The students in February 2016:
Selman Bulut, Nicolai Kastelic, Kamila Kutz, Alessandra Zappulo, Ana Miguel Fernandes, Panagiotis Papavasileiou, Laura Breimann (left to right); Mahmoud Ibrahim (top circle)
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.
Laura Breimann (2016-): TBC
Supervisory team: Stephan Preibisch and TBC
Selman Bulut (2016-): TBC
Supervisory team: Baris Tursun and Sevinc Ercan
Ana Miguel Fernandes (2014-): Dynamic regulation of co-transcriptional processes during neuronal maturation
Supervisory team: Ana Pombo and Esteban O. Mazzoni
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-): TBC
Supervisory team: Markus Landthaler and Esteban O. Mazzoni
Kamila Kutz (2014-): TBC
Supervisory team: Matthias Selbach and Richard Bonneau
Mahmoud Ibrahim (2013-): Probabilistic modeling methods to identify chromatin state transitions in time course data
Supervisory team: Uwe Ohler and Esteban O. Mazzoni
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-): Biogenesis and function of circular and other ncRNAs in development
Supervisory team: Nikolaus Rajewsky and Claude Desplan
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-): Subcellular mRNA localization and translation in mESC derived neurons
Supervisory team: Marina Chekulaeva and Esteban O. Mazzoni
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
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.