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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, 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: 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, 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) - [j55]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): 19019-19048 (2023) - 2022
- [j54]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): 4100-4108 (2022) - [j53]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): 18 (2022) - [c30]Marius Knaust, Enrico Seiler, Knut Reinert, Thomas Steinke:
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, 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): 642-663 (2021) - [j51]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): 426-428 (2021) - [j50]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): 3934-3935 (2021) - [j49]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): 255-260 (2021) - [c29]Marie Hoffmann, Michael T. Monaghan, Knut Reinert:
PriSeT: efficient de novo primer discovery. BCB 2021: 2:1-2:12 - 2020
- [j48]Christopher Pockrandt, Mai Alzamel, Costas S. Iliopoulos, Knut Reinert:
GenMap: ultra-fast computation of genome mappability. Bioinform. 36(12): 3687-3692 (2020) - [j47]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): i12-i20 (2020) - [j46]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) - [i11]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 abs/2006.03104 (2020)
2010 – 2019
- 2018
- [j45]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): i766-i772 (2018) - [j44]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): 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, Knut Reinert:
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, Sandra Gesing, Knut Reinert, Oliver Kohlbacher:
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, Knut Reinert, Tandy J. Warnow:
Next Generation Sequencing (Dagstuhl Seminar 16351). Dagstuhl Reports 6(8): 91-130 (2016) - 2015
- [j41]Jialu Hu, Knut Reinert:
LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks. Bioinform. 31(3): 363-372 (2015) - [j40]Manuel Holtgrewe, Léon Kuchenbecker, Knut Reinert:
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, 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): 2963-2971 (2015) - [c26]Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau:
CIDANE: Comprehensive Isoform Discovery and Abundance Estimation. RECOMB 2015: 60-61 - 2014
- [j38]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): 540-548 (2014) - [j37]Hannes Hauswedell, Jochen Singer, Knut Reinert:
Lambda: the local aligner for massive biological data. Bioinform. 30(17): 349-355 (2014) - [j36]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): 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, Knut Reinert:
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, Knut Reinert, Stefan Canzar:
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, 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): 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, 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: 34 (2012) - [j27]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): 385-394 (2012) - [c23]Birte Kehr, Knut Reinert, Aaron E. Darling:
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, 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: 140 (2011) - [j25]Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert:
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, David Weese, Knut Reinert, Silke R. Sperling:
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, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner:
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, Hartmut Schlüter, Joachim Thiemann, Klaus Unger:
Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min. 2 (2009) - [j20]Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert:
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, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert:
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, David Weese, Tobias Rausch, Knut Reinert:
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, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert:
LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinform. 9 (2008) - [j15]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) - [j14]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): 685-704 (2008) - [c21]Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert:
Segment-based multiple sequence alignment. ECCB 2008: 187-192 - [c20]Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert, Martin Vingron:
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, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm:
TOPP - the OpenMS proteomics pipeline. Bioinform. 23(2): 191-197 (2007) - [j12]Markus Bauer, Gunnar W. Klau, Knut Reinert:
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinform. 8 (2007) - [j11]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): 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, Knut Reinert:
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, Peter Jungblut, Knut Reinert:
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, 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: 285 (2005) - [c15]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: 151-162 - [c14]Markus Bauer, Gunnar W. Klau, Knut Reinert:
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization. CompLife 2005: 217-228 - [c13]Markus Bauer, Gunnar W. Klau, Knut Reinert:
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, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert:
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, Eugene W. Myers:
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, Granger G. Sutton:
Comparing Assemblies Using Fragments and Mate-Pairs. WABI 2001: 294-306 - 2000
- [j5]Knut Reinert, Jens Stoye, Torsten Will:
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, Knut Reinert, Martin Vingron:
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, Martin Vingron:
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, Kurt Mehlhorn, John D. Kececioglu:
A branch-and-cut algorithm for multiple sequence alignment. RECOMB 1997: 241-250 - 1996
- [c1]