Suffix Trees in the Functional Programming Paradigm. - Robert Giegerich; Stefan Kurtz (ESOP, 1994)

A Comparison of Imperative and Purely Functional Suffix Tree Constructions. - Robert Giegerich; Stefan Kurtz (Sci. Comput. Program., 1995)

Fundamental algorithms for a declarative pattern matching system. - Stefan Kurtz (1995)

Estimating the Probability of Approximate Matches. - Stefan Kurtz; Gene Myers (CPM, 1997)

From Ukkonen to McCreight and Weiner: A Unifying View of Linear-Time Suffix Tree Construction. - Robert Giegerich; Stefan Kurtz (Algorithmica, 1997)

Modifications of the Burrows and Wheeler Data Compression Algorithm. - Bernhard Balkenhol; Stefan Kurtz; Yuri M. Shtarkov (Data Compression Conference, 1999)

REPuter: fast computation of maximal repeats in complete genomes. - Stefan Kurtz; Chris Schleiermacher (Bioinform., 1999)

Reducing the space requirement of suffix trees. - Stefan Kurtz (Softw. Pract. Exp., 1999)

Computation and Visualization of Degenerate Repeats in Complete Genomes. - Stefan Kurtz; Enno Ohlebusch; Chris Schleiermacher; Jens Stoye; Robert Giegerich (ISMB, 2000)

Universal Data Compression Based on the Burrows-Wheeler Transformation: Theory and Practice. - Bernhard Balkenhol; Stefan Kurtz (IEEE Trans. Computers, 2000)

HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns. - Stefan Gräf; Dirk Strothmann; Stefan Kurtz; Gerhard Steger (Nucleic Acids Res., 2001)

Efficient multiple genome alignment. - Michael Höhl; Stefan Kurtz; Enno Ohlebusch (ISMB, 2002)

Optimal Exact Strring Matching Based on Suffix Arrays. - Mohamed Ibrahim Abouelhoda; Enno Ohlebusch; Stefan Kurtz (SPIRE, 2002)

The Enhanced Suffix Array and Its Applications to Genome Analysis. - Mohamed Ibrahim Abouelhoda; Stefan Kurtz; Enno Ohlebusch (WABI, 2002)

Rapid development of nucleic acid diagnostics. - J. Patrick Fitch; Shea N. Gardner; Thomas A. Kuczmarski; Stefan Kurtz; Rich Myers; Linda L. Ott; Thomas R. Slezak; Elizabeth A. Vitalis; Adam T. Zemla; Paula M. McCready (Proc. IEEE, 2002)

Local Similarity in RNA Secondary Structures. - Matthias Höchsmann; Thomas Töller; Robert Giegerich; Stefan Kurtz (CSB, 2003)

An Applications-focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges. - Patrick S. G. Chain; Stefan Kurtz; Enno Ohlebusch; Tom Slezak (Briefings Bioinform., 2003)

RNA-related tools on the Bielefeld Bioinformatics Server. - Alexander Sczyrba; Jan Krüger; Henning Mersch; Stefan Kurtz; Robert Giegerich (Nucleic Acids Res., 2003)

Efficient implementation of lazy suffix trees. - Robert Giegerich; Stefan Kurtz; Jens Stoye (Softw. Pract. Exp., 2003)

PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays. - Michael Beckstette; Dirk Strothmann; Robert Homann; Robert Giegerich; Stefan Kurtz (German Conference on Bioinformatics, 2004)

GenAlyzer: interactive visualization of sequence similarities between entire genomes. - Jomuna V. Choudhuri; Chris Schleiermacher; Stefan Kurtz; Robert Giegerich (Bioinform., 2004)

Replacing suffix trees with enhanced suffix arrays. - Mohamed Ibrahim Abouelhoda; Stefan Kurtz; Enno Ohlebusch (J. Discrete Algorithms, 2004)

