Publications by authors named "Knut Reinert"

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Engineering rank queries on bit vectors and strings.
Simon Gene Gottlieb, Knut Reinert

Algorithms Mol Biol· December 2025

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ganon2: up-to-date and scalable metagenomics analysis.
Vitor C Piro, Knut Reinert

NAR Genom Bioinform· September 2025

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TetRex: a novel algorithm for index-accelerated search of highly conserved motifs.
Remy M Schwab, Simon Gene Gottlieb, Knut Reinert

NAR Genom Bioinform· June 2025

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FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events.
Yannek Nowatzky, Francesco Friedrich Russo, Jan Lisec, Alexander Kister, Knut Reinert

Nat Commun· March 2025

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SeArcH schemes for Approximate stRing mAtching.
Simon Gene Gottlieb, Knut Reinert

NAR Genom Bioinform· March 2025

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Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil.
Mădălina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocío Chamorro González, Lotte Brückner, Knut Reinert

Genome Res· October 2024

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Leaf: an ultrafast filter for population-scale long-read SV detection.
Chenxu Pan, Knut Reinert

Genome Biol· June 2024

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Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences.
Hannes Hauswedell, Sara Hetzel, Simon G Gottlieb, Helene Kretzmer, Alexander Meissner, Knut Reinert

Bioinformatics· March 2024

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A simple refined DNA minimizer operator enables 2-fold faster computation.
Chenxu Pan, Knut Reinert

Bioinformatics· February 2024

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Mistle: bringing spectral library predictions to metaproteomics with an efficient search index.
Yannek Nowatzky, Philipp Benner, Knut Reinert, Thilo Muth

Bioinformatics· June 2023

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Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.
Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Knut Reinert

Genome Biol· May 2023

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Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models.
Chenxu Pan, René Rahn, David Heller, Knut Reinert

Brief Bioinform· March 2023

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A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data.
Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Knut Reinert

Bioinformatics· January 2023

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Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments.
Mitra Darvish, Enrico Seiler, Svenja Mehringer, René Rahn, Knut Reinert

Bioinformatics· September 2022

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Critical Assessment of Metagenome Interpretation: the second round of challenges.
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Knut Reinert

Nat Methods· April 2022

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LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.
Jörg Winkler, Gianvito Urgese, Elisa Ficarra, Knut Reinert

BMC Bioinformatics· January 2022

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Correction to: Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures.
Kerstin Neubert, Eric Zuchantke, Robert Maximilian Leidenfrost, Röbbe Wünschiers, Josephine Grützke, Knut Reinert

BMC Genomics· December 2021

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RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data.
Sara Hetzel, Pay Giesselmann, Knut Reinert, Alexander Meissner, Helene Kretzmer

Bioinformatics· November 2021

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Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures.
Kerstin Neubert, Eric Zuchantke, Robert Maximilian Leidenfrost, Röbbe Wünschiers, Josephine Grützke, Knut Reinert

BMC Genomics· November 2021

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The Collaborative Research Center FONDA.
Ulf Leser, Marcus Hilbrich, Claudia Draxl, Peter Eisert, Lars Grunske, Knut Reinert

Datenbank Spektrum· November 2021

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Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, Knut Reinert

iScience· July 2021

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SCORE: Smart Consensus Of RNA Expression-a consensus tool for detecting differentially expressed genes in bacteria.
Silver A Wolf, Lennard Epping, Sandro Andreotti, Knut Reinert, Torsten Semmler

Bioinformatics· April 2021

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Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, Knut Reinert

Brief Bioinform· March 2021

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Profiling of Sub-Lethal in Vitro Effects of Multi-Walled Carbon Nanotubes Reveals Changes in Chemokines and Chemokine Receptors.
Sandeep Keshavan, Fernando Torres Andón, Audrey Gallud, Wei Chen, Knut Reinert

Nanomaterials (Basel)· March 2021

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Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire.
Robert Pieper, Temesgen H Dadi, Laura Pieper, Wilfried Vahjen, André Franke, Knut Reinert

ISME J· November 2020

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