Jens Stoye

发表

Simone Dantas, Luis Antonio Brasil Kowada, Daniel Doerr, 2016, RECOMB.

The Genesis of the DCJ Formula

Jens Stoye, Anne Bergeron, J. Stoye, 2013, Models and Algorithms for Genome Evolution.

Linear time algorithms for finding and representing all the tandem repeats in a string

Jens Stoye, Dan Gusfield, J. Stoye, 2004, J. Comput. Syst. Sci..

Counting suffix arrays and strings

Jens Stoye, Klaus-Bernd Schürmann, J. Stoye, 2005, Theor. Comput. Sci..

Combinatorial Pattern Matching

Jens Stoye, Juha Kärkkäinen, 2012, Lecture Notes in Computer Science.

An incomplex algorithm for fast suffix array construction

Jens Stoye, Klaus-Bernd Schürmann, 2007 .

Reversal Distance without Hurdles and Fortresses

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2004, CPM.

On motifs in colored graphs pdf

Jens Stoye, Diego P Rubert, Eloi Araujo, 2020, ArXiv.

FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment

Jens Stoye, Vincent Moulton, Sören W. Perrey, 1997 .

Computational Short Read Metagenomics

Jens Stoye, 2009 .

Algorithms for Phylogenetic Reconstructions

Martin Vingron, Jens Stoye, Hannes Luz, 2006 .

An iterative method for faster sum-of-pairs multiple sequence alignment

Jens Stoye, Knut Reinert, Torsten Will, 2000, Bioinform..

A new linear time algorithm to compute the genomic distance via the double cut and join distance

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2009, Theor. Comput. Sci..

Common intervals and sorting by reversals: a marriage of necessity

Jens Stoye, Anne Bergeron, Steffen Heber, 2002, ECCB.

Finding Maximal Pairs with Bounded Gap

Jens Stoye, Christian N. S. Pedersen, Gerth Stølting Brodal, 1999, CPM.

THE NUMBER OF STANDARD AND OF EFFECTIVE MULTIPLE ALIGNMENTS

Jens Stoye, Burkhard Morgenstern, Andreas W. M. Dress, 1998 .

Comparing Tandem Repeats with Duplications and Excisions of Variable Degree

Jens Stoye, Michael Sammeth, J. Stoye, 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Genomic Distance with DCJ and Indels

Jens Stoye, Marília D. V. Braga, Eyla Willing, 2010, WABI.

A Unifying View of Genome Rearrangements

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2006, WABI.

Algorithmic complexity of protein identification

Thomas Erlebach, Jens Stoye, Mark Cieliebak, 2001 .

Fast and Simple Jumbled Indexing for Binary RLE Strings pdf

Simone Dantas, Luis Antonio Brasil Kowada, Jens Stoye, 2017, ArXiv.

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length

Eugene W. Myers, Jens Stoye, Kim R. Rasmussen, 2006, J. Comput. Biol..

an OpenSource Software Framework and User Interface for High{Throughput Metabolomics

Jens Stoye, Mathias Wilhelm, Nils Homann, 2012 .

Jens Stoye, Anne Bergeron, 2006, J. Comput. Biol..

Algorithms for Finding Gene Clusters

Jens Stoye, Steffen Heber, J. Stoye, 2001, WABI.

Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment

Jens Stoye, Knut Reinert, Torsten Will, 1999, German Conference on Bioinformatics.

UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ

Jens Stoye, Christian N. S. Pedersen, Rolf Hilker, 2012, Bioinform..

Statistics for approximate gene clusters

Jens Stoye, Katharina Jahn, Sebastian Böcker, 2013, BMC Bioinformatics.

An incomplex algorithm for fast suffix array construction

Jens Stoye, Klaus-Bernd Schürmann, J. Stoye, 2007, ALENEX/ANALCO.

Phylogenetic comparative assembly

Jens Stoye, Peter Husemann, J. Stoye, 2009, Algorithms for Molecular Biology.

Suffix Tree Construction

Jens Stoye, 2016, Encyclopedia of Algorithms.

