Saez-Rodriguez Group

Systems Biomedicine

Research

Group Leader

Julio Saez-Rodriguez

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Secretary

Erika Schulz

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Staff Scientist

Marzia Sidri

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Bioinformatician

Eleanor Fewings

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Postdocs

Denes Turei

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Attila Gabor

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Jovan Tanevski

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Rosa Hernansaiz Ballesteros

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Javier Perales-Patón

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Bartosz Bartmanski

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Katharina Zirngibl

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Arezou Rahimi

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Martín Garrido Rodríguez-Córdoba

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Sebastian Lobentanzer

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PhD Students

Aurélien Dugourd

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Ricardo O. Ramirez-Flores

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Olga Ivanova

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Daniel Dimitrov

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Pau Badia i Mompel

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Sophia Müller-Dott

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Associated members

Christian Holland

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Jan Lanzer

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Rebecca Terrall Levinson

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Monica Toft Hannani

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Nadine Tüchler

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Bence Szalai

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The following people spent over 6 months with us:

Name Duration Position
Igor Bulanov 2019-2020 intern
Minoo Ashtiani 2019-2020 intern
Alice Driessen 2019-2020 intern
Ana Victoria Ponce-Bobadilla 2019-2020 Postdoc
Alberto Valdeolivas Urbelz 2019-2020 Postdoc
Charlie Pieterman 2018-2018 intern
Anika Liu 2018-2018 Master Thesis
Hyojin Kim 2017-2020 Phd student
Nicolas Palacio-Escat 2017-2020 PhD Student
Panuwat Trairatphisan 2017-2019 Postdoc
Bence Szalai 2017-2018 Postdoc
Ferenc Tajti 2017-2018 Intern
Francesco Ceccarelli 2017-2018 intern
Vigneshwari Subramanian 2017-2018 Postdoc
Mahmoud Ibrahim 2017 -2017 Postdoc
Enio Gjerga 2016-2020 Phd student
Luis Tobalina Segura 2016-2019 Postdoc
Melanie Rinas 2016-2019 Postdoc
Mi Yang 2015-2019 PhD Student / Postdoc
Angeliki Kalamara 2015-2019 PhD Student
Jakob Wirbel 2015-2017 Intern & Master Thesis
Fatemeh Ghavidel 2015-2016 Postdoc (w O Stegle & A Brazma)
Pisanu Buphamalai 2015-2016 Trainee (w. M Brehme)
Ricardo Ramirez 2015-2016 Trainee
Luz Garcia-Alonso 2014-2018 Postdoc
Johannes Stephan 2014-2015 Postdoc (w O Stegle)
Claudia Hernandez 2014-2015 Trainee
Martí Bernardo-Faura 2013-2015 Postdoc
Ioannis Melas 2013-2014 Postdoc
Vitor Costa 2013-2013 Master Thesis
Luca Cerone 2013-2013 Postdoc
Emanuel Gonçalves 2012-2017 PhD Student
Michael Schubert 2012-2016 PhD Student
Michael Menden 2011-2016 PhD student
Thomas Cokelaer 2011-2015 Staff Scientist
Martijn van Iersel 2011-2012 Postdoc
Federica Eduati 2011 - 2017 Postdoc
Francesco Iorio 2010-2017 Postdoc / Senior Bioinformatician
Aidan MacNamara 2010-2014 Postdoc
Camille Terfve 2010-2014 PhD Student
David Henriques 2010-2011 Master Thesis

Publications

Latest Publications

Preprints

Spatial multi-omic map of human myocardial infarction

Kuppe, Ramirez Flores, Li, et al. 2020

BioServices

Python package to access Bioinformatics Web Services.

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Birewire

R package for the randomisation of bipartite graphs.

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Cyrface

Interface between R and Cytoscape.

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CySBGN

Cytoscape plug-in for SBGN maps.

More about CySBGN

DREAMTools

Code used in the scoring of DREAM challenges.

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DrugVsDisease

R/Cytoscape pipeline to compare drug and disease gene expression profiles.

More about DrugVsDisease

GDSCTools

Python library dedicated to the study pharmacogenomic relationships.

More about GDSCTools

iNRG-cMap

An R package for interactive network guided connectivity mapping.

More about iNRG-cMap

KinAct

Python package to infer kinase activities from phosphoproteomics datasets.

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lipyd

lipyd is a Python module for lipidomics LC MS/MS data analysis.

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MEIGO

Global optimization toolbox including metaheuristic and Bayesian methods.

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SLAPenrich

R package to identify pathway-level enrichments of genetic alterations.

More about SLAPenrich
Duration Name Agency
2021-2025

DECIDER: Improved clinical decisions via integrating multiple data levels to overcome chemotherapy resistance in high-grade serous ovarian cancer

European Union
2021

Analysis of essentiality in cancer using CRISPR-Cas9 screenings

Sanofi
2020-2022

MSCare-A Systems Medicine Approach to Stratification of  Cancer Recurrence

German Ministry of Education and Research (BMBF)
2020-2022

Analysis of multi-omics and spatial transcriptomics data

GSK
2020-2021

BioDATEN : Bioinformatics DATa Environment

Ministry of Science, Research and Art, Baden Wuerttemberg
2020-2021

Single cell resolution of human chronic kidney disease for precision medicine in nephrology

DFG German Research Council
2020 - 2024

StrategyCKD: System omics to unravel the gut-kidney axis in Chronic Kidney Disease

European Uunion H220-MSCA-ITN
2020 - 2022

HPC Center of Excellence in Personalised Medicine – PerMedCoE

European Union (H2020-EU.1.4.1.3)
2019-2022

individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology

European Union H2020 Health
2019-2022

LaMarcK: Longitudinal Multiomics Characterization of disease using prior Knowledge

German Ministry of Education and Research (BMBF)
2019-2022

Validating microfluidics-based personalized cancer therapy in mouse models

DFG German Research Council
2019-2021

Informatics for Life

Klaus-Tschira Stiftung
2017-2021

TransQST: Translational quantitative systems toxicology to improve the understanding of the safety of medicines

EU IMI Innovative Medicines Initiative
2017-2018

Analysis of mass spectrometry proteomics and drug treatment

OncoSignature/Acrivon
2016-2020

LiSym: Liver systems medicine

BMBF
2016-2019

SYS4MS: Personalizing health care in Multiple Sclerosis using sytems medicine tools

BMBF
2016-2018

PrECISE: Personalized engine for Cancer integrative study and evaluation

EU H2020 Health
2016-2018

CPTAC DREAM Challenge

National Cancer Institute (USA)
2015-2019

Joint Research Center for Computational Biomedicine

Bayer AG
2015-2018

SyMBioSys : Systematic Models for Biological Systems Engineering Training Network

EU H2020 Health MSCA-ITN
2014-2016

Novel Target Identification Through Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cancer Cell Lines

Center for Therapeutic Target Validation
2014-2016

Target identification and validation using pathway activities derived from functional genomics data

Center for Therapeutic Target Validation
2013-2014

CombiMS: a novel drug discovery method based on systems biology: combination therapy and biomarkers for Multiple Sclerosis

EU H2020 Health
2012-2015

BioPreDyn: New Bioinformatics Methods and Tools for Data-Driven Predictive Dynamic Modelling in Biotechnological Applications

EU H2020 Health
2012-2014

Understanding drug mode of action via statistical integration of functional genomic studies and literature-derived signalling networks

Medical Research Council (UK)
2011-2012

Analysis of mass spectrometry phosphoproteomics data in the context of insulin signal processing and functional alterations thereof

Sanofi

Jobs