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Knut Reinert
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- affiliation: Free University of Berlin, Germany
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2020 – today
- 2024
- [c33]Ninon De Mecquenem, Simon Bosse, Vasilis Bountris, Somayeh Mohammadi, Knut Reinert, Ulf Leser:
CuttleFlow: Infrastructure-Specific Workflow Adaption for Improved Reusability. e-Science 2024: 1-10 - [c32]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 - [c31]Madalina Giurgiu
, Nadine Wittstruck, Elias Rodriguez-Fos, Rocío Chamorro González, Lotte Brückner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt
Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. RECOMB 2024: 406-411 - 2023
- [j57]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) - [j56]Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Fashuai Wu, Knut Reinert
A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. Bioinform. 39(1) (2023) - [j55]Somayeh Mohammadi
A mathematical programming approach for resource allocation of data analysis workflows on heterogeneous clusters. J. Supercomput. 79(17): 19019-19048 (2023) - 2022
- [j54]Mitra Darvish
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinform. 38(17): 4100-4108 (2022) - [j53]Jörg Winkler
LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences. BMC Bioinform. 23(1): 18 (2022) - [c30]Marius Knaust, Enrico Seiler, Knut Reinert
Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. FPGA 2022: 180-189 - 2021
- [j52]Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22(2): 642-663 (2021) - [j51]Silver A. Wolf, Lennard Epping, Sandro Andreotti
SCORE: Smart Consensus Of RNA Expression - a consensus tool for detecting differentially expressed genes in bacteria. Bioinform. 37(3): 426-428 (2021) - [j50]Sara Hetzel
RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. Bioinform. 37(21): 3934-3935 (2021) - [j49]Ulf Leser, Marcus Hilbrich
The Collaborative Research Center FONDA. Datenbank-Spektrum 21(3): 255-260 (2021) - [c29]Marie Hoffmann, Michael T. Monaghan
PriSeT: efficient de novo primer discovery. BCB 2021: 2:1-2:12 - 2020
- [j48]Christopher Pockrandt, Mai Alzamel
GenMap: ultra-fast computation of genome mappability. Bioinform. 36(12): 3687-3692 (2020) - [j47]Vitor Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinform. 36(Supplement-1): i12-i20 (2020) - [j46]M-Hossein Moeinzadeh
Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLoS Comput. Biol. 16(5) (2020) - [i11]Christopher Schiefer, Marc Bux, Jörgen Brandt, Clemens Messerschmidt
Portability of Scientific Workflows in NGS Data Analysis: A Case Study. CoRR abs/2006.03104 (2020)
2010 – 2019
- 2018
- [j45]Temesgen Hailemariam Dadi, Enrico Siragusa, Vitor Piro, Andreas Andrusch, Enrico Seiler, Bernhard Y. Renard
DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinform. 34(17): i766-i772 (2018) - [j44]René Rahn, Stefan Budach, Pascal Costanza, Marcel Ehrhardt
Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. Bioinform. 34(20): 3437-3445 (2018) - 2017
- [j43]Johannes T. Roehr, Christoph Dieterich, Knut Reinert
Flexbar 3.0 - SIMD and multicore parallelization. Bioinform. 33(18): 2941-2942 (2017) - [c28]Christopher Pockrandt, Marcel Ehrhardt
EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices. RECOMB 2017: 190-206 - [c27]Jongkyu Kim, Knut Reinert
Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence. WABI 2017: 13:1-13:14 - [e3]Russell Schwartz, Knut Reinert:
17th International Workshop on Algorithms in Bioinformatics, WABI 2017, August 21-23, 2017, Boston, MA, USA. LIPIcs 88, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2017, ISBN 978-3-95977-050-7 [contents] - [i10]Kiavash Kianfar, Christopher Pockrandt, Bahman Torkamandi, Haochen Luo, Knut Reinert:
