ALIGNMENT OF MINISATELLITE MAPS: A MINIMUM SPANNING TREE BASED APPROACH (2009)
Mohamed I. Abouelhoda, Robert Giegerich
In addition to the well-known edit operations, the alignment of minisatellite maps includes duplication events. We model these duplications using a special kind of spanning trees and deduce an...
the Identification of Conserved (2009)
Jomuna Veronica Choudhuri, M. Sc. Jomuna, Veronica Choudhuri, Ag Praktische Informatik, ...
I would like to express my gratitude to my two supervisors, Prof. Dr. Robert Giegerich and Dr. Thomas Schmitt-John, for their careful guidance in these years, for their keen sense of timing and,...
Abteilung Informationstechnik, Jomuna V. Choudhuri, Chris Schleiermacher, Impressum Herausgeber, Robert Giegerich, ...
GenAlyzer:
mkESA: enhanced suffix array construction tool (2009)
Homann, Robert, Fleer, David, Giegerich, Robert, Rehmsmeier, Marc
Summary: We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly...
Wolfgang Gerlach, Robert Giegerich, Martin Bishop
Motivation: RNA secondary structure analysis often requires searching for potential helices in large sequence data. Results: We present a utility program GUUGle that efficiently locates potential...
Xenopus Laevis, Alexander Sczyrba, Ag Praktische Informatik, ...
am 30.03.2007 verteidigt und genehmigt.
DISTANCE EDUCATION THROUGH THE INTERNET: THE GNA-VSNS BIOCOMPUTING COURSE (2008)
Francisco M. De, La Vega, Robert Giegerich, Georg Fuellen A
A prototype course on biocomputing was delivered via international computer networks in early summer 1995. The course lasted 11 weeks, and was o ered free of charge. It was organized by the...
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI (2008)
Lamprecht, Anna-Lena, Margaria, Tiziana, Steffen, Bernhard, Sczyrba, Alexander, Hartmeier, Sven, Giegerich, Robert
Abstract Background PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using...
Janina Reeder, Jens Reeder, Robert Giegerich
Motivation and Results: Motivated by the recent rise of interest in small regulatory RNAs, we present Locomotif—a new approach for locating RNA motifs that goes beyond the previous ones in three...
Peter Steffen, Björn Voß, Marc Rehmsmeier, Jens Reeder, Robert Giegerich
Summary: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape...
BIOINFORMATICS ORIGINAL PAPER Structural bioinformatics (2008)
doi:10.1093/bioinformatics/bti577
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...
Suffix Tree Construction and Storage with Limited Main Memory (2008)
Abteilung Informationstechnik, Klaus-bernd Schürmann, Jens Stoye, Impressum Herausgeber, Robert Giegerich, ...
Abstract. Suffix trees have been established as one of the most versatile index structures for unstructured string data like genomic sequences and other strings. In this work, our goal is the...
Towards a Discipline of Dynamic Programming (2008)
Robert Giegerich, Carsten Meyer, Peter Steffen
Abstract. Dynamic programming is a classic programming technique, applicable in a wide variety of domains, like stochastic systems analysis, operations research, combinatorics of discrete structures,...
Algebraic Dynamic Programming Algebraic Dynamic Programming (2008)
Robert Giegerich, Robert Giegerich, Carsten Meyer
Abstract. Dynamic programming is a classic programming technique, applicable in a wide variety of domains, like stochastic systems analysis, operations research, combinatorics of discrete structures,...
Analyzing Ambiguity of Context-Free Grammars (2008)
Claus Brabr, Robert Giegerich, Anders Møller
Abstract. It has been known since 1962 that the ambiguity problem for context-free grammars is undecidable. Ambiguity in context-free grammars is a recurring problem in language design and parser...
Challenges in the Compilation of a Domain Specific Language for Dynamic Programming ABSTRACT (2008)
Many combinatorial optimization problems in biosequence analysis are solved via dynamic programming. To increase programming productivity and program reliability, a domain specific language embedded...
