PhD students

 

Emel Comak

Inference of cis-regulatory mutations in cancer

1. supervisor: Martin Vingron

2. supervisor: Frederick Klauschen

  • Student speaker 2019/20
 

Clemens Messerschmidt

Learning from Background for Omics Data Analysis

1. supervisor: Ulf Leser

  • Student speaker 2019/20
Tincy Simon

Tincy Simon

Genomic and epigenomic alterations in Pancreatic Neuroendocrine tumors

1. supervisor: Christine Sers

2. supervisor: Nils Blüthgen

  • organizer of clinical visits program
Tzu-Ting Wei

Tzu-Ting Wei

Predicting the functional importance of variants from allele-specific expression and chromatin accessibility data

supervisors: Roland Schwarz, Christine Sers

Cindy received her Master’s degree in Translational Medical Research majoring in Molecular Oncology at Heidelberg University. She is a second-year PhD student in the group of Dr. Roland Schwarz at Max Delbrück Center for Molecular Medicine.  Her current research interest is to study the cis-regulatory mechanism in pan-cancer with the focus on understanding the function and effect of somatic variants together with allele-specific expression and chromatin features using machine learning methods.

Follow me on Twitter @TzuTingCindy

Bettina Schmidt

Bettina Schmidt

Unsupervised single cell mapping in CyTOF experiments

1. supervisor: Nils Blüthgen

2. supervisor: Dagmar Kainmüller

I approach modern challenges in single cell data analysis from a mathematical perspective. A lot of theoretical concepts from the statistics / applied mathematics communities are unknown in cancer research – though they might significantly improve the data analysis pipeline of the later. My challenge is to implement and adapt mentioned concepts into algorithms suitable for the use of system biologists / bioinformaticians. Currently, I am working on a Bayesian estimator for the Kullback-Leiber divergence that uses the nearest neighbour algorithm. The divergence is a dissimilarity measure that can be applied to multivariate probability distributions. In terms of single cell data, this method can help to determine the effect of potential cancer treatment drugs.

  • organizer of students retreat
  • Student speaker 2020/21
 

Samuele Garda (associated)

 

1. supervisor: Ulf Leser

My research focuses on the automatic extraction of structured information from the scientific literature. The aim is to accelerate the integration of new knowledge into resources crucial for biomedical research, including personalized cancer treatment. Specifically, I am interested in retrieving information regarding non-coding DNA sequences and the disease potential of their variants.

 
  • https://www2.informatik.hu-berlin.de/~gardasam/
Matthias Fischer

Matthias Fischer

Population dynamics of tumoural cell populations

supervisors: Nils Blüthgen, Hanspeter Herzel, Christine Sers

The intestinal epithelium is one of the fastest renewing tissues in mammals with an average turnover time of only three to five days, and shows a remarkable degree of stability towards external perturbations. My research is mainly focussed on using methods from dynamical systems and the analysis of experimental data, mainly obtained by mass cytometry and single-cell RNA sequencing of colon organoids to understand how a healthy homoeostatic tissue such as the intestinal epithelium may lose its homoeostasis and instead switch to a qualitatively different behaviour of unbounded growth, thereby giving rise to a cancerous lesion. I am especially interested in the very first steps of healthy colon tissue towards colorectal cancer, which often consist of a very specific set of somatic mutations, often also occurring in a characteristic order. I study how these mutations are able to affect the behaviour and interaction of different cell types, and thereby affect the overall behviour of the system.

 
 

Eleonora Usatikova

Modeling crosstalk between circadian clock and oncogenic signaling

1. supervisor: Hanspeter Herzel

2. supervisor: Christine Sers

 
 

Sinduja Chandrasekaran

Analyses of genomic rearrangement breakpoints in neuroblastoma

1. supervisor: Birte Kehr

2. supervisor: Johannes Schulte

 
 

Lorenz Rumberger

 

1. supervisor: Dagmar Kainmüller

 
 

Louisa Krützfeldt

 

1. supervisor: Johannes Schulte

 
 

Wanja Kassuhn (associated)

Identification and evaluation of novel therapeutic approaches to distinct molecular subtypes of high-grade serous ovarian cancer

1. supervisor: Hagen Kulbe

2. supervisor: Nils Blüthgen

3. supervisor: Ulf Leser

 
Rosario Astaburuaga

Rosario Astaburuaga (associated)

Signalling pathways governing cell fate decisions upon radiation and molecular targets to break radioresistance

1. supervisor: Nils Blüthgen

 
Stefan Peidli

Stefan Peidli (associated)

A holistic integration model for scalable and single cell based systems biology in cancer

supervisors: Nils Blüthgen, Chris Sander, Dagmar Kainmüller

My aim is to dissect the effects of and responses to perturbations (drugs/inhibitors, CRISPR) on a single cell level using various machine learning techniques in collaboration with other labs in Berlin and Boston. Maybe we can use this knowledge to develop efficient combination therapies against cancer and understand the drug response on the transcript/protein level. More broadly, I am interested in systems biology and the regulatory circuitry in human cells. Especially incorporating multiple layers of cellular features (genetics aberrations, gene expression, epigenetics, proteins, phenotypes, ...) and their regulation in multi-omic single cell data might prove crucial for advancement in modern perturbation biology and cancer research. As a mathematician with a love for natural sciences, I find the greatest joy in the richness of problems and challenges that single cell data provide us. It gives me space to be creative and ask a lot of unsolved questions.

  • Student speaker 2020/21
  • twitter: @SPeidli
  • GitHub: https://github.com/stefanpeidli
Jennifer Wiederspahn

Jennifer Wiederspahn (associated)

 

1. supervisor: Chris Sander

2. supervisor: Nils Blüthgen

 
Maja-Celine Cwikla

Maja-Celine Cwikla (associated)

 

1. supervisor: Roland Schwarz

 
 

Fabian Reith

 

1. supervisor: Dagmar Kainmüller

 
 

Saskia Grabe

 

1. supervisor: Hanspeter Herzel