Research experience

Staff scientist [2013-present]

Institut Pasteur (Paris, France), Computational Imaging & Modeling Uniit

  • Development of quantitative imaging methods to study the spatial-temporal dimension of transcription

In a collaboration with E. Bertrand (IGMM Montpellier), we used the MS2 approach to analyze transcription of an HIV reporter in live cells . We found that HIV-1 RNA synthesis is achieved by groups of evenly spaced polymerases that move synchronously as a polymerase convoy. We further showed that different promoter elements control stochasticity on specific time-scales, suggesting that promoter architecture may be tailored to produce transcripts with a specific temporal sequence.

I currently focus on projects investigating the spatial dimension of transcription at different scales. First, we study non-random mRNA molecules distribute within cells, and develop tools to identify and quantify these non-random mRNA localisation patterns. Second, I work on projects to infer and qualitatively describe mRNA localisation in the context developing embryos or tissue, e.g. to spatially localize different cell types.

Postdoc [2010-2013]

Ecole Normale Supérieure (Paris, France), Functional Imaging and Transcription Group

Institut Pasteur (Paris, France), Computational Imaging & Modeling Group

  • Development of computational tools for automatic detection and quantification of mRNA-FISH and MS2 data to study gene expression in single-cells.

The experience of my first Postdoc, fuelled my interested in transcription. To pursue this interest, I did a joint-PostDoc in the labs of Xavier Darzacq (ENS Paris) and Christophe Zimmer (Institut Pasteur). These groups started together with the group of Edouard Bertrand (IGMM Montpellier) an effort to study gene expression in live and fixed cells. I occupied a central role in this project by developing and implementing the necessary image analysis and modelling tools.

A central development was the analysis software FISH-quant allowing to measure mature and nascent mRNA levels in individual cells from 3D smFISH images. This software is now widely used by main research labs for the analysis of data in different organism from yeast to drosophila embryos.

We used FISH-quant to study the transcriptional regulation of the proto-oncogene c-Fos. We investigated how the activating transcription factors (TF) affect c-FOS bursting. We linked TF concentration with transcription burst frequency, TF-DNA association with burst duration, and TF transactivation domain strength with polymerase initiation frequency. This work illustrates how TFs can regulate different bursting parameters, offering a vast, evolutionarily tunable knob.

Postdoc [2009-2010]

National Institutes of Health (USA, Bethesda), Fluorescence Imaging Group

  • Implementation of Monte Carlo simulations to study limitations of competition ChIP experiments. Development and validation of an improved analytical model to analyze competition ChIP data.
  • Cross-validation of in-vivo measurement of binding rates by FRAP and FCS (Fluorescence Correlation Spectroscopy). Investigation of the role of reversible photobleaching in FRAP.

After finishing my PhD I decided to stay for two more years in the group of Dr. McNally to complete some of the projects that I had begun near the end of my thesis work. Most notably, I was working on a project to model data from a biochemical assay which also allows measurement of DNA binding in-vivo (competition ChIP-chip, collaboration with the lab of Jason Lieb). In order to successfully work on this project I had to acquired the skills needed to critically evaluate these experiments, both from an experimental and a theoretical perspective.

Predoctoral fellow [2005-2008]

National Institutes of Health (USA, Bethesda), Fluorescence Imaging Group

  • Investigation of the in-vivo binding behavior of nuclear proteins by combining live-cell microscopy and mathematical modeling. This involved the development and improvement of FRAP procedures.
  • Involved in various collaborative projects and development of novel tools for visualization and classification of FRAP data for different research questions.

I obtained a master degree in computational physics from the Karl-Franzens University Graz (Austria). During the final years of this program I developed an interest in biophysical methods used in cell biology. For his master thesis I then conducted research at the Technical University Graz and I developed a numeric simulation environment which allowed a detailed investigation of the underlying assumptions in FRAP (Fluorescence Recovery After Photobleaching) experiments. This experience fueled my interest to pursue a scientific career area and I decided to continue working on this topic as a graduate student.

Therefore, I joined the lab of Dr. James McNally at NIH as a graduate student in March 2005. Dr. McNally is one of the leading experts in the study of the nuclear mobility of proteins by in-vivo microscopy approaches like FRAP. The general aim of my doctoral thesis was to investigate the in-vivo binding behavior of nuclear proteins to nuclear scaffolds like DNA with a special focus on extracting quantitative information from microscopy experiments. I obtained the necessary quantitative background to work on this project from the master program. The group of Dr. McNally and the NIH provided an excellent framework to learn the other necessary skills.

I obtained extensive training in imaging techniques such as FRAP and FCS (Fluorescence Correlation Spectroscopy) which encompassed the entire workflow from data acquisition and processing to the quantification. I also completed several courses of the Biotrac-Program at NIH to get practical training in various wet-lab procedures (Tissue culture, molecular biology techniques). Furthermore I attended a number of seminar and lecture series at NIH with a focus on nuclear cell biology and transcription to further deepen my biological knowledge. In addition I was involved in a number of collaborative research projects which not only allowed me to directly apply my acquired knowledge, it was also of invaluable help for me to learn how to successfully work in an international interdisciplinary environment.