Martin Luther University Halle-Wittenberg

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Liste der Publikationen

List of publications

  • Christoph Ruttkies, Steffen Neumann and Stefan Posch. "Improving  metfrag with statistical learning of fragment annotations". BMC  bioinformatics, 20(1):376, 2019
  • Jan Grau, Stefan Posch  and Jens Keilwagen. "Aus Fehlern lernen - wo binden  Transkriptionsfaktoren an die DNA?" BIOspektrum, 25(3):346–347, 2019.
  • Jens Keilwagen, Stefan Posch and Jan Grau. "Accurate prediction of cell type-specific trans- cription factor binding". Genome biology, 20(1):9, 2019
  • B. Möller, H. Chen, T.  Schmidt, A. Zieschank, R. Patzak, M. Türke,  A. Weigelt and S. Posch, "rhizo Trak: A flexible open source Fiji plugin for user-friendly manual annotation of time-series images from minirhizotrons". In Plant and Soil, September 2019. [bib]
    Below you can download the peer-reviewed pre-production version of our article, the final version can be found at Springer's Plant and Soil website.    rhizoTrak-MoellerChen-PLSO-D-19-00329-final-1.pdf (2 MB)  vom 16.09.2019
  • Jens Keilwagen, Stefan Posch and Jan Grau. "Learning from mistakes: Accurate prediction of cell type-specific transcription factor binding". bioRxiv, 230011, 2018.
  • S. Posch and B. Möller, ''Alida - Advanced Library for Integrated Development of Data Analysis Applications''. In Journal of Open Research Software, 5(1):7, 2017. [bib]
  • B. Möller, M. Glaß, D. Misiak, and S. Posch, ''MiToBo - a toolbox for image processing and analysis''. In Journal of Open Research Software, 4(1):e17, 2016. [bib]
  • S. Posch and B. Möller, ''Design and implementation of the Alida framework to ease the development of image analysis algorithms''. In Pattern Recognition and Image Analysis, 26(1):181-189, 2016. [bib]
  • Jan  Grau, Ivo Grosse, Stefan Posch and Jens Keilwagen. "Motif clustering  with implications for transcription factor interactions". e1601, PeerJ  PrePrints, 2015
  • Martin Nettling, Hendrik  Treutler, Jan Grau, Jens Keilwagen, Stefan Posch and Ivo Grosse.  "Difflogo: a comparative visualization of sequence motifs". BMC  bioinformatics, 16(1):387, 2015
  • Stefan Posch and  Birgit Möller, Design and Implementation of the  Alida Framework to  Ease the Development of Image Analysis Algorithms,  9th Open German-Russian Worokshop on Pattern Recognition and Image  Understanding (OGRW 2014), Koblenz, December 2015 [bib]
  • Danny  Misiak, Stefan Posch, Marcell Lederer, Claudia Reinke, Stefan   Hüttelmaier and Birgit Möller, "Extraction of protein profiles from   primary neurons using active contour models and wavelets", Journal of   Neuroscience Methods, vol. 225, pp. 1-12, March 2014. [bib]
  • Jan Grau, Jens Boch and Stefan Posch, TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics,2013. [bib]
  • Jan Grau, Stefan Posch, Ivo Grosse and Jens Keilwagen, A general  approach for discriminative de-novo motif discovery from high-throughput  data. Nucleic Acids Research, doi: 10.1093/nar/gkt831, 2013. [bib]
  • Jan  Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch and  Jens  Boch, Computational Predictions Provide Insights into the Biology  of  TAL Effector Target Sites.  PLoS Comput Biol, no. 3, vol. 9,  e1002962,  March 2013. [bib]
  • Jan  Grau, Jens Keilwagen, André Gohr, Ivan A. Paponov, Stefan Posch,   Michael Seifert, Marc Strickert and Ivo Grosse, Dispom: A   Discriminative De-novo Motif Discovery Tool Based On The Jstacs  Library.  Journal of Bioinformatics and Computational Biology, no. 1,  vol. 11,  2013. [bib]
