Knut Reinert - researchr alias

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2011

2010

MicroRazerS: rapid alignment of small RNA readsAnne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert, Silke R. Sperling. bioinformatics, 26(1):123-124, 2010. [doi]

Oops I Did it Again... Sustainability in Sequence Analysis via Software LibrariesKnut Reinert. ercim, 2010(82):13, 2010. [doi]

2009

Integer Linear Programming in Computational BiologyErnst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert. BIRTHDAY 2009: 199-218 [doi]

Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String DescriptorsRaphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner. algorithms, 2(2):692-709, 2009. [doi]

A consistency-based consensus algorithm for ::::de novo:::: and reference-guided sequence assembly of short readsTobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert. bioinformatics, 25(9):1118-1124, 2009. [doi]

Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experimentsOle Schulz-Trieglaff, Egidijus Machtejevas, Knut Reinert, Hartmut SchlÃ¼ter, Joachim Thiemann, Klaus Unger. biodatamining, 2, 2009. [doi]

2008

An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure AlignmentMarkus Bauer, Gunnar W. Klau, Knut Reinert. aor, 3(2), 2008. [doi]

SeqAn An efficient, generic C++ library for sequence analysisAndreas Döring, David Weese, Tobias Rausch, Knut Reinert. bmcbi, 9, 2008. [doi]

Robust consensus computationTobias Rausch, Anne-Katrin Emde, Knut Reinert. bmcbi, 9(S-10), 2008. [doi]

Segment-based multiple sequence alignmentTobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert. eccb 2008: 187-192 [doi]

LC-MSsim - a simulation software for liquid chromatography mass spectrometry dataOle Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert. bmcbi, 9, 2008. [doi]

Computational Quantification of Peptides from LC-MS DataOle Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Leinenbach, Andreas Hildebrandt, Christian G. Huber, Knut Reinert. jcb, 15(7):685-704, 2008. [doi]

Fast and Adaptive Variable Order Markov Chain ConstructionMarcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert, Martin Vingron. wabi 2008: 306-317 [doi]

OpenMS - An open-source software framework for mass spectrometryMarc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher. bmcbi, 9, 2008. [doi]

2007

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimizationMarkus Bauer, Gunnar W. Klau, Knut Reinert. bmcbi, 8, 2007. [doi]

Integer linear programming approaches for non-unique probe selectionGunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert. DAM, 155(6-7):840-856, 2007. [doi]

TOPP - the OpenMS proteomics pipelineOliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm. bioinformatics, 23(2):191-197, 2007. [doi]

A geometric approach for the alignment of liquid chromatography - mass spectrometry dataEva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian G. Huber, Knut Reinert. ismb 2007: 273-281 [doi]

A General Paradigm for Fast, Adaptive Clustering of Biological SequencesKnut Reinert, Markus Bauer, Andreas Döring, Gunnar W. Klau, Aaron L. Halpern. gcb 2007: 15-29

A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry DataOle Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Hildebrandt, Knut Reinert. recomb 2007: 473-487 [doi]

2006

A branch-and-cut algorithm for multiple sequence alignmentErnst Althaus, Alberto Caprara, Hans-Peter Lenhof, Knut Reinert. mp, 105(2-3):387-425, 2006. [doi]

Computational Proteomics, 20.-25. November 2005Christian G. Huber, Oliver Kohlbacher, Knut Reinert, editors, Volume 05471 of Dagstuhl Seminar Proceedings, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany, 2006.

