MDC-NYU PhD Exchange Program

Bilateral Meeting at the Center for Genomics and Systems Biology in New York in 2015.

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.

December 2019: MDC-NYU exchange program fellows, BIMSB and NYU faculty discuss ongoing and new collaborations during the annual bilateral meeting at the Center for Genomics and Systems Biology in New York.

As of December 2019, a total of 22 MDC-NYU program fellows have co-authored 46 publications. The success of the program is highlighted by 11 joint publications with NYU faculty.

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 novel sequencong applications, multi-omics approaches, organoid models and bioinformatics
  • an extensive and comprehensive archive of animal model systems for evo-devo or translational 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
Up to 10 interdisciplinary graduate students join the program.

MDC-NYU students in 2019: BIMSB group leader Markus Landthaler, Thomas Sparks, MDC-NYU program alumni Mathias Munschauer, Liene Astica, Laura Breimann, Simone Del Giudice, Maria Stella deBiase, Lorena Lopez Zepeda

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 including the student's first author publications.

Simone Del Giudice (2019-)

Supervisory team: Markus Landthaler and Lionel Christiaen
Simone Del Giudice

Miriam Wandres (2019-)

Supervisory team: Nikolaus Rajewsky and TBA
Miriam Wandres

Liene Astica (2018-)

Role of CTCF in the evolution of metazoan chromatin architecture

Supervisory team: Dario Lupianez and Robert Zinzen and Lionel Christiaen
Liene Astica

Jonathan Alles (2017-)

Poly(A) tails in eukaryotic gene expression control

Supervisory team: Nikolaus Rajewsky and Carlos Carmona-Fontaine
Jonathan Alles

Alles J*, Karaiskos N*, Praktiknjo SD, Grosswendt S, Wahle P, Ruffault PL, Ayoub S, Schreyer L, Boltengagen A, Birchmeier C, Zinzen R, Kocks C, Rajewsky N. (2017) Cell fixation and preservation for droplet-based single-cell transcriptomics. BMC Biol. 2017 May 19;15(1):44.

Legnini I*, Alles J*, Karaiskos N, Ayoub S, Rajewsky N. (2019) FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control. Nat Methods. 2019 Sep;16(9):879-886

Thomas Maximilian Sparks (2017-)

Incorporating RNA detection into Genome Architecture Mapping

Supervisory team: Ana Pombo and Richard Bonneau
Thomas Sparks

Maria Stella de Biase (2017-)

Understanding the aetiology of intra-tumour heterogeneity and its functional consequences

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

Lorena Sofia Lopez Zepeda (2017-)

Using CRISRR screens to understand genomic regulation in a motor neuron programming model

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

Laura Breimann (2016-2019)

Dissecting the role of chromosome condensation on transcription regulation in C.elegans
Supervisory team: Stephan Preibisch and Sevinc Ercan
Laura Breimann

Breimann L., Preusser F., Preibisch S. (2019) Light-microscopy methods in C.elegans research. Curr Opin Syst Biol 13: 82-92

Selman Bulut (2016-2019)

Tissue-specific ChIP-seq to Study Tissue-specificity of CHE-1-mediated Conversion and Genomic Distribution of Histone Variants
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

Nicolai Kastelic (2014-2019)

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

Kastelic N, Landthaler M. (2017). mRNA interactome capture in mammalian cells. Methods.;126:38-43

Kamila Kutz (2014-2017)

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

Mahmoud Ibrahim (2013-2017)

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

Ibrahim MM, Lacadie SA, Ohler U. (2015) JAMM: a peak finder for joint analysis of NGS replicates. Bioinformatics. 2015 Jan 1;31(1):48-55

Velasco, S.*, Ibrahim, M.M.*, Kakumanu, A., Garipler, G., Aydin, B., Al-Sayegh, M.A., Hirsekorn, A., Abdul-Rahman, F., Satija, R., Ohler, U., Mahony, S., Mazzoni, E.O. (2017). A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. Cell Stem Cell 20, 205-217.e208.

Ibrahim MM, Karabacak A, Glahs A, Kolundzic E, Hirsekorn A, Carda A, Tursun B, Zinzen RP, Lacadie SA, Ohler U. (2018) Determinants of promoter and enhancer transcription directionality in metazoans. Nat Commun. 2018 Oct 26;9(1):4472.

