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Schwartz, Russell and Reinert, Knut, eds. (2017) 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). LIPICS, 88 . Dagstuhl LIPIcs, Saarbrücken/Wadern. ISBN 978-3-95977-050-7

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

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

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

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

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).

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.

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.

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.

Andreotti, Sandro (2015) Linear Programming and Integer Linear Programming in Bioinformatics. PhD thesis, Freie Universität Berlin.

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

Bafna, V. and Reinert, K. (2005) Mass Spectrometry and Computational Proteomics. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley-Eastern.

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.

Bais, Abha Singh (2008) Annotated Alignments. PhD thesis, Freie Universität Berlin.

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.

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

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).

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.

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.

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

Bauer, Chris (2014) Exploiting Proteomics Data. PhD thesis, Freie Universität Berlin.

Bauer, Markus Johann (2008) A combinatorial approach to RNA sequence-structure alignments. PhD thesis, Freie Universität Berlin.

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 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

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

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.

Bielow, Chris (2012) Quantification and simulation of liquid chromatography-mass spectrometry data. PhD thesis, Freie Universität Berlin.

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.

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.

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 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. (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. (2007) Generating labeled planar graphs uniformly at random. Theoretical Computer Science, 379 (3). pp. 377-386.

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

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.

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).

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.

Busch, Anne and Thomas, Prasad and Zuchantke, Eric and Brendebach, Holger and Neubert, Kerstin and Gruetzke, Josephine and Al Dahouk, Sascha and Peters, Martin and Hotzel, Helmut and Neubauer, Heinrich and Tomaso, Herbert (2018) Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis. Frontiers in Microbiology, 9 . ISSN 1664-302X

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

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

Conrad, T. O. F. (2008) New statistical algorithms for the analysis of mass spectrometry time-of- flight mass data with applications in clinical diagnostics. PhD thesis, Freie Universität Berlin.

Dadi, Temesgen Hailemariam (2019) Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities. PhD thesis, Freie Universität Berlin.

Dadi, Temesgen Hailemariam and Renard, Bernhard Y. and Wieler, Lothar H. and Semmler, Torsten and Reinert, Knut (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ, 5 . e3138. ISSN 2167-8359

Dadi, Temesgen Hailemariam and Siragusa, Enrico and Piro, Vitor C and Andrusch, Andreas and Seiler, Enrico and Renard, Bernhard Y and Reinert, Knut (2018) DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinformatics, 34 (17). i766-i772. ISSN 1367-4803

Darvish, Mitra and Seiler, Enrico and Mehringer, Svenja and Rahn, René and Reinert, Knut and Ponty, Yann (2022) Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinformatics, 38 (17). pp. 4100-4108. ISSN 1367-4803

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.

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

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.

Emde, Anne-Katrin (2013) Next-generation sequencing algorithms - from read mapping to variant detection. PhD thesis, Freie Universität Berlin.

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.

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.

Gholami, Jafar and Kamankesh, Mohamad Reza and Mohammadi, Somayeh and Hosseinkhani, Elahe and Abdi, Somayeh (2022) Powerful enhanced Jaya algorithm for efficiently optimizing numerical and engineering problems. Soft Computing . ISSN 1432-7643

Giesselmann, Pay (2021) Genome Analysis Methods using Long Read Nanopore Sequencing. PhD thesis, Freie Universität Berlin.

Giurgiu, Mădălina and Wittstruck, Nadine and Rodriguez-Fos, Elias and Chamorro González, Rocío and Brückner, Lotte and Krienelke-Szymansky, Annabell and Helmsauer, Konstantin and Hartebrodt, Anne and Koche, Richard P. and Haase, Kerstin and Reinert, Knut and Henssen, Anton G. (2023) Decoil: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data. bioRxiv - The Preprint Server for Biology .

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

Gogol-Döring, Andreas (2009) SeqAn. PhD thesis, Freie Universität Berlin.

Grześkowiak, Łukasz and Martínez-Vallespín, Beatriz and Dadi, Temesgen H and Radloff, Judith and Amasheh, Salah and Heinsen, Femke-Anouska and Franke, Andre and Reinert, Knut and Vahjen, Wilfried and Zentek, Jürgen and Pieper, Robert (2018) Formula Feeding Predisposes Neonatal Piglets to Clostridium difficile Gut Infection. The Journal of Infectious Diseases, 217 (9). pp. 1442-1452. ISSN 0022-1899

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

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

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

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.

