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Number of items at this level: 145.

2017

Audain, Enrique and Uszkoreit, Julian and Sachsenberg, Timo and Pfeuffer, Julianus and Liang, Xiao and Hermjakob, Henning and Sanchez, Aniel and Eisenacher, Martin and Reinert, Knut and Tabb, David L. and Kohlbacher, Oliver and Perez-Riverol, Yasset (2017) In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics, 150 . pp. 170-182. ISSN 18743919

Reinert, Knut and Dadi, Temesgen Hailemariam and Ehrhardt, Marcel and Hauswedell, Hannes and Mehringer, Svenja and Rahn, René and Kim, Jongkyu and Pockrandt, Christopher and Winkler, Jörg and Siragusa, Enrico and Urgese, Gianvito and Weese, David (2017) The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology . ISSN 01681656

Vatansever, 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

2016

Canzar, 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

Jäger, Marten and Schubach, Max and Zemojtel, Tomasz and Reinert, Knut and Church, Deanna M. and Robinson, Peter N. (2016) Alternate-locus aware variant calling in whole genome sequencing. Genome Medicine, 8 (1). ISSN 1756-994X

Marschall, T. and Reinert, K. and others, (59 authors in total) (2016) Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics . ISSN 1477-4054 (Online)

2015

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

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

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

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

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

Schultz, 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

Wilmes, Anja and Bielow, Chris and Ranninger, Christina and Bellwon, Patricia and Aschauer, Lydia and Limonciel, Alice and Chassaigne, Hubert and Kristl, Theresa and Aiche, Stephan and Huber, Christian G. and Guillou, Claude and Hewitt, Philipp and Leonard, Martin O. and Dekant, Wolfgang and Bois, Frederic and Jennings, Paul (2015) Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics. Toxicology in Vitro, 30 (1, Part A). pp. 117-127. ISSN 08872333

2014

Hauswedell, H. and Singer, J. and Reinert, K. (2014) Lambda: the local aligner for massive biological data. Bioinformatics (Oxford, England), 30 (17). i349-i355.

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

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

Neu, 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.

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

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.

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

Walzer, M. and Pernas, L. E. and Nasso, S. and Bittremieux, W. and Nahnsen, S. and Kelchtermans, P. and Pichler, P. and van den Toorn, H. W. P. and Staes, A. and Vandenbussche, J. and Mazanek, M. and Taus, T. and Scheltema, R. A. and Kelstrup, C. D. and Gatto, L. and van Breukelen, B. and Aiche, S. and Valkenborg, D. and Laukens, K. and Lilley, K. S. and Olsen, J. V. and Heck, A. J. R. and Mechtler, K. and Aebersold, R. and Gevaert, K. and Vizcaino, J. A. and Hermjakob, H. and Kohlbacher, O. and Martens, L. (2014) qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments. Molecular & Cellular Proteomics, 13 (8). pp. 1905-1913. ISSN 1535-9476

Wandelt, S. and Deng, D. and Gerdjikov, S. and Mishra, S. and Mitankin, P. and Patil, M. and Siragusa, E. and Tiskin, A. and Wang, W. and Wang, J. and Leser, U. (2014) State-of-the-art in String Similarity Search and Join. SIGMOD Record, 43 (1).

2013

Aiche, S. (2013) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data. PhD thesis, Freie Universität Berlin.

Andreotti, 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

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

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

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

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.

Steijger, T. and Abril, J. F. and Engström, P. G. and Kokocinski, F. and The RGASP Consortium, and Richard, H. and Schulz, M. H. and Weese, D. and Hubbard, T. and Guigó, R. and Harrow, J. and Bertone, P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184.

Weese, D. (2013) Indices and Applications in High-Throughput Sequencing. PhD thesis, Freie Universität Berlin.

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

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.

2012

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

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.

Bielow, C. (2012) Quantification and Simulation of Liquid Chromatography-Mass Spectrometry Data. PhD thesis, Freie Universität Berlin.

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.

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

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

Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599.

2011

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.

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.

Böcker, S. and Kehr, B. and Rasche, F. (2011) Determination of Glycan Structure from Tandem Mass Spectra. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 8 (4). pp. 976-986. ISSN 1545-4963

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

Kehr, B. and Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (S9). S15. ISSN 1471-2105

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

2010

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

Birn, M. and Holtgrewe, M. and Sanders, P. and Singler, J. (2010) Simple and Fast Nearest Neighbor Search. 2010 Proceedings of the Twelfth Workshop on Algorithm Engineering and Experiments (ALENEX) . pp. 43-54.

