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Group by: Date | Item Type Number of items: 99. 2022Meyer, F. and Fritz, A. and Deng, Z.-L. and Koslicki, D. and Gurevich, A. and Robertson, G. and Alser, M. and Antipov, D. and Beghini, F. and Bertrand, D. and Brito, J. J. and Brown, C.T. and Buchmann, J. and Buluç, A. and Chen, B. and Chikhi, R. and Clausen, P. T. and Cristian, A. and Dabrowski, P. W. and Darling, A. E. and Egan, R. and Eskin, E. and Georganas, E. and Goltsman, E. and Gray, M. A. and Hansen, L. H. and Hofmeyr, S. and Huang, P. and Irber, L. and Jia, H. and Jørgensen, T. S. and Kieser, S. D. and Klemetsen, T. and Kola, A. and Kolmogorov, M. and Korobeynikov, A. and Kwan, J. and LaPierre, N. and Lemaitre, C. and Li, C. and Limasset, A. and Malcher-Miranda, F. and Mangul, S. and Marcelino, V. R. and Marchet, C. and Marijon, P. and Meleshko, D. and Mende, D. R. and Milanese, A. and Nagarajan, N. and Nissen, J. and Nurk, S. and Oliker, L. and Paoli, L. and Peterlongo, P. and Piro, V. C. and Porter, J. S. and Rasmussen, S. and Rees, E. R. and Reinert, K. and Renard, B. and Robertsen, E. M. and Rosen, G. L. and Ruscheweyh, H.-J. and Sarwal, V. and Segata, N. and Seiler, E. and Shi, L. and Sun, F. and Sunagawa, S. and Sørensen, S. J. and Thomas, A. and Tong, C. and Trajkovski, M. and Tremblay, J. and Uritskiy, G. and Vicedomini, R. and Wang, Zi. and Wang, Zhe. and Wang, Zho. and Warren, A. and Willassen, N. P. and Yelick, K. and You, R. and Zeller, G. and Zhao, Z. and Zhu, S. and Zhu, J. and Garrido-Oter, R. and Gastmeier, P. and Hacquard, S. and Häußler, S. and Khaledi, A. and Maechler, F. and Mesny, F. and Radutoiu, S. and Schulze-Lefert, P. and Smit, N. and Strowig, T. and Bremges, A. and Sczyrba, A. and McHardy, A. C. (2022) Critical Assessment of Metagenome Interpretation - the second round of challenges. Nature Methods, 19 (4). pp. 429-440. ISSN 1548-7091 2020Kim, J.J. and Kim, J. and Reinert, K. (2020) Vaquita-LR: A new bioinformatics tool for identifying structural variants using long and short reads. In: Abstracts from the 53rd European Society of Human Genetics (ESHG) Conference: Interactive e-Posters. In: 53rd European Society of Human Genetics (ESHG) Conference, June 6–9, 2020, virtual. 2018Marschall, T. and Reinert, K. and others, (59 authors in total) (2018) Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19 (1). pp. 118-135. ISSN 1467-5463 (Print), 1477-4054 (Online) 2017Vatansever, B. and Muñoz, A. and Klein, C. L. and Reinert, K. (2017) Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis. Analytical and Bioanalytical Chemistry, 409 (4). pp. 989-997. ISSN 1618-2642 2016Canzar, S. and Andreotti, S. and Weese, D. and Reinert, K. and Klau, G. W. (2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology, 17 (1). ISSN 1474-760X 2015Schultz, L. and Zurich, M.-G. and Culot, M. and da Costa, A. and Landry, C. and Bellwon, P. and Kristl, T. and Hörmann, K. and Ruzek, S. and Aiche, S. and Reinert, K. and Bielow, C. and Gosselet, F. and Cecchelli, R. and Huber, C. G. and Schroeder, O. H.-U. and Gramowski-Voss, A. and Weiss, D. G. and Bal-Price, A. (2015) Evaluation of drug-induced neurotoxicity based on metabolomics, proteomics and electrical activity measurements in complementary CNS in vitro models. Toxicology in Vitro, 30 (1). pp. 138-165. ISSN 08872333 Reinert, K. and Langmead, B. and Weese, D. and Evers, D.J. (2015) Alignment of Next-Generation Sequencing Reads. Annual Review of Genomics and Human Genetics, 16 (1). pp. 133-151. ISSN 1527-8204 Aiche, S. and Sachsenberg, T. and Kenar, E. and Walzer, M. and Wiswedel, B. and Kristl, T. and Boyles, M. and