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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

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

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

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

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

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

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

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

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

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

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

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

Smith, M. and Smyth, R.P. and Marquet, R. and von Kleist, M. (2016) MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments. Bioinformatics, 32 (21). pp. 3369-3370. ISSN 1367-4803

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

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

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

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

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

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

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.

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

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, 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

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, 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.

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.