GISMO - Prokaryotic Gene Identification using a Support Vector Machine for ORF Classification

Jens Stoye, Lutz Krause, Alice C. McHardy, 2007 .

Generic Software Frameworks for GC-MS Based Metabolomics

Jens Stoye, Nils Hoffmann, J. Stoye, 2012 .

Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences

Jens Stoye, Thomas Schmidt, J. Stoye, 2004, CPM.

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length

Eugene W. Myers, Jens Stoye, Kim R. Rasmussen, 2005, RECOMB.

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

Daniel Doerr, Jens Stoye, Sonja J. Prohaska, 2014, PloS one.

Indexing and Searching a Mass Spectrometry Database

Benno Schwikowski, Jens Stoye, Søren Besenbacher, 2010, Algorithms and Applications.

Algorithms in Bioinformatics

Jens Stoye, Aaron E. Darling, J. Stoye, 2013, Lecture Notes in Computer Science.

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

Jens Stoye, Cédric Chauve, Roland Wittler, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions

Folker Meyer, Jens Stoye, Dirk Evers, 1997, ISMB.

Counting Suffix Arrays and Strings

Jens Stoye, Klaus-Bernd Schürmann, J. Stoye, 2005, SPIRE.

The Solution Space of Sorting by DCJ

Jens Stoye, Marília D. V. Braga, J. Stoye, 2010, J. Comput. Biol..

Computation and Visualization of Degenerate Repeats in Complete Genomes

Enno Ohlebusch, Robert Giegerich, Jens Stoye, 2000, ISMB.

A Novel Approach to Remote Homology Detection: Jumping Alignments

Jens Stoye, Rainer Spang, Marc Rehmsmeier, 2002, J. Comput. Biol..

Multiple genome comparison based on overlap regions of pairwise local alignments

Jens Stoye, Katharina Jahn, Henner Sudek, 2012, BMC Bioinformatics.

Computing the Genomic Distance in Linear Time

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2010 .

Evaluation of the Jumping Alignment algorithm with artificial and biological data

Jens Stoye, Constantin Bannert, 2003, German Conference on Bioinformatics.

Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery

Daniel Doerr, Jens Stoye, Tizian Schulz, 2017, RECOMB-CG.

Computation of Median Gene Clusters

Jens Stoye, Katharina Jahn, Sebastian Böcker, 2009, J. Comput. Biol..

Panta rhei (QAlign2): an open graphical environment for sequence analysis

Jens Stoye, Michael Sammeth, Thasso Griebel, 2006, Bioinform..

The Problem of Chromosome Reincorporation in DCJ Sorting and Halving

Jens Stoye, Marília D. V. Braga, Jakub Kovác, 2010, RECOMB-CG.

Jens Stoye, Anne Bergeron, J. Stoye, 2003, COCOON.

Computing the Inversion-Indel Distance

Jens Stoye, Eyla Willing, Mar'ilia D. V. Braga, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching

Jens Stoye, Juha Kärkkäinen, 2012 .

Dynamic Alignment-Free and Reference-Free Read Compression

Faraz Hach, Jens Stoye, Roland Wittler, 2018, J. Comput. Biol..

A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates

Jens Stoye, Pedro Feijão, Marília D. V. Braga, 2016, WABI.

Consistency of Sequence-Based Gene Clusters

Jens Stoye, Roland Wittler, 2010, RECOMB-CG.

Detecting High Scoring Local Alignments in Pangenome Graphs

Faraz Hach, Jens Stoye, Roland Wittler, 2020, bioRxiv.

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment

Jens Stoye, Vincent Moulton, Andreas W. M. Dress, 1997, Comput. Appl. Biosci..

Identifying Maximal Perfect Haplotype Blocks

Luis Antonio Brasil Kowada, Jens Stoye, Yoan Diekmann, 2018, BSB.

Finding Nested Common Intervals Efficiently

Jens Stoye, Guillaume Blin, 2009, RECOMB-CG.

BIOINFORMATICS APPLICATIONS NOTE

Jens Stoye, Peter Husemann, J. Stoye, 2009 .

Character sets of strings

Jens Stoye, Dekel Tsur, Gilles Didier, 2007, J. Discrete Algorithms.