2-Stage Fault Tolerant Interval Group Testing (2008)
Abteilung Informationstechnik, Ferdinando Cicalese, José Augusto, Amgarten Quitzau, Impressum Herausgeber, ...
Abstract. We study the following fault tolerant variant of the interval group testing model: Given three positive integers n, p,e, determine the minimum number of questions needed to identify a...
Anna-lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Er Sczyrba, Robert Giegerich
on the development of new technologies in proteomics, glycoanalysis, proteinbiochips, biostatistics and bioinformatics in terms of Life-Science (see the Website at www.zap-do.de). PCR primer design...
Efficient computation of absent words in genomic sequences (2008)
Herold, Julia, Kurtz, Stefan, Giegerich, Robert
Abstract Background Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so...
Shape based indexing for faster search of RNA family databases (2008)
Janssen, Stefan, Reeder, Jens, Giegerich, Robert
Abstract Background Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally annotated...
The BREW workshop series: a stimulating experience in PhD education (2008)
Giegerich, Robert, Brazma, Alvis, Ukkonen, Esko, Vingron, Martin
Over recent years, five European PhD programmes have organized a series of ‘Bioinformatics Research and Education Workshops’. These workshops address the needs of first-year PhD students and have...
KnotInFrame: prediction of -1 ribosomal frameshift events (2008)
Theis, Corinna, Reeder, Jens, Giegerich, Robert
Programmed −1 ribosomal frameshift (−1 PRF) allows for alternative reading frames within one mRNA. First found in several viruses, it is now believed to exist in all kingdoms of life. Strong...
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI (2008)
Bmc Bioinformatics, Anna-lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Er Sczyrba, Sven Hartmeier, ...
This article is available from:
Distance Education Through The Internet: The Gna-Vsns Biocomputing Course (2007)
Francisco M. De, Robert Giegerich, Georg Fuellen
This paper describes the aims and organization of the course, and gives a preliminary account of this novel experience in distance education. 1 Introduction
Semantic Matching for Left-Linear Convergent Rewrite Systems (2007)
Bernd Butow, Robert Giegerich, Enno Ohlebusch, Stephan Thesing
In this paper, a calculus for solving the semantic matching problem w.r.t. left-linear or variable-preserving convergent term rewriting systems is presented. Narrowing calculi usually use advanced...
Pairwise Sequence Alignment (2007)
Robert Giegerich, David Wheeler
alphabets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 11.5 Some examples of taking subsequences . . . . . . . . . . . . . . . . . . . . . . 17 11.6 Some simple properties of...
Pairwise Sequence Alignment (2007)
Robert Giegerich, David Wheeler
alphabets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 6.5 Some examples of taking subsequences . . . . . . . . . . . . . . . . . . . . . . 17 6.6 Some simple properties of...
Walter Gr Uner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, ...
c;d, and Peter Schuster a;c;d; a
Abteilung Informationstechnik, Impressum Herausgeber, Robert Giegerich, Alois Knoll, Helge Ritter, ...
Universit at Bielefeld, Technische Fakult at, AG Technische Informatik,
Standard Models of Fuzzy Quantification (2007)
Abteilung Informationstechnik, Impressum Herausgeber, Robert Giegerich, Alois Knoll, Helge Ritter, ...
Contents 1 The axiomatics of fuzzy quantification 3 2 The class of MB-DFSes 19 3 The class of Fξ-DFSes 27
Abteilung Informationstechnik, Impressum Herausgeber, Robert Giegerich, Alois Knoll, Helge Ritter, ...
Anschrift:
An Axiomatic Theory of Fuzzy Quantifiers in Natural Languages (2007)
Abteilung Informationstechnik, Impressum Herausgeber, Robert Giegerich, Alois Knoll, Peter Ladkin, ...
Abstract Many applications e.g. in approximate reasoning, data summarisation, information retrieval etc. can profit from the use of fuzzy quantifiers like “almost all ” or “many”, which...
