Knut Reinert

ORCID

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 30

Top Venues

Saarland University, Saarbrücken, Germany (PHD)

Education History

Saarland University, Saarbrücken, Germany

PHD

Publications

Somayeh Mohammadi, Latif Pourkarimi, Manuel Zschäbitz, Tristan Aretz, Ninon De Mecquenem, Ulf Leser, Knut Reinert
Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous Cluster Infrastructures. EDBT/ICDT Workshops (2024)
Madalina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocío Chamorro González, Lotte Brückner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Philipp Euskirchen, Richard P. Koche, Kerstin Haase, Knut Reinert, Anton G. Henssen
Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. RECOMB (2024)
Chenxu Pan, René Rahn, David Heller, Knut Reinert
Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models. Briefings Bioinform. 24 (2) (2023)
Somayeh Mohammadi, Latif Pourkarimi, Felix Droop, Ninon De Mecquenem, Ulf Leser, Knut Reinert
A mathematical programming approach for resource allocation of data analysis workflows on heterogeneous clusters. J. Supercomput. 79 (17) (2023)
Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Fashuai Wu, Knut Reinert, Xuequn Shang, Hui Yang, Jialu Hu
A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. Bioinform. 39 (1) (2023)
Mitra Darvish, Enrico Seiler, Svenja Mehringer, René Rahn, Knut Reinert
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinform. 38 (17) (2022)
Jörg Winkler, Gianvito Urgese, Elisa Ficarra, Knut Reinert
LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences. BMC Bioinform. 23 (1) (2022)
Marius Knaust, Enrico Seiler, Knut Reinert, Thomas Steinke
Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. FPGA (2022)
Silver A. Wolf, Lennard Epping, Sandro Andreotti, Knut Reinert, Torsten Semmler
SCORE: Smart Consensus Of RNA Expression - a consensus tool for detecting differentially expressed genes in bacteria. Bioinform. 37 (3) (2021)
Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria Jesus Martin, Roman Martin, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna J. Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22 (2) (2021)
Marie Hoffmann, Michael T. Monaghan, Knut Reinert
primer discovery. BCB (2021)
Sara Hetzel, Pay Giesselmann, Knut Reinert, Alexander Meissner, Helene Kretzmer
RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. Bioinform. 37 (21) (2021)
Ulf Leser, Marcus Hilbrich, Claudia Draxl, Peter Eisert, Lars Grunske, Patrick Hostert, Dagmar Kainmüller, Odej Kao, Birte Kehr, Timo Kehrer, Christoph Koch, Volker Markl, Henning Meyerhenke, Tilmann Rabl, Alexander Reinefeld, Knut Reinert, Kerstin Ritter, Björn Scheuermann, Florian Schintke, Nicole Schweikardt, Matthias Weidlich
The Collaborative Research Center FONDA. Datenbank-Spektrum 21 (3) (2021)
Vitor Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert, Bernhard Y. Renard
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinform. 36 (Supplement-1) (2020)
Christopher Pockrandt, Mai Alzamel, Costas S. Iliopoulos, Knut Reinert
GenMap: ultra-fast computation of genome mappability. Bioinform. 36 (12) (2020)
Christopher Schiefer, Marc Bux, Jörgen Brandt, Clemens Messerschmidt, Knut Reinert, Dieter Beule, Ulf Leser
Portability of Scientific Workflows in NGS Data Analysis: A Case Study. CoRR (2020)
M-Hossein Moeinzadeh, Jun Yang, Evgeny Muzychenko, Giuseppe Gallone, David Heller, Knut Reinert, Stefan A. Haas, Martin Vingron
Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLoS Comput. Biol. 16 (5) (2020)
René Rahn, Stefan Budach, Pascal Costanza, Marcel Ehrhardt, Jonny Hancox, Knut Reinert
Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. Bioinform. 34 (20) (2018)
Temesgen Hailemariam Dadi, Enrico Siragusa, Vitor Piro, Andreas Andrusch, Enrico Seiler, Bernhard Y. Renard, Knut Reinert
DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinform. 34 (17) (2018)
Jongkyu Kim, Knut Reinert
Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence. WABI (2017)
Johannes T. Roehr, Christoph Dieterich, Knut Reinert
