Jens Stoye

Possui mestrado em Informatics in the Natural Sciences pela Bielefeld University(1995), doutorado em Naturwissenschaftliche Informatik pela Bielefeld University(1997), pós-doutorado pela Bielefeld University(1997), pós-doutorado pela University of California Davis(1998) e pós-doutorado pela Deutsches Krebsforschungszentrum(2001). Atualmente é Full Professor "Genome Informatics" da Bielefeld University, Membro de corpo editorial da IEEE/ACM Transactions on Computational Biology and Bioinformatics (Print) e Membro de comitê assessor da Deutscher Akademischer Austauschdienst. Tem experiência na área de Ciência da Computação. Atuando principalmente nos seguintes temas:affix trees.

Informações coletadas do Lattes em 04/11/2022

Acadêmico

Formação acadêmica

Doutorado em Naturwissenschaftliche Informatik

1995 - 1997

Bielefeld University
Título: Divide-and-Conquer Multiple Sequence Alignment
Orientador: Andreas Dress and Robert Giegerich
Bolsista do(a): .

Mestrado em Informatics in the Natural Sciences

1990 - 1995

Bielefeld University
Orientador: Robert Giegerich
Coorientador: Enno Ohlebusch. Palavras-chave: affix trees.Grande área: Ciências Exatas e da Terra / Área: Ciência da Computação / Subárea: stringology.

Pós-doutorado

1998 - 2001

Pós-Doutorado. , Deutsches Krebsforschungszentrum. , Bolsista do(a): Deutsches Krebsforschungszentrum. , Grande área: Ciências da Saúde / Área: Medicina / Subárea: Clínica Médica / Especialidade: Cancerologia. , Grande Área: Ciências Exatas e da Terra / Área: Ciência da Computação.

1997 - 1998

Pós-Doutorado. , University of California Davis. , Bolsista do(a): Deutscher Akademischer Austauschdienst, DAAD, Alemanha. , Grande área: Ciências Exatas e da Terra / Área: Ciência da Computação.

1997 - 1997

Pós-Doutorado. , Bielefeld University. , Bolsista do(a): Deutsche Forschungsgemeinschaft, DFG, Alemanha. , Grande área: Ciências Exatas e da Terra / Área: Matemática / Subárea: Structure Formation.

Idiomas

Inglês

Compreende Bem, Fala Bem, Lê Bem, Escreve Bem.

Alemão

Compreende Bem, Fala Bem, Lê Bem, Escreve Bem.

Áreas de atuação

Grande área: Ciências Exatas e da Terra / Área: Ciência da Computação.

Orientou

Linda Katharina Sundermann

ChimP -- Chimera Prediction with the Jumping Alignment Algorithm; 2014; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Svea Kokott

Comparison of Insertion Predictions using an Error-Tolerant Similarity Model; 2014; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Tina Zekic

Reconstructing Modular Phage Recombinations with the Crisscross Jumping Alignment Algorithm; 2014; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Christian Bender

Highspeed calculation of isotopic distributions using OpenCL and Fourier transformations; 2014; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Kai Bernd Stadermann

Integration of differential expression analysis capabilities into a Viewer for Next Generation Sequencing Data utilizing baySeq, DESeq and an own approach; 2013; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Sascha McSporran

Effiziente Kompression von Biosequenzen; 2013; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Andreas Klötgen

Netzwerkbasierte Analysen genetischer Assoziationen zur Identifikation krankheitsrelevanter biologischer Prozesse; 2013; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Henner Sudek

Multiple genome comparison based on overlap regions of pairwise local alignments; 2013; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Nina Luhmann

Detection of small inserted DNA fragments at deletion break-points using paired-end sequencing data; 2013; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Jennifer He

Funktionelle Annotation von Polymorphismen; 2013; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Maureen Smith

Unraveling Overlapping Insertions with Agglomerative Clustering; 2013; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Yvonne Nelly Herrmann

Comparison of Metagenomic Data by identifying enriched Pathways in Metabolic Networks; 2012; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Alexander Berhörster

Integration und Analyse von Genotyp-Phänotyp-Assoziationsdaten; 2012; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Jasmin Straube

Biomarker discovery for personalized treatment -- Mining complex, multidimensional and heterogeneous data sets; 2012; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Mathias Wilhelm

Computational Mass Spectrometry Method Development and Clinical Application; 2011; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Pina Krell

Segment-based (reference-) alignment of short reads -- Profiling the T-cell receptor (beta chain) repertoire using next-generation sequencing; 2010; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Eyla Willing

The Double Cut and Join Model with Insertions and Deletions; 2010; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Rolf Hilker

Unified Model of Genomic Distance Computation; 2010; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Daniel Dörr

Non-additive Substitution Rate Functions in Distance-Based Phylogenetic Reconstructions; 2010; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Niels Kleinbölting

Protein Clustering using an Ant Colony Layouting approach; 2009; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Coorientador: Jens Stoye;