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows (2007)
Reeder, Jens, Steffen, Peter, Giegerich, Robert
RNA pseudoknots are an important structural feature of RNAs, but often neglected in computer predictions for reasons of efficiency. Here, we present the pknotsRG Web Server for single sequence RNA...
Surprises in approximating Levenshtein distances (2006)
Baake, Michael, Grimm, Uwe, Giegerich, Robert
The Levenshtein distance is an important tool for the comparison of symbolic sequences, with many appearances in genome research, linguistics and other areas. For efficient applications, an...
XML schemas for common bioinformatic data types and their application in workflow systems (2006)
Seibel, Philipp N, Krüger, Jan, Hartmeier, Sven, Schwarzer, Knut, Löwenthal, Kai, Mersch, Henning, ...
Abstract Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create...
Fast index based algorithms and software for matching position specific scoring matrices (2006)
Beckstette, Michael, Homann, Robert, Giegerich, Robert, Kurtz, Stefan
Abstract Background In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching...
Correction: versatile and declarative dynamic programming using pair algebras (2006)
Steffen, Peter, Giegerich, Robert
No abstract available.
Complete probabilistic analysis of RNA shapes (2006)
Voß, Björn, Giegerich, Robert, Rehmsmeier, Marc
Abstract Background Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve...
Surprises in approximating Levenshtein distances (2006)
Baake, Michael, Grimm, Uwe, Giegerich, Robert
The Levenshtein distance is an important tool for the comparison of symbolic sequences, with many appearances in genome research, linguistics and other areas. For efficient applications, an...
On Common Intervals with Errors (2006)
Abteilung Informationstechnik, Cedric Chauve, Yoan Diekmann, Steffen Heber, Julia Mixtacki, ...
The information that groups of genes co-occur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene...
Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz, Biomed Central, Robert Giegerich, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
On Common Intervals with Errors (2006)
Abteilung Informationstechnik, Cedric Chauve, Yoan Diekmann, Steffen Heber, Julia Mixtacki, ...
The information that groups of genes co-occur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene...
Table design in dynamic programming (2006)
Peter Steffen, Robert Giegerich
Dynamic Programming solves combinatorial optimization problems by recursive decomposition and tabulation of intermediate results. The first step in the design of a dynamic programming algorithm is to...
Gerlach, Wolfgang, Giegerich, Robert
Motivation: RNA secondary structure analysis often requires searching for potential helices in large sequence data. Results: We present a utility program GUUGle that efficiently locates potential...
Pair Algebras, Peter Steffen, Robert Giegerich, Steffen P, Giegerich R Versatile
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis (2005)
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H, Giegerich, Robert, Altmann, Curtis R
Abstract Background Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts...
Versatile and declarative dynamic programming using pair algebras (2005)
Steffen, Peter, Giegerich, Robert
Abstract Background Dynamic programming is a widely used programming technique in bioinformatics. In sharp contrast to the simplicity of textbook examples, implementing a dynamic programming...
Effective ambiguity checking in biosequence analysis (2005)
Reeder, Janina, Steffen, Peter, Giegerich, Robert
Abstract Background Ambiguity is a problem in biosequence analysis that arises in various analysis tasks solved via dynamic programming, and in particular, in the modeling of families of RNA...
Theoretical Bioinformatics Group (2005)
Abteilung Theoretische Informatik, Leiter Prof, Dr. Uwe Schöning, Amtierender Dekan, Prof Dr, H. Partsch, ...
vorgelegt von
Counting Suffix Arrays and Strings (2005)
Abteilung Informationstechnik, Klaus-bernd Schürmann, Jens Stoye, Impressum Herausgeber, Robert Giegerich, ...
Suffix arrays are used in various application and research areas like data compression or computational biology. In this work, our goal is to characterize the combinatorial properties of suffix...
Peter F. Stadler, Mario Mörl Leipzig, Robert Giegerich Bielefeld, Prof Dr, Peter F. Stadler, Prof Dr, ...
