Publications of Knut Reinert
All genres
Journal Article (14)
1.
Journal Article
40 (3), btae097 (2024)
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics 2.
Journal Article
A simple refined DNA minimizer operator enables twofold faster computation. Bioinformatics, btae045 (2024)
3.
Journal Article
24 (1), 131 (2023)
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries. Genome Biology: Biology for the Post-Genomic Era 4.
Journal Article
24 (2), bbad071 (2023)
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 5.
Journal Article
28 (17), pp. 4100 - 4108 (2022)
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinformatics 6.
Journal Article
19 (4), pp. 429 - 440 (2022)
Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods 7.
Journal Article
23, 18 (2022)
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences. BMC Bioinformatics 8.
Journal Article
37 (21), pp. 3934 - 3935 (2021)
RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data. Bioinformatics 9.
Journal Article
24 (7), 102782 (2021)
Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience 10.
Journal Article
36 (suppl.1), pp. i12 - i20 (2020)
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics 11.
Journal Article
11, 11:636 (2020)
Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping. Frontiers in Microbiology 12.
Journal Article
GenMap: Ultra-fast Computation of Genome Mappability. Bioinformatics, btaa222 (2020)
13.
Journal Article
34 (17), pp. i766 - 1772 (2018)
DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinformatics 14.
Journal Article
261, pp. 157 - 168 (2017)
The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology Conference Paper (1)
15.
Conference Paper
Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. In: FPGA '22, pp. 180 - 189. FPGA '22: Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays, Virtual Event, February 27, 2022 - March 01, 2022. Association for Computing Machinery, New York, NY (2022)
Thesis - PhD (4)
16.
Thesis - PhD
Algorithms for finding RNA sequence-structure motifs. Dissertation, XIII, 137 pp. (2023)
17.
Thesis - PhD
Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities. Dissertation, viii, 145 pp. (2019)
18.
Thesis - PhD
Approximate String Matching: Improving Data Structures and Algorithms. Dissertation, 175 pp. (2019)
19.
Thesis - PhD
Analysis of Antigen Receptor Repertoires Captured by High Throughput Sequencing. Dissertation, vii, 164 pp. (2018)