Tim Schäfer -- rcmd.org/ts/

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This is the professional website of Tim Schäfer. I am a bioinformatician, currently employed as software developer at Molecular Health, Heidelberg, Germany. I finished my Ph.D. at the Department of Molecular Bioinformatics (group of Prof. Dr. Ina Koch) at Goethe-University Frankfurt am Main, Germany in November 2016. Before starting my Ph.D., I studied Bioinformatics at Goethe-University. I have also worked as a programmer, system administrator, and IT trainer.





Current work


I currently work as a software developer at Molecular Health GmbH in Heidelberg, Germany.

PhD projects


Digital pathology: The spatial distribution of immune cells in Hodgkin lymphoma

We are working on the analysis of Hodgkin lymphoma, a cancer of the lymphatic system, based on high-resolution images. In this project, we are 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 University Hospital Frankfurt, Dr Senckenberg Institute of Pathology.

Hodgkin lymphoma cell graph

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.

Protein structure

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)



Other Articles (Non-Peer Reviewed)



Conference Talks



Posters and Conferences

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CV




DateJob and description
2016-11 to presentSoftware developer at Molecular Health GmbH, Heidelberg, Germany
2011-09 to 2016-10Ph.D. student and Wissenschaftlicher Mitarbeiter at Goethe-University, Frankfurt am Main, Germany
  • Dissertation on Nov 24, 2016 (Dr. rer. nat., summa cum laude)
  • Ph.D. thesis submitted on May 31, 2016. Title: Application of Graph Theory to the Topologies of Proteins and Hodgkin Lymphoma
  • Image analysis and mathematical modeling of Hodgkin Lymphoma
  • Computation and analysis of Protein topology graphs
  • Teaching
2005-10 to 2011-07Diploma in Bioinformatics at Goethe-University, Frankfurt am Main, Germany
  • Overall grade: 1.1 (Very good)
  • Diploma thesis: Analysis of protein topologies using graph-theoretical methods
    • Grade for thesis: 1.0 (Very good)
  • Worked as a tutor at Goethe-University during studies
2006-10 to 2008-10Freelance IT-Trainer, Frankfurt am Main, Germany
  • Part-time job to pay for studies
  • Preparation and Implementation of technical IT courses (Linux Server and Network Administration)
  • Worked for New Horizons CLC Kassel GmbH, GENIUS Education GmbH
2005-07 to 2005-09Programmer and IT-Trainer at New Horizons Computer Learning Center Kassel GmbH, Kassel, Germany
  • Programming (Java, PHP)
  • System administration Windows and Linux
  • Technical IT support (Windows)
  • Preparation and Implementation of technical IT courses (Linux Server and Network Administration)
2002-08 to 2005-06Industrial training as Application Programmer at New Horizons Computer Learning Center Kassel GmbH, Kassel, Germany
  • Grade: very good / good
  • Tasks
    • Programming (Java, PHP, C++)
    • System administration Windows and Linux
    • Network and security administration Linux
  • I took additional commercial courses and exams to be able to work as an IT-Trainer, including:
    • Microsoft Certified Professional (MCP) certification
    • Linux Professional Institute LPIC-1 certification
2001-10 to 2002-07Studied Biology at University Kassel, Kassel, Germany
2000-09 to 2001-08Alternative civilian service at Klinikum Wahrendorff GmbH, Sehnde, Germany
1993-07 to 2000-07Abitur at Gymnasium Gross Ilsede, Germany


Professional profiles on other websites


Here are my profiles at BeKnown/Monster, Research Gate, Xing, and LinkedIn.

Contact and Imprint


Feel free to contact me via email. My email address is:

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Please do not use my address at Goethe-University any more.

Imprint






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