Katrin Rademacher

The interaction of skipped exons with variable flanking splice sites; 2009; Dissertação (Mestrado em Naturwissenschaftliche Informatik) - Bielefeld University,; Coorientador: Jens Stoye;

Christina Ander

Erweiterung des Sequence Analysis and Management Systems (SAMS); 2009; Dissertação (Mestrado em Bioinformatik und Genomforschung) - Bielefeld University,; Orientador: Jens Stoye;

Martin Mascher

POPSEQ: Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing; 2014; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Nils Hoffmann

Computational Methods for High-Throughput Metabolomics; 2014; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Christina Ander

Bioinformatic methods for the analysis and comparison of metagenomes and metatranscriptomes; 2014; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Jochen Blom

Comparative genomics on gene and single nucleotide level; 2013; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Wolfgang Gerlach

Taxonomic Classification of Metagenomic Sequences; 2012; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Patrick Schwientek

Genomics and Transcriptomics of the Industrial Acarbose Producer Actinoplanes sp; SE50/110; 2012; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Alexander Bunkowski

MCC-IMS data analysis using automated spectra processing and explorative visualisation methods; 2012; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Martha Zakrzewski

Development of computational methods for the analysis or metagenome and metatranscriptome data; 2012; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Peter Husemann

Bioinformatic Approaches for Genome Finishing; 2011; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Tobias Wittkop

Clustering biological data by unraveling hidden transitive substructures; 2010; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Coorientador: Jens Stoye;

Roland Wittler

Phylogeny-based analysis of gene clusters; 2010; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

José Augusto Amgarten Quitzau

Biological applications for de Bruijn subgraphs and interval group testing; 2010; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Katharina Jahn

Approximate Common Intervals Based Gene Cluster Models; 2010; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Constantin Bannert

Flexible protein annotation with sequence- and secondary structure information; 2009; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Epameinondas Fritzilas

Combinatorial aspects of low-rank matrix factorization and two applications in bioinformatics; 2009; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Coorientador: Jens Stoye;

Travis Gagie

New algorithms and lower bounds for sequential-access data compression; 2009; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Coorientador: Jens Stoye;

Inke Herms

Probabilistic arithmetic automata: applications of a stochastic computational framework in biological sequence analysis; 2009; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Coorientador: Jens Stoye;

Sebastian Oehm

Comparing organisms on the level of metabolism; 2009; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Heiko Neuweger

MeltDB: a software platform for the analysis and integration of metabolomics experiment data; 2009; Tese (Doutorado em Naturwissenschaftliche Informatik) - Bielefeld University,; Orientador: Jens Stoye;

