Center for Computational and Theoretical Biology

Ankenbrand, Markus (Dr.)

Dr. Markus Ankenbrand

Group Leader - BioMedical Data Science

Tel: 0931 31-85754



I'm group leader of the BioMedical Data Science group at the Center for Computational and Theoretical Biology (CCTB).
I studied Biology und Informatics at the University of Würzburg and did my PhD in the Graduate School of Life Sciences.

My research interests are the development and application of algorithms, tools and workflows to generate knowledge from biological and medical data.
Currently my focus is on multi-modal methods and model interpretability in machine learning.


2024[ to top ]
  • Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. Quaresma, Andreia; Ankenbrand, Markus J.; Garcia, Carlos Ariel Yadr{ó}; Rufino, Jos{é}; Honrado, M{ó}nica; Amaral, Joana; Brodschneider, Robert; Brusbardis, Valters; Gratzer, Kristina; Hatjina, Fani; Kilpinen, Ole; Pietropaoli, Marco; Roessink, Ivo; van der Steen, Jozef; Vejsn{\ae}s, Flemming; Pinto, M. Alice; Keller, Alexander. In Scientific Data, 11(1), bl 129. 2024.
  • Cardiac function in a large animal model of myocardial infarction at 7 T: deep learning based automatic segmentation increases reproducibility. Kollmann, Alena; Lohr, David; Ankenbrand, Markus J.; Bille, Maya; Terekhov, Maxim; Hock, Michael; Elabyad, Ibrahim; Baltes, Steffen; Reiter, Theresa; Schnitter, Florian; Bauer, Wolfgang R.; Hofmann, Ulrich; Schreiber, Laura M. In Scientific Reports, 14(1), bl 11009. 2024.
2023[ to top ]
  • MyoPS: A benchmark of myocardial pathology segmentation combining three-sequence cardiac magnetic resonance images. Li, Lei; Wu, Fuping; Wang, Sihan; Luo, Xinzhe; Martín-Isla, Carlos; Zhai, Shuwei; Zhang, Jianpeng; Liu, Yanfei; Zhang, Zhen; Ankenbrand, Markus J.; Jiang, Haochuan; Zhang, Xiaoran; Wang, Linhong; Arega, Tewodros Weldebirhan; Altunok, Elif; Zhao, Zhou; Li, Feiyan; Ma, Jun; Yang, Xiaoping; Puybareau, Elodie; Oksuz, Ilkay; Bricq, Stephanie; Li, Weisheng; Punithakumar, Kumaradevan; Tsaftaris, Sotirios A.; Schreiber, Laura M.; Yang, Mingjing; Liu, Guocai; Xia, Yong; Wang, Guotai; Escalera, Sergio; Zhuang, Xiahai. In Medical Image Analysis, bl 102808. 2023.
  • Ten (mostly) simple rules to future-proof trait data in ecological and evolutionary sciences. Keller, Alexander; Ankenbrand, Markus J.; Bruelheide, Helge; Dekeyzer, Stefanie; Enquist, Brian J.; Erfanian, Mohammad Bagher; Falster, Daniel S.; Gallagher, Rachael V.; Hammock, Jennifer; Kattge, Jens; Leonhardt, Sara D.; Madin, Joshua S.; Maitner, Brian; Neyret, Margot; Onstein, Renske E.; Pearse, William D.; Poelen, Jorrit H.; Salguero-Gomez, Roberto; Schneider, Florian D.; Tóth, Anikó B.; Penone, Caterina. In Methods in Ecology and Evolution, 14(2), K. Bacon (red.), bll 444–458. 2023.
  • Recognition and reconstruction of cell differentiation patterns with deep learning. Dirk, Robin; Fischer, Jonas L.; Schardt, Simon; Ankenbrand, Markus J.; Fischer, Sabine C. In PLOS Computational Biology, 19(10), bll 1–29. Public Library of Science, 2023.
  • {Opportunistic Bacteria of Grapevine Crown Galls Are Equipped with the Genomic Repertoire for Opine Utilization}. Faist, Hanna; Ankenbrand, Markus J; Sickel, Wiebke; Hentschel, Ute; Keller, Alexander; Deeken, Rosalia. In Genome Biology and Evolution, 15(12), bl evad228. 2023.