  • Birgit  Möller and Stefan Posch, "A Framework Unifying the  Development of  Image Analysis Algorithms and Associated User  Interfaces". In Proc. of  13th IAPR International Conference on Machine  Vision Applications  (MVA), pp. 447-450, Kyoto, Japan, May 2013. [bib]
  • Jan  Grau, Jens Keilwagen, André Gohr, Berit Haldemann, Stefan Posch  and  Ivo Grosse, Jstacs: A Java Framework for Statistical Analysis and   Classification of Biological Sequences. Journal of Machine Learning   Research, pp. 1967-1971, vol. 13,June 2012. [bib]
  • Birgit Möller and Stefan Posch. Comparing Active Contours for the Segmentation of Biomedical Images. In Proc. of IEEE International Symposium on Biomedical Imaging (ISBI     '12), Barcelona, Spain, May 2012. [bib]
  • Stefan  Posch and Birgit Möller. Alida - Automatic Generation of User   Interfaces for Data Analysis Algorithms. Poster presentation at IEEE International Symposium on Biomedical Imaging (ISBI), Bioimage Analysis Workshop, Barcelona, Spain, April 2012. [bib]
  • Oliver Greß and Stefan Posch. Parametric Data Association Prior for  Multi-Target Tracking Based on Rao-Blackwellized  Monte Carlo Data  Association. International Conference on Computer  Vision Theory and  Applications 2012, vol. 2, pages 387-394, Rom, Italia, February, 2012. [bib]
  • Birgit Möller, Oliver Greß, Nadine Stöhr, Stefan Hüttelmaier and Stefan Posch. VISIGRAPP 2010, Revised Selected Papers of Int. Joint Conf. on Computer  Vision, Imaging and Computer Graphics. Theory and Applications. Communications in Computer and Information Science, pages 154-169, 2011. [bib]
  • Birgit Möller and Stefan Posch.   MiCA - easy cell image analysis with normalized snakes.   In International Workshop on Microscopic Image Analysis with   Applications in Biology, September 2011. [bib]
  • Jens Keilwagen, Jan Grau, Ivan A. Paponov, Stefan Posch, Marc  Strickert, and   Ivo Grosse.   De-novo discovery of differentially  abundant transcription factor   binding sites including their positional  preference. PLoS Comput Biol, 7(2):e1001070, February 2011. [bib]
  • Manuela  Hesse, Edith Willscher, Benjamin Schmiedel, Stefan Posch,  Ralph  Golbik,   and Martin Staege.   Sequence and expression of the  chicken  membrane-associated   phospholipases a1 alpha (liph) and beta  (lipi). Molecular Biology Reports, pages 1-9, 2011. [bib]
  • Markus Glaß and Birgit Möller and Anne Zirkel and Kristin Wächter and Stefan Hüttelmaier and Stefan Posch. Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measures.  Proc. of 5th Iberian Conference on Pattern Recognition and Image  Analysis (IbPRIA '11) pp. 100-108, Gran Canaria, Spain, 2011. [bib]
  • Birgit Möller, Oliver Greß and Stefan Posch. Knowing what happened - Automatic Documentation of Image Analysis Processes. Proceedings of 8th International Conference on Computer Vision Systems,   pp. 1-10, Sophia Antipolis, France, 2011. Springer [bib]
  • Birgit Möller, Nadine Stöhr, Stefan Hüttelmaier and Stefan Posch. Cascaded Segmentation of Grained Cell Tissue with Active Contour Models. In Proc. of Int. Conf. on Pattern Recognition (ICPR), IEEE, pp. 1481-1484, Istanbul, Turkey, August 2010. [bib]
  • Birgit Möller, Oliver Greß, Nadine Stöhr, Stefan Hüttelmaier, and Stefan Posch. Adaptive segmentation of cells and particles in fluorescent microscope images. In Proc. of International Conference on Computer Vision Theory and Applications (VISAPP '10), vol. 2, pp. 97-106, Angers, France, May 2010. [bib]
