Publications

You can find my google scholar profile here.

  • J. Kippnich, F. Benz, H. Uecker, F. Baumdicker (2024). Effectiveness of CRISPR-Cas in Sensitizing Bacterial Populations with Plasmid-Encoded Antimicrobial Resistance (view biorxiv preprint)

  • A. Gavriilidou, E. Paulitz, C. Resl, N. Ziemert, A. Kupczok, F. Baumdicker (2024). Goldfinder: Unraveling Networks of Gene Co-occurrence and Avoidance in Bacterial Pangenomes (view biorxiv preprint)

  • K. Burger, S. Klepper, U. von Luxburg, F. Baumdicker (2024).  Inferring Ancestry with the Hierarchical Soft Clustering Approach tangleGen (view biorxiv preprint) (accepted in Genome Research)

  • A Fehrenbach, A Mitrofanov, OS Alkhnbashi, R Backofen, F Baumdicker (2024). SpacerPlacer: Ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions, Nucleic Acids Research (view biorxiv preprint) (view paper)

  • F. Baumdicker, A. Kupczok (2023). Tackling the pangenome dilemma requires the concerted analysis of multiple population genetic processes, Genome Biology and Evolution (view paper)

  • E. Lauterbur, et al. (2023). Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations (view biorxiv preprint) (view paper)

  • K. Burger, P. Pfaffelhuber, F. Baumdicker (2022). Neural Networks for self-adjusting Mutation Rate Estimation when the Recombination Rate is unknown, PLOS Computational Biology (view biorxiv preprint) (view paper)

  • P. Pfaffelhuber, E. Sester-Huss, F. Baumdicker, J. Naue, S. Lutz-Bonengel, F. Staubach (2022) Inference of recent admixture using genotype data, Forensic Science International: Genetics (view biorxiv preprint) (view paper)

  • F. Baumdicker, G. Bisschop, D. Goldstein, G. Gower, A. Ragsdale, G. Tsambos, S. Zhu, et al. (2021) Efficient ancestry and mutation simulation with msprime 1.0, Genetics (view biorxiv preprint) (view paper)

  • Y. Wang, F. Baumdicker, P. Schweiger, S. Kuenzel, F. Staubach (2021) Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila, BMC Biology (view biorxiv preprint) (view paper)

  • J. Adrion et al. (2020). A community-maintained standard library of population genetic models. eLife 2020;9:e54967, (view paper)

  • F. Baumdicker, E. Huss, P. Pfaffelhuber (2020). Modifiers of mutation rate in selectively fluctuating environments. Stochastic Processes and their Applications, (view paper) (view arxiv preprint)

  • P. Pfaffelhuber, F. Grundner-Culemann, V. Lipphardt, F. Baumdicker (2020). How to choose sets of ancestry informative markers: A supervised feature selection approach. Forensic Science International: Genetics, (view article)(view biorxiv preprint)

  • F. Baumdicker, U. Hölker (2020). Method comparison with repeated measurements - Passing-Bablok regression for grouped data with errors in both variables. Statistics & Probability Letters, (view article)(view arxiv preprint)

  • F. Baumdicker, A. M. I. Huebner, and P. Pfaffelhuber (2018). The ordered independent loss model for the evolution of CRISPR spacers. Theoretical Population Biology, 119, 72-82 , (view pdf) (view arxiv preprint)

  • W. Ding, F. Baumdicker, and R. A. Neher (2018). panX: pan-genome analysis and exploration. Nucleic Acids Research, 46, 1, e5, (view pdf) (view biorxiv preprint)

  • F. Baumdicker (2015). The site frequency spectrum of dispensable genes. Theoretical Population Biology, 100, 13-25. (view pdf)

  • F. Baumdicker (2014). Bacterial Population Genomics - towards a population genetics view of bacterial evolution, Dissertation (view pdf)

  • F. Baumdicker and P. Pfaffelhuber (2014). The infinitely many genes model with horizontal gene transfer, Electronic Journal of Probability 19 (view pdf)

  • Baumdicker F., W. R. Hess, and P. Pfaffelhuber (2012). The infinitely many genes model for the distributed genome of bacteria, Genome Biology and Evolution 2012 (view pdf)

  • F. Baumdicker and P. Pfaffelhuber (2011). Evolution of bacterial genomes under horizontal gene transfer, arXiv:1105.5014v1 [q-bio.PE] (view pdf)

  • Baumdicker, F., W. R. Hess, and P. Pfaffelhuber (2010). The diversity of a distributed genome in bacterial populations, Annals of Applied Probability 20 (5), 1567-1606. (view pdf)