HASLR: Fast Hybrid Assembly of Long Reads

Faraz Hach, Jens Stoye, Cedric Chauve, 2020, iScience.

Restricted DCJ-Indel Model Revisited

Jens Stoye, Marília D. V. Braga, J. Stoye, 2013, BSB.

Gene family assignment-free comparative genomics

Daniel Doerr, Jens Stoye, Annelyse Thévenin, 2012, BMC Bioinformatics.

Efficient implementation of lazy suffix trees

Robert Giegerich, Jens Stoye, Stefan Kurtz, 1999, Softw. Pract. Exp..

Bloom Filter Trie - A Data Structure for Pan-Genome Storage

Jens Stoye, Roland Wittler, Guillaume Holley, 2015, WABI.

Suffix Tree Construction in RAM

Jens Stoye, 2008, Encyclopedia of Algorithms.

Divide-and-conquer multiple alignment with segment-based constraints

Jens Stoye, Burkhard Morgenstern, Michael Sammeth, 2003, ECCB.

Resampling Methods in Physical Mapping

Martin Vingron, Jens Stoye, Marcus Frohme, 2002 .

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jens Stoye, Alexander Goesmann, Tobias Jakobi, 2011, Bioinform..

Finding All Maximal Perfect Haplotype Blocks in Linear Time

Jens Stoye, Hideo Bannai, Pierre Peterlongo, 2019, WABI.

Rearrangement Models and Single-Cut Operations

Jens Stoye, Anne Bergeron, Paul Medvedev, 2010, J. Comput. Biol..

On Sorting by Translocations

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2006, J. Comput. Biol..

Consistency of Sequence-Based Gene Clusters

Ján Manuch, Jens Stoye, Murray Patterson, 2011, J. Comput. Biol..

MeltDB: a software platform for the analysis and integration of metabolomics experiment data

Jens Stoye, Alexander Goesmann, Karsten Niehaus, 2008, Bioinform..

Approximative Gencluster und ihre Anwendung in der komparativen Genomik

Jens Stoye, Katharina Jahn, 2009, Informatik-Spektrum.

Swiftly Computing Center Strings

Jens Stoye, Katharina Jahn, Sebastian Böcker, 2010, BMC Bioinformatics.

On the inversion-indel distance

Jens Stoye, Simone Zaccaria, Marília D. V. Braga, 2013, BMC Bioinformatics.

Two applications of the divide&conquer principle in the molecular sciences

Jens Stoye, Andreas W. M. Dress, Gunnar Brinkmann, 1997, Math. Program..

On Sorting by Translocations

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2005, RECOMB.

Updating benchtop sequencing performance comparison

Jens Stoye, Alexander Goesmann, Arndt von Haeseler, 2013, Nature Biotechnology.

Finding novel genes in bacterial communities isolated from the environment

Daniela Bartels, Folker Meyer, Jens Stoye, 2006, ISMB.

Algorithms for Computing the Family-Free Genomic Similarity Under DCJ

Jens Stoye, Edna Ayako Hoshino, Marília D. V. Braga, 2017, RECOMB-CG.

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage

Jens Stoye, Roland Wittler, Guillaume Holley, 2016, Algorithms for Molecular Biology.

Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings

Simone Dantas, Luis Antonio Brasil Kowada, Jens Stoye, 2017, CPM.

Eloi Araujo, Simone Dantas, Luis Antonio Brasil Kowada, 2016, RECOMB.

Overview of the data sets used in this study and their sequencing yield.

Jens Stoye, Alexander Goesmann, Stefan P. Albaum, 2014 .

Phylogenetic Comparative Assembly

Jens Stoye, Peter Husemann, 2009, WABI.

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences

Jens Stoye, Ole Schulz-Trieglaff, Anthony J. Cox, 2013, BMC Bioinformatics.

On Simultaneous versus Iterative Multiple Sequence Alignment

Jens Stoye, Vincent Moulton, Andreas W. M. Dress, 1997 .

Comparative Pathway Analyzer—a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms

Andreas Tauch, Jens Stoye, David R. Gilbert, 2008, Nucleic Acids Res..