  • Oliver Greß, Birgit Möller, Nadine Stöhr, Stefan Hüttelmaier and Stefan Posch. Scale-adaptive wavelet-based particle detection in microscopy images. In Hans-Peter Meinzer, Thomas Martin Deserno, Heinz Handels, andThomas Tolxdorff, editors, Bildverarbeitung für die Medizin, pages 266-270, Berlin, March 2010. Springer [bib]
  • Stefan  Posch, Jan Grau, André Gohr, Jens Keilwagen, and Ivo Grosse.   Probabilistic approaches to transcription factor binding site   prediction. In Istvan Ladunga, editor, The Computational Biology of Transcription Factor Binding, Methods in Molecular Biology. Springer Press, 2010. in preparation. [bib]
  • Jens  Keilwagen, Jan Grau, Stefan Posch, Marc Strickert, and Ivo  Grosse.  Unifying generative and discriminative learning principles. BMC Bioinformatics, 11(1):98, 2010. [bib]
  • Jens  Keilwagen, Jan Grau, Stefan Posch, and Ivo Grosse.   Apples and   oranges: avoiding different priors in Bayesian DNA   sequence analysis.   BMC Bioinformatics, 11(1):149, 2010. [bib]
  • Jan  Grau, Daniel Arend, Ivo Grosse, Artemis G. Hatzigeorgiou, Jens   Keilwagen,   Manolis Maragkakis, Claus Weinholdt, and Stefan Posch.   Predicting miRNA targets utilizing an extended profile HMM.   In  Dietmar  Schomburg and Andreas Grote, editors, German   Conference on Bioinformatics, volume P-173 of Lecture Notes in   Informatics (LNI) - Proceedings, pages 81-91, Bonn, 2010. Gesellschaft   für Informatik. [bib]
  • Birgit Möller and Stefan Posch. Robust features for 2-d electrophoresis gel image registration. Electrophoresis, 30:4137-4148, 2009.   [bib]
  • Danny Misiak, Stefan Posch, Nadine Stöhr, Stefan Hüttelmaier, and Birgit Möller. Automatic analysis of fluorescence labeled neurites in microscope images. In IEEE Workshop on Applications of Computer Vision (WACV '09), pages 118-124, 2009. IEEE Catalog Number: CFP09082-CDR.   [bib]
  • Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter  F. Stadler, editors.German Conference on Bioinformatics 2009,volume 157  of LNI. GI, 2009.   [bib]
  • Birgit Möller, Oliver Gress, and Stefan Posch. A comparative study of robust feature detectors for 2d electrophoresis gel image registration. In Proc. of German Conference on Bioinformatics, LNI P-136, pages 138-147, Dresden, Germany, September 2008.   [bib]
  • Jörg Wensch, Alf Gerisch, and Stefan Posch. Optimised coupling of hierarchies in image registration. Image and Vision Computing, 26(7), 2008.   [bib]
  • Birgit Möller and Stefan Posch. An integrated analysis concept for errors in image registration. Int. Journal on Pattern Recognition and Image Analysis (PRIA), 18(2):201-206, 2008.   [bib]
  • Birgit Möller and Stefan Posch. An iconic scene memory approach for mobile robots interacting with humans. Technical Report 2007-03, Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany, December 2007.   [bib]
  • Birgit Möller and Stefan Posch. Identifying lens distortions in image registration by learning from examples. In Proc. of British Machine Vision Conference (BMVC '07), pages I:152-161, University of Warwick, Coventry, UK, September 2007.   [bib]
  • Birgit Möller and Stefan Posch. An integrated analysis concept for errors in image registration. In Proc. of 7th Open German/Russian Workshop on Pattern Recognition and Image Understanding (OGRW '07), Ettlingen, Germany, August 2007.   [bib]
  • Birgit Möller and Stefan Posch. Automatic analysis of lens distortions in image registration. In Proc.   of Int. Conf. on Computer Vision Systems (ICVS '07), Workshop on  Camera  Calibration Methods for Computer Vision Systems (CCMVS '07), Bielefeld, Germany, March 2007.   [bib]
