Constantin Bannert, Martin Vingron, Jens Stoye, Hannes Luz, Sebastian Böcker
These lecture notes are the result of a collaborative effort of many people. They result from a series of lectures given by Martin Vingron (MPI/FU Berlin) and Jens Stoye (Bielefeld University) and a...
On optimal comparability editing with applications to molecular diagnostics (2009)
Böcker, Sebastian, Briesemeister, Sebastian, Klau, Gunnar W
Abstract Background The C OMPARABILITY E DITING problem appears in the context of hierarchical disease classification based on noisy data. We are given a directed graph G representing hierarchical...
SIRIUS: decomposing isotope patterns for metabolite identification (2009)
Böcker, Sebastian, Letzel, Matthias C., Lipták, Zsuzsanna, Pervukhin, Anton
Motivation: High-resolution mass spectrometry (MS) is among the most widely used technologies in metabolomics. Metabolites participate in almost all cellular processes, but most metabolites still...
Timm, Wiebke, Scherbart, Alexandra, Böcker, Sebastian, Kohlbacher, Oliver, Nattkemper, Tim W
Abstract Background Mass spectrometry is a key technique in proteomics and can be used to analyze complex samples quickly. One key problem with the mass spectrometric analysis of peptides and...
THE MONEY CHANGING PROBLEM REVISITED: COMPUTING THE FROBENIUS NUMBER IN TIME O(k a1) (2008)
Abteilung Informationstechnik, Sebastian Böcker, Zsuzsanna Lipták, Impressum Herausgeber, Robert Giegerich, ...
Abstract. The Money Changing Problem is as follows: Let a1 < a2 < · · · < ak be fixed positive integers with gcd(a1,..., ak) = 1. Given some integer n, are there non-negative integers...
ABSTRACT Efficient Mass Decomposition (2008)
Sebastian Böcker, Zsuzsanna Lipták, Ag Genominformatik
We study the problem of decomposing a positive integer M over a (fixed and finite) weighted alphabet Σ: We want to find non-negative integers ci such that M = c1a1+...+ckak, where the ai are the...
Combinatorial Approaches for Mass Spectra Recalibration (2008)
Sebastian Böcker, Veli Mäkinen, Ag Genominformatik
Contact:
Computation of Median Gene Clusters (2008)
Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
Abstract. Whole genome comparison based on gene order has become a popular approach in comparative genomics. An important task in this field is the detection of gene clusters, i.e. sets of genes that...
Towards de novo identification of metabolites by analyzing tandem mass spectra (2008)
Böcker, Sebastian, Rasche, Florian
Mass spectrometry is among the most widely used technologies in proteomics and metabolomics. For metabolites, de novo interpretation of spectra is even more important than for protein data, because...
Combinatorial Approaches for Mass Spectra Recalibration (2008)
Böcker, Sebastian, Mäkinen, Veli
The authors were supported by “Deutsche Forschungsgemeinschaft” (BO 1910/1-1) within the Computer Science Action Program. Second author was also partially supported by the Academy of Finland.
DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem (2008)
Böcker, Sebastian, Lipták, Zsuzsanna, Martin, Marcel, Pervukhin, Anton, Sudek, Henner
Summary: We introduce Decomp, a tool that computes the sum formula of all molecules whose mass equals the input mass. This problem arises frequently in biochemistry and mass spectrometry (MS), when...
EPoS: a modular software framework for phylogenetic analysis (2008)
Griebel, Thasso, Brinkmeyer, Malte, Böcker, Sebastian
Summary: Estimating Phylogenies of Species (EPoS) is a modular software framework for phylogenetic analysis, visualization and data management. It provides a plugin-based system that integrates a...
and consensus tree methods (2007)
Simple but fundamental limitations on supertree
Algorithmic aspects of tree (2007)
Sebastian Böcker, Gk Strukturbildungsprozesse, Fsp Mathematisierung, David Bryant, ...
‡ Mike Steel thanks the New Zealand Marsden Fund (UOC-MIS-003) for supporting this research 1 2 BÖCKER, BRYANT, DRESS, STEEL Proposed running head: Tree amalgamation
SAMPI: Protein Identification with Mass Spectra Alignments (2007)
Kaltenbach, Hans-Michael, Wilke, Andreas, Böcker, Sebastian
Abstract Background Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its...
SAMPI: Protein Identification with Mass Spectra Alignments (2007)
Kaltenbach, Hans-Michael, Wilke, Andreas, Böcker, Sebastian
Abstract Background Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its...
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry (2007)
Motivation: Single Nucleotide Polymorphisms (SNPs) are believed to contribute strongly to the genetic variability in living beings, and SNP and mutation discovery are of great interest in today's...
Böcker, Sebastian, Letzel, Matthias C., Lipták, Zsuzsanna, Pervukhin, Anton
Metabolites, small molecules that are intermediates and products of the metabolism, participate in almost all cellular processes such as signal transduction and stress response. There exist several...
SOM-based Peptide Prototyping for Mass Spectrometry Peak Intensity Prediction (2007)
Scherbart, Alexandra, Timm, Wiebke, Böcker, Sebastian, Nattkemper, Tim W.
In todays bioinformatics, Mass spectrometry (MS) is the key technique for the identification of proteins. A prediction of spectrum peak intensities from pre computed molecular features would pave the...
Combinatorial Approaches for Mass Spectra Recalibration (2006)
Böcker, Sebastian, Mäkinen, Veli
Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger datasets, the automated recalibration of mass spectra becomes...