Simple and flexible detection of contiguous repeats using a suffix tree

Jens Stoye, Dan Gusfield, J. Stoye, 1998, Theor. Comput. Sci..

The inversion distance problem

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2007, Mathematics of Evolution and Phylogeny.

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

Jens Stoye, Cedric Chauve, Roland Wittler, 2014, BSB.

Partitioning biological data with transitivity clustering

Dorothea Emig, Mario Albrecht, Jens Stoye, 2010, Nature Methods.

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

Jens Stoye, Paul Medvedev, Michael Brudno, 2009, Bioinform..

Large scale hierarchical clustering of protein sequences

Martin Vingron, Jens Stoye, Antje Krause, 2005, BMC Bioinformatics.

Contig selection in physical mapping

Martin Vingron, Jens Stoye, Steffen Heber, 2000, RECOMB '00.

HASLR: Fast Hybrid Assembly of Long Reads

Faraz Hach, Jens Stoye, Cedric Chauve, 2020, bioRxiv.

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

Jens Stoye, Mathias Wilhelm, Karsten Niehaus, 2012, BMC Bioinformatics.

Divide-and-Conquer Multiple Sequence Alignment

Jens Stoye, J. Stoye, 1997 .

ReadXplorer—visualization and analysis of mapped sequences

Jens Stoye, Alexander Goesmann, Jörn Kalinowski, 2014, Bioinform..

Finding all maximal perfect haplotype blocks in linear time

Jens Stoye, Pierre Peterlongo, Jarno Alanko, 2019, Algorithms for Molecular Biology.

Double Cut and Join with Insertions and Deletions

Jens Stoye, Eyla Willing, Marília D V Braga, 2011, J. Comput. Biol..

Protein Annotation by Secondary Structure Based Alignments (PASSTA)

Jens Stoye, Constantin Bannert, J. Stoye, 2005, CompLife.

Balanced vertices in trees and a simpler algorithm to compute the genomic distance pdf

Jens Stoye, Péter L. Erdös, Lajos Soukup, 2011, Appl. Math. Lett..

Index Structures for Large Sequence Data: Suffix Trees and Affix Trees

Jens Stoye, 2002, GI Jahrestagung.

25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241)

Jens Stoye, Travis Gagie, Giovanni Manzini, 2019, Dagstuhl Reports.

Common Intervals of Multiple Permutations

Jens Stoye, Richard Mayr, Steffen Heber, 2011, Algorithmica.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

Gad M. Landau, Steven Skiena, Roded Sharan, 2006, WABI 2012.

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

Gunnar Rätsch, Jens Stoye, Quaid Morris, 2020, bioRxiv.

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

Jens Stoye, Nils Hoffmann, J. Stoye, 2009, Bioinform..

Finding All Common Intervals of k Permutations

Jens Stoye, Steffen Heber, J. Stoye, 2001, CPM.

On the weight of indels in genomic distances

Jens Stoye, Raphael Machado, Marília D. V. Braga, 2011, BMC Bioinformatics.

Simple and flexible detection of contiguous repeats using a suffix tree

Jens Stoye, Dan Gusfield, 2002, Theor. Comput. Sci..

Maltcms an Application Framework for Processing of Metabolomics{Data

Jens Stoye, Mathias Wilhelm, Karsten Niehaus, 2009 .

Dynamic Alignment-Free and Reference-Free Read Compression

Faraz Hach, Jens Stoye, Roland Wittler, 2018, J. Comput. Biol..

Repeat-aware Comparative Genome Assembly

Jens Stoye, Peter Husemann, J. Stoye, 2010, GCB.

Faster Jumbled Indexing for Binary Run-Length Encoded Strings

Luis Antonio Brasil Kowada, Jens Stoye, Travis Gagie, 2017 .

On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2008, RECOMB-CG.

Counting All DCJ Sorting Scenarios

Jens Stoye, Marília D. V. Braga, J. Stoye, 2009, RECOMB-CG.

BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry

Jens Stoye, Mathias Wilhelm, Karsten Niehaus, 2014, Bioinform..

Suffix Tree Construction in RAM (1997; Farach-Colton)

Jens Stoye, 2008 .

