Publications

336 entries « 7 of 7 »

Dönnes, Pierre; Höglund, Annette; Sturm, Marc; Comtesse, Nicole; Backes, Christina; Meese, Eckart; Kohlbacher, Oliver; Lenhof, Hans-Peter

Integrative analysis of cancer-related data using CAP

FASEB Journal, 18 (12), pp. 1465-1467, 2004.

(Links | BibTeX)

Dönnes, Pierre; Höglund, Annette

Predicting Protein Subcellular Localization: Past, Present, and Future

Genomics Proteomics Bioinformatics, 2 (4), pp. 209–215, 2004.

(Abstract | Links | BibTeX)

Kerzmann, Andreas; Neumann, Dirk; Kohlbacher, Oliver

High-Accuracy Prediction of Protein-Carbohydrate Interactions

Trends in Glycoscience and Glycotechnology, 16 , pp. S26, 2004.

(BibTeX)

Florea, Liliana; Halldórsson, Bjarni; Kohlbacher, Oliver; Schwartz, Russell; Hoffman, Stephen; Istrail, Sorin

Epitope Prediction Algorithms for Peptide based Vaccine Design

Proceedings of the 2nd IEEE Computer Society Conference on Bioinformatics, pp. 17-26, IEEE Computer Society, 2003, (PMID: 16826643).

(Links | BibTeX)

Hildebrandt, Andreas; Kohlbacher, Oliver; Blossey, Ralf; Lenhof, Hans-Peter

Using nonlocal electrostatics for solvation free energy computations: ions and small molecules

2003.

(Links | BibTeX)

Sandelin, Albin; Höglund, Annette; Lenhard, Boris; Wasserman, Wyeth

Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes

Funct Integr Genomics, 3 (3), pp. 125-134, 2003.

(BibTeX)

Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans Peter; Müller, Peter

A Combinatorial Approach to Protein Docking with Flexible Side-Chains

J. Comput. Biol., 9 (4), pp. 597-612, 2002.

(Abstract | Links | BibTeX)

Neumann, Dirk; Kohlbacher, Oliver; Lenhof, Hans-Peter; Lehr, Claus-Michael

Protein-sugar interactions: Calculated versus experimental binding energies

Eur. J. Biochem., 269 (5), pp. 1518-1524, 2002.

(Links | BibTeX)

Neumann, Dirk; Kerzmann, Andreas; Kohlbacher, Oliver

Modelling the sugar-lectin interaction by computer simulated docking

Abstracts of the 20th Interlec Meeting, pp. 116, University of Copenhagen, Copenhagen, Denmark, 2002.

(BibTeX)

Sirava, Marite; Schäfer, Thomas; Eiglsperger, Markus; Kaufmann, Michael; Kohlbacher, Oliver; Bornberg-Bauer, Erich; Lenhof, Hans-Peter

BioMiner - modeling, analysing, and visualizing biochemical pathways and networks

Bioinformatics, 19 (10), pp. S219-230, 2002.

(Links | BibTeX)

Dönnes, Pierre; Elofsson, Arne

Prediction of MHC class I binding peptides, using SVMHC

BMC Bioinformatics, 3 (25), 2002.

(Links | BibTeX)

Kohlbacher, Oliver; Burchardt, Andreas; Moll, Andreas; Hildebrandt, Andreas; Bayer, Peter; Lenhof, Hans-Peter

Structure prediction of protein complexes by a NMR-based protein docking algorithm

J. Biomol. NMR, 20 , pp. 15-21, 2001.

(Abstract | Links | BibTeX)

Turner, Russell J; Chaturvedi, Kabir; Edwards, Nathan J; Fasulo, Daniel; Halpern, Aaron L; Huson, Daniel H; Remington, Karin A; Schwartz, Russell; Walenz, Brian; Yooseph, Shibu; Istrail, Sorin

Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm

Proceedings of the IEEE Symposium on Parallel and Large-Data Visualization and Graphics (PVG2001), pp. 7–18, San Diego, USA,, 2001.

(BibTeX)

Kohlbacher, Oliver; Burchardt, Andreas; Hildebrandt, Andreas; Moll, Andreas; Bayer, Peter; Lenhof, Hans-Peter

A NMR-spectra-based scoring function for protein docking

Sankoff, David; Lengauer, Thomas (Ed.): RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, pp. 169-177, ACM press, 2001.

(Links | BibTeX)

Kohlbacher, Oliver

BALL - A Framework for Rapid Application Development in Molecular Modeling

Beiträge zum Heinz-Billing-Preis 2000, pp. 13-28, Gesellschaft für wissenschaftliche Datenverarbeitung mbH, Göttingen, 2001.

