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Personal Homepage of Nils Hoffmann

Nils Hoffmann

Postal Address:	Universität Bielefeld AG Genominformatik 33594 Bielefeld Germany
Office:	U10-144
Office Phone:	+49-(0)521-106-4342
E-mail:	nils.hoffmanncebitec.uni-bielefeld.de

Research Interests

Algorithms for analytical high-throughput applications, e.g. GC, GCxGC, and LC-MS
Chem(o)informatics, QSPR
Scientific visualization
Software engineering

Publications

2012
Generic Software Frameworks for GC-MS Based Metabolomics (pdf)
Nils Hoffmann; Jens Stoye
Metabolomics, Ute Roessner (Ed.), ISBN: 978-953-51-0046-1, InTech
Publication

2009
ChromA: Signal Based Retention Time Alignment for Chromatography-Mass Spectrometry Data (pdf)
Nils Hoffmann; Jens Stoye
Bioinformatics 2009; doi: 10.1093/bioinformatics/btp343
Publication

Posters

2012
Proteus, An interactive Laboratory Journal Application for Gel-based Proteomics (pdf)
Konstantin Otte, Nils Hoffmann, Fabian Schulte, Karsten Niehaus, Jens Stoye
Presented at FGP 2012

2011
Maui and Maltcms a Graphical User Interface and Application Framework for High-Throughput Metabolomics (pdf)
Nils Hoffmann, Mathias Wilhelm, Kai Stadermann, Jens Stoye
Presented at GCB 2011

The mzML vendor-neutral data format for chromatography-mass spectrometry (link)
Sean O'Callaghan, Steffen Neumann, Nils Hoffmann, Eric Deutsch, Vladimir A. Likic
Presented at Metabolomics 2011

2010
ChromAUI - An integrated OpenSource Application for Metabolomics based on the Netbeans Rich Client Platform (pdf)
Nils Hoffmann, Mathias Wilhelm, Matthias Keck, Anja Döbbe, Karsten Niehaus, Olaf Kruse, Jens Stoye
Presented at Perspektive science fair 2010

2010
ChromA4D - an integrated OpenSource Application Framework for comprehensive GCxGC-MS-based Metabolomics (pdf)
Nils Hoffmann, Mathias Wilhelm, Matthias Keck, Anja Döbbe, Karsten Niehaus, Olaf Kruse, Jens Stoye
Presented at Metabolomics 2010

2010
Maltcms - an Application Framework for Processing of Metabolomics Data (Release 1.0) (pdf)
Mathias Wilhelm, Nils Hoffmann, Kai-Bernd Stadermann, Matthias Keck, Karsten Niehaus, Jens Stoye
Presented at Metabolomics 2010

2009
Maltcms - an Application Framework for Processing of Metabolomics Data (pdf)
Nils Hoffmann, Mathias Wilhelm, Matthias Keck, Anja Döbbe, Karsten Niehaus, Jens Stoye
Presented at GCB 2009

Teaching
Winter Term 2009/2010

Teaching assistant/organization of tutorials: Foundations of Sequence Analysis

Summer Term 2009

Seminar: Bioinformatics in Metabolomics and Proteomics

Teaching assistant/organization of tutorials: Advanced Algorithms in Sequence Analysis

Project: Random-model of simulated evolution

Winter Term 2008/2009

Organization of tutorials: Foundations of Sequence Analysis

Seminar: Genome Informatics Journal Club

Seminar: Genome Informatics Group Seminar

Summer Term 2008

Seminar: Bioinformatics in Metabolomics and Proteomics

Practical course: Sequence Analysis

Seminar: Genome Informatics Group Seminar

Winter Term 2007/2008

Teaching Assistant for Algorithms and Datastructures I

Seminar: Genome Informatics Group Seminar

Seminar: Genome Informatics Journal Club

Links

Projects

ChromA
Alignment of GC- and LC-MS data using a constrained and customizable variant of dynamic time warping.
Visit ChromA on BiBiServ

Maltcms/ChromA[1D,2D,4D]
The Modular Application Toolkit for Chromatography-Mass Spectrometry provides a comprehensive, modular and easily extendible basis for the creation of rich applications in the context of metabolomics and proteomics research. It is licensed as open source under the GNU L-GPL v3
Visit project Maltcms on sourceforge

Maui (formerly ChromAUI)
Maui is the Maltcms User Interface, a rich client application for the interactive visualization, organization and analysis of GC-MS and GCxGC-MS data from metabolomics experiments. It is currently under development and will be available here.

Collaborations

Molecular Phytopathology
Chemical Ecology