FAMOUS: Fast Approximate string Matching using OptimUm search Schemes. CoRR abs/1711.02035 (2017) - 2016
- [j42]Luis de la Garza, Johannes Veit, András Szolek, Marc Röttig, Stephan Aiche
From the desktop to the grid: scalable bioinformatics via workflow conversion. BMC Bioinform. 17: 127 (2016) - [i9]Christopher Pockrandt, Marcel Ehrhardt, Knut Reinert:
Constant-time and space-efficient unidirectional and bidirectional FM-indices using EPR-dictionaries. CoRR abs/1608.02413 (2016) - [i8]Gene Myers, Mihai Pop
Next Generation Sequencing (Dagstuhl Seminar 16351). Dagstuhl Reports 6(8): 91-130 (2016) - 2015
- [j41]Jialu Hu
LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks. Bioinform. 31(3): 363-372 (2015) - [j40]Manuel Holtgrewe
Methods for the detection and assembly of novel sequence in high-throughput sequencing data. Bioinform. 31(12): 1904-1912 (2015) - [j39]Léon Kuchenbecker, Mikalai Nienen
IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinform. 31(18): 2963-2971 (2015) - [c26]Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert
CIDANE: Comprehensive Isoform Discovery and Abundance Estimation. RECOMB 2015: 60-61 - 2014
- [j38]Jialu Hu
NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinform. 30(4): 540-548 (2014) - [j37]Hannes Hauswedell
Lambda: the local aligner for massive biological data. Bioinform. 30(17): 349-355 (2014) - [j36]Marcel H. Schulz
Fiona: a parallel and automatic strategy for read error correction. Bioinform. 30(17): 356-363 (2014) - [j35]Kathrin Trappe, Anne-Katrin Emde, Hans-Christian Ehrlich, Knut Reinert
Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinform. 30(24): 3484-3490 (2014) - [j34]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): 3499-3505 (2014) - [j33]Birte Kehr, Kathrin Trappe, Manuel Holtgrewe
Genome alignment with graph data structures: a comparison. BMC Bioinform. 15: 99 (2014) - 2013
- [j32]Alexandra Zerck, Eckhard Nordhoff, Hans Lehrach, Knut Reinert
Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinform. 14: 56 (2013) - [j31]Sandro Andreotti
The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees. J. Comput. Biol. 20(9): 643-659 (2013) - [c25]Enrico Siragusa, David Weese, Knut Reinert
Scalable string similarity search/join with approximate seeds and multiple backtracking. EDBT/ICDT Workshops 2013: 370-374 - [c24]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 - 2012
- [j30]Anne-Katrin Emde, Marcel H. Schulz
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinform. 28(5): 619-627 (2012) - [j29]David Weese, Manuel Holtgrewe, Knut Reinert
RazerS 3: Faster, fully sensitive read mapping. Bioinform. 28(20): 2592-2599 (2012) - [j28]Chris Bauer, Frank Kleinjung, Dorothea Rutishauser
PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. BMC Bioinform. 13: 34 (2012) - [j27]Sandro Andreotti
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 9(2): 385-394 (2012) - [c23]Birte Kehr, Knut Reinert
Hidden Breakpoints in Genome Alignments. WABI 2012: 391-403 - [i7]Enrico Siragusa, David Weese, Knut Reinert:
Fast and sensitive read mapping with approximate seeds and multiple backtracking. CoRR abs/1208.4238 (2012) - 2011
- [j26]Chris Bauer, Frank Kleinjung, Celia J. Smith, Mark W. Towers, Ali Tiss
Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset. BMC Bioinform. 12: 140 (2011) - [j25]Manuel Holtgrewe
A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinform. 12: 210 (2011) - [j24]Birte Kehr, David Weese, Knut Reinert
STELLAR: fast and exact local alignments. BMC Bioinform. 12(S-9): S15 (2011) - [i6]Sandro Andreotti, Gunnar W. Klau, Knut Reinert:
