M Holtgrewe, L Kuchenbecker, K Reinert (2015) Methods for the detection and assembly of novel sequence in high-throughput sequencing data. Bioinformatics, 31 (12): 1904-12
S Aiche et al. (2015) Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. Proteomics, 15 (8): 1443-7
V Neu, C Bielow, K Reinert, CG Huber (2014) Ultrahigh-performance liquid chromatography-ultraviolet absorbance detection-high-resolution-mass spectrometry combined with automated data processing for studying the kinetics of oxidative thermal degradation of thyroxine in the solid state. J Chromatogr A., 1371:196-203
J Hu, K Reinert (2015) LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks. Bioinformatics, 31 (3): 363-72
H Hauswedell, J Singer, K Reinert (2014) Lambda: the local aligner for massive biological data. Bioinformatics, 30 (17): i349-i355
MH Schulz et al. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics, 30 (17): i356-i363
B Kehr, K Trappe, M Holtgrewe, K Reinert (2014) Genome alignment with graph data structures: a comparison. BMC Bioinformatics, 15 (1): 99
J Hu, B Kehr, K Reinert (2013) NetCoffee: A fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics, 30 (4): 540-8
S Andreotti, K Reinert, S Canzar (2013) The duplication-loss small phylogeny problem: from cherries to trees. J Comput Biol., 20 (9): 643-59
A Zerck, E Nordhoff, H Lehrach, K Reinert (2013) Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinformatics, 14 (1): 56
V Neu et al. (2013) Rapid and comprehensive impurity profiling of synthetic thyroxine by UHPLC-HR-MS. Anal Chem., 85 (6): 3309-17
E Siragusa, D Weese, K Reinert (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res., 41 (7): e78
V Neu, C Bielow, P Schneider, K Reinert, H Stuppner, CG Huber (2013) Investigation of reaction mechanisms of drug-degradation in the solid-state: a kinetic study implementing ultrahigh-performance liquid chromatography and high-resolution mass spectrometry for thermally stressed thyroxine. Anal Chem., 85 (4): 2385-90
S Nahnsen, C Bielow, K Reinert, O Kohlbacher (2012) Tools for label-free peptide quantification. Mol Cell Proteomics., 12 (3): 549-56
D Weese, M Holtgrewe, K Reinert (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20): 2592-9
S Aiche, K Reinert, C Schütte, D Hildebrand, H Schlüter, TO Conrad (2012) Inferring proteolytic processes from mass spectrometry time series data using degradation graphs. PLoS One, 7 (7): e40656
J Junker, C Bielow, A Bertsch, M Sturm, K Reinert, O Kohlbacher (2012) TOPPAS: A graphical workflow editor for the analysis of high-throughput proteomics data. J Proteome Res., 11 (7): 3914-20
C Bauer et al. (2012) PPINGUIN: Peptide profiling guided identification of proteins improves quantification of iTRAQ ratios. BMC Bioinformatics, 13 (1): 34
AK Emde, MH Schulz, D Weese, R Sun, M Vingron, VM Kalscheuer, SA Haas, K Reinert (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5): 619-27
B Kehr, D Weese, K Reinert (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12(Suppl 9): S15
M Holtgrewe, AK Emde, D Weese, K Reinert (2011) A novel and well-defined benchmarking method for second generation read mapping. BMC Bioinformatics, 12 (1): 210
C Bauer et al. (2011) Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset. BMC Bioinformatics, 12 (1): 140
C Bielow, S Aiche, S Andreotti, K Reinert (2011) MSSimulator: Simulation of mass spectrometry data. J Proteome Res., 10 (7): 2922-9
S Andreotti, GW Klau, K Reinert (2011) Antilope - a Lagrangian relaxation approach to the de novo peptide sequencing problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9 (2):385-94
A Bertsch, C Gröpl, K Reinert, O Kohlbacher (2011) OpenMS and TOPP: Open Source Software for LC-MS Data Analysis. Methods Mol Biol., 696:353-67
D Hüser, A Gogol-Döring, T Lutter, S Weger, K Winter, EM Hammer, T Cathomen, K Reinert, R Heilbronn (2010) Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome. PLoS Pathog., 6(7):e1000985
C Bielow, S Ruzek, CG Huber, K Reinert (2010) Optimal decharging and clustering of charge ladders generated in ESI-MS. J Proteome Res, 9(5):2688-95
