomas Bourgeron (PI)

Gravity (for Gene inteRaction Analysis of Variants in Individuals: a Tool for You) provides a visualisation of genetic data from SNP array, whole genome and whole exome data in the context of protein-protein interactions. […]
Software
Ongoing
2 Members

Cytoscape: Visualization and analysis of omics data in interaction networks

Benno Schwikowski (PI)

Cytoscape is the worldwide standard open-source platform for network visualization and data integration. This project, which we started at the Institute for Systems Biology in Seattle, provides a universal, customizable tool for the network-based […]

CV

Current position

Directeur de Recherche and Chef de Laboratoire (Institut Pasteur)

Research interests

Computational and predictive medicine

Network biology, Statistical data analysis, Machine learning, Algorithms

Infection and immunity, cancer

Publication statistics

Google Scholar profile: http://bit.ly/scholar-bs

Named by Researchgate.net as the currently most cited researcher at Institut Pasteur http://bit.ly/ipmostcited

Previous positions

04/04   Visiting Professor Epigenomics Project/Génopole Evry, France

01/01 – 08/09   Affiliate Assistant Professor, member of the graduate faculty
Dept. of Computer Science and Engineering, University of Washington, Seattle, USA

10/01 – 03/04   Assistant Professor for Computational Biology
04/00 – 09/01   Senior Researcher
Institute for Systems Biology, Seattle, USA

10/98 – 03/00   Postdoctoral Fellow
With Richard M. Karp, U. Washington, Seattle, USA

03/95 – 09/98   Doctoral student
With Martin Vingron and Thomas Lengauer, GMD St. Augustin and DKFZ Heidelberg

Publications

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