Duschl, A. and Huber, C. G. and Berthold, M. R. and Reinert, K. and Kohlbacher, O. (2015) Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. PROTEOMICS, 15 (8). pp. 1443-1447. ISSN 16159853 Kuchenbecker, L. and Nienen, M. and Hecht, J. and Neumann, A. U. and Babel, N. and Reinert, K. and Robinson, P. N. (2015) IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics, 31 (18). pp. 2963-2971. ISSN 1367-4803 Hu, J. and Reinert, K. (2015) LocalAli: An Evolutionary-based Local Alignment Approach to Identify Functionally Conserved Modules in Multiple Networks. Bioinformatics, 30 (1). pp. 363-372. ISSN 1367-4803 Holtgrewe, M. and Kuchenbecker, L. and Reinert, K. (2015) Methods for the Detection and Assembly of Novel Sequence in High-Throughput Sequencing Data. Bioinformatics, 31 (12). pp. 1904-1912. ISSN 1367-4803 2014Neu, V. and Bielow, C. and Reinert, K. and Huber, C. G. (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. Journal of chromatography A, 1371 . pp. 196-203. Hauswedell, H. and Singer, J. and Reinert, K. (2014) Lambda: the local aligner for massive biological data. Bioinformatics (Oxford, England), 30 (17). i349-i355. Rahn, R. and Weese, D. and Reinert, K. (2014) Journaled string tree--a scalable data structure for analyzing thousands of similar genomes on your laptop. Bioinformatics . ISSN Online ISSN 1460-2059 - Print ISSN 1367-4803 Trappe, K. and Emde, A.-K. and Ehrlich, H.-C. and Reinert, K. (2014) Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics, 30 (24). pp. 3484-3490. ISSN 1367-4803 Kehr, B. and Trappe, K. and Holtgrewe, M. and Reinert, K. (2014) Genome alignment with graph data structures: a comparison. BMC Bioinformatics, 15 . ISSN 1471-2105 Hu, J. and Kehr, B. and Reinert, K. (2014) NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics, 30 (4). pp. 540-548. ISSN 1367-4803 Schulz, M. H. and Weese, D. and Holtgrewe, M. and Dimitrova, V. and Niu, S. and Reinert, K. and Richard, H. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics, 30 (17). i356-i363. 2013Andreotti, S. and Reinert, K. and Canzar, S. (2013) The duplication-loss small phylogeny problem: from cherries to trees. Journal of Computational Biology, 20 (9). pp. 643-59. Nahnsen, S. and Bielow, C. and Reinert, K. and Kohlbacher, O. (2013) Tools for Label-free Peptide Quantification. Molecular & Cellular Proteomics, 12 (3). pp. 549-556. ISSN 1535-9476 Zerck, A. and Nordhoff, E. and Lehrach, H. and Reinert, K. (2013) Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinformatics, 14 (1). p. 56. ISSN 1471-2105 Neu, V. and Bielow, C. and Gostomski, I. and Wintringer, R. and Braun, R. and Reinert, K. and Schneider, P. and Stuppner, H. and Huber, C. (2013) Rapid and Comprehensive Impurity Profiling of Synthetic Thyroxine by Ultrahigh-Performance Liquid Chromatography–High-Resolution Mass Spectrometry. Analytical Chemistry, 85 (6). pp. 3309-3317. ISSN 0003-2700 Siragusa, E. and Weese, D. and Reinert, K. (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Oxford Journals, 41 (7). e78. ISSN Print ISSN 0305-1048; Online ISSN 1362-4962 Neu, V. and Bielow, C. and Schneider, P. and Reinert, K. and Stuppner, H. and Huber, C. (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. Analytical Chemistry, 85 (4). pp. 2385-2390. ISSN 0003-2700 de la Garza, L. and Krüger, J. and Schärfe, Ch. and Röttig, M. and Aiche, S. and Reinert, K. and Kohlbacher, O. (2013) From the Desktop to the Grid: conversion of KNIME Workflows to gUSE. In: IWSG (International Workshop on Science Gateways), 3-5 June 2013, Zurich, Switzerland. Siragusa, E. and Weese, D. and Reinert, K. (2013) Scalable string similarity search/join with approximate seeds and multiple backtracking. In: Proceedings of the Joint EDBT/ICDT 2013 Workshops, Genoa, Italy. 