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Dr. Anna-Katharina Hildebrandt

Employment: 
Researcher
Personal: 

This is the personal site of Anna-Katharina Hildebrandt, aka Dehof :-).

 

 

 

Education: 
since 04/2012 Postdoctoral researcher at chair of Prof. Lenhof, Center for Bioinformatics
03/2012 PhD-thesis at Graduate School of Saarland University, chair of Prof. Lenhof, Center for Bioinformatics
04/2007 Master's Degree, Saarland University
10/2005 Bachelor's Degree, Saarland University
2004 Summer placement at the Bioinformatics Research Center at Glasgow University
2002-2007 Studies in Computational Biology at Saarland University
1999-2002 Job training as Mathematisch-Technische Assistentin/Informatik (IHK) at AXA Tech

 

Research: 

My current research interests are in the fields of structure based bioinformatics and eLearning:

  • NMR-based structure analysis and docking algorithms (Drug Design and Machine Learning)
  • Real time ray tracing techniques in Molecular Visualization for the molecular viewing and editing tool BALLView
  • Optimization techniques, e.g., for bond order assignment (Cheminformatics)
  • Computational Proteomics
  • Image Processing
  • The BALL project
  • Development of web interfaces for bioinformatic services (ballaxy)
  • Bioinformatics education, e.g. MSWissenschaft
Teaching: 
Lectures, seminars, courses
  • TA Bioinformatics 1 (WS 07/08, WS 08/09, WS 09/10, WS 10/11, WS 11/12, WS 12/13, WS 13/14)
  • TA Bioinformatics 2 (SS 06, SS 07, SS 09, SS 11, SS 12, SS 13)
  • TA "Fighting Cancer in Bioinformatics"(SS 08)
  • Proseminar "Bioinformatic Approaches for Cancer Research" (repeatedly 2007-2013)
  • Proseminar "Efficient Algorithms for RNA molecules" (repeatedly 2007-2013)
  • Seminar "Modelling and Analyzing Biological Networks" (repeatedly 2007-2013)
  • Seminar "Selected Topics in Molecular Docking" (repeatedly 2007-2013)
  • Seminar "Computation in Systems Biology" (WS 07/08)
  • Girl's Day / Girl's Camp (SS07, SS 08, SS09, WS 09/10)
Diploma, Bachelor's and Master's thesis
  • "Implementation of RNA shift prediction in BALL" (Christina Kiefer WS13/14)
  • "XML3D based molecular structure visualization using BALLView and BALLaxy" (Lukas Brausch WS13/14)
  • "Segmentation of biological images based on space and colour neighbourhood" (Sebastian Schattner, SS13)
  • "Normal Mode Based Structure Recognition for Scoring Cryo-EM Images" (Vanessa Morguet, SS13)
  • "Erweiterung und Evaluierung von BALLView und des Präsentationsframeworks PresentaBALL für den Einsatz im Chemieunterricht an weiterführenden Schulen" (Markus Konietzko, SS12)
  • "Design and implementation of the functionality to align sequences and structures into the Biochemical Algorithms Library" (Nikola Koch, SS12)
  • "Implementation of a Graph Coloring Algorithm for InChi Computation" (Alexander Zapp, SS12)
  • "pKa-dependent Bond Order Assignment of Organic Molecules" (Adrian Fritz, WS11/12)
  • "Statistical Analysis of Bond Orders in Ligand Molecules" (Alexander Gress, SS12)
  • "A hybrid model for NMR chemical shift prediction" (Simon Loew, WS10/11)
  • "Structural Stability and Immunogenicity of Peptides" (Eva Kranz, WS09/10)
  • "TNF alpha antibody design" (Miriam Mangels , WS09/10)

My Publications

2015

[DOT+15] Dietzen, M., Kalinina, O.V., Taskova, K., Kneissl, B., Hildebrandt, A.-K., Jaenicke, E., Decker, H., Lengauer, T., and Hildebrandt, A.:Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces. Proteins: Structure, Function, and Bioinformatics. 2015
[HSH+15] Hoang-Vu, D., Schmidt, B., Hildebrandt, A., Tran, T.T. and Hildebrandt, A.-K: CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm International Journal of High Performance Computing Applications, 2015

2014

[AKH+14] Hildebrandt, A. K., Stöckel D., Fischer, N. M., de la Garza, L., Krüger, J., Nickels, S., Röttig, M., Schärfe, C., Schumann, M., Thiel, P., Lenhof, H.-P., Kohlbacher, O., and Andreas Hildebrandt, ballaxy: web services for structural bioinformatics, Bioinformatics 2014, doi: 10.1093/bioinformatics/btu574
[AHH14] Althaus, E., Hildebrandt, A. and Hildebrandt, A.K. A Greedy Algorithm for Hierarchical Complete Linkage Clustering. 1st International Conference on Algorithms for Computational Biology (AlCoB 2014)
[HDL+14] Hildebrandt, A.K., Dietzen, M., Lengauer, T., Lenhof, H.-P., Althaus, E., and Hildebrandt, A. Efficient computation of root mean square deviations under rigid transformations. J Comput Chem. 35(10):765–771, 2014
[HSH+14] Hoang-Vu Dang and Schmidt, B. and Hildebrandt, A. and Hildebrandt, A.K. Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs. 22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP). ISSN:1066-6192, 2014