Flexbar 3.0 - SIMD and multicore parallelization. Bioinform. 33 (18) (2017)
Christopher Pockrandt, Marcel Ehrhardt, Knut Reinert
EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices. RECOMB (2017)
Kiavash Kianfar, Christopher Pockrandt, Bahman Torkamandi, Haochen Luo, Knut Reinert
FAMOUS: Fast Approximate string Matching using OptimUm search Schemes. CoRR (2017)
Christopher Pockrandt, Marcel Ehrhardt, Knut Reinert
Constant-time and space-efficient unidirectional and bidirectional FM-indices using EPR-dictionaries. CoRR (2016)
Gene Myers, Mihai Pop, Knut Reinert, Tandy J. Warnow
Next Generation Sequencing (Dagstuhl Seminar 16351). Dagstuhl Reports 6 (8) (2016)
Luis de la Garza, Johannes Veit, András Szolek, Marc Röttig, Stephan Aiche, Sandra Gesing, Knut Reinert, Oliver Kohlbacher
From the desktop to the grid: scalable bioinformatics via workflow conversion. BMC Bioinform. 17 (2016)
Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
CIDANE: Comprehensive Isoform Discovery and Abundance Estimation. RECOMB (2015)
Léon Kuchenbecker, Mikalai Nienen, Jochen Hecht, Avidan U. Neumann, Nina Babel, Knut Reinert, Peter N. Robinson
IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinform. 31 (18) (2015)
Jialu Hu, Knut Reinert
modules in multiple networks. Bioinform. 31 (3) (2015)
Manuel Holtgrewe, Léon Kuchenbecker, Knut Reinert
Methods for the detection and assembly of novel sequence in high-throughput sequencing data. Bioinform. 31 (12) (2015)
Hannes Hauswedell, Jochen Singer, Knut Reinert
Lambda: the local aligner for massive biological data. Bioinform. 30 (17) (2014)
Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard
Fiona: a parallel and automatic strategy for read error correction. Bioinform. 30 (17) (2014)
René Rahn, David Weese, Knut Reinert
Journaled string tree - a scalable data structure for analyzing thousands of similar genomes on your laptop. Bioinform. 30 (24) (2014)
Jialu Hu, Birte Kehr, Knut Reinert
NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinform. 30 (4) (2014)
Birte Kehr, Kathrin Trappe, Manuel Holtgrewe, Knut Reinert
Genome alignment with graph data structures: a comparison. BMC Bioinform. 15 (2014)
Kathrin Trappe, Anne-Katrin Emde, Hans-Christian Ehrlich, Knut Reinert
Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinform. 30 (24) (2014)
Sandro Andreotti, Knut Reinert, Stefan Canzar
The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees. J. Comput. Biol. 20 (9) (2013)
Luis de la Garza, Jens Krüger, Charlotta Schärfe, Marc Röttig, Stephan Aiche, Knut Reinert, Oliver Kohlbacher
From the Desktop to the Grid: conversion of KNIME Workflows to gUSE. IWSG (2013)
Enrico Siragusa, David Weese, Knut Reinert
Scalable string similarity search/join with approximate seeds and multiple backtracking. EDBT/ICDT Workshops (2013)
Alexandra Zerck, Eckhard Nordhoff, Hans Lehrach, Knut Reinert
Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinform. 14 (2013)
Birte Kehr, Knut Reinert, Aaron E. Darling
Hidden Breakpoints in Genome Alignments. WABI (2012)
Sandro Andreotti, Gunnar W. Klau, Knut Reinert
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (2) (2012)
Chris Bauer, Frank Kleinjung, Dorothea Rutishauser, Christian Panse, Alexandra Chadt, Tanja Dreja, Hadi Al-Hasani, Knut Reinert, Ralph Schlapbach, Johannes Schuchhardt
PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. BMC Bioinform. 13 (2012)
David Weese, Manuel Holtgrewe, Knut Reinert
RazerS 3: Faster, fully sensitive read mapping. Bioinform. 28 (20) (2012)
Enrico Siragusa, David Weese, Knut Reinert
Fast and sensitive read mapping with approximate seeds and multiple backtracking CoRR (2012)
Anne-Katrin Emde, Marcel H. Schulz, David Weese, Ruping Sun, Martin Vingron, Vera M. Kalscheuer, Stefan A. Haas, Knut Reinert
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinform. 28 (5) (2012)
Chris Bauer, Frank Kleinjung, Celia J. Smith, Mark W. Towers, Ali Tiss, Alexandra Chadt, Tanja Dreja, Dieter Beule, Hadi Al-Hasani, Knut Reinert, Johannes Schuchhardt, Rainer Cramer
Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset. BMC Bioinform. 12 (2011)
Sandro Andreotti, Gunnar W. Klau, Knut Reinert
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem CoRR (2011)
Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert
A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinform. 12 (2011)
Birte Kehr, David Weese, Knut Reinert
STELLAR: fast and exact local alignments. BMC Bioinform. 12 (S-9) (2011)
Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert, Silke R. Sperling
MicroRazerS: rapid alignment of small RNA reads. Bioinform. 26 (1) (2010)
Knut Reinert
Oops I Did it Again... Sustainability in Sequence Analysis via Software Libraries. ERCIM News 2010 (82) (2010)
Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert
and reference-guided sequence assembly of short reads. Bioinform. 25 (9) (2009)
Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2 (2) (2009)
Ole Schulz-Trieglaff, Egidijus Machtejevas, Knut Reinert, Hartmut Schlüter, Joachim Thiemann, Klaus Unger
Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min. 2 (2009)
Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert
Integer Linear Programming in Computational Biology. Efficient Algorithms (2009)
Tobias Rausch, Anne-Katrin Emde, Knut Reinert
Robust consensus computation. BMC Bioinform. 9 (S-10) (2008)
Knut Reinert, Christian G. Huber, Kathrin Marcus, Michal Linial, Oliver Kohlbacher
08101 Abstracts Collection - Computational Proteomics. Computational Proteomics (2008)
Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert
LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinform. 9 (2008)
Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert, Martin Vingron
Fast and Adaptive Variable Order Markov Chain Construction. WABI (2008)
Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert
Segment-based multiple sequence alignment. ECCB (2008)
Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher
OpenMS - An open-source software framework for mass spectrometry. BMC Bioinform. 9 (2008)
Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Leinenbach, Andreas Hildebrandt, Christian G. Huber, Knut Reinert
Computational Quantification of Peptides from LC-MS Data. J. Comput. Biol. 15 (7) (2008)
Andreas Döring, David Weese, Tobias Rausch, Knut Reinert
SeqAn An efficient, generic C++ library for sequence analysis. BMC Bioinform. 9 (2008)
Markus Bauer, Gunnar W. Klau, Knut Reinert
An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Oper. Res. 3 (2) (2008)
Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian G. Huber, Knut Reinert
A geometric approach for the alignment of liquid chromatography - mass spectrometry data. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm
TOPP - the OpenMS proteomics pipeline. Bioinform. 23 (2) (2007)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
Integer linear programming approaches for non-unique probe selection. Discret. Appl. Math. 155 (6-7) (2007)
Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Hildebrandt, Knut Reinert
A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data. RECOMB (2007)
Markus Bauer, Gunnar W. Klau, Knut Reinert
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinform. 8 (2007)
Knut Reinert, Markus Bauer, Andreas Döring, Gunnar W. Klau, Aaron L. Halpern
A General Paradigm for Fast, Adaptive Clustering of Biological Sequences. German Conference on Bioinformatics (2007)
Ernst Althaus, Alberto Caprara, Hans-Peter Lenhof, Knut Reinert
A branch-and-cut algorithm for multiple sequence alignment. Math. Program. 105 (2-3) (2006)
Eva Lange, Clemens Gröpl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt
High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques. Pacific Symposium on Biocomputing (2006)
Markus Bauer, Gunnar W. Klau, Knut Reinert
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization. CompLife (2005)
Christian G. Huber, Oliver Kohlbacher, Knut Reinert
05471 Abstract Collection - Computational Proteomics. Computational Proteomics (2005)
