Saez-Rodriguez Group

Systems Biomedicine

Our goal is to acquire a functional understanding of the deregulation of signalling networks in disease and to apply this knowledge to develop novel therapeutics. We focus on cancer, auto-immune and fibrotic disease.

We are at the Institute for Computational Biomedicine at the Medical Faculty of Heidelberg University and Heidelberg University Hospital. We are also  part of the Molecular Medicine Partnership Unit (MMPU) between the Medical Faculty of the University of Heidelberg and the European Molecular Biology Laboratory (EMBL).


Our research is hypothesis-driven and tailored towards producing mathematical models that integrate diverse data sources. Because of this, we collaborate closely with experimental groups.
A key emphasis is to build models that are both mechanistic (to provide understanding) and predictive (to generate novel hypotheses). To build these models, we combine existing biochemical knowledge with functional data. A major focus of our group is the development of logic models of signaling networks. We train these models with data generated with mass spectrometry and antibody-based technologies. We are also very interested in the use of single-cell data.
In parallel, we analyse genomic and phenotypic data collected in large-scale drug screenings. We combine this information with our prior knowledge of the underlying pathways. Thereby, we aim to improve our ability to dissect the mode of action of therapies and provide avenues for developing new ones. While our research is driven by applications, we develop open-source computational tools that share freely with the scientific community.
Finally, we support scientific crowdsourcing, specifically collaboratives competitions, through the DREAM challenges.
Click below for a list of our main ongoing projects.

Group Leader

Julio Saez-Rodriguez



Erika Schulz



Eleanor Fewings



Denes Turei


Attila Gabor


Jovan Tanevski


Rosa Hernansaiz Ballesteros


Javier Perales-Patón


PhD Students

Aurélien Dugourd


Nicolàs Palacio


Christian Holland


Hyojin Kim


Ricardo O. Ramirez-Flores


Olga Ivanova


Daniel Dimitrov


Pau Badia i Mompel


Associated members

Jan Lanzer


Rebecca Terrall Levinson


Monica Toft Hannani


Nadine Tüchler


Bence Szalai


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
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



Python package to access Bioinformatics Web Services.

More about BioServices


R package for the randomisation of bipartite graphs.

More about Birewire


Interface between R and Cytoscape.

More about Cyrface


Cytoscape plug-in for SBGN maps.

More about CySBGN


Code used in the scoring of DREAM challenges.

More about DREAMTools


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

More about DrugVsDisease


Python library dedicated to the study pharmacogenomic relationships.

More about GDSCTools


An R package for interactive network guided connectivity mapping.

More about iNRG-cMap


Python package to infer kinase activities from phosphoproteomics datasets.

More about KinAct


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

More about lipyd


Global optimization toolbox including metaheuristic and Bayesian methods.

More about MEIGO


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

More about SLAPenrich

The wordcloud is based on the number of joint publications with our collaborators


We are thankful to our present and past collaborators, including (in alphabetic order):

  • Ruedi Aebersold, ETH Zurich
  • Leonidas G. Alexopoulos, National Technical University of Athens
  • Bernd Bodenmiller, University of Zurich
  • Julio Banga, (Bio)Process Engineering Group, CSIC
  • Pedro Beltrao, EMBL-EBI
  • CoLoMoTo Consortium, in particular Claudine Chaouiya, Denis Thieffry, Tomas Helikar, and Laurence Calzone
  • Thorsten Cramer, RWTH Aachen
  • Pedro R. Cutillas, Barts
  • Christian Frezza, MRC – Cambridge
  • DREAM Challenges, in particular Gustavo Stolovitzky
  • Mathew Garnett and Ultan McDermott, Sanger Institute
  • Anne-Claude Gavin, EMBL Heidelberg
  • Steffen Klamt, Max Planck Institute
  • Tamás Korcsmáros, Earlham Institute and Institute of Food Research
  • Rafael Kramann, RWTH Aachen
  • Douglas Lauffenburger, Massachusetts Institute of Technology
  • Christoph Merten, EMBL
  • Alexander Mitsos, RTWH Aachen, Germany
  • Rainer Pepperkok, EMBL
  • Miguel Angel Pujana, IDIBELL
  • Miguel Rocha, University of Minho
  • Eduard Sabido, CRG
  • Anne Siegel, INRIA/IRISA
  • Peter K. Sorger, Harvard Medical School
  • Oliver Stegle, EMBL-EBI
  • Pablo Villoslada, IDIBAPS – Hospital Clinic of Barcelona
  • Martin Zeier and Susanne Delecluse, Kidney Center Heidelberg
Duration Name Agency

BioDATEN : Bioinformatics DATa Environment

Ministry of Science, Research and Art, Baden Wuerttemberg

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

DFG German Research Council
2020 - 2022

HPC Center of Excellence in Personalised Medicine – PerMedCoE

European Union (H2020-EU.

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

EU H2020 Health

LaMarcK: Longitudinal Multiomics Characterization of disease using prior Knowledge


Validating microfluidics-based personalized cancer therapy in mouse models

DFG German Research Council

Informatics for Life

Klaus-Tschira Stiftung

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

EU IMI Innovative Medicines Initiative

Analysis of mass spectrometry proteomics and drug treatment


LiSym: Liver systems medicine


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


PrECISE: Personalized engine for Cancer integrative study and evaluation

EU H2020 Health


National Cancer Institute (USA)

Joint Research Center for Computational Biomedicine

Bayer AG

SyMBioSys : Systematic Models for Biological Systems Engineering Training Network

EU H2020 Health MSCA-ITN

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

Center for Therapeutic Target Validation

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

Center for Therapeutic Target Validation

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

EU H2020 Health

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

EU H2020 Health

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

Medical Research Council (UK)

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



For all positions, candidates should email their CV (including names of three references) and a letter of interest to jobs.saez {at}  The letter of interest has to be tailored to our group, mentioning projects or articles of our group that you find interesting, and explaining how you would fit in our group. Please also provide a pointer to a code repository if possible.  Non-specific applications without this tailored expression of interest or sent to a different address will not be considered.

1. We have currently Postdoctoral and PhD positions in medical bioinformatics. The positions are in the context of various national and international collaborations to study clinical multi-omics data sets, including single-cell data, to develop and apply computational methods to better understand and treat cancer.

2. We also have an opening for a Research Software Engineer in the context of a PerMedCoE, a recently granted European project that aims at the refactoring of system biology simulation tools for High Performance Computing (HPC) and exascale architectures.  You are expected to hold a degree in statistics, mathematics, physics, engineering or computer science, or a degree in biological science with substantial experience in computational and statistical work.


3. We also have opportunities for student assistants (HiWi), master thesis, and internships, for a period of typically at least six months. We have often funding available for these positions.