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staff:martin [2014-08-01 12:48]
Marcel Martin
staff:martin [2015-09-11 10:19]
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-/* no table of contents */ 
-~~NOTOC~~ 
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-==== Marcel Martin ==== 
- 
-| Room: | 209 | 
-| Phone: | +49 231 755-7745 | 
-| Fax: | +49 231 755-7740 | 
-| E-Mail: | marcel //dot// martin //at// tu //dash// dortmund //dot// de | 
-| ORCID: | http://​orcid.org/​0000-0002-0680-200X | 
- 
-I am a PhD student at [[http://​www.tu-dortmund.de|TU Dortmund]], [[http://​www.cs.uni-dortmund.de|Department of Computer Science]], [[http://​ls11-www.cs.tu-dortmund.de|Chair of Algorithm Engineering]] within the group //​Bioinformatics for High-Throughput Technologies//​ of [[http://​www.rahmannlab.de/​| Prof. Dr. Sven Rahmann]]. 
- 
-==== Teaching ==== 
- 
-  * Winter 2012/13: [[staff:​martin:​algoseq|Algorithmen auf Sequenzen]] (Vorlesung und Übung) 
-  * Summer 2012: [[http://​www.rahmannlab.de/​lehre/​pg-567-computational-epigenomics|Projektgruppe 567 Computational Epigenomics]] 
-  * Winter 2011/12: [[http://​ls1-www.cs.uni-dortmund.de/​cms/​lehre/​blog-2|Einführung in die Informatik für Logistiker und Wirtschaftsingenieure]] 
-  * Summer 2010: [[:​teaching:​angebio | Einführung in die angewandte Bioinformatik]] 
-  * Winter 2009/10: [[http://​eini-lw.wikidot.com | Einführung in die Informatik für Logistiker und Wirtschaftsingenieure]] 
-  * Summer 2009: [[http://​bioinfo.wikidot.com/​ | Einführung in die angewandte Bioinformatik]] 
-  * Winter 2008/9: [[http://​eini-lw.wikidot.com | Einführung in die Informatik für Logistiker und Wirtschaftsingenieure]] 
-  * Summer 2008: [[http://​bioinfo.wikidot.com/​ | Einführung in die angewandte Bioinformatik]] 
-  * Winter 2007/8: Einführung in die Informatik für Logistiker und Wirtschaftsingenieure 
- 
-/* 
-==== Reviews ==== 
-  * 2011: Bioinformatics 
-  * 2011: BMC Bioinformatics 
-  * 2011: JCSS Elsevier 
-  * 2010: IEEE/ACM Transactions on Computational Biology and Bioinformatics 
-  * SEA 2009 
-  * ISBRA 2009 
- 
-==== Workshops, Conferences ==== 
-  * German Conference on Bioinformatics (GCB) 2013, Göttingen 
-  * German Conference on Bioinformatics (GCB) 2012, Jena 
-  * WABI 2010, Liverpool 
-  * The Computational Challenges of the Next Generation DNA Sequencing, January 15-16, 2009, Uppsala 
-  * ISMB/ECCB 2009, Stockholm 
-  * WABI/ESA 2008, Karlsruhe, September 15-17, 2008 
-  * RECOMB 2008, Singapore 
-  * [[http://​www.madalgo.au.dk/​html_sider/​2_5_Events/​SS2007/​FrontPage_SS2007.html| MADALGO Summer School on Data Stream Algorithms (Denmark, Aarhus, 2007)]] 
- 
-betreute Diplomarbeiten 
-  * Djamila Lindemann 
-  * Torsten Glebocki 
-  * Henning Timm 
- 
-Bachelorarbeiten 
-  * Manuel Allhoff 
-  * Diana Howey 
-*/ 
- 
-==== Peer-Reviewed Publications ==== 
- 
-Marcel Martin, Sven Rahmann.\\ 
