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ORCIDBibTeX records: Knut Reinert
@inproceedings{DBLP:conf/edbt/MohammadiPZAMLR24,
author = {Somayeh Mohammadi and
Latif Pourkarimi and
Manuel Zsch{\"{a}}bitz and
Tristan Aretz and
Ninon De Mecquenem and
Ulf Leser and
Knut Reinert},
editor = {Themis Palpanas and
H. V. Jagadish},
title = {Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous
Cluster Infrastructures},
booktitle = {Proceedings of the Workshops of the {EDBT/ICDT} 2024 Joint Conference
co-located with the {EDBT/ICDT} 2024 Joint Conference, Paestum, Italy,
March 25, 2024},
series = {{CEUR} Workshop Proceedings},
volume = {3651},
publisher = {CEUR-WS.org},
year = {2024},
url = {https://ceur-ws.org/Vol-3651/DARLI-AP-15.pdf},
timestamp = {Wed, 03 Apr 2024 17:09:53 +0200},
biburl = {https://dblp.org/rec/conf/edbt/MohammadiPZAMLR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PanRHR23,
author = {Chenxu Pan and
Ren{\'{e}} Rahn and
David Heller and
Knut Reinert},
title = {Linear: a framework to enable existing software to resolve structural
variants in long reads with flexible and efficient alignment-free
statistical models},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad071},
doi = {10.1093/BIB/BBAD071},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/PanRHR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLZZHWRSYH23,
author = {Yuwei Wang and
Bin Lian and
Haohui Zhang and
Yuanke Zhong and
Jie He and
Fashuai Wu and
Knut Reinert and
Xuequn Shang and
Hui Yang and
Jialu Hu},
title = {A multi-view latent variable model reveals cellular heterogeneity
in complex tissues for paired multimodal single-cell data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad005},
doi = {10.1093/BIOINFORMATICS/BTAD005},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLZZHWRSYH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tjs/MohammadiPDMLR23,
author = {Somayeh Mohammadi and
Latif Pourkarimi and
Felix Droop and
Ninon De Mecquenem and
Ulf Leser and
Knut Reinert},
title = {A mathematical programming approach for resource allocation of data
analysis workflows on heterogeneous clusters},
journal = {J. Supercomput.},
volume = {79},
number = {17},
pages = {19019--19048},
year = {2023},
url = {https://doi.org/10.1007/s11227-023-05325-w},
doi = {10.1007/S11227-023-05325-W},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tjs/MohammadiPDMLR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DarvishSMRR22,
author = {Mitra Darvish and
Enrico Seiler and
Svenja Mehringer and
Ren{\'{e}} Rahn and
Knut Reinert},
title = {Needle: a fast and space-efficient prefilter for estimating the quantification
of very large collections of expression experiments},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4100--4108},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac492},
doi = {10.1093/BIOINFORMATICS/BTAC492},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DarvishSMRR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WinklerUFR22,
author = {J{\"{o}}rg Winkler and
Gianvito Urgese and
Elisa Ficarra and
Knut Reinert},
title = {LaRA 2: parallel and vectorized program for sequence-structure alignment
of {RNA} sequences},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {18},
year = {2022},
url = {https://doi.org/10.1186/s12859-021-04532-7},
doi = {10.1186/S12859-021-04532-7},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WinklerUFR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fpga/KnaustSR022,
author = {Marius Knaust and
Enrico Seiler and
Knut Reinert and
Thomas Steinke},
editor = {Michael Adler and
Paolo Ienne},
title = {Co-Design for Energy Efficient and Fast Genomic Search: Interleaved
Bloom Filter on {FPGA}},
booktitle = {{FPGA} '22: The 2022 {ACM/SIGDA} International Symposium on Field-Programmable
Gate Arrays, Virtual Event, USA, 27 February 2022 - 1 March 2022},
pages = {180--189},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3490422.3502366},
doi = {10.1145/3490422.3502366},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fpga/KnaustSR022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HufskyLAAABBBBC21,
author = {Franziska Hufsky and
Kevin Lamkiewicz and
Alexandre Almeida and
Abdel Aouacheria and
Cecilia N. Arighi and
Alex Bateman and
Jan Baumbach and
Niko Beerenwinkel and
Christian Brandt and
Marco Cacciabue and
Sara Chuguransky and
Oliver Drechsel and
Robert D. Finn and
Adrian Fritz and
Stephan Fuchs and
Georges Hattab and
Anne{-}Christin Hauschild and
Dominik Heider and
Marie Hoffmann and
Martin H{\"{o}}lzer and
Stefan Hoops and
Lars Kaderali and
Ioanna Kalvari and
Max von Kleist and
Ren{\'{o}} Kmiecinski and
Denise K{\"{u}}hnert and
Gorka Lasso and
Pieter Libin and
Markus List and
Hannah F. L{\"{o}}chel and
Maria Jesus Martin and
Roman Martin and
Julian O. Matschinske and
Alice C. McHardy and
Pedro Mendes and
Jaina Mistry and
Vincent Navratil and
Eric P. Nawrocki and
{\'{A}}ine Niamh O'toole and
Nancy Ontiveros{-}Palacios and
Anton I. Petrov and
Guillermo Rangel{-}Pineros and
Nicole Redaschi and
Susanne Reimering and
Knut Reinert and
Alejandro Reyes and
Lorna J. Richardson and
David L. Robertson and
Sepideh Sadegh and
Joshua B. Singer and
Kristof Theys and
Chris Upton and
Marius Welzel and
Lowri Williams and
Manja Marz},
title = {Computational strategies to combat {COVID-19:} useful tools to accelerate
SARS-CoV-2 and coronavirus research},
journal = {Briefings Bioinform.},
volume = {22},
number = {2},
pages = {642--663},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa232},
doi = {10.1093/BIB/BBAA232},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HufskyLAAABBBBC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WolfEARS21,
author = {Silver A. Wolf and
Lennard Epping and
Sandro Andreotti and
Knut Reinert and
Torsten Semmler},
title = {{SCORE:} Smart Consensus Of {RNA} Expression - a consensus tool for
detecting differentially expressed genes in bacteria},
journal = {Bioinform.},
volume = {37},
number = {3},
pages = {426--428},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa681},
doi = {10.1093/BIOINFORMATICS/BTAA681},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WolfEARS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HetzelGRMK21,
author = {Sara Hetzel and
Pay Giesselmann and
Knut Reinert and
Alexander Meissner and
Helene Kretzmer},
title = {{RLM:} fast and simplified extraction of read-level methylation metrics
from bisulfite sequencing data},
journal = {Bioinform.},
volume = {37},
number = {21},
pages = {3934--3935},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab663},
doi = {10.1093/BIOINFORMATICS/BTAB663},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HetzelGRMK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dbsk/LeserHDEGHKKKKK21,
author = {Ulf Leser and
Marcus Hilbrich and
Claudia Draxl and
Peter Eisert and
Lars Grunske and
Patrick Hostert and
Dagmar Kainm{\"{u}}ller and
Odej Kao and
Birte Kehr and
Timo Kehrer and
Christoph Koch and
Volker Markl and
Henning Meyerhenke and
Tilmann Rabl and
Alexander Reinefeld and
Knut Reinert and
Kerstin Ritter and
Bj{\"{o}}rn Scheuermann and
Florian Schintke and
Nicole Schweikardt and
Matthias Weidlich},
title = {The Collaborative Research Center {FONDA}},
journal = {Datenbank-Spektrum},
volume = {21},
number = {3},
pages = {255--260},
year = {2021},
url = {https://doi.org/10.1007/s13222-021-00397-5},
