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| + | ==== Dr. Dominik Kopczynski ==== | ||
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| + | | E-Mail: | [vorname].[nachname]{{:staff:at.gif|}}tu-dortmund.de| | ||
| + | | ORCID: | [[http://orcid.org/0000-0001-5885-4568|http://orcid.org/0000-0001-5885-4568]] | | ||
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| + | ==== Teaching (in German) ==== | ||
| + | == Sommersemester 2015 == | ||
| + | * Vorlesung [[staff:kopczynski:algoseq|Algorithmen auf Sequenzen]] | ||
| + | == Wintersemester 2014/15 == | ||
| + | * [[:teaching:ep1415sopra | Praktikum]] der Exportveranstaltung [[/people/rudolph/teaching/lectures/EINI/WS2014-15/lecture.jsp | Einführung in die Programmierung]] | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/pg583|PG 583 "Algorithmen zur Entdeckung krebsauslösender Genvarianten"]] | ||
| + | == Sommersemester 2014 == | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/pg583|PG 583 "Algorithmen zur Entdeckung krebsauslösender Genvarianten"]] | ||
| + | == Wintersemester 2013/14 == | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/pg572-imobspi|PG 572 "IMobSPi"]] | ||
| + | == Sommersemester 2013 == | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/pg572-imobspi|PG 572 "IMobSPi"]] | ||
| + | == Wintersemester 2012/13 == | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/pg-567-computational-epigenomics|PG 567 "Computational Epigenomics"]] | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/ps-python|Proseminar "DAP mit Python"]] | ||
| + | == Sommersemester 2012 == | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/pg-567-computational-epigenomics|PG 567 "Computational Epigenomics"]] | ||
| + | * Betreuung [[http://www.rahmannlab.de/lehre/ps-python|Proseminar "DAP mit Python"]] | ||
| + | == Wintersemester 2011/12 == | ||
| + | * Praktikum [[http://www.rahmannlab.de/lehre/v-computational-omics | Computational Omics]] | ||
| + | == Sommersemester 2011 == | ||
| + | * Übung [[http://www.rahmannlab.de/lehre/v-algo-seq | Algorithmen auf Sequenzen]] | ||
| + | == Wintersemester 2009/10 == | ||
| + | * Praktikum [[http://ls5-www.cs.tu-dortmund.de/html/EIP-Praktikum-0910.htm|EINI]] | ||
| + | == Sommersemester 2009 == | ||
| + | * Praktikum [[http://ls11-www.cs.tu-dortmund.de/people/gutweng/DAP2-09/dap2p.jsp|DAP2]] | ||
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| + | |||
| + | ==== Research Topics ==== | ||
| + | * Resource-constrained analysis of spectrometry data | ||
| + | * Online peak parametrization in [[http://www.rahmannlab.de/research/ims|IMS]] measurements | ||
| + | * Prediction of spectra in [[http://www.rahmannlab.de/research/ims|IMS]] measurements | ||
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| + | ==== Supervised and Co-supervised Diploma / Bachelor / Master Theses ==== | ||
| + | List of ongoing and completed Theses: | ||
| + | * Helge Michels (D): Bestimmung des Potentials volatiler Metabolite der Saccharomyces cerevisiae in silico, 2015 | ||
| + | * Benjamin Borchert (B): Partitionierung von DNS-Reads anhand gegebener Strukturdefinitionen, 2015 | ||
| + | * Tom Eckelmann (D): Probabilistisches Flowgram-String Alignment, 2014 | ||
| + | * Till Hartmann (B): Automatisierte Bestimmung verwendeter Adapter bei DNA-Sequenzierung, 2014 | ||
| + | * Henning Funke (B): Fast Analysis of MCC/IMS Data using GPGPU Programming, 2013 | ||
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| + | ==== Publications ==== | ||
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| + | == Conference Paper == | ||
| + | * Dominik Kopczynski, Sven Rahmann. {{http://link.springer.com/content/pdf/10.1007%2F978-3-662-44753-6_18.pdf|An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data}}. //Proceedings of the 14th Workshop on Algorithms in Bioinformatics (WABI 2014)//, Wrocław, Poland, 2014. | ||
| + | * Dominik Kopczynski, Jörg Ingo Baumbach, Sven Rahmann. {{http://www.eurasip.org/Proceedings/Eusipco/Eusipco2012/Conference/papers/1569581297.pdf|Peak Modeling for Ion Mobility Spectrometry Measurements}}. //Proceedings of the 20th European Signal Processing Conference (EUSIPCO 2012)//, Bucharest, Romania, 2012. | ||