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 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 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.

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).

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.

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.

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.

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).

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

Hauswedell, Hannes and Hetzel, Sara and Gottlieb, Simon G and Kretzmer, Helene and Meissner, Alexander and Reinert, Knut and Cowen, Lenore (2024) Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics, 40 (3). ISSN 1367-4811

Hauswedell, Hannes Peer (2021) SeqAn3 – Sequence Analysis and Modern C++. PhD thesis, Freie Universität Berlin.

Hetzel, Sara and Giesselmann, Pay and Reinert, Knut and Meissner, Alexander and Kretzmer, Helene and Alkan, Can (2021) RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. Bioinformatics, 37 (21). pp. 3934-3935. ISSN 1367-4803

Hoffmann, Marie and Monaghan, Michael T. and Reinert, Knut (2021) PriSeT: Efficient De Novo Primer Discovery. Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics . pp. 1-12.

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

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

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 .

Holtgrewe, Manuel (2015) Engineering Algorithms for Personal Genome Pipelines. PhD thesis, Freie Universität Berlin.

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

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

Hu, Jialu (2015) Algorithms to Identify Functional Orthologs And Functional Modules from High- Throughput Data. PhD thesis, Freie Universität Berlin.

Hufsky, Franziska and Lamkiewicz, Kevin and Almeida, Alexandre and Aouacheria, Abdel and Arighi, Cecilia and Bateman, Alex and Baumbach, Jan and Beerenwinkel, Niko and Brandt, Christian and Cacciabue, Marco and Chuguransky, Sara and Drechsel, Oliver and Finn, Robert D and Fritz, Adrian and Fuchs, Stephan and Hattab, Georges and Hauschild, Anne-Christin and Heider, Dominik and Hoffmann, Marie and Hölzer, Martin and Hoops, Stefan and Kaderali, Lars and Kalvari, Ioanna and von Kleist, Max and Kmiecinski, Renó and Kühnert, Denise and Lasso, Gorka and Libin, Pieter and List, Markus and Löchel, Hannah F and Martin, Maria J and Martin, Roman and Matschinske, Julian and McHardy, Alice C and Mendes, Pedro and Mistry, Jaina and Navratil, Vincent and Nawrocki, Eric P and O’Toole, Áine Niamh and Ontiveros-Palacios, Nancy and Petrov, Anton I and Rangel-Pineros, Guillermo and Redaschi, Nicole and Reimering, Susanne and Reinert, Knut and Reyes, Alejandro and Richardson, Lorna and Robertson, David L and Sadegh, Sepideh and Singer, Joshua B and Theys, Kristof and Upton, Chris and Welzel, Marius and Williams, Lowri and Marz, Manja (2020) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22 (2). pp. 642-663. ISSN 1467-5463

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. (2002) The Greedy Path-Merging Algorithm for Sequence Assembly. Journal of the ACM, 49 (5). pp. 603-615.

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).

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

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.

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

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

Jäger, Marten (2020) Annotation und Interpretation von Varianten und Polymorphismen im humanen Genom. PhD thesis, Freie Universität Berlin.

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.

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

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

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

Kehr, Birte (2014) Contributions to computing and modeling multiple whole-genome alignments. PhD thesis, Freie Universität Berlin.

Keshavan, Sandeep and Andón, Fernando Torres and Gallud, Audrey and Chen, Wei and Reinert, Knut and Tran, Lang and Fadeel, Bengt (2021) Profiling of Sub-Lethal in Vitro Effects of Multi-Walled Carbon Nanotubes Reveals Changes in Chemokines and Chemokine Receptors. Nanomaterials, 11 (4). p. 883. ISSN 2079-4991

Kianfar, Kiavash and Pockrandt, Christopher and Torkamandi, Bahman and Luo, Haochen and Reinert, Knut (2018) Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index. bioRxiv, The Preprint Server for Biology .

Kim, 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.

Kim, Jongkyu and Reinert, Knut (2017) Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence. In: 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). LIPICS (88). Dagstuhl LIPIcs, Saarbrücken/Wadern, 185(13:1)-198(13:14). ISBN 978-3-95977-050-7

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.