Produções bibliográficas

BRAGA, MARILIA ; STOYE, JENS . Sorting linear genomes with rearrangements and indels. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Print) , v. 99, p. 1-1, 2014.
SCHWIENTEK, PATRICK ; NESHAT, ARMIN ; KALINOWSKI, JÖRN ; KLEIN, ANDREAS ; RÜCKERT, CHRISTIAN ; SCHNEIKER-BEKEL, SUSANNE ; WENDLER, SERGEJ ; STOYE, JENS ; PÜHLER, ALFRED . Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5--ends of primary transcripts. Journal of Biotechnology , v. 190, p. 85-95, 2014.
JAKOBI, TOBIAS ; BRINKROLF, KARINA ; TAUCH, ANDREAS ; NOLL, THOMAS ; STOYE, JENS ; PÜHLER, ALFRED ; GOESMANN, ALEXANDER . Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology , v. 190, p. 64-75, 2014.
DOERR, DANIEL ; STOYE, JENS ; BÖCKER, SEBASTIAN ; JAHN, KATHARINA . Identifying gene clusters by discovering common intervals in indeterminate strings. BMC Genomics , v. 15, p. S2, 2014.
JÜNEMANN, SEBASTIAN ; PRIOR, KAROLA ; ALBERSMEIER, ANDREAS ; ALBAUM, STEFAN ; KALINOWSKI, JÖRN ; GOESMANN, ALEXANDER ; STOYE, JENS ; HARMSEN, DAG . GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers. Plos One , v. 9, p. e107014, 2014.
LECHNER, MARCUS ; HERNANDEZ-ROSALES, MARIBEL ; DOERR, DANIEL ; WIESEKE, NICOLAS ; THÉVENIN, ANNELYSE ; STOYE, JENS ; HARTMANN, ROLAND K. ; PROHASKA, SONJA J. ; STADLER, PETER F. . Orthology Detection Combining Clustering and Synteny for Very Large Datasets. Plos One , v. 9, p. e105015, 2014.
HILKER, R. ; STADERMANN, K. B. ; DOPPMEIER, D. ; KALINOWSKI, J. ; STOYE, J. ; STRAUBE, J. ; WINNEBALD, J. ; GOESMANN, A. . ReadXplorer--visualization and analysis of mapped sequences. Bioinformatics (Oxford. Print) , v. 30, p. 2247-2254, 2014.
HENRICH, BIRGIT ; RUMMING, MADIS ; SCZYRBA, ALEXANDER ; VELLEUER, EUNIKE ; DIETRICH, RALF ; GERLACH, WOLFGANG ; GOMBERT, MICHAEL ; RAHN, SEBASTIAN ; STOYE, JENS ; BORKHARDT, ARNDT ; FISCHER, UTE . Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma. Plos One , v. 9, p. e92297, 2014.
HOFFMANN, N. ; WILHELM, M. ; DOEBBE, A. ; NIEHAUS, K. ; STOYE, J. . BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinformatics (Oxford. Print) , v. 30, p. 988-995, 2014.
JAHN, KATHARINA ; WINTER, SASCHA ; STOYE, JENS ; BÖCKER, SEBASTIAN . Statistics for approximate gene clusters. BMC Bioinformatics , v. 14, p. S14, 2013.
WILLING, EYLA ; ZACCARIA, SIMONE ; BRAGA, MARÍLIA DV ; STOYE, JENS . On the inversion-indel distance. BMC Bioinformatics , v. 14, p. S3, 2013.
KRELL, P. F. I. ; REUTHER, S. ; FISCHER, U. ; KELLER, T. ; WEBER, S. ; GOMBERT, M. ; SCHUSTER, F. R. ; ASANG, C. ; STEPENSKY, P. ; STRAHM, B. ; MEISEL, R. ; STOYE, J. ; BORKHARDT, A. . Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a chain CDR3 sequence associated with hepatitis-induced pathogenesis. Haematologica (Roma) , v. 98, p. 1388-1396, 2013.
SCHWIENTEK, PATRICK ; WENDLER, SERGEJ ; NESHAT, ARMIN ; EIRICH, CHRISTINA ; RÜCKERT, CHRISTIAN ; KLEIN, ANDREAS ; WEHMEIER, UDO F. ; KALINOWSKI, JÖRN ; STOYE, JENS ; PÜHLER, ALFRED . Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media. Journal of Biotechnology , v. 167, p. 166-177, 2013.
ZAKRZEWSKI, MARTHA ; BEKEL, THOMAS ; ANDER, CHRISTINA ; PÜHLER, ALFRED ; RUPP, OLIVER ; STOYE, JENS ; SCHLÜTER, ANDREAS ; GOESMANN, ALEXANDER . MetaSAMS-A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology , v. 167, p. 156-165, 2013.
ANDER, CHRISTINA ; SCHULZ-TRIEGLAFF, OLE B ; STOYE, JENS ; COX, ANTHONY J . metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics , v. 14, p. S2, 2013.
JÜNEMANN, SEBASTIAN ; SEDLAZECK, FRITZ JOACHIM ; PRIOR, KAROLA ; ALBERSMEIER, ANDREAS ; JOHN, UWE ; KALINOWSKI, JÖRN ; MELLMANN, ALEXANDER ; GOESMANN, ALEXANDER ; VON HAESELER, ARNDT ; STOYE, JENS ; HARMSEN, DAG . Updating benchtop sequencing performance comparison. Nature Biotechnology (Print) , v. 31, p. 294-296, 2013.
JÜNEMANN, SEBASTIAN ; SEDLAZECK, FRITZ JOACHIM ; PRIOR, KAROLA ; ALBERSMEIER, ANDREAS ; JOHN, UWE ; KALINOWSKI, JÖRN ; MELLMANN, ALEXANDER ; GOESMANN, ALEXANDER ; VON HAESELER, ARNDT ; STOYE, JENS ; HARMSEN, DAG . Corrigendum: Updating benchtop sequencing performance comparison. Nature Biotechnology (Print) , v. 31, p. 1148-1148, 2013.
