Martin Strauch

PhD student

Martin Strauch .

Universität Konstanz
Fachbereich Biologie

D-78457 Konstanz, Germany

Tel: +49-7531-88-2102

room: M 1124a

email: martin.strauch/-/uni-konstanz.de

web: https://neuro.uni-konstanz.de

Curriculum vitae

since 2007 : University of Konstanz, Germany (Department of Neurobiology, associated with the DFG graduate school for computer science)

2003            : Flinders University, Adelaide, Australia

2000-2007 : University of Tübingen, Germany (diploma in computer science/bioinformatics)

Neuroinformatics: Video mining, pattern detection

In the BMBF-funded project 'Olfactory Coding', we are working towards understanding how information about odorant stimuli is represented and processed in the brain of insects. We are particularly interested in the antennal lobe of the honeybee Apis mellifera .

My part in this project is the analysis of optical recordings from the antennal lobe, a brain compartment that collects and processes information from olfactory receptor neurons. Combinatorial activity patterns of cells called glomeruli encode the identiy of odorants.
Using calcium-imaging techniques we are able to record movies that show these patterns over time in the resting state and when an odorant stimulus is presented.

I am developing methods to automatically extract glomerular patterns from batch recordings as well as from video streams. In the end, hours of raw recordings are condensed to clean spatio-temporal activity patterns that are then subject to higher-level data analysis.

My collaborators in this project are:
Julia Rein , Giovanni Galizia (Konstanz), Thomas Nowotny (Informatics, Sussex), Ina Klinke, Michael Schmuker , Randolf Menzel (Neurobiology, FU Berlin)

References: [3], [A1-3, A5]

Bio-/Neuroinformatics: Integrating heterogeneous datasets

Suppose we want to know as much as possible about odorant responses of this tiny and strange insect called Drosophila melanogaster , i.e. which odorants elicit which response in which olfactory receptor neuron.

Suppose we are also a bit lazy and think that others have already performed a lot of nice experiments that each give us a part of the answer. Unfortunately, they worked on their own, using different techniques: some recorded spikes, others changes in calcium concentration.

In our DoOR (Database of Odorant Responses) project we propose a method for joining all of these datasets together, resulting in a comprehensive data repository.

My collaborators in this project are: Shouwen Ma, Daniel Münch, Anja Nissler, C. Giovanni Galizia (Konstanz)

References: [A4]

Bioinformatics: Gene expression, bayesian networks, biclustering

During my time in the group of Andreas Zell (ZBIT, Tübingen) I contributed to the JCell project:
Jcell - A Java based framework to reconstruct genetic interactions from microarray data.

Later, in my diploma thesis, I developed algorithms for the analysis of three-dimensional (genes, time, experimental conditions) gene expression data.

The project was a collaboration with Jochen Supper (Bioinformatics, Tübingen) and Dierk Wanke (Plant Physiology, Tübingen) .
We characterised the gene regulatory response of Arabidopsis thaliana to abiotic stress factors.

Matlab sources and datasets from this project can be found here .

References: [1,2]

Strauch M, Lüdke A, Münch D, Laudes T, Galizia CG, Martinelli E, Lavra L, Paolesse R, Ulivieri A, Catini A, Capuano R, Di Natale C (2014) More than Apples and Oranges - Detecting Cancer with a Fruit Fly’s Antenna.
Scientific Reports
4 (January 6, 2014). doi:10.1038/srep03576.

Strauch M, Müthing C, Broeg MP, Szyszka P, Münch D, Laudes T, Deussen O, Galizia CG, Merhof D (2013)
The looks of an odour - Visualising neural odour response patterns in real time.
BMC Bioinformatics 2013, 14(Suppl 19):S6

Beran J, Weiershaeuser A, Galizia CG, Rein J, Smith BH, Strauch M (2013)
On piecewise polynomial regression under general dependence conditions, with an application to calcium-imaging data.
Sankhya B

Julia Rein, Julie A. Mustard, Martin Strauch, Brian H. Smith, C. Giovanni Galizia:
Octopamine modulates activity of neural networks in the honey bee antennal lobe,
Journal of Comparative Physiology A, May 2013

Martin Strauch, Julia Rein, Christian Lutz,  C. Giovanni Galizia:(2013)
Signal extraction from movies of honeybee brain activity by convex analysis: The ImageBee plugin for KNIME,
extended journal version, BMC Bioinformatics 14: (Suppl 18):S4 

Strauch M, Ditzen M, Galizia CG (2012)
Keeping their distance? Odor response patterns along the concentration range.
Front Syst Neurosci doi: 10.3389 / fnsys.2012.00071