2013

[CEG+13] Cabezas-Wallscheid, N., Eichwald, V., de Graaf, J., Löwer, M., Lehr, H.-A., Kreft, A., Eshkind, L., Hildebrandt, A., Abassi, Y., Heck, R., Dehof, A. K., Ohngemach, S., Sprengel, R., Wörtge, S., Schmitt, S., Lotz, J., Meyer, C., Kindler, T., Zhang, D.-E., Kaina, B., Castle, J. C., Trumpp, A., Sahin, U. and Bockamp, E.: Instruction of haematopoietic lineage choices, evolution of transcriptional landscapes and cancer stem cell hierarchies derived from an AML1-ETO mouse model. EMBO Mol Med. doi: 10.1002/emmm.201302661, 2013.
[NSM+13] Nickels, S., Stöckel, D., Mueller, S.C., Lenhof, H.-P., Hildebrandt, A., and Dehof, A.K.: PresentaBALL – a Powerful Package for Presentations and Lessons in Structural Biology. BioVis - 3rd IEEE Symposium on Biological Data Visualization, 2013.
[HEL+13] Hildebrandt, A.K., Althaus, E., Lenhof, H.P., Hung, C.W., Tholey, A., and Hildebrandt, A.: Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics. Proceedings of the German Conference on Bioinformatics (GCB), 2013.
[DLL+13] Dehof, A.K., Loew, S., Lenhof, H.-P., & Hildebrandt, A.: NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction. BMC Bioinformatics, 14(1):98, 2013.

2012

[NSM+12] Nickels, S, Sminia, H, Mueller, S, Kools, B, A.K. Dehof, H.-P. Lenhof, and A. Hildebrandt: (2012) ProteinScanAR - An augmented reality web application for high school education in biomolecular life sciences. Proceedings of the 6th International Symposium on Information Visualization in Biomedical Informatics (IVBI 2012).

2011

[DLH11] Dehof, A.K., Lenhof, H.-P., and Hildebrandt, A.: Predicting Protein NMR Chemical Shifts in the Presence of Ligands and Ions using Force Field-based Features. Proceedings of the German Conference on Bioinformatics (GCB), 2011.
[DRB+11] Dehof, A.K., Rurainski, A., Bui, Q.B.A., Böcker, S., Lenhof, H.-P. & Hildebrandt, A.: Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 27(13), 2011.

2010

[HDR+10] Hildebrandt, A., Dehof, A.K., Rurainski, A., Bertsch, A., Schumann, M., Toussaint, N.C., Moll, A., Stöckel, D., Nickels, S., Müller, S.C., Lenhof, H.-P. & Kohlbacher, O.: BALL - Biochemical Algorithms Library 1.3. BMC Bioinformatics, 11:531, 2010.
[SER+10] Singh, K.K., Erkelenz, S., Rattay, S., Dehof, A.-K., Hildebrandt, A., Schulze-Osthoff, K., Schaal, H., and Schwerk, C.: Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold. RNA, 2010, 16(12), 2442-2454, 2010.
[MDG+10] Marsalek, L., Georgiev, I., Dehof, A.K., Lenhof, H.-P., Slusallek, P., and Hildebrandt, A.: Real-time Ray Tracing of Complex Molecular Scenes. Proceedings of the IVbm 10 - Information Visualization in Biomedical Informatics, 2010.
[PGDN+10] M. Phillips, I. Georgiev, A.K. Dehof, L. Marsalek, H.-P. Lenhof, A. Hildebrandt, and P. Slusallek: (2010) Measuring Properties of Molecular Surfaces Using Ray Casting. HiCOMB 2010, Proceedings of 9th International Workshop on High Performance Computational Biology

2009

[DGMS+09] A. K. Dehof, I. Georgiev, L. Marsalek, D. Stöckel, S. Nickels, H.-P. Lenhof, P. Slusallek and A. Hildebrandt (2009): Visual Computing in Computer Aided Drug Design. Visual Computing Research Conference, Saarbrücken, Germany, 8-10 December 2009
[DRL+09] Dehof, A. K., Rurainski, A., Lenhof, H.-P., and Hildebrandt, A.: Automated Bond Order Assignment as an Optimization Problem. Proceedings of the German Conference on Bioinformatics (GCB), Lecture Notes in Informatics, 2009.
[BRFD+05] K.H. Brämswig, A.B. Riemer, E. Förster-Waldl, A. Dehof, D. Neumann, H.N. Lode, C. Zielinski, O. Scheiner, H. Pehamberger, E. Jensen-Jarolim (2005): Generation of Peptide mimics of Melanoma Antigen GD2. Proceedings of the 35th Annual European Society for Dermatological Research (ESDR) Meeting, Journal of Investigative Dermatology 125(S1:A35)
[FRDN+05] E. Förster-Waldl, A.B. Riemer, A.K. Dehof, D. Neumann, K.H. Brämswig, G. Boltz-Nitulescu, H. Pehamberger, C. Zielinski, O. Scheiner, A. Plloak, H.N. Lode, and E. Jensen-Jarolim: (2004) Isolation and structural analysis of peptide mimotopes for the disialoganglioside GD2, a neuroblastoma tumor antigen Molecular Immunology

Contact

Address:
Center for Bioinformatics
Saarland University
Building E 2.1
Room 402
P.O. Box 15 11 50
Email:
anna.hildebrandt@bioinf.uni-sb.de
Fax:
+49-681-302-64719
Phone:
+49-681-302-68613