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. Towards this goal, we integrate big (‘Omics’) data with mechanistic molecular knowledge into statistical and machine learning methods, and we share our tools as free open-source packages.

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 application-driven and tailored towards producing computational models that integrate diverse data sources to better understand and treat diseases. Because of this, we collaborate closely with experimental groups. A major emphasis is to build context-specific models that are both mechanistic (to provide understanding) and predictive (to generate novel hypotheses). To build these models, we combine existing biochemical knowledge with different types of large scale data. We believe that this biological knowledge can be instrumental to move from pure correlation to causation in large data sets, and thereby identify the molecular processes that underlie specific phenomena.
 
We develop and apply methods to extract mechanistic features from diverse omics data,  recently also for single-cell data. We then combine these multi-omics data sets into causal networks. Finally, we build dynamic models of specific subsystems using logic formalisms that we can analyze and simulate to predict the effect of new perturbations.
 
We apply these strategies in the context of many disease conditions. Particular areas of interest for us are cancer, in particular  large-scale drug screenings,  fibrosis (in particular in kidney, heart, and liver), and co-morbidities in heart failure
 
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

More...

Secretary

Erika Schulz

More...

Staff Scientist

Marzia Sidri

More...

Postdocs

Denes Turei

More...

Attila Gabor

More...

Jovan Tanevski

More...

Rosa Hernansaiz Ballesteros

More...

Javier Perales-Patón

More...

Bartosz Bartmanski

More...

Katharina Zirngibl

More...

Arezou Rahimi

More...

Martín Garrido Rodríguez-Córdoba

More...

Sebastian Lobentanzer

More...

Ahmet Sureyya Rifaioglu

More...

PhD Students

Aurélien Dugourd

More...

Ricardo O. Ramirez-Flores

More...

Olga Ivanova

More...

Daniel Dimitrov

More...

Pau Badia i Mompel

More...

Sophia Müller-Dott

More...

Associated members

Jan Lanzer

More...

Rebecca Terrall Levinson

More...

Monica Toft Hannani

More...

Nadine Tüchler

More...

Bence Szalai

More...

The following people spent over 6 months with us:

Name Duration Position
Eleanor Fewings 2020-2021 Bioinformatician
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
Christian Holland 2017 -2021 PhD Student
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

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

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
  • Christian Frezza, MRC – Cambridge
  • DREAM Challenges, in particular Gustavo Stolovitzky
  • Mathew Garnett and Ultan McDermott, Sanger Institute
  • 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 Rocha, University of Minho
  • 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
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

For all positions, candidates should email their CV and a letter of interest to jobs.saez {at} bioquant.uni-heidelberg.de, including names of (ideally 3) references.  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 do not have any specific PostDoctoral and PhD positions but we welcome spontaneous applications of qualified candidates.

2. We have opportunities for student assistants (HiWi), master thesis, and internships. In general, these are for a period of six months or longer, although shorter internships are sometimes possible. Please include information on the lectures you have attended.