Benny Kneissl, Dr.

Research Associate

Room: 03-435

Johannes Gutenberg-Universität Mainz
Institut für Informatik
Staudingerweg 9
55128 Mainz, Germany

E-Mail: bkneissl@uni-mainz.de

Office Phone: +49-6131-39-22838
Fax number: +49-6131-39-23534

Research Interests:

Structural Molecular Biology, Machine Learning, Optimization Problems, Chemoinformatics, Drug Design, Molecular Dynamics, G-Protein Coupled Receptors,...

Publications:

Kneissl, B, Müller, SC, Tautermann, CS, and Hildebrandt, A (2011).
String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins
Journal of Chemical Information and Modeling, 51(11):3017-3025.

Kneissl, B, Leonhardt, B, Hildebrandt, A, and Tautermann, CS (2009).
Revisiting Automated G-Protein Coupled Receptor Modeling: The Benefit of Additional Template Structures for a Neurokinin-1 Receptor Model
Journal of Medicinal Chemistry, 52(10):3166-3173.

Leinenbach, A, Hartmer, R, Lubeck, M, Kneissl, B, Elnakady, YA, Baessmann, C, Müller, R, and Huber, CG (2009).
Proteome Analysis of Sorangium cellulosum Employing 2D-HPLC-MS/MS and Improved Database Searching Strategies for CID and ETD Fragment Spectra
Journal of Proteome Research, 8(9):4350-4361.

Backes, C, Keller, A, Küntzer, J, Kneissl, B, Comtesse, N, Elnakady, YA, Müller, R, Meese, E, and Lenhof, H (2007).
GeneTrail—advanced gene set enrichment analysis
Nucleic Acids Research, 35(2):W186-W192.

Küntzer, J, Kneissl, B, Kohlbacher, O, and Lenhof, H (2007).
Abstract analysis of pathways using the BN++ software framework
BMC Systems Biology, 1(2):24.

Short Scientific CV:

since 03/2011		Research Associate at Johannes Gutenberg - University Mainz
01/2008 - 12/2012		Ph.D. student at Saarland University in cooperation with Boehringer Ingelheim
10/2010 - 02/2011		Research Associate at Max-Planck-Institute for Computer Science
05/2007 - 12/2007		Ph.D. student at Boehringer Ingelheim Pharma GmbH & Co. KG
09/2006 - 03/2007		Research Associate at Center for Bioinformatics, Saarland University
10/2005 - 09/2006		Master of Science in Bioinformatics, Saarland University
10/2002 - 10/2005		Bachelor of Science in Bioinformatics, Saarland University

Teaching:

Lectures, seminars, courses

Assistent in Software Engineering (2013 at JGU)
Own Practical Course in C++ (2011 at JGU, 2013 at JGU)
Tutor in Software Engineering (2012 at JGU)
Assistent in Modeling and Simulation (2012 at JGU)
Bioinformatics Seminar (2012 at JGU)

Assistent in Structure based Bioinformatics (2006 at UdS, 2011 at JGU, 2012 at JGU)

Assistent in Sequence based Bioinformatics (2011 and 2012 at JGU)
Assistent in Practical Course Programming with CUDA (2009 at UdS)

Assistent in Scientific Computing in Molecular Modeling (2009 at UdS)

Assistent in Parallel Programming for Bioinformatics (2008 at UdS)

Assistent in Docking (2007 and 2008 at UdS)

Tutor in Docking (2005 at UdS)

Tutor in Sequence based Bioinformatics (2004 at UdS)

Diploma, Bachelor's and Master's thesis

Bachelor's thesis: Including Ligand Information in GPCR Modeling - A Promising Step towards Improved Binding Pocket Accuracy? (Tim Seifert, 2013 at JGU)
Bachelor's thesis: Analyzing Molecular Dynamic Trajectories of Peptides by means of GPCR Helices (Andreas Lund, 2011 at JGU)

Bachelor's thesis: Identication and Similarity Measurement of GPCR Binding Pockets (Debora Ernst, 2011 at UdS)

Master's thesis: The Applicability of Artificial Evolution for modeling transmembrane helices by means of GPCRs (Alexander Baldauf, 2011 at UdS)

Master's thesis: Kink prediction in α-helices using string kernels for support vector machines (Sabine Müller, 2009 at UdS)

Bachelor's thesis: Topology prediction of protein structures using a Hidden Markov Model (Jan Riehm, 2009 at UdS)

Diploma thesis: Optimierung von Helix-Helix Interaktionen bei G-Protein-gekoppelten Rezeptoren (Thomas Thies, 2008 at EKU)

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