doi = {10.1007/S13222-021-00397-5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dbsk/LeserHDEGHKKKKK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/HoffmannMR21,
author = {Marie Hoffmann and
Michael T. Monaghan and
Knut Reinert},
editor = {Hongmei Jiang and
Xiuzhen Huang and
Jiajie Zhang},
title = {PriSeT: efficient \emph{de novo} primer discovery},
booktitle = {{BCB} '21: 12th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Gainesville, Florida,
USA, August 1-4, 2021},
pages = {2:1--2:12},
publisher = {{ACM}},
year = {2021},
url = {https://doi.org/10.1145/3459930.3469546},
doi = {10.1145/3459930.3469546},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/HoffmannMR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PockrandtAIR20,
author = {Christopher Pockrandt and
Mai Alzamel and
Costas S. Iliopoulos and
Knut Reinert},
title = {GenMap: ultra-fast computation of genome mappability},
journal = {Bioinform.},
volume = {36},
number = {12},
pages = {3687--3692},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa222},
doi = {10.1093/BIOINFORMATICS/BTAA222},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PockrandtAIR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PiroDSRR20,
author = {Vitor Piro and
Temesgen Hailemariam Dadi and
Enrico Seiler and
Knut Reinert and
Bernhard Y. Renard},
title = {ganon: precise metagenomics classification against large and up-to-date
sets of reference sequences},
journal = {Bioinform.},
volume = {36},
number = {Supplement-1},
pages = {i12--i20},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa458},
doi = {10.1093/BIOINFORMATICS/BTAA458},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PiroDSRR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MoeinzadehYMGHR20,
author = {M{-}Hossein Moeinzadeh and
Jun Yang and
Evgeny Muzychenko and
Giuseppe Gallone and
David Heller and
Knut Reinert and
Stefan A. Haas and
Martin Vingron},
title = {Ranbow: {A} fast and accurate method for polyploid haplotype reconstruction},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {5},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1007843},
doi = {10.1371/JOURNAL.PCBI.1007843},
timestamp = {Wed, 11 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/MoeinzadehYMGHR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2006-03104,
author = {Christopher Schiefer and
Marc Bux and
J{\"{o}}rgen Brandt and
Clemens Messerschmidt and
Knut Reinert and
Dieter Beule and
Ulf Leser},
title = {Portability of Scientific Workflows in {NGS} Data Analysis: {A} Case
Study},
journal = {CoRR},
volume = {abs/2006.03104},
year = {2020},
url = {https://arxiv.org/abs/2006.03104},
eprinttype = {arXiv},
eprint = {2006.03104},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-03104.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DadiSPASRR18,
author = {Temesgen Hailemariam Dadi and
Enrico Siragusa and
Vitor Piro and
Andreas Andrusch and
Enrico Seiler and
Bernhard Y. Renard and
Knut Reinert},
title = {DREAM-Yara: an exact read mapper for very large databases with short
update time},
journal = {Bioinform.},
volume = {34},
number = {17},
pages = {i766--i772},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty567},
doi = {10.1093/BIOINFORMATICS/BTY567},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DadiSPASRR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RahnBCEHR18,
author = {Ren{\'{e}} Rahn and
Stefan Budach and
Pascal Costanza and
Marcel Ehrhardt and
Jonny Hancox and
Knut Reinert},
title = {Generic accelerated sequence alignment in SeqAn using vectorization
and multi-threading},
journal = {Bioinform.},
volume = {34},
number = {20},
pages = {3437--3445},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty380},
doi = {10.1093/BIOINFORMATICS/BTY380},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RahnBCEHR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoehrDR17,
author = {Johannes T. Roehr and
Christoph Dieterich and
Knut Reinert},
title = {Flexbar 3.0 - {SIMD} and multicore parallelization},
journal = {Bioinform.},
volume = {33},
number = {18},
pages = {2941--2942},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx330},
doi = {10.1093/BIOINFORMATICS/BTX330},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoehrDR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/PockrandtER17,
author = {Christopher Pockrandt and
Marcel Ehrhardt and
Knut Reinert},
editor = {S{\"{u}}leyman Cenk Sahinalp},
title = {EPR-Dictionaries: {A} Practical and Fast Data Structure for Constant
Time Searches in Unidirectional and Bidirectional {FM} Indices},
booktitle = {Research in Computational Molecular Biology - 21st Annual International
Conference, {RECOMB} 2017, Hong Kong, China, May 3-7, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10229},
pages = {190--206},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-56970-3\_12},
doi = {10.1007/978-3-319-56970-3\_12},
timestamp = {Sat, 30 May 2020 20:04:52 +0200},
biburl = {https://dblp.org/rec/conf/recomb/PockrandtER17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/KimR17,
author = {Jongkyu Kim and
Knut Reinert},
editor = {Russell Schwartz and
Knut Reinert},
title = {Vaquita: Fast and Accurate Identification of Structural Variation
Using Combined Evidence},
booktitle = {17th International Workshop on Algorithms in Bioinformatics, {WABI}
2017, August 21-23, 2017, Boston, MA, {USA}},
series = {LIPIcs},
volume = {88},
pages = {13:1--13:14},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2017},
url = {https://doi.org/10.4230/LIPIcs.WABI.2017.13},
doi = {10.4230/LIPICS.WABI.2017.13},
timestamp = {Tue, 11 Feb 2020 15:52:14 +0100},
biburl = {https://dblp.org/rec/conf/wabi/KimR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wabi/2017,
editor = {Russell Schwartz and
Knut Reinert},
title = {17th International Workshop on Algorithms in Bioinformatics, {WABI}
2017, August 21-23, 2017, Boston, MA, {USA}},
series = {LIPIcs},
volume = {88},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2017},
url = {http://www.dagstuhl.de/dagpub/978-3-95977-050-7},
isbn = {978-3-95977-050-7},
timestamp = {Tue, 11 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/2017.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1711-02035,
author = {Kiavash Kianfar and
Christopher Pockrandt and
Bahman Torkamandi and
Haochen Luo and
Knut Reinert},
title = {{FAMOUS:} Fast Approximate string Matching using OptimUm search Schemes},
journal = {CoRR},
volume = {abs/1711.02035},
year = {2017},
url = {http://arxiv.org/abs/1711.02035},
eprinttype = {arXiv},
eprint = {1711.02035},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1711-02035.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GarzaVSRAGRK16,
author = {Luis de la Garza and
Johannes Veit and
Andr{\'{a}}s Szolek and
Marc R{\"{o}}ttig and
Stephan Aiche and
Sandra Gesing and
Knut Reinert and
Oliver Kohlbacher},
title = {From the desktop to the grid: scalable bioinformatics via workflow
conversion},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {127},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-0978-9},
doi = {10.1186/S12859-016-0978-9},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GarzaVSRAGRK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/PockrandtER16,
author = {Christopher Pockrandt and
Marcel Ehrhardt and
Knut Reinert},
