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Dr. Tom Hartmann
– Ph.D. in Computer Science –

Picture of CS

Since March 2019, I am a full-time researcher at the Bioinformatics Group of the Leipzig University.

My research is about the algorithmic study of biologically motivated problems. It focusses on the development of algorithms solving problems that are related to genome rearrangements and graph theory. I also have interests in swarm intelligence algorithms, computational complexity, combinatorics, computational biology and many others in computer science and discrete mathematics. For more information click here to see my dissertation or analyze the wordcloud below. Additionally, you can find me on the following webpages:
                                                       Research Gate Google Scholar Orcid Phönix Leipzig GitHub
If you have questions, comments or suggestions, please, feel free to write an email to tom@bioinf.uni-leipzig.de.

Wordcloud
CV

Education

TimeDescription
Mar. 2019 – now Postdoctoral Fellow at the Leipzig University (Bioinformatics Group)
Mar. 2019 Ph.D. in Computer Science (under Prof. Middendorf; Leipzig University)
Apr. 2014 – Feb. 2019 Ph.D. Student at the Leipzig University (Swarm Intelligence and Complex Systems Group)
Mar. 2014 Diploma Degree in Mathematics (under Prof. Middendorf; Leipzig University)
Oct. 2009 – Mar. 2014 Diploma student in Mathematics with Biology at the Leipzig University

Travel

TimeDescription
Sep. 2018 – Dec. 2018 Spain: Technical University of Catalonia, Barcelona
Jul. 2017 – Sep. 2017 Taiwan: Summer Institute Programme (DAAD 57342485)
Feb. 2016 – Mar. 2016 India: Soft Computing Lab of Indian Institute Technology Roorkee (DAAD 57130298)
Feb. 2015 – Apr. 2015 India: Soft Computing Lab of Indian Institute Technology Roorkee (DAAD 57130298)
Publications

Submitted

  • T. Hartmann, M. Bannach, M. Middendorf, N. Wieseke, P. F. Stadler, M. Hellmuth
        Complete Edge-Colored Permutation Graphs
        [ResearchGate, arXiv]

    • Journal Publications

  • T. Hartmann, M. Bannach, and M. Middendorf
        Sorting Signed Permutations by Inverse Tandem Duplication Random Losses
        IEEE/ACM Transactions on Computational Biology and Bioinformatics (in press)
        [ResearchGate]
  • T. Hartmann, M. Bernt, and M. Middendorf
        An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements
        IEEE/ACM Transactions on Computational Biology and Bioinformatics 16.1 (2019): 52–62
        [Publisher's page]
  • T. Hartmann, M. Middendorf, and M. Bernt
        EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
        BMC Bioinformatics 19 (2018): 192
        [Publisher's page]
  • T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, and M. Bernt
        Genome Rearrangement with ILP
        IEEE/ACM Transactions on Computational Biology and Bioinformatics 15.5 (2018): 1585–1593
        [Publisher's page]
  • T. Hartmann, A. Chu, M. Middendorf, and M. Bernt
        Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes
        IEEE/ACM Transactions on Computational Biology and Bioinformatics 15.1 (2018): 83–95
        [Publisher's page]
  • Y.-C. Cheng, T. Hartmann, P.-Y. Tsai, and M. Middendorf
        Population Based Ant Colony Optimization for Reconstructing ECG Signals
        Evolutionary Intelligence 9.3 (2016): 55–66
        [Publisher's page]
  • N. Wieseke, T. Hartmann, M. Bernt, and M. Middendorf
        Cophylogenetic Reconciliation with ILP
        IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.6 (2015): 1227–1235
        [Publisher's page]

    • Monographs

  • T. Hartmann
        Models and Algorithms for Sorting Permutations with Tandem Duplication and Random Loss
        PhD Thesis
        Leipzig University 2019
        [Leipzig University Library]

    • Book Chapters

  • T. Hartmann, M. Middendorf, and M. Bernt
        Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches
        In: Setubal J., Stoye J., Stadler P. (eds) Comparative Genomics. Methods in Molecular Biology, 1704 (2018)
        Humana Press, New York, NY
        [Publisher's page]

