PD Dr. habil. Dominik Heider

Department: Center for Medical Biotechnology, Department of Bioinformatics Address: Universitaetsstr. 1-5, 45117 Essen, Germany Room: S03 S03 A44 Phone: +49 201 183-3975 Fax: +49 201 183-3437 E-mail: dominik.heider@uni-due.de

Professional Experience:

Sep 2012 - present	Akademischer Rat, Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
Jun 2012 - present	Privatdozent (eq. Associate Professor), Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
Mar 2011 - present	Member of the Executive Board, Center for Medical Biotechnology, Essen, Germany
Jul 2012 + Mar 2011 + Sep 2009	Visiting Professor, Department of Electrical and Electronic Engineering, Universita di Cagliari, Cagliari, Italy
Apr 2009 - Sep 2011	Visiting Lecturer, Department of Experimental Tumorbiology, University of Muenster, Muenster, Germany
Nov 2008 - Sep 2012	Postdoctoral Research Associate, Department of Bioinformatics, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
Oct 2008 - Mar 2009	Lehrbeauftragter (eq. Lecturer), Institute of Computer Science, University of Muenster, Muenster, Germany
Oct 2006 - Sep 2008	Research Assistant, Institute of Computer Science, University of Muenster, Muenster, Germany
Education:
June 2012	Habilitation (Venia Legendi) in Bioinformatics, University of Duisburg-Essen, Essen, Germany
Oct 2006 - Oct 2008	Dr. rer. nat. (eq. Ph.D.), University of Muenster, Muenster, Germany
Oct 2002 - Sep 2006	Diploma in Computer Science (eq. M.C.S.), University of Muenster, Muenster, Germany