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).

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.

Knaust, Marius and Seiler, Enrico and Reinert, Knut and Steinke, Thomas (2022) Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. In: The 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays (FPGA '22), 27 February - 1 March 2022, virtual.

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).

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

Krakau, Sabrina (2020) Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data. PhD thesis, Freie Universität Berlin.

Krannich, Thomas (2022) Contributions to the detection of non-reference sequences in population-scale NGS data. PhD thesis, Freie Universität Berlin.

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

Kuchenbecker, Sven-Leon (2018) Analysis of Antigen Receptor Repertoires Captured by High Throughput Sequencing. PhD thesis, Freie Universität Berlin.

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

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).

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

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)

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).

Lange, Eva (2008) Analysis of mass spectrometric data - peak picking and map alignment. PhD thesis, Freie Universität 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.

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).

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.

Leser, Ulf and Hilbrich, Marcus and Draxl, Claudia and Eisert, Peter and Grunske, Lars and Hostert, Patrick and Kainmüller, Dagmar and Kao, Odej and Kehr, Birte and Kehrer, Timo and Koch, Christoph and Markl, Volker and Meyerhenke, Henning and Rabl, Tilmann and Reinefeld, Alexander and Reinert, Knut and Ritter, Kerstin and Scheuermann, Björn and Schintke, Florian and Schweikardt, Nicole and Weidlich, Matthias (2021) The Collaborative Research Center FONDA. Datenbank-Spektrum, 21 (3). pp. 255-260. ISSN 1618-2162

Löber, Ulrike (2019) Development of Bioinformatic Tools for Retroviral Analysis from High Throughput Sequence Data. PhD thesis, Freie Universität Berlin.

Marschall, 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)

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.

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.

Mehringer, Svenja and Seiler, Enrico and Droop, Felix and Darvish, Mitra and Rahn, René and Vingron, Martin and Reinert, Knut (2023) Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries. Genome Biology, 24 (131). ISSN 1474-760X

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

Meyer, 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

Meyers, Gene and Pop, Mihai and Reinert, Knut and Warnow, Tandy (2017) Dagstuhl Reports, Vol. 6, No. 8, pp. 91-130: Next Generation Sequencing (Dagstuhl Seminar 16351). Documentation. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany.

Mohammadi, Somayeh and PourKarimi, Latif and Droop, Felix and De Mecquenem, Ninon and Leser, Ulf and Reinert, Knut (2023) A mathematical programming approach for resource allocation of data analysis workflows on heterogeneous clusters. The Journal of Supercomputing, 79 (17). pp. 19019-19048. ISSN 0920-8542

Mohammadi, Somayeh and PourKarimi, Latif and Zschäbitz, Manuel and Aretz, Tristan and De Mecquenem, Ninon and Leser, Ulf and Reinert, Knut (2024) Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous Cluster Infrastructures. In: EDBT/ICDT 2024 Joint Conference: 8th International workshop on Data Analytics solutions for Real-LIfe APplications (DARLI-AP).

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.

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.

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 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.

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

Neubert, Kerstin and Zuchantke, Eric and Leidenfrost, Robert Maximilian and Wünschiers, Röbbe and Grützke, Josephine and Malorny, Burkhard and Brendebach, Holger and Al Dahouk, Sascha and Homeier, Timo and Hotzel, Helmut and Reinert, Knut and Tomaso, Herbert and Busch, Anne (2021) Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures. BMC Genomics, 22 (1). p. 822. ISSN 1471-2164

Niehus, Sebastian (2022) Multi-Sample Approaches and Applications for Structural Variant Detection. PhD thesis, Freie Universität Berlin.

Nowatzky, Yannek and Benner, Philipp and Reinert, Knut and Muth, Thilo (2023) Mistle: bringing spectral library predictions to metaproteomics with an efficient search index. Bioinformatics, 39 (6). ISSN 1367-4811

Ntini, Evgenia and Budach, Stefan and Vang Ørom, Ulf A and Marsico, Annalisa (2020) Predictive modeling of long non-coding RNA chromatin (dis-)association. bioRxiv .

Okonechnikov, Konstantin (2016) High-throughput RNA sequencing: a step forward in transcriptome analysis. PhD thesis, Freie Universität Berlin.