Witold E. Wolski, Maciej Lalowski, Peter Martus, Ralf Herwig, Patrick Giavalisco, Johan Gobom, Albert Sickmann, Hans Lehrach, Knut Reinert
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinform. 6 (2005)
Witold E. Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert
Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinform. 6 (2005)
Markus Bauer, Gunnar W. Klau, Knut Reinert
Multiple Structural RNA Alignment with Lagrangian Relaxation. WABI (2005)
Nathanaël Delmotte, Bettina M. Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph L. Klein, Christian G. Huber
Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins. Computational Proteomics (2005)
Christian G. Huber, Oliver Kohlbacher, Knut Reinert
05471 Executive Summary - Computational Proteomics. Computational Proteomics (2005)
Clemens Gröpl, Eva Lange, Knut Reinert, Oliver Kohlbacher, Marc Sturm, Christian G. Huber, Bettina M. Mayr, Christoph L. Klein
Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples. CompLife (2005)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
Optimal robust non-unique probe selection using Integer Linear Programming. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Oliver Kohlbacher, Knut Reinert
Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges). it Inf. Technol. 46 (1) (2004)
Ernst Althaus, Alberto Caprara, Hans-Peter Lenhof, Knut Reinert
Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. ECCB (2002)
Aaron L. Halpern, Daniel H. Huson, Knut Reinert
Segment Match Refinement and Applications. WABI (2002)
Daniel H. Huson, Knut Reinert, Eugene W. Myers
The greedy path-merging algorithm for contig scaffolding. J. ACM 49 (5) (2002)
Daniel H. Huson, Knut Reinert, Saul A. Kravitz, Karin A. Remington, Arthur L. Delcher, Ian M. Dew, Michael Flanigan, Aaron L. Halpern, Zhongwu Lai, Clark M. Mobarry, Granger G. Sutton, Eugene W. Myers
Design of a compartmentalized shotgun assembler for the human genome. ISMB (Supplement of Bioinformatics) (2001)
Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton
Comparing Assemblies Using Fragments and Mate-Pairs. WABI (2001)
Russell J. Turner, Kabir Chaturvedi, Nathan Edwards, Daniel P. Fasulo, Aaron L. Halpern, Daniel H. Huson, Oliver Kohlbacher, Jason R. Miller, Knut Reinert, Karin A. Remington, Russell Schwartz, Brian Walenz, Shibu Yooseph, Sorin Istrail
Visualization challenges for a new cyberpharmaceutical computing paradigm. IEEE Symposium on Parallel and Large-Data Visualization and Graphics (2001)
Daniel H. Huson, Knut Reinert, Eugene W. Myers
The greedy path-merging algorithm for sequence assembly. RECOMB (2001)
Martin Lermen, Knut Reinert
The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. J. Comput. Biol. 7 (5) (2000)
John D. Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron
A polyhedral approach to sequence alignment problems. Discret. Appl. Math. 104 (1-3) (2000)
Knut Reinert, Jens Stoye, Torsten Will
An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinform. 16 (9) (2000)
Knut Reinert, Jens Stoye, Torsten Will
-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment. German Conference on Bioinformatics (1999)
Hans-Peter Lenhof, Burkhard Morgenstern, Knut Reinert
An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinform. 15 (3) (1999)
Knut Reinert, Hans-Peter Lenhof, Burkhard Morgenstern
An exact solution for the Segment-to-Segment multiple sequence alignment problem. German Conference on Bioinformatics (1998)
Hans-Peter Lenhof, Knut Reinert, Martin Vingron
A polyhedral approach to RNA sequence structure alignment. RECOMB (1998)
Hans-Peter Lenhof, Knut Reinert, Martin Vingron
A Polyhedral Approach to RNA Sequence Structure Alignment. J. Comput. Biol. 5 (3) (1998)
Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu
A branch-and-cut algorithm for multiple sequence alignment. RECOMB (1997)
Phillip G. Bradford, Knut Reinert
Lower Bounds for Row Minima Searching (Extended Abstract). ICALP (1996)

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Publication Activity (10 Years)

Top Topics

Top Venues

Knut Reinert