title = {Constant-time and space-efficient unidirectional and bidirectional
FM-indices using EPR-dictionaries},
journal = {CoRR},
volume = {abs/1608.02413},
year = {2016},
url = {http://arxiv.org/abs/1608.02413},
eprinttype = {arXiv},
eprint = {1608.02413},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/PockrandtER16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dagstuhl-reports/MyersPRW16,
author = {Gene Myers and
Mihai Pop and
Knut Reinert and
Tandy J. Warnow},
title = {Next Generation Sequencing (Dagstuhl Seminar 16351)},
journal = {Dagstuhl Reports},
volume = {6},
number = {8},
pages = {91--130},
year = {2016},
url = {https://doi.org/10.4230/DagRep.6.8.91},
doi = {10.4230/DAGREP.6.8.91},
timestamp = {Sat, 16 Sep 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dagstuhl-reports/MyersPRW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuR15,
author = {Jialu Hu and
Knut Reinert},
title = {LocalAli: an evolutionary-based local alignment approach to identify
functionally \emph{conserved} modules in multiple networks},
journal = {Bioinform.},
volume = {31},
number = {3},
pages = {363--372},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu652},
doi = {10.1093/BIOINFORMATICS/BTU652},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoltgreweKR15,
author = {Manuel Holtgrewe and
L{\'{e}}on Kuchenbecker and
Knut Reinert},
title = {Methods for the detection and assembly of novel sequence in high-throughput
sequencing data},
journal = {Bioinform.},
volume = {31},
number = {12},
pages = {1904--1912},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv051},
doi = {10.1093/BIOINFORMATICS/BTV051},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HoltgreweKR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuchenbeckerNHN15,
author = {L{\'{e}}on Kuchenbecker and
Mikalai Nienen and
Jochen Hecht and
Avidan U. Neumann and
Nina Babel and
Knut Reinert and
Peter N. Robinson},
title = {{IMSEQ} - a fast and error aware approach to immunogenetic sequence
analysis},
journal = {Bioinform.},
volume = {31},
number = {18},
pages = {2963--2971},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv309},
doi = {10.1093/BIOINFORMATICS/BTV309},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuchenbeckerNHN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/CanzarAWRK15,
author = {Stefan Canzar and
Sandro Andreotti and
David Weese and
Knut Reinert and
Gunnar W. Klau},
editor = {Teresa M. Przytycka},
title = {{CIDANE:} Comprehensive Isoform Discovery and Abundance Estimation},
booktitle = {Research in Computational Molecular Biology - 19th Annual International
Conference, {RECOMB} 2015, Warsaw, Poland, April 12-15, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9029},
pages = {60--61},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-16706-0\_8},
doi = {10.1007/978-3-319-16706-0\_8},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/CanzarAWRK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuKR14,
author = {Jialu Hu and
Birte Kehr and
Knut Reinert},
title = {NetCoffee: a fast and accurate global alignment approach to identify
functionally conserved proteins in multiple networks},
journal = {Bioinform.},
volume = {30},
number = {4},
pages = {540--548},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt715},
doi = {10.1093/BIOINFORMATICS/BTT715},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuKR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HauswedellSR14,
author = {Hannes Hauswedell and
Jochen Singer and
Knut Reinert},
title = {Lambda: the local aligner for massive biological data},
journal = {Bioinform.},
volume = {30},
number = {17},
pages = {349--355},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu439},
doi = {10.1093/BIOINFORMATICS/BTU439},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HauswedellSR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchulzWHDNRR14,
author = {Marcel H. Schulz and
David Weese and
Manuel Holtgrewe and
Viktoria Dimitrova and
Sijia Niu and
Knut Reinert and
Hugues Richard},
title = {Fiona: a parallel and automatic strategy for read error correction},
journal = {Bioinform.},
volume = {30},
number = {17},
pages = {356--363},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu440},
doi = {10.1093/BIOINFORMATICS/BTU440},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchulzWHDNRR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TrappeEER14,
author = {Kathrin Trappe and
Anne{-}Katrin Emde and
Hans{-}Christian Ehrlich and
Knut Reinert},
title = {Gustaf: Detecting and correctly classifying SVs in the {NGS} twilight
zone},
journal = {Bioinform.},
volume = {30},
number = {24},
pages = {3484--3490},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu431},
doi = {10.1093/BIOINFORMATICS/BTU431},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TrappeEER14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RahnWR14,
author = {Ren{\'{e}} Rahn and
David Weese and
Knut Reinert},
title = {Journaled string tree - a scalable data structure for analyzing thousands
of similar genomes on your laptop},
journal = {Bioinform.},
volume = {30},
number = {24},
pages = {3499--3505},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu438},
doi = {10.1093/BIOINFORMATICS/BTU438},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RahnWR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KehrTHR14,
author = {Birte Kehr and
Kathrin Trappe and
Manuel Holtgrewe and
Knut Reinert},
title = {Genome alignment with graph data structures: a comparison},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {99},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-99},
doi = {10.1186/1471-2105-15-99},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KehrTHR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZerckNLR13,
author = {Alexandra Zerck and
Eckhard Nordhoff and
Hans Lehrach and
Knut Reinert},
title = {Optimal precursor ion selection for {LC-MALDI} {MS/MS}},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {56},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-56},
doi = {10.1186/1471-2105-14-56},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZerckNLR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AndreottiRC13,
author = {Sandro Andreotti and
Knut Reinert and
Stefan Canzar},
title = {The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees},
journal = {J. Comput. Biol.},
volume = {20},
number = {9},
pages = {643--659},
year = {2013},
url = {https://doi.org/10.1089/cmb.2013.0057},
doi = {10.1089/CMB.2013.0057},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/AndreottiRC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/edbt/SiragusaWR13,
author = {Enrico Siragusa and
David Weese and
Knut Reinert},
editor = {Giovanna Guerrini},
title = {Scalable string similarity search/join with approximate seeds and
multiple backtracking},
booktitle = {Joint 2013 {EDBT/ICDT} Conferences, {EDBT/ICDT} '13, Genoa, Italy,
March 22, 2013, Workshop Proceedings},
pages = {370--374},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2457317.2457386},
doi = {10.1145/2457317.2457386},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/edbt/SiragusaWR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwsg/Garza0SRARK13,
author = {Luis de la Garza and
Jens Kr{\"{u}}ger and
Charlotta Sch{\"{a}}rfe and
Marc R{\"{o}}ttig and
Stephan Aiche and
Knut Reinert and
Oliver Kohlbacher},
