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. 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.
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.
Further information on application deadlines and how to apply can be found at the.
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.
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.
Supervisory team: Markus Landthaler and Lionel Christiaen
Supervisory team: Nikolaus Rajewsky and TBA
Role of CTCF in the evolution of metazoan chromatin architecture
Supervisory team: Dario Lupianez and Robert Zinzen and Lionel Christiaen
Poly(A) tails in eukaryotic gene expression control
Supervisory team: Nikolaus Rajewsky and Carlos Carmona-Fontaine
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
Incorporating RNA detection into Genome Architecture Mapping
Supervisory team: Ana Pombo and Richard Bonneau
Understanding the aetiology of intra-tumour heterogeneity and its functional consequences
Supervisory team: Roland Schwarz and Mark Siegal
Using CRISRR screens to understand genomic regulation in a motor neuron programming model
Supervisory team: Uwe Ohler and Neville Sanjana
Dissecting the role of chromosome condensation on transcription regulation in C.elegans
Supervisory team: Stephan Preibisch and Sevinc Ercan
Breimann L., Preusser F., Preibisch S. (2019) Light-microscopy methods in C.elegans research. Curr Opin Syst Biol 13: 82-92
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
Dynamic regulation of co-transcriptional processes during neuronal maturation
Supervisory team: Ana Pombo and Esteban O. Mazzoni
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
Proteomic identification and characterization of micropeptides
Supervisory team: Matthias Selbach and Richard Bonneau
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.
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
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.
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
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).
Genome wide DNA CpG methylation profiling using massive parallel bisulfite sequencing
Supervisory team: Wei Chen and Fei Li
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.
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
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
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
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