J. Wolf Lab

Our group develops and analyses mathematical models of signaling pathways and gene-regulatory networks in normal and disease states. We focus on processes in cancer biology and early development as well as design principles of biological networks.

Complex diseases are often characterized by an accumulation of multiple perturbations, such as mutations or over-expression of proteins, in rather large and complex cellular networks. The consequences of these perturbations can hardly be analyzed by pure reasoning.

Here, mathematical modelling and computational analyses contribute to a deeper understanding of the regulatory systems. They provide a rational basis for the interpretation and integration of multi-omics or high-throughput data and identification of effective drug targets paving the way for a patient-specific understanding of diseases.

In the last years, we analysed gene expression and signal transduction, in particular the NF-κB/IKK, p53, Wnt/β-catenin and Hes1 pathways that are crucial for cell fate decisions. Moreover, we studied the effect of oncogenes in cellular metabolism. In many of our projects we closely collaborate with experimental and clinical partners in and outside of the MDC.

Staff

Tino Marwin Petrov

TinoMarwin.Petrov@mdc-berlin.de

PhD student

Yozlem Bahar

31.1: Max-Delbrück-Haus

Room: 5015.2

Yozlem.Bahar@mdc-berlin.de

+49 30 9406-2465

Zsófia Bujtár

Zsofia.Bujtar@mdc-berlin.de

Graduate and Undergraduate

Dana Barilan

Dana.Barilan@mdc-berlin.de

Sina Glöckner

Sina.Gloeckner@mdc-berlin.de

Daria Komkova

Daria.Komkova@mdc-berlin.de

November 01, 2023 / Bioinformatics

PEDL+: Protein-centered relation extraction from PubMed at your fingertip

L. Weber
F. Barth
L. Lorenz
F. Konrath
K. Huska
J. Wolf
U. Leser

October 20, 2023 / iScience

A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1

F. Konrath
M. Willenbrock
D. Busse
C. Scheidereit
J. Wolf

January 01, 2023 / Methods Mol Biol

Resolving crosstalk between signaling pathways using mathematical modeling and time-resolved single cell data

F. Konrath
A. Loewer
J. Wolf

November 18, 2022 / Database

Chemical-protein relation extraction with ensembles of carefully tuned pretrained language models

L. Weber
M. Sänger
S. Garda
F. Barth
C. Alt
U. Leser

July 12, 2022 / J Chem Theory Comput

Graph neural networks for learning molecular excitation spectra

K. Singh
J. Münchmeyer
L. Weber
U. Leser
A. Bande

June 10, 2022 / Interface Focus

Time-keeping and decision-making in living cells: Part II

J.J. Tyson
A. Csikasz-Nagy
D. Gonze
J.K. Kim
S. Santos
J. Wolf

June 06, 2022 / Interface Focus

Time-keeping and decision-making in living cells: Part I

J.J. Tyson
A. Csikasz-Nagy
D. Gonze
J.K. Kim
S. Santos
J. Wolf

May 01, 2022

Dataset debt in biomedical language modeling

J.A. Fries
N. Seelam
G. Altay
L. Weber
M. Kang
D. Datta
R. Su
S. Garda
B. Wang
S. Ott
M. Samwald
W. Kusa

April 29, 2022 / Metabolites

A flexible tool to correct superimposed mass isotopologue distributions in GC-APCI-MS flux experiments

J. Langenhan
C. Jaeger
K. Baum
M. Simon
J. Lisec

December 15, 2021 / Exp Cell Res

An oscillatory network controlling self-renewal of skeletal muscle stem cells

I. Lahmann
Y. Zhang
K. Baum
J. Wolf
C. Birchmeier

Science July 06, 2022

The modeler of life

Jana Wolf draws on experimental data and the growing knowledge of cellular mechanisms to translate disease processes into mathematical models. Her models aim to represent the complexity of life as realistically as possible and to help develop therapies that are precisely tailored to the patient.

Light sheet microscopy image of the hepato-pancreato-biliary organ system and gastrointestinal tract of a mouse embryo

Science September 29, 2021

The regenerative power of progenitors

Studies at the MDC and the BIH have revealed that the liver, gallbladder and pancreas arise from a common pool of progenitor cells and that the supply of cells from this pool is inexhaustible. These findings may contribute to the development of new regenerative therapies, the researchers write in the journal “Nature”.