editor = {Tam{\'{a}}s Kiss},
title = {From the Desktop to the Grid: conversion of {KNIME} Workflows to gUSE},
booktitle = {Proceedings of the 5th International Workshop on Science Gateways,
Zurich, Switzerland, 3-5 June, 2013},
series = {{CEUR} Workshop Proceedings},
volume = {993},
publisher = {CEUR-WS.org},
year = {2013},
url = {https://ceur-ws.org/Vol-993/paper9.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:48 +0100},
biburl = {https://dblp.org/rec/conf/iwsg/Garza0SRARK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EmdeSWSVKHR12,
author = {Anne{-}Katrin Emde and
Marcel H. Schulz and
David Weese and
Ruping Sun and
Martin Vingron and
Vera M. Kalscheuer and
Stefan A. Haas and
Knut Reinert},
title = {Detecting genomic indel variants with exact breakpoints in single-
and paired-end sequencing data using SplazerS},
journal = {Bioinform.},
volume = {28},
number = {5},
pages = {619--627},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts019},
doi = {10.1093/BIOINFORMATICS/BTS019},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EmdeSWSVKHR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeeseHR12,
author = {David Weese and
Manuel Holtgrewe and
Knut Reinert},
title = {RazerS 3: Faster, fully sensitive read mapping},
journal = {Bioinform.},
volume = {28},
number = {20},
pages = {2592--2599},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts505},
doi = {10.1093/BIOINFORMATICS/BTS505},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeeseHR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BauerKRPCDARSS12,
author = {Chris Bauer and
Frank Kleinjung and
Dorothea Rutishauser and
Christian Panse and
Alexandra Chadt and
Tanja Dreja and
Hadi Al{-}Hasani and
Knut Reinert and
Ralph Schlapbach and
Johannes Schuchhardt},
title = {{PPINGUIN:} Peptide Profiling Guided Identification of Proteins improves
quantitation of iTRAQ ratios},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {34},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-34},
doi = {10.1186/1471-2105-13-34},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BauerKRPCDARSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/AndreottiKR12,
author = {Sandro Andreotti and
Gunnar W. Klau and
Knut Reinert},
title = {Antilope - {A} Lagrangian Relaxation Approach to the de novo Peptide
Sequencing Problem},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {2},
pages = {385--394},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2011.59},
doi = {10.1109/TCBB.2011.59},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/AndreottiKR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/KehrRD12,
author = {Birte Kehr and
Knut Reinert and
Aaron E. Darling},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {Hidden Breakpoints in Genome Alignments},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {391--403},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_31},
doi = {10.1007/978-3-642-33122-0\_31},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/KehrRD12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1208-4238,
author = {Enrico Siragusa and
David Weese and
Knut Reinert},
title = {Fast and sensitive read mapping with approximate seeds and multiple
backtracking},
journal = {CoRR},
volume = {abs/1208.4238},
year = {2012},
url = {http://arxiv.org/abs/1208.4238},
eprinttype = {arXiv},
eprint = {1208.4238},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1208-4238.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BauerKSTTCDBARSC11,
author = {Chris Bauer and
Frank Kleinjung and
Celia J. Smith and
Mark W. Towers and
Ali Tiss and
Alexandra Chadt and
Tanja Dreja and
Dieter Beule and
Hadi Al{-}Hasani and
Knut Reinert and
Johannes Schuchhardt and
Rainer Cramer},
title = {Biomarker Discovery and Redundancy Reduction towards Classification
using a Multi-factorial {MALDI-TOF} {MS} {T2DM} Mouse Model Dataset},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {140},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-140},
doi = {10.1186/1471-2105-12-140},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BauerKSTTCDBARSC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HoltgreweEWR11,
author = {Manuel Holtgrewe and
Anne{-}Katrin Emde and
David Weese and
Knut Reinert},
title = {A Novel And Well-Defined Benchmarking Method For Second Generation
Read Mapping},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {210},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-210},
doi = {10.1186/1471-2105-12-210},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HoltgreweEWR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KehrWR11,
author = {Birte Kehr and
David Weese and
Knut Reinert},
title = {{STELLAR:} fast and exact local alignments},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-9}},
pages = {S15},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S9-S15},
doi = {10.1186/1471-2105-12-S9-S15},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KehrWR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1102-4016,
author = {Sandro Andreotti and
Gunnar W. Klau and
Knut Reinert},
title = {Antilope - {A} Lagrangian Relaxation Approach to the de novo Peptide
Sequencing Problem},
journal = {CoRR},
volume = {abs/1102.4016},
year = {2011},
url = {http://arxiv.org/abs/1102.4016},
eprinttype = {arXiv},
eprint = {1102.4016},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1102-4016.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EmdeGWRS10,
author = {Anne{-}Katrin Emde and
Marcel Grunert and
David Weese and
Knut Reinert and
Silke R. Sperling},
title = {MicroRazerS: rapid alignment of small {RNA} reads},
journal = {Bioinform.},
volume = {26},
number = {1},
pages = {123--124},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btp601},
doi = {10.1093/BIOINFORMATICS/BTP601},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EmdeGWRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/daglib/p/ReinertK10,
author = {Knut Reinert and
Oliver Kohlbacher},
editor = {Simon J. Hubbard and
Andrew R. Jones},
title = {OpenMS and {TOPP:} Open Source Software for {LC-MS} Data Analysis},
booktitle = {Proteome Bioinformatics},
pages = {201--211},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-1-60761-444-9\_14},
doi = {10.1007/978-1-60761-444-9\_14},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/books/daglib/p/ReinertK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ercim/Reinert10,
author = {Knut Reinert},
title = {Oops {I} Did it Again... Sustainability in Sequence Analysis via Software
Libraries},
journal = {{ERCIM} News},
volume = {2010},
number = {82},
pages = {13},
year = {2010},
url = {http://ercim-news.ercim.eu/en82/special/sustainability-in-sequence-analysis-via-software-libraries},
timestamp = {Wed, 22 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ercim/Reinert10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/daglib/0024077,
author = {Andreas Gogol{-}D{\"{o}}ring and
Knut Reinert},
title = {Biological Sequence Analysis Using the SeqAn {C++} Library},
series = {Chapman and Hall / {CRC} mathematical and computational biology series},
publisher = {{CRC} Press},
year = {2009},
isbn = {978-1-4200-7623-3},
timestamp = {Fri, 28 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/daglib/0024077.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/BauerRMRSBP09,
author = {Raphael Andr{\'{e}} Bauer and
