Prof. Dr. Jens Stoye

Education:

• 10/1991-05/1995 Diploma studies Informatics in the Natural Sciences, Faculty of Technology, Bielefeld University. Thesis title: Affix Trees (advisor: Robert Giegerich)
• 05/1995-01/1997 PhD studies, Faculty of Technology, Bielefeld University. Thesis title: Divide-and-Conquer Multiple Sequence Alignment (advisors: Andreas Dress, Robert Giegerich)

Employment:

• 05/1995-02/1997 Staff scientist at the Interdisciplinary Research Center on Structure Formation (FSPM), Bielefeld University
• 03/1997-08/1997 Postdoc at the DFG Research Training Group Structure Formation, FSPM, Bielefeld University
• 09/1997-08/1998 Postdoc (DAAD-funded) at the Department of Computer Science, University of California at Davis
• 09/1998-02/2001 Postdoc at the Theoretical Bioinformatics division, German Cancer Research Center (DKFZ) Heidelberg
• 03/2001-02/2002 Head of junior research group Algorithmic Bioinformatics at the Max Planck Institute for Molecular Genetics, Berlin
• since 03/2002 Full university professor (C4) for Genome Informatics, Faculty of Technology, Bielefeld University

Academic service:

• since 01/2004 Associate editor of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
• 01/2010-10/2013 Associate editor of BMC Bioinformatics
• 02/2019-11/2020 Section Editor "Sequence Analysis" of BMC Bioinformatics
• since 04/2019 Editorial board member of NAR Genomics and Bioinformatics
• since 11/2020 Senior Editorial board member of BMC Bioinformatics
• since 04/2021 Editor "Computational Molecular Biology" of Discrete Applied Mathematics

Theses advised (by end of 2024):

• 58 Bachelor Theses
• 71 Master and Diploma Theses
• 36 PhD Theses

Member of scientific advisory boards:

• 12/2019-11/2023 SeqDigger – Search engine for genomic sequencing data (ANR project)
• 01/2021-06/2024 OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon (EU H2020-WIDESPREAD-2020-5 project)

Member of conference steering committees:

• since 09/2012 Workshop on Algorithms in Bioinformatics (WABI)
• 10/2014-11/2022 Bioinformatics Research and Education Workshop (BREW)

Member of conference program committees:

• GCB: 2000 (co-chair), 2004 (co-chair), 2010, 2011, 2012, 2013, 2014
• WABI: 2002, 2003, 2004, 2005, 2007, 2008, 2009, 2010, 2011, 2012, 2013 (co-chair), 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022
• ISMB: 2003, 2004, 2009, 2010, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022
• RECOMB: 2004, 2006, 2008, 2009, 2012, 2017, 2018, 2019, 2020, 2021, 2022, 2023
• ECCB: 2004, 2005, 2009, 2012, 2013, 2014, 2015, 2016, 2017, 2019, 2020, 2021
• RECOMB-CG: 2005, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 (co-chair), 2016, 2017, 2018, 2019
• IWBRA/ISBRA: 2006, 2007, 2008, 2009, 2010, 2011
• CPM: 2006, 2010, 2012 (co-chair), 2013, 2014, 2015, 2019
• SPIRE: 2006, 2010, 2011, 2017, 2020, 2021
• ALENEX: 2007
• IEEE BIBM: 2007, 2013, 2019
• SHORT-SIG/HiTSeq: 2009 (co-chair), 2010 (co-chair), 2011 (co-chair), 2017
• LATA: 2011, 2012, 2017
• ACM-BCB: 2011, 2012, 2013, 2019
• RECOMB-Seq: 2012, 2013, 2016
• ESA: 2012
• RECOMB-AB: 2012
• Others: CompLife 2005, ISBB 2006, ICCABS 2010, ITMAB 2011, FAW-AAIM 2013, BSB 2013, BSB 2018, APBC 2019, ITAT 2021

Member of conference organizing committees:

• GCB: 2000, 2004, 2014 (chair), 2024 (co-chair)

Best paper award:

• CPM 2008: HP Distance via Double Cut and Join (A. Bergeron, J. Mixtacki, J. Stoye)

Invited speaker:

• JOBIM 2006: Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back
• JOBIM 2009: Computational Short Read Metagenomics
• BSB 2012: Genome Rearrangement by Double Cut and Join
• ALGO 2012: Algorithms for Genome Rearrangement by Double Cut and Join
• MAGE 2013: The potential of family-free genome comparison
• SocBiN 2014: Family-free genome comparison
• BSB 2020: Searching for Genomic Variants in Multiple Genomes at Once

Administration:

• 10/2002-09/2014 Vice-Speaker of the Board of Directors, German Bioinformatics Society (GI-Fachgruppe BIOINF)
• 10/2002-09/2014 and since 10/2018 Member of the Faculty Assembly of the Faculty of Technology, Bielefeld University
• 12/2002-12/2015 Speaker of the Institute for Bioinformatics, Center for Biotechnology (CeBiTec), Bielefeld University
• 01/2004-09/2024 Member of the Board of Directors, Center for Biotechnology (CeBiTec), Bielefeld University
• 10/2002-03/2007 Head of Examination Board, Diploma program Informatics in the Natural Sciences, Faculty of Technology, Bielefeld University
• 10/2007-09/2012 and 04/2020-01/2023 Head of Selection Board, Master program Informatics in the Natural Sciences, Faculty of Technology, Bielefeld University
• 10/2007-09/2012 and since 04/2023 Head of Examination Board, Master program Informatics in the Natural Sciences, Faculty of Technology, Bielefeld University
• 04/2007-09/2009 and 10/2010-09/2013 Dean of the Faculty of Technology, Bielefeld University
• 10/2009-09/2010 Vice-dean of the Faculty of Technology, Bielefeld University
• 10/2013-09/2019 Speaker of the International DFG Research Training Group Computational Methods for the Analysis of the Diversity and Dynamics of Genomes, Faculty of Technology, Bielefeld University
• 01/2014-12/2025 Member of the DAAD Selection Committee for Postdoc Fellowships
• 04/2015-02/2018 Special Visiting Researcher, UFF Niterói, Brazil
• 12/2015-09/2024 Speaker of the Research Area Large Scale Genomics and Big Data Bioinformatics, Center for Biotechnology (CeBiTec), Bielefeld University
• 10/2017-09/2025 Member of the Board of Directors, Center for Interdisciplinary Research (ZiF), Bielefeld University
• since 06/2019 Managing Director of the Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University
• 10/2023-09/2025 Executive Director of the Center for Interdisciplinary Research (ZiF), Bielefeld University
• since 01/2025 Member of the Steering Committee, Freiburg Institute for Advanced Studies (FRIAS)