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. CoRR abs/1102.4016 (2011) - 2010
- [j23]Anne-Katrin Emde, Marcel Grunert
MicroRazerS: rapid alignment of small RNA reads. Bioinform. 26(1): 123-124 (2010) - [p1]Knut Reinert, Oliver Kohlbacher
OpenMS and TOPP: Open Source Software for LC-MS Data Analysis. Proteome Bioinformatics 2010: 201-211 - [i5]Knut Reinert:
Oops I Did it Again... Sustainability in Sequence Analysis via Software Libraries. ERCIM News 2010(82): 13 (2010)
2000 – 2009
- 2009
- [b2]Andreas Gogol-Döring, Knut Reinert:
Biological Sequence Analysis Using the SeqAn C++ Library. Chapman and Hall / CRC mathematical and computational biology series, CRC Press 2009, ISBN 978-1-4200-7623-3, pp. 1-311 - [j22]Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2(2): 692-709 (2009) - [j21]Ole Schulz-Trieglaff, Egidijus Machtejevas, Knut Reinert
Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min. 2 (2009) - [j20]Tobias Rausch
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinform. 25(9): 1118-1124 (2009) - [c22]Ernst Althaus, Gunnar W. Klau
Integer Linear Programming in Computational Biology. Efficient Algorithms 2009: 199-218 - 2008
- [j19]Markus Bauer, Gunnar W. Klau, Knut Reinert:
An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Oper. Res. 3(2) (2008) - [j18]Andreas Döring
SeqAn An efficient, generic C++ library for sequence analysis. BMC Bioinform. 9 (2008) - [j17]Tobias Rausch, Anne-Katrin Emde, Knut Reinert:
Robust consensus computation. BMC Bioinform. 9(S-10) (2008) - [j16]Ole Schulz-Trieglaff, Nico Pfeifer
LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinform. 9 (2008) - [j15]Marc Sturm
OpenMS - An open-source software framework for mass spectrometry. BMC Bioinform. 9 (2008) - [j14]Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Leinenbach, Andreas Hildebrandt
Computational Quantification of Peptides from LC-MS Data. J. Comput. Biol. 15(7): 685-704 (2008) - [c21]Tobias Rausch
Segment-based multiple sequence alignment. ECCB 2008: 187-192 - [c20]Marcel H. Schulz
Fast and Adaptive Variable Order Markov Chain Construction. WABI 2008: 306-317 - [e2]Christian G. Huber, Oliver Kohlbacher, Michal Linial, Kathrin Marcus, Knut Reinert:
Computational Proteomics, 02.03. - 07.03.2008. Dagstuhl Seminar Proceedings 08101, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2008 [contents] - [i4]Knut Reinert, Christian G. Huber, Kathrin Marcus, Michal Linial, Oliver Kohlbacher:
08101 Abstracts Collection - Computational Proteomics. Computational Proteomics 2008 - 2007
- [j13]Oliver Kohlbacher
TOPP - the OpenMS proteomics pipeline. Bioinform. 23(2): 191-197 (2007) - [j12]Markus Bauer, Gunnar W. Klau
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinform. 8 (2007) - [j11]Gunnar W. Klau
Integer linear programming approaches for non-unique probe selection. Discret. Appl. Math. 155(6-7): 840-856 (2007) - [c19]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: 15-29 - [c18]Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian G. Huber
A geometric approach for the alignment of liquid chromatography - mass spectrometry data. ISMB/ECCB (Supplement of Bioinformatics) 2007: 273-281 - [c17]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: 473-487 - 2006
- [j10]Ernst Althaus, Alberto Caprara, Hans-Peter Lenhof, Knut Reinert
A branch-and-cut algorithm for multiple sequence alignment. Math. Program. 105(2-3): 387-425 (2006) - [c16]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: 243-254 - [e1]Christian G. Huber, Oliver Kohlbacher, Knut Reinert:
Computational Proteomics, 20.-25. November 2005. Dagstuhl Seminar Proceedings 05471, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2006 [contents] - 2005