  • Birgit Möller, Rafael Garcia, and Stefan Posch. Towards objective quality assessment of image registration results. In Proc. of International Conference on Computer Vision Theory and Applications (VISAPP '07), pages 233-240, Barcelona, Spain, March 2007.   [bib]
  • Lennart Opitz, Alexander Schliep, and Stefan Posch. Joint analysis of in-situ hybridization and gene expression data. In Reinhold Decker and Hans J. Lenz, editors, Advances in Data Analysis: Proceedings of the 30th Annual Conference of the Gesellschaft für Klassifikation e.V.,, pages 577-584. Springer, 2007.   [bib]
  • Stefan Posch, Jan Grau, Andre Gohr, Irad Ben-Gal, Alexander Kel, and  Ivo Grosse. Recognition of cis-regulatory elements with VOMBAT. Journal of Bioinformatics and Computational Biology, 5(02B):561-577, 2007.   [bib]
  • Jan Grau, Jens Keilwagen, Alexander Kel, Ivo Grosse, and Stefan Posch. Supervised posteriors for dna-motif classification. In German Conference on Bioinformtics, pages 123-134, 2007.   [bib]
  • Jan  Grau, Jens Keilwagen, Ivo Grosse, and Stefan Posch. On the  relevance  of model orders to discriminative learning of markov models.  In  Alexander Hinneburg, editor, LWA: Lernen - Wissen - Adaption, pages 61-66, 2007.   [bib]
  • Jens  Keilwagen, Jan Grau, Stefan Posch, and Ivo Grosse. Recognition  of  splice sites using maximum conditional likelihood. In Alexander   Hinneburg, editor, LWA: Lernen - Wissen - Adaption, pages 67-72, 2007.   [bib]
  • Birgit Möller and Stefan Posch. A space- and time-efficient mosaic-based iconic memory for interactive systems. In Proc. of International Conference on Computer Vision Theory and Applications (VISAPP '06), pages 413-421, Setúbal, Portugal, February 2006. [ bib ]
  • Jan Grau, Irad Ben-Gal, Andre Gohr, Alexander Kel, Olga  Kel-Margoulis,  Stefan Posch, and Ivo Grosse. Prediction of eukaryotic  transcription  factor binding sites using variable order markov models.  In GCB, pages 5-6, 2006. [ bib ]
  • Jan Grau, Irad Ben-Gal, Ivo Grosse, and Stefan Posch. Vombat: A  web-server  for predicting transcription factor binding sites using  variable order  markov models and variable order bayesian trees. In GCB, Short paper, 2006. [ bib ]
  • Yvonne  Pöschl, Christoph Böttcher, Stephan Clemens, Dierk Scheel,  Stefan  Posch, and Steffen Neumann. Analysis of metabolite relations in  lcms  data using bayesian networks. In GCB, Short paper, pages 17-18, 2006. [ bib ]
  • Jan Grau, Irad Ben-Gal,  Stefan Posch, and Ivo Grosse. VOMBAT:  Prediction of transcription  factor binding sites using variable order  bayesian trees. Nucleic Acids Research, 34(suppl_2):W529-533, 2006. [ bib ]
  • Gregor Erz and Stefan Posch. Root detection by hierarchical seed expansion. In Proceedings of Eurocon 2005, pages 963-966, Belgrade, November 2005. IEEE Computer Society Press. [ bib ]
  • Birgit  Möller, Stefan Posch, Axel Haasch, Jannik Fritsch, and  Gerhard  Sagerer. Interactive object learning for robot companions using  mosaic  images. In Proc. IEEE/RSJ Int. Conf. on Intelligent Robots and Systems, pages 371-376, Edmonton, Alberta, Canada, August 2005. [ bib ]
  • Birgit Möller and Stefan Posch. A mosaic-based visual memory with applications to active scene exploration. In Proc. of Mirage, Computer Vision / Computer Graphics Collaboration Techniques and Applications, pages 117-125, INRIA Rocquencourt, France, March 2005.
  • Birgit Möller and Stefan Posch. Visual scene memory based on multi-mosaics. In Dietrich Paulus and Detlev Droege, editors, Mixed-reality as a challenge to image understanding and artificial intelligence, pages 27-32, Koblenz, 2005. Universität Koblenz-Landau, Institut für Informatik.
