Jens Stoye

According to our database1, Jens Stoye authored at least 117 papers between 1997 and 2020.

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Bibliography

2020
Computing the rearrangement distance of natural genomes.
CoRR, 2020

2019
25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241).
Dagstuhl Reports, 2019

Computing the Inversion-Indel Distance.
CoRR, 2019

Finding All Maximal Perfect Haplotype Blocks in Linear Time.
Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

2018
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

Dynamic Alignment-Free and Reference-Free Read Compression.
Journal of Computational Biology, 2018

Computing the family-free DCJ similarity.
BMC Bioinformatics, 2018

Identifying Maximal Perfect Haplotype Blocks.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2018

2017
New Genome Similarity Measures based on Conserved Gene Adjacencies.
Journal of Computational Biology, 2017

Fast and Simple Jumbled Indexing for Binary RLE Strings.
CoRR, 2017

Approximating the DCJ distance of balanced genomes in linear time.
Algorithms for Molecular Biology, 2017

Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery.
Proceedings of the Comparative Genomics - 15th International Workshop, 2017

Algorithms for Computing the Family-Free Genomic Similarity Under DCJ.
Proceedings of the Comparative Genomics - 15th International Workshop, 2017

Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings.
Proceedings of the 28th Annual Symposium on Combinatorial Pattern Matching, 2017

2016
Suffix Tree Construction.
Encyclopedia of Algorithms, 2016

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.
Algorithms for Molecular Biology, 2016

A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates.
Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

New Genome Similarity Measures Based on Conserved Gene Adjacencies.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015
Sorting Linear Genomes with Rearrangements and Indels.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

On the family-free DCJ distance and similarity.
Algorithms for Molecular Biology, 2015

Bloom Filter Trie - A Data Structure for Pan-Genome Storage.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

2014
Editorial.
J. Discrete Algorithms, 2014

BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry.
Bioinformatics, 2014

ReadXplorer - visualization and analysis of mapped sequences.
Bioinformatics, 2014

On the Family-Free DCJ Distance.
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

2013
On the inversion-indel distance.
BMC Bioinformatics, 2013

Statistics for approximate gene clusters.
BMC Bioinformatics, 2013

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.
BMC Bioinformatics, 2013

Restricted DCJ-Indel Model Revisited.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013

The Potential of Family-Free Genome Comparison.
Proceedings of the Models and Algorithms for Genome Evolution, 2013

The Genesis of the DCJ Formula.
Proceedings of the Models and Algorithms for Genome Evolution, 2013

2012
Multiple genome comparison based on overlap regions of pairwise local alignments.
BMC Bioinformatics, 2012

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.
BMC Bioinformatics, 2012

Gene family assignment-free comparative genomics.
BMC Bioinformatics, 2012

UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ.
Bioinformatics, 2012

2011
Consistency of Sequence-Based Gene Clusters.
Journal of Computational Biology, 2011

Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation.
Journal of Computational Biology, 2011

Double Cut and Join with Insertions and Deletions.
Journal of Computational Biology, 2011

Swiftly Computing Center Strings.
BMC Bioinformatics, 2011

On the weight of indels in genomic distances.
BMC Bioinformatics, 2011

Genomic distance under gene substitutions.
BMC Bioinformatics, 2011

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.
Bioinformatics, 2011

Balanced vertices in trees and a simpler algorithm to compute the genomic distance.
Appl. Math. Lett., 2011

Common Intervals of Multiple Permutations.
Algorithmica, 2011

2010
The Solution Space of Sorting by DCJ.
Journal of Computational Biology, 2010

Finding Nested Common Intervals Efficiently.
Journal of Computational Biology, 2010

Rearrangement Models and Single-Cut Operations.
Journal of Computational Biology, 2010

r2cat: synteny plots and comparative assembly.
Bioinformatics, 2010

Phylogenetic comparative assembly.
Algorithms for Molecular Biology, 2010

Genomic Distance with DCJ and Indels.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Consistency of Sequence-Based Gene Clusters.
Proceedings of the Comparative Genomics - International Workshop, 2010

The Problem of Chromosome Reincorporation in DCJ Sorting and Halving.
Proceedings of the Comparative Genomics - International Workshop, 2010

Repeat-aware Comparative Genome Assembly.
Proceedings of the German Conference on Bioinformatics 2010, 2010

Indexing and Searching a Mass Spectrometry Database.
Proceedings of the Algorithms and Applications, 2010

2009
A new linear time algorithm to compute the genomic distance via the double cut and join distance.
Theor. Comput. Sci., 2009

A Unified Approach for Reconstructing Ancient Gene Clusters.
IEEE/ACM Trans. Comput. Biology Bioinform., 2009

