Knut Reinert

Alexandra Zerck, Eckhard Nordhoff, Hans Lehrach, Knut Reinert: Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinformatics 14: 56 (2013)

Enrico Siragusa, David Weese, Knut Reinert: Scalable string similarity search/join with approximate seeds and multiple backtracking. EDBT/ICDT Workshops 2013: 370-374

Anne-Katrin Emde, Marcel H. Schulz, David Weese, Ruping Sun, Martin Vingron, Vera M. Kalscheuer, Stefan A. Haas, Knut Reinert: Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics 28(5): 619-627 (2012)

David Weese, Manuel Holtgrewe, Knut Reinert: RazerS 3: Faster, fully sensitive read mapping. Bioinformatics 28(20): 2592-2599 (2012)

Chris Bauer, Frank Kleinjung, Dorothea Rutishauser, Christian Panse, Alexandra Chadt, Tanja Dreja, Hadi Al-Hasani, Knut Reinert, Ralph Schlapbach, Johannes Schuchhardt: PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. BMC Bioinformatics 13: 34 (2012)

Sandro Andreotti, Gunnar W. Klau, Knut Reinert: Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE/ACM Trans. Comput. Biology Bioinform. 9(2): 385-394 (2012)

Birte Kehr, Knut Reinert, Aaron E. Darling: Hidden Breakpoints in Genome Alignments. WABI 2012: 391-403

Enrico Siragusa, David Weese, Knut Reinert: Fast and sensitive read mapping with approximate seeds and multiple backtracking. CoRR abs/1208.4238 (2012)

Chris Bauer, Frank Kleinjung, Celia J. Smith, Mark W. Towers, Ali Tiss, Alexandra Chadt, Tanja Dreja, Dieter Beule, Hadi Al-Hasani, Knut Reinert, Johannes Schuchhardt, Rainer Cramer: Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset. BMC Bioinformatics 12: 140 (2011)

Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert: A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics 12: 210 (2011)

Birte Kehr, David Weese, Knut Reinert: STELLAR: fast and exact local alignments. BMC Bioinformatics 12(S-9): S15 (2011)

Sandro Andreotti, Gunnar W. Klau, Knut Reinert: Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. CoRR abs/1102.4016 (2011)

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert, Silke R. Sperling: MicroRazerS: rapid alignment of small RNA reads. Bioinformatics 26(1): 123-124 (2010)

Knut Reinert: Oops I Did it Again... Sustainability in Sequence Analysis via Software Libraries. ERCIM News 2010(82): 13 (2010)

Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner: Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2(2): 692-709 (2009)

Ole Schulz-Trieglaff, Egidijus Machtejevas, Knut Reinert, Hartmut Schlüter, Joachim Thiemann, Klaus Unger: Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Mining 2 (2009)

Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert: A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics 25(9): 1118-1124 (2009)

Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert: Integer Linear Programming in Computational Biology. Efficient Algorithms 2009: 199-218

Markus Bauer, Gunnar W. Klau, Knut Reinert: An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Operations Research 3(2) (2008)

Andreas Döring, David Weese, Tobias Rausch, Knut Reinert: SeqAn An efficient, generic C++ library for sequence analysis. BMC Bioinformatics 9 (2008)

Tobias Rausch, Anne-Katrin Emde, Knut Reinert: Robust consensus computation. BMC Bioinformatics 9(S-10) (2008)

Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert: LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics 9 (2008)

Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher: OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics 9 (2008)

Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Leinenbach, Andreas Hildebrandt, Christian G. Huber, Knut Reinert: Computational Quantification of Peptides from LC-MS Data. Journal of Computational Biology 15(7): 685-704 (2008)

Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert: Segment-based multiple sequence alignment. ECCB 2008: 187-192

Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert, Martin Vingron: Fast and Adaptive Variable Order Markov Chain Construction. WABI 2008: 306-317

Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm: TOPP - the OpenMS proteomics pipeline. Bioinformatics 23(2): 191-197 (2007)

Markus Bauer, Gunnar W. Klau, Knut Reinert: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics 8 (2007)

Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert: Integer linear programming approaches for non-unique probe selection. Discrete Applied Mathematics 155(6-7): 840-856 (2007)

Knut Reinert, Markus Bauer, Andreas Döring, Gunnar W. Klau, Aaron L. Halpern: A General Paradigm for Fast, Adaptive Clustering of Biological Sequences. German Conference on Bioinformatics 2007: 15-29

Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian G. Huber, Knut Reinert: A geometric approach for the alignment of liquid chromatography - mass spectrometry data. ISMB/ECCB (Supplement of Bioinformatics) 2007: 273-281

Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Hildebrandt, Knut Reinert: A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data. RECOMB 2007: 473-487

Ernst Althaus, Alberto Caprara, Hans-Peter Lenhof, Knut Reinert: A branch-and-cut algorithm for multiple sequence alignment. Math. Program. 105(2-3): 387-425 (2006)

