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 scientific software developer in the Fries Lab at ESI.
I received my PhD in bioinformatics at the Molecular Bioinformatics group of Prof. Dr. Ina Koch at Goethe-University Frankfurt in 2016. I have industry experience as a software engineer at Molecular Health and systems administrator at New Horizons CLC.
I have contributed to a range of open source projects and I am the author and maintainer of some neuroimaging software tools, including the freesurferformats and fsbrain packages for R, and libraries providing access to neuroimaging data for C++, Julia, Rust and Python. You can find the source code for some of my projects on my github profile.
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Current work
I am a scientific software developer in the Fries Lab at ESI, working on the syncopy Python package for electrophysiology data analysis.
Previous projects
Ecker Lab
I was 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 from 03/2018 - 04/2022. We used structural magnetic resonance imaging (sMRI) in combination with genetic data to
uncover the mechanisms of autism spectrum disorders. We applied statistical and machine learning methods implemented in R, Python and Matlab to surface-based cortical reconstructions generated with Freesurfer. See the website of the Laboratory of Neuroimaging and the list of publications below for more details.
Visualization of neuroimaging data, created with fsbrain. A Visualization of raw morphometry data (cortical thickness) from native space on the white surface of a subject. The view shows the data in tiles from 8 different angles. B Arbitrary data (p-values in this case) visualized on the regions of the Desikan atlas, using the surface of the fsaverage (standard space template) subject from FreeSurfer. The view shows the data in tiles from 4 different angles. C The regions of the Desikan atlas on the white surface of a subject. The colors were loaded from the respective annotation file.
Koch Lab
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
Here are my records on ORCID and Google Scholar, which may be more up-to-date than this list.
Journal Articles (Peer reviewed)
- Bienek, V., Bletsch, A., Mann, C., Schaefer, T., ..., Ecker, C. (2021) Longitudinal Changes in Cortical Thickness in Adolescents with Autism Spectrum Disorder and Their Association with Restricted and Repetitive Behaviors. Genes 2021, 12(12). doi.org/10.3390/genes12122024
- Ecker, C., Pretzsch, C. M., Bletsch, A., Mann, C., Schaefer, T., Ambrosino, S., ... & Murphy, D. G. (2021). Interindividual Differences in Cortical Thickness and Their Genomic Underpinnings in Autism Spectrum Disorder. American Journal of Psychiatry, appi-ajp. doi.org/10.1176/appi.ajp.2021.20050630
- Bletsch, A., Schäfer, T., Mann, C., Andrews, D. S., Daly, E., Gudbrandsen, M., ... & Ecker, C. (2021). Atypical measures of diffusion at the gray‐white matter boundary in autism spectrum disorder in adulthood. Human brain mapping, 42(2), 467-484. doi.org/10.1002/hbm.25237
- Schäfer, T., Mann, C., Bletsch, A., Zimmermann, J., Seelemeyer, H., Herøy, N., & Ecker, C. (2021). Die Kortexdicke bei Autismus-Spektrum-Störung wird moduliert durch eine komorbide Aufmerksamkeitsdefizit-/Hyperaktivitätsstörung. Kindheit und Entwicklung. doi.org/10.1026/0942-5403/a000329
- Caroline Mann, Tim Schäfer, Anke Bletsch, Maria Gudbrandsen, Eileen Daly, John Suckling, Edward T. Bullmore et al. Examining volumetric gradients based on the frustum surface ratio in the brain in autism spectrum disorder. Human brain mapping 42, no. 4 (2021): 953-966. doi.org/10.1002/hbm.25270
- 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)]
Preprints and Other Articles (Non-Peer Reviewed)
- Viola Hollestein, Geert Poelmans, Natalie J Forde, Christian F Beckmann, Christine Ecker, Caroline Mann, Tim Schäfer,..., Jilly Naaijen. (2021) Excitatory/inhibitory imbalance in autism: the role of glutamate and GABA gene-sets in symptoms and cortical brain structure Preprint at biorxiv
- Tim Schäfer and Christine Ecker. (2020) fsbrain: an R package for the visualization of structural neuroimaging data. Preprint at biorxiv
- 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 and Christine Ecker. Managing and Visualizing Freesurfer Neuroimaging Data in R – the Freesurferformats and Fsbrain Packages. INSAR 2020 Annual Meeting, (virtual), June 3 (2020). [Abstract] [ePoster]
- 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