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 (20)

Journal Article
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)
Journal Article
Gottlieb, S. G.; Reinert, K.: SeArcH schemes for Approximate stRing mAtching. NAR: genomics and bioinformatics 7 (1), Article lqaf025 (2025)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
Pan, C.; Reinert, K.: A simple refined DNA minimizer operator enables 2-fold faster computation. Bioinformatics 40 (2), Article btae045 (2024)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
Journal Article
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)
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