-//Aligning Flowgrams to DNA Sequences//​\\ 
-German Conference on Bioinformatics,​ 2013.\\ 
-DOI: [[http://​dx.doi.org/​10.4230/​OASIcs.GCB.2013.125|10.4230/​OASIcs.GCB.2013.125]] 
- 
-Claudia Voigt, André Mégarbané,​ Kornelia Neveling, Johanna Christina Czeschik, Beate Albrecht, Bert Callewaert, Florian von Deimling, Andreas Hehr, Marie Falkenberg Smeland, Rainer König, Alma Kuechler, Carlo Marcelis, Maria Puiu, Willie Reardon, Hilde Monica Riise Stensland, Bernd Schweiger, Marloes Steehouwer, Christopher Teller, Marcel Martin, Sven Rahmann, Ute Hehr, Han G Brunner, Hermann-Josef Lüdecke and Dagmar Wieczorek.\\ 
-//​Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies - expanding the phenotypes associated with EFTUD2 mutations//​\\ 
-Orphanet Journal of Rare Diseases, 2013.\\ 
-DOI [[http://​dx.doi.org/​10.1186/​1750-1172-8-110|10.1186/​1750-1172-8-110]] 
- 
-M. Martin, L. Maßhöfer,​ P. Temming, S. Rahmann, C. Metz, N. Bornfeld, J. van de Nes, L. Klein-Hitpass,​ A. G. Hinnebusch, ​ 
-B. Horsthemke, D. R. Lohmann, M. Zeschnigk.\\ 
-//Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3//\\ 
-Nature Genetics, 2013.\\ 
-DOI: [[http://​dx.doi.org/​10.1038/​ng.2674|10.1038/​ng.2674]] 
- 
-J.C. Czeschik and C. Voigt and Y. Alanay and B. Albrecht and A. Avci and D. FitzPatrick and D.R. Goudie and A.J. Hoogeboom and H. Kayserili and O.S. Kiper and A. Kuechler and V. Lopez-Gonzalez and M. Martin and S. Rahmann and B. Schweiger and M. Splitt and B. Wollnik and H.-J. Lüdecke and M. Zeschnigk and D. Wieczorek.\\ 
-//Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome//​\\ 
-Human Genetics, Springer-Verlag,​ 2013, 1-14.\\ 
-DOI: [[http://​dx.doi.org/​10.1007/​s00439-013-1295-2|10.1007/​s00439-013-1295-2]] 
-        ​ 
-Sven Rahmann, Marcel Martin, Johannes H. Schulte, Johannes Köster, Tobias Marschall, Alexander Schramm.\\ 
-//​Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data//\\ 
-Methods 2012.\\ 
-DOI: [[http://​dx.doi.org/​10.1016/​j.ymeth.2012.10.005|10.1016/​j.ymeth.2012.10.005]] 
- 
-A. Schramm, B. Schowe, K. Fielitz, M. Heilmann, M. Martin, T. Marschall, J. Köster, J. Vandesompele,​ J. Vermeulen, K. de Preter, J. Koster, R. Versteeg, R. Noguera, F. Speleman, S. Rahmann, A. Eggert, K. Morik, J. H. Schulte\\ 
-//​Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome//\\ 
-//British Journal of Cancer//, 2012, 107(8):​1409-1417.\\ 
-DOI: [[http://​dx.doi.org/​10.1038/​bjc.2012.391|10.1038/​bjc.2012.391]] 
- 
-Alexander Schramm, Johannes Köster, Tobias Marschall, Marcel Martin, Melanie Schwermer, Kathrin Fielitz, Gabriele Büchel, Matthias Barann, Daniela Esser, Philip Rosenstiel, Sven Rahmann, Angelika Eggert, Johannes H. Schulte\\ 
-//​Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma//​\\ 
-In //​International Journal of Cancer, 2012//\\ 
-DOI: [[http://​dx.doi.org/​10.1002/​ijc.27787|10.1002/​ijc.27787]] 
- 