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

Holtgrewe, M. and Sanders, P. and Schulz, C. (2010) Engineering a scalable high quality graph partitioner. 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS) . pp. 1-12. ISSN 1530-2075

Holtgrewe, M. (2010) Mason – A Read Simulator for Second Generation Sequencing Data. Technical Report FU Berlin .

Hüser, 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

2009

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

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.

Weese, 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 .

2008

Bauer, M. and Klau, G. W. and Reinert, K. (2008) An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Operations Research .

Bodirsky, M. and Gröpl, C. and Kang, M. (2008) Generating unlabeled connected cubic planar graphs uniformly at random. Random Structures and Algorithms, 32 (2). pp. 157-180.

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.

Lange, E. and Tautenhahn, R. and Neumann, S. and Gröpl, C. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomic measurements. BMC Bioinformatics, 9 (375).

Rausch, T. and Emde, A.-K. and Reinert, K. (2008) Robust consensus computation. BMC Bioinformatics, 9 (Suppl 10). P4.

Rausch, T. and Thomas, A. and Camp, N. J. and Facelli, L. A. (2008) A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease. Comput. Biol. Med., 38 . pp. 826-836.

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.

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 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.

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).

Weese, D. and Schulz, M. H. (2008) Efficient String Mining under Constraints via the Deferred Frequency Index. In: Proceedings of the 8th Industrial Conference on Data Mining (ICDM'08).

2007

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.

Bodirsky, M. and Gröpl, C. and Johannsen, D. and Kang, M. (2007) A direct decomposition of 3-connected planar graphs. Séminaire Lotharingien de Combinatoire, B54Ak . 15 pages.

Bodirsky, M. and Gröpl, C. and Kang, M. (2007) Generating labeled planar graphs uniformly at random. Theoretical Computer Science, 379 (3). pp. 377-386.

Fasulo, D. and Emde, A.-K. and Wang, L.-Y. and Edwards, N. J. (2007) Alignment of Mass Spectrometry Data by Clique Finding and Optimization. In: Systems Biology and Computational Proteomics.

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.

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)

May, P. and Klau, G. W. and Bauer, M. and Steinke, T. (2007) Accelerated microRNA Precursor Detection Using the Smith-Waterman Algorithm on FPGAs. In: Proc. of GCCB 2006.

Meier, Ch. (2007) Bioinformatik: Aktuelle Proteinausstattung erlaubt Aussagen über den Gesundheitszustand. Software hilft Ärzten künftig bei der Diagnose. UNSPECIFIED.

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).

Reinert, K. and Huson, D. H. (2007) Sequence Assembly. In: UNSPECIFIED Bioinformatics - From Genomes to Therapies, 1 . Wiley-VCH, Weinheim, pp. 25-55.

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).

2006

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.

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).

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).

Mayr, 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.

Rausch, T. (2006) Discovering causes of multifactorial diseases. Masters thesis, Hasso-Plattner-Institut für Softwaresystemtechnik GmbH, Universität Potsdam.

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.

Weese, D. (2006) Entwurf und Implementierung eines generischen Substring-Index. Other thesis, Humboldt-University.

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.

2005

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) Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Relaxation. In: Proceedings of the 1st International Symposium on Computational Life Science (CompLife-05).

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).

Bodirsky, M. and Gröpl, C. and Johannsen, D. and Kang, M. (2005) A direct decomposition of 3-connected planar graphs. In: Proceedings of the 17th Annual International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC05).

Bodirsky, M. and Gröpl, C. and Kang, M. (2005) Sampling Unlabeled Biconnected Planar Graphs. In: Proceedings of the 16th Annual International Symposium on Algorithms and Computation (ISAAC05).

Gröpl, C. (2005) An Algorithm for Feature Finding in LC/MS Raw Data. In: Computational Proteomics.

Gröpl, C. and Hildebrandt, A. and Lange, E. and Lövenich, S. and Sturm, M. (2005) OpenMS - Software for Mass Spectrometry. UNSPECIFIED.

Gröpl, C. and Hildebrandt, A. and Lange, E. and Sturm, M. (2005) OpenMS - a generic open source framework for HPLC/MS-based proteomics. UNSPECIFIED.

Gröpl, 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).

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.

Lange, E. and Gröpl, C. and Reinert, K. and Hildebrandt, A. (2005) High-accuracy peak picking of proteomics data. In: Computational Proteomics.

