Tim Schäfer -- rcmd.org/ts/
current work || projects || publications || contact
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This is the professional website of Dr. Tim Schäfer. I am a bioinformatician and currently a postdoc in computational neuroimaging at the Laboratory of Neuroimaging, University Hospital Frankfurt, Germany.
I finished my doctorate in bioinformatics at the Department of Molecular Bioinformatics (group of Prof. Dr. Ina Koch) at Goethe-University Frankfurt in 2016. I also worked in the industry as a software engineer, system administrator, and IT trainer. You can find the source code for some of my projects on my github profile.
I am the author and maintainer of some neuroimaging software tools, including the freesurferformats and fsbrain packages for GNU R, and the brainload module for Python.
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Current work
I am a postdoc in Computational Neuroimaging at University Hospital Frankfurt, Department of Child
and Adolescent Psychiatry, Psychosomatics and Psychotherapy in the group of Prof Christine Ecker. We use magnetic resonance imaging (MRI) in combination with computational methods to
uncover the mechanisms of mental disorders. See the website of the Laboratory of Neuroimaging for more details.
Brain surface mesh.
Previous projects
I finished my doctorate in 2016 and mainly worked on the following two projects in the fields of digital pathology and structural biology:
Digital pathology: The spatial distribution of immune cells in Hodgkin lymphoma
In this project, I worked on the analysis of Hodgkin lymphoma, a cancer of the lymphatic system, based on high-resolution images. We were interested in better understanding the way tumour cells interact with their environment, communicate and spread through the lymphatic system. We implemented a digital image analysis pipeline to perform cell detection, description and classification.
We used graphs to model and compare spatial cell distributions in different Hodgkin lymphoma subtypes as well as lymphadenitis. This is a collaboration with the Senckenberg Institute of Pathology at University Hospital Frankfurt.
Part of a whole slide image from a Hodgkin lymphoma case. Cell nuclei are stained in blue, and CD30+ cells in red. A cell graph is displayed as an overlay. Each vertex represents a cell detected by our imaging pipeline. Edges are added between cells which are close to each other. The graphs can be used to quantify clustering and to compare cell distributions.
Structural biology: The new Protein Topology Graph Library (PTGL) webserver
My diploma thesis dealt with modeling protein structure topologies by graph-theoretical methods. A part of the thesis was the development of the Visualization of Protein Ligand Graphs (VPLG) software. VPLG computes and visualizes protein ligand graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. The graphs can be saved to a database or exported in standard graph formats for further analysis.
VPLG is free software and available from the project websites at Sourceforge and GitHub. It powers the PTGL protein topology database, a web server which also supports motif detection and other advanced queries based on the graphs computed for all proteins of the RCSB Protein Data Bank.
From 3D atom data to protein graph. The 3D atom coordinates and the secondary structure assignments are used to compute contacts between secondary structure elements (SSEs). In the final cell graph, each vertex represents an SSE, and edges model spatial contacts and relative spatial orientations between SSEs.
Publications
Journal Articles (Peer reviewed)
- Jennifer Hannig, Hendrik Schäfer, Jörg Ackermann, Marie Hebel, Tim Schäfer, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann and Ina Koch. Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma. PLOS Computational Biology, 2020. DOI: 10.1371/journal.pcbi.1007516 [Article at PLOS Computational Biology (Open Access)]
- Ina Koch and Tim Schäfer. Protein super-secondary structure and quaternary structure topology: theoretical description and application. Current Opinion in Structural Biology 50:134-143, 2018. DOI: 10.1016/j.sbi.2018.02.005
- Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, and Ina Koch. The new Protein Topology Graph Library web server. Bioinformatics, 32(3):474–476, 2016. DOI: 10.1093/bioinformatics/btv574 [Abstract at Oxford Bioinformatics]
- Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch. CD30 cell graphs of Hodgkin lymphoma are not scale-free -- An image analysis approach. Bioinformatics, 32(1):122–129, 2016. DOI 10.1093/bioinformatics/btv542 [Abstract at PubMed]
- Tim Schäfer, Hendrik Schäfer, Alexander Schmitz, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch. Image database analysis of Hodgkin lymphoma. Computational Biology and Chemistry 46C:1-7, 2013. DOI 10.1016/j.compbiolchem.2013.04.003 [Article DOI link]
- Tim Schäfer, Patrick May, and Ina Koch. Computation and Visualization of Protein Topology Graphs Including Ligand Information. German Conference on Bioinformatics 2012 (Proceedings). [Article DOI link (Open Access)]
Other Articles (Non-Peer Reviewed)
- Jennifer Scheidel, Hendrik Schäfer, Jörg Ackermann, Marie Hebel, Tim Schäfer, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch. Bioinformatics analysis quantifies neighborhood preferences of
cancer cells in Hodgkin lymphoma. DOI: http://dx.doi.org/10.1101/22898, Preprint at bioRxiv
- Alexander Schmitz, Tim Schäfer, Hendrik Schäfer, Claudia Döring, Jörg Ackermann, Norbert Dichter, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch. Automated Image Analysis of Hodgkin lymphoma. Dagstuhl Seminar 12291 "Structure Discovery in Biology: Motifs, Networks & Phylogenies". arXiv:1209.3189 [q-bio.TO]
Conference Talks
- Tim Schäfer, Caroline Mann, Anke Bletsch, Eva Loth, Declan Murphy, Jan Buitelaar, Tony Charman, Tobias Banaschewski, Simon Baron-Cohen, Sven Bölte, Sarah Durston, the EU-AIMS LEAP consortium and Christine Ecker. Atypical Scaling Between the Inner and Outer Curvature of the Brain in Autism Spectrum Disorder. INSAR Annual Meeting 2019, Montreal, Canada, May 1-4 (2019).