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

Wolfgang Gerlach, Jens Stoye, Alexander Goesmann, 2009, BMC Bioinformatics.

Corrigendum: Updating benchtop sequencing performance comparison

Jens Stoye, Alexander Goesmann, Arndt von Haeseler, 2013, Nature Biotechnology.

Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, Germany, October 4-6, 2004

Robert Giegerich, Jens Stoye, 2004, German Conference on Bioinformatics.

Rose: generating sequence families

Folker Meyer, Jens Stoye, Dirk Evers, 1998, Bioinform..

Finding Nested Common Intervals Efficiently

Jens Stoye, Guillaume Blin, David Faye, 2010, J. Comput. Biol..

Proceedings of the 13th Workshop on Algorithms in Bioinformatics (WABI2013)

Jens Stoye, Aaron Darling, 2013 .

HP Distance Via Double Cut and Join Distance

Jens Stoye, Anne Bergeron, Julia Mixtacki, 2008, CPM.

Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment

Jens Stoye, Sören W. Perrey, J. Stoye, 1996 .

Computing the rearrangement distance of natural genomes pdf

Daniel Doerr, Jens Stoye, Marília D. V. Braga, 2020, RECOMB.

Swiftly Computing Center Strings

Jens Stoye, Katharina Jahn, Sebastian Böcker, 2010, WABI.

Searching and inferring colorful topological motifs in vertex-colored graphs

Jens Stoye, Marco A. Stefanes, Eloi Araujo, 2020, J. Comb. Optim..

Approximating the DCJ distance of balanced genomes in linear time

Jens Stoye, Pedro Feijão, Diego P. Rubert, 2017, Algorithms for Molecular Biology.

Computing the family-free DCJ similarity

Jens Stoye, Edna Ayako Hoshino, Marília D. V. Braga, 2018, BMC Bioinformatics.

Benchmarking tools for the alignment of functional noncoding DNA

Jens Stoye, Michael B. Eisen, Casey M. Bergman, 2004, BMC Bioinformatics.

On the Family-Free DCJ Distance

Jens Stoye, Pedro Feijão, Marília D. V. Braga, 2014, WABI.

A Unified Approach for Reconstructing Ancient Gene Clusters

Jens Stoye, Roland Wittler, J. Stoye, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Efficient implementation of lazy suffix trees

Robert Giegerich, Jens Stoye, Stefan Kurtz, 2003, Softw. Pract. Exp..

Algorithmic complexity of protein identification: combinatorics of weighted strings

Thomas Erlebach, Jens Stoye, Zsuzsanna Lipták, 2004, Discret. Appl. Math..

Pan-Genome Storage and Analysis Techniques.

Jens Stoye, Guillaume Holley, Tina Zekic, 2018, Methods in molecular biology.

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

Daniela Bartels, Folker Meyer, Jens Stoye, 2005, Bioinform..

Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)

Jens Stoye, Michael Sammeth, Dag Harmsen, 2005, WABI.

Proceedings of the German Conference on Bioinformatics (GCB 2000), Heidelberg, October 5-7, 2000

Jens Stoye, Erich Bornberg-Bauer, Ursula Rost, 2000, German Conference on Bioinformatics.

Computation of Median Gene Clusters

Jens Stoye, Katharina Jahn, Sebastian Böcker, 2008, RECOMB.

The SYSTERS protein sequence cluster set

Martin Vingron, Jens Stoye, Antje Krause, 2000, Nucleic Acids Res..

The SYSTERS Protein Family Webserver

Martin Vingron, Jens Stoye, Hannes Luz, 2002 .

Detecting Repeat Families in Incompletely Sequenced Genomes

Jens Stoye, José Augusto Amgarten Quitzau, J. Stoye, 2008, WABI.

Gecko and GhostFam

Jens Stoye, Thomas Schmidt, J. Stoye, 2007 .

The Potential of Family-Free Genome Comparison

Daniel Doerr, Jens Stoye, Cédric Chauve, 2013, Models and Algorithms for Genome Evolution.

Digital extractor: analysis of digital differential display output

Jens Stoye, Jürgen Albert, Michael Sammeth, 2003, Bioinform..