DOERR, DANIEL ; THÉVENIN, ANNELYSE ; STOYE, JENS . Gene family assignment-free comparative genomics. BMC Bioinformatics , v. 13, p. S3, 2012.
JAHN, K. ; SUDEK, H. ; STOYE, J. . Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics , v. 13, p. S7, 2012.
HILKER, R. ; SICKINGER, C. ; PEDERSEN, C. N. S. ; STOYE, J. . UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics (Oxford. Print) , v. 28, p. 2509-2511, 2012.
HOFFMANN, NILS ; KECK, MATTHIAS ; NEUWEGER, HEIKO ; WILHELM, MATHIAS ; HÖGY, PETRA ; NIEHAUS, KARSTEN ; STOYE, JENS . Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics , v. 13, p. 214, 2012.
JÜNEMANN, SEBASTIAN ; PRIOR, KAROLA ; SZCZEPANOWSKI, RAFAEL ; HARKS, INGA ; EHMKE, BENJAMIN ; GOESMANN, ALEXANDER ; STOYE, JENS ; HARMSEN, DAG . Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing. Plos One , v. 7, p. e41606, 2012.
SCHWIENTEK, PATRICK ; SZCZEPANOWSKI, RAFAEL ; RUCKERT, CHRISTIAN ; KALINOWSKI, JORN ; KLEIN, ANDREAS ; SELBER, KLAUS ; WEHMEIER, UDO F ; STOYE, JENS ; PUHLER, ALFRED . The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics , v. 13, p. 112, 2012.
BRAGA, MARÍLIA D V ; MACHADO, RAPHAEL ; RIBEIRO, LEONARDO C ; STOYE, JENS . On the weight of indels in genomic distances. BMC Bioinformatics , v. 12, p. S13, 2011.
BRAGA, MARÍLIA D V ; MACHADO, RAPHAEL ; RIBEIRO, LEONARDO C ; STOYE, JENS . Genomic distance under gene substitutions. BMC Bioinformatics , v. 12, p. S8, 2011.
KOVÁ', JAKUB ; WARREN, ROBERT ; BRAGA, MARÍLIA D.V. ; STOYE, JENS . Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. Journal of Computational Biology , v. 18, p. 1231-1241, 2011.
BRAGA, MARÍLIA D.V. ; WILLING, EYLA ; STOYE, JENS . Double Cut and Join with Insertions and Deletions. Journal of Computational Biology , v. 18, p. 1167-1184, 2011.
WITTLER, ROLAND ; MAň ; PATTERSON, MURRAY ; STOYE, JENS . Consistency of Sequence-Based Gene Clusters. Journal of Computational Biology , v. 18, p. 1023-1039, 2011.
SCHWIENTEK, PATRICK ; SZCZEPANOWSKI, RAFAEL ; RÜCKERT, CHRISTIAN ; STOYE, JENS ; PÜHLER, ALFRED . Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology , v. 155, p. 68-77, 2011.
GERLACH, W. ; STOYE, J. . Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Research , v. 39, p. e91-e91, 2011.
HEBER, STEFFEN ; MAYR, RICHARD ; STOYE, JENS . Common Intervals of Multiple Permutations. Algorithmica , v. 60, p. 175-206, 2011.
BLOM, J. ; JAKOBI, T. ; DOPPMEIER, D. ; JAENICKE, S. ; KALINOWSKI, J. ; STOYE, J. ; GOESMANN, A. . Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics (Oxford. Print) , v. 27, p. 1351-1358, 2011.
HUFSKY, FRANZISKA ; KUCHENBECKER, LÉON ; JAHN, KATHARINA ; STOYE, JENS ; BÖCKER, SEBASTIAN . Swiftly Computing Center Strings. BMC Bioinformatics , v. 12, p. 106, 2011.
ERD'S, PÉTER L. ; SOUKUP, LAJOS ; STOYE, JENS . Balanced vertices in trees and a simpler algorithm to compute the genomic distance. Applied Mathematics Letters , v. 24, p. 82-86, 2011.
TROST, EVA ; OTT, LISA ; SCHNEIDER, JESSICA ; SCHRÖDER, JASMIN ; JAENICKE, SEBASTIAN ; GOESMANN, ALEXANDER ; HUSEMANN, PETER ; STOYE, JENS ; DORELLA, FERNANDA ; ROCHA, FLAVIA ; DE CASTRO SOARES, SIOMAR ; D'AFONSECA, VÍVIAN ; MIYOSHI, ANDERSON ; RUIZ, JERONIMO ; SILVA, ARTUR ; AZEVEDO, VASCO ; BURKOVSKI, ANDREAS ; GUISO, NICOLE ; JOIN-LAMBERT, OLIVIER F ; KAYAL, SAMER ; TAUCH, ANDREAS . 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. BMC Genomics , v. 11, p. 728, 2010.
BERGERON, ANNE ; MEDVEDEV, PAUL ; STOYE, JENS . Rearrangement Models and Single-Cut Operations. Journal of Computational Biology , v. 17, p. 1213-1225, 2010.
BLIN, GUILLAUME ; FAYE, DAVID ; STOYE, JENS . Finding Nested Common Intervals Efficiently. Journal of Computational Biology , v. 17, p. 1183-1194, 2010.
BRAGA, MARÍLIA D.V. ; STOYE, JENS . The Solution Space of Sorting by DCJ. Journal of Computational Biology , v. 17, p. 1145-1165, 2010.