AK Emde, M Grunert, D Weese, K Reinert, SR Sperling (2010) MicroRazerS: rapid alignment of small RNA reads. Bioinformatics, 26(1):123-4
K Reinert and O Kohlbacher (2010) OpenMS and TOPP: open source software for LC-MS data analysis. Methods Mol Biol., 604:201-11
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D Weese, AK Emde, T Rausch, A Döring, K Reinert (2009) RazerS--fast read mapping with sensitivity control. Genome Res., 19(9):1646-54
A Zerck et al (2009) An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics. J Proteome Res., 8(7):3239-51
T Rausch, S Koren, G Denisov, D Weese, AK Emde, A Dö, K Reinert (2009) A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25(9):1118-24
O Schulz-Trieglaff, E Machtejevas, K Reinert, H Schlüter, J Thiemann, K Unger (2009) Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min., 2(1):4
O Schulz-Trieglaff, N Pfeifer, C Gröpl, O Kohlbacher, K Reinert (2008) LC-MSsim--a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics, 9:423
O Schulz-Trieglaff, R Hussong, C Gröpl, A Leinenbach, A Hildebrandt, C Huber, K Reinert (2008) Computational quantification of peptides from LC-MS data. J Comput Biol., 15(7):685-704
T Rausch, AK Emde, D Weese, A Döring, C Notredame, K Reinert Segment-based multiple sequence alignment. Bioinformatics, 24(16):i187-92
M Sturm et al (2008) OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics, 9:163
A Döring, D Weese, T Rausch, K Reinert (2008) SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9:11
O Schulz-Trieglaff, R Hussong, C Gröpl, A Hildebrandt, K Reinert (2007) A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry data. In "Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007)", pages 473-487, 2007.
E Lange, C Gröpl, O Schulz-Trieglaff, K Reinert A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data. In "Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), 2007.
M Bauer, G Klau, K Reinert (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, number 1, volume 8, pages 271
G Klau, S Rahmann, A Schliep, M Vingron, K Reinert (2007) Integer Linear Programming Approaches for Non-unique Probe Selection. Discrete Applied Mathematics, 155, pages 840-856
M Bauer, GW Klau, K Reinert (2005) Multiple Structural RNA Alignment with Lagrangian Relaxation. In "Proceedings of the 5th Workshop on Algorithms Bioinformatics (WABI-05), pages 303-314
K Reinert, O Kohlbacher, C Gröpl, E Lange, O Schulz-Trieglaff, M Sturm, N Pfeifer (2005) OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In "Computational Proteomics", IBFI, 2005. Dagstuhl Online Publication Server (DROPS).
G Klau, S Rahmann, A Schliep, M Vingron, K Reinert Optimal Robust Non-Unique Probe Selection Using Integer Linear Programming. In "Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology (ISMB-04)", pages 186-193, 2004.
A Halpern, D Huson and K Reinert (2002) Segment match refinment and applications. Proceedings of the 2nd Workshop on Algorithms Bioinformatics (WABI-02), 126-139.
DH Huson, K Reinert and EW Myers (2002) The greedy path-merging algorithm for sequence assembly. J. of the ACM49(5), 603-615.
DH Huson, D.H., AL Halpern, Z Lai, EW Myers, K Reinert and GG Sutton (2001) Comparing assemblies using fragments and mate-pairs. Proc. of the 1st Workshop on Algorithms Bioinformatics (WABI-01), 294-306.
DH Huson, K Reinert, SA Kravitz, KA Remington, AL Delcher, IM Dew, M Flanigan, AL Halpern, Z Lai, CM Mobarry, GG Sutton and EW Myers (2001) Design of a compartmentalized shotgun assembler for the human genome. Proc. of the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB01), 132-139.
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K Reinert, J Stoye and T Will (2000) An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinformatics16(9), 808- 814.
JD Kececioglu, HP Lenhof, K Mehlhorn, P Mutzel, K Reinert and M Vingron (2000). A polyhedral approach to sequence alignment problems. Discr. Appl. Mathematics104, 143-186.
HP Lenhof, K Reinert and M Vingron (1998) A polyhedral approach to RNA sequence structure alignment. J. Comp. Biol.5(3), 517-530.