-Jing-Woei Li, Keith Robison, Marcel Martin, Andreas Sjödin, Björn Usadel, Matthew Young, Eric C. Olivares, Dan M. Bolser.\\ 
-//​SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis//​\\ 
-Nucleic Acids Research, 2012, 40(D1):​D1313-D1317.\\ 
-DOI: [[http://​dx.doi.org/​10.1093/​nar/​gkr1058|10.1093/​nar/​gkr1058]] 
- 
-Marcel Martin.\\ 
-//​[[http://​journal.embnet.org/​index.php/​embnetjournal/​article/​view/​200|Cutadapt removes adapter sequences from high-throughput sequencing reads]]//\\ 
-In //​EMBnet.journal//,​ 17, May 2011\\ 
-DOI: [[http://​dx.doi.org/​10.14806/​ej.17.1.200|10.14806/​ej.17.1.200]] 
- 
-Johannes H. Schulte, Tobias Marschall, Marcel Martin, Philipp Rosenstiel, Pieter Mestdagh, Stefanie Schlierf, Theresa Thor, Jo Vandesompele,​ Angelika Eggert, Stefan Schreiber, Sven Rahmann and Alexander Schramm.\\ 
-//Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma//​\\ 
-DOI: [[http://​dx.doi.org/​10.1093/​nar/​gkq342|10.1093/​nar/​gkq342]] 
- 
-Marcel Martin, Jonathan Maycock, Florian Paul Schmidt, Oliver Kramer.\\ 
-//​Recognition of Manual Actions Using Vector Quantization and Dynamic Time Warping//​.\\ 
-In //​Proceedings of 5th Int. Conf. on Hybrid Artificial Intelligence Systems (HAIS 2010)// 221-228. 
- 
-Michael Zeschnigk, Marcel Martin, Gisela Betzl, Andreas Kalbe, Caroline Sirsch, Karin Buiting, Stephanie Gross, Epameinondas Fritzilas, Bruno Frey, Sven Rahmann and Bernhard Horsthemke.\\ 
-//Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete//​.\\ 
-DOI: [[http://​dx.doi.org/​10.1093/​hmg/​ddp054|10.1093/​hmg/​ddp054]] 
- 
-Sebastian Böcker, Zsuzsanna Lipták, Marcel Martin, Anton Pervukhin, Henner Sudek.\\ 
-//​DECOMP---from interpreting Mass Spectrometry peaks to solving the Money Changing Problem//​.\\ 
-Bioinformatics 24(4):​591-593 (2008).\\ 
-DOI: [[http://​dx.doi.org/​10.1093/​bioinformatics/​btm631|10.1093/​bioinformatics/​btm631]] 
- 
-Sven Rahmann, Tobias Wittkop, Jan Baumbach, Marcel Martin, Anke Truß, and Sebastian Böcker.\\ 
-[[http://​www.lifesciencessociety.org/​CSB2007/​toc/​391.2007.html|Exact and Heuristic Algorithms for Weighted Cluster Editing]].\\ 
-In //​Proceedings of the Conference Computational Systems Bioinformatics//,​ volume 6, pages 391–401, August 2007. 
- 
-Thomas Plötz, Gernot A Fink, Peter Husemann, Sven Kanies, Kai Lienemann, Tobias Marschall, Marcel Martin, Lars Schillingmann,​ Matthias Steinrücken,​ Henner Sudek.\\ 
-//Automatic Detection of Song Changes in Music Mixes Using Stochastic Models//. 
-Proc. of the Int. Conf. on Pattern Recognition (ICPR'​06) \\ 
-DOI: [[http://​dx.doi.org/​10.1109/​ICPR.2006.297| 10.1109/​ICPR.2006.297]] 
- 
-==== Book Chapter ==== 
- 
-Tobias Marschall, Marcel Martin, and Sven Rahmann. //Extending SeqAn with a BWT-based suffix array construction.//​ In Knut Reinert and Andreas Gogol-Döring,​ editors, Biological Sequence Analysis Using the Seqan C++ Library. CRC Press Inc, 2009. ISBN 978-1420076233. 