This workshop will bring together the RNA Research Community from Germany and neighboring countries. It strives to provide a program that emphasizes the common interests of experimentalists and...
Peter Steffen, Robert Giegerich
Background: Dynamic programming is a widely used programming technique in bioinformatics. In sharp contrast to the simplicity of textbook examples, implementing a dynamic programming algorithm for a...
Wolfgang Gerlach, Robert Giegerich
Motivation: RNA secondary structure analysis often requires searching for potential helices in large sequence data. Results: We present a utility program GUUGle that efficiently locates potential...
Reeder, Jens, Giegerich, Robert
Motivation: The well-known Sankoff algorithm for simultaneous RNA sequence alignment and folding is currently considered an ideal, but computationally over-expensive method. Available tools implement...
Reeder, Jens, Giegerich, Robert
Motivation: The well-known Sankoff algorithm for simultaneous RNA sequence alignment and folding is currently considered an ideal, but computationally over-expensive method. Available tools implement...
RNAshapes: an integrated RNA analysis package based on abstract shapes (2005)
Steffen, Peter, Voß, Björn, Rehmsmeier, Marc, Reeder, Jens, Giegerich, Robert
Summary: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape...
A comprehensive comparison of comparative RNA structure prediction approaches (2004)
Gardner, Paul P, Giegerich, Robert
Abstract Background An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent...
Reeder, Jens, Giegerich, Robert
Abstract Background The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include arbitrary...
Genlight: Interactive high-throughput sequence analysis and comparative genomics (2004)
Beckstette, Michael, Mailänder, Jens T., Marhöfer, Richard J., Sczyrba, Alexander, Ohlebusch, Enno, Giegerich, Robert, ...
With rising numbers of fully sequenced genomes the importance of comparative genomics is constantly increasing. Although several software systems for genome comparison analyses do exist, their...
Robert Giegerich, Björn Voß, Marc Rehmsmeier
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of...
Abteilung Informationstechnik, Ferdinando Cicalese, Peter Damaschke, Ugo Vaccaro, Impressum Herausgeber, ...
We consider the following constrained version of the classical Group Testing Problem: Given a finite set of items identified with the set of natural numbers 2, . . . , n} and an unknown distinguished...
Bmc Bioinformatics, Paul P Gardner, Robert Giegerich, Biomed Central
A comprehensive comparison of comparative RNA structure
BMC Bioinformatics BioMed Central (2004)
Research article Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
A discipline of dynamic programming over sequence data (2004)
Robert Giegerich, Carsten Meyer, Peter Steffen
Abstract. Dynamic programming is a classical programming technique, applicable in a wide variety of domains such as stochastic systems analysis, operations research, combinatorics of discrete...
Research article Effective ambiguity checking in biosequence analysis (2004)
Bmc Bioinformatics, Janina Reeder, Peter Steffen, Robert Giegerich, Biomed Central, Robert Giegerich
© 2005 Reeder et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Fast and effective prediction of microRNA/target duplexes (2004)
REHMSMEIER, MARC, STEFFEN, PETER, HÖCHSMANN, MATTHIAS, GIEGERICH, ROBERT
MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a...
Evaluating the predictability of conformational switching in RNA (2004)
Voss, Björn, Meyer, Carsten, Giegerich, Robert
Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural...
Evaluating the predictability of conformational switching in RNA (2004)
Vofl, Björn, Meyer, Carsten, Giegerich, Robert
Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural...
GenAlyzer: interactive visualization of sequence similarities between entire genomes (2004)
Choudhuri, Jomuna V., Schleiermacher, Chris, Kurtz, Stefan, Giegerich, Robert
Summary: GenAlyzer is a software tool designed for the interactive visualization of sequence matches between DNA or Protein sequences. It provides visualizations on different levels of granularity,...
Giegerich, Robert, Voß, Björn, Rehmsmeier, Marc
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of...
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, Giegerich, Robert
e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable...
