Publikationen von Knut Reinert

Simon Gene Gottlieb and Knut Reinert, "SeArcH schemes for Approximate stRing mAtching," NAR: genomics and bioinformatics 7 (1), Article lqaf025 (2025).

Yannek Nowatzky, Francesco Friedrich Russo, Jan Lisec, Alexander Kister, Knut Reinert, Thilo Muth, and Philipp Benner, "FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events," Nature Communications 16 (1), Article 2298 (2025).

Madalina Giurgiu , Nadine Wittstruck, Elias Rodriguez-Fos, Rocío Chamorro González , Lotte Brückner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Philipp Euskirchen, Richard P. Koche, Kerstin Haase, Knut Reinert, and Anton G. Henssen, "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil," Genome Research 34 (9), 1355-1364 (2024).

Chenxu Pan and Knut Reinert, "Leaf: an ultrafast filter for population-scale long-read SV detection," Genome Biology: Biology for the Post-Genomic Era 25 (1), Article 155 (2024).

Hannes Hauswedell , Sara Hetzel, Simon G. Gottlieb , Helene Kretzmer, Alexander Meissner, and Knut Reinert, "Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences," Bioinformatics 40 (3), Article btae097 (2024).

Chenxu Pan and Knut Reinert, "A simple refined DNA minimizer operator enables 2-fold faster computation," Bioinformatics 40 (2), Article btae045 (2024).

Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron, and Knut Reinert, "Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries," Genome Biology: Biology for the Post-Genomic Era 24 (1), 131 (2023).

Chenxu Pan, René Rahn , David Heller, and Knut Reinert, "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), bbad071 (2023).

Mitra Darvish, Enrico Seiler, Svenja Mehringer, René Rahn, and Knut Reinert, "Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments," Bioinformatics 28 (17), 4100-4108 (2022).

F. Meyer, A. Fritz, Z.-L. Deng, D. Koslicki, T. R. Lesker, A. Gurevich, G. Robertson, M. Alser, D. Antipov, F. Beghini, D. Bertrand, J. J. Brito, C. T. Brown, J. Buchmann, A. Buluc, B. Chen, R. Chikhi, P. T. L. C. Clausen, Al. Cristian, P. W. Dabrowski, A. E. Darling, R. Egan, El. Eskin, E. Georganas, E. Goltsman, M. A. Gray, L. H. Hansen, S. Hofmeyr, P. Huang, L. Irber, H. Jia, T. S. Jorgensen, S. D. Kieser, T. Klemetsen, A. Kola, M. Kolmogorov, A. Korobeynikov, J. Kwan, N. LaPierre, C. Lemaitre, C. Li, A. Limasset, F. Malcher-Miranda, S. Mangul, V. R. Marcelino, C. Marchet, P. Marijon, D. Meleshko, D. R. Mende, A. Milanese, N. Nagarajan, J. Nissen, S. Nurk, L. Oliker, L. Paoli, P. Peterlongo, V. C. Piro, J. S. Porter, S. Rasmussen, E. R. Rees, K. Reinert, B. Renard, E. M. Robertsen, G. L. Rosen, H.-J. Ruscheweyh, V. Sarwal, N. Segata, E. Seiler, L. Shi, F. Sun, S. Sunagawa, S. J. Sorensen, A. Thomas, C. Tong, M. Trajkovski, J. Tremblay, G. Uritskiy, R. Vicedomini, Z. Wang, Z. Wang, Z. Wang, A. Warren, N. Willassen, K. Yelick, R. You, G. Zeller, Z. Zhao, S. Zhu, J. Zhu, R. Garrido-Oter, P. Gastmeier, S. Hacquard, S. Haeussler, A. Khaledi, F. Maechler, F. Mesny, S. Radutoiu, P. Schulze-Lefert, N. Smit, T. Strowig, A. Bremges, A. Sczyrba, and A. C. McHardy, "Critical Assessment of Metagenome Interpretation: the second round of challenges," Nature Methods 19 (4), 429-440 (2022).

Jörg Winkler, Gianvito Urgese, Elisa Ficarra, and Knut Reinert, "LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences," BMC Bioinformatics 23, 18 (2022).

Sara Hetzel, Pay Gießelmann, Knut Reinert, Alexander Meissner, and Helene Kretzmer, "RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data," Bioinformatics 37 (21), 3934-3935 (2021).

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

Vitor C. Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert, and Bernhard Y. Renard, "ganon: precise metagenomics classification against large and up-to-date sets of reference sequences," Bioinformatics 36 (suppl.1), i12-i20 (2020).

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

Natalie Witt, Sandro Andreotti, Anne Busch, Kerstin Neubert, Knut Reinert, Herbert Tomaso, and David Meierhofer, "Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping," Frontiers in Microbiology 11, 11:636 (2020).

Christopher M. Pockrandt, Mai Alzamel, Costas S. Iliopoulos, and Knut Reinert, "GenMap: Ultra-fast Computation of Genome Mappability," Bioinformatics 36 (12), 3687-3692 (2020).

Temesgen Hailemariam Dadi, Enrico Siragusa, Vitor C. Piro, Andreas Andrusch, Enrico Seiler, Bernhard Y. Renard, and Knut Reinert, "DREAM-Yara: an exact read mapper for very large databases with short update time," Bioinformatics 34 (17), i766-1772 (2018).

Knut Reinert, Temesgen Hailemariam Dadi, Marcel Ehrhardt, Hannes Hauswedell , Svenja Mehringer, René Rahn, Jongkyu Kim, Christopher Pockrandt, Jörg Winkler, Enrico Siragusa, Gianvito Urgese, and David Weese, "The SeqAn C++ template library for efficient sequence analysis: A resource for programmers," Journal of Biotechnology 261, 157-168 (2017).

Marius Knaust, Enrico Seiler, Knut Reinert, and Thomas Steinke, "Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA", in FPGA '22, (Association for Computing Machinery, New York, NY, 2022), pp. 180-189.