© Felix Petermann, MDC_portrait_wolf, jana-8592.jpg

Institute & Campus June 15, 2020

Professorship for Jana Wolf

Dr. Jana Wolf heads the Mathematical Modeling of Cellular Processes Lab at the MDC. On June 15 she will begin a professorship at FU Berlin. She looks forward to exchanging expertise and ideas with her new colleagues – and to leveraging this knowledge to develop new medical models.

Science February 27, 2018

MINT400 Forum at the MDC: Why math is an indispensable tool

Basic medical research would be impossible without math and chemistry. At this year's MINT400 Forum, 350 schoolchildren and 50 teachers from all over Germany came together to learn about the importance of interdisciplinary research for science today.

Institute & Campus February 10, 2017

Of bits, bytes, and bacteria: a week of systems biology at the MDC

Can the lives of microorganisms be described through mathematics? It is one of the questions that pupils participating in the MINT Excellence Academy in “Systems Biology” have asked scientists during their visit to the MDC from Feb. 6 to 10 this year. Twenty pupils from across Germany have come to catch a glimpse of how researchers combine laboratory and computational science into models of biological processes.

Press Release No. 15 July 31, 2015 Berlin

RNA-binding Protein Influences Key Mediator of Cellular Inflammation and Stress Responses

Messenger (mRNA) molecules are a key component of protein biosynthesis. They are first transcribed as a “working copy” of the DNA and then translated into protein molecules. RNA-binding proteins such as RC3H1 (also known as ROQUIN) regulate the degradation of the mRNA molecules and thus prevent the production of specific proteins. Researchers at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) have now shown that ROQUIN binds several thousand mRNA molecules. They demonstrated that ROQUIN also influences the gene regulator NF-kappaB, a key mediator of cellular inflammation and stress responses (Nature Communications, Article number: 7367)*.

Science February 17, 2012 By Russell Hodge

Tipping the balance on Alzheimer's disease

In 1906, while peering at brain tissue through a microscope, Aloysius Alzheimer discovered one of the main hallmarks of the disease that now bears his name.

Science July 04, 2011 By Russell Hodge

The first full census of a mammalian cell

A cell's functions and behavior depend on the total population of molecules present in it at any...

Press Release No. 6 May 19, 2011 Berlin

From Gene to Protein – New Insights of MDC Researchers

The Berlin Institute for Medical Systems Biology (BIMSB) was launched by the MDC in 2008, supported...

Leonie Lorenz, Master student, went to EMBL-EBI
Ziyue Chen, Master student
Daria Komkova, Master student
Katharina Baum, PhD student and Postdoc, went to Hasso-Plattner-Institute, Potsdam
Uwe Benary, PhD student and Postdoc, went to Omikron Data Quality GmbH
Janina Mothes, PhD student and Postdoc, went to Bayer AG
Laura Stumpf, Master student, went to Insilico Biotechnology
Bente Kofahl, PhD student and Postdoc, went to Freiburg University
Dorothea Busse, Postdoc, went to IRI LifeSciences, Humboldt-University Berlin
Alexandra Iovkova, scientist, went to TU Munich
Christian Brettschneider, Postdoc, went to Atos Consulting
Jana Schütze, PhD student, went to Humboldt-University Berlin
Antonio Politi, Postdoc, went to EMBL Heidelberg

Guests and internships

Yukino Fujiya, internship 2023
Leonie Lorenz, internship 2021
Ziyue Chen, internship 2020/2021
Daria Komkova, internship 2021
Bashar Morouj, Student research assistant, 2021
Lucas Arnoldt, internship 2020
Florian Auer, internship 2020
Jonathan Grill, Bachelor student 2018/2019
Sandra Krüger, internship 2018
Janosch Brandhorst, Bachelor student 2017/2018
Mirjam van Bentum, Charité MoIMed rotation student 2016
Pia Brechmann, internship 2016
Maria Trofimova, internship 2016
Luis Martini, internship 2015
Dominik Otto, internship 2014
Kristin Meisel, internship 2011
Niklas Hartung, guest PhD student

We always welcome applications from motivated individuals for internships or positions as a Master student, PhD student or PostDoc. Ideally, applicants already have a background in the field of biology as well as computer science/modeling.

If you are interested in joining our lab, please contact our secretary Constanze Dahl (constanze.dahl@mdc-berlin.de) and include the following documents in your application: CV, relevant certificates/ university transcripts (listing the courses and grades), a short text describing why you are interested in joining our lab (email text is fine), when you would like to start (for interns: how long you would like to join us).