  • Gregor Erz, Maik Veste, Heiko Anlauf, Siegmar-Walter  Breckle, and  Stefan Posch. A region and contour based technique for  automatic  detection of of tomatoe roots in minirhizotron images. Journal of Applied Botany and Food Quality, 79:83-88, 2005. [ bib ]
  • I. Ben-Gal,  A. Shani, A. Gohr, J. Grau, S. Arviv, A. Shmilovici, S.  Posch, and I.  Grosse. Identification of transcription factor binding  sites with  variable-order bayesian networks. Bioinformatics, 21:2657-2666, 2005. [ bib ]
  • Irad Ben-Gal,  Sigal Arviv, Andre Gohr, Jan Grau an d Stefan Posch,  Armin Shmilovici,  and Ivo Grosse. Computational identification of  transcription factor  binding si tes with variable-order markov models.  In ISMB/ECCB, Poster Abstract, 2004. [ bib ]
  • Andreas  Stephanik, Steffen Neumann, Lothar Altschmied, David L.  Müller, Stefan  Posch, and Ivo Grosse. SMArrT: Smarrt: An integrated  workflow for  array an integrated workflow for array analysis. In GCB, Poster Abstract, 2004. [ bip ]
  • Birgit Möller, Denis Williams, and Stefan Posch. Towards a mosaic-based visual representation of large scenes. Int. Journal on Pattern Recognition and Image Analysis (PRIA), Spec. Issue, 14(2):262-266, 2004. [ bib ]
  • Gregor  Erz and Stefan Posch. A region based seed detection for root  detection  in minirhizotron images. In B. Michaelis and G. Krell,  editors, Pattern Recognition, Proc. of 25th DAGM Symposium, LNCS 2781, pages 482-489, Magdeburg, Germany, September 2003. Springer. [ bib ]
  • Birgit Möller, Denis Williams, and Stefan Posch. Robust image sequence mosaicing. In B. Michaelis and G. Krell, editors, Pattern Recognition, Proc. of 25th DAGM Symposium, LNCS 2781, pages 386-293, Magdeburg, Germany, September 2003. Springer. [ bib ]
  • Birgit Möller, Denis Williams, and Stefan Posch. Towards a mosaic-based visual representation of large scenes. In Proc. of 6th Open German-Russian Workshop (IAPR), pages 108-111, Katun Village, Altai Region, Russian Federation, 25.-30. August 2003. [ bib ]
  • Jörg Weitzenberg and Stefan Posch. Using Hidden-Markov-Models to analyze Concentrations from Biosensor Curves. In Proc. Int. Conference Signal Processing, Pattern Recognition, & Applications, pages 98-103, Rhodes, 2003. IASTED.
  • Denis  Williams, Birgit Möller, and Stefan Posch. Integrated system  for a  visual memory based on mosaics. In H. R. Arabnia and Youngsong  Mun,  editors, Proc. of International Conference on Imaging Science, Systems, and Technology (CISST'03), pages II: 633-639, Las Vegas, USA, 23.-26.June 2003. CSREA Press. [ bib ]
  • Birgit Möller and Stefan Posch. Analysis of object interactions in dynamic scenes.In L. van Gool, editor, Pattern Recognition. 24. DAGM-Symposium, LNCS 2449, pages 361-369, Zurich, Switzerland, September 2002. Springer.
  • Jörg Weitzenberg, Stefan Posch, and Manfred Rost. Analysis of  amperometric biosensor curves using hidden- markov-modells. In Luc Van  Gool, editor, Pattern Recognition. 24. DAGM-Symposium, pages 182-189, 2002. [ bib ]
  • Birgit  Möller and Stefan Posch. Detection and tracking of moving  objects for  mosaic image generation. In B. Radig and S. Florczyk,  editors, Pattern Recognition, Proc. of 23rd DAGM Symposium, LNCS 2191, pages 208-215, Munich, Germany, September 2001. Springer.
  • J.  Weitzenberg, S. Posch, C. Bauer, M. Rost, and B. Gründig.  Analysis of  amperometric biosensor data using fuzzy logic and discrete  hidden-  markov-models. In H.R. Tränkler, editor, SENSOR 2001, pages Volume II: 493-498, 2001. [ bib ]
  • Daniel Schlüter, Sven Wachsmuth, Gerhard Sagerer, and Stefan Posch.  Towards an integrated framework for contour-based grouping and object  recognition using markov random fields. In Proc. International Conference on Image Processing, volume II, pages 100-103. IEEE, 2000.