Projects:
DNA-Crypt
JACVANN
BrainBlend
Interpol


Papers:
Pubmed

1. Pyka M., Hahn T., Heider D., Krug A., Sommer J., Kircher T., Jansen A.: Baseline Activity Predicts Working Memory Load Of Preceding Task Condition, Human Brain Mapping 2012, in press.
2. Sowa J.-P., Heider D., Bechmann L. P., Gerken G., Hoffmann D., Canbay A.: Novel algorithm for non-invasive assessment of fibrosis in NAFLD, PLoS ONE 2013, in press.
3. Heider D., Bartenhagen C., Dybowski J.N., Hauke S., Pyka M., Hoffmann D.: Unsupervised dimension reduction methods for protein sequence classification, Data Analysis, Machine Learning and Knowledge Discovery 2013, in press.
4. Wang Y., Rawi R., Wilms C., Heider D., Yang R., Hoffmann D.: A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes, PLoS ONE 2013, 8(3): e58804.
5. Jiang Q.Q., Bartsch L., Sicking W., Wich P.R., Heider D., Hoffmann D., Schmuck C.: A new approach to inhibit human Beta-tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms, Organic and Biomolecular Chemistry 2013, 11(10):1631-1639..
6. Ertle J. M., Heider D., Wichert M., Keller B., Kueper R., Hilgard P., Gerken G., Schlaak J. F.: Combination of Alphafetoprotein and Des-Gamma-Carboxy Prothrombin is superior in detection of Hepatocellular Carcinoma, Digestion 2013, 87(2):121-131.
7. Pyka M., Kircher T., Hauke S., Heider D.: The Brain in a box: an encoding scheme for natural neural networks, Proceedings of the 4th International Joint Conference on Computational Intelligence 2012, Barcelona, Spain, 196-201.
8. Wünsch D., Fetz V., Heider D., Tenzer S., Bier C., Kunst L., Knauer S., Stauber R.: Chemico-genetic strategies to inhibit the leukemic potential of Threonine Aspartase-1, Blood Cancer Journal 2012, 2:e77.
9. van den Boom J., Heider D., Martin S. R., Pastore A., Mueller J. W.: 3'-Phospho-adenosine-5'-phosphosulphate (PAPS) Synthases - Naturally Fragile Enzymes Specifically Stabilised by Nucleotide Binding, Journal of Biological Chemistry 2012, 87(21):17645-17655.
10. Kessler D., Gruen G. C., Heider D., Morgner J., Reis H., Schmid K. W., Jendrossek V.: Concerted Action of Rab11 and Rab25 in Vesicle Trafficking during Cell Migration, Cellular Physiology and Biochemistry 2012, 29:647-656.
11. Dybowski J.N., Riemenschneider M., Hauke S., Pyka M., Verheyen J., Hoffmann D., Heider D.: Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers, BioData Mining 2011, 4:26
12. Driver J., Heider D., Hauke S., Borschbach M., Pyka M.: Hierarchical Text Clustering Based on Independent Component Analysis, Proceedings of the Computational Linguistics-Applications Conference 2011, Warsaw, Poland, ISBN: 978-83-60810-47-7, 17-21.
13. Winkler J., Armano G., Dybowski J. N., Kuhn O., Ledda F., Heider D.: Computational Design of a DNA- and Fc-binding Fusion Protein, Advances in Bioinformatics 2011, 2011:457578
14. Lederer C., Heider D., van den Boom J., Hoffmann D., Mueller J.W., Bayer P.: Single-domain parvulins constitute a specific marker for recently proposed deep-branching archaeal subgroups, Evolutionary Bioinformatics 2011, 7:135-148.
15. Heider D., Barnekow A.: DNA Watermarking: Challenging Perspectives for Biotechnological Applications, Current Bioinformatics 2011, 6(3):375-382.
16. Hauke S., Pyka M., Heider D.: Group-Agreement as a Reliability Measure for Witness Recommendations in Reputation-Based Trust Protocols, Transactions on Computational Science XII, Lecture Notes in Computer Science 2011, 6670:231-255.
17. Heider D., Hoffmann D.: Interpol: An R package for preprocessing of protein sequences, BioData Mining 2011, 4:16
18. Heider D., Verheyen J., Hoffmann D.: Machine learning on normalized protein sequences, BMC Research Notes 2011, 4:94
19. Pyka M.*, Heider D.*, Hauke S., Kircher T., Jansen A.: Dynamic Causal Modeling with Genetic Algorithms, Journal of Neuroscience Methods 2011, 194(2):402-406. * contributed equally
20. Dybowski J. N., Heider D., Hoffmann D.: Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism, AIDS Research and Therapy 2010, 7:41
21. Hauke S., Pyka M., Borschbach M., Heider D.: Reputation-Based Trust Diffusion in Complex Socio-Economic Networks, Information Retrieval and Mining in Distributed Environments, Studies in Computational Intelligence 2010, Springer-Verlag, ISBN 978-3-642-16088-2, 21-40.
22. Hauke S., Pyka M., Heider D.: Towards Improved Trust Diffusion Through Active Recommender Propagation, Systemics and Informatics World Network 2010, 10:121-129
23. Winkler J., Hauke S., Pyka M., Heider D.: JACVANN: A Java Framework For Complex Valued Artificial Neural Networks, Systemics and Informatics World Network 2010, 10:48-55
24. Hauke S., Pyka M., Borschbach M., Heider D.: Augmenting Reputation-based Trust Metrics with Rumor-like Dissemination of Reputation Information, IFIP Advances in Information and Communication Technology 2010, 330:136-147
25. Heider D., Hauke S., Pyka M., Kessler D.: Insights into the classification of small GTPases, Advances and Applications in Bioinformatics and Chemistry 2010, 3:15-24
26. Dybowski J. N.*, Heider D.*, Hoffmann D.: Prediction of co-receptor usage of HIV-1 from genotype, PLoS Comp Biol 2010, 6(4): e1000743. * contributed equally
27. Heider D., Verheyen J., Hoffmann D.: Predicting Bevirimat resistance of HIV-1 from genotype, BMC Bioinformatics 2010, 11:37
28. Pyka M., Hertog M., Fernandez R., Hauke S., Heider D., Dannlowski U. and Konrad C.: fMRI data visualization with BrainBlend and Blender, Neuroinformatics 2010, 8(1): 21-31
29. Pyka M., Beckmann C. F., Schöning S., Hauke S., Heider D., Kugel H., Arolt V., Konrad C.: Impact of working memory load on fMRI resting state pattern in subsequent resting phase, PLoS ONE 2009, 4(9): e7198
30. Heider D., Appelmann J., Bayro T., Dreckmann W., Held A., Winkler J., Barnekow A., Borschbach M.: A computational approach for the identification of small GTPases based on preprocessed amino acid sequences, Technology in Cancer Research and Treatment 2009, 8(5):333-342
31. Heider D., Pyka M., Barnekow A.: DNA watermarks in non-coding regulatory sequences, BMC Research Notes 2009, 2:125
32. Hauke S., Pyka M., Heider D., M. Borschbach: A reputation-based trust framework leveraging the dynamics of complex socio-economic networks for information dissemination, Communications of SIWN 2009, 7:53-58
33. Borschbach M., Hauke S., Pyka M., Heider D.: Opportunities and limitations of a principal component analysis optimized machine learning approach for the identification and classification of cancer involved proteins, Communications of SIWN 2009, 6:85-89
34. Heider D., Kessler D., Barnekow A.: Watermarking sexually reproducing diploid organisms, Bioinformatics 2008, 24(17):1961-1962
35. Heider D., Barnekow A.: DNA watermarks: A proof of concept, BMC Molecular Biology 2008, 9:40
36. Heider D.: A genetic algorithm for producing analogous proteins, Proceedings of the 1st Interdisciplinary Conference on Applied Soft-Computing (ICASC 2008), Muenster, Germany, no pp. given
37. Heider D., Barnekow A.: DNA-based watermarks using the DNA-Crypt algorithm, BMC Bioinformatics 2007, 8:176

