Stefan Kurtz

According to our database1, Stefan Kurtz authored at least 44 papers between 1994 and 2019.

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Bibliography

2019
GfaViz: flexible and interactive visualization of GFA sequence graphs.
Bioinform., 2019

2017
GfaPy: a flexible and extensible software library for handling sequence graphs in Python.
Bioinform., 2017

2014
FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.
J. Clin. Bioinform., 2014

2013
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.
BMC Bioinform., 2013

2012
A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Readjoiner: a fast and memory efficient string graph-based sequence assembler.
BMC Bioinform., 2012

2011
CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.
J. Integr. Bioinform., 2011

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
J. Clin. Bioinform., 2011

Structator: fast index-based search for RNA sequence-structure patterns.
BMC Bioinform., 2011

2009
Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures.
PLoS Comput. Biol., 2009

<i>AnnotationSketch</i>: a genome annotation drawing library.
Bioinform., 2009

Significant speedup of database searches with HMMs by search space reduction with PSSM family models.
Bioinform., 2009

2008
Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences.
J. Comput. Biol., 2008

Efficient computation of absent words in genomic sequences.
BMC Bioinform., 2008

<i>LTRharvest</i>, an efficient and flexible software for <i>de novo </i>detection of LTR retrotransposons.
BMC Bioinform., 2008

CoCoNUT: an efficient system for the comparison and analysis of genomes.
BMC Bioinform., 2008

2007
Optimising oligonucleotide array design for ChIP-on-chip.
BMC Bioinform., 2007

Optimized design and assessment of whole genome tiling arrays.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006
Fast index based algorithms and software for matching position specific scoring matrices.
BMC Bioinform., 2006

2005
Engineering a software tool for gene structure prediction in higher organisms.
Inf. Softw. Technol., 2005

2004
Computational Biology.
Proceedings of the Handbook of Data Structures and Applications., 2004

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences.
Nucleic Acids Res., 2004

Replacing suffix trees with enhanced suffix arrays.
J. Discrete Algorithms, 2004

GenAlyzer: interactive visualization of sequence similarities between entire genomes.
Bioinform., 2004

<i>PoSSuMsearch</i>: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays.
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004

2003
Efficient implementation of lazy suffix trees.
Softw. Pract. Exp., 2003

RNA-related tools on the Bielefeld Bioinformatics Server.
Nucleic Acids Res., 2003

An Applications-focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges.
Briefings Bioinform., 2003

Local Similarity in RNA Secondary Structures.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
The Enhanced Suffix Array and Its Applications to Genome Analysis.
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

Optimal Exact Strring Matching Based on Suffix Arrays.
Proceedings of the String Processing and Information Retrieval, 2002

Efficient multiple genome alignment.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001
HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns.
Nucleic Acids Res., 2001

2000
Universal Data Compression Based on the Burrows-Wheeler Transformation: Theory and Practice.
IEEE Trans. Computers, 2000

Computation and Visualization of Degenerate Repeats in Complete Genomes.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999
Reducing the space requirement of suffix trees.
Softw. Pract. Exp., 1999

REPuter: fast computation of maximal repeats in complete genomes.
Bioinform., 1999

Modifications of the Burrows and Wheeler Data Compression Algorithm.
Proceedings of the Data Compression Conference, 1999

1997
From Ukkonen to McCreight and Weiner: A Unifying View of Linear-Time Suffix Tree Construction.
Algorithmica, 1997

Estimating the Probability of Approximate Matches.
Proceedings of the Combinatorial Pattern Matching, 8th Annual Symposium, 1997

1995
Fundamental algorithms for a declarative pattern matching system.
PhD thesis, 1995

A Comparison of Imperative and Purely Functional Suffix Tree Constructions.
Sci. Comput. Program., 1995

1994
Suffix Trees in the Functional Programming Paradigm.
Proceedings of the Programming Languages and Systems, 1994


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