WITTKOP, TOBIAS ; EMIG, DOROTHEA ; LANGE, SITA ; RAHMANN, SVEN ; ALBRECHT, MARIO ; MORRIS, JOHN H ; BÖCKER, SEBASTIAN ; STOYE, JENS ; BAUMBACH, JAN . Partitioning biological data with transitivity clustering. Nature Methods , v. 7, p. 419-420, 2010.
HUSEMANN, P. ; STOYE, J. . r2cat: synteny plots and comparative assembly. Bioinformatics (Oxford. Print) , v. 26, p. 570-571, 2010.
HUSEMANN, PETER ; STOYE, JENS . Phylogenetic comparative assembly. Algorithms for Molecular Biology , v. 5, p. 3, 2010.
GERLACH, WOLFGANG ; JÜNEMANN, SEBASTIAN ; TILLE, FELIX ; GOESMANN, ALEXANDER ; STOYE, JENS . WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics , v. 10, p. 430, 2009.
BERGERON, ANNE ; MIXTACKI, JULIA ; STOYE, JENS . A new linear time algorithm to compute the genomic distance via the double cut and join distance. Theoretical Computer Science , v. 410, p. 5300-5316, 2009.
BRUDNO, M. ; MEDVEDEV, P. ; STOYE, J. ; DE LA VEGA, F. M. . A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinformatics (Oxford. Print) , v. 25, p. 2863-2864, 2009.
STOYE, J. ; WITTLER, R. . A Unified Approach for Reconstructing Ancient Gene Clusters. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Print) , v. 6, p. 387-400, 2009.
BÖCKER, SEBASTIAN ; JAHN, KATHARINA ; MIXTACKI, JULIA ; STOYE, JENS . Computation of Median Gene Clusters. Journal of Computational Biology , v. 16, p. 1085-1099, 2009.
HOFFMANN, N. ; STOYE, J. . ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics (Oxford. Print) , v. 25, p. 2080-2081, 2009.
JAHN, KATHARINA ; STOYE, JENS . Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Informatik-Spektrum , v. 32, p. 288-300, 2009.
BEKEL, THOMAS ; HENCKEL, KOLJA ; KÜSTER, HELGE ; MEYER, FOLKER ; MITTARD RUNTE, VIRGINIE ; NEUWEGER, HEIKO ; PAARMANN, DANIEL ; RUPP, OLIVER ; ZAKRZEWSKI, MARTHA ; PÜHLER, ALFRED ; STOYE, JENS ; GOESMANN, ALEXANDER . 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. Journal of Biotechnology , v. 140, p. 3-12, 2009.
NEUWEGER, H. ; ALBAUM, S. P. ; DONDRUP, M. ; PERSICKE, M. ; WATT, T. ; NIEHAUS, K. ; STOYE, J. ; GOESMANN, A. . MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics (Oxford. Print) , v. 24, p. 2726-2732, 2008.
KRAUSE, LUTZ ; DIAZ, NARYTTZA N. ; EDWARDS, ROBERT A. ; GARTEMANN, KARL-HEINZ ; KRÖMEKE, HOLGER ; NEUWEGER, HEIKO ; PÜHLER, ALFRED ; RUNTE, KAI J. ; SCHLÜTER, ANDREAS ; STOYE, JENS ; SZCZEPANOWSKI, RAFAEL ; TAUCH, ANDREAS ; GOESMANN, ALEXANDER . Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. Journal of Biotechnology , v. 136, p. 91-101, 2008.
OEHM, S. ; GILBERT, D. ; TAUCH, A. ; STOYE, J. ; GOESMANN, A. . Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Research , v. 36, p. W433-W437, 2008.
SCHÜRMANN, KLAUS-BERND ; STOYE, JENS . Counting suffix arrays and strings. Theoretical Computer Science , v. 395, p. 220-234, 2008.
KRAUSE, L. ; DIAZ, N. N. ; GOESMANN, A. ; KELLEY, S. ; NATTKEMPER, T. W. ; ROHWER, F. ; EDWARDS, R. A. ; STOYE, J. . Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research , v. 36, p. 2230-2239, 2008.
MELLMANN, ALEXANDER ; WENIGER, THOMAS ; BERSSENBRÜGGE, CHRISTOPH ; ROTHGÄNGER, JÖRG ; SAMMETH, MICHAEL ; STOYE, JENS ; HARMSEN, DAG . Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms. BMC Microbiology (Online) , v. 7, p. 98, 2007.
DIDIER, GILLES ; SCHMIDT, THOMAS ; STOYE, JENS ; TSUR, DEKEL . Character sets of strings. Journal of Discrete Algorithms (Print) , v. 5, p. 330-340, 2007.
SCHÜRMANN, KLAUS-BERND ; STOYE, JENS . An incomplex algorithm for fast suffix array construction. Software, Practice & Experience (Print) , v. 37, p. 309-329, 2007.
KRAUSE, L. ; MCHARDY, A. C. ; NATTKEMPER, T. W. ; PUHLER, A. ; STOYE, J. ; MEYER, F. . GISMO--gene identification using a support vector machine for ORF classification. Nucleic Acids Research , v. 35, p. 540-549, 2006.
SAMMETH, MICHAEL ; STOYE, JENS . Comparing Tandem Repeats with Duplications and Excisions of Variable Degree. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Print) , v. 3, p. 395-407, 2006.
BERGERON, ANNE ; STOYE, JENS . On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. Journal of Computational Biology , v. 13, p. 1340-1354, 2006.