    • Publications in Conference Proceedings

  • T. Gatter, S. Von Loehneysen, P. Drozdova, T. Hartmann, P. F. Stadler
        Economic Genome Assembly from Low Coverage Illumina and Nanopore Data
        accepted for Workshop on Algorithms in BioInformatics (WABI 2020)
        [BioRxiv]
  • D. Abitz, T. Hartmann, M. Middendorf
        A Weighted Population Update Rule for PACO Applied to the Single Machine Total Weighted Tardiness Problem
        accepted for The Genetic and Evolutionary Computation Conference (GECCO 2020)
        [arXiv]
  • T. Hartmann, M. Bannach, and M. Middendorf
        Sorting Signed Permutations by Inverse Tandem Duplication Random Losses
        17th Asia Pacific Bioinformatics Conference (APBC 2019)
  • T. Hartmann, M. Bernt, and M. Middendorf
        An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements
        16th Asia Pacific Bioinformatics Conference (APBC 2018)
  • T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, and M. Bernt
        Genome Rearrangement with ILP
        15th Asia Pacific Bioinformatics Conference (APBC 2017)
  • Y.-C. Cheng, T. Hartmann, P.-Y. Tsai, and M. Middendorf
        Population Based Ant Colony Optimization for Reconstructing ECG Signals
        Applications of Evolutionary, Computation Lecture Notes in Computer Science 9597 (2016): 770–785
        [Publisher's page]
  • N. Wieseke, T. Hartmann, M. Bernt, and M. Middendorf
        Cophylogenetic Reconciliation with ILP
        13th Asia Pacific Bioinformatics Conference (APBC 2015)
    • Supervised Theses
    If you are interested in working with a group of highly motivated and friendly people, don't hesitate to contact me!

    Supervised Master Theses

  • E. Kupfer
        Entwicklung und Untersuchung eines hierarchischen populationsbasierten Ameisenalgorithmus für das statische und
        dynamische Traveling Salesperson Problem
        University Leipzig (2020)
  • K. Hainke
        Einsatz von PQ-Bäumen für populationsbasierte Ameisenalgorithmen
        University Leipzig (2019)
  • D. Abitz
        Entwicklung und Untersuchung eines populationbasierten Ameisenalgorithmus für ein Ein-Maschinen-Scheduling
        mit gewichteten Jobs
        University Leipzig (2019)
  • D. M. Anglés
        Ein Softwarewerkzeug zur Konstruktion und Ausführung von populationsbasierten Optimierungsalgorithmen
        University Leipzig (2019)
  • R. Terbach
        A Population-Based Swarm Algorithm With Charged Particles for Dynamic Travelling Salesperson Problems
        University Leipzig (2017)

    • Supervised Diploma Theses

  • P. Geser
        Zur Komplexität des 2-Maschinen-Flow-Shop-Problems mit Zwischenspeicher
        University Leipzig (2017)
  • M. Winkel
        Flowshop-Probleme mit Puffern: Analyse und Entwurf eines Ameisenalgorithmus
        University Leipzig (2015)

    • Supervised Bachelor Theses

  • B. Schmidt
        Exploring weighting schemes for comparative mitochondrial genome rearrangement analysis with CREx2
        University Leipzig (2019)
  • L. Janik
        The Influence of Correlation on the non-dominated Front of an Ant Colony Optimization Algorithm for Multi-Criteria Traveling     Salesman Problems
        University Leipzig (2019)
  • M. Kriegs
        Entwicklung eines Populationsbasierten Ameisenalgorithmus zum Sortieren von Permutationen durch Inversionen
        University Leipzig (2018)
  • K. Schreiblehner
        On Some Properties of the Condorcet Method and Its Use for Particle Swarm Optimization
        University Leipzig (2017)

    • Reviewing Activities

    Contact

    Contact Information:

    address Dr. Tom Hartmann
    Bioinformatics Group (4th floor)
    Department of Computer Science
    Leipzig University
    Härtelstraße 16-18
    Room 440
    D-04107 Leipzig
    Germany
    phone +49 341 97 16663
    e-mail tom@bioinf.uni-leipzig.de