Martin Strauch, Marc P. Broeg, Clemens Müthing, Paul Szyszka, Oliver Deussen, C. Giovanni Galizia, Dorit Merhof (2012)
INCIDE the brain of a bee: Visualising honeybee brain activity in real time by semantic segmentation.
Proceedings of BioVis 2012, Seattle (USA),
(download preprint)

[6] Martin Strauch, Julia Rein , C.Giovanni Galizia (2012)
Signal extraction from movies of honeybee brain activity by convex analysis.
Proceedings of ICCABS, Las Vegas (USA), IEEE, 2012
(link to PDF)
(download preprint)

[5] Martin Strauch, C.Giovanni Galizia (2011)
Fast PCA for Processing Calcium-imaging Data from the Brain of Drosophila Melanogaster.
Proceedings of DTMBIO'11, ISBN: 978-1-4503-0717-8, pp 3-10, ACM, 2011 
(download PDF)

[4] C.Giovanni Galizia , Daniel Münch, Martin Strauch, Anja Nissler A, Shouwen Ma (2010)
Integrating heterogeneous odor response data into a common response model: A DoOR to the complete olfactome.
Chemical Senses35: 551-563
(download PDF)

[3] Martin Strauch, C.Giovanni Galizia (2008)
Registration to a neuroanatomical reference atlas - identifying glomeruli in optical recordings of the honeybee brain.
Lecture Notes in Informatics , P-136, pp 85-95, 2008
(download preprint) , published in: (GI-Edition LNI)

[2] Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, Andreas Zell (2007)
EDISA: extracting biclusters from multiple time-series of gene expression profiles.
BMC Bioinformatics 8: 334, 2007
(download PDF)

[1] Martin Strauch, Jochen Supper, Christian Spieth, Dierk Wanke, Joachim Kilian, Klaus Harter, Andreas Zell (2007)
A Two-Step Clustering for 3-D Gene Expression Data Reveals the Main Features of the Arabidopsis Stress Response.
Journal of Integrative Bioinformatics 4: 54, 2007
(download PDF)

Bibtex-entries are provided by CSB .

Abstracts in conference proceedings

[A7]Strauch M, Julia Rein, C. Giovanni Galizia (2009)
Pattern mining in spontaneous background activity from the honeybee antennal lobe.
Bernstein Conference on Computational Neuroscience in Frankfurt, Germany, 2009

[A6] Martin Strauch, Christian Lutz, David Samuelson, C. Giovanni Galizia (2009)
Connecting insect brain imaging to data mining tools - a neuroimage extension for the KNIME platform.
Frontiers in Neuroinformatics, read the abstract here
2nd INCF Congress of Neuroinformatics, Pilsen, Czech Republic, Sep 6-8, 2009

[A5] Julia Rein, Martin Strauch, C. Giovanni Galizia (2009)
Novel techniques for the exploration of the honeybee antennal lobe.
Neuroforum Feb 2009(1) Vol.XV, ISSN 0947-0875, Supplement p. 958,
8th Meeting of the German Neuroscience Society, Göttingen, Germany, Mar 25-29, 2009

[A4] Shouwen Ma, Martin Strauch, Daniel Münch, C. Giovanni Galizia (2009)
DoOR - a Database of Odorant Responses.
Neuroforum Feb 2009(1) Vol.XV, ISSN 0947-0875, Supplement p. 957,
8th Meeting of the German Neuroscience Society, Göttingen, Germany, Mar 25-29, 2009

[A3] Ina Klinke, Julia Rein, Michael Schmuker, Martin Strauch, Thomas Nowotny, C. Giovanni Galizia, Randolf Menzel (2008)
The Bernstein Partner project 'Olfactory Coding': A joint effort to reveal the neural basis of olfaction.
Frontiers in Computational Neuroscience , doi:10.3389/conf.neuro.10.2008.01.073
4th Bernstein Symposium, Munich, Germany, Oct 8-10, 2008

[A2] Ina Klinke, Julia Rein, Michael Schmuker, Martin Strauch, Thomas Nowotny, C. Giovanni Galizia, Randolf Menzel (2007)
Olfactory coding: integrating experimental and theoretical approaches.
NNCN meeting : Midterm evaluation of the German National Network for Computational Neuroscience, Proceedings, p 129, Berlin, Germany, Dec 3-4, 2007

[A1] Martin Strauch, Julia Rein, C. Giovanni Galizia (2007)
Towards understanding olfactory information processing in the antennal lobes of Apis mellifera.
3rd Bernstein Symposium for Computational Neuroscience , Proceedings, p 100,
Göttingen, Germany, Sep 24-27, 2007