Computation of Median Gene Clusters.
Journal of Computational Biology, 2009

Approximative Gencluster und ihre Anwendung in der komparativen Genomik.
Informatik Spektrum, 2009

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
BMC Bioinformatics, 2009

ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.
Bioinformatics, 2009

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).
Bioinformatics, 2009

Rearrangement Models and Single-Cut Operations.
Proceedings of the Comparative Genomics, International Workshop, 2009

Counting All DCJ Sorting Scenarios.
Proceedings of the Comparative Genomics, International Workshop, 2009

Finding Nested Common Intervals Efficiently.
Proceedings of the Comparative Genomics, International Workshop, 2009

2008
Suffix Tree Construction in RAM.
Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Counting suffix arrays and strings.
Theor. Comput. Sci., 2008

Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms.
Nucleic Acids Research, 2008

MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Bioinformatics, 2008

Detecting Repeat Families in Incompletely Sequenced Genomes.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios.
Proceedings of the Comparative Genomics, International Workshop, 2008

HP Distance Via Double Cut and Join Distance.
Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

2007
An incomplex algorithm for fast suffix array construction.
Softw., Pract. Exper., 2007

Character sets of strings.
J. Discrete Algorithms, 2007

2006
Comparing Tandem Repeats with Duplications and Excisions of Variable Degree.
IEEE/ACM Trans. Comput. Biology Bioinform., 2006

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length.
Journal of Computational Biology, 2006

On the Similarity of Sets of Permutations and Its Applications to Genome Comparison.
Journal of Computational Biology, 2006

On Sorting by Translocations.
Journal of Computational Biology, 2006

Panta rhei (QAlign2): an open graphical environment for sequence analysis.
Bioinformatics, 2006

A Unifying View of Genome Rearrangements.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Finding novel genes in bacterial communities isolated from the environment.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005
Large scale hierarchical clustering of protein sequences.
BMC Bioinformatics, 2005

BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
Bioinformatics, 2005

Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length.
Proceedings of the Research in Computational Molecular Biology, 2005

Protein Annotation by Secondary Structure Based Alignments (PASSTA).
Proceedings of the Computational Life Sciences, First International Symposium, 2005

2004
Linear time algorithms for finding and representing all the tandem repeats in a string.
J. Comput. Syst. Sci., 2004

Algorithmic complexity of protein identification: combinatorics of weighted strings.
Discrete Applied Mathematics, 2004

Correction: Benchmarking tools for the alignment of functional noncodingDNA.
BMC Bioinformatics, 2004

Benchmarking tools for the alignment of functional noncoding DNA.
BMC Bioinformatics, 2004

Suboptimal Local Alignments Across Multiple Scoring Schemes.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences.
Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

Reversal Distance without Hurdles and Fortresses.
Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

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

Digital extractor: analysis of digital differential display output.
Bioinformatics, 2003

Evaluation of the Jumping Alignment algorithm with artificial and biological data.
Proceedings of the German Conference on Bioinformatics, 2003

Divide-and-conquer multiple alignment with segment-based constraints.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002
Simple and flexible detection of contiguous repeats using a suffix tree.
Theor. Comput. Sci., 2002

A Novel Approach to Remote Homology Detection: Jumping Alignments.
Journal of Computational Biology, 2002

Algorithmic Complexity of Protein Identification: Searching in Weighted Strings.
Proceedings of the Foundations of Information Technology in the Era of Networking and Mobile Computing, 2002

Index Structures for Large Sequence Data: Suffix Trees and Affix Trees.
Proceedings of the Informatik bewegt: Informatik 2002 - 32. Jahrestagung der Gesellschaft für Informatik e.v. (GI), 30. September, 2002

Common intervals and sorting by reversals: a marriage of necessity.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001
Algorithms for Finding Gene Clusters.
Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

Sequence Database Search Using Jumping Alignments.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

Finding All Common Intervals of k Permutations.
Proceedings of the Combinatorial Pattern Matching, 12th Annual Symposium, 2001

2000
The SYSTERS protein sequence cluster set.
Nucleic Acids Research, 2000

Contig Selection in Physical Mapping.
Journal of Computational Biology, 2000

An iterative method for faster sum-of-pairs multiple sequence alignment.
Bioinformatics, 2000

Contig selection in physical mapping.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

Sequence Database Search Using Jumping Alignments.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

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

1999
Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment.
Proceedings of the German Conference on Bioinformatics, 1999

Finding Maximal Pairs with Bounded Gap.
Proceedings of the Combinatorial Pattern Matching, 10th Annual Symposium, 1999

1998
Rose: generating sequence families.
Bioinformatics, 1998

Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version).
Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998

1997
Two applications of the Divide&Conquer principle in the molecular sciences.
Math. Program., 1997

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.
Computer Applications in the Biosciences, 1997

Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997


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