BMC Bioinformatics BioMed Central Poster presentation Robust consensus computation (2009)
Tobias Rausch, Anne-katrin Emde, Knut Reinert, Tobias Rausch
We used a read simulator and real data from the NCBI trace archive to evaluate our consensus tool. The main parameters of the read simulator are the source sequence length, the average read length,...
Schulz-Trieglaff, Ole, Machtejevas, Egidijus, Reinert, Knut, Schlüter, Hartmut, Thiemann, Joachim, Unger, Klaus
Abstract Background Quality assessment methods, that are common place in engineering and industrial production, are not widely spread in large-scale proteomics experiments. But modern technologies...
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors (2009)
Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, ...
This work presents a generalized approach for the fast structural alignment of thousands of macromolecular structures. The method uses string representations of a macromolecular structure and a hash...
Rausch, Tobias, Koren, Sergey, Denisov, Gennady, Weese, David, Emde, Anne-Katrin, Döring, Andreas, ...
Motivation: Novel high-throughput sequencing technologies pose new algorithmic challenges in handling massive amounts of short-read, high-coverage data. A robust and versatile consensus tool is of...
RazerS--fast read mapping with sensitivity control (2009)
Weese, David, Emde, Anne-Katrin, Rausch, Tobias, Döring, Andreas, Reinert, Knut
Second-generation sequencing technologies deliver DNA sequence data at unprecedented high throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly...
Apweiler, Rolf, Aslanidis, Charalampos, Deufel, Thomas, Gerstner, Andreas, Hansen, Jens, Hochstrasser, Dennis, ...
The field of clinical proteomics offers opportunities to identify new disease biomarkers in body fluids, cells and tissues. These biomarkers can be used in clinical applications for diagnosis,...
am Fachbereich Mathematik und Informatik (2008)
Sven Rahmann, Prof Dr, Martin Vingron, Prof Dr, Knut Reinert, ...
Tag der Promotion:
Robust consensus computation (2008)
Rausch, Tobias, Emde, Anne-Katrin, Reinert, Knut
No abstract available.
LC-MSsim – a simulation software for liquid chromatography mass spectrometry data (2008)
Schulz-Trieglaff, Ole, Pfeifer, Nico, Gröpl, Clemens, Kohlbacher, Oliver, Reinert, Knut
Abstract Background Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an...
Vol. 23 ISMB/ECCB 2007, pages i273–i281 BIOINFORMATICS doi:10.1093/bioinformatics/btm209 (2008)
Eva Lange, Clemens Gröpl, Ole Schulz-trieglaff, Andreas Leinenbach, Christian Huber, Knut Reinert
A geometric approach for the alignment of liquid chromatography—mass spectrometry data
Eva Lange, Clemens Gropl, Knut Reinert, Oliver Kohlbacher
Analysis of mass spectrometry data using subspectra and wavelets Spectra resulting from Surface-Enhanced Laser Desorption/Ionisation (SELDI) mass spectrometry measurements are constructed by...
doi:10.1093/bioinformatics/btl299 (2008)
Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-trieglaff, ...
Vol. 23 ECCB 2006, pages e191–e197
Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins (2008)
Nathanaël Delmotte, Bettina Mayr, Andreas Leinenbach, Knut Reinert, Christoph Klein, Christian Huber, ...
Abstract. The potential of mass spectrometric peptide identification in complex mixtures by means of peptide mass fingerprinting (PMF) and peptide fragment fingerprinting (PFF) was evaluated and...
A Branch-and-Cut Algorithm for Multiple Sequence Alignment (2008)
Ernst Althaus, Alberto Caprara, Hans-peter Lenhof, Knut Reinert
Abstract. We consider a branch-and-cut approach for solving the multiple sequence alignment problem, which is a central problem in computational biology. We propose a general model for this problem...
OpenMS- A Software Platform for Shotgun Proteomics (2008)
Marc Sturm, Eva Lange, Clemens Gröpl, Ole Schulz-trieglaff, Nico Pfeifer, Oliver Kohlbacher, ...
Over the last few years numerous experimental techniques for the differential analysis of proteome expression levels have been developed and HPLC-MS has become one of the standard techniques in...
