Dr. Sarah Gerster

Homepage www.echinops.ch

Current position

• Since December 2007: Ph.D. student and assistant at the Seminar für Statistik

Research interests

Coming from a computational science and engineering background, I am particularly interested in using computational statistics to solve interdisciplinary problems.

I am collaborating with different labs to focus on:

• protein identification
• protein quantification

From a statistical point of view, this means mostly working on:

• mixture models
• Markovian assumptions on k-partite graphs

Publications

• Gerster, S., Qeli, E., Ahrens, C.H. and Bühlmann, P. (2010). Protein and gene model inference based on statistical modeling in k-partite graphs . PNAS 107(27): 12101-12106.
• Dolenc, J., Gerster, S. and van Gunsteren, W.F. (2010). Molecular Dynamics Simulations Shed Light on the Enthalpic and Entropic Driving Forces That Govern the Sequence Specific Recognition between Netropsin and DNA. J. Phys. Chem. B, 2010, 114 (34): 11164-11172.
• Master thesis (2007). Learning Graphs from Data: A comparison of Different Algorithms with Application to Tissue Microarray Expreriments.

Talks & posters

• Statistical approach to protein quantification presented at ECCB'12 (the European Conference on Computational Biology) in Basel. Co-authors:Christina Ludwig (IMSB), Mariette Matondo (IMSB), Ruedi Aebersold (IMSB) and Peter Bühlmann (SfS).
• Statistical approach to protein quantification presented at the RECOMB Satellite Conference on Computational Proteomics 2012 in San Diego. Co-authors:Christina Ludwig (IMSB), Mariette Matondo (IMSB), Ruedi Aebersold (IMSB) and Peter Bühlmann (SfS).
• Statistical approach to absolute protein quantification presented at the ISMB/ECCB conference, Vienna 2011. Co-author: Peter Bühlmann (SfS).
• Statistical approach to absolute protein quantification presented at the workshop on Statistical Challenges and Biomedical Applications of Deep Sequencing Data, Ascona 2011. Co-author: Peter Bühlmann (SfS).
• Protein identification based on rigorous statistical modeling in bipartite graphs presented at the Statistical advances in Genome-scale Data Analysis - Workshop, Ascona 2009. Joint work with Ermir Qeli (Q-MOP), Christian Ahrens (Q-MOP) and Peter Bühlmann (SfS).

R code

R implementation of the MIPGEM approach for protein and gene model inference (Gerster et al. PNAS 2010).

Personal interests

I am only a part time Ph.D. student in order to have time for all my activities outside of ETH ;-)

Volunteering activities

• since 2008: steering group member of an international working group of Service Civil International, the The Long Term Exchange Group, which aims at strengthening and improving the long term volunteer exchanges within the SCI network.
• since 2006: member of the long term volunteering working group of the Swiss branch of SCI.
• since 2004: part of the crew of the Magasin du Monde in Saignelégier.

Gardening, farming and nature in general

My parents live in the countryside and I have the opportunity to help with many gardening and farming tasks. I especially enjoy:

• apiculture: my mother and I take care of about 10 bee colonies
• orchard: we have over 15 fruit trees (apples, cherries, pears, plums, quince and walnuts). I help to tend and prune the trees as well as to collect and process the harvest.

Playing in a recorder quartet

After over 10 years of recorder lessons, I decided to quit the class in 2002 when I started university. However, I kept meeting 3 of my former fellow students to play together and we finally became the quartet "Les flutes au bec" which still exists today. We meet regularly to play together on a large game of recorders (from sopranino to contra bass). We give concerts 3 or 4 times a year.

Discovering new cultures

• in 2005/2006, after my bachelor's degree, I spent 4 months volunteering in a Russian children's home (in Ulan-Ude, Siberia)
• in 1999/2000 I spent a year in the USA (Houston, TX) as an exchange student during high school
• furthermore, I travelled to many European countries as well as to Cameroon, China, Japan, Moldova, Mongolia and North Korea. I like to get to know local culture and life and hence always combine my journeys either with visiting friends, or with the participation in an SCI project.