List of works - Jens Stoye

A novel approach to remote homology detection: jumping alignments

scientific article published on 01 January 2002

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

scientific article published on 24 September 2009

A unified approach for reconstructing ancient gene clusters

scientific article published in July 2009

Algorithmic complexity of protein identification: combinatorics of weighted strings

journal article from 'Discrete Applied Mathematics' published in 2004

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

scientific article published on 16 April 2020

Approximating the DCJ distance of balanced genomes in linear time.

scientific article

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

scientific article published on 28 October 2004

Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing

scientific article

Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms

scientific article

Benchmarking tools for the alignment of functional noncoding DNA

scientific article

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

scientific article published on 20 December 2013

Bioinformatics for NGS-based metagenomics and the application to biogas research.

scientific article

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

scientific article

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

scientific article

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

scientific article

Common Intervals of Multiple Permutations

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

scientific article published on 6 June 2008

Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media

Comparing tandem repeats with duplications and excisions of variable degree

scientific article published in October 2006

Computation of median gene clusters

scientific article published in August 2009

Computing the Inversion-Indel Distance

scientific article published on 21 April 2020

Computing the Rearrangement Distance of Natural Genomes

scientific article published on 30 December 2020

Computing the family-free DCJ similarity.

scientific article published on 8 May 2018

Consistency of sequence-based gene clusters

scientific article

Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing

scientific article

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

scientific article published on 01 October 2003

Double cut and join with insertions and deletions

scientific article

Dynamic Alignment-Free and Reference-Free Read Compression

scientific article published on 01 July 2018

Editorial: Computational Methods for Microbiome Analysis

scientific article published on 11 December 2020

Efficient q-gram filters for finding all epsilon-matches over a given length

scientific article

Erratum: Corrigendum: Updating benchtop sequencing performance comparison

scholarly article published in Nature Biotechnology

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

scientific article published on 30 March 2011

Family-Free Genome Comparison

scientific article published in January 2018

Finding all maximal perfect haplotype blocks in linear time

scientific article published on 10 February 2020

Finding approximate gene clusters with Gecko 3.

scientific article

Finding nested common intervals efficiently.

scientific article published in September 2010

Finding novel genes in bacterial communities isolated from the environment

article

Flexible metagenome analysis using the MGX framework

scientific article published on 24 April 2018

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers

scientific article

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

scientific article published on 14 December 2006

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

scientific article published in January 2007

Gene family assignment-free comparative genomics

scientific article

Genomic distance under gene substitutions

scientific article

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

scientific article published on 8 May 2018

HASLR: Fast Hybrid Assembly of Long Reads

scientific article published on 25 July 2020

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach

scientific article published on 17 December 2019

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma

scientific article published on 10 February 2016

Identifying Maximal Perfect Haplotype Blocks

Identifying gene clusters by discovering common intervals in indeterminate strings

scientific article published on 17 October 2014

Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts

scientific article published on 15 March 2014

Indexing and Searching a Mass Spectrometry Database

Large scale hierarchical clustering of protein sequences

scientific article

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

scientific article

MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets

scientific article published on 29 September 2012

Multiple genome comparison based on overlap regions of pairwise local alignments

scientific article

Multiple sequence alignment with the divide-and-conquer method ⬇️

scientific article published on May 12, 1998

Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma

scientific article

NFDI4Microbiota – national research data infrastructure for microbiota research

New Genome Similarity Measures based on Conserved Gene Adjacencies

scientific article published on June 2017

Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a β chain CDR3 sequence associated with hepatitis-induced pathogenesis.

scientific article published on 28 May 2013

On sorting by translocations

scientific article published in March 2006

On the family-free DCJ distance and similarity

scientific article

On the inversion-indel distance

scientific article

On the similarity of sets of permutations and its applications to genome comparison

scientific article published in September 2006

On the weight of indels in genomic distances

scientific article

Orthology detection combining clustering and synteny for very large datasets

scientific article

Pan-Genome Storage and Analysis Techniques

scientific article

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

scientific article published on 17 January 2006

Partitioning biological data with transitivity clustering

scientific article

Phylogenetic classification of short environmental DNA fragments

scientific article (publication date: April 2008)