Pan, Chenxu and Rahn, René and Heller, David and Reinert, Knut (2023) Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models. Briefings in Bioinformatics, 24 (2). ISSN 1467-5463; Online ISSN 1477-4054

Pan, Chenxu and Reinert, Knut and Valencia, Alfonso (2024) A simple refined DNA minimizer operator enables 2-fold faster computation. Bioinformatics, 40 (2). ISSN 1367-4811

Pfeuffer, Julianus and Sachsenberg, Timo and Alka, Oliver and Walzer, Mathias and Fillbrunn, Alexander and Nilse, Lars and Schilling, Oliver and Reinert, Knut and Kohlbacher, Oliver (2017) OpenMS – A platform for reproducible analysis of mass spectrometry data. Journal of Biotechnology, 261 . pp. 142-148. ISSN 01681656

Pfeuffer, Julianus and Sachsenberg, Timo and Dijkstra, Tjeerd M. H. and Serang, Oliver and Reinert, Knut and Kohlbacher, Oliver (2020) EPIFANY: A Method for Efficient High-Confidence Protein Inference. Journal of Proteome Research, 19 (3). pp. 1060-1072. ISSN 1535-3893

Pieper, Robert and Dadi, Temesgen H. and Pieper, Laura and Vahjen, Wilfried and Franke, André and Reinert, Knut and Zentek, Jürgen (2020) Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire. The ISME Journal, 14 (11). pp. 2783-2793. ISSN 1751-7362

Piro, Vitor C (2018) Reference and taxonomy based methods for classification and abundance estimation of organisms in metagenomic samples. PhD thesis, Freie Universität Berlin.

Piro, Vitor C and Renard, Bernhard Y (2023) Contamination detection and microbiome exploration with GRIMER. GigaScience, 12 . ISSN 2047-217X

Piro, Vitor C. and Reinert, Knut (2023) ganon2: up-to-date and scalable metagenomics analysis. bioRxiv preprint .

Pockrandt, Christopher and Ehrhardt, Marcel and Reinert, Knut (2017) EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices. In: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science (LNCS), 10229 . Springer, Cham, pp. 190-206. ISBN 978-3-319-56970-3 (elektronisch)

Pockrandt, Christopher Maximilian (2019) Approximate String Matching - Improving Data Structures and Algorithms. PhD thesis, Freie Universität Berlin.

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

Rahn, René and Budach, Stefan and Costanza, Pascal and Ehrhardt, Marcel and Hancox, Jonny and Reinert, Knut (2018) Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. Bioinformatics, 34 (20). pp. 3437-3445. ISSN 1367-4803

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

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

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

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.

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.

Rausch, Tobias (2010) Dissecting multiple sequence alignment methods. PhD thesis, Freie Universität Berlin.

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 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.

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.

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

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.

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

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).

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, 261 . pp. 157-168. ISSN 01681656

Reinert, Knut and Iliopoulos, Costas S and Alzamel, Mai and Pockrandt, Christopher and Xu, Jinbo (2020) GenMap: ultra-fast computation of genome mappability. Bioinformatics, 36 (12). pp. 3687-3692. ISSN 1367-4803

Renard, Bernhard Y and Reinert, Knut and Seiler, Enrico and Dadi, Temesgen H and Piro, Vitor C (2020) ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics, 36 (Supple). i12-i20. ISSN 1367-4803

Roehr, Johannes T. and Dieterich, Christoph and Reinert, Knut (2017) Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics, 33 (18). pp. 2941-2942. ISSN 1367-4803

Rungsarityotin, Wasinee (2007) Algorithm to identify protein complexes from high-throughput data. PhD thesis, Freie Universität Berlin.

Röst, Hannes L and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and Liang, Xiao and Nahnsen, Sven and Nilse, Lars and Pfeuffer, Julianus and Rosenberger, George and Rurik, Marc and Schmitt, Uwe and Veit, Johannes and Walzer, Mathias and Wojnar, David and Wolski, Witold E and Schilling, Oliver and Choudhary, Jyoti S and Malmström, Lars and Aebersold, Ruedi and Reinert, Knut and Kohlbacher, Oliver (2016) OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods, 13 (9). pp. 741-748. ISSN 1548-7091

Schiefer, Christopher and Bux, Marc and Brandt, Joergen and Messerschmidt, Clemens and Reinert, Knut and Beule, Dieter and Leser, Ulf (2020) Portability of Scientific Workflows in NGS Data Analysis: A Case Study. Other. arXiv.org. (Submitted)

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

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, 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.