- 
-==== Posters ==== 
- 
-//​[[http://​ls11-www.cs.tu-dortmund.de/​people/​martin/​poster/​gcb2012-mmartin-flowgrams.pdf|Alignment of Flowgrams to Strings]]// by M. Martin, presented at German Conference on Bioinformatics (GCB) 2012, Jena, Germany (second place poster award) 
- 
-//​[[http://​journal.embnet.org/​index.php/​embnetjournal/​article/​view/​272|From cutadapt to sequencetools (sqt): a versatile toolset for sequencing projects]]//​ M. Martin and S. Rahmann 
- 
-//A Symbol-Oriented Approach to Motion Analysis// by O. Kramer, J. Maycock, F. P. Schmidt, and M. Martin, Intelligence and Action II - New Perspectives in Dance and Cognitive Science, (2009) 
- 
-//A Heuristic Clustering Algorithm Using Graph Transitivity//​ by M. Martin, S. Rahmann, presented at RECOMB 2008, Singapore 
- 
-MADALGO Summer School on Data Stream Algorithms (2007) 
- 
-==== Software ==== 
- 
-=== FlowG (2013) === 
- 
-This tool is a proof-of-concept implementation of flowgram-string alignment as described in the submitted GCB 2013 paper “Aligning Flowgrams to DNA Sequences”. See http://​www.rahmannlab.de/​software . 
- 
-=== cutadapt (2010–) === 
- 
-This tool removes adapter sequences from high-throughput sequencing reads. Available at http://​code.google.com/​p/​cutadapt/​ . 
- 
-=== sqt (2011–) === 
- 
-This is a set of Unix command-line tools for working with high-throughput sequencing data. Available at http://​code.google.com/​p/​sqt/​ . 
- 
-=== Verjinxer (2008–2010) === 
- 
-This //Versatile Java-based indexer// is a framework for the development of indexing algorithms in high-throughput sequencing applications. I contributed bisulfite read mapping functionality. Available at http://​code.google.com/​p/​verjinxer/​ . 
- 
-=== Decomp (2008) === 
- 
-Used in mass spectrometry,​ this tool decomposes a given mass into sum formulas. Frontend available at http://​bibiserv.techfak.uni-bielefeld.de/​decomp/​ . 
- 
-=== SBBI (2007) === 
- 
-Motivated by genome rearrangement,​ this tool sorts a given permutation into ascending order using only block interchanges. Available at http://​bibiserv.techfak.uni-bielefeld.de/​sbbi/​ . 
- 
-/* [[http://​www.citeulike.org/​user/​mmartin| My CiteULike library]] */ 
- 
-==== Talks (mostly German) ==== 
- 
-=== Erste Schritte mit Git === 
- 
-  * [[/​people/​martin/​git/​erste-schritte-mit-git.html | Die Folien zu meinem Vortrag "Erste Schritte mit Git"]] (Taste '​t'​ drücken, um zwischen Slideshow und Komplettansicht umzuschalten) 
-  * [[/​people/​martin/​git/​erste-schritte-mit-git.md | Der Markdown-Quellcode]] 
- 
-Die Folien wurden im [[http://​daringfireball.net/​projects/​markdown/​ | Markdown-Format]] geschrieben und mit [[http://​johnmacfarlane.net/​pandoc/​ | pandoc]] in eine [[http://​meyerweb.com/​eric/​tools/​s5/​|S5-Präsentation]] im HTML-Format konvertiert. Die Befehlzeile lautet: 
- 
-  pandoc --smart -s -m --offline -t s5 erste-schritte-mit-git.md | sed '​s|text-transform:​ capitalize;​||'​ > erste-schritte-mit-git.html 
- 
-=== Python im Bioinformatiker-Alltag === 
- 
-Dieser Vortrag wurde von mir auf der PyCon DE 2011 in Leipzig gehalten. 
- 
-  * [[/​people/​martin/​pycon/​pycon-de-2011-marcel-martin.pdf|Die Folien als PDF]] 
-  * [[http://​blip.tv/​show/​708134|Das Video des Vortrags]] 
- 
-=== PyDay: praktische Module in der Standardbibliothek;​ Pakete selbst bauen === 
- 
-  * [[/​people/​martin/​pyday/​pakete.html | Die Folien zu meinem lehrstuhlinternen PyDay-Vortrag]] (Taste '​t'​ drücken, um zwischen Slideshow und Komplettansicht umzuschalten) 
-  * [[/​people/​martin/​pyday/​pakete.md | Der Markdown-Quellcode]] 
- 
  
 
Last modified: 2015-09-11 10:19 (external edit)
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