(Links | BibTeX)

Neumann, Dirk; Kohlbacher, Oliver; Haltner, Eleonore; Lenhof, Hans-Peter; Lehr, Claus-Michael

Modeling the Sugar Lectin Interaction by Computational Chemistry Relevant to Drug Design

Proc. 3rd World Meeting on Pharmaceutics, Biopharmaceutics and Pharmaceutical Technology, pp. 233, 2000.

(BibTeX)

Kohlbacher, Oliver; Lenhof, Hans-Peter

BALL - Rapid Software Prototyping in Computational Molecular Biology

Bioinformatics, 16 (9,), pp. 815–824, 2000.

(Abstract | Links | BibTeX)

Boghossian, N P; Kohlbacher, O; Lenhof, H P

Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL)

J. Exp. Algorithmics, 5 , pp. 16, 2000.

(BibTeX)

Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans-Peter; Müller, Peter

A Combinatorial Approach to Protein Docking with Flexible Side-Chains

Shamir, Ron; Miyano, Satoru; Istrail, Sorin; Pevzner, Pavel; Waterman, Michael (Ed.): RECOMB 2000 -- Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, pp. 15–24, ACM press, 2000.

(BibTeX)

Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans-Peter; Müller, Peter

A branch and cut algorithm for the optimal solution of the side-chain placement problem

Max-Planck-Institute für Informatik Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany, (MPI-I-2000-1-001), 2000.

(Links | BibTeX)

Kohlbacher, O; Lenhof, H -P

Rapid Software Prototyping in Computational Molecular Biology

Proceedings of the German Conference on Bioinformatics (GCB'99), 1999.

(BibTeX)

Boghossian, Nicolas Pascal; Kohlbacher, Oliver; Lenhof, Hans-Peter

BALL: Biochemical Algorithms Library

Vitter, J S; Zaroliagis, C D (Ed.): Algorithm Engineering, 3rd International Workshop, WAE'99, Proceedings, pp. 330-344, Springer, 1999.

(BibTeX)

Boghossian, Nicolas Pascal; Kohlbacher, Oliver; Lenhof, Hans-Peter

BALL: Biochemical Algorithms Library

Max-Planck-Institut für Informatik Saarbrücken, Germany, (MPI-I-99-1-002), 1999.

(Links | BibTeX)

Neumann, Dirk; Haltner, Elleonore; Lehr, Claus-Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

Investigating the Sugar-Lectin Interaction by Computational Chemistry: Tunneling the Epithelial Barrier

Abstracts of the 18th Interlec Meeting, pp. 549, 1998.

(BibTeX)

Friedrich, Andreas; de la Garza, Luis; Kohlbacher, Oliver

0000.

(BibTeX)

Lara Schneider Tim Kehl, Kristina Thedinga Nadja Grammes Christina Backes Christopher Mohr Benjamin Schubert Kerstin Lenhof Nico Gerstner Andreas Daniel Hartkopf Markus Wallwiener Oliver Kohlbacher Andreas Keller Eckart Meese Norbert Graf Hans-Peter Lenhof L

ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification

Bioinformatics, Forthcoming.

(BibTeX)

Bernadette Richter Marc Rurik, Stephanie Gurk Oliver Kohlbacher Markus Fischer

Food monitoring: Screening of the geographical origin of white asparagus using FT-NIR and machine learning

Food Control, Forthcoming.

(BibTeX)

Choobdar, Sarvenaz; Ahsen, Mehmet E; Crawford, Jake; Tomasoni, Mattia; Fang, Tao; Lamparter, David; Lin, Junyuan; Hescott, Benjamin; Hu, Xiaozhe; Mercer, Johnathan; Natoli, Ted; Narayan, Rajiv; and Subramanian, Aravind; Zhang, Jitao D; Stolovitzky, Gustavo; Kutalik, Zoltán; Lage, Kasper; Slonim, Donna K; Saez-Rodriguez, Julio; Cowen, Lenore J; Bergmann, Sven; Marbach, Daniel

Assessment of network module identification across complex diseases

Nat. Methods, 16 , pp. 843–852, 0000.

(Abstract | Links | BibTeX)

Samuel Wein Byron Andrews, Timo Sachsenberg Helena Santos-Rosa Oliver Kohlbacher Tony Kouzarides Benjamin Garcia ; Weisser, Hendrik

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Nat. Commun., Forthcoming.

(BibTeX)

Jeong, Kyowon; Kim, Jihyung; Gaikwad, Manasi; Hidayah, Siti Nurul; Heikaus, Laura; Schlüter, Hartmut; Kohlbacher, Oliver

FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics

Cell Systems, Forthcoming, ISSN: 2405-4712.