  • Novel integrative elements and genomic plasticity in ocean ecosystems. Hackl, Thomas; Laurenceau, Raphaël; Ankenbrand, Markus J.; Bliem, Christina; Cariani, Zev; Thomas, Elaina; Dooley, Keven D.; Arellano, Aldo A.; Hogle, Shane L.; Berube, Paul; Leventhal, Gabriel E.; Luo, Elaine; Eppley, John M.; Zayed, Ahmed A.; Beaulaurier, John; Stepanauskas, Ramunas; Sullivan, Matthew B.; DeLong, Edward F.; Biller, Steven J.; Chisholm, Sallie W. In Cell, 186(1), bll 47–62.e16. Elsevier, 2023.
2022[ to top ]
  • A data-driven semantic segmentation model for direct cardiac functional analysis based on undersampled radial MR cine series. Wech, Tobias; Ankenbrand, Markus Johannes; Bley, Thorsten Alexander; Heidenreich, Julius Frederik. In Magnetic Resonance in Medicine, 87(2), bll 972–983. 2022.
  • In Vitro Rearing Changes Social Task Performance and Physiology in Honeybees. Schilcher, Felix; Hilsmann, Lioba; Rauscher, Lisa; Değirmenci, Laura; Krischke, Markus; Krischke, Beate; Ankenbrand, Markus; Rutschmann, Benjamin; Mueller, Martin J.; Steffan-Dewenter, Ingolf; Scheiner, Ricarda. In Insects, 13(1). 2022.
  • Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions. John, Maura; Ankenbrand, Markus J; Artmann, Carolin; Freudenthal, Jan A; Korte, Arthur; Grimm, Dominik G. In Bioinformatics, 38(Supplement\_2), bll ii5-ii12. 2022.
2021[ to top ]
  • Dealing with software complexity in individual-based models. Vedder, Daniel; Ankenbrand, Markus; Cabral, Juliano. In Methods in Ecology and Evolution, 12, bll 2324–2333. 2021.
  • Inferring core genome phylogenies for bacteria. Keller, Alexander; Ankenbrand, Markus J. In Bacterial Pangenomics (in press), A. Mengoni, M. Fondi, G. Bacci (reds.). Springer Verlag, Heidelberg, Germany, 2021.
  • B0 shimming of the human heart at 7T. Hock, Michael; Terekhov, Maxim; Stefanescu, Maria Roxana; Lohr, David; Herz, Stefan; Reiter, Theresa; Ankenbrand, Markus; Kosmala, Aleksander; Gassenmaier, Tobias; Juchem, Christoph; Schreiber, Laura Maria. In Magnetic Resonance in Medicine, 85(1), bll 182–196. 2021.
  • On the way to routine cardiac MRI at 7 Tesla - a pilot study on consecutive 84 examinations. Reiter, Theresa; Lohr, David; Hock, Michael; Ankenbrand, Markus Johannes; Stefanescu, Maria Roxana; Kosmala, Aleksander; Kaspar, Mathias; Juchem, Christoph; Terekhov, Maxim; Schreiber, Laura Maria. In PLOS ONE, 16(7), bll 1–18. Public Library of Science, 2021.
  • Open Science principles for accelerating trait-based science across the Tree of Life. Gallagher, Rachael; Falster, Daniel S.; Maitner, Brian; Enquist, Brian; Ankenbrand, Markus; Balk, Meghan; Bland, Lucie; Boyle, Brad; Bravo, Catherine; Cavazos, Brittany; Fadrique, Belen; Feng, Xiao; Halbritter, Aud; Hammock, Jennifer; Hogan, James Aaron; Iversen, Colleen; Jochum, Malte; Kattge, Jens; Keller, Alexander; Madin, Joshua; Manning, Peter; McCormack, Luke; Michaletz, Sean; Park, Daniel; Pearse, William; Penone, Caterina; Perez, Timothy; Pineda-Munoz, Silvia; Poelen, Joritt; Ray, Courtenay; Salguero-Gomez, Roberto; Sauquet, Herve; Schneider, Florian; Spasojevic, Marko J.; Vandvik, Vigdis; Violle, Cyrille; Weiss, Katherine. In Nature Ecology \& Evolution, bll 294–303. Nature Publishing Group, 2021.
  • Self-configuring nnU-net pipeline enables fully automatic infarct segmentation in late enhancement MRI after myocardial infarction. Heidenreich, Julius F.; Gassenmaier, Tobias; Ankenbrand, Markus J.; Bley, Thorsten A.; Wech, Tobias. In European Journal of Radiology, 141, bl 109817. 2021.
