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Computer Science

D-Index
48
Citations
11075
World Ranking
6115
National Ranking
285

Overview

Jens Stoye is affiliated with Bielefeld University in Germany and has contributed extensively to the field of Biochemistry, Genetics, and Molecular Biology, particularly focusing on Molecular Biology and Genetics. Their research spans several relevant subfields including Plant Science, Artificial Intelligence, and Cancer Research.

Their work encompasses a range of main topics including Genomics and Phylogenetic Studies, Chromosomal and Genetic Variations, Genome Rearrangement Algorithms, Gene expression and cancer classification, RNA and protein synthesis mechanisms, Algorithms and Data Compression, and Genetic diversity and population structure.

Jens Stoye has been published regularly in various scientific venues, with a notable frequency in:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Zenodo (CERN European Organization for Nuclear Research)
  • Algorithms for Molecular Biology
  • arXiv (Cornell University)
  • iScience

Frequent coauthors collaborating with Stoye include:

  • Roland Wittler
  • Leonard Bohnenkämper
  • Daniel Doerr
  • Luca Parmigiani
  • Alexander Goesmann

The following are some recent publications by Jens Stoye, highlighting key research outcomes and publication venues:

  • HASLR: Fast Hybrid Assembly of Long Reads, 2020, iScience
  • Computing the Rearrangement Distance of Natural Genomes, 2021, Journal of Computational Biology
  • Applying rearrangement distances to enable plasmid epidemiology with pling, 2024, Microbial Genomics
  • Finding all maximal perfect haplotype blocks in linear time, 2020, Algorithms for Molecular Biology
  • Panacus: fast and exact pangenome growth and core size estimation, 2024, Bioinformatics

Best Publications

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

    Stefan Kurtz;Jomuna V. Choudhuri;Enno Ohlebusch;Chris Schleiermacher

  • Updating benchtop sequencing performance comparison

    Sebastian Jünemann;Sebastian Jünemann;Fritz Joachim Sedlazeck;Karola Prior;Andreas Albersmeier

  • A unifying view of genome rearrangements

    Anne Bergeron;Julia Mixtacki;Jens Stoye

  • Phylogenetic classification of short environmental DNA fragments

    Lutz Krause;Naryttza N. Diaz;Alexander Goesmann;Scott Kelley

  • Rose: generating sequence families.

    Jens Stoye;Dirk Evers;Folker Meyer

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

    Lutz Krause;Naryttza N. Diaz;Robert A. Edwards;Robert A. Edwards;Karl Heinz Gartemann

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

    Alexander Mellmann;Thomas Weniger;Christoph Berssenbrügge;Jörg Rothgänger

  • Efficient implementation of lazy suffix trees

    Robert Giegerich;Stefan Kurtz;Jens Stoye

  • Finding Maximal Pairs with Bounded Gap

    Gerth Stølting Brodal;Rune B. Lyngsø;Christian N. S. Pedersen;Jens Stoye

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

    Jens Stoye;Vincent Moulton;Andreas W.M. Dress

  • Benchmarking tools for the alignment of functional noncoding DNA

    Daniel A Pollard;Casey M Bergman;Casey M Bergman;Jens Stoye;Susan E Celniker

  • Efficient Q-Gram Filters for Finding All Epsilon-Matches Over a Given Length

    Kim R. Rasmussen;Jens Stoye;Eugene W. Myers

  • Orthology detection combining clustering and synteny for very large datasets.

    Marcus Lechner;Maribel Hernandez-Rosales;Daniel Doerr;Nicolas Wieseke

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

    Dan Gusfield;Jens Stoye

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

    Anne Bergeron;Jens Stoye

  • Taxonomic classification of metagenomic shotgun sequences with CARMA3

    Wolfgang Gerlach;Jens Stoye

  • Finding All Common Intervals of k Permutations

    Steffen Heber;Jens Stoye

  • r2cat: synteny plots and comparative assembly

    Peter Husemann;Jens Stoye

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

    Jens Stoye

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

    Heiko Neuweger;Stefan P. Albaum;Michael Dondrup;Marcus Persicke

Frequent Co-Authors

Alexander Goesmann
Alexander Goesmann University of Giessen
Alfred Pühler
Alfred Pühler Bielefeld University
Jörn Kalinowski
Jörn Kalinowski Bielefeld University
Andreas W. M. Dress
Andreas W. M. Dress Max Planck Institute for Mathematics in the Sciences
Sebastian Böcker
Sebastian Böcker Friedrich Schiller University Jena
Lutz Krause
Lutz Krause University of Queensland
Dag Harmsen
Dag Harmsen University of Münster
Folker Meyer
Folker Meyer Argonne National Laboratory
Gunnar Rätsch
Gunnar Rätsch ETH Zurich
Martin Vingron
Martin Vingron Max Planck Society

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