1. Kälsch J., Kälsch H., Heider D., Sowa J.-P., Bechmann L., Kahraman A., Moebus S., Slomiany U., Erbel R., Jöckel K.-H., Gerken G., Canbay A.: Are current normal ranges settled to high? Prevalence of abnormal liver transaminases in a populationbased cohort - the Heinz Nixdorf Recall Study, Proc. 119th Kongress der Deutschen Gesellschaft für Innere Medizin e.V. 2013, Wiesbaden, Germany.
2. Budeus B., Heider D., Verheyen J., Hoffmann D.: Co-receptor tropism of HIV-1 is highly significantly associated with non-V3 residues in Env, Proc. 23nd Annual Meeting of the Society for Virology 2013, Kiel, Germany.
3. Sierra S., Dybowski J., Pironti A., Gueney L., Thielen A., Reuter S., Esser S., Fätkenheuer G., Lengauer T., Heider D., Hoffmann D., Pfister H., Jensen B., Kaiser R.: Optimisation of baseline genotypic testing for safe and efficient maraviroc administration, Journal of the International AIDS Society 2012, 15(Suppl 4):18134.
4. Wang Y., Rawi R., Heider D., Dybowski J.N., Hoffmann D.: V3 Loops of HIV-1 gp120 in Chinese and Non-Chinese Show Small Set of Distinct Sequence Features, Proc. 22nd Annual Meeting of the Society for Virology 2012, Essen, Germany
5. Winkler J., Heider D.: ProteinReactor: A novel algorithm for designing chimeric proteins, Proc. 25th German Conference on Bioinformatics 2010, Braunschweig, Germany
6. Dybowski J.N., Heider D., Hoffmann D.: Prediction of coreceptor usage from HIV-1 genotype and application to deep sequencing, 18th International AIDS Conference (AIDS 2010), Vienna, Austria
7. Winkler J., Heider D.: ProteinReactor: A Genetic Algorithm to Generate Protein Sequences, 6th NanoBio-Europe 2010, Muenster, Germany
8. Dybowski J. N., Heider D., Hoffmann D.: Genotypic Prediction of HIV-1 Coreceptor Usage and Application to Deep Sequencing, RIBS Forum, Essen, Germany
9. Pyka M., Hauke S., Heider D., Dannlowski U., Konrad C.: Modelling effective connectivity in fMRI data with artificial neural networks, Frontiers in Neuroinformatics, 2nd INCF Congress of Neuroinformatics 2009, Pilsen, Czech Republic
10. Borschbach M., Hauke S., Pyka M., Heider D.: A preprocessing scheme to reduce the computational complexity of prediction, identification and classification of cancer involved proteins based on machine learning, 17th International Conference on Computing (CIC 2008), Mexico City, Mexico
11. Heider D., Barnekow A.: DNA watermarks and sexual transmission, Europ. J. Cell Biol. 2008, 87S1, 58
12. Heider D., Barnekow A.: DNA watermarks in living organisms, Proceedings of the GBM Fall Meeting 2007, Hamburg, Germany