GenAlyzer: interactive visualization of sequence similarities between entire genomes (2004)
Choudhuri, Jomuna V., Schleiermacher, Chris, Kurtz, Stefan, Giegerich, Robert
Summary: Genalyzer is a software tool designed for the interactive visualization of sequence matches between DNA or protein sequences. It provides visualizations on different levels of granularity,...
Evaluating the predictability of conformational switching in RNA (2004)
Vofl, Björn, Meyer, Carsten, Giegerich, Robert
Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural...
GenAlyzer: interactive visualization of sequence similarities between entire genomes (2004)
Choudhuri, Jomuna V., Schleiermacher, Chris, Kurtz, Stefan, Giegerich, Robert
Summary: GenAlyzer is a software tool designed for the interactive visualization of sequence matches between DNA or Protein sequences. It provides visualizations on different levels of granularity,...
The Rise of Bioinformatics (2003)
Paul A. David, Lynda Ellis, Blanche Feck, E. Olusegun George, Robert Giegerich
discipline
DOI: 10.1093/nar/gkg576 RNA-related tools on the Bielefeld (2003)
Bioinformatics Server, Er Sczyrba, Jan Krüger, Henning Mersch, Stefan Kurtz, Robert Giegerich
We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison...
On the Similarity of Sets of Permutations and its Applications to Genome Comparison (2003)
Abteilung Informationstechnik, Impressum Herausgeber, Robert Giegerich, Ralf Hofestädt, Peter Ladkin, Helge Ritter, ...
The comparison of genomes with the same gene content relies on our ability to compare permutations, either by measuring how much they di#er, or by measuring how much they are alike. With the notable...
Local similarity in RNA secondary structures (2003)
Matthias Höchsmann, Thomas Töller, Robert Giegerich, Stefan Kurtz
Abstract. We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et....
RNA-related tools on the Bielefeld Bioinformatics Server (2003)
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, Giegerich, Robert
We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison...
GenDB--an open source genome annotation system for prokaryote genomes (2003)
Meyer, Folker, Goesmann, Alexander, McHardy, Alice C., Bartels, Daniela, Bekel, Thomas, Clausen, Jörn, ...
The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To...
Folker Meyer, Er Goesmann, Alice C. Mchardy, Daniela Bartels, Thomas Bekel, Joè Rn Clausen, ...
GenDBÐan open source genome annotation system
Matching and significance evaluation of combined sequence-structure motifs in RNA (2002)
Carsten Meyer, Robert Giegerich
Abstract. The discipline of Algebraic Dynamic Programming is a powerful method to design and implement versatile pattern matching algorithms on sequences; here we consider mixed sequence and...
EIMaR: A Protein Docking System using Flexibility Information (2002)
Abteilung Informationstechnik, Frank Zöllner, Steffen Neumann, Kerstin Koch, ...
We give an overview of the ELMAR Docking System. Using a distributed modular and optionally parallel architecture results can be obtained within a few minutes. ELMAR incorporates protein flexibility...
Implementing algebraic dynamic programming in the functional and the imperative paradigm (2002)
Robert Giegerich, Peter Steffen
Abstract. Algebraic dynamic programming is a new method for developing and reasoning about dynamic programming algorithms. In this approach, so-called yield grammars and evaluation algebras...
Algebraic dynamic programming (2002)
Robert Giegerich, Carsten Meyer
Abstract. Dynamic programming is a classic programming technique, applicable in a wide variety of domains, like stochastic systems analysis, operations research, combinatorics of discrete structures,...
PathFinder: reconstruction and dynamic visualization of metabolic pathways (2002)
Goesmann, Alexander, Haubrock, Martin, Meyer, Folker, Kalinowski, Jörn, Giegerich, Robert
Motivation: Beyond methods for a gene-wise annotation and analysis of sequenced genomes new automated methods for functional analysis on a higher level are needed. The identification of realized...
REPuter: the manifold applications of repeat analysis on a genomic scale (2001)
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, Giegerich, Robert
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The...