Eva Lange, Clemens Gröpl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt: High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques. Pacific Symposium on Biocomputing 2006: 243-254

Christian G. Huber, Oliver Kohlbacher, Knut Reinert (Eds.): Computational Proteomics, 20.-25. November 2005. Dagstuhl Seminar Proceedings 05471, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2006

Witold E. Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert: Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics 6: 203 (2005)

Witold E. Wolski, Maciej Lalowski, Peter Martus, Ralf Herwig, Patrick Giavalisco, Johan Gobom, Albert Sickmann, Hans Lehrach, Knut Reinert: Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics 6: 285 (2005)

Clemens Gröpl, Eva Lange, Knut Reinert, Oliver Kohlbacher, Marc Sturm, Christian G. Huber, Bettina M. Mayr, Christoph L. Klein: Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples. CompLife 2005: 151-162

Markus Bauer, Gunnar W. Klau, Knut Reinert: Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization. CompLife 2005: 217-228

Nathanaël Delmotte, Bettina M. Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph L. Klein, Christian G. Huber: Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins. Computational Proteomics 2005

Christian G. Huber, Oliver Kohlbacher, Knut Reinert: 05471 Executive Summary - Computational Proteomics. Computational Proteomics 2005

Christian G. Huber, Oliver Kohlbacher, Knut Reinert: 05471 Abstract Collection - Computational Proteomics. Computational Proteomics 2005

Markus Bauer, Gunnar W. Klau, Knut Reinert: Multiple Structural RNA Alignment with Lagrangian Relaxation. WABI 2005: 303-314

Knut Reinert: A polyhedral approach to sequence alignment problems. Saarland University 2004

Oliver Kohlbacher, Knut Reinert: Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges). it - Information Technology 46(1): 31-38 (2004)

Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert: Optimal robust non-unique probe selection using Integer Linear Programming. ISMB/ECCB (Supplement of Bioinformatics) 2004: 186-193

Daniel H. Huson, Knut Reinert, Eugene W. Myers: The greedy path-merging algorithm for contig scaffolding. J. ACM 49(5): 603-615 (2002)

Ernst Althaus, Alberto Caprara, Hans-Peter Lenhof, Knut Reinert: Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. ECCB 2002: 4-16

Aaron L. Halpern, Daniel H. Huson, Knut Reinert: Segment Match Refinement and Applications. WABI 2002: 126-139

Daniel H. Huson, Knut Reinert, Saul A. Kravitz, Karin A. Remington, Arthur L. Delcher, Ian M. Dew, Michael Flanigan, Aaron L. Halpern, Zhongwu Lai, Clark M. Mobarry, Granger G. Sutton, Eugene W. Myers: Design of a compartmentalized shotgun assembler for the human genome. ISMB (Supplement of Bioinformatics) 2001: 132-139

Russell J. Turner, Kabir Chaturvedi, Nathan Edwards, Daniel P. Fasulo, Aaron L. Halpern, Daniel H. Huson, Oliver Kohlbacher, Jason R. Miller, Knut Reinert, Karin A. Remington, Russell Schwartz, Brian Walenz, Shibu Yooseph, Sorin Istrail: Visualization challenges for a new cyberpharmaceutical computing paradigm. IEEE Symposium on Parallel and Large-Data Visualization and Graphics 2001: 7-18

Daniel H. Huson, Knut Reinert, Eugene W. Myers: The greedy path-merging algorithm for sequence assembly. RECOMB 2001: 157-163

Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton: Comparing Assemblies Using Fragments and Mate-Pairs. WABI 2001: 294-306

Knut Reinert, Jens Stoye, Torsten Will: An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinformatics 16(9): 808-814 (2000)

John D. Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron: A polyhedral approach to sequence alignment problems. Discrete Applied Mathematics 104(1-3): 143-186 (2000)

Martin Lermen, Knut Reinert: The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. Journal of Computational Biology 7(5): 655-671 (2000)

Hans-Peter Lenhof, Burkhard Morgenstern, Knut Reinert: An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics 15(3): 203-210 (1999)

Knut Reinert, Jens Stoye, Torsten Will: Combining Divide-and-Conquer, the A^*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment. German Conference on Bioinformatics 1999: 17-24

Hans-Peter Lenhof, Knut Reinert, Martin Vingron: A Polyhedral Approach to RNA Sequence Structure Alignment. Journal of Computational Biology 5(3): 517-530 (1998)

Knut Reinert, Hans-Peter Lenhof, Burkhard Morgenstern: An exact solution for the Segment-to-Segment multiple sequence alignment problem. German Conference on Bioinformatics 1998

Hans-Peter Lenhof, Knut Reinert, Martin Vingron: A polyhedral approach to RNA sequence structure alignment. RECOMB 1998: 153-162

Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu: A branch-and-cut algorithm for multiple sequence alignment. RECOMB 1997: 241-250

Phillip G. Bradford, Knut Reinert: Lower Bounds for Row Minima Searching (Extended Abstract). ICALP 1996: 454-465