{{ :staff:schaefer.png?180|}} ====== Till Schäfer ====== ^ Room | OH 14 / 238 | ^ Phone | +49 231 755-7707 | ^ Fax | +49 231 755-7740 | ^ E-Mail | till2.schaefer{{:staff:at.gif|}}tu-dortmund.de ([[https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79|PGP-Key]]) | ===== Research Interests ===== * Clustering * Subgraph Mining * Visual Analytics * Applications in Cheminformatics ===== Projects ===== * [[http://sourceforge.net/projects/scaffoldhunter/|Scaffold Hunter]] - A free software tool for analysis and exploration of chemical space * OpenTox Euro 2013: [[http://old.opentox.org/meet/opentoxeu2013/opentoxeuro13awards|Best Software Award]] * Google Summer Of Code 2013: [[https://www.google-melange.com/gsoc/project/details/google/gsoc2013/lappie/5662278724616192|Mentored Project]] * Google Summer Of Code 2014: [[https://www.google-melange.com/gsoc/project/details/google/gsoc2014/sturm89/5634387206995968|Mentored Project]] * [[https://www.big-data-spp.de/projects/graph-based-methods-for-rational-drug-design|Graph-Based Methods for Rational Drug Design]] - DFG Priority Programme [[http://www.big-data-spp.de/|Algorithms for Big Data]] (SPP 1736) * [[https://do-foss.de|Do-FOSS (private project)]] ===== Publications ===== All data and source code that is referenced in my publications can be found [[staff:schaefer:publication_data | here]] === Journal Articles === * **[[https://doi.org/10.1002/cmdc.201700689|CHIPMUNK: A Virtual Synthesizable Small‐Molecule Library for Medicinal Chemistry, Exploitable for Protein–Protein Interaction Modulators ]]** \\ Lina Humbeck, Sebastian Weigang, Till Schäfer, Petra Mutzel, Oliver Koch \\ ChemMedChem, 2018. ({{ :staff:schaefer:hws_2018.bib | BIBTEX}}) * Very Important Paper Award * [[https://doi.org/10.1002/cmdc.201800126|Cover Feature]] * [[https://www.big-data-spp.de/publications/awards|Interdisciplinary Award (SPP Big Data)]] * One of the 20 most read ChemMedChem articles in 2017-2018 * **[[https://dx.doi.org/10.1186/s13321-017-0213-3|Scaffold Hunter: A comprehensive visual analytics framework for drug discovery]]** \\ Till Schäfer, Nils Kriege, Lina Humbeck, Karsten Klein, Oliver Koch, Petra Mutzel \\ Journal of Cheminformatics, 9:28, 2017. ([[https://citation-needed.springer.com/v2/references/10.1186/s13321-017-0213-3?format=bibtex&flavour=citation|BIBTEX]]) * **[[https://dx.doi.org/10.7155/jgaa.00338|Practical SAHN Clustering for Very Large Data Sets and Expensive Distance Metrics]]** \\ Nils Kriege, Petra Mutzel, Till Schäfer \\ Journal of Graph Algorithms and Applications (JGAA), vol. 18, no. 4, 577-602, 2014 ([[http://dblp.uni-trier.de/rec/bibtex/journals/jgaa/KriegeMS14|BIBTEX]]) * **[[https://dx.doi.org/10.1002/minf.201300087|Visual Analysis of Biological Activity Data with Scaffold Hunter]]**\\ //Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel and Till Schäfer// \\ Molecular Informatics, WILEY-VCH Verlag, 2013 ([[http://scaffoldhunter.sourceforge.net/klein2013.bib|BIBTEX]]) === Refereed Conference Proceedings === * **[[https://doi.org/10.1007/978-3-030-32047-8_27|Protein Complex Similarity based on Weisfeiler-Lehman labeling]]** ([[https://doi.org/10.7287/peerj.preprints.26612v1|PeerJ Preprints, vol. 6, e26612v1]]) \\ Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils Kriege, Sven Rahmann \\ International Conference on Similarity Search and Applications (SISAP) 2019, 308-322. ([[https://citation-needed.springer.com/v2/references/10.1007/978-3-030-32047-8_27?format=bibtex&flavour=citation|BIBTEX]]) * **[[https://doi.org/10.1007/978-3-319-69179-4_24|StruClus: Scalable Structural Graph Set Clustering with Representative Sampling]]**\\ //Till Schäfer , Petra Mutzel// \\ Advanced Data Mining and Applications (ADMA) 2017, LNCS 10604, pp. 343-359, 2017 ([[https://citation-needed.springer.com/v2/references/10.1007/978-3-319-69179-4_24?format=bibtex&flavour=citation|BIBTEX]]) * **[[http://dx.doi.org/10.2312/cgvc.20151247|Extending the Scaffold Hunter