Minimum conflict: a divide-and-conquer approach to phylogeny estimation (2001)
Fuellen, Georg, Wägele, Johann-Wolfgang, Giegerich, Robert
Motivation: Fast and reliable phylogeny estimation is rapidly gaining importance as more and more genomic sequence information is becoming available, and the study of the evolution of genes and...
Computation and visualization of degenerate repeats in complete genomes (2000)
Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The...
Explaining and Controlling Ambiguity in Dynamic Programming (2000)
. Ambiguity in dynamic programming arises from two independent sources, the non-uniqueness of optimal solutions and the particular recursion scheme by which the search space is evaluated. Ambiguity,...
Computation and Visualization of Degenerate Repeats in Complete Genomes (2000)
Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The...
Computation and Visualization of Degenerate Repeats in Complete Genomes (2000)
Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The...
Explaining and controlling ambiguity in dynamic programming (2000)
Abstract. Ambiguity in dynamic programming arises from two independent sources, the non-uniqueness of optimal solutions and the particular recursion scheme by which the search space is evaluated....
A systematic approach to dynamic programming in bioinformatics (2000)
Motivation: Dynamic programming is probably the most popular programming method in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are...
Editorial Board: H. Aït-Kaci L. Augustsson (1999)
Ch. Brzoska, J. Darlington, Y. Guo, M. Hagiya, M. Hanus, T. Ida, ...
other articles see:
A Systematic Approach to Dynamic Programming in Bioinformatics (1999)
Motivation: Dynamic programming is probably the most popular programming method in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are...
An Algebraic Dynamic Programming Approach to the Analysis of Recombinant DNA Sequences (1999)
Robert Giegerich, Stefan Kurtz, Georg F. Weiller
Evaluator and Evaluation Algebras According to [4], an abstract evaluator is obtained by abstracting from the constructors of the underlying datatype Alignment. Additionally, an abstract choice...
Straight to the Heart of Computer Science via Functional Programming (1999)
Robert Giegerich, Ralf Hinze, Stefan Kurtz
We outline a deductive concept for an introductory course to computer science aimed at CS students as well as students from other disciplines. The emphasis is on introducing fundamental concepts of...
A General Pattern Matching Language for Specific Motifs in RNA Secondary Structure (1999)
Dirk Evers Robert, Robert Giegerich, Stefan Kurtz
Introduction The problem of RNA folding has been approached by dynamic programming, simulated annealing, and a variety of combinatorial approaches. For recognition of structural motifs, specific...
Straight to the Heart of Computer Science via Functional Programming (1999)
Robert Giegerich, Ralf Hinze, Stefan Kurtz
We outline a deductive concept for an introductory course to computer science aimed at CS students as well as students from other disciplines. The emphasis is on introducing fundamental concepts of...
Efficient Implementation of Lazy Suffix Trees (1999)
Robert Giegerich, Stefan Kurtz, Jens Stoye
Abstract. We present an efficient implementation of a write-only topdown construction for suffix trees. Our implementation is based on a new, space-efficient representation of suffix trees which...
A new approach to the systematic development of dynamic programming algorithms is presented and applied to RNA folding. Analyses of the potential foldings of an RNA molecule have mainly been...
A General Technique to Improve Filter Algorithms for Approximate String Matching (1997)
Robert Giegerich, Frankk Hischke, Stefan Kurtz, Enno Ohlebusch
. Approximate string matching searches for occurrences of a pattern in a text, where a certain number of character differences (errors) is allowed. Fast methods use filters: A fast preprocessing...
Ingo Glöckner, Forschungsberichte Der, Abteilung Informationstechnik, Ingo Gl Ockner, Impressum Herausgeber, ...
The processing of natural language (NL) queries and the search for semantic matches between such queries and the contents of multimedia documents necessitate powerful quantifiers that adequately...
Rose: Generating Sequence Families (1997)
Forschungsbericht Der, Abteilung Informationstechnik, Jens Stoye, Dirk Evers, Folker Meyer, Impressum Herausgeber, ...