Kristian Rother and
Peter Moor and
Knut Reinert and
Thomas Steinke and
Janusz M. Bujnicki and
Robert Preissner},
title = {Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams
and String Descriptors},
journal = {Algorithms},
volume = {2},
number = {2},
pages = {692--709},
year = {2009},
url = {https://doi.org/10.3390/a2020692},
doi = {10.3390/A2020692},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithms/BauerRMRSBP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodatamining/Schulz-TrieglaffMRSTU09,
author = {Ole Schulz{-}Trieglaff and
Egidijus Machtejevas and
Knut Reinert and
Hartmut Schl{\"{u}}ter and
Joachim Thiemann and
Klaus Unger},
title = {Statistical quality assessment and outlier detection for liquid chromatography-mass
spectrometry experiments},
journal = {BioData Min.},
volume = {2},
year = {2009},
url = {https://doi.org/10.1186/1756-0381-2-4},
doi = {10.1186/1756-0381-2-4},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodatamining/Schulz-TrieglaffMRSTU09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RauschKDWEDR09,
author = {Tobias Rausch and
Sergey Koren and
Gennady Denisov and
David Weese and
Anne{-}Katrin Emde and
Andreas D{\"{o}}ring and
Knut Reinert},
title = {A consistency-based consensus algorithm for \emph{de novo} and reference-guided
sequence assembly of short reads},
journal = {Bioinform.},
volume = {25},
number = {9},
pages = {1118--1124},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp131},
doi = {10.1093/BIOINFORMATICS/BTP131},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RauschKDWEDR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/AlthausKKLR09,
author = {Ernst Althaus and
Gunnar W. Klau and
Oliver Kohlbacher and
Hans{-}Peter Lenhof and
Knut Reinert},
editor = {Susanne Albers and
Helmut Alt and
Stefan N{\"{a}}her},
title = {Integer Linear Programming in Computational Biology},
booktitle = {Efficient Algorithms, Essays Dedicated to Kurt Mehlhorn on the Occasion
of His 60th Birthday},
series = {Lecture Notes in Computer Science},
volume = {5760},
pages = {199--218},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-03456-5\_14},
doi = {10.1007/978-3-642-03456-5\_14},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/birthday/AlthausKKLR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/aor/BauerKR08,
author = {Markus Bauer and
Gunnar W. Klau and
Knut Reinert},
title = {An Exact Mathematical Programming Approach to Multiple {RNA} Sequence-Structure
Alignment},
journal = {Algorithmic Oper. Res.},
volume = {3},
number = {2},
year = {2008},
url = {http://journals.hil.unb.ca/index.php/AOR/article/view/9700},
timestamp = {Wed, 10 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/aor/BauerKR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DoringWRR08,
author = {Andreas D{\"{o}}ring and
David Weese and
Tobias Rausch and
Knut Reinert},
title = {SeqAn An efficient, generic {C++} library for sequence analysis},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-11},
doi = {10.1186/1471-2105-9-11},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DoringWRR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RauschER08,
author = {Tobias Rausch and
Anne{-}Katrin Emde and
Knut Reinert},
title = {Robust consensus computation},
journal = {{BMC} Bioinform.},
volume = {9},
number = {{S-10}},
year = {2008},
url = {http://www.biomedcentral.com/1471-2105/9/S10/P4},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RauschER08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Schulz-TrieglaffPGKR08,
author = {Ole Schulz{-}Trieglaff and
Nico Pfeifer and
Clemens Gr{\"{o}}pl and
Oliver Kohlbacher and
Knut Reinert},
title = {LC-MSsim - a simulation software for liquid chromatography mass spectrometry
data},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-423},
doi = {10.1186/1471-2105-9-423},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Schulz-TrieglaffPGKR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SturmBGHHLPSZRK08,
author = {Marc Sturm and
Andreas Bertsch and
Clemens Gr{\"{o}}pl and
Andreas Hildebrandt and
Rene Hussong and
Eva Lange and
Nico Pfeifer and
Ole Schulz{-}Trieglaff and
Alexandra Zerck and
Knut Reinert and
Oliver Kohlbacher},
title = {OpenMS - An open-source software framework for mass spectrometry},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-163},
doi = {10.1186/1471-2105-9-163},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SturmBGHHLPSZRK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Schulz-TrieglaffHGLHHR08,
author = {Ole Schulz{-}Trieglaff and
Rene Hussong and
Clemens Gr{\"{o}}pl and
Andreas Leinenbach and
Andreas Hildebrandt and
Christian G. Huber and
Knut Reinert},
title = {Computational Quantification of Peptides from {LC-MS} Data},
journal = {J. Comput. Biol.},
volume = {15},
number = {7},
pages = {685--704},
year = {2008},
url = {https://doi.org/10.1089/cmb.2007.0117},
doi = {10.1089/CMB.2007.0117},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Schulz-TrieglaffHGLHHR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/RauschEWDNR08,
author = {Tobias Rausch and
Anne{-}Katrin Emde and
David Weese and
Andreas D{\"{o}}ring and
C{\'{e}}dric Notredame and
Knut Reinert},
title = {Segment-based multiple sequence alignment},
booktitle = {ECCB'08 Proceedings, Seventh European Conference on Computational
Biology, 22-26 September 2008, Cagliari, Italy},
pages = {187--192},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn281},
doi = {10.1093/BIOINFORMATICS/BTN281},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/eccb/RauschEWDNR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SchulzWRDRV08,
author = {Marcel H. Schulz and
David Weese and
Tobias Rausch and
Andreas D{\"{o}}ring and
Knut Reinert and
Martin Vingron},
editor = {Keith A. Crandall and
Jens Lagergren},
title = {Fast and Adaptive Variable Order Markov Chain Construction},
booktitle = {Algorithms in Bioinformatics, 8th International Workshop, {WABI} 2008,
Karlsruhe, Germany, September 15-19, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5251},
pages = {306--317},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87361-7\_26},
doi = {10.1007/978-3-540-87361-7\_26},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SchulzWRDRV08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/dagstuhl/2008P8101,
editor = {Christian G. Huber and
Oliver Kohlbacher and
Michal Linial and
Kathrin Marcus and
Knut Reinert},
title = {Computational Proteomics, 02.03. - 07.03.2008},
series = {Dagstuhl Seminar Proceedings},
volume = {08101},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"{u}}r Informatik
(IBFI), Schloss Dagstuhl, Germany},
year = {2008},
url = {http://drops.dagstuhl.de/portals/08101/},
timestamp = {Thu, 10 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dagstuhl/2008P8101.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dagstuhl/ReinertHMLK08,
author = {Knut Reinert and
Christian G. Huber and
Kathrin Marcus and
Michal Linial and
Oliver Kohlbacher},
editor = {Christian G. Huber and
Oliver Kohlbacher and
Michal Linial and
Kathrin Marcus and
Knut Reinert},
title = {08101 Abstracts Collection - Computational Proteomics},
booktitle = {Computational Proteomics, 02.03. - 07.03.2008},
series = {Dagstuhl Seminar Proceedings},
volume = {08101},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"{u}}r Informatik