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.

Schulz-Trieglaff, O. (2005) Modelling the Randomness in Biological Systems. UNSPECIFIED.

Schulz-Trieglaff, O. (2005) Software Platforms for Computational Proteomics. In: Computational Proteomics.

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.

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.

2004

Bauer, M. and Klau, G. W. (2004) Structural Alignment of Two RNA Sequences with Lagrangian Relaxation. In: Proceedings of the 15th International Symposium, ISAAC 2004, Hong Kong.

Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2004) Ordered binary decision diagrams and the Shannon effect. Discrete Applied Mathematics, 142 . pp. 67-85.

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.

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).

Kohlbacher, O. and Reinert, K. (2004) Differenzielle Proteomanalyse -- Experimentelle Methoden, Algorithmische Herausforderungen. it -- Information technology, 46 . pp. 31-38.

Lange, E. (2004) Peak picking in mass spectra. UNSPECIFIED.

2003

Bodirsky, M. and Gröpl, C. and Kang, M. (2003) Decomposing, Counting, and Generating Unlabeled Cubic Planar Graphs. In: European Conference on Combinatorics, Graph Theory, and Applications EUROCOMB'03 Prague.

Bodirsky, M. and Gröpl, C. and Kang, M. (2003) Generating labeled planar graphs uniformly at random. In: Proceedings of ICALP 2003.

Frömmel, C. and Gille, Ch. and Goede, A. and Gröpl, C. and Hougardy, S. and Nierhoff, T. and Preissner, R. and Thimm, M. (2003) Accelerating screening of 3D protein data with a graph theoretical approach. Bioinformatics, 19 (18). pp. 2442-2447.

Gröpl, C. (2003) Algorithmen in der Bioinformatik. UNSPECIFIED.

2002

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.

Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2002) Steiner trees in uniformly quasi-bipartite graphs. Information Processing Letters, 83 . pp. 195-200.

Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. and Thimm, M. (2002) Approximationsalgorithmen für das Steinerbaumproblem in Graphen. UNSPECIFIED.

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).

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.

Mural, 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.

2001

Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2001) Approximation Algorithms for the Steiner Tree Problem in Graphs. In: Steiner Trees in Industry. Kluwer Academic Publishers, pp. 235-279.

Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2001) Lower bounds for approximation algorithms for the Steiner tree problem. In: Proceedings of the 27th International Workshop on Graph-Theoretic Concepts in Computer Science (2001).

Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2001) On the Evolution of the Worst-Case OBDD Size. Information Processing Letters, 77 . pp. 1-7.

Huson, 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).

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.

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.

2000

UNSPECIFIED (2000) The Genome Sequence of Drosophila melanogaster. Science, 287 (5461). pp. 2185-2195.

Baudis, G. and Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2000) Approximating Minimum Spanning Sets in Hypergraphs and Polymatroids. Technical Report. UNSPECIFIED.

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.

Reinert, 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.

1999

Gröpl, C. (1999) Binary Decision Diagrams for Random Boolean Functions. PhD thesis, Humboldt-Universität zu Berlin.

Lenhof, 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.

1998

Gröpl, C. and Prömel, H.-J. and Srivastav, A. (1998) Size and Structure of Random Ordered Binary Decision Diagrams (Extended Abstract). In: STACS 98.

Gröpl, C. and Skutella, M. (1998) Parallel Repetition of MIP(2,1) Systems. In: Lectures on Proof Verification and Approximation Algorithms. Lecture Notes in Computer Science, 1367 . Springer, pp. 161-177.

Lenhof, 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).

1997

Block, M. and Gröpl, C. and Preuss, H. and Prömel, H. J. and Srivastav, A. (1997) Efficient ordering of state variables and transition relation partitions in symbolic model checking. Technical Report. UNSPECIFIED.

Reinert, 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).

1996

Bradford, P. G. and Reinert, K. (1996) Lower Bounds for Row Minima Searching. In: Proceedings of the 23rd International Colloquium on Automata, Languages, and Programming 1996 (ICALP-96), LNCS 1099.

Gröpl, C. (1996) Über Approximationsalgorithmen zur Färbung k-färbbarer Graphen, die vektorchromatische Zahl und andere Varianten der vartheta-Funktion. Masters thesis, Rheinische Friedrich-Wilhelms-Universität Bonn.

This list was generated on Mon Sep 25 20:35:04 2017 CEST.