OpenMS – An open-source software framework for mass spectrometry (2008)
Sturm, Marc, Bertsch, Andreas, Gröpl, Clemens, Hildebrandt, Andreas, Hussong, Rene, Lange, Eva, ...
Abstract Background Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass...
SeqAn An efficient, generic C++ library for sequence analysis (2008)
Döring, Andreas, Weese, David, Rausch, Tobias, Reinert, Knut
Abstract Background The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome 1 would not have been possible...
Segment-based multiple sequence alignment (2008)
Rausch, Tobias, Emde, Anne-Katrin, Weese, David, Döring, Andreas, Notredame, Cedric, Reinert, Knut
Motivation: Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools,...
Fast and adaptive variable order Markov chain construction (2008)
Schulz, Marcel H., Weese, David, Rausch, Tobias, Döring, Andreas, Reinert, Knut, Vingron, Martin
Variable order Markov chains (VOMCs) are a flexible class of models that extend the well-known Markov chains. They have been applied to a variety of problems in computational biology, e.g. protein...
08101 Abstracts Collection -- Computational Proteomics (2008)
Reinert, Knut, Huber, Christian, Marcus, Kathrin, Linial, Michal, Kohlbacher, Oliver
The second Dagstuhl Seminar on emph{Computational Proteomics} took place from March 3rd to 7th, 2008 in Schloss Dagstuhl--Leibniz Center for Informatics. This highly international meeting brought...
An Exact Solution for the Segment-to-Segment Multiple Sequence Alignment Problem (2007)
Hans-peter Lenhof, Burkhard Morgenstern, Knut Reinert
In molecular biology sequence alignment is a crucial tool in studying structure and function of molecules as well as evolution of species. In the segment-to-segment variation of the multiple...
Lower Bounds for Row Minima Searching (Extended Abstract) (2007)
P.G. Bradford, Phillip G. Bradford, Knut Reinert
) Phillip G. Bradford and Knut Reinert Max-Planck-Institut fur Informatik, Im Stadtwald, D-66123 Saarbrucken, Germany. f bradford, kreinert g@mpi-sb.mpg.de Abstract. This paper shows that finding the...
Bauer, Markus, Klau, Gunnar W, Reinert, Knut
Abstract Background The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however,...
TOPP--the OpenMS proteomics pipeline (2007)
Kohlbacher, Oliver, Reinert, Knut, Gröpl, Clemens, Lange, Eva, Pfeifer, Nico, Schulz-Trieglaff, Ole, ...
Motivation: Experimental techniques in proteomics have seen rapid development over the last few years. Volume and complexity of the data have both been growing at a similar rate. Accordingly, data...
Integer linear programming approaches for non-unique probe selection. (2007)
Klau, Gunnar W., Rahmann, Sven, Schliep, Alexander, Vingron, Martin, Reinert, Knut
In addition to their prevalent use for analyzing gene expression, DNA microarrays are an efficient tool for biological, medical, and industrial applications because of their ability to assess the...
Markus Bauer, Gunnar W. Klau, Knut Reinert, Markus Bauer, Gunnar W. Klau, Knut Reinert
Background: The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at...
Markus Bauer, Gunnar W Klau, Knut Reinert, Open Access
© 2007 Bauer et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Analytical model of peptide mass cluster centres with applications (2006)
Wolski, Witold E, Farrow, Malcolm, Emde, Anne-Katrin, Lehrach, Hans, Lalowski, Maciej, Reinert, Knut
Abstract Background The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to...
Analytical model of peptide mass cluster centres with applications (2006)
Wolski, Witold E., Farrow, Malcolm, Emde, Anne-Katrin, Lehrach, Hans, Lalowski, Maciej, Reinert, Knut
Background The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate...
High accuracy peak-picking of proteomics data using wavelet techniques (2006)
Eva Lange, Clemens Gropl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebr, Eva Lange, ...
A new peak picking algorithm for the analysis of mass spectrometric (MS) data is presented. It is independent of the underlying machine or ionization method, and is able to resolve highly convoluted...