Statistics of cleavage fragments in random weighted strings (2005)
Kaltenbach, Hans-Michael, Sudek, Henner, Böcker, Sebastian, Rahmann, Sven
Peptide mass fingerprinting is an important technique that allows to identify a protein from its fragment masses obtained by mass spectrometry after enzymatic fragmentation: An experimental mass...
Zsuzsanna Lipták, Dr. Sebastian Böcker, Dr. Sebastian Böcker, Prof Dr, Jens Stoye, For Nando
This thesis treats two problem areas in bioinformatics which can both be beneficially formalized as string problems. The first (and larger) part deals with weighted string problems as they arise from...
Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS (2005)
Ehrich, Mathias, Böcker, Sebastian, Van Den Boom, Dirk
The completion of the Human Genome Project provides researchers with a reference sequence that covers about 99% of the gene-containing regions and is more than 99.9% accurate. Sequence drafts and...
High-Throughput MALDI-TOF Discovery of Genomic Sequence Polymorphisms (2004)
Stanssens, Patrick, Zabeau, Marc, Meersseman, Geert, Remes, Gwen, Gansemans, Yannick, Storm, Niels, ...
We describe a comparative sequencing strategy that is based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analyses of complete base-specific cleavage...
SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry (2003)
Motivation: Single Nucleotide Polymorphisms (SNPs) are believed to contribute strongly to the genetic variability in living beings, in particular their disease or drug side effect predispositions....
Algorithmic aspects of tree (2000)
Sebastian Böcker, Gk Strukturbildungsprozesse, Fsp Mathematisierung, David Bryant, ...
‡ Mike Steel thanks the New Zealand Marsden Fund (UOC-MIS-003) for supporting this research 1 2 BÖCKER, BRYANT, DRESS, STEEL Proposed running head: Tree amalgamation
Algorithmic Aspects of Tree Amalgamation (2000)
Sebastian Böcker, David Bryant, Mike A. Steel
this paper, we consider the question ofdetermining whether the collection of input trees uniquely determines a possible supertree. Webeg4 by introducing some terminologM We will view (leaf-labeled)...
Sebastian Böcker, Mike A. Steel
Abstract. A fundamental problem in many areas of classification, and particularly in biology, is the reconstruction of a leaf-labeled tree from just a subset of its induced subtrees. Without loss of...
Sebastian Böcker, Cc C Implies, Cc C C
. In this note, we want to introduce a concept that---as we shall see---exhibits an interesting relationship with hierarchies: We define a collection C ` P(X) of subsets of a set X to be a patchwork...
Sebastian Böcker, Mike A. Steel
. A fundamental problem in many areas of classification, and particularly in biology, is the reconstruction of a leaf-labeled tree from just a subset of its induced subtrees. Without loss of...
Von Wintzingerode, Friedrich, Böcker, Sebastian, Schlötelburg, Cord, Chiu, Norman H. L., Storm, Niels, Jurinke, Christian, ...
A rapid approach to the 16S rRNA gene (16S rDNA)-based bacterial identification has been developed that combines uracil-DNA-glycosylase (UDG)-mediated base-specific fragmentation of PCR products with...
High-Throughput MALDI-TOF Discovery of Genomic Sequence Polymorphisms
Stanssens, Patrick, Zabeau, Marc, Meersseman, Geert, Remes, Gwen, Gansemans, Yannick, Storm, Niels, ...
We describe a comparative sequencing strategy that is based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analyses of complete base-specific cleavage...
Novel Mass Spectrometry-Based Tool for Genotypic Identification of Mycobacteria
Lefmann, Michael, Honisch, Christiane, Böcker, Sebastian, Storm, Niels, Von Wintzingerode, Friedrich, Schlötelburg, Cord, ...
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR amplified and in vitro-transcribed 16S rRNA gene (rDNA) was used for...
Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS
Ehrich, Mathias, Böcker, Sebastian, Van Den Boom, Dirk
The completion of the Human Genome Project provides researchers with a reference sequence that covers about 99% of the gene-containing regions and is more than 99.9% accurate. Sequence drafts and...
Von Wintzingerode, Friedrich, Böcker, Sebastian, Schlötelburg, Cord, Chiu, Norman H. L., Storm, Niels, Jurinke, Christian, ...
A rapid approach to the 16S rRNA gene (16S rDNA)-based bacterial identification has been developed that combines uracil-DNA-glycosylase (UDG)-mediated base-specific fragmentation of PCR products with...
High-Throughput MALDI-TOF Discovery of Genomic Sequence Polymorphisms
Stanssens, Patrick, Zabeau, Marc, Meersseman, Geert, Remes, Gwen, Gansemans, Yannick, Storm, Niels, ...
We describe a comparative sequencing strategy that is based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analyses of complete base-specific cleavage...
Novel Mass Spectrometry-Based Tool for Genotypic Identification of Mycobacteria
Lefmann, Michael, Honisch, Christiane, Böcker, Sebastian, Storm, Niels, Von Wintzingerode, Friedrich, Schlötelburg, Cord, ...
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR amplified and in vitro-transcribed 16S rRNA gene (rDNA) was used for...
Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS
Ehrich, Mathias, Böcker, Sebastian, Van Den Boom, Dirk
The completion of the Human Genome Project provides researchers with a reference sequence that covers about 99% of the gene-containing regions and is more than 99.9% accurate. Sequence drafts and...
SIRIUS: decomposing isotope patterns for metabolite identification†
Böcker, Sebastian, Letzel, Matthias C., Lipták, Zsuzsanna, Pervukhin, Anton
Motivation: High-resolution mass spectrometry (MS) is among the most widely used technologies in metabolomics. Metabolites participate in almost all cellular processes, but most metabolites still...