2012Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599. Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203 Junker, J. and Bielow, C. and Bertsch, A. and Sturm, M. and Reinert, K. and Kohlbacher, O. (2012) TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J. Proteome Res., 11 (7). pp. 3914-3920. ISSN 1535-3893 Andreotti, S. and Klau, G. W. and Reinert, K. (2012) Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) , 9 (2). pp. 385-394. Emde, A.-K. and Schulz, M. H. and Weese, D. and Sun, R. and Vingron, M. and Kalscheuer, V. M. and Haas, S. A. and Reinert, K. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5). pp. 619-627. Kehr, B. and Reinert, K. and Darling, A. E. (2012) Hidden Breakpoints in Genome Alignments. In: Lecture Notes in Computer Science: Algorithms in Bioinformatics. Springer-Verlag, Berlin, pp. 391-403. ISBN 978-3-642-33121-3 2011Kehr, B. and Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (S9). S15. ISSN 1471-2105 Bielow, C. and Aiche, S. and Andreotti, S. and Reinert, K. (2011) MSSimulator: Simulation of Mass Spectrometry Data. Journal of Proteome Research, 10 (7). pp. 2922-2929. Holtgrewe, M. and Emde, A.-K. and Weese, D. and Reinert, K. (2011) A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics, 12 (120). ISSN 1471-2105 Bielow, C. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2011) Bioinformatics for qualitative and quantitative proteomics. In: Bioinformatics for Omics Data Methods and Protocols. Humana Press, pp. 331-49. Rausch, T. and Reinert, K. (2011) Practical multiple Sequence alignment. In: Problem Solving Handbook in Computational Biology and Bioinformatics. Springer Science+Business Media, pp. 21-43. ISBN 978-0-387-09759-6 2010Hüser, D. and Gogol-Döring, A. and Lutter, T. and Weger, S. and Winter, K. and Hammer, E.-M. and Cathomen, T. and Reinert, K. and Heilbronn, R. (2010) Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome. PLoS Pathogens, 6 (7). e1000985. ISSN 1553-7374 Bielow, C. and Ruzek, S. and Huber, C. and Reinert, K. (2010) Optimal Decharging and Clustering of Charge Ladders Generated in ESI−MS. J. Proteome Res., 9 (5). pp. 2688-2695. ISSN 1535-3893 Emde, A.-K. and Grunert, M. and Weese, D. and Reinert, K. and Sperling, S. R. (2010) MicroRazerS: Rapid alignment of small RNA reads. Bioinformatics, 26 (1). pp. 123-124. ISSN 1367-4803 Gogol-Döring, A. and Reinert, K. (2010) Biological Sequence Analysis using the SeqAn C++ Library. Chapman & Hall/CRC Mathematical & Computational Biology (1). CRC Press, Boca Raton, USA. ISBN 9781420076233 2009Weese, D. and Emde, A.-K. and Rausch, T. and Döring, A. and Reinert, K. (2009) RazerS - Fast Read Mapping with Sensitivity Control. Genome Research, 19 (9). pp. 1646-1654. Zerck, A. and Nordhoff, E. and Reseman, A. and Mirgorodskaya, E. and Suckau, D. and Reinert, K. and Lehrach, H. and Gobom, J. (2009) An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics. Journal of Proteome Research . Bauer, R. A. and Rother, K. and Moor, P. and Reinert, K. and Steinke, T. and Bujnicki, J. M. and Preissner, R. (2009) Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms and Molecular Sciences, 2 (2). pp. 692-709. ISSN 1999-4893 Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2009) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining, 2 (4). Rausch, T. and Koren, S. and Denisov, G. and Weese, D. and Emde, A.-K. and Döring, A. and Reinert, K. (2009) A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25 (9). pp. 1118-1124. 