(IBFI), Schloss Dagstuhl, Germany},
year = {2008},
url = {http://drops.dagstuhl.de/opus/volltexte/2008/1784/},
timestamp = {Thu, 10 Jun 2021 13:02:06 +0200},
biburl = {https://dblp.org/rec/conf/dagstuhl/ReinertHMLK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KohlbacherRGLPSS07,
author = {Oliver Kohlbacher and
Knut Reinert and
Clemens Gr{\"{o}}pl and
Eva Lange and
Nico Pfeifer and
Ole Schulz{-}Trieglaff and
Marc Sturm},
title = {{TOPP} - the OpenMS proteomics pipeline},
journal = {Bioinform.},
volume = {23},
number = {2},
pages = {191--197},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl299},
doi = {10.1093/BIOINFORMATICS/BTL299},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KohlbacherRGLPSS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BauerKR07,
author = {Markus Bauer and
Gunnar W. Klau and
Knut Reinert},
title = {Accurate multiple sequence-structure alignment of {RNA} sequences
using combinatorial optimization},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-271},
doi = {10.1186/1471-2105-8-271},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BauerKR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/KlauRSVR07,
author = {Gunnar W. Klau and
Sven Rahmann and
Alexander Schliep and
Martin Vingron and
Knut Reinert},
title = {Integer linear programming approaches for non-unique probe selection},
journal = {Discret. Appl. Math.},
volume = {155},
number = {6-7},
pages = {840--856},
year = {2007},
url = {https://doi.org/10.1016/j.dam.2005.09.021},
doi = {10.1016/J.DAM.2005.09.021},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/KlauRSVR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/ReinertBDKH07,
author = {Knut Reinert and
Markus Bauer and
Andreas D{\"{o}}ring and
Gunnar W. Klau and
Aaron L. Halpern},
editor = {Claudia Falter and
Alexander Schliep and
Joachim Selbig and
Martin Vingron and
Dirk Walther},
title = {A General Paradigm for Fast, Adaptive Clustering of Biological Sequences},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 2007,
September 26-28, 2007, Potsdam, Germany},
series = {{LNI}},
volume = {{P-115}},
pages = {15--29},
publisher = {{GI}},
year = {2007},
url = {https://dl.gi.de/handle/20.500.12116/22371},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/ReinertBDKH07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/LangeGSLHR07,
author = {Eva Lange and
Clemens Gr{\"{o}}pl and
Ole Schulz{-}Trieglaff and
Andreas Leinenbach and
Christian G. Huber and
Knut Reinert},
title = {A geometric approach for the alignment of liquid chromatography -
mass spectrometry data},
booktitle = {Proceedings 15th International Conference on Intelligent Systems for
Molecular Biology {(ISMB)} {\&} 6th European Conference on Computational
Biology (ECCB), Vienna, Austria, July 21-25, 2007},
pages = {273--281},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm209},
doi = {10.1093/BIOINFORMATICS/BTM209},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/LangeGSLHR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Schulz-TrieglaffHGHR07,
author = {Ole Schulz{-}Trieglaff and
Rene Hussong and
Clemens Gr{\"{o}}pl and
Andreas Hildebrandt and
Knut Reinert},
editor = {Terence P. Speed and
Haiyan Huang},
title = {A Fast and Accurate Algorithm for the Quantification of Peptides from
Mass Spectrometry Data},
booktitle = {Research in Computational Molecular Biology, 11th Annual International
Conference, {RECOMB} 2007, Oakland, CA, USA, April 21-25, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4453},
pages = {473--487},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71681-5\_33},
doi = {10.1007/978-3-540-71681-5\_33},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/Schulz-TrieglaffHGHR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mp/AlthausCLR06,
author = {Ernst Althaus and
Alberto Caprara and
Hans{-}Peter Lenhof and
Knut Reinert},
title = {A branch-and-cut algorithm for multiple sequence alignment},
journal = {Math. Program.},
volume = {105},
number = {2-3},
pages = {387--425},
year = {2006},
url = {https://doi.org/10.1007/s10107-005-0659-3},
doi = {10.1007/S10107-005-0659-3},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mp/AlthausCLR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LangeGRKH06,
author = {Eva Lange and
Clemens Gr{\"{o}}pl and
Knut Reinert and
Oliver Kohlbacher and
Andreas Hildebrandt},
editor = {Russ B. Altman and
Tiffany Murray and
Teri E. Klein and
A. Keith Dunker and
Lawrence Hunter},
title = {High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques},
booktitle = {Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2006},
pages = {243--254},
publisher = {World Scientific},
year = {2006},
url = {http://psb.stanford.edu/psb-online/proceedings/psb06/lange.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LangeGRKH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/dagstuhl/2005P5471,
editor = {Christian G. Huber and
Oliver Kohlbacher and
Knut Reinert},
title = {Computational Proteomics, 20.-25. November 2005},
series = {Dagstuhl Seminar Proceedings},
volume = {05471},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"{u}}r Informatik
(IBFI), Schloss Dagstuhl, Germany},
year = {2006},
url = {http://drops.dagstuhl.de/portals/05471/},
timestamp = {Thu, 10 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dagstuhl/2005P5471.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WolskiLJR05,
author = {Witold E. Wolski and
Maciej Lalowski and
Peter Jungblut and
Knut Reinert},
title = {Calibration of mass spectrometric peptide mass fingerprint data without
specific external or internal calibrants},
journal = {{BMC} Bioinform.},
volume = {6},
pages = {203},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-203},
doi = {10.1186/1471-2105-6-203},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WolskiLJR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WolskiLMHGGSLR05,
author = {Witold E. Wolski and
Maciej Lalowski and
Peter Martus and
Ralf Herwig and
Patrick Giavalisco and
Johan Gobom and
Albert Sickmann and
Hans Lehrach and
Knut Reinert},
title = {Transformation and other factors of the peptide mass spectrometry
pairwise peak-list comparison process},
journal = {{BMC} Bioinform.},
volume = {6},
pages = {285},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-285},
doi = {10.1186/1471-2105-6-285},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WolskiLMHGGSLR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/complife/GroplLRKSHMK05,
author = {Clemens Gr{\"{o}}pl and
Eva Lange and
Knut Reinert and
Oliver Kohlbacher and
Marc Sturm and
Christian G. Huber and
Bettina M. Mayr and
Christoph L. Klein},
editor = {Michael R. Berthold and
Robert C. Glen and
Kay Diederichs and
Oliver Kohlbacher and
Ingrid Fischer},
title = {Algorithms for the Automated Absolute Quantification of Diagnostic
Markers in Complex Proteomics Samples},
booktitle = {Computational Life Sciences, First International Symposium, CompLife
2005, Konstanz, Germany, September 25-27, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3695},
pages = {151--162},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11560500\_14},
doi = {10.1007/11560500\_14},
timestamp = {Wed, 25 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/complife/GroplLRKSHMK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/complife/BauerKR05,
author = {Markus Bauer and