KRAUSE, L. ; DIAZ, N. N. ; BARTELS, D. ; EDWARDS, R. A. ; PUHLER, A. ; ROHWER, F. ; MEYER, F. ; STOYE, J. . Finding novel genes in bacterial communities isolated from the environment. Bioinformatics (Oxford. Print) , v. 22, p. e281-e289, 2006.
BERGERON, ANNE ; MIXTACKI, JULIA ; STOYE, JENS . On Sorting by Translocations. Journal of Computational Biology , v. 13, p. 567-578, 2006.
RASMUSSEN, KIM R. ; STOYE, JENS ; MYERS, EUGENE W. . Efficient -Gram Filters for Finding All -Matches over a Given Length. Journal of Computational Biology , v. 13, p. 296-308, 2006.
SAMMETH, M. ; GRIEBEL, T. ; TILLE, F. ; STOYE, J. . Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinformatics (Oxford. Print) , v. 22, p. 889-890, 2006.
BARTELS, D. ; KESPOHL, S. ; ALBAUM, S. ; DRUKE, T. ; GOESMANN, A. ; HEROLD, J. ; KAISER, O. ; PUHLER, A. ; PFEIFFER, F. ; RADDATZ, G. ; STOYE, J. ; MEYER, F. ; SCHUSTER, S. C. . BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics (Oxford. Print) , v. 21, p. 853-859, 2005.
KRAUSE, ANTJE ; STOYE, JENS ; VINGRON, MARTIN . Large Scale Hierarchical Clustering of Protein Sequences. BMC Bioinformatics , v. 6, p. 15, 2005.
GUSFIELD, DAN ; STOYE, JENS . Linear time algorithms for finding and representing all the tandem repeats in a string. Journal of Computer and System Sciences (Print) , v. 69, p. 525-546, 2004.
CIELIEBAK, MARK ; ERLEBACH, THOMAS ; LIPTÁK, ZSUZSANNA ; STOYE, JENS ; WELZL, EMO . Algorithmic complexity of protein identification: combinatorics of weighted strings. Discrete Applied Mathematics , v. 137, p. 27-46, 2004.
POLLARD, DANIEL A ; BERGMAN, CASEY M ; STOYE, JENS ; CELNIKER, SUSAN E ; EISEN, MICHAEL B . Benchmarking Tools for the Alignment of Functional Noncoding DNA. BMC Bioinformatics , v. 5, p. 6, 2004.
POLLARD, DA ; BERGMAN, CM ; STOYE, J ; CELNIKER, SE ; EISEN, MB . Correction: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics , v. 5, p. 73, 2004.
SAMMETH, M. ; MORGENSTERN, B. ; STOYE, J. . Divide-and-conquer multiple alignment with segment-based constraints. Bioinformatics (Oxford. Print) , v. 19, p. ii189-ii195, 2003.
GIEGERICH, R. ; KURTZ, S. ; STOYE, J. . Efficient implementation of lazy suffix trees. Software, Practice & Experience (Print) , v. 33, p. 1035-1049, 2003.
SAMMETH, M. ; ROTHGANGER, J. ; ESSER, W. ; ALBERT, J. ; STOYE, J. ; HARMSEN, D. . QAlign: quality-based multiple alignments with dynamic phylogenetic analysis. Bioinformatics (Oxford. Print) , v. 19, p. 1592-1593, 2003.
SPANG, RAINER ; REHMSMEIER, MARC ; STOYE, JENS . A Novel Approach to Remote Homology Detection: Jumping Alignments. Journal of Computational Biology , v. 9, p. 747-760, 2002.
BERGERON, A. ; HEBER, S. ; STOYE, J. . Common intervals and sorting by reversals: a marriage of necessity. Bioinformatics (Oxford. Print) , v. 18, p. S54-S63, 2002.
STOYE, JENS ; GUSFIELD, DAN . Simple and flexible detection of contiguous repeats using a suffix tree. Theoretical Computer Science , v. 270, p. 843-856, 2002.
REINERT, K. ; STOYE, J. ; WILL, T. . An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinformatics (Oxford. Print) , v. 16, p. 808-814, 2000.
HEBER, STEFFEN ; STOYE, JENS ; FROHME, MARCUS ; HOHEISEL, JÖRG ; VINGRON, MARTIN . Contig Selection in Physical Mapping. Journal of Computational Biology , v. 7, p. 395-408, 2000.
DRESS, A. ; MORGENSTERN, B. ; STOYE, J. . The number of standard and of effective multiple alignments. Applied Mathematics Letters , v. 11, p. 43-49, 1998.
STOYE, JENS . Multiple sequence alignment with the divide-and-conquer method. Gene (Amsterdam) , v. 211, p. GC45-GC56, 1998.
STOYE, J. ; EVERS, D. ; MEYER, F. . Rose: generating sequence families. Bioinformatics (Oxford. Print) , v. 14, p. 157-163, 1998.
STOYE, JENS ; MOULTON, VINCENT ; DRESS, ANDREAS W.M. . DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Bioinformatics (Oxford. Print) , v. 13, p. 625-626, 1997.
BRINKMANN, G. ; DRESS, A. W. M. ; PERREY, S. W. ; STOYE, J. . Two applications of the divide&conquer principle in the molecular sciences. Mathematical Programming , v. 79, p. 71-97, 1997.