Phylogenetic comparative assembly

scientific article

REPuter: the manifold applications of repeat analysis on a genomic scale ⬇️

scientific article (publication date: 15 November 2001)

ReadXplorer--visualization and analysis of mapped sequences

scientific article published on 30 April 2014

Rearrangement models and single-cut operations

scientific article published in September 2010

Restricted DCJ model: rearrangement problems with chromosome reincorporation

scientific article

Rose: generating sequence families ⬇️

scientific article published on January 1, 1998

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

scientific article published on 15 March 2018

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology

scientific article published on 23 April 2011

Sorting Linear Genomes with Rearrangements and Indels

scientific article published on May 2015

Statistics for approximate gene clusters

scientific article

Swiftly computing center strings ⬇️

scientific article

Taxonomic classification of metagenomic shotgun sequences with CARMA3.

scientific article

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

scientific article published on 20 June 2008

The European conference on computational biology

scientific article published in February 2003

The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies

scientific article

The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence ⬇️

scientific article

The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.

scientific article

The solution space of sorting by DCJ.

scientific article published in September 2010

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

scientific article published on 18 July 2012

Updating benchtop sequencing performance comparison

scientific article published in April 2013

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

scientific article

Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium

scientific article published on 23 January 2019

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

scientific article

r2cat: synteny plots and comparative assembly

scientific article published on 16 December 2009

List of works by Jens Stoye

A novel approach to remote homology detection: jumping alignments

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

A unified approach for reconstructing ancient gene clusters

Algorithmic complexity of protein identification: combinatorics of weighted strings

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

Approximating the DCJ distance of balanced genomes in linear time.

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

Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing

Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms

Benchmarking tools for the alignment of functional noncoding DNA

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

Bioinformatics for NGS-based metagenomics and the application to biogas research.

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

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

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

Common Intervals of Multiple Permutations

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

Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media

Comparing tandem repeats with duplications and excisions of variable degree

Computation of median gene clusters

Computing the Inversion-Indel Distance

Computing the Rearrangement Distance of Natural Genomes

Computing the family-free DCJ similarity.

Consistency of sequence-based gene clusters

Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing

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

Double cut and join with insertions and deletions

Dynamic Alignment-Free and Reference-Free Read Compression

Editorial: Computational Methods for Microbiome Analysis

Efficient q-gram filters for finding all epsilon-matches over a given length

Erratum: Corrigendum: Updating benchtop sequencing performance comparison

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

Family-Free Genome Comparison

Finding all maximal perfect haplotype blocks in linear time

Finding approximate gene clusters with Gecko 3.

Finding nested common intervals efficiently.

Finding novel genes in bacterial communities isolated from the environment

Flexible metagenome analysis using the MGX framework

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers

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

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

Gene family assignment-free comparative genomics

Genomic distance under gene substitutions

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

HASLR: Fast Hybrid Assembly of Long Reads

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma

Identifying Maximal Perfect Haplotype Blocks

Identifying gene clusters by discovering common intervals in indeterminate strings

Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts

Indexing and Searching a Mass Spectrometry Database

Large scale hierarchical clustering of protein sequences

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

MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets

Multiple genome comparison based on overlap regions of pairwise local alignments

Multiple sequence alignment with the divide-and-conquer method ⬇️

Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma

NFDI4Microbiota – national research data infrastructure for microbiota research

New Genome Similarity Measures based on Conserved Gene Adjacencies

Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a β chain CDR3 sequence associated with hepatitis-induced pathogenesis.

On sorting by translocations

On the family-free DCJ distance and similarity

On the inversion-indel distance

On the similarity of sets of permutations and its applications to genome comparison

On the weight of indels in genomic distances

Orthology detection combining clustering and synteny for very large datasets

Pan-Genome Storage and Analysis Techniques

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

Partitioning biological data with transitivity clustering

Phylogenetic classification of short environmental DNA fragments

Phylogenetic comparative assembly

REPuter: the manifold applications of repeat analysis on a genomic scale ⬇️

ReadXplorer--visualization and analysis of mapped sequences

Rearrangement models and single-cut operations

Restricted DCJ model: rearrangement problems with chromosome reincorporation

Rose: generating sequence families ⬇️

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology

Sorting Linear Genomes with Rearrangements and Indels