BIMSB

Medical Systems Biology

The Berlin Institute for Medical Systems Biology (BIMSB)

MDC-NYU PhD Exchange Program

Systems biology combines molecular biology, biochemistry, computational sciences, mathematics and physics to quantitatively capture and predict complex processes of life.

The MDC-NYU PhD Exchange program was launched in 2009 to train the next generation of systems biologists. Ten BIMSB PhD students are able to to spend up to two years working and studying at the Center for Genomics and Systems Biology at New York University. Students can also take advantage of our state of the art technology platforms and a training programme of specialist courses and personal development opportunities.

BIMSB and NYU Biology are committed to sharing their scientific and educational expertise with their respective student bodies.

Information on BIMSB

How to Apply

Further information on application deadlines and how to apply can be found at the MDC Graduate Office Website.

Research Training

The Berlin Institute for Medical Systems Biology offers an exceptional PhD Exchange Program to support interdisciplinary research projects and international PhD education.

PhD topics are structured as collaborative projects between the Center for Genomics and Systems Biology at New York University and the Berlin Institute for Medical Systems Biology at the MDC. A Principal Investigator from each institution supervises each student, students who are expected to divide their time between Berlin and New York, taking advantage of complimentary research and training expertise. Resources are available for travel from Berlin to New York for short and long term working periods as well as for course and conference participation. The regular guidance of an international PhD Committee supports the creation of individual research and training portfolios.

Our program offers:

  • interdisciplinary research training in top ranking labs
  • projects that are dually mentored by a group leader from MDC and NYU
  • students are supported to spend up to fifty percent of their time at NYU
  • access to and training in high-end technologies, such as deep sequencing, mass spectrometry, bioinformatics
  • an extensive and comprehensive archive of animal model systems and "evo-devo" approaches
  • participation in interdisciplinary classes, soft skills courses, student focussed seminars and specialist summer schools
  • the regular opportunity to present your research at the BIMSB Student Seminar and attend the Systems Biology Lecture Series

More about PhD programmes at the MDC

More about the Center for Genomics and Systems Biology at NYU

Student Profiles

 

The students in March 2018: Lorena Sofia Lopez Zepeda, Selman Bulut, Laura Breimann, Maria Stella deBiase, Thomas Sparks, Jonathan Alles, Ana Miguel Fernandes, Nicolai Kastelic (left to right)

Here we introduce the MDC-NYU students and their joint projects with the Center for Genomics and Systems Biology and the Department of Biology at NYU.

Jonathan Alles (2017-)

TBC
Supervisory team: Nikolaus Rajewsky and Rahul Satija
Jonathan Alles

I am interested in developing experimental and computational approaches for analyzing RNA isoform expression at single cell resolution. Therefore I modify existing high-thoughput single cell sequencing protocols as DropSeq or InDrop and develop new computational pipelines for data analysis. I will apply these methods to neuronal differentiation systems as iPS cell derived neurons or human cerebral organoids in order to gain new insight about how genes are regulated in different cell types and over time.

Thomas Maximilian Sparks (2017-)

TBC
Supervisory team: Ana Pombo and Richard Bonneau
Thomas Sparks

Maria Stella de Biase (2017-)

TBC
Supervisory team: Roland Schwarz and Mark Siegal
Maria Stelle de Biase

Lorena Sofia Lopez Zepeda (2017-)

TBC
Supervisory team: Uwe Ohler and Neville Sanjana
Lorena Sofia Lopez Zepeda

Laura Breimann (2016-)

TBC
Supervisory team: Stephan Preibisch and Sevinc Ercan
Laura Breimann

Dissecting the role of chromosome condensation on transcription regulation in C.elegans.

I use quantitative single-cell imaging to characterise transcription regulation in C. elegans. In particular I study X-chromosome condensation and the dynamics of condensin DC binding during embryogenesis in C. elegans . To determine the effect of condensin DC on transcription, I quantify gene expression using single molecule RNA fluorescence in situ hybridization (smFISH) and live transcription imaging technologies.

Selman Bulut (2016-)

TBC
Supervisory team: Baris Tursun and Sevinc Ercan
Selman Bulut

Ana Miguel Fernandes (2014-2017)

Dynamic regulation of co-transcriptional processes during neuronal maturation
Supervisory team: Ana Pombo and Esteban O. Mazzoni
Ana Miguel Fernandes

I am interested in exploring the mechanisms underlying co-transcriptional RNA processing events relevant for neuronal maturation. My studies will focus on chromatin-related processes mediated by signalling through post-transcriptional modification of RNA polyermerase II.