Visualization Toolkit with Interactive Heatmaps]]**\\ //Werner Sturm , Till Schäfer , Tobias Schreck , Andreas Holzinger and Torsten Ullrich// \\ Computer Graphics & Visual Computing (CGVC) 2015, The Eurographics Association ([[https://diglib.eg.org/handle/10.2312/cgvc20151247|BIBTEX]]) * **[[http://dx.doi.org/10.1007/978-3-319-04657-0_11|SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search]]** \\ //Till Schäfer, Petra Mutzel, Nils Kriege// \\ International Workshop on Algorithms and Computation (WALCOM) 2014, LNCS 8344, pp. 90–101, 2014 ([[http://dblp.uni-trier.de/rec/bibtex/conf/walcom/KriegeMS14|BIBTEX]]) === Posters === * **Chemogenomics analysis of small molecule bioactivity data: Privileged scaffolds and conserved structural elements in proteins** \\ Lina Humbeck, Till Schäfer, Nils Kriege, Petra Mutzel, Oliver Koch \\ 10th International Conference on Chemical Structures, Noordwijkerhout, Netherlands, 2014 * **Scaffold Hunter: Visual Analysis of Biological Activity Data** \\ Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer \\ German Conference on Chemoinformatics, Fulda, Germany, 2013. === Technical Reports & Unrefereed Publications === * ** [[https://arxiv.org/abs/1609.09000|arXiv: StruClus: Structural Clustering of Large-Scale Graph Databases]]** \\ //Till Schäfer, Petra Mutzel//, 2016 * ** {{:techreports:tr13-02.pdf|TR13-1-002: Beschleunigung hierarchischer Clusterverfahren für allgemeine metrische Distanzmaße }}** \\ //Till Schäfer//, Diploma Thesis, TU Dortmund, June 2013 ===== Teaching ===== === Online Tutorials === * **[[staff:kriege:opentox2013workshop|Using Scaffold Hunter for the Visual Analysis of Chemical Datasets]]** \\ Nils Kriege, Till Schäfer, Hands-on Workshops, OpenTox Euro 2013, Mainz, **Best Software Award** === Supervised Bachelor/Master/Diploma Theses === * **[[https://www.cs.hhu.de/de/lehrstuehle-und-arbeitsgruppen/algorithmische-bioinformatik/unser-team.html|Sven Schrinner]]**: //Diskriminatives Subgraph Mining in großen Datenmengen mit Hilfe von Sampling-Techniken//, Master Thesis, 2016/17 * **Sven Brümmer**: //Lokale Cluster-Split-Verfahren für repräsentantenbasiertes strukturelles Clustering//, Bachelor Thesis, 2016 * **Nane Wessels**: //Word Clouds - Übersicht über die algorithmischen Varianten und Bewertungskritieren in Bezug auf verschiedene Anwendungsfälle//, Bachelor Thesis, 2016 * **Markus Kloss**: //Multi-Pattern Coverage in Large Graph Data Sets//, Master Thesis, 2015 * **Emil Tanev**: //Berechnung und Visualisierung von Netzwerkumgebungen im Scaffold-Baum//, Bachelor Thesis, 2015 === Courses (in German) === == Sommersemester 2016 == * [[:teaching:seminar-gdm-ss2016 | Seminar Graph Data Mining]] * [[:teaching:seminarae-ss2016 | Seminar Algorithm Engineering]] == Wintersemester 2015/16 == * [[:teaching:seminarae-ws2015 | Seminar Algorithm Engineering]] == Sommersemester 2015 == * [[:teaching:seminarae-ss2015 | Seminar Algorithm Engineering]] == Wintersemester 2014/15 == * [[:teaching:ep1415sopra | Praktikum]] der Exportveranstaltung [[/people/rudolph/teaching/lectures/EINI/WS2014-15/lecture.jsp | Einführung in die Programmierung]] * [[:teaching:seminarae-ws2014 | Seminar Algorithm Engineering]] == Sommersemester 2014 == * [[:staff:schaefer:ea-ueb-2014 | Effiziente Algorithmen (Übung)]] == Wintersemester 2013/14 == * [[:teaching:ep1314sopra | Praktikum]] der Exportveranstaltung [[/people/rudolph/teaching/lectures/EINI/WS2013-14/lecture.jsp | Einführung in die Programmierung]] * [[:teaching:seminarae-ws2013 | Seminar Algorithm Engineering]] == Sommersemester 2013 == * [[:staff:schaefer:ea-ueb-2013 | Effiziente Algorithmen (Übung)]] * [[:teaching:seminarae-ss2013 | Seminar Algorithm Engineering]] == Wintersemester 2012/13 == * [[:teaching:ep1213sopra | Praktikum]] der Exportveranstaltung [[/people/rudolph/teaching/lectures/EINI/WS2012-13/lecture.jsp | Einführung in die Programmierung]] * [[:teaching:seminarae-ws2012 | Seminar Algorithm Engineering]]