05471 Executive Summary -- Computational Proteomics (2006)
Huber, Christian G., Kohlbacher, Oliver, Reinert, Knut
The Dagstuhl Seminar on Computational Proteomics brought together researchers from computer science and from proteomics to discuss the state of the art and future developments at the interface...
Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins (2006)
Delmotte, Nathanaël, Mayr, Bettina, Leinenbach, Andreas, Reinert, Knut, Kohlbacher, Oliver, Klein, Christoph, ...
The serum complexity makes the absolute quantitative analysis of medium to low-abundant proteins very challenging. Tens of thousands proteins are present in human serum and dispersed over an...
05471 Abstract Collection -- Computational Proteomics (2006)
Huber, Christian G., Kohlbacher, Oliver, Reinert, Knut
From 20.11.05 to 25.11.05, the Dagstuhl Seminar 05471 ``Computational Proteomics'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several...
OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics (2006)
Reinert, Knut, Kohlbacher, Oliver, Gröpl, Clemens, Lange, Eva, Schulz-Trieglaff, Ole, Sturm, Marc, ...
In the talk we describe the freely available software library OpenMS which is currently under development at the Freie Universität Berlin and the Eberhardt-Karls Universität...
Wolski, Witold E, Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, ...
Abstract Background: Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides,...
Wolski, Witold E, Lalowski, Maciej, Jungblut, Peter, Reinert, Knut
Abstract Background Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally...
Wolski, Witold E., Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, ...
Background: Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is...
Optimal robust non-unique probe selection using Integer Linear Programming (2004)
Klau,Gunnar W., Rahmann,Sven, Schliep,Alexander, Vingron,Martin, Reinert,Knut
Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the...
A polyhedral approach to sequence alignment problems (2004)
We study two problems in sequence alignment both from a theoretical and a practical point of view. For the first time in sequence alignment, we use tools from combinatorial optimization to develop...
Leverandørvalg ved offentlige anskaffelser (2004)
Målet med denne fremstillingen er å drøfte hvordan regelverket om offentlige anskaffelser, påvirker oppdragsgivers valg av leverandør. Spesielt de begrensningene som regelverket legger på...
Optimal robust non-unique probe selection using Integer Linear Programming (2004)
Klau, Gunnar W., Rahmann, Sven, Schliep, Alexander, Vingron, Martin, Reinert, Knut
Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the...
Whole-genome shotgun assembly and comparison of human genome assemblies. (2004)
Istrail, Sorin, Sutton, Granger G., Florea, Liliana, Halpern, Aaron L., Mobarry, Clark M., Lippert, Ross, ...
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in...
using Integer Linear Programming (2004)
Gunnar W. Klau, Sven Rahmann, Er Schliep, Martin Vingron, Knut Reinert
Vol. 20 Suppl. 1 2004, pages i186–i193
Optimal Robust Non-Unique Probe Selection Using Integer Linear Programming (2004)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Er Schliep B, Martin Vingron, Knut Reinert
Motivation Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical, and industrial applications due to their ability to assess the...
Mass Spectrometry is the tool of choice for Proteomics, with applications to peptide sequencing, protein structure prediction, protein-protein interactions, and many others. Continued improvements in...
Mass Spectrometry is the tool of choice for Proteomics, with applications to peptide sequencing, protein structure prediction, protein-protein interactions, and many others. Continued improvements in...
Optimal robust non-unique probe selection using Integer Linear Programming (2004)
Klau, Gunnar W., Rahmann, Sven, Schliep, Alexander, Vingron, Martin, Reinert, Knut
Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the...
Althaus,Ernst, Caprara,Alberto, Lenhof,Hans-Peter, Reinert,Knut
Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In...
Althaus, Ernst, Caprara, Alberto, Lenhof, Hans-Peter, Reinert, Knut, Lengauer, Thomas
Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In...
Althaus, Ernst, Caprara, Alberto, Lenhof, Hans-Peter, Reinert, Knut
Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In...
Comparing Assemblies Using Fragments and Mate Pairs (2001)
Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton
Abstract. Using current technology, large consecutive stretches of DNA (such as whole chromosomes) are usually assembled from short fragments obtained by shotgun sequencing, or from fragments and...