Gunnar W. Klau and
Knut Reinert},
editor = {Michael R. Berthold and
Robert C. Glen and
Kay Diederichs and
Oliver Kohlbacher and
Ingrid Fischer},
title = {Fast and Accurate Structural {RNA} Alignment by Progressive Lagrangian
Optimization},
booktitle = {Computational Life Sciences, First International Symposium, CompLife
2005, Konstanz, Germany, September 25-27, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3695},
pages = {217--228},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11560500\_20},
doi = {10.1007/11560500\_20},
timestamp = {Tue, 26 Mar 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/complife/BauerKR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BauerKR05,
author = {Markus Bauer and
Gunnar W. Klau and
Knut Reinert},
editor = {Rita Casadio and
Gene Myers},
title = {Multiple Structural {RNA} Alignment with Lagrangian Relaxation},
booktitle = {Algorithms in Bioinformatics, 5th International Workshop, {WABI} 2005,
Mallorca, Spain, October 3-6, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3692},
pages = {303--314},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11557067\_25},
doi = {10.1007/11557067\_25},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BauerKR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dagstuhl/DelmotteMLRKKH05,
author = {Nathana{\"{e}}l Delmotte and
Bettina M. Mayr and
Andreas Leinenbach and
Knut Reinert and
Oliver Kohlbacher and
Christoph L. Klein and
Christian G. Huber},
editor = {Christian G. Huber and
Oliver Kohlbacher and
Knut Reinert},
title = {Evaluation of {LC-MS} data for the absolute quantitative analysis
of marker proteins},
booktitle = {Computational Proteomics, 20.-25. November 2005},
series = {Dagstuhl Seminar Proceedings},
volume = {05471},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"{u}}r Informatik
(IBFI), Schloss Dagstuhl, Germany},
year = {2005},
url = {http://drops.dagstuhl.de/opus/volltexte/2006/539},
timestamp = {Thu, 10 Jun 2021 13:02:10 +0200},
biburl = {https://dblp.org/rec/conf/dagstuhl/DelmotteMLRKKH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dagstuhl/HuberKR05,
author = {Christian G. Huber and
Oliver Kohlbacher and
Knut Reinert},
editor = {Christian G. Huber and
Oliver Kohlbacher and
Knut Reinert},
title = {05471 Executive Summary - Computational Proteomics},
booktitle = {Computational Proteomics, 20.-25. November 2005},
series = {Dagstuhl Seminar Proceedings},
volume = {05471},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"{u}}r Informatik
(IBFI), Schloss Dagstuhl, Germany},
year = {2005},
url = {http://drops.dagstuhl.de/opus/volltexte/2006/540},
timestamp = {Thu, 23 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dagstuhl/HuberKR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dagstuhl/HuberKR05a,
author = {Christian G. Huber and
Oliver Kohlbacher and
Knut Reinert},
editor = {Christian G. Huber and
Oliver Kohlbacher and
Knut Reinert},
title = {05471 Abstract Collection - Computational Proteomics},
booktitle = {Computational Proteomics, 20.-25. November 2005},
series = {Dagstuhl Seminar Proceedings},
volume = {05471},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"{u}}r Informatik
(IBFI), Schloss Dagstuhl, Germany},
year = {2005},
url = {http://drops.dagstuhl.de/opus/volltexte/2006/556},
timestamp = {Thu, 23 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dagstuhl/HuberKR05a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/it/KohlbacherR04,
author = {Oliver Kohlbacher and
Knut Reinert},
title = {Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische
Herausforderungen (Differential Analysis in Proteomics: Experimental
Methods, Algorithmic Challenges)},
journal = {it Inf. Technol.},
volume = {46},
number = {1},
pages = {31--38},
year = {2004},
url = {http://www.extenza-eps.com/extenza/loadHTML?objectIDValue=26506\&\#38;type=abstract},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/it/KohlbacherR04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KlauRSVR04,
author = {Gunnar W. Klau and
Sven Rahmann and
Alexander Schliep and
Martin Vingron and
Knut Reinert},
title = {Optimal robust non-unique probe selection using Integer Linear Programming},
booktitle = {Proceedings Twelfth International Conference on Intelligent Systems
for Molecular Biology/Third European Conference on Computational Biology
2004, Glasgow, UK, July 31-August 4, 2004},
pages = {186--193},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth936},
doi = {10.1093/BIOINFORMATICS/BTH936},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/KlauRSVR04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jacm/HusonRM02,
author = {Daniel H. Huson and
Knut Reinert and
Eugene W. Myers},
title = {The greedy path-merging algorithm for contig scaffolding},
journal = {J. {ACM}},
volume = {49},
number = {5},
pages = {603--615},
year = {2002},
url = {https://doi.org/10.1145/585265.585267},
doi = {10.1145/585265.585267},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jacm/HusonRM02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/AlthausCLR02,
author = {Ernst Althaus and
Alberto Caprara and
Hans{-}Peter Lenhof and
Knut Reinert},
title = {Multiple sequence alignment with arbitrary gap costs: Computing an
optimal solution using polyhedral combinatorics},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2002), October 6-9, 2002, Saarbr{\"{u}}cken, Germany},
pages = {4--16},
year = {2002},
timestamp = {Thu, 23 Jun 2016 15:53:27 +0200},
biburl = {https://dblp.org/rec/conf/eccb/AlthausCLR02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/HalpernHR02,
author = {Aaron L. Halpern and
Daniel H. Huson and
Knut Reinert},
editor = {Roderic Guig{\'{o}} and
Dan Gusfield},
title = {Segment Match Refinement and Applications},
booktitle = {Algorithms in Bioinformatics, Second International Workshop, {WABI}
2002, Rome, Italy, September 17-21, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2452},
pages = {126--139},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45784-4\_10},
doi = {10.1007/3-540-45784-4\_10},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/HalpernHR02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/HusonRKRDDFHLMSM01,
author = {Daniel H. Huson and
Knut Reinert and
Saul A. Kravitz and
Karin A. Remington and
Arthur L. Delcher and
Ian M. Dew and
Michael Flanigan and
Aaron L. Halpern and
Zhongwu Lai and
Clark M. Mobarry and
Granger G. Sutton and
Eugene W. Myers},
title = {Design of a compartmentalized shotgun assembler for the human genome},
booktitle = {Proceedings of the Ninth International Conference on Intelligent Systems
for Molecular Biology, July 21-25, 2001, Copenhagen, Denmark},
pages = {132--139},
year = {2001},
timestamp = {Mon, 12 Sep 2005 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/HusonRKRDDFHLMSM01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pvg/TurnerCEFHHKMRRSWYI01,
author = {Russell J. Turner and
Kabir Chaturvedi and
Nathan Edwards and
Daniel P. Fasulo and
Aaron L. Halpern and
Daniel H. Huson and
Oliver Kohlbacher and
Jason R. Miller and
Knut Reinert and
Karin A. Remington and
Russell Schwartz and
Brian Walenz and
Shibu Yooseph and
Sorin Istrail},
editor = {David E. Breen and
Alan Heirich and
Anton H. J. Koning},
title = {Visualization challenges for a new cyberpharmaceutical computing paradigm},
booktitle = {Proceedings of the {IEEE} 2001 Symposium on Parallel and Large-Data