High-Accuracy Peak Picking of Proteomics Data Using Wavelet TechniquesEva Lange, Clemens Gröpl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt. psb 2006: 243-254 [doi]

2005

Multiple Structural RNA Alignment with Lagrangian RelaxationMarkus Bauer, Gunnar W. Klau, Knut Reinert. wabi 2005: 303-314 [doi]

Fast and Accurate Structural RNA Alignment by Progressive Lagrangian OptimizationMarkus Bauer, Gunnar W. Klau, Knut Reinert. complife 2005: 217-228 [doi]

Evaluation of LC-MS data for the absolute quantitative analysis of marker proteinsNathanaël Delmotte, Bettina M. Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph L. Klein, Christian G. Huber. dagstuhl 2006: [doi]

Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics SamplesClemens Gröpl, Eva Lange, Knut Reinert, Oliver Kohlbacher, Marc Sturm, Christian G. Huber, Bettina M. Mayr, Christoph L. Klein. complife 2005: 151-162 [doi]

05471 Abstract Collection - Computational ProteomicsChristian G. Huber, Oliver Kohlbacher, Knut Reinert. dagstuhl 2006: [doi]

05471 Executive Summary - Computational ProteomicsChristian G. Huber, Oliver Kohlbacher, Knut Reinert. dagstuhl 2006: [doi]

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison processWitold E. Wolski, Maciej Lalowski, Peter Martus, Ralf Herwig, Patrick Giavalisco, Johan Gobom, Albert Sickmann, Hans Lehrach, Knut Reinert. bmcbi, 6:285, 2005. [doi]

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrantsWitold E. Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert. bmcbi, 6:203, 2005. [doi]

2004

Optimal robust non-unique probe selection using Integer Linear ProgrammingGunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert. ismb 2004: 186-193 [doi]

Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges)Oliver Kohlbacher, Knut Reinert. it, 46(1):31-38, 2004. [doi]

2002

Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatoricsErnst Althaus, Alberto Caprara, Hans-Peter Lenhof, Knut Reinert. eccb 2002: 4-16

Segment Match Refinement and ApplicationsAaron L. Halpern, Daniel H. Huson, Knut Reinert. wabi 2002: 126-139 [doi]

The greedy path-merging algorithm for contig scaffoldingDaniel H. Huson, Knut Reinert, Eugene W. Myers. JACM, 49(5):603-615, 2002. [doi]

2001

Comparing Assemblies Using Fragments and Mate-PairsDaniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton. wabi 2001: 294-306 [doi]

The greedy path-merging algorithm for sequence assemblyDaniel H. Huson, Knut Reinert, Eugene W. Myers. recomb 2001: 157-163 [doi]

Design of a compartmentalized shotgun assembler for the human genomeDaniel 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. ismb 2001: 132-139

Visualization challenges for a new cyberpharmaceutical computing paradigmRussell 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. pvg 2001: 7-18 [doi]

2000

A polyhedral approach to sequence alignment problemsJohn D. Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron. DAM, 104(1-3):143-186, 2000.

The Practical Use of the A* Algorithm for Exact Multiple Sequence AlignmentMartin Lermen, Knut Reinert. jcb, 7(5):655-671, 2000.

An iterative method for faster sum-of-pairs multiple sequence alignmentKnut Reinert, Jens Stoye, Torsten Will. bioinformatics, 16(9):808-814, 2000.

1999

An exact solution for the segment-to-segment multiple sequence alignment problemHans-Peter Lenhof, Burkhard Morgenstern, Knut Reinert. bioinformatics, 15(3):203-210, 1999.

Combining Divide-and-Conquer, the A:::*:::-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence AlignmentKnut Reinert, Jens Stoye, Torsten Will. gcb 1999: 17-24

1998

A Polyhedral Approach to RNA Sequence Structure AlignmentHans-Peter Lenhof, Knut Reinert, Martin Vingron. jcb, 5(3):517-530, 1998.

A polyhedral approach to RNA sequence structure alignmentHans-Peter Lenhof, Knut Reinert, Martin Vingron. recomb 1998: 153-162 [doi]

An exact solution for the Segment-to-Segment multiple sequence alignment problemKnut Reinert, Hans-Peter Lenhof, Burkhard Morgenstern. gcb 1998:

1997

A branch-and-cut algorithm for multiple sequence alignmentKnut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu. recomb 1997: 241-250 [doi]

1996

Lower Bounds for Row Minima Searching (Extended Abstract)Phillip G. Bradford, Knut Reinert. icalp 1996: 454-465