  • Sensitivity analysis for interpretation of machine learning based segmentation models in cardiac {MRI}. Ankenbrand, Markus J.; Shainberg, Liliia; Hock, Michael; Lohr, David; Schreiber, Laura M. In BMC Medical Imaging, 21(1), bl 27. 2021.
  • Standard methods for pollen research. Campos, Maria G.; Anjos, Ofélia; Chica, Manuel; Campoy, Pascual; Nozkova, Janka; Almaraz-Abarca, Norma; Barreto, Lidia M. R. C.; Nordi, João Carlos; Estevinho, Leticia M.; Pascoal, Ananias; Paula, Vanessa Branco; Chopina, Altino; Dias, Luis G.; j. Tešić, Živoslav L.; Mosić, Mirjana D.; Kostić, Aleksandar Ž.; Pešić, Mirjana B.; Milojković-Opsenica, Dušanka M.; Sickel, Wiebke; Ankenbrand, Markus J.; Grimmer, Gudrun; Steffan-Dewenter, Ingolf; Keller, Alexander; Förster, Frank; Tananaki, Chrysoula H.; Liolios, Vasilios; Kanelis, Dimitrios; Rodopoulou, Maria-Anna; Thrasyvoulou, Andreas; Paulo, Luísa; Kast, Christina; Lucchetti, Matteo A.; Glauser, Gaëtan; Lokutova, Olena; de Almeida-Muradian, Ligia Bicudo; Szczęsna, Teresa; Carreck, Norman L. In Journal of Apicultural Research, 60(4), bll 1–109. Taylor & Francis, 2021.
  • Deep learning-based cardiac cine segmentation: Transfer learning application to 7T ultrahigh-field MRI. Ankenbrand, Markus Johannes; Lohr, David; Schlötelburg, Wiebke; Reiter, Theresa; Wech, Tobias; Schreiber, Laura Maria. In Magnetic Resonance in Medicine, 86(4), bll 2179–2191. 2021.
2020[ to top ]
  • BCdatabaser: on-the-fly reference database creation for DNA (meta-)barcoding. Keller, Alexander; Hohlfeld, Sonja; Kolter, Andreas; Schultz, Jörg; Gemeinholzer, Birgit; Ankenbrand, Markus J. In Bioinformatics, 36(8), bll 2630–2631. 2020.
  • Chronic exposure to the pesticide flupyradifurone can lead to premature onset of foraging in honeybees (Apis mellifera). Hesselbach, Hannah; Seeger, Johannes; Schilcher, Felix; Ankenbrand, Markus; Scheiner, Ricarda. In Journal of Applied Ecology, 57, bll 609–618. 2020.
  • A systematic comparison of chloroplast genome assembly tools. Freudenthal, Jan A.; Pfaff, Simon; Terhoeven, Niklas; Korte, Arthur; Ankenbrand, Markus J.; F{ö}rster, Frank. In Genome Biology, 21(1), bl 254. 2020.
  • {{G}enomes of the {V}enus {F}lytrap and {C}lose {R}elatives {U}nveil the {R}oots of {P}lant {C}arnivory}. Palfalvi, G.; Hackl, T.; Terhoeven, N.; Shibata, T. F.; Nishiyama, T.; Ankenbrand, M.; Becker, D.; Förster, F.; Freund, M.; Iosip, A.; Kreuzer, I.; Saul, F.; Kamida, C.; Fukushima, K.; Shigenobu, S.; Tamada, Y.; Adamec, L.; Hoshi, Y.; Ueda, K.; Winkelmann, T.; Fuchs, J.; Schubert, I.; Schwacke, R.; Al-Rasheid, K.; Schultz, J.; Hasebe, M.; Hedrich, R. In Current Biology, 30(12), bll 2312–2320. 2020.
  • Exploring Ensemble Applications for Multi-sequence Myocardial Pathology Segmentation. Ankenbrand, Markus J.; Lohr, David; Schreiber, Laura M. In Myocardial Pathology Segmentation Combining Multi-Sequence Cardiac Magnetic Resonance Images, X. Zhuang, L. Li (reds.), bll 60–67. Springer International Publishing, Cham, 2020.
2019[ to top ]
  • Linking pollen foraging of megachilid bees to their nest bacterial microbiota. Voulgari-Kokota, Anna; Ankenbrand, Markus; Grimmer, Gudrun; Steffan-Dewenter, Ingolf; Keller, Alexander. In Ecology and Evolution, 9(18), bll 10788–10800. 2019.
2018[ to top ]
  • Wild bees and their nests host Paenibacillus bacteria with functional potential of avail. Keller, Alexander; Brandel, Annette; Becker, Mira C.; Balles, Rebecca; Abdelmohlsen, Usama R.; Ankenbrand, Markus J.; Sickel, Wiebke. In Microbiome, (6), bl 229. 2018.
  • Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest. Too, Chin Chin; Ong, Kuan Shion; Ankenbrand, Markus J; Lee, Sui Mae; Yule, Catherine M; Keller, Alexander. In Genome announcements, 6(25), bll e00561–18. Am Soc Microbiol, 2018.
  • Draft Genome Sequence of Klebsiella sp. Strain C31 Isolated from a Malaysian Tropical Peat Swamp Forest. Too, Chin Chin; Ong, Kuan Shion; Ankenbrand, Markus J; Lee, Sui Mae; Yule, Catherine M; Keller, Alexander. In Genome announcements, 6(25), bll e00560–18. Am Soc Microbiol, 2018.
  • FENNEC - Functional Exploration of Natural Networks and Ecological Communities. Ankenbrand, Markus J.; Hohlfeld, Sonja C. Y.; Foerster, Frank; Keller, Alexander. In Methods in Ecology and Evolution, bll 2028–2033. 2018.
2017[ to top ]
  • AliTV - interactive visualization of whole genome comparisons. Ankenbrand, Markus J.; Hohlfeld, Sonja; Hackl, Thomas; Förster, Frank. In PeerJ Comput. Sci., 3, bl e116. 2017.
2016[ to top ]
  • DNA-Metabarcoding – ein neuer Blick auf organismische Diversität. Keller, Alexander; Grimmer, Gudrun; Sickel, Wiebke; Ankenbrand, Markus J. In BioSpektrum, 22, bll 147–150. 2016.
  • {{V}enus flytrap carnivorous lifestyle builds on herbivore defense strategies}. Bemm, F.; Becker, D.; Larisch, C.; Kreuzer, I.; Escalante-Perez, M.; Schulze, W. X.; Ankenbrand, M.; Van de Weyer, A. L.; Krol, E.; Al-Rasheid, K. A.; Mithofer, A.; Weber, A. P.; Schultz, J.; Hedrich, R. In Genome Res., 26(6), bll 812–825. 2016.
  • TBro: visualization and management of de novo transcriptomes. Ankenbrand, Markus J.; Weber, Lorenz; Becker, Dirk; Förster, Frank; Bemm, Felix. In Database, 2016. 2016.
  • biojs-io-biom, a {BioJS} component for handling data in Biological Observation Matrix ({BIOM}) format. Ankenbrand, Markus J.; Terhoeven, Niklas; Hohlfeld, Sonja; Förster, Frank; Keller, Alexander. In F1000Research, 5, bl 2348. F1000 Research, Ltd., 2016.
  • bcgTree: automatized phylogenetic tree building from bacterial core genomes. Ankenbrand, Markus J; Keller, Alexander. In Genome, 59, bll 783–791. 2016.
2015[ to top ]
  • Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples. Keller, Alexander; Danner, Nadja; Grimmer, Gudrun; Ankenbrand, Markus; {von der Ohe}, Katharina; {von der Ohe}, Werner; Rost, Simone; Härtel, Stephan; Steffan-Dewenter, Ingolf. In Plant Biology, 17, bll 558–566. 2015.
  • {{I}{T}{S}2 {D}atabase {V}: {T}wice as {M}uch}. Ankenbrand, M. J.; Keller, A.; Wolf, M.; Schultz, J.; Forster, F. In Mol. Biol. Evol., 32(11), bll 3030–3032. 2015.
  • ITS2 Database V: Twice as Much. Ankenbrand, Markus J.; Keller, Alexander; Wolf, Matthias; Schultz, Jörg; Förster, Frank. In Molecular Biology and Evolution, 32(11), bll 3030–3032. 2015.
  • Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. Sickel, Wiebke; Ankenbrand, Markus; Grimmer, Gudrun; Holzschuh, Andrea; Härtel, Stephan; Lanzen, Jonathan; Steffan-Dewenter, Ingolf; Keller, Alexander. In BMC Ecology, 15, bl 20. 2015.
2013[ to top ]
  • Compensatory Base Changes in {ITS}2 Secondary Structures Correlate with the Biological Species Concept Despite Intragenomic Variability in {ITS}2 Sequences {\textendash} A Proof of Concept. Wolf, Matthias; Chen, Shilin; Song, Jingyuan; Ankenbrand, Markus; Müller, Tobias. In {PLoS} {ONE}, 8(6), J. E. Stajich (red.), bl e66726. Public Library of Science ({PLoS}), 2013.