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).

Research

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

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Secretary

Erika Schulz

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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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Alberto Valdeolivas Urbelz

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PhD Students

Aurélien Dugourd

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Nicolàs Palacio

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Christian Holland

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Hyojin Kim

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Ricardo O. Ramirez-Flores

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Olga Ivanova

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Associated members

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
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

Publications

BioServices

Python package to access Bioinformatics Web Services.

More about BioServices

Birewire

R package for the randomisation of bipartite graphs.

More about Birewire

Cyrface

Interface between R and Cytoscape.

More about Cyrface

CySBGN

Cytoscape plug-in for SBGN maps.

More about CySBGN

DREAMTools

Code used in the scoring of DREAM challenges.

More about DREAMTools

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.

More about KinAct

lipyd

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

More about lipyd

MEIGO

Global optimization toolbox including metaheuristic and Bayesian methods.

More about MEIGO

SLAPenrich

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
2020-2021

BioDATEN : Bioinformatics DATa Environment

Ministry of Science, Research and Art, Baden Wuerttemberg
2019-2022

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

EU H2020 Health
2019-2022

LaMarcK: Longitudinal Multiomics Characterization of disease using prior Knowledge

BMBF
2019-2021

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

1. We have currently one postdoctoral position in the context of a recently granted European project that aims at the refactoring of system biology simulation tools for High Performance Computing (HPC) and exascale architectures. More information here.
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. Candidates should email their CV (including names of three references) and a letter of interest to jobs.saez {at} bioquant.uni-heidelberg.de.  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. Deadline September 1st.

2. We always welcome spontaneous applications for  Postdocs or PhD students. Candidates should apply as explained above for the postdoc position.

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. Candidates should apply as explained above for the postdoc position.

4. There is an opening for a junior group leader in computational pathology to work with us in the Institute for Computational Biomedicine in collaboration with the Institute of Pathology, within the HIGHmed medical informatics initiative. More information here. Deadline September 15.