Panagiotis Papavasileiou (2013-2017)

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

Memczak S*, Papavasileiou P*, Peters O, Rajewsky N. (2015). Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood. PLoS One;10(10):e0141214. *equal contribution

Alessandra Zappulo (2013-2017)

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

Zappulo, A., Van Den Bruck, D., Ciolli Mattioli, C., Franke, V., Imami, K., McShane, E., Moreno-Estelles, M., Calviello, L., Filipchyk, A., Peguero-Sanchez, E., Müller, T., Woehler, A., Birchmeier, C., Merino, E., Rajewsky, N., Ohler, U., Mazzoni, E.O., Selbach, M., Akalin, A., Chekulaeva, M. (2017). RNA localization is a key determinant of neurite-enriched proteome. Nat Commun 8, 583.

Fabian Bindel (2010-2014)

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

Rohwer N*, Bindel F*, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T. (2016) Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. Oncotarget. 2016 Feb 9;7(6):6693-710. doi: 10.18632/oncotarget.6793

Mathias Munschauer (2010-2014)

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

Graf R*, Munschauer M*, Mastrobuoni G, Mayr F, Heinemann U, Kempa S, Rajewsky N, Landthaler M. (2013) Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation. RNA Biol. 2013 Jul;10(7):1146-59.

Schueler M*, Munschauer M*, Gregersen LH, Finzel A, Loewer A, Chen W, Landthaler M, Dieterich C. (2014) Differential protein occupancy profiling of the mRNA transcriptome. Genome Biol. 2014 Jan 13;15(1):R15.

Munschauer M, Schueler M, Dieterich C, Landthaler M. (2014) High-resolution profiling of protein occupancy on polyadenylated RNA transcripts. Methods. 2014 Feb;65(3):302-9

Munschauer M., Vogel J. (2018). Nuclear lncRNA stabilization in the host response to bacterial infection. EMBO J. 2018 Jul 2;37(13).

Martina Weigt (2010-)

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

Rina Ahmed (2009-2014)

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

Ahmed R, Chang Z, Younis AE, Langnick C, Li N, Chen W, Brattig N, Dieterich C. (2013). Conserved miRNAs are candidate post-transcriptional regulators of developmental arrest in free-living and parasitic nematodes. Genome Biol Evol. 2013;5(7):1246-60.

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

Baltz AG., Munschauer M., Schwanhaeusser B., Vasile A., Murakawa Y., Schueler M., Youngs N., Penfold-Brown D., Drew K., Milek M., Wyler E., Bonneau R., Selbach M., Dieterich C., Landthaler M. (2012). The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell. 46 (5): 674-690

Jiaxuan Chen (2009-2015)

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

Sury MD*, Chen JX*, Selbach M. (2010) The SILAC fly allows for accurate protein quantification in vivo. Mol Cell Proteomics. 2010 Oct;9(10):2173-83 *equal contribution

Sury MD*, Chen JX*, Selbach M. (2014) In vivo stable isotope labeling by amino acids in Drosophila melanogaster. Methods Mol Biol. ;1188:85-93. *equal contribution

Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M. (2016). In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics. Mol Cell Proteomics;15(5):1642-57

Anna-Carina Jungkamp (2009-2012)

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

Jungkamp, A.C., Stoeckius, M., Mecenas, D., Grün, D., Mastrobuoni, G., Kempa, S., Rajewsky, N. (2011). In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites. Mol Cell. 4: 828-40

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

Stoeckius M., Maaskola J., Colombo T., Rahn H.P., Friedlaender M.R., Li N.; Chen W., Piano F., Rajewsky N. (2009-10). Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nature Methods 6 (10): 745-751

Stoeckius M, Grün D, Rajewsky N. (2014) Paternal RNA contributions in the Caenorhabditis elegans zygote. EMBO J. 2014 Aug 18;33(16):1740-50.

Stoeckius M., Gruen D., Kirchner M., Ayoub S., Torti F., Piano F., Herzog M., Selbach M., Rajewsky N. (2014). Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism EMBO J. 33(16): 1751-1766



BIMSB and MDC Faculty

NYU Faculty

Justin Blau
Transcriptional Regulation in Circadian Pacemaker Neurons

Richard Bonneau
Network Inference and Protein Structure Design and Prediction

Carlos Carmona-Fontaine
Understanding multicellular organization

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

Mark Siegal
Robustness and Evolution of Complex Phenotypes

Stephen Small
Transcriptional Networks in Developmental Patterning

Christine Vogel
Proteomics and Regulation of Protein Expression