Visualization and Graphics, {PVG} 2001, San Diego, California, USA,
October 22-23, 2001},
pages = {7--18},
publisher = {{IEEE}},
year = {2001},
url = {https://dl.acm.org/doi/10.5555/502125.502127},
doi = {10.5555/502125.502127},
timestamp = {Thu, 02 Jun 2022 12:38:21 +0200},
biburl = {https://dblp.org/rec/conf/pvg/TurnerCEFHHKMRRSWYI01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HusonRM01,
author = {Daniel H. Huson and
Knut Reinert and
Eugene W. Myers},
editor = {Thomas Lengauer},
title = {The greedy path-merging algorithm for sequence assembly},
booktitle = {Proceedings of the Fifth Annual International Conference on Computational
Biology, {RECOMB} 2001, Montr{\'{e}}al, Qu{\'{e}}bec, Canada,
April 22-25, 2001},
pages = {157--163},
publisher = {{ACM}},
year = {2001},
url = {https://doi.org/10.1145/369133.369190},
doi = {10.1145/369133.369190},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HusonRM01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/HusonHLMRS01,
author = {Daniel H. Huson and
Aaron L. Halpern and
Zhongwu Lai and
Eugene W. Myers and
Knut Reinert and
Granger G. Sutton},
editor = {Olivier Gascuel and
Bernard M. E. Moret},
title = {Comparing Assemblies Using Fragments and Mate-Pairs},
booktitle = {Algorithms in Bioinformatics, First International Workshop, {WABI}
2001, Aarhus, Denmark, August 28-31, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2149},
pages = {294--306},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44696-6\_23},
doi = {10.1007/3-540-44696-6\_23},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/HusonHLMRS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReinertSW00,
author = {Knut Reinert and
Jens Stoye and
Torsten Will},
title = {An iterative method for faster sum-of-pairs multiple sequence alignment},
journal = {Bioinform.},
volume = {16},
number = {9},
pages = {808--814},
year = {2000},
url = {https://doi.org/10.1093/bioinformatics/16.9.808},
doi = {10.1093/BIOINFORMATICS/16.9.808},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReinertSW00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/KececiogluLMMRV00,
author = {John D. Kececioglu and
Hans{-}Peter Lenhof and
Kurt Mehlhorn and
Petra Mutzel and
Knut Reinert and
Martin Vingron},
title = {A polyhedral approach to sequence alignment problems},
journal = {Discret. Appl. Math.},
volume = {104},
number = {1-3},
pages = {143--186},
year = {2000},
url = {https://doi.org/10.1016/S0166-218X(00)00194-3},
doi = {10.1016/S0166-218X(00)00194-3},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/KececiogluLMMRV00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/LermenR00,
author = {Martin Lermen and
Knut Reinert},
title = {The Practical Use of the A* Algorithm for Exact Multiple Sequence
Alignment},
journal = {J. Comput. Biol.},
volume = {7},
number = {5},
pages = {655--671},
year = {2000},
url = {https://doi.org/10.1089/106652701446134},
doi = {10.1089/106652701446134},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/LermenR00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/de/Reinert2004,
author = {Knut Reinert},
title = {A polyhedral approach to sequence alignment problems},
school = {Saarland University, Saarbr{\"{u}}cken, Germany},
year = {1999},
url = {http://scidok.sulb.uni-saarland.de/volltexte/2004/220/index.html},
urn = {urn:nbn:de:bsz:291-scidok-2202},
timestamp = {Sat, 17 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/de/Reinert2004.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LenhofMR99,
author = {Hans{-}Peter Lenhof and
Burkhard Morgenstern and
Knut Reinert},
title = {An exact solution for the segment-to-segment multiple sequence alignment
problem},
journal = {Bioinform.},
volume = {15},
number = {3},
pages = {203--210},
year = {1999},
url = {https://doi.org/10.1093/bioinformatics/15.3.203},
doi = {10.1093/BIOINFORMATICS/15.3.203},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LenhofMR99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/ReinertSW99,
author = {Knut Reinert and
Jens Stoye and
Torsten Will},
title = {Combining Divide-and-Conquer, the A\({}^{\mbox{*}}\)-Algorithm, and
Successive Realignment Approaches to Speed Multiple Sequence Alignment},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1999,
October 4-6, 1999, Hannover, Germany},
pages = {17--24},
year = {1999},
timestamp = {Fri, 02 Aug 2019 15:48:16 +0200},
biburl = {https://dblp.org/rec/conf/gcb/ReinertSW99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/LenhofRV98,
author = {Hans{-}Peter Lenhof and
Knut Reinert and
Martin Vingron},
title = {A Polyhedral Approach to {RNA} Sequence Structure Alignment},
journal = {J. Comput. Biol.},
volume = {5},
number = {3},
pages = {517--530},
year = {1998},
url = {https://doi.org/10.1089/cmb.1998.5.517},
doi = {10.1089/CMB.1998.5.517},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/LenhofRV98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/ReinertLM98,
author = {Knut Reinert and
Hans{-}Peter Lenhof and
Burkhard Morgenstern},
title = {An exact solution for the Segment-to-Segment multiple sequence alignment
problem},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1998,
University of Cologne, Germany, October 1998},
publisher = {Oxford University Press},
year = {1998},
timestamp = {Fri, 02 Aug 2019 15:48:14 +0200},
biburl = {https://dblp.org/rec/conf/gcb/ReinertLM98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/LenhofRV98,
author = {Hans{-}Peter Lenhof and
Knut Reinert and
Martin Vingron},
editor = {Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {A polyhedral approach to {RNA} sequence structure alignment},
booktitle = {Proceedings of the Second Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1998, New York, NY, USA,
March 22-25, 1998},
pages = {153--162},
publisher = {{ACM}},
year = {1998},
url = {https://doi.org/10.1145/279069.279109},
doi = {10.1145/279069.279109},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/LenhofRV98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ReinertLMMK97,
author = {Knut Reinert and
Hans{-}Peter Lenhof and
Petra Mutzel and
Kurt Mehlhorn and
John D. Kececioglu},
editor = {Michael S. Waterman},
title = {A branch-and-cut algorithm for multiple sequence alignment},
booktitle = {Proceedings of the First Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1997, Santa Fe, NM, USA,
January 20-23, 1997},
pages = {241--250},
publisher = {{ACM}},
year = {1997},
url = {https://doi.org/10.1145/267521.267845},
doi = {10.1145/267521.267845},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/ReinertLMMK97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/BradfordR96,
author = {Phillip G. Bradford and
Knut Reinert},
editor = {Friedhelm Meyer auf der Heide and
Burkhard Monien},
title = {Lower Bounds for Row Minima Searching (Extended Abstract)},
booktitle = {Automata, Languages and Programming, 23rd International Colloquium,
ICALP96, Paderborn, Germany, 8-12 July 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1099},
pages = {454--465},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/3-540-61440-0\_150},
doi = {10.1007/3-540-61440-0\_150},
timestamp = {Tue, 14 May 2019 10:00:44 +0200},
biburl = {https://dblp.org/rec/conf/icalp/BradfordR96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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