2008Conrad, T. O. F. and Reinert, K. and Kohlbacher, O. (2008) Bioinformatics Support for Mass Spectrometry Quality Control. In: Proteomics Sample Preparation. Wiley-Vch, p. 485. Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Hildebrandt, A. and Huber, Ch. and Reinert, K. (2008) Computational Quantification of Peptides from LC-MS data. Journal of Computational Biology, 15 (7). pp. 685-704. Bauer, M. and Klau, G. W. and Reinert, K. (2008) An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Operations Research . Schulz, M. H. and Weese, D. and Rausch, T. and Döring, A. and Reinert, K. and Vingron, M. (2008) Fast and Adaptive Variable Order Markov Chain Construction. In: Proceedings of the 8th International Workshop in Algorithms in Bioinformatics (WABI'08). Schulz-Trieglaff, O. and Pfeifer, N. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2008) LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics, 9 (423). Sturm, M. and Andreas, B. and Gröpl, C. and Hussong, R. and Lange, E. and Pfeifer, N. and Schulz-Trieglaff, O. and Zerck, A. and Reinert, K. and Kohlbacher, O. (2008) OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics, 9 (163). Rausch, T. and Emde, A.-K. and Reinert, K. (2008) Robust consensus computation. BMC Bioinformatics, 9 (Suppl 10). P4. Rausch, T. and Emde, A.-K. and Weese, D. and Notredame, C. and Reinert, K. (2008) Segment-based multiple sequence alignment. Bioinformatics, 24 (16). i187-192. Döring, A. and Weese, D. and Rausch, T. and Reinert, K. (2008) SeqAn -- An efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9 (1). p. 11. Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2008) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining . accepted for publication. (In Press) 2007Reinert, K. and Huson, D. H. (2007) Sequence Assembly. In: UNSPECIFIED Bioinformatics - From Genomes to Therapies, 1 . Wiley-VCH, Weinheim, pp. 25-55. Bauer, M. and Klau, G. W. and Reinert, K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8 (1). p. 271. Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Reinert, K. (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). Lange, E. and Gröpl, C. and Schulz-Trieglaff, O. and Leinenbach, A. and Huber, Ch. and Reinert, K. (2007) A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data. Oxford Journals, 23 (13). i273-i281. ISSN 1460-2059 (online), 1367-4803 (print) Klau, G. W. and Rahmann, S. and Schliep, A. and Vingron, M. and Reinert, K. (2007) Integer Linear Programming Approaches for Non-unique Probe Selection. Discrete Applied Mathematics, 155 . pp. 840-856. Reinert, K. and Bauer, M. and Döring, A. and Halpern, A. L. (2007) A general paradigm for fast and adaptive clustering of biological sequences. In: German Conference on Bioinformatics (GCB 2007). 2006Mayr, B. M. and Kohlbacher, O. and Reinert, K. and Gröpl, C. and Lange, E. and Klein, C. L. and Huber, Ch. (2006) Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms. Journal of Proteome Research, 5 . pp. 414-421. Wolski, W. E. and Farrow, M. and Emde, A.-K. and Maciej, L. and Lehrach, H. and Reinert, K. (2006) Analytical model of peptide mass cluster centres with applications. Proteome Science, 4 (18). doi:10.1186/1477-5956. Althaus, E. and Caprara, A. and Lenhof, H.-P. and Reinert, K. (2006) A Branch-and-Cut Algorithm for Multiple Sequence Alignment. Mathematical Programming (105). pp. 387-425. Lange, E. and Gröpl, C. and Reinert, K. and Hildebrandt, A. (2006) High Accuracy Peak-Picking of Proteomics Data using Wavelet Techniques. In: Proceedings of the 11th Pacific Symposium on Biocomputing (PSB-06). Reinert, K. and Kohlbacher, O. and Gröpl, C. and Lange, E. and Schulz-Trieglaff, O. and Sturm, M. and Pfeifer, N. (2006) OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In: Computational Proteomics. Kohlbacher, O. and Reinert, K. and Gröpl, C. and Lange, E. and Pfeiffer, N. and Schulz-Trieglaff, O. and Sturm, M. (2006) TOPP - The OpenMS Proteomics Pipeline. In: Proceedings of the 5th European Conference on Computational Biology (ECCB 2006). 