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. - Jan Krüger; Alexander Sczyrba; Stefan Kurtz; Robert Giegerich (Nucleic Acids Res., 2004)

Computational Biology. - Stefan Kurtz; Stefano Lonardi (Handbook of Data Structures and Applications, 2004)

Engineering a software tool for gene structure prediction in higher organisms. - Gordon Gremme; Volker Brendel; Michael E. Sparks; Stefan Kurtz (Inf. Softw. Technol., 2005)

Fast index based algorithms and software for matching position specific scoring matrices. - Michael Beckstette; Robert Homann; Robert Giegerich; Stefan Kurtz (BMC Bioinform., 2006)

Optimized design and assessment of whole genome tiling arrays. - Stefan Gräf; Fiona G. G. Nielsen; Stefan Kurtz; Martijn A. Huynen; Ewan Birney; Henk Stunnenberg; Paul Flicek (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Optimising oligonucleotide array design for ChIP-on-chip. - Fiona G. G. Nielsen; Stefan Gräf; Xinmin Zhang; Stefan Kurtz; Sergei Denissov; Roland Green; Ewan Birney; Paul Flicek; Martijn A. Huynen; Henk Stunnenberg (BMC Bioinform., 2007)

CoCoNUT: an efficient system for the comparison and analysis of genomes. - Mohamed Ibrahim Abouelhoda; Stefan Kurtz; Enno Ohlebusch (BMC Bioinform., 2008)

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. - David Ellinghaus; Stefan Kurtz; Ute Willhoeft (BMC Bioinform., 2008)

Efficient computation of absent words in genomic sequences. - Julia Herold; Stefan Kurtz; Robert Giegerich (BMC Bioinform., 2008)

Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences. - Enno Ohlebusch; Stefan Kurtz (J. Comput. Biol., 2008)

Significant speedup of database searches with HMMs by search space reduction with PSSM family models. - Michael Beckstette; Robert Homann; Robert Giegerich; Stefan Kurtz (Bioinform., 2009)

AnnotationSketch: a genome annotation drawing library. - Sascha Steinbiss; Gordon Gremme; Christin Schärfer; Malte Mader; Stefan Kurtz (Bioinform., 2009)

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. - Steve Hoffmann; Christian Otto; Stefan Kurtz; Cynthia M. Sharma; Philipp Khaitovich; Jörg Vogel 002; Peter F. Stadler; Jörg Hackermüller (PLoS Comput. Biol., 2009)

Structator: fast index-based search for RNA sequence-structure patterns. - Fernando Meyer; Stefan Kurtz; Rolf Backofen; Sebastian Will; Michael Beckstette (BMC Bioinform., 2011)

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. - Malte Mader; Ronald Simon; Sascha Steinbiss; Stefan Kurtz (J. Clin. Bioinform., 2011)

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data. - Malik Alawi; Stefan Kurtz; Michael Beckstette (J. Integr. Bioinform., 2011)

Readjoiner: a fast and memory efficient string graph-based sequence assembler. - Giorgio Gonnella; Stefan Kurtz (BMC Bioinform., 2012)

A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences. - Sascha Steinbiss; Stefan Kurtz (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns. - Fernando Meyer; Stefan Kurtz; Michael Beckstette (BMC Bioinform., 2013)

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations. - Gordon Gremme; Sascha Steinbiss; Stefan Kurtz (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research. - Malte Mader; Ronald Simon; Stefan Kurtz (J. Clin. Bioinform., 2014)

GfaPy: a flexible and extensible software library for handling sequence graphs in Python. - Giorgio Gonnella; Stefan Kurtz (Bioinform., 2017)

GfaViz: flexible and interactive visualization of GFA sequence graphs. - Giorgio Gonnella; Niklas Niehus; Stefan Kurtz (Bioinform., 2019)

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention. - Fabian Hausmann; Stefan Kurtz (Algorithms Mol. Biol., 2021)