(Abstract | Links | BibTeX)

Schulte-Schrepping, J; Reusch, N; Paclik, D; Ba?ler, K; Schlickeiser, S; Zhang, B; Kr?mer, B; Krammer, T; Brumhard, S; Bonaguro, L; Domenico, De E; Wendisch, D; Grasshoff, M; Kapellos, T S; Beckstette, M; Pecht, T; Saglam, A; Dietrich, O; Mei, H E; Schulz, A R; Conrad, C; Kunkel, D; Vafadarnejad, E; Xu, C J; Horne, A; Herbert, M; Drews, A; Thibeault, C; Pfeiffer, M; Hippenstiel, S; Hocke, A; M?ller-Redetzky, H; Heim, K M; Machleidt, F; Uhrig, A; de Jarcy, Bosquillon L; J?rgens, L; Stegemann, M; Gl?senkamp, C R; Volk, H D; Goffinet, C; Landthaler, M; Wyler, E; Georg, P; Schneider, M; Dang-Heine, C; Neuwinger, N; Kappert, K; Tauber, R; Corman, V; Raabe, J; Kaiser, K M; Vinh, M T; Rieke, G; Meisel, C; Ulas, T; Becker, M; Geffers, R; Witzenrath, M; Drosten, C; Suttorp, N; von Kalle, C; Kurth, F; H?ndler, K; Schultze, J L; Aschenbrenner, A C; Li, Y; Nattermann, J; Sawitzki, B; Saliba, A E; Sander, L E; Angelov, A; Bals, R; Bartholom?us, A; Becker, A; Bezdan, D; Bonifacio, E; Bork, P; Clavel, T; Colome-Tatche, M; Diefenbach, A; Dilthey, A; Fischer, N; F?rstner, K; Frick, J S; Gagneur, J; Goesmann, A; Hain, T; Hummel, M; Janssen, S; Kalinowski, J; Kallies, R; Kehr, B; Keller, A; Kim-Hellmuth, S; Klein, C; Kohlbacher, O; Korbel, J O; Kurth, I; Landthaler, M; Li, Y; Ludwig, K; Makarewicz, O; Marz, M; McHardy, A; Mertes, C; N?then, M; N?rnberg, P; Ohler, U; Ossowski, S; Overmann, J; Peter, S; Pfeffer, K; Poetsch, A R; P?hler, A; Rajewsky, N; Ralser, M; Rie?, O; Ripke, S; da Rocha, Nunes U; Rosenstiel, P; Saliba, A E; Sander, L E; Sawitzki, B; Schiffer, P; Schulte, E C; Schultze, J L; Sczyrba, A; Stegle, O; Stoye, J; Theis, F; Vehreschild, J; Vogel, J; von Kleist, M; Walker, A; Walter, J; Wieczorek, D; Ziebuhr, J

Severe COVIĐ-19 Is Marked by a Đysregulated Myeloid Cell Compartment

Cell, 0000.

(Abstract | BibTeX)

Klare Juliane; Rurik, Marc; Rottmann Eric; Bollen Anke; Kohlbacher Oliver; Fischer Markus; Hackl Thomas

Determination of the Geographical Origin of Asparagus officinalis L. by 1H‐NMR‐Spectroscopy

J. Agricult. Food Chem., Forthcoming.

(BibTeX)

et al., Eugen Netz

OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS

Mol. Cell. Prot., Forthcoming.

(BibTeX)

Alexander Leitner Alexandre M.J.J. Bonvin, Christoph Borchers Robert Chalkley Julia Chamot-Rooke Colin Combe Jürgen Cox Meng-Qiu Dong Lutz Fischer Michael Götze Fabio Gozzo Albert Heck Michael Hoopmann Lan Huang Yasushi Ishihama Andrew Jones Nir Kalisman Oliver Kohlbacher Karl Mechtler Robert Moritz Eugen Netz Petr Novak Evgeniy Petrotchenko Andrej Sali Richard Scheltema Carla Schmidt David Schriemer Andrea Sinz Frank Sobott Florian Stengel Konstantinos Thalassinos Henning Urlaub Rosa Viner Juan Vizcaino Marc Wilkins Juri Rappsilber H J W C J R R R L A A R

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

Structure, Forthcoming.

(Abstract | Links | BibTeX)

B, Richter; M, Rurik; S, Gurk; O, Kohlbacher; M, Fischer

Food monitoring: Screening of the geographical origin of white asparagus using FT-NIR and machine learning

Food Control, 104 , pp. 318-325, 0000.

(Abstract | Links | BibTeX)

Arndt, Maike; Rurik, Marc; Drees, Alissa; Ahlers, Christian; Feldmann, Simon; Kohlbacher, Oliver; Fischer, Markus

Food Authentication: Determination of the geographical origin of almonds (Prunus dulcis MILL.) via near-infrared spectroscopy

Microchem. J., Forthcoming.

(BibTeX)

336 entries « 7 of 7 »

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