2005Gröpl, C. and Lange, E. and Reinert, K. and Sturm, M. and Huber, Ch. and Mayr, B. M. and Klein, C. L. (2005) Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples. In: Proceedings of the 1st International Symposium on Computational Life Science (CompLife05). Wolski, W. E. and Lalowski, M. and Jungblut, P. and Reinert, K. (2005) Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics, 6 (203). http://www.biomedcentral.com/1471-2105/6/203. Bauer, M. and Klau, G. W. and Reinert, K. (2005) Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Relaxation. In: Proceedings of the 1st International Symposium on Computational Life Science (CompLife-05). Lange, E. and Gröpl, C. and Reinert, K. and Hildebrandt, A. (2005) High-accuracy peak picking of proteomics data. In: Computational Proteomics. Bafna, V. and Reinert, K. (2005) Mass Spectrometry and Computational Proteomics. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley-Eastern. Bauer, M. and Klau, G. W. and Reinert, K. (2005) Multiple Structural RNA Alignment with Lagrangian Relaxation. In: Proceedings of the 5th Workshop on Algorithms Bioinformatics (WABI-05). Reinert, K. and Kohlbacher, O. and Gröpl, C. and Lange, E. and Schulz-Trieglaff, O. and Sturm, M. and Pfeifer, N. (2005) OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In: Computational Proteomics. Klein, C. L. and Kohlbacher, O. and Reinert, K. (2005) Reference methods and materials in standardisation and quality assurance (abstract). FEBS Journal, 272 (Supplement 1). pp. 490-504. Wolski, E. and Lalowski, M. and Martus, P. and Giavalisco, P. and Gobom, J. and Sickmann, A. and Lehrach, H. and Reinert, K. (2005) Transformation and other factors of the peptide mass spectormetry pairwise peaklist comparison process. BMC Bioinformatics, 6 (285). http://www.biomedcentral.com/1471-2105/6/285. 2004Kohlbacher, O. and Reinert, K. (2004) Differenzielle Proteomanalyse -- Experimentelle Methoden, Algorithmische Herausforderungen. it -- Information technology, 46 . pp. 31-38. Klau, G. W. and Rahmann, S. and Schliep, A. and Reinert, K. (2004) 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). Istrail, S. and Sutton, G. G. and Florea, L. and Mobarry, C. M. and Lippert, R. and Walenz, B. and Shatkay, H. and Dew, Ian and Miller, J. R. and Flanigan, M. J. and Edwards, N. J. and Bolanos, R. and Fasulo, D. and Halldorsson, B. V. and Hannenhalli, S. and Turner, R. J. and Yooseph, S. and Lu, Fu and Nusskern, D. R. and Shue, B. C. and Zheng, X. H. and Zhong, F. and Delcher, A. L. and Huson, D. H. and Kravitz, S. A. and Mouchard, L. and Reinert, K. and Remington, K. A. and Clark, A. G. and Waterman, M. S. and Eichler, E. E. and Adams, M. D. and Hunkapillar, M. W. and Myers, E. W. and Venter, J. C. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the national academy of science (PNAS), 101 (7). pp. 1916-1921. 2002Mural, Richard and Adams, M. D. and Reinert, K. (2002) A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. Science, 296 . pp. 1661-1671. Huson, D. H. and Reinert, K. and Myers, E. W. (2002) The Greedy Path-Merging Algorithm for Sequence Assembly. Journal of the ACM, 49 (5). pp. 603-615. Althaus, E. and Caprara, A. and Lenhof, H.