Nicolai Kastelic (2014-2018)

RNA-based regulation in pluripotency and differentiation
Supervisory team: Markus Landthaler and Esteban O. Mazzoni
Nicolai Kastelic

Kamila Kutz (2014-2017)

Proteomic identification and characterization of micropeptides
Supervisory team: Matthias Selbach and Richard Bonneau
Kamila Kutz

Understanding the full protein-coding potential of the genome and its biological function is one of the greatest challenges in the post-genomic era. Current genome annotation methods categorize open reading frames of less than 100 amino acids as non-protein coding portion of the genome. The aim of my research is to identify and characterize these so-called micropeptides using mass spectrometry-based and computational approaches.

Mahmoud Ibrahim (2013-2017)

Probabilistic modeling methods to identify chromatin state transitions in time course data
Supervisory team: Uwe Ohler and Esteban O. Mazzoni
Mahmoud Ibrahim

In my PhD project I will apply probabilistic modeling methods to identify chromatin state transitions in time course data. In particular, I will try to understand how changes in histone modifications and chromatin structure determine gene expression changes for the differentiation of cell types during development.

Panagiotis Papavasileiou (2013-2017)

Biogenesis and function of circular and other ncRNAs in development
Supervisory team: Nikolaus Rajewsky and Claude Desplan
Panagoitis Papavasileiou

In order to improve the understanding of biogenesis and function of circular RNAs, I am working on their screening in a variety of organisms and cell cultures. In particular, I'm interested in the impact of circular RNAs in development and differentiation of D. melanogaster.

Alessandra Zappulo (2013-2017)

Subcellular mRNA localization and translation in mESC derived neurons
Supervisory team: Marina Chekulaeva and Esteban O. Mazzoni
Alessandra Zappulo

My project is focusing on dissecting the roles of miRNAs in mRNA localization and local translation. These processes are crucial for establishment of body axis, cell migration, synaptic plasticity and cell growth. To analyze the effects of miRNAs on these processes, I am using an approach that allows me to biochemically separate different cell compartments of neurons differentiated from mESCs for spatial transcriptomic, proteomic and bioinformatic analyses. This analysis aims to generate unique datasets of localized transcriptome and proteome and clarify the mechanisms underlying mRNA localization and localized translation.

Fabian Bindel (2010-2014)

Deciphering links between transcription factor signaling and cancer metabolism
Supervisory team: Stefan Kempa and Richard Bonneau

Cancer is a disease of imbalance in cell cycle regulation and consequently in cell growth. To acquire a cancer phenotype, a cell has to undergo a series of gene alterations which regulate cell proliferation, differentiation and apoptosis. Cancer cells can be characterized by their abnormal proliferation rate. Even if the in vivo concentration of the nutrients remain the same, some cancer cells are able to increase their proliferation rate. My question is: What are the mechanisms that transform the metabolism to enable such altered proliferation rate? The underlying feature behind different cell phenotypes is the different regulation of the metabolism despite the fundamental pathways being the same. These changes are reflected on the different molecular levels of a cell. To identify possible regulatory events changing a cell phenotypic behavior we will investigate the cell metabolism using stable isotope labeled substrates over different time spans. This allows us to monitor pathway activities in a dynamic way. Simultaneously, we will analyze the proteome to identify connections to an altered proliferation rate (e.g. isoform switching) by Stable Isotope Labeling by Amino acids in Cell culture (SILAC). Transcriptomic analysis (RNA-Seq) will be used for gene expression profiling. The combined data analysis of these different levels will further the identification of new potential targets for anticancer drugs.

Fabian successfully defended his thesis with the grade magna cum laude at Humboldt-Universität zu Berlin on 02 March 2015.

Mathias Munschauer (2010-2014)

High-resolution profiling of protein-RNA interactions
Supervisory team: Markus Landthaler and Christine Vogel

The goal of my PhD project is to study translational regulatory mechanisms by in vivo crosslinking approaches and small RNA sequencing.

Mathias successfully defended his thesis with the grade summa cum laude at  Freie Universität Berlin on 22 August 2014.

Martina Weigt (2010-)

Genome wide DNA CpG methylation profiling using massive parallel bisulfite sequencing
Supervisory team: Wei Chen and Fei Li
Martina Weigt

DNA methylation is, besides histone modyfication, the key feature of epigenetic modification. It holds multiple functions in plants and higher animal phylia. In mammals, CpG methylation is generally regarded as a regulator of transcription and is essential for processes such as development, parental allele-specific imprinting and dosage compensation by X inactivation in females. It has been also implicated in many human pathologies including cancer. During my study to investigate the CpG methylation profile on a genome wide scale, I will first set up the technique of reduced representation bisulfite sequencing (RRBS) and then apply it in different biological systems.