Genomic distance under gene substitutions

Jens Stoye, Raphael Machado, Marília D. V. Braga, 2011, BMC Bioinformatics.

Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation

Jens Stoye, Robert Warren, Marília D. V. Braga, 2011, J. Comput. Biol..

Sorting Linear Genomes with Rearrangements and Indels

Jens Stoye, Marilia D. V. Braga, J. Stoye, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Algorithmic Complexity of Protein Identification: Searching in Weighted Strings

Thomas Erlebach, Jens Stoye, Zsuzsanna Lipták, 2002, IFIP TCS.

Suboptimal Local Alignments Across Multiple Scoring Schemes

Jens Stoye, Christoph Dieterich, Morris Michael, 2004, WABI.

Rearrangement Models and Single-Cut Operations

Jens Stoye, Paul Medvedev, J. Stoye, 2009, RECOMB-CG.

On the family-free DCJ distance and similarity

Jens Stoye, Pedro Feijão, Marília D. V. Braga, 2015, Algorithms for Molecular Biology.

Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning

Paola Bonizzoni, Yuri Pirola, Jens Stoye, 2021, AlCoB.

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

Gunnar Rätsch, Jens Stoye, Quaid Morris, 2021, PLoS Comput. Biol..

Detecting high-scoring local alignments in pangenome graphs

Faraz Hach, Jens Stoye, Sven Rahmann, 2021, Bioinform..

Computing the Rearrangement Distance of Natural Genomes

Daniel Doerr, Jens Stoye, Marília D. V. Braga, 2021, J. Comput. Biol..

Gecko and GhostFam: rigorous and efficient gene cluster detection in prokaryotic genomes.

Jens Stoye, Thomas Schmidt, 2007, Methods in molecular biology.

Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

Jens Stoye, Alexander Goesmann, Dag Harmsen, 2012, PloS one.

Identifying gene clusters by discovering common intervals in indeterminate strings

Daniel Doerr, Jens Stoye, Katharina Jahn, 2014, BMC Genomics.

Finding Maximal Pairs with Bounded Gap

Jens Stoye, Christian N. S. Pedersen, Gerth Stølting Brodal, 1999 .

GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers

Jens Stoye, Alexander Goesmann, Stefan P. Albaum, 2014, PloS one.

Algorithms for Finding Gene

Jens Stoye, J. Stoye, ClustersSte en Heber, 2001 .

On Parsimony Haplotyping

Franz Kummert, Jens Stoye, Gerhard Sagerer, 2008 .

The European conference on computational biology.

Jens Stoye, Steffen Heber, 2003, Drug discovery today.

On Common Intervals with Errors

Jens Stoye, Cedric Chauve, Sven Rahmann, 2006 .

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data

Daniel Doerr, Jens Stoye, Tizian Schulz, 2018, BMC Genomics.

A space efficient representation for sparse de Bruijn subgraphs

Jens Stoye, José Augusto Amgarten Quitzau, 2008 .

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Alexander Sczyrba, Andreas Keller, Christian Drosten, 2020, Cell.

Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment

Jens Stoye, Andreas W. M. Dress, Sören W. Perrey, 1997 .

GISMO—gene identification using a support vector machine for ORF classification

Folker Meyer, Jens Stoye, Tim W. Nattkemper, 2006, Nucleic acids research.

Suffix Tree Construction and Storage with Limited Main Memory

Jens Stoye, Klaus-Bernd Schrmann, 2003 .

Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants

Daniel Doerr, Jens Stoye, Diego P. Rubert, 2020, BMC Genomics.

Online Abelian Pattern Matching

Jens Stoye, Sven Rahmann, Tahir Ejaz, 2008 .

Finding approximate gene clusters with Gecko 3

Jens Stoye, Katharina Jahn, Manja Marz, 2016, Nucleic acids research.

A Unified Approach for Reconstructing Ancient Gene Clusters

Jens Stoye, Roland Wittler, J. Stoye, 2009, TCBB.

Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.

Andreas Tauch, Jens Stoye, Robert A Edwards, 2008, Journal of biotechnology.