  • Daniel  Schlüter, Franz Kummert, Gerhard Sagerer, and Stefan Posch.   Integration of regions and contours for object recognition. In Proc. International Conference on Pattern Recognition, volume 1, pages 944-947. IEEE, 2000.
  • Denis  Williams and Stefan Posch. Stereozuordnung von hierachischen   Konturgruppen mit Markov Random Fields. In Gerald Sommer, Norbert   Krüger, and Christian Perwass, editors, Mustererkennug 2000. Proceedings 22. DAGM-Symposium, Informatik Aktuell, pages 7-16. Springer, 2000. [ bib ]
  • Jörg  Weitzenberg, Stefan Posch, and Manfred Rost. Diskrete Hidden  Markov  Modelle zur Analyse von Meßkurven amperometrischer Biosensoren.  In  Gerald Sommer, Norbert Krüger, and Christian Perwass, editors, Mustererkennug 2000. Proceedings 22. DAGM-Symposium, Informatik Aktuell, pages 317-324. Springer, 2000.
  • Steffen Neumann, Stefan Posch, and Gerhard Sagerer. Towards evaluation of docking hypotheses using elasic matching. In Computer Sciene and Biology: Proceedings of the German Conference on Bioinformatics, page 220, October 1999.
  • Stefan Posch. Perzeptives Gruppieren und Bildanalyse. Deutscher Universitäts Verlag, 1999.
  • Christian  Bauckhage, Gernot A. Fink, Franz Kummert, Stefan Posch,  Gerhard  Sagerer, and Daniel Schlüter. Towards and image understanding   architecture for a situatedartificial communicator. In Bernd Radig,   Heinrich Niemann, Yuri Zhuravlev, Igor Gourevitch, and Ivan Laptev,   editors, Pattern Recognition and Image Understanding,pages 203-210, Sankt Augustin, 1999. infix.
  • Friedrich Ackermann, Grit Herrmann, Stefan Posch, and Gerhard Sagerer. Estimation and filtering of potential protein-protein docking positions. Bioinformatics, 14(2):196-205, 1998
  • Stefan Posch and Helge Ritter, editors. Dynamische Perzeption, Proceedings on Artificial Intelligence. infix, 1998.
  • Daniel  Schlüter and Stefan Posch. Combining contour and region  information  for perceptual grouping. In P. Levi, R.-J. Ahlers, F. May,  and M.  Schanz, editors,  Mustererkennug 1998. Proceedings 20. DAGM-Symposium, Informatik Aktuell, pages 393-401. Springer, 1998.
  • Stefan  Posch and Daniel Schlüter. Perceptual grouping using markov  random  fields and cue integration of contour and region information.  Technical  Report 98/10, SFB 360, Universität Bielefeld, 1998.
  • A. Maßmann, S. Posch, G. Sagerer, and D. Schlüter. Using markov random fields for contour-based grouping. In Proc. International Conference on Image Processing, volume II, pages 207-210. IEEE, 1997.
  • Thorsten Bomberg and Stefan Posch. Regionensegmentierung von Farbbildfolgen. In E. Paulus and F.M.Wahl, editors, Mustererkennug 1997. Proceedings 19. DAGM-Symposium, Informatik Aktuell, pages 63-70. Springer, 1997.
  • Grit  Herrmann, Franz Kummert, Stefan Posch, and Gerhard Sagerer.   Kontrollstrategie für ein wissensbasiertes System zur Makromolekularen   Erkennung. In E. Paulus and F.M.Wahl, editors, Mustererkennug 1997. Proceedings 19. DAGM-Symposium, Informatik Aktuell, pages 602-609. Springer, 1997.
  • F.  Ackermann, A. Maßmann, S. Posch, G. Sagerer, and D. Schlüter.   Perceptual grouping of contour segments using markov random fields.   International Journal of Pattern Recognition and Image Analysis,   7(1):11-17, 1997.

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