STOYE, J. ; PERREY, S.W. ; DRESS, A.W.M. . Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment. Applied Mathematics Letters , v. 10, p. 67-73, 1997.
TÖNGES, UDO ; PERREY, SÖREN W. ; STOYE, JENS ; DRESS, ANDREAS W.M. . A general method for fast multiple sequence alignment. Gene (Amsterdam) , v. 172, p. GC33-GC41, 1996.
DARLING, A. ; Stoye, J. . Algorithms in Bioinformatics. 1. ed. , 2013.
KARKKAINEN, J. ; Stoye, J. . Combinatorial Pattern Matching. 1. ed. , 2012.
GIEGERICH, R. ; Stoye, J. . Proceedings of the German Conference on Bioinformatics, GCB 2004. 1. ed. , 2004.
BORNBERG-BAUER, E. ; ROST, U. ; STOYE, J ; VINGRON, M. . Proceedings of the German Conference on Bioinformatics, GCB 2000. 1. ed. , 2000.
Luhmann, Nina ; Chauve, Cedric ; Stoye, Jens ; WITTLER, ROLAND . Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2014, v. , p. 135-143.
Martinez, Fábio V. ; Feijão, Pedro ; Braga, Marília D. V. ; Stoye, Jens . On the Family-Free DCJ Distance. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2014, v. , p. 174-186.
Stoye, Jens . Suffix Tree Construction. Encyclopedia of Algorithms. 1ed.: Springer US, 2014, v. , p. 1-6.
Braga, Marília D. V. ; Chauve, Cedric ; DOERR, DANIEL ; JAHN, KATHARINA ; Stoye, Jens ; THÉVENIN, ANNELYSE ; WITTLER, ROLAND . The Potential of Family-Free Genome Comparison. Computational Biology. 1ed.: Springer London, 2013, v. 19, p. 287-307.
BERGERON, ANNE ; Stoye, Jens . The Genesis of the DCJ Formula. Computational Biology. 1ed.: Springer London, 2013, v. , p. 63-81.
GERLACH, WOLFGANG ; Stoye, Jens . Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3. Encyclopedia of Metagenomics. 1ed.: Springer New York, 2013, v. , p. 1-8.
Braga, Marília D. V. ; Stoye, Jens . Restricted DCJ-Indel Model Revisited. Lecture Notes in Computer Science. 1ed.: Springer International Publishing, 2013, v. , p. 36-46.
HOFFMANN, NILS ; Stoye, Jens . Generic Software Frameworks for GC-MS Based Metabolomics. Metabolomics. 1ed.: InTech, 2012, v. , p. 73-98.
Besenbacher, S ren ; Schwikowski, Benno ; Stoye, Jens . Indexing and Searching a Mass Spectrometry Database. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2010, v. , p. 62-76.
Braga, Marília D. V. ; WILLING, EYLA ; Stoye, Jens . Genomic Distance with DCJ and Indels. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2010, v. , p. 90-101.
Kováč ; Braga, Marília D. V. ; Stoye, Jens . The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2010, v. , p. 13-24.
HUFSKY, FRANZISKA ; KUCHENBECKER, LÉON ; JAHN, KATHARINA ; Stoye, Jens ; BÖCKER, SEBASTIAN . Swiftly Computing Center Strings. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2010, v. , p. 325-336.
WITTLER, ROLAND ; Stoye, Jens . Consistency of Sequence-Based Gene Clusters. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2010, v. , p. 252-263.
MEDVEDEV, PAUL ; Stoye, Jens . Rearrangement Models and Single-Cut Operations. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2009, v. , p. 84-97.
HUSEMANN, PETER ; Stoye, Jens . Phylogenetic Comparative Assembly. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2009, v. , p. 145-156.
Braga, Marília D. V. ; Stoye, Jens . Counting All DCJ Sorting Scenarios. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2009, v. , p. 36-47.
BLIN, GUILLAUME ; Stoye, Jens . Finding Nested Common Intervals Efficiently. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2009, v. , p. 59-69.
Stoye, Jens . Suffix Tree Construction in RAM. Encyclopedia of Algorithms. 1ed.: Springer US, 2008, v. , p. 925-928.
BERGERON, ANNE ; MIXTACKI, JULIA ; Stoye, Jens . HP Distance Via Double Cut and Join Distance. Combinatorial Pattern Matching. 1ed.: Springer Berlin Heidelberg, 2008, v. , p. 56-68.
Amgarten Quitzau, José Augusto ; Stoye, Jens . Detecting Repeat Families in Incompletely Sequenced Genomes. Algorithms in Bioinformatics. 1ed.: Springer Berlin Heidelberg, 2008, v. , p. 342-353.