- Tim Schäfer, Patrick May, and Ina Koch. Computation and Visualization of Protein Topology Graphs including ligand information. Talk at German Conference on Bioinformatics 2012, Jena, Germany [slides @figshare, @f1000]
- Tim Schäfer, Hendrik Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch. Analysis of the distribution of CD30+ cells in classical Hodgkin lymphoma and Lymphadenitis using graph-based methods. Talk at 99. Jahrestagung der Deutschen Gesellschaft für Pathologie, Frankfurt am Main, Germany (2015). [Slides at figshare, Abstract published in the journal 'Der Pathologe'. Edition 36, Supplement 1, May 2015 (PDF)]
- Tim Schäfer, Hendrik Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch. CD30 cell graphs of Hodgkin lymphoma are not scale-free -- an image analysis approach. Highlight talk at Intelligent Systems for Molecular Biology 2016. Orlando, FL, USA [slides @slideshare]
Posters and Conferences
- Tim Schäfer, Caroline Mann, Anke Bletsch, Eva Loth, Declan Murphy, Jan Buitelaar, Tony Charman, Tobias Banaschewski, Simon Baron-Cohen, Sven Bölte, Sarah Durston, the EU-AIMS LEAP consortium and Christine Ecker. Atypical Scaling Between the Inner and Outer Curvature of the Brain in Autism Spectrum Disorder. OHBM 2019, Rome, Italy, June 9-13 (2019).
- Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann and Ina Koch. Graph-based analysis of CD30+ cell distributions in Hodgkin Lymphoma. ISMB 2016, Orlando, FL, USA, July 8-12 (2016).
- Tim Schäfer, Ben Haladik, Julian Gruber-Roet, Andreas Scheck and Ina Koch. The Protein Topology Graph Library web server. ISMB 2016, Orlando, FL, USA, July 8-12 (2016). [@f1000]
- Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann and Ina Koch. Graph-based analysis of CD30+ cell distributions in Hodgkin Lymphoma. GCB 2015, Dortmund, Germany, September 27-30 (2015). Abstracts at PeerJ
- Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann and Ina Koch. Spatial distribution of cells in Hodgkin Lymphoma. GCB 2013, Göttingen, Germany, September 10-13 (2013)
[@figshare, @f1000]
- Tatiana Bakirova, Tim Schäfer, Ina Koch. Comparison of protein topology graphs using graphlet-based methods. GCB 2013, Göttingen, Germany, September 10-13 (2013) [@figshare, @f1000]
- Tim Schäfer and Ina Koch. Computation and Visualization of Protein Topology Graphs including ligand information. GCB 2012, Jena, Germany [@f1000, @figshare]
- Tim Schäfer, Patrick May and Ina Koch. Extension of protein topologies by ligand interactions: computation and visualization. Molecular Life Sciences 2011. Frankfurt, Germany, September 25-29 (2011). [@figshare]
- Tim Schäfer, Patrick May and Ina Koch.Analysis of protein topology by graph theoretical methods. German Conference on Bioinformatics 2011. Weihenstephan, Germany, September 7-9 (2011).
- A. Schmitz, T. Schäfer, H. Schäfer, C. Döring, J. Ackermann, N. Dichter, S. Hartmann, M.-L. Hansmann, and I. Koch. Automated Image Analysis of Hodgkin lymphoma. German Conference on Bioinformatics, Jena, Germany, September 19-22 (2012). [@figshare]
Contact
My email address is:
You can also contact me on Research Gate or find my office phone number and address at KGU on the website of the Laboratory of Neuroimaging.
current work || projects || publications || contact