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 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).

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).

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

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

Schulz-Trieglaff, Ole (2009) Computational methods for Quantitative Peptide Mass Spectrometry. PhD thesis, Freie Universität Berlin.

Schönhuth, Alexander and Moeinzadeh, M-Hossein and Yang, Jun and Muzychenko, Evgeny and Gallone, Giuseppe and Heller, David and Reinert, Knut and Haas, Stefan and Vingron, Martin (2020) Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLOS Computational Biology, 16 (5). e1007843. ISSN 1553-7358

Seiler, Enrico and Mehringer, Svenja and Darvish, Mitra and Turc, Etienne and Reinert, Knut (2021) Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience, 24 (7). p. 102782. ISSN 25890042

Seiler, Enrico and Trappe, Kathrin and Renard, Bernhard Y. (2019) Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation. PLOS Computational Biology, 15 (7). e1007208. ISSN 1553-7358

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.

Siragusa, Enrico (2015) Approximate string matching for high-throughput sequencing. PhD thesis, Freie Universität Berlin.

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.

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).

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

Trappe, Kathrin (2018) Computational Methods for Integrative Structural Variant Analysis Across Species Boundaries. PhD thesis, Freie Universität Berlin.

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.

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

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.

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).

Wang, Yuwei and Lian, Bin and Zhang, Haohui and Zhong, Yuanke and He, Jie and Wu, Fashuai and Reinert, Knut and Shang, Xuequn and Yang, Hui and Hu, Jialu and Mathelier, Anthony (2023) A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. Bioinformatics, 39 (1). ISSN 1367-4803

Weber, Britta (2015) Reconstruction of Microtubule Centerlines from Electron Tomograms. PhD thesis, Freie Universität Berlin.

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).

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

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

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.

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

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

Wilson, Laurence O. W. and Hetzel, Sara and Pockrandt, Christopher and Reinert, Knut and Bauer, Denis C. (2019) VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9. BMC Biotechnology, 19 (1). ISSN 1472-6750

Winkler, Jörg and Urgese, Gianvito and Ficarra, Elisa and Reinert, Knut (2022) LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences. BMC Bioinformatics, 23 (1). ISSN 1471-2105

Witt, Natalie and Andreotti, Sandro and Busch, Anne and Neubert, Kerstin and Reinert, Knut and Tomaso, Herbert and Meierhofer, David (2020) Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping. Frontiers in Microbiology, 11 . ISSN 1664-302X

Wolf, Silver A and Epping, Lennard and Andreotti, Sandro and Reinert, Knut and Semmler, Torsten and Birol, Inanc (2021) SCORE: Smart Consensus Of RNA Expression—a consensus tool for detecting differentially expressed genes in bacteria. Bioinformatics, 37 (3). pp. 426-428. ISSN 1367-4803

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.

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.

Wolski, Witold Eryk (2007) Analysis of sets and collections of Peptide Mass Fingerprint data. PhD thesis, Freie Universität Berlin.

You, Xintian Arthur (2015) Tailored Analysis in Studying Transcriptome Landscape. 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

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 .

Zerck, Alexandra (2014) Optimal precursor ion selection for LC-MS/MS based proteomics. PhD thesis, Freie Universität Berlin.

Zühlke, Martin and Riebe, Daniel and Beitz, Toralf and Löhmannsröben, Hans-Gerd and Andreotti, Sandro and Reinert, Knut and Zenichowski, Karl and Diener, Marc (2016) High-performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization, data management, and applications. Journal of Separation Science, 39 (24). pp. 4756-4764. ISSN 16159306

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.

de la Garza, Luis and Veit, Johannes and Szolek, Andras and Röttig, Marc and Aiche, Stephan and Gesing, Sandra and Reinert, Knut and Kohlbacher, Oliver (2016) From the desktop to the grid: scalable bioinformatics via workflow conversion. BMC Bioinformatics, 17 (1). ISSN 1471-2105