| + | |||
| + | == Journal Paper == | ||
| + | * Dominik Kopczynski, Sven Rahmann. {{http://www.almob.org/content/10/1/17/abstract|An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data}}. //Algorithms for Molecular Biology//, 10(1):17, 2015. | ||
| + | * Dominik Kopczynski, Sven Rahmann. {{http://arxiv.org/pdf/1405.5501v1.pdf|Using the Expectation Maximization Algorithm with Heterogeneous Mixture Components for the Analysis of Spectrometry Data}}. //arXiv:1405.5501,// (under review). | ||
| + | * Marianna D'Addario, Dominik Kopczynski, Jörg Ingo Baumbach, Sven Rahmann. {{http://www.biomedcentral.com/content/pdf/1471-2105-15-25.pdf|A modular computational framework for automated peak extraction from ion mobility spectra}}. //BMC Bioinformatics//, 15(1):25, 2014. | ||
| + | * Anne-Christin Hauschild, Dominik Kopczynski, Marianna D'Addario, Jörg Ingo Baumbach, Sven Rahmann, Jan Baumbach. {{http://www.mdpi.com/2218-1989/3/2/277/pdf|Peak Detection Method Evaluation for Ion Mobility Spectrometry by Using Machine Learning Approaches}}. //Metabolites//, p277-293, 2013. (Metabolites best paper award 2015) | ||
| + | |||
| + | == Poster == | ||
| + | * Dominik Kopczynski, Sven Rahmann. {{:staff:kopczyns:online-poster.pdf|An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data}}. //18th German Conference on Bioinformatics (GCB 2014)//, Bielefeld Germany, 2014. | ||
| + | * Dominik Kopczynski, Sven Rahmann. {{:staff:kopczyns:meds-for-bs.pdf|A Memory-Efficient Data Structure for Pattern Matching in DNA with Backward Search}}. //17th German Conference on Bioinformatics (GCB 2013)//, Göttingen Germany, 2013. | ||
| + | * Dominik Kopczynski, Marianna D'Addario, Jörg Ingo Baumbach, Sven Rahmann. {{:staff:kopczyns:poster-pipeline.png?linkonly|Automated Peak Extraction for MCC/IMS Measurements of Exhaled Breath}}. //International Conference on Breath Research (Breath 2013)//, Wallerfangen Germany, 2013. | ||
| + | * Anne-Christin Hauschild, Dominik Kopczynski, Marianna D'Addario, Jörg Ingo Baumbach, Sven Rahmann, Jan Baumbach. {{:staff:kopczyns:bitmap-poster.png?linkonly|Evaluation of Peak Detection Methods for MCC/IMS Measurements in Clinical Breath Studies}}. //International Conference on Breath Research (Breath 2013)//, Wallerfangen Germany, 2013. | ||
| + | * Dominik Kopczynski, Sven Rahmann. {{:staff:kopczyns:approx-bs-kopczynski.pdf|An Automaton-Based View on Error-Tolerant Pattern Matching with Backward Search}}. //16th German Conference on Bioinformatics (GCB 2012)//, Jena Germany, 2012. | ||
| + | * Dominik Kopczynski, Sven Rahmann. {{:staff:kopczyns:doktorandenkolleg-2011-kopczynski.pdf|Resource-Constrained Analysis of Spectrometry Data}}. //At the Doktorantenkolleg Informatik Ruhr 2011//, Valbert Germany, 2011. | ||
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| + | == Invited Talks == | ||
| + | * {{:staff:kopczyns:kdml-talk-kopczynski-2012.pdf|Peak Modeling for Ion Mobility Spectrometry Measurements}}. //14th Workshop on Knowledge Discovery, Data Mining and Machine Learning (KDML 2012)//, Dortmund, Germany, Sep. 12, 2012. | ||
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| + | == Tech Reports == | ||
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| + | * Dominik Kopczynski. {{{{:techreports:tr11-04.pdf|Datenreduktion und Merkmalsextraktion bei IMS-Messungen}}. Technische Universität Dortmund, 2011. | ||
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| + | ==== Brief Biography ==== | ||
| + | Currently I am a PhD student at TU Dortmund, Department of Computer Science, Chair of Algorithm Engineering within the group Bioinformatics for High-Throughput Technologies of Prof. Dr. Sven Rahmann. | ||
| + | Between 2004 and the end of 2010, I studied computer science with a focus on intelligent systems and algorithmic at TU Dortmund. | ||
| + | * 01/2011 - today: PhD student at the Department of Computer Science, Chair of Algorithm Engineering within the group Bioinformatics for High-Throughput Technologies at TU Dortmund, Dortmund, Germany | ||
| + | * 10/2004 - 06/2010: Diploma student in Computer Science at TU Dortmund, Dortmund, Germany | ||