-P. and Reinert, K. (2002) Multiple Sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. In: Proceedings of the 1st European Conference on Computational Biology (ECCB 2002). Bailey, J. A. and Gu, Z. and Clark, R. A. and Reinert, K. and Samonte, R. V. and Schwartz, S. S. and Adams, M. D. and Myers, E. W. and Li, P. and Eichler, E. E. (2002) Recent Segmental Duplications in the Human Genome. Science, 297 . pp. 1003-1007. Halpern, A. L. and Huson, D. H. and Reinert, K. (2002) Segment Match refinment and applications. In: Proceedings of the 2nd Workshop on Algorithms Bioinformatics (WABI-02). 2001Huson, D. H. and Halpern, A. L. and Lai, Z. and Myers, E. W. and Reinert, K. and Sutton, G. G. (2001) Comparing Assemblies using Fragments and Mate-pairs. In: Proceedings of the 1st Workshop on Algorithms Bioinformatics (WABI-01). Huson, D. H. and Reinert, K. and Kravitz, S. A. and Remington, K. A. and Delcher, A. L. and Dew, I. M. and Flanigan, M. J. and Halpern, A. L. and Lai, Z. and Mobarry, C. M. and Sutton, G. G. and Myers, E. W. (2001) Design of a compartmentalized Shotgun Assembler for the Human Genome. In: Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB-01). Huson, D. H. and Reinert, K. and Myers, E. W. (2001) The Greedy Path-Merging Algorithm for Sequence Assembly. In: Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01). Venter, J. C. and Adams, M. D. and Myers, E. W. and Reinert, K. and et al, . (2001) The Sequence of the Human Genome. Science, 291 (5507). pp. 1304-1351. Turner, R. J. and Chaturvedi, K. and Edwards, N. J. and Halpern, A. L. and Huson, D. H. and Kohlbacher, O. and Miller, J. R. and Reinert, K. and Remington, K. A. and Schwartz, R. and Walenz, B. and Yooseph, S. and Istrail, S. (2001) Visualization Challenges for a New Cyberpharmaceutical Computing. In: IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics. 2000Reinert, K. and Stoye, J. and Will, T. (2000) An Iterative Methods for Faster Sum-of-Pairs Multiple Sequence Alignment. BIOINFORMATICS, 16 (9). pp. 808-814. Kececioglu, J. D. and Lenhof, H.-P. and Mehlhorn, K. and Reinert, K. and Vingron, M. (2000) A Polyhedral Approach to Sequence Alignment Problems. Discrete Applied Mathematics, 104 . pp. 143-186. Lermen, M. and Reinert, K. (2000) The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. Journal of Computational Biology . pp. 655-671. Myers, E. W. and Sutton, G. G. and Delcher, A. L. and Dew, D. P. and Flanigan, M. J. and Kravitz, S. A. and Mobarry, C. M. and Reinert, K. and Remington, K. A. and Anson, E. L. and Bolanos, R. and Chou, H.-H. and Jordan, C. M. and Halpern, A. L. and Lonardi, S. and Beasly, E. M. and Brandon, R. C. and Chen, L. and Dunn, P. J. and Lai, Z. and Liang, Y. and Nusskern, D. R. and Zhan, M. and Zhang, Q. and Zheng, X. H. and Rubin, G. M. and Adams, M. D. and Venter, J. C. (2000) A Whole-Genome Assembly of Drosophila. Science, 287 (5461). pp. 2196-2203. 1999Lenhof, H.-P. and Morgenstern, B. and Reinert, K. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. BIOINFORMATICS, 15 (3). pp. 203-210. 1998Lenhof, H.-P. and Reinert, K. and Vingron, M. (1998) A Polyhedral Approach to RNA Sequence Structure Alignment. Journal of Computational Biology, 5 (3). pp. 517-530. Lenhof, H.-P. and Reinert, K. and Vingron, M. (1998) A polyhedral approach to RNA sequence structure alignment. In: Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB-98). 1997Reinert, K. and Lenhof, H.-P. and Mutzel, P. and Kececioglu, J. D. (1997) A branch-and-Cut algorithm for multiple sequence alignment. In: Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB-97). 1996Bradford, P. G. and Reinert, K. (1996) Lower Bounds for Row Minima Searching. 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