Publications

The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.

Journal Article (21)

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Gottlieb, S. G.; Reinert, K.: Engineering rank queries on bit vectors and strings. Algorithms for Molecular Biology 20, 21 (2025)
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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)
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Gottlieb, S. G.; Reinert, K.: SeArcH schemes for Approximate stRing mAtching. NAR: genomics and bioinformatics 7 (1), Article lqaf025 (2025)
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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)
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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)
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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)
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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)
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Pan, C.; Reinert, K.: A simple refined DNA minimizer operator enables 2-fold faster computation. Bioinformatics 40 (2), Article btae045 (2024)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Pockrandt, C. M.; Alzamel, M.; Iliopoulos, C. S.; Reinert, K.: GenMap: Ultra-fast Computation of Genome Mappability. Bioinformatics 36 (12), pp. 3687 - 3692 (2020)
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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)
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