Rina Ahmed (2009-2014)

Bioinformatic analysis of microRNA genes in free-living and parasitic nematodes
Supervisory team: Christoph Dieterich and Kris Gunsalus

In my PhD project, I will investigate the evolution of microRNA genes in the phylum of nematodes. For this, we will perform small RNA next-generation sequencing on a genus-wide level.

Rina successfully defended her thesis at Freie Universität Berlin on 26 February 2015.

Alexander Baltz (2009-2013)

The mRNA-bound Proteome of a human cell-line and in early Drosophila embryogenesis
Supervisory team: Markus Landthaler and Stephen Small

The aim of my PhD project is to investigate transcriptome-wide protein-mRNA interactions in mammalian cells and during development and differentiation in D. melanogaster.

Alex successfully defended his thesis with the grade summa cum laude at Freie Universität Berlin on 05 May 2014.

Jiaxuan Chen (2009-2015)

Analysis of protein-protein interaction during embryogenesis in C. elegans
Supervisory team: Matthias Selbach and Fabio Piano

The aim of my PhD project is to study protein-protein interaction during early C. elegans development. Combining an in vivo SILAC approach and high-throughput quantiative mass spectrometry, I will investigate the binding partners of proteins that are important for C. elegans embryogenesis.

Jiaxuan successfully defended his thesis with the grade magna cum laude at Humboldt Universität zu Berlin on 21 September 2015.

Anna-Carina Jungkamp (2009-2012)

In vivo and transcriptome-wide identification of RNA binding protein target sites
Supervisory team: Nikolaus Rajewsky and Fabio Piano

During my PhD project, I will study post-transcriptional regulation of gene expression in vivo. I will establish a technique to identify transcriptome-wide target sites of RNA-binding proteins in the nematode C. elegans. These data will then be combined with RNAi experiments, RNA-seq and high-throughput quantitative in vivo proteomics to study the function of particular RNA binding proteins. As a member of the MDC-NYU PhD Exchange Program, I have already visited Fabio Piano's lab to learn basic C.elegans techniques and during my PhD project and regular visits to his lab are planned. Some of the experiments are planned as joint projects with a PhD student in his lab.

Anna-Carina successfully defended her thesis with the grade summa cum laude at Humboldt-Universität-zu Berlin on 16 May 2013.

Marlon Stoeckius (2009-2011)

High resolution transcriptome and proteome profiling during oocyte to embryo transition in C.elegans
Supervisory team: Nikolaus Rajewsky and Fabio Piano

My PhD project was part of a long-standing collaboration with the lab of Fabio Piano at New York University. I spent several months in New York to learn C. elegans methods which enabled me to establish those used in Berlin. We recently published a method to sort specific stages of C.elegans embryogenesis (Stoeckius et al, 2009) as a part of my MDC-NYU PhD project.

Marlon successfully defended his thesis with the grade summa cum laude at Humboldt-Universität-zu Berlin on 20 June 2011.

Faculty

 

BIMSB and MDC Faculty

NYU Faculty

Justin Blau
Transcriptional Regulation in Circadian Pacemaker Neurons

Richard Bonneau
Network Inference and Protein Structure Design and Prediction

Lionel Christiaen
Gene Network Models for Heart and Skeletal Muscle Development

Claude Desplan 
Stochastic Mechanisms and Evolution of Development

Sevinc Ercan
Regulation of Transcription by Chromatin Structure

David Fitch
Gene-Interaction Networks Regulating Sexually Dimorphic Morphogenesis & its Evolution

David Gresham
Systems Biology of Cell Growth and RNA Degradation

Kris Gunsalus
Developmental Systems Biology

Andreas Hochwagen
Chromosome Organization and Repetitive DNA

Fei Li  
Chromatin Organization and Epigenetics

Esteban Mazzoni
Neural Differentiation of Embryonic Stem Cells

Fabio Piano 
Systems Biology and Evolution of Embryogenesis

Christine Rushlow
Transcriptional Programming in Fly Development

Neville Sanjana
sanjanalab.org

Mark Siegal
Robustness and Evolution of Complex Phenotypes

Stephen Small
Transcriptional Networks in Developmental Patterning

Christine Vogel
Proteomics and Regulation of Protein Expression

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