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...
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...
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...
An overview of the wcd EST clustering tool (2008)
Hazelhurst, Scott, Hide, Winston, Lipták, Zsuzsanna, Nogueira, Ramon, Starfield, Richard
Summary: The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d...
Judith Zimmermann, Zsuzsanna Lipták, Scott Hazelhurst
We present a method for evaluating the suitability of different string dissimilarity measures and clustering algorithms for EST clustering, one of the main techniques used in transcriptome projects....
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...
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...
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...
Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl
We investigate a problem which arises in computational biology: Given a constant– size alphabet A with a weight function µ: A → N, find an efficient data structure and query algorithm solving...
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...
An overview of the wcd EST clustering tool
Hazelhurst, Scott, Hide, Winston, Lipták, Zsuzsanna, Nogueira, Ramon, Starfield, Richard
Summary: The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d...