BÖCKER, SEBASTIAN ; JAHN, KATHARINA ; MIXTACKI, JULIA ; Stoye, Jens . Computation of Median Gene Clusters. Research in Computational Molecular Biology. 1ed.: Springer Berlin Heidelberg, 2008, v. , p. 331-345.
BERGERON, ANNE ; MIXTACKI, JULIA ; Stoye, Jens . On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2008, v. , p. 226-240.
SCHMIDT, THOMAS ; Stoye, Jens . Gecko and GhostFam. Methods in Molecular Biology. 1ed.: Humana Press, 2007, v. , p. 165-182.
BERGERON, ANNE ; MIXTACKI, JULIA ; Stoye, Jens . A Unifying View of Genome Rearrangements. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2006, v. , p. 163-173.
BERGERON, A. ; MIXTACKI, J. ; Stoye, J. . The Inversion Distance Problem. Mathematics of Evolution and Phylogeny. 1ed.: Olivier Gascuel, 2005, v. , p. 262-290.
Bannert, Constantin ; Stoye, Jens . Protein Annotation by Secondary Structure Based Alignments (PASSTA). Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2005, v. , p. 79-90.
BERGERON, ANNE ; MIXTACKI, JULIA ; Stoye, Jens . On Sorting by Translocations. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2005, v. , p. 615-629.
SCHÜRMANN, KLAUS-BERND ; Stoye, Jens . Counting Suffix Arrays and Strings. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2005, v. , p. 55-66.
SCHÜRMANN, KLAUS-BERND ; STOYE, JENS . An Incomplex Algorithm for Fast Suffix Array Construction. Proc. of ALENEX/ANALCO 2005. 1ed.: , 2005, v. , p. 77-85.
SAMMETH, MICHAEL ; WENIGER, THOMAS ; HARMSEN, DAG ; Stoye, Jens . Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2005, v. , p. 276-290.
RASMUSSEN, KIM R. ; Stoye, Jens ; MYERS, EUGENE W. . Efficient q-Gram Filters for Finding All ε-Matches over a Given Length. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2005, v. , p. 189-203.
SCHMIDT, THOMAS ; Stoye, Jens . Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2004, v. , p. 347-358.
Michael, Morris ; Dieterich, Christoph ; Stoye, Jens . Suboptimal Local Alignments Across Multiple Scoring Schemes. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2004, v. , p. 99-110.
BERGERON, ANNE ; MIXTACKI, JULIA ; Stoye, Jens . Reversal Distance without Hurdles and Fortresses. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2004, v. , p. 388-399.
BERGERON, ANNE ; Stoye, Jens . On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2003, v. , p. 68-79.
HEBER, STEFFEN ; Stoye, Jens . Algorithms for Finding Gene Clusters. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2001, v. , p. 252-263.
HEBER, STEFFEN ; Stoye, Jens . Finding All Common Intervals of k Permutations. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 2001, v. , p. 207-218.
BRODAL, G. S. ; LYNGS , R. B. ; PEDERSEN, C. N. S. ; Stoye, J. . Finding Maximal Pairs with Bounded Gap. Matching Patterns (Journal of Discrete Algorithms). 1ed.: , 2000, v. , p. 77-104.
Giegerich, Robert ; Kurtz, Stefan ; Stoye, Jens . Efficient Implementation of Lazy Suffix Trees. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 1999, v. , p. 30-42.
Brodal, Gerth St lting ; Lyngs , Rune B. ; Pedersen, Christian N. S. ; Stoye, Jens . Finding Maximal Pairs with Bounded Gap. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 1999, v. , p. 134-149.
Stoye, Jens ; GUSFIELD, DAN . Simple and flexible detection of contiguous repeats using a suffix tree Preliminary Version. Lecture Notes in Computer Science. 1ed.: Springer Berlin Heidelberg, 1998, v. , p. 140-152.

Histórico profissional

Endereço profissional

Bielefeld University, Faculty of Technology. , Universitätsstr. 25, Schildesche, 33615 - Bielefeld, - Alemanha, Telefone: (49521) 1063852, URL da Homepage:

Experiência profissional

2014 - Atual

Deutscher Akademischer Austauschdienst

Vínculo: Membro de comitê assessor, Enquadramento Funcional:

2002 - Atual

Bielefeld University

Vínculo: Servidor Público, Enquadramento Funcional: Full Professor "Genome Informatics", Carga horária: 40, Regime: Dedicação exclusiva.

2001 - 2002

Max-Planck-Institut für Molekulare Genetik

Vínculo: Celetista, Enquadramento Funcional: Group Leader "Algorithmic Bioinformatics", Carga horária: 40, Regime: Dedicação exclusiva.