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staff:kopczynski [2017-12-15 15:59] (current)
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 +{{ :​staff:​dommi.jpg|}}
 +
 +==== Dr. Dominik Kopczynski ====
 +
 +| 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]] |
 +
 +==== 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]]
 +
 +
 +==== 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
 +
 +==== 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
 +
 +==== Publications ====
 +
 +== 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.
 +
 +== 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.
 +
 +== Tech Reports ==
 +
 +  * Dominik Kopczynski. {{{{:​techreports:​tr11-04.pdf|Datenreduktion und Merkmalsextraktion bei IMS-Messungen}}. Technische Universität Dortmund, 2011.
 +
 +
 +==== 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
  
 
Last modified: 2017-12-15 15:59 (external edit)
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