- [j9]Witold E. Wolski, Maciej Lalowski
Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinform. 6: 203 (2005) - [j8]Witold E. Wolski, Maciej Lalowski
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinform. 6: 285 (2005) - [c15]Clemens Gröpl, Eva Lange, Knut Reinert, Oliver Kohlbacher, Marc Sturm, Christian G. Huber
Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples. CompLife 2005: 151-162 - [c14]Markus Bauer, Gunnar W. Klau
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization. CompLife 2005: 217-228 - [c13]Markus Bauer, Gunnar W. Klau
Multiple Structural RNA Alignment with Lagrangian Relaxation. WABI 2005: 303-314 - [i3]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 - [i2]Christian G. Huber, Oliver Kohlbacher, Knut Reinert:
05471 Executive Summary - Computational Proteomics. Computational Proteomics 2005 - [i1]Christian G. Huber, Oliver Kohlbacher, Knut Reinert:
05471 Abstract Collection - Computational Proteomics. Computational Proteomics 2005 - 2004
- [j7]Oliver Kohlbacher, Knut Reinert:
Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges). it Inf. Technol. 46(1): 31-38 (2004) - [c12]Gunnar W. Klau
Optimal robust non-unique probe selection using Integer Linear Programming. ISMB/ECCB (Supplement of Bioinformatics) 2004: 186-193 - 2002
- [j6]Daniel H. Huson, Knut Reinert
The greedy path-merging algorithm for contig scaffolding. J. ACM 49(5): 603-615 (2002) - [c11]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: 4-16 - [c10]Aaron L. Halpern, Daniel H. Huson, Knut Reinert:
Segment Match Refinement and Applications. WABI 2002: 126-139 - 2001
- [c9]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: 132-139 - [c8]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: 7-18 - [c7]Daniel H. Huson, Knut Reinert, Eugene W. Myers:
The greedy path-merging algorithm for sequence assembly. RECOMB 2001: 157-163 - [c6]Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert
Comparing Assemblies Using Fragments and Mate-Pairs. WABI 2001: 294-306 - 2000
- [j5]Knut Reinert
An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinform. 16(9): 808-814 (2000) - [j4]John D. Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel
A polyhedral approach to sequence alignment problems. Discret. Appl. Math. 104(1-3): 143-186 (2000) - [j3]Martin Lermen, Knut Reinert
The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. J. Comput. Biol. 7(5): 655-671 (2000)
1990 – 1999
- 1999
- [b1]Knut Reinert:
A polyhedral approach to sequence alignment problems. Saarland University, Saarbrücken, Germany, 1999, pp. 1-168 - [j2]Hans-Peter Lenhof, Burkhard Morgenstern, Knut Reinert
An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinform. 15(3): 203-210 (1999) - [c5]Knut Reinert, Jens Stoye, Torsten Will:
Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment. German Conference on Bioinformatics 1999: 17-24 - 1998
- [j1]Hans-Peter Lenhof, Knut Reinert
A Polyhedral Approach to RNA Sequence Structure Alignment. J. Comput. Biol. 5(3): 517-530 (1998) - [c4]Knut Reinert, Hans-Peter Lenhof, Burkhard Morgenstern:
An exact solution for the Segment-to-Segment multiple sequence alignment problem. German Conference on Bioinformatics 1998 - [c3]Hans-Peter Lenhof, Knut Reinert, Martin Vingron:
A polyhedral approach to RNA sequence structure alignment. RECOMB 1998: 153-162 - 1997
- [c2]Knut Reinert, Hans-Peter Lenhof, Petra Mutzel
A branch-and-cut algorithm for multiple sequence alignment. RECOMB 1997: 241-250 - 1996
- [c1]Phillip G. Bradford, Knut Reinert:
Lower Bounds for Row Minima Searching (Extended Abstract). ICALP 1996: 454-465
Coauthor Index
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