The greedy path-merging algorithm for sequence assembly (2001)
Daniel H. Huson, Knut Reinert, Eugene W. Myers
Two different approaches to determining the human genome are currently being pursued: one is the “clone-by-clone ” approach, employed by the publicly-funded Human Genome Project, and the other is...
Comparing Assemblies Using Fragments and Mate Pairs (2001)
Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, G. Sutton
Abstract. Using current technology, large consecutive stretches of DNA (such as whole chromosomes) are usually assembled from short fragments obtained by shotgun sequencing, or from fragments and...
Design of a compartmentalized shotgun assembler for the human genome (2001)
Huson, Daniel H., Reinert, Knut, Kravitz, Saul A., Remington, Karin A., Delcher, Art L., Dew, Ian M., ...
Two different strategies for determining the human genome are currently being pursued: one is the “clone-by-clone” approach, employed by the publicly funded project, and the other is the “whole...
A polyhedral approach to sequence alignment problems (2000)
Kececioglu, John, Lenhof, Hans-Peter, Mehlhorn, Kurt, Mutzel, Petra, Reinert, Knut, Vingron, Martin
An iterative method for faster sum-of-pairs multiple sequence alignment (2000)
Reinert, Knut, Stoye, Jens, Will, Torsten
Motivation: Multiple sequence alignment is an important tool in computational biology. In order to solve the task of computing multiple alignments in affordable time, the most commonly used multiple...
A polyhedral approach to sequence alignment problems (1999)
We study two problems in sequence alignment both from a theoretical and a practical point of view. For the first time in sequence alignment, we use tools from combinatorial optimization to develop...
A polyhedral approach to sequence alignment problems / (1999)
Saarbrücken, University, Diss., 1999.
Dekan der technischen Fakultät: (1999)
We study two problems in sequence alignment both from a theoretical and a practical point of view. For the first time in sequence alignment, we use tools from combinatorial optimization to develop...
A Polyhedral Approach to RNA Sequence Structure Alignment (1998)
Hans-peter Lenhof, Knut Reinert, Martin Vingron
Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It generally is a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to...
A Polyhedral Approach to Sequence Alignment Problems (1998)
John D. Kececioglu, Hans-peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron
We study two new problems in sequence alignment both from a practical and a theoretical view, using tools from combinatorial optimization to develop branchand -cut algorithms. The Generalized Maximum...
The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment (1997)
Multiple alignment is an important problem in computational biology. It is well known that it can be solved exactly by a dynamic programming algorithm which in turn can be interpreted as a shortest...
A Branch-And-Cut algorithm for multiple sequence alignment (1997)
Reinert, Knut, Lenhof, Hans-Peter, Mehlhorn, Kurt, Mutzel, Petra, Kececioglu, John
The Sequence of the Human Genome (1304)
T He, H Uman, G Enome, J. Craig Venter, Mark D. Adams, Eugene W. Myers, ...
Whole-genome shotgun assembly and comparison of human genome assemblies
Istrail, Sorin, Sutton, Granger G., Florea, Liliana, Halpern, Aaron L., Mobarry, Clark M., Lippert, Ross, ...
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in...
Wolski, Witold E, Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, ...
Analytical model of peptide mass cluster centres with applications
Wolski, Witold E, Farrow, Malcolm, Emde, Anne-Katrin, Lehrach, Hans, Lalowski, Maciej, Reinert, Knut
Whole-genome shotgun assembly and comparison of human genome assemblies
Istrail, Sorin, Sutton, Granger G., Florea, Liliana, Halpern, Aaron L., Mobarry, Clark M., Lippert, Ross, ...
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in...
Wolski, Witold E, Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, ...
Analytical model of peptide mass cluster centres with applications
Wolski, Witold E, Farrow, Malcolm, Emde, Anne-Katrin, Lehrach, Hans, Lalowski, Maciej, Reinert, Knut
SeqAn An efficient, generic C++ library for sequence analysis
Döring, Andreas, Weese, David, Rausch, Tobias, Reinert, Knut
OpenMS – An open-source software framework for mass spectrometry
Sturm, Marc, Bertsch, Andreas, Gröpl, Clemens, Hildebrandt, Andreas, Hussong, Rene, Lange, Eva, ...