Publications of Knut Reinert

Schwab, R. M.; Gottlieb, S. G.; Reinert, K.: TetRex: a novel algorithm for index-accelerated search of highly conserved motifs. NAR: genomics and bioinformatics 7 (2), Article lqaf039 (2025)

Gottlieb, S. G.; Reinert, K.: SeArcH schemes for Approximate stRing mAtching. NAR: genomics and bioinformatics 7 (1), Article lqaf025 (2025)

Nowatzky, Y.; Russo, F. F.; Lisec, J.; Kister, A.; Reinert, K.; Muth, T.; Benner, P.: FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events. Nature Communications 16 (1), Article 2298 (2025)

Giurgiu , M.; Wittstruck, N.; Rodriguez-Fos, E.; González , R. C.; Brückner, L.; Krienelke-Szymansky, A.; Helmsauer, K.; Hartebrodt, A.; Euskirchen, P.; Koche, R. P. et al.; Haase, K.; Reinert, K.; Henssen, A. G.: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Research 34 (9), pp. 1355 - 1364 (2024)

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

Hauswedell , H.; Hetzel, S.; Gottlieb , S. G.; Kretzmer, H.; Meissner, A.; Reinert, K.: Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics 40 (3), Article btae097 (2024)

Pan, C.; Reinert, K.: A simple refined DNA minimizer operator enables 2-fold faster computation. Bioinformatics 40 (2), Article btae045 (2024)

Mehringer, S.; Seiler, E.; Droop, F.; Darvish, M.; Rahn, R.; Vingron, M.; Reinert, K.: Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries. Genome Biology: Biology for the Post-Genomic Era 24 (1), 131 (2023)

Pan, C.; Rahn , R.; Heller, D.; Reinert, K.: 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)

Darvish, M.; Seiler, E.; Mehringer, S.; Rahn, R.; Reinert, K.: Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinformatics 28 (17), pp. 4100 - 4108 (2022)

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

Winkler, J.; Urgese, G.; Ficarra, E.; Reinert, K.: LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences. BMC Bioinformatics 23, 18 (2022)

Hetzel, S.; Gießelmann, P.; Reinert, K.; Meissner, A.; Kretzmer, H.: RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data. Bioinformatics 37 (21), pp. 3934 - 3935 (2021)

Seiler, E.; Mehringer, S.; Darvish, M.; Turc, E.; Reinert, K.: Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience 24 (7), 102782 (2021)

Piro, V. C.; Dadi, T. H.; Seiler, E.; Reinert, K.; Renard, B. Y.: ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics 36 (suppl.1), pp. i12 - i20 (2020)

Moeinzadeh, M.-H.; Yang, Jun; Muzychenko, E.; Gallone, G.; Heller, D.; Reinert, K.; Haas, S.; Vingron, M.: Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLOS Computational Biology 16 (5), e1007843 (2020)

Witt, N.; Andreotti, S.; Busch, A.; Neubert, K.; Reinert, K.; Tomaso, H.; Meierhofer, D.: Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping. Frontiers in Microbiology 11, 11:636 (2020)

Pockrandt, C. M.; Alzamel, M.; Iliopoulos, C. S.; Reinert, K.: GenMap: Ultra-fast Computation of Genome Mappability. Bioinformatics 36 (12), pp. 3687 - 3692 (2020)

Dadi, T. H.; Siragusa, E.; Piro, V. C.; Andrusch, A.; Seiler, E.; Renard, B. Y.; Reinert, K.: DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinformatics 34 (17), pp. i766 - 1772 (2018)

Reinert, K.; Dadi, T. H.; Ehrhardt, M.; Hauswedell , H.; Mehringer, S.; Rahn, R.; Kim, J.; Pockrandt, C.; Winkler, J.; Siragusa, E. et al.; Urgese, G.; Weese, D.: The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology 261, pp. 157 - 168 (2017)