Martin Luther University Halle-Wittenberg

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Conference Contributions & Journal Papers

2019

  • 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
  • B. Möller, L. Zergiebel and K. Bürstenbinder, "Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D". In Plant Cell Morphogenesis: Methods and Protocols (10), 151-171, 2019. [bib]
  • B. Möller, Y. Poeschl, S. Klemm and K. Bürstenbinder, "Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant". In Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant (22), 329-349, 2019. [bib]
  • B. Möller and K. Bürstenbinder, ''Semi-automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level''. In Proc. of IEEE International Symposium on Biomedical Imaging (ISBI '19   ), Venice, Italy, April 2019, accepted. [bib]
  • B. Möller and M. Schattat, ''Quantification of Stromule Frequencies in Microscope Images of Plastids combining Ridge Detection and Geometric Criteria''. In Proc. of 6th Int. Conf. on Bioimaging (BIOIMAGING '19   ), Prague, Czech Republic, February 2019, accepted. [bib]
  • D. Mitra, S. Klemm, P. Kumari, J. Quegwer, B. Möller, Y. Poeschl, P. Pflug, G. Stamm, S. Abel, K. Bürstenbinder, ''Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana''. In Journal of Experimental Botany, 70(2):529-543, January 2019. [bib]

2018

  • Jens Keilwagen, Stefan Posch and Jan Grau. "Learning from mistakes: Accurate prediction of cell type-specific transcription factor binding". bioRxiv, 230011, 2018.

2017

  • 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]
  • K. Bürstenbinder, B. Möller, R. Plötner, G. Stamm, G. Hause, D. Mitra, and S. Abel, ''The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus''. In Plant Physiology, 173(3):1692-1708, March 2017. [bib]

2016

  • 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]

2015

  • 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
  • L. Franke, B. Storbeck, J. L. Erickson, D.  Rödel, D. Schröter, B. Möller and Martin Hartmut Schattat,The 'MTB Cell Counter' a versatile tool for the semi-automated quantification of sub-cellular phenotypes in fluorescence microscopy images. A case study on plastids, nuclei and peroxisomes. Journal of Endocytobiosis and Cell Research, vol. 26, pp. 31-42, 2015 [bib]
  • 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]

2014

  • N. Bley, M. Lederer, B. Pfalz, C. Reinke, T. Fuchs, Markus Glaß, Birgit Möller and Stefan Hüttelmaier,   Stress granules are dispensable for {mRNA} stabilization during cellular stress, Nucleic Acids Research vol. 43 No. 4, pages e26, December 2014 [bib]
  • Birgit Möller, E. Piltz and N. Bley, Quantification of Actin Structures  using Unsupervised Pattern Analysis Techniques, Proceedings of Int. Conf. on Pattern Recognition (ICPR), pp. 3251-3256, Stockholm, Sweden, 2014 [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]

2013

  • 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]

2012

This contribution won the 'Best Scientific Poster' - Award!

  • 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]
  • Steffen Neumann, Andrea Thum and Christoph Böttcher. Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data. Metabolomics (15 February 2012), pp. 1-8, doi: 10.1007/s11306-012-0401-0 [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]
    Parametric Data Association Prior for Multi-Target Tracking Based on Rao-Blackwellized Monte Carlo Data Association gress2012parametric-1.pdf


2011

  • 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]

2010

  • 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]

2009

  • 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]

2008

  • Birgit Möller, Thomas Plötz, and Gernot Fink. Calibration-free camera hand-over for fast and reliable person tracking in multi-camera setups. In Proc. of Int. Conf. on Pattern Recognition (ICPR '08). Tampa, Florida, USA, December 2008.  [bib]
  • Armagan Elibol, Birgit Möller, and Rafael Garcia. Perspectives of auto-correcting lens distortions in mosaic-based underwater navigation. In Proc. of 23rd IEEE Int. Symposium on Computer and Information Sciences (ISCIS '08), pages 1-6, Istanbul, Turkey, October 2008.   [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]

2007

  • 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]

2006

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.

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.

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.

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.

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.

2005

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.

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.

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.

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.

2004

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.

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.

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.

2003

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.

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.

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.

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.

2002

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.

2001

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.

2000

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.

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.

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