piwik-script

Center for Computational and Theoretical Biology

Ankenbrand, Markus (Dr.)

Dr. Markus Ankenbrand

Group Leader - BioMedical Data Science

Tel: 0931 31-85754

eMail: markus.ankenbrand@uni-wuerzburg.de

Research

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.

Publications

2023[ to top ]
  • 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, (K. Bacon, red.) (2023). 14(2) 444–458.
  • 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 (2023). 186(1) 47–62.e16.
  • 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 (2023). 102808.
2022[ to top ]
  • 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 (2022). 13(1)
  • 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 (2022). 38(Supplement\_2) ii5-ii12.
  • 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 (2022). 87(2) 972–983.
2021[ to top ]
  • 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 (2021). 60(4) 1–109.
  • 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 (2021). 21(1) 27.
  • 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 (2021). 141 109817.
  • 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 (2021). 294–303.
  • 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 (2021). 16(7) 1–18.
  • Inferring core genome phylogenies for bacteria Keller, Alexander; Ankenbrand, Markus J in Bacterial Pangenomics (in press), A. Mengoni, M. Fondi, G. Bacci (reds.) (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 (2021). 86(4) 2179–2191.
  • Dealing with software complexity in individual-based models Vedder, Daniel; Ankenbrand, Markus; Cabral, Juliano in Methods in Ecology and Evolution (2021). 12 2324–2333.
  • 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 (2021). 85(1) 182–196.
2020[ to top ]
  • {{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 (2020). 30(12) 2312–2320.
  • 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.) (2020). 60–67.
  • 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 (2020). 57 609–618.
  • 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 (2020). 36(8) 2630–2631.
  • A systematic comparison of chloroplast genome assembly tools Freudenthal, Jan A.; Pfaff, Simon; Terhoeven, Niklas; Korte, Arthur; Ankenbrand, Markus J.; F{\"o}rster, Frank in Genome Biology (2020). 21(1) 254.
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 (2019). 9(18) 10788–10800.
2018[ to top ]
  • {chloroExtractor}: extraction and assembly of the chloroplast genome from whole genome shotgun data Ankenbrand, Markus J; Pfaff, Simon; Terhoeven, Niklas; Qureischi, Musga; Gündel, Maik; Wei{\ss}, Clemens L.; Hackl, Thomas; Förster, Frank in The Journal of Open Source Software (2018). 3(21) 464.
  • 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 (2018). (6) 229.
  • 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 (2018). 2028–2033.
  • 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 (2018). 6(25) e00561–18.
  • 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 (2018). 6(25) e00560–18.
2017[ to top ]
  • AliTV - interactive visualization of whole genome comparisons. Ankenbrand, Markus J.; Hohlfeld, Sonja; Hackl, Thomas; Förster, Frank in PeerJ Comput. Sci. (2017). 3 e116.
2016[ to top ]
  • {{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. (2016). 26(6) 812–825.
  • TBro: visualization and management of de novo transcriptomes. Ankenbrand, Markus J.; Weber, Lorenz; Becker, Dirk; Förster, Frank; Bemm, Felix in Database (2016). 2016
  • DNA-Metabarcoding – ein neuer Blick auf organismische Diversität Keller, Alexander; Grimmer, Gudrun; Sickel, Wiebke; Ankenbrand, Markus J in BioSpektrum (2016). 22 147–150.
  • 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 (2016). 5 2348.
  • bcgTree: automatized phylogenetic tree building from bacterial core genomes Ankenbrand, Markus J; Keller, Alexander in Genome (2016). 59 783–791.
2015[ to top ]
  • {{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. (2015). 32(11) 3030–3032.
  • ITS2 Database V: Twice as Much Ankenbrand, Markus J.; Keller, Alexander; Wolf, Matthias; Schultz, Jörg; Förster, Frank in Molecular Biology and Evolution (2015). 32(11) 3030–3032.
  • 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 (2015). 15 20.
  • 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 (2015). 17 558–566.
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}, (J. E. Stajich, red.) (2013). 8(6) e66726.