2 2 Introduction 3 3 Systems and Methods 5 4 Algorithm 6 4.1 The Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 4.2 The Root Sequence . . . . . . . . . . . . . . . . . . . . . ....
Divide-and-Conquer Multiple Sequence Alignment (1997)
Abteilung Informationstechnik, Jens Stoye, Impressum Herausgeber, Robert Giegerich, Alois Knoll, ...
Contents 1 Introduction 1 1.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.3...
From Ukkonen to McCreight and Weiner: A Unifying View of Linear-Time Suffix Tree Construction (1997)
Robert Giegerich, Stefan Kurtz
We review the linear time suffix tree constructions by Weiner, McCreight, and Ukkonen. We use the terminology of the most recent algorithm, Ukkonen's online construction, to explain its historic...
DFS - An Axiomatic Approach to Fuzzy Quantification (1997)
Ingo Glöckner, Abteilung Informationstechnik, Impressum Herausgeber, Robert Giegerich, Alois Knoll, ...
Contents 1 Introduction 1 1.1 Fuzzy quantifiers: statement of the problem . . . . . . . . . . . . . . . . . . . . . 1 1.2 Outline of DFS solution . . . . . . . . . . . . . . . . . . . . . . . . . . ....
Static and Dynamic Filtering Methods for Approximate String Matching (1996)
Abteilung Informationstechnik, Impressum Herausgeber, Alois Knoll, Peter Ladkin, Helge Ritter, ...
this paper improves on this by merging the filtering and the checking phase. It evaluates the statically derived filter information during the checking phase, strengthening it by information...
Instructing Cooperating Assembly Robots through Situated Dialogues in Natural Language (1996)
Abteilung Informationstechnik, A. Knoll, B. Hildebrandt, J. Zhang, Impressum Herausgeber, ...
We present an assembly cell consisting of two cooperating robots and a variety of sensors. It offers a number of complex skills necessary for constructing aggregates from elements of a toy...
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration - I. Neutral Networks (1996)
Walter Grüner, Walter Gr Uner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, ...
Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU...
Walter Grüner, Walter Gr Uner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, ...
The relations between RNA sequences and secondary structures are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The technique of tries is used for economic...
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration (1996)
Walter Grüner, Walter Gr Uner, Robert Giegerich, Dirk Strohmann, Christian Reidys, Jacqueline Weber, ...
The mapping from RNA sequences to their secondary structures is investigated by exhaustively folding all GC and AU sequences with chain lengths up to 30. We analyse the distribution of secondary...
Bielefeld Workshop on RNA Structure Exploration (1996)
Andreas Dress, Fsp Mathematisierung, Dirk Evers, Robert Giegerich, Robert Giegerich, ...
Contents Schedule 1 Dirk Evers and Robert Giegerich RNA Movies 3 Fabrice Lefebvre A new grammar formalism for sequence analysis models 4 Gerhard Steger Interpretation of experimentally determined RNA...
A New Calculus for Semantic Matching (1995)
Bernd Butow, Robert Giegerich, Enno Ohlebusch, Stephan Thesing
. In this paper, we present Reverse Restructuring, a new calculus for solving the semantic matching problem. For narrowing, advanced selection rules are commonly seen as an appropriate method to...
A Comparison of Imperative and Purely Functional Suffix Tree Constructions (1995)
Robert Giegerich, Stefan Kurtz
We explore the design space of implementing suffix tree algorithms in the functional paradigm. We review the linear time and space algorithms of McCreight and Ukkonen. Based on a new terminology of...
Basic Semantics for Computer Arithmetic (1994)
Abteilung Informationstechnik, M. Freericks, A. Fauth, A. Knoll, Impressum Herausgeber, ...
This report defines a framework that supports a generic model of numeric representations and operations on them. We try to model all user-relevant notions such as "representation",...
Searching Correspondences in Colour Stereo Images - Recent Results Using the Fuzzy Integral (1994)
André Wolfram, Forschungsberichte Der, Abteilung Informationstechnik, Impressum Herausgeber, Robert Giegerich, ...
Introduction 3 Table of Contents 1 Introduction 3 2 Experimental Set-Up 4 3 Search for Correspondences 5 3.1 Correspondence Search with Colour Images . . . . . . . . . . . . . . . . . . . . . . . 6...
Embedding Sequence Analysis in the Functional Programming Paradigm - A Feasibility Study (1992)
ion: From a set of sequences that are known to share a certain biological function, the tool should aid the researcher in the task to extract the important characteristics. Consensus symbols, as used...
Invariance of Approximative Semantics with Respect to Program Transformations (1981)
Robert Giegerich, Ulrich Moncke, Reinhard Wilhelm
Program transformations, as used for optimizations and sometimes for program development, utilize information about the program which is derived by the method of abstract interpretation within...
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, Giegerich, Robert
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The...
GenDB—an open source genome annotation system for prokaryote genomes
Meyer, Folker, Goesmann, Alexander, McHardy, Alice C., Bartels, Daniela, Bekel, Thomas, Clausen, Jörn, ...
The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To...
RNA-related tools on the Bielefeld Bioinformatics Server
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, Giegerich, Robert
We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison...
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, Giegerich, Robert
e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable...
Giegerich, Robert, Voß, Björn, Rehmsmeier, Marc
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of...
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H, Giegerich, Robert, Altmann, Curtis R
Fast and effective prediction of microRNA/target duplexes
REHMSMEIER, MARC, STEFFEN, PETER, HÖCHSMANN, MATTHIAS, GIEGERICH, ROBERT
MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a...
Fast index based algorithms and software for matching position specific scoring matrices
Beckstette, Michael, Homann, Robert, Giegerich, Robert, Kurtz, Stefan
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, Giegerich, Robert
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The...
GenDB—an open source genome annotation system for prokaryote genomes
Meyer, Folker, Goesmann, Alexander, McHardy, Alice C., Bartels, Daniela, Bekel, Thomas, Clausen, Jörn, ...
The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To...
RNA-related tools on the Bielefeld Bioinformatics Server
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, Giegerich, Robert
We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison...
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, Giegerich, Robert
e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable...
Giegerich, Robert, Voß, Björn, Rehmsmeier, Marc
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of...
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H, Giegerich, Robert, Altmann, Curtis R
Fast and effective prediction of microRNA/target duplexes
REHMSMEIER, MARC, STEFFEN, PETER, HÖCHSMANN, MATTHIAS, GIEGERICH, ROBERT
MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a...
Fast index based algorithms and software for matching position specific scoring matrices
Beckstette, Michael, Homann, Robert, Giegerich, Robert, Kurtz, Stefan
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
Reeder, Jens, Steffen, Peter, Giegerich, Robert
RNA pseudoknots are an important structural feature of RNAs, but often neglected in computer predictions for reasons of efficiency. Here, we present the pknotsRG Web Server for single sequence RNA...
XML schemas for common bioinformatic data types and their application in workflow systems
Seibel, Philipp N, Krüger, Jan, Hartmeier, Sven, Schwarzer, Knut, Löwenthal, Kai, Mersch, Henning, ...
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI
Lamprecht, Anna-Lena, Margaria, Tiziana, Steffen, Bernhard, Sczyrba, Alexander, Hartmeier, Sven, Giegerich, Robert
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
Walter Gruner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, ...
Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU...
KnotInFrame: prediction of −1 ribosomal frameshift events
Theis, Corinna, Reeder, Jens, Giegerich, Robert
Programmed −1 ribosomal frameshift (−1 PRF) allows for alternative reading frames within one mRNA. First found in several viruses, it is now believed to exist in all kingdoms of life. Strong...
mkESA: enhanced suffix array construction tool
Homann, Robert, Fleer, David, Giegerich, Robert, Rehmsmeier, Marc
Summary: We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly...