Chair for Computational and Theoretical Biology

Publications

2026[ to top ]
  • Wnt/β-catenin signalling modulates the timing of cell fate decision making in the early mouse embryo. Lilao-Garzón, Joaquin; Corujo-Simon, Elena; Vinyoles, Meritxell; Fischer, Sabine C.; Guillén, José; Balayo, Tina; Muñoz-Descalzo, Silvia. In PLOS ONE, 21(3), pp. 1–25. Public Library of Science, 2026.
2025[ to top ]
  • Detection of Local Prostate Cancer Recurrence from PET/CT Scans Using Deep Learning. Korb, Marko; Efetürk, Hülya; Jedamzik, Tim; Hartrampf, Philipp E.; Kosmala, Aleksander; Serfling, Sebastian E.; Dirk, Robin; Michalski, Kerstin; Buck, Andreas K.; Werner, Rudolf A.; Schlötelburg, Wiebke; Ankenbrand, Markus J. In Cancers, 17(9), p. 1575. MDPI AG, 2025.
  • Broad geographic dispersal is not a diversification driver for Emberizoidea. Arango, Axel; Pinto-Ledezma, Jesús; Rojas-Soto, Octavio; Villalobos, Fabricio. In Proceedings of the Royal Society B: Biological Sciences, 292(2039). The Royal Society, 2025.
  • Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in situ sequencing (mudRapp-seq). Ahmad, Shazeb; Li, Jianhui; Schaust, Joél; Gribling-Burrer, Anne-Sophie; Geiger, Nina; Fischer, Sabine C; Ambi, Uddhav B; Backes, Simone; Ankenbrand, Markus J; Smyth, Redmond P. In Nucleic Acids Research, 53(11). Oxford University Press (OUP), 2025.
  • VESNA: an open-source tool for automated 3D vessel segmentation and network analysis. Schüttler, Magdalena; Dogan, Leyla; Kirchner, Jana; Ergün, Süleyman; Wörsdörfer, Philipp; Fischer, Sabine C. In BMC Bioinformatics, 26(1), p. 254. 2025.
  • Collective cooperative intelligence. Barfuss, Wolfram; Flack, Jessica; Gokhale, Chaitanya S.; Hammond, Lewis; Hilbe, Christian; Hughes, Edward; Leibo, Joel Z.; Lenaerts, Tom; Leonard, Naomi; Levin, Simon; Sehwag, Udari Madhushani; McAvoy, Alex; Meylahn, Janusz M.; Santos, Fernando P. In Proceedings of the National Academy of Sciences, 122(25), p. e2319948121. 2025.
  • Compartment model of strategy-dependent time delays in replicator dynamics. Fic, Małgorzata; Bastian, Frank; Miȩkisz, Jacek; Gokhale, Chaitanya S. In Journal of Theoretical Biology, 601, p. 112044. 2025.
  • The cost of fungicide resistance evolution in multi-field plant epidemics. Mikaberidze, Alexey; Gokhale, Chaitanya S.; Bargués-Ribera, Maria; Verma, Prateek. In PLOS Sustainability and Transformation, 4(6), pp. 1–24. Public Library of Science, 2025.
  • An agent-based model of Trypanosoma brucei social motility to explore determinants of colony pattern formation. Kuhn, Andreas; Kr{ü}ger, Timothy; Engstler, Markus; Fischer, Sabine C. In bioRxiv. Cold Spring Harbor Laboratory, 2025.
  • On multiple infections by parasites with complex life cycles. Nguyen, Phuong L.; Gokhale, Chaitanya S. In Oikos, p. e10493. 2025.
2024[ to top ]
  • 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), p. 11009. 2024.
  • Catalysing cooperation: the power of collective beliefs in structured populations. Fic, Małgorzata; Gokhale, Chaitanya S. In npj Complex, 1(1), p. 6. 2024.
  • The Free-Running Circasemilunar Period Is Determined by Counting Circadian Clock Cycles in the Marine Midge Clunio Marinus. Neumann, Jule; Rajendra, Dharanish; Kaiser, Tobias S. In Journal of Biological Rhythms, 39(4), pp. 379–391. SAGE Publications, 2024.
  • mTOR controls growth and internal architecture of human breast cancer spheroids. Hötte, Katharina; Fischer, Sabine C.; Schmitz, Alexander; Koch, Michael; Saeifar, Sanam; Stelzer, Ernst H.K.; Pampaloni, Francesco. In bioRxiv, p. 2024.02.24.580871. Cold Spring Harbor Laboratory, 2024.
  • 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), p. 129. 2024.
  • Insights into the relationship between hydraulic safety, hydraulic efficiency and tree structural complexity from terrestrial laser scanning and fractal analysis. Dorji, Yonten; Isasa, Emilie; Pierick, Kerstin; Sarmento Cabral, Juliano; Tobgay, Tashi; Annighöfer, Peter; Schuldt, Bernhard; Seidel, Dominik. In Trees, 38(221-239). 2024.
  • Inference of alveolar capillary network connectivity from blood flow dynamics. Schmid, Kerstin; Olivares, Andy L.; Camara, Oscar; Kuebler, Wolfgang M.; Ochs, Matthias; Hocke, Andreas C.; Fischer, Sabine C. In American Journal of Physiology-Lung Cellular and Molecular Physiology. American Physiological Society, 2024.
  • Effects of time spent in pregnancy or brooding on immunocompetence. Revathi Venkateswaran, Vandana; Gokhale, Chaitanya S.; Mangel, Marc; Eliassen, Sigrunn. In Ecology and Evolution, 14(1), p. e10764. 2024.
  • Self-organization as a mechanism of resilience in dryland ecosystems. Kéfi, Sonia; Génin, Alexandre; Garcia-Mayor, Angeles; Guirado, Emilio; Cabral, Juliano S.; Berdugo, Miguel; Guerber, Josquin; Solé, Ricard; T. Maestre, Fernando. In PNAS, 121, p. e2305153121. 2024.
2023[ to top ]
  • 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), pp. 47–62.e16. Elsevier, 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), p. evad228. 2023.
  • Optimizing crop rotations via {Parrondo}’s paradox for sustainable agriculture. Gokhale, Chaitanya S.; Sharma, Nikhil. In R. Soc. Open Sci., 10(5), p. 221401. 2023.
  • 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, p. 102808. 2023.
  • Potential change in the future spatial distribution of submerged macrophyte species and species richness: the role of today’s lake type and strength of compounded environmental change. Lewerentz, Anne; Hoffmann, Markus; Hovestadt, Thomas; Raeder, Uta; Sarmento Cabral, Juliano. In Oikos, accepted. 2023.
  • Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities. Gaube, Paul; Marchenko, Polina; Müller, Caroline; Schweiger, Rabea; Tenhaken, Raimund; Keller, Alexander; Junker, Robert R. In Environmental Microbiology. Wiley, 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), pp. 1–29. Public Library of Science, 2023.
  • Formative Integration of Julia Code into the Unity Game Engine:The Use Case of Diving into Aquatic Plant Growth. Lewerentz, Anne; Manke, Nico; Schantz, David; Cabral, Juliano S.; von Mammen, Sebastian. 2023.
  • Adjusting the range of cell--cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing. Schardt, Simon; Fischer, Sabine C. In Journal of Mathematical Biology, 87(4), p. 54. 2023.
  • Theoretical assessment of persistence and adaptation in weeds with complex life cycles. Lauenroth, Dana; Gokhale, Chaitanya S. In Nat. Plants, 9(8), pp. 1267–1279. 2023.
  • The salt-and-pepper pattern in mouse blastocysts is compatible with signalling beyond the nearest neighbours. Fischer, Sabine; Schardt, Simon; Lilao-Garzon, Joaquin; Munoz-Descalzo, Silvia. In iScience, p. 108106. Elsevier {BV}, 2023.
  • Assessing the agreement between the pneumatic and the flow-centrifuge method for estimating xylem safety in temperate diffuse-porous tree species. Paligi, Sharath Shyamappa; Link, Roman M.; Isasa, Emilie; Bittencourt, Paulo; Cabral, Juliano Sarmento; Jansen, Steven; Oliveira, Rafael S; Pereira, Luciano; Schuldt, Bernhard. In Plant Biology, 25, pp. 1171–1185. 2023.
  • The road to integrate climate change effects on land-use change in regional biodiversity models. Sarmento Cabral, Juliano; Mendoza-Ponce, Alma; da Silva, André Pinto; Oberpriller, Johannes; Mimet, Anne; Kieslinger, Julia; Berger, Thomas; Blechschmidt, Jana; Brönner, Maximilian; Classen, Alice; Fallert, Stefan; Hartig, Florian; Hof, Christian; Hoffmann, Markus; Knoke, Thomas; Krause, Andreas; Lewerentz, Anne; Pohle, Perdita; Raeder, Uta; Rammig, Anja; Redlich, Sarah; Rubanschi, Sven; Stetter, Christian; Weisser, Wolfgang; Vedder, Daniel; Verburg, Peter H.; Zurell, Damaris. In People & Nature, accepted. 2023.
  • {The Effect of Mating Complexity on Gene Drive Dynamics}. Verma, Prateek; Reeves, R Guy; Simon, Samson; Otto, Mathias; Gokhale, Chaitanya S. In The American Naturalist, 201(1), pp. E1-E22. 2023.
  • The {Effect} of {Mating} {Complexity} on {Gene} {Drive} {Dynamics}. Verma, Prateek; Reeves, R Guy; Simon, Samson; Otto, Mathias; Gokhale, Chaitanya S. In Am. Nat., 201(1), pp. E1-E22. 2023.
  • Tissues as networks of cells: towards generative rules of complex organ development. Fischer, Sabine C.; Bassel, George W.; Kollmannsberger, Philip. In Journal of The Royal Society Interface, 20(204), p. 20230115. The Royal Society, 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 (ed.), pp. 444–458. 2023.
  • User-Centered Engineering of an Interactive Land Use Exploration Tool. Buhl, Tobias; Marcomin, David; Fallert, Stefan; Blechschmidt, Jana; Bönisch, Franziska; Mark, Robert; Cabral, Juliano S.; von Mammen, Sebastian. In Workshop on Visualisation in Environmental Sciences (EnvirVis), S. Dutta, K. Feige, K. Rink, D. Zeckzer (eds.). The Eurographics Association, 2023.
2022[ to top ]
  • New proposal of epiphytic Bromeliaceae functional groups to include nebulophytes and shallow tanks. Reyes-García, Casandra; Pereira-Zaldívar, Narcy Anai; Espadas-Manrique, Celene; Tamayo-Chim, Manuela; Chilpa-Galván, Nahlleli Civi; Cach-Pérez, Manuel Jesús; Ramírez-Medina, Marypaz; Benavides, Ana María; Hietz, Peter; Zotz, Gerhard; Andrade, José Luis; Cardelús, Catherine; Oliveiras, Rodolfo De Paula; Einzmann, Helena J.R.; Guzmán Jacob, Valeria; Krömer, Thorsten; Pinzón, Juan Pablo; Sarmento Cabral, Juliano; Wanek, Wolfgang; Woods, Carrie. In Plants, p. accepted. 2022.
  • Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing. Schardt, Simon; Fischer, Sabine C. In arXiv, p. 2211.07241. 2022.
  • Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus. Schmid, Kerstin; Knote, Andreas; Mück, Alexander; Pfeiffer, Keram; von Mammen, Sebastian; Fischer, Sabine C. In Frontiers in Bioinformatics. Frontiers, 2022.
  • Spatiotemporal dynamics of freshwater macrophytes in Bavarian lakes under environmental change. Lewerentz, Anne F. Universität Würzburg, 2022.
  • Phylogenetic relatedness of food plants reveals highest insect herbivore specialisation at intermediate temperatures along a broad climatic gradient. König, Sebastian; Krauss, Jochen; Keller, Alexander; Bofinger, Lukas; Steffan-Dewenter, Ingolf. In Global Change Biology, p. in press. 2022.
  • Recognition and reconstruction of cell differentiation patterns with deep learning. Dirk, Robin; Fischer, Jonas L.; Schardt, Simon; Ankenbrand, Markus J.; Fischer, Sabine C. In arXiv, p. 2212.10058. 2022.
  • Critical links between biodiversity, nutrition and health in wild bee conservation. Parreno, M.A.; Alaux, C.; Brunet, J.-L.; Butschkau, S.; Buydens, L.; Filipiak, M.; Henry, M.; Keller, Alexander; Klein, A.-M.; Kuhlmann, M; Leroy, C.; Meeus, I; Palmer-Young, E; Piot, N.; Requier, F.; Ruedenauer, F.; Smagghe, G.; Stevenson, P.C; Leonhardt, S.D. In Trends in Ecology and Evolution, p. in press. 2022.
  • Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. Moraes, Ana Paula; Engel, Thaissa; Forni-Martins, Eliana; Felix, Leonardo; Cabral, Juliano. In Annals of Botany, 130, pp. 11–25. 2022.
  • 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), pp. 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.
  • Putting vascular epiphytes on the traits map. Hietz, Peter; Wagner, Katrin; Nunes Ramos, Flavio; Cabral, Juliano; Agudelo, Claudia; Benavides, Ana Maria; Cach-Pérez, Manuel Jesús; Cardelús, Catherine; Chilpa Galván, Nahlleli; Costa, Lucas; de Paula Oliveira, Rodolfo; Einzmann, Helena; Farias, Rafael; Guzmán Jacob, Valeria; Kattge, Jens; Kessler, Michael; Kirby, Catherine; Kreft, Holger; Kromer, Thorsten; Males, Jamie; Monsalve Correa, Samuel; Moreno-Chacón, Maria; Petter, Gunnar; Reyes-Garcia, Casandra; Saldana, Alfredo; Schellenberger Costa, David; Taylor, Amanda; Velázquez Rosas, Noé; Wanek, Wolfgang; Woods, Carrie; Zotz, Gerhard. In Journal of Ecology, 110, pp. 340–358. 2022.
  • Forest landscapes increase diversity of honeybee diets in the tropics. Cannizzaro, Chris; Keller, Alexander; Wilson, Rachele S.; Elliott, Brittany; Newis, Ryan; Ovah, Raywin; Inae, Kelly; Kerlin, Douglas H.; Bar, Ido; Kämper, Wiebke; Shapcott, Alison; Wallace, Helen M. In Forest Ecology and Management, p. in press. 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), pp. ii5-ii12. 2022.
  • Scaling up our understanding of tipping points. Kéfi, Sonia; Saade, Camille; Berlow, Eric; Cabral, Juliano S. Cabral; Fronhofer, Emanuel. In Philosophical Transactions of the Royal Society B, 377, p. 20210386. 2022.
2021[ to top ]
  • Transmission of Bacterial Symbionts With and Without Genome Erosion Between a Beetle Host and the Plant Environment. Wierz, Jürgen C.; Gaube, Paul; Klebsch, Dagmar; Kaltenpoth, Martin; Flórez, Laura V. In Frontiers in Microbiology, 12. Frontiers Media {SA}, 2021.
  • Identifying {New} {Potential} {Biomarkers} in {Adrenocortical} {Tumors} {Based} on {mRNA} {Expression} {Data} {Using} {Machine} {Learning}. Marquardt, André; Landwehr, Laura-Sophie; Ronchi, Cristina L.; di Dalmazi, Guido; Riester, Anna; Kollmannsberger, Philip; Altieri, Barbara; Fassnacht, Martin; Sbiera, Silviu. In Cancers, 13(18), p. 4671. 2021.
  • How bees find a way in European cities: pollen metabarcoding unravels multiple feeding strategies and their effects on distribution patterns in four wild bee species. Casanelles Abella, Joan; Müller, Stefanie; Keller, Alexander; Aleixo, Cristiana; Alós Orti, Marta; Chiron, François; Deguines, Nicolas; Hallikma, Tiit; Laanisto, Lauri; Pinho, Pedro; Samson, Roeland; Tryjanowski, Piotr; Van Mensel, Anskje; Pellissier, Loïc; Moretti, Marco. In Journal of Applied Ecology, p. in press. 2021.
  • gen3sis: The GENeral Engine for Eco-Evolutionary SImulationS on the origins of biodiversity. Hagen, Oskar; Flück, Benjamin; Fopp, Fabian; Cabral, Juliano S.; Hartig, Florian; Pontarp, Mikael; Rangel, Thiago F.; Pellissier, Loïc. In Plos Biology, 19, p. e3001340. 2021.
  • Many small rather than few large sources identified in long-term bee pollen diets in agroecosystems. Wilson, Rachele; Keller, Alexander; Shapcott, Alison; Leonhardt, Sara D.; Sickel, Wiebke; Hardwick, J. L.; Heard, Tim; Kaluza, Benjamin F; and Wallace, Helen. In Agriculture, Ecosystems and Environment. 2021.
  • Functional resin use in solitary bees. Chui, Shao Xiong; Keller, Alexander; Leonhardt, Sara. In Ecological Entomology, p. in press. 2021.
  • Inferring core genome phylogenies for bacteria. Keller, Alexander; Ankenbrand, Markus J. In Bacterial Pangenomics (in press), A. Mengoni, M. Fondi, G. Bacci (eds.). Springer Verlag, Heidelberg, Germany, 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), p. 27. 2021.
  • Niche evolution reveals disparate signatures of speciation in the ‘great speciator‘ (White-eyes, Aves: genus Zosterops). Engler, Jan O.; Lawrie, Yvonne; Cabral, Juliano S.; Lens, Luc. In Journal of Biogeography, 48, pp. 1981–1993. 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), pp. 1–18. Public Library of Science, 2021.
  • Osmotic adaptation and compatible solute biosynthesis of phototrophic bacteria as revealed from genome analyses. Imhoff, Johannes F.; Rahn, Tanja; Künzel, Sven; Keller, Alexander; Neulinger, Sven C. In Microorganisms, 9(1), p. 46. 2021.
  • Pollen diets and niche overlap of honey bees and native bees in protected areas. Elliott, Brittany; Wilson, Rachele; Shapcott, Alison; Keller, Alexander; Newis, Ryan; Cannizzaro, Chris; Burwell, Chris; Smith, Tobias; Leonhardt, Sara D.; Kämper, Wiebke; Wallace, Helen. In Basic and Applied Ecology, Special issue: Sequence based molecular ecology. 2021.
  • Preservation methods of honey-bee collected pollen are not a source of bias in ITS2 metabarcoding. Quaresma, Andreia; Brodschneider, Robert; Gratzer, Kristina; Gray, Alison; Keller, Alexander; Kilpinen, Ole; Rufino, Jose; van der Steen, Jozef; Vejsnaes, Flemming; Pinto, Maria Alice. In Environmental Monitoring and Assessment, p. in press. 2021.
  • Temporal environmental variation imposes differential selection on both genomic and ecological traits. Leidinger, Ludwig; Vedder, Daniel; Cabral, Juliano S. In Oikos, 130, pp. 1100–1115. 2021.
  • Propagule pressure and an invasion syndrome determine invasion success in a plant community model. Vedder, Daniel; Leidinger, Ludwig; Sarmento Cabral, Juliano. In Ecology and Evolution, 11, pp. 17106–17116. 2021.
  • Putative roles of bacteria in the carbon and nitrogen cycles in a tropical peat swamp forest. Too, Chin Chin; Ong, Kuan Shion; Lee, Sui Mae; Yule, Catherine M.; Keller, Alexander. In Basic and Applied Ecology, Special issue: Predictors of microbiomes. 2021.
  • Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections. Pauli, Martin; Paul, Mila M.; Proppert, Sven; Mrestani, Achmed; Sharifi, Marzieh; Repp, Felix; Kürzinger, Lydia; Kollmannsberger, Philip; Sauer, Markus; Heckmann, Manfred; Sirén, Anna-Leena. In Communications Biology, 4(1), pp. 1–13. 2021.
  • Subgroup-{Independent} {Mapping} of {Renal} {Cell} {Carcinoma}—{Machine} {Learning} {Reveals} {Prognostic} {Mitochondrial} {Gene} {Signature} {Beyond} {Histopathologic} {Boundaries}. Marquardt, André; Solimando, Antonio Giovanni; Kerscher, Alexander; Bittrich, Max; Kalogirou, Charis; Kübler, Hubert; Rosenwald, Andreas; Bargou, Ralf; Kollmannsberger, Philip; Schilling, Bastian; Meierjohann, Svenja; Krebs, Markus. In Frontiers in Oncology, 11. 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), pp. 1–109. Taylor & Francis, 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, p. 109817. 2021.
  • Species richness is more important for ecosystem functioning than species turnover along an elevational gradient. Albrecht, Joerg; Peters, Marcell K.; Classen, Alice; Becker, Joscha N.; Behler, Christina; Ensslin, Andreas; Ferger, Stefan W.; Gebert, Friederike; Helbig-Bonitz, Maria; Kindeketa, William J.; Mayr, Antonia V.; {Njovu, Henry K. Pabst}; Pommer, Ulf; Röder, Juliane; Rutten, Gemma; Schellenberger Costa, David; Sierra-Cornejo, Natalia; Vogeler, Anna; Vollstädt, Maximilian G. R.; Dulle, Hamadi I.; Eardley, Connal D.; Howell, Kim M.; Keller, Alexander; Peters, Ralph S.; Kakengi, Victor; Hemp, Claudia; Zhang, Jie; Manning, Peter; Müller, Thomas; Böhning-Gaese, Katrin; Brandl, Roland; Hertel, Dietrich; Kiese, Ralf; Kleyer, Michael; Kuzyakov, Yakov; Nauss, Thomas; Tschapka, Marco; Fischer, Markus; Hemp, Andreas; Steffan-Dewenter, Ingolf; Schleuning, Matthias. In Nature Ecology and Evolution, p. in press. 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, pp. 294–303. Nature Publishing Group, 2021.
  • (More than) Hitchhikers through the network: The shared microbiome of bees and flowers. Keller, Alexander; McFrederick, Quinn S.; Dharampal, Prarthana; Steffan, Shawn; Danforth, Bryan N.; Leonhardt, Sara D. In Current Opinion in Insect Science. 2021.
  • Changes amid constancy: flower and leaf microbiomes along land use gradients and between bioregions. Gaube, Paul; Junker, Robert R.; Keller, Alexander. In Basic and Applied Ecology, 50, pp. 1–15. Elsevier {BV}, 2021.
  • Active zone compaction correlates with presynaptic homeostatic potentiation. Mrestani, Achmed; Pauli, Martin; Kollmannsberger, Philip; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, Sören; Sauer, Markus; Sirén, Anna-Leena; Heckmann, Manfred; Paul, Mila M. In Cell Reports, 37(1). 2021.
  • Cryptic species and hidden ecological interactions of halictine bees along an elevational gradient. Mayr, Antonia V.; Keller, Alexander; Peters, Marcell K.; Grimmer, Gudrun; Krischke, Beate; Geyer, Mareen; Schmitt, Thomas; Steffan-Dewenter, Ingolf. In Ecology and Evolution. 2021.
  • Dealing with software complexity in individual-based models. Vedder, Daniel; Ankenbrand, Markus; Cabral, Juliano. In Methods in Ecology and Evolution, 12, pp. 2324–2333. 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), pp. 2179–2191. 2021.
  • Defining the {Basis} of {Cyanine} {Phototruncation} {Enables} a {New} {Approach} to {Single}-{Molecule} {Localization} {Microscopy}. Matikonda, Siddharth S.; Helmerich, Dominic A.; Meub, Mara; Beliu, Gerti; Kollmannsberger, Philip; Greer, Alexander; Sauer, Markus; Schnermann, Martin J. In ACS Central Science, 7(7), pp. 1144–1155. 2021.
  • Depth diversity gradients of macrophytes: shape, drivers and recent shifts. Lewerentz, Anne; Hoffmann, Markus; Cabral, Juliano Sarmento. In Ecology and Evolution, 11, pp. 13830–13845. 2021.
  • Depth diversity gradients of macrophytes: Shape, drivers, and recent shifts. Lewerentz, Anne; Hoffmann, Markus; Cabral, Juliano Sarmento. In Ecology and Evolution, 11(20), pp. 13830–13845. Wiley, 2021.
  • DNA sequence-based biodiversity and interaction ecology. Tiede, Julia; Keller, Alexander; Eitzinger, Bernhard. In Basic and Applied Ecology. 2021.
  • bioDIVERsity. Ein Computerspiel gegen das Imageproblem von Wasserpflanzen. Lewerentz, Anne; Schantz, David; Gröh, Julian; Knote, Andreas; Mammen, Sebastian von; Cabral, Juliano Sarmento. In Mitteilungen der Fränkischen Geographischen Gesellschaft, (67), pp. 29–36. 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), pp. 182–196. 2021.
  • Anthropogenic and environmental drivers shape diversity of non-native plants across the Pacific. Wohlwend, Michael; Craven, Dylan; Weigelt, Patrick; Seebens, Hanno; Kreft, Holger; Winter, Marten; Zurell, Damaris; Cabral, Juliano Sarmento; Essl, Franz; van Kleunen, Mark; Pergl, Jan; Pysek, Petr; Knight, Tiffany. In Diversity and Distributions, 27, pp. 1120–1133. 2021.
  • Agent-based modeling of the effects of forest dynamics, selective logging, and fragment size on epiphyte communities. Petter, Gunnar; Zotz, Gerhard; Kreft, Holger; Cabral, Juliano Sarmento. In Ecology and Evolution, (11), pp. 2937–2951. 2021.
  • Effects of three flower field types on bumblebees and their pollen diets. Piko, Julia; Keller, Alexander; Geppert, Costanza; Batáry, Péter; Tscharntke, Teja; Westphal, Catrin; Hass, Annika L. In Basic and Applied Ecology, 52, pp. 95–108. 2021.
  • An integrative environmental pollen diversity assessment and its importance for the Sustainable Development Goals. Hornick, Thomas; Bastl, M; Bohlmann, S; Bonn, A; Bumberger, J; Dietrich, P; Gemeinholzer, B.; Grote, R; Harpole, W. S.; Heinold, B; Keller, Alexander; Luttkus, M. L.; Mäder, P.; Motivans, E.; Passonneau, S.; Punyasena, S.W.; Rakosy, Demetra; Richter, A.; Richter, R.; Sickel, W.; Steffan-Dewenter, I.; Theodorou, P.; Treudler, R.; Werchan, B.; Werchan, M.; Wolke, R.; Dunker, S. In Plants, People, Planet, p. in press. 2021.
2020[ to top ]
  • Floral Species Richness Correlates with Changes in the Nutritional Quality of Larval Diets in a Stingless Bee. Trinkl, Moritz; Kaluza, Benjamin F.; Wallace, Helen; Heard, Tim A.; Keller, A.; Leonhardt, Sara D. In Insects, 11(2). 2020.
  • Macroecology in the age of big data – where to go from here? Wüest, Rafael O.; Zimmermann, Niklaus E.; Zurell, Damaris; Alexander, Jake; Fritz, Susanne A.; Hof, Christian; Kreft, Holger; Normand, Signe; Sarmento Cabral, Juliano; Szekely, Eniko; Thuiller, Wilfried; Wikelski, Martin; Karger, Dirk Nikolaus. In Journal of Biogeography, 47, pp. 1–12. 2020.
  • CRISPR/Cas 9 mediated mutations as a new tool for studying taste in honeybees. Degirmenci, Laura; Geiger, Dietmar; Rogé Ferreira, Fábio Luiz; Keller, Alexander; Krischke, Beate; Beye, Martin; Steffan-Dewenter, Ingolf; Scheiner, Ricarda. In Chemical Senses, p. bjaa063. 2020.
  • Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach. Liebisch, Tim; Drusko, Armin; Mathew, Biena; Stelzer, Ernst H. K.; Fischer, Sabine C.; Matthäus, Franziska. In Scientific Reports, 10(1), p. 22405-. 2020.
  • DeepCLEM: automated registration for correlative light and electron microscopy using deep learning [version 1; peer review: awaiting peer review]. Seifert, R; Markert, SM; Britz, S; Perschin, V; Erbacher, C; Stigloher, C; Kollmannsberger, P. In F1000Research, 9(1275). 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 (eds.), pp. 60–67. Springer International Publishing, Cham, 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), p. 254. 2020.
  • Disentangling the drivers of local species richness using probabilistic species pools. Karger, Dirk Nikolaus; Wüest, Rafael; König, Christian; Cabral, Juliano; Weigelt, Patrick; Zimmermann, Nikaus; Linder, Peter. In Journal of Biogeography, (47), pp. 879–889. 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 Curr Biol, 30(12), pp. 2312–2320. 2020.
  • Biological network growth in complex environments – a computational framework. Paul, Torsten Johann; Kollmannsberger, Philip. In PLOS Computational Biology, 16(11), p. e1008003. 2020.
  • Haruspex: {A} {Neural} {Network} for the {Automatic} {Identification} of {Oligonucleotides} and {Protein} {Secondary} {Structure} in {Cryo}-{Electron} {Microscopy} {Maps}. Mostosi, Philipp; Schindelin, Hermann; Kollmannsberger, Philip; Thorn, Andrea. In Angewandte Chemie International Edition, n/a(n/a). 2020.
  • 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, p. in press. 2020.
  • Strong phylogenetic constraint on transition metal incorporation in the mandibles of the hyper-diverse Hymenoptera (Insecta). Polidori, Carlo; Jorge, Alberto; Keller, Alexander; Ornosa, Concepcion; Tormos, Jose; Asis, Josep Daniel; Nieves-Aldrey, Jose Luis. In Organisms, Diversity and Evolution, p. in press. 2020.
  • Modeling how community assembly alters the functioning of ecosystems. Koffel, Thomas; Kremer, Colin T.; Bannar-Martin, Katherine; Ernest, S. K. Morgan; Eisenhauer, Nico; Roscher, Christiane; Cabral, Juliano Sarmento; Leibold, Mathew A. In bioRxiv. 2020.
  • Efficient {Classification} of {White} {Blood} {Cell} {Leukemia} with {Improved} {Swarm} {Optimization} of {Deep} {Features}. Sahlol, Ahmed T.; Kollmannsberger, Philip; Ewees, Ahmed A. In Scientific Reports, 10(1), p. 2536. 2020.
  • Mapping human pressures on biodiversity across the planet uncovers anthropogenic threat complexes. Bowler, D. E.; Bjorkman, A.D.; Dornelas, M.; Myers-Smith, I.; O’Connor, M.; Navarro, L.M.; Niamir, A.; Supp, S.R.; Waldock, C.; Vellend, M.; Blowes, S.A.; Böhning-Gaese, K.; Bruelheide, H.; Elahi, R.; Antão, L.H.; Hines, J.; Isbell, F.; Jones, H.P.; Magurran, A.E.; Cabral, J.S.; Winter, M.; Bates, A.E. In People and Nature, 2, pp. 380–394. 2020.
  • Susceptibility of red mason bee larvae to bacterial threats due to microbiome exchange with imported pollen provisions. Voulgari-Kokota, Anna; Steffan-Dewenter, Ingolf; Keller, Alexander. In Insects, 11(6). 2020.
  • Tracking beekeepers in floristic regions of Iran: employing DNA metabarcoding to determine the geographical origin of honey. Khansaritoreh, Elmira; Salamaki, Y; Ramezani, E; Akbari-Azirani, T; Keller, Alexander; Neumann, Katrin; Alizadeh, K; Zarre, S; Beckh, G; Behling, H. In Heliyon. 2020.
  • Integrating the underlying structure of stochasticity into community ecology. Shoemaker, Lauren G.; Sullivan, Lauren L.; Donohue, Ian; Cabral, Juliano S.; Williams, Ryan J.; Mayfield, Margaret M.; Chase, Jonathan M.; Chu, Chengjin; Harpole, W. Stanley; Huth, Andreas; HilleRisLambers, Janneke; James, Aubrie R.M.; Kraft, Nathan J.B.; May, Felix; Muthukrishnan, Ranjan; Satterlee, Sean; Taubert, Franziska; Wang, Xugao; Wiegand, Thorsten; Yang, Qiang; Abbott, Karen C. In Ecology, 101, p. e02922. 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, pp. 609–618. 2020.
  • The effect of species extinctions on island biogeographic patterns. Matthews, Tom; Leidinger, Ludwig; Cabral, Juliano. In Ecological Research, 35, pp. 372–381. 2020.
  • The genus Micromonospora as a model microorganism for bioactive natural product discovery. Hifnawy, Mohamed S.; Fouda, Mohamed M.; Sayed, Ahmed M.; Mohammed, Rabab; Hassan, Hossam M.; AbouZid, Sameh F.; Rateb, Mostafa E.; Keller, Alexander; Adamek, Martina; Ziemert, Nadine; Abdelmohsen, Usama Ramadan. In Royal Society of Chemistry Advances, 10(35), pp. 20939–20959. The Royal Society of Chemistry, 2020.
  • {{H}ow to {G}row a {T}ree: {P}lant {V}oltage-{D}ependent {C}ation {C}hannels in the {S}potlight of {E}volution}. Dreyer, I.; Sussmilch, F. C.; Fukushima, K.; Riadi, G.; Becker, D.; Schultz, J.; Hedrich, R. In Trends Plant Sci. 2020.
  • Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations. Bargués-Ribera, Maria; Gokhale, Chaitanya S. In PLoS Comput. Biol., 16(1), M. Bargués-Ribera; C. S. Gokhale (eds.). Center for Computational and Theoretical Biology (CCTB), 2020.
  • Introduced bees (Osmia cornifrons) collect pollen from both coevolved and novel host-plant species within their family-level phylogenetic preferences. Vaudo, Anthony D.; Biddinger, David J.; Sickel, Wiebke; Keller, Alexander; López-Uribe, Margarita M. In Royal Society Open Science, p. in press. 2020.
  • {{T}he {V}enus flytrap trigger hair-specific potassium channel {K}{D}{M}1 can reestablish the {K}+ gradient required for hapto-electric signaling}. Iosip, A. L.; Böhm, J.; Scherzer, S.; Al-Rasheid, K. A. S.; Dreyer, I.; Schultz, J.; Becker, D.; Kreuzer, I.; Hedrich, R. In PLoS Biol, 18(12), p. e3000964. 2020.
  • The transition from local to global patterns governs the differentiation of mouse blastocysts. Fischer, Sabine C.; Corujo-Simon, Elena; Lilao-Garzon, Joaquin; Stelzer, Ernst H. K.; Muñoz-Descalzo, Silvia. In PLOS ONE, 15(5), pp. 1–29. Public Library of Science, 2020.
  • {Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations}. Bargués-Ribera, Maria; Gokhale, Chaitanya S. In PLoS Computational Biology, 16(1), p. e1007546. 2020.
2019[ to top ]
  • Active zone compaction for presynaptic strength. Mrestani, Achmed; Kollmannsberger, Philip; Pauli, Martin; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, S{ö}ren; Sauer, Markus; Sir{é}n, Anna-Leena; Heckmann, Manfred; Paul, Mila M. In bioRxiv. Cold Spring Harbor Laboratory, 2019.
  • A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics. Steuer Costa, Wagner; Van der Auwera, Petrus; Glock, Caspar; Liewald, Jana F.; Bach, Maximilian; Schüler, Christina; Wabnig, Sebastian; Oranth, Alexandra; Masurat, Florentin; Bringmann, Henrik; Schoofs, Liliane; Stelzer, Ernst H.K.; Fischer, Sabine C.; Gottschalk, Alexander. In Nature Communications, 10(4095). 2019.
  • A minimal model for the latitudinal diversity gradient suggests a dominant role for ecological limits. Etienne, Rampal S.; Cabral, Juliano S.; Hagen, Oskar; Hartig, Florian; Hurlbert, Allen H.; Pellissier, Loïc; Pontarp, Mikael; Storch, David. In The American Naturalist, (194), pp. E122-E133. 2019.
  • {{V}enus flytrap microbiotas withstand harsh conditions during prey digestion}. Sickel, W.; Van de Weyer, A. L.; Bemm, F.; Schultz, J.; Keller, A. In FEMS Microbiol. Ecol., 95(3). 2019.
  • Venus flytrap microbiota withstand harsh conditions during prey digestion. Sickel, Wiebke; Van der Weyer, Anna-Lena; Bemm, Felix; Schultz, Jörg; Keller, Alexander. In FEMS Microbiology Ecology, p. fiz010. 2019.
  • An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians. Fischer, Sabine C. In Computational Biology, H. Husi (ed.). Codon Publications, Brisbane, Australia, 2019.
  • {{A}cquiring {C}ontrol: {T}he {E}volution of {S}tomatal {S}ignalling {P}athways}. Sussmilch, F. C.; Schultz, J.; Hedrich, R.; Roelfsema, M. R. G. In Trends Plant Sci., 24(4), pp. 342–351. 2019.
  • The latitudinal diversity gradient - novel understanding through mechanistic eco-evolutionary models. Pontarp, Mikael; Bunnefeld, Lynsey; Cabral, Juliano Sarmento; Etienne, Rampal S.; Fritz, Susanne A.; Gillespie, Rosemary; Graham, Catherine H.; Hagen, Oskar; Hartig, Florian; Huang, Shan; Jansson, Roland; Maliet, Odile; Münkemüller, Tamara; Pellissier, Loïc; Rangel, Thiago F.; Storch, David; Wiegand, Thorsten; Hurlbert, Allen H. In Trends in Ecology & Evolution, 34, pp. 211–223. 2019.
  • Species richness change across spatial scales. Chase, Jonathan; McGill, Brian; Thompson, Patrick; Antao, Laura; Bates, Amanda; Blowes, Shane; Dornelas, Maria; Gonzalez, Andrew; Magurran, Anne; Supp, Sarah; Winter, Marten; Bjorkman, Anne; Bruelheide, Helge; Byrnes, Jarrett; Cabral, Juliano Sarmento; Elahi, Robin; Gomez, Catalina; Guzmán, Héctor; Isbell, Forest; Myers-Smith, Isla; Jones, Holly; Hines, Jessica; Vellend, Mark; Waldock, Conor; O’Connor, Mary. In Oikos. 2019.
  • Bacterial community structure and succession in nests of two megachilid bee genera. Voulgari-Kokota, Anna; Grimmer, Gudrun; Steffan-Dewenter, Ingolf; Keller, Alexander. In FEMS Microbiology Ecology, 95(1), p. fiy218. 2019.
  • Understanding extinction debts: spatio-temporal scales, mechanisms and a roadmap for future research. Figueiredo, Ludmilla; Krauß, Jochen; Steffan-Dewenter, Ingolf; Sarmento Cabral, Juliano. In Ecography, 42, pp. 1973–1990. 2019.
  • Surface tension determines tissue shape and growth kinetics. Ehrig, Sebastian; Bidan, Cécile M.; West, Alan; Jacobi, Cornelius; Lam, Karen; Kollmannsberger, Philip; Petersen, Ansgar; Tomancak, Pavel; Kommareddy, Krishna; Fischer, Franz Dieter; Fratzl, Peter; Dunlop, John W. C. In Science Advances, 5(9), p. eaav9394. 2019.
  • Assessing predicted isolation effects from the general dynamic model of island biogeography with an eco-evolutionary model for plants. Cabral, J.S.; Whittaker, R.J.; Wiegand, K.; Kreft, H. In Journal of Biogeography, 46, pp. 1569–1581. 2019.
  • The dimensionality of stability depends on disturbance type. Radchuk, Viktoriia; De Laender, Frederik; Sarmento Cabral, Juliano; Boulangeat, Isabelle; Crawford, Michael; Bohn, Friedrich; De Raedt, Jonathan; Scherer, Cedric; Svenning, Jens-Christian; Thonicke, Kirsten; Schurr, Frank; Grimm, Volker; Kramer-Schadt, Stephanie. In Ecology Letters, 22, pp. 674–684. 2019.
  • Towards a {Connectomic} {Description} of the {Osteocyte} {Lacunocanalicular} {Network} in {Bone}. Weinkamer, Richard; Kollmannsberger, Philip; Fratzl, Peter. In Current Osteoporosis Reports. 2019.
  • Cold-adaptation of Subtercola vilae DB165T, an isolate from a high-altitude cold volcano lake, as revealed by its genome analysis. Villalobos, Alvaro S; Wiese, Jutta; Imhoff, Johannes F; Dorador, Cristina; Keller, Alexander; Hentschel, Ute. 2019.
  • Climate–land-use interactions shape tropical mountain biodiversity and ecosystem functions. Peters, Marcell K.; Hemp, Andreas; Appelhans, Tim; Becker, Joscha N.; Behler, Christina; Classen, Alice; Detsch, Florian; Ensslin, Andreas; Ferger, Stefan W.; Frederiksen, Sara B.; Gebert, Friederike; Gerschlauer, Friederike; Gütlein, Adrian; Helbig-Bonitz, Maria; Hemp, Claudia; Kindeketa, William J.; Kühnel, Anna; Mayr, Antonia V.; Mwangomo, Ephraim; Ngereza, Christine; Njovu, Henry K.; Otte, Insa; Pabst, Holger; Renner, Marion; Röder, Juliane; Rutten, Gemma; Schellenberger Costa, David; Sierra-Cornejo, Natalia; Vollstädt, Maximilian G. R.; Dulle, Hamadi I.; Eardley, Connal D.; Howell, Kim M.; Keller, Alexander; Peters, Ralph S.; Ssymank, Axel; Kakengi, Victor; Zhang, Jie; Bogner, Christina; Böhning-Gaese, Katrin; Brandl, Roland; Hertel, Dietrich; Huwe, Bernd; Kiese, Ralf; Kleyer, Michael; Kuzyakov, Yakov; Nauss, Thomas; Schleuning, Matthias; Tschapka, Marco; Fischer, Markus; Steffan-Dewenter, Ingolf. In Nature. 2019.
  • Mouse ICM organoids reveal three-dimensional cell fate clustering. Mathew, Biena; Muñoz-Descalzo, Silvia; Corujo Simon, Elena; Schröter, Christian; Stelzer, Ernst H.K; Fischer, Sabine C. In Biophysical Journal, 116, pp. 127–141. Elsevier, 2019.
  • Honey bee waggle dance communication increases diversity of pollen diets in intensively managed agricultural landscapes. Nürnberger, Fabian; Keller, Alexander; Härtel, Stephan; Steffan-Dewenter, Ingolf. In Molecular Ecology, p. in press. 2019.
  • Electron tomography of mouse LINC complexes at meiotic telomere attachment sites with and without microtubules. Spindler, Marie-Christin; Redolfi, Josef; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian; Benavente, Ricardo. In Communications Biology, 2(1), p. 376-. 2019.
  • Immersive Analysis of 3D Multi-cellular In-Vitro and In-Silico Cell Cultures. Knote, Andreas; Fischer, Sabine C.; Cussat-Blanc, Sylvain; Niebling, Florian; Bernard, David; Cogoni, Florian; von Mammen, Sebastian. In 2019 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR), pp. 82–89. 2019.
  • Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of insular plant diversity. Cabral, J.S.; Wiegand, K.; Kreft, H. In Journal of Biogeography, 46, pp. 1582–1597. 2019.
  • Drivers, diversity and functions of solitary bee microbiota. Voulgari-Kokota, Anna; McFrederick, Quinn; Steffan-Dewenter, Ingolf; Keller, Alexander. In Trends in Microbiology, p. in press. 2019.
  • Linking the foraging patterns of megachilid bee species to nest bacteria. Voulgari-Kokota, Anna; Ankenbrand, Markus; Grimmer, Gudrun; Steffan-Dewenter, Ingolf; Keller, Alexander. In Ecology and Evolution, p. in press. 2019.
2018[ to top ]
  • Draft Genome Sequence of Dyella sp. Strain C9, Isolated from a Malaysian Tropical Peat Swamp Forest. Too, Chin Chin; Ong, Kuan Shion; Lee, Sui Mae; Yule, Catherine M; Keller, Alexander. In Microbiol Res Announc, 7(12), pp. e01083–18. Am Soc Microbiol, 2018.
  • Microbial community structure in a Malaysian tropical peat swamp forest: the influence of tree species and depth. Too, Chin Chin; Keller, Alexander; Sickel, Wiebke; Lee, Sui Mae; Yule, Catherine M. In Frontiers in Microbiology, 9, p. 2859. 2018.
  • 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), p. 229. 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, pp. 2028–2033. 2018.
  • reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. Terhoeven, Niklas; Schultz, Jörg; Hackl, Thomas. In Journal of Open Source Software, 3(22), p. 527. 2018.
  • Physical contact between mesenchymal stem cells and endothelial precursors induces distinct signatures with relevance to the very early phase of regeneration. Hafen, Bettina; Wiesner, Susanne; Schlegelmilch, Katrin; Keller, Alexander; Seefried, Lothar; Ebert, Regina; Walles, Heike; Jakob, Franz; Schütze, Norbert. In Journal of Cellular Biochemistry. 2018.
  • The characterization of the circadian clock in the olive fly Bactrocera oleae (Diptera: Tephritidae) reveals a Drosophila-like organization. Bertolini, Enrico; Kistenpfennig, Christa; Menegazzi, Pamela; Keller, Alexander; Koukidou, Martha; Helfrich-F{ö}rster, Charlotte. In Scientific Reports, 8(1), p. 816. 2018.
  • Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts. Kollmannsberger, Philip; Bidan, Cécile M; Dunlop, John; Fratzl, Peter; Vogel, Viola. In Science Advances, 4(1), p. eaao4881. 2018.
  • Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest. Too, Chin Chin; Ong, Kuan Shion; Lee, Sui Mae; Yule, Catherine M; Keller, Alexander. In Genome announcements, 6(25), pp. e00459–18. Am Soc Microbiol, 2018.
  • Integrating community assembly and biodiversity reveals new dimensions of ecosystem functions: the Community Assembly and the Functioning of Ecosystems (CAFE) approach. Bannar-Martin, Katherine; Kremer, Colin; Ernest, Morgan; Leibold, Mathew; Auge, Harald; Chase, Jonathan; Declerck, Steven; Eisenhauer, Nico; Harpole, Stanley; Hillebrand, Helmut; Isbell, Forest; Koffel, Thomas; Larsen, Stefano; Narwani, Anita; Petermann, Jana; Roscher, Christiane; Sarmento Cabral, Juliano; Supp, Sarah. In Ecology Letters, 21, pp. 167–180. 2018.
  • Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning. Kaltdorf, Kristin V; Theiss, Maria; Markert, Sebastian M; Zhen, Mei; Dandekar, Thomas; Stigloher, Christian; Kollmannsberger, Philip. In PLoS one, 13(10), p. e0205348. Public Library of Science, 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). American Society for Microbiology Journals, 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), pp. e00561–18. Am Soc Microbiol, 2018.
  • Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition. Bouain, Nadia; Satbhai, Santosh B.; Korte, Arthur; Saenchai, Chorpet; Desbrosses, Guilhem; Berthomieu, Pierre; Busch, Wolfgang; Rouached, Hatem. In PLOS Genetics, 14(4), pp. 1–23. Public Library of Science, 2018.
  • Spatial scaling of extinction rates: theory and data reveal non-linearity, and a major upscaling and downscaling challenge. Keil, P.; Pereira, H.M.; Cabral, J.S.; Chase, J.; May, F.; Martins, I.S.; Winter, M. In Global Ecology and Biogeography, 27, pp. 2–13. 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), pp. e00560–18. Am Soc Microbiol, 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, p. e116. 2017.
  • {Social dilemma in the external immune system of the red flour beetle? It is a matter of time}. Gokhale, Chaitanya S.; Traulsen, Arne; Joop, Gerrit. In Ecology and Evolution, 7(17), pp. 6758–6765. 2017.
  • FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Dandekar, Thomas; Stigloher, Christian. In PLOS Computational Biology, 13(1), pp. 1–21. Public Library of Science, 2017.
  • Spatial heterogeneity in the canalicular density of the osteocyte network in human osteons. Repp, Felix; Kollmannsberger, Philip; Roschger, Andreas; Kerschnitzki, Michael; Berzlanovich, Andrea; Gruber, Gerlinde M.; Roschger, Paul; Wagermaier, Wolfgang; Weinkamer, Richard. In Bone Reports, 6, pp. 101–108. 2017.
  • Genetic Components of Root Architecture Remodeling in Response to Salt Stress. Julkowska, Magdalena; Koevoets, Iko Tamar; Mol, Selena; Hoefsloot, Huub CJ; Feron, Richard; Tester, Mark; Keurentjes, Joost J.B.; Korte, Arthur; Haring, Michel A; de Boer, Gert-Jan; Testerink, Christa. In The Plant Cell. American Society of Plant Biologists, 2017.
  • Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. Danner, Nadja; Keller, Alexander; H{ä}rtel, Stephan; Steffan-Dewenter, Ingolf. In PloS one, 12(8), p. e0183716. Public Library of Science, 2017.
  • Flagship umbrella species needed for conservation of overlooked biodiversity. Kalinkat, G.; Cabral, J.S.; Darwall, W.; Ficetola, F.; Fisher, J.; Giling, D.; Gosselin, M.-P.; Grossart, H.-P.; Jähnig, S.; Jeschke, J.; Knopf, K.; Larsen, S.; Onandia, G.; Pätzig, M.; Saul, W.-C.; Singer, G.; Jarić, I. In Conservation Biology, 31, pp. 481–485. 2017.
  • Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps. Wurdack, Mareike; Polidori, Carlo; Keller, Alexander; Feldhaar, Heike; Schmitt, Thomas. In Evolution, in press. 2017.
  • Effects of time and isolation on plant diversity: testing island biogeography theory with an eco-evolutionary model. Cabral, J.S.; Whittaker, R.J.; Wiegand, K.; Kreft, H. In bioRxiv, (100289). 2017.
  • The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone. Kollmannsberger, Philip; Kerschnitzki, Michael; Repp, Felix; Wagermaier, Wolfgang; Weinkamer, Richard; Fratzl, Peter. In New Journal of Physics, 19, p. 073019. 2017.
  • Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of island biodiversity. Cabral, J.S.; Wiegand, K.; Kreft, H. In bioRxiv, (099978). 2017.
  • Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone. Repp, Felix; Kollmannsberger, Philip; Roschger, Andreas; Berzlanovich, Andrea; Gruber, Gerlinde; Roschger, Paul; Wagermaier, Wolfgang; Weinkamer, Richard. In Journal of Stuctural Biology, 199, pp. 177–186. 2017.
  • AraPheno: a public database for Arabidopsis thaliana phenotypes. Seren, {Ü}mit; Grimm, Dominik; Fitz, Joffrey; Weigel, Detlef; Nordborg, Magnus; Borgwardt, Karsten; Korte, Arthur. In Nucleic acids research, 45(D1), pp. D1054-D1059. Oxford University Press, 2017.
  • Biodiversity dynamics on islands: explicitly accounting for causality in mechanistic models. Leidinger, Ludwig; Cabral, Juliano Sarmento. In Diversity, 9(30). 2017.
  • An individual-based model for the collective cancer cell migration explains speed dynamics and phenotype variability in response to growth factors. Stichel, D.; Middleton, A.M.; M{ü}ller, B.F.; Depner, S.; Klingm{ü}ller, U.; Breuhahn, K.; Matth{ä}us, F. In NPJ Systems Biology and Applications, 3, p. Art. no. 5. 2017.
  • Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. Moraes, A.; de Mesquita Filho, J.; Koehler, S.; Cabral, J.; Lopes Gomes, S.; Viccini, L.; Barros, F.; Felix, L.; Guerra, M.; Forni-Martins, E. In Plant Biology, 19, pp. 298–308. 2017.
  • Mechanistic models in macroecology and biogeography: state-of-art and prospects. Cabral, Juliano Sarmento; Valente, Luis; Hartig, Florian. In Ecography, 40(267-280). 2017.
  • The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. Togninalli, Matteo; Seren, Ümit; Meng, Dazhe; Fitz, Joffrey; Nordborg, Magnus; Weigel, Detlef; Borgwardt, Karsten; Korte, Arthur; Grimm, Dominik G. In Nucleic Acids Research, p. gkx954. 2017.
2016[ to top ]
  • 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, p. 2348. F1000 Research, Ltd., 2016.
  • {{A}{L}{V}{I}{S}: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments}. Schwarz, R. F.; Tamuri, A. U.; Kultys, M.; King, J.; Godwin, J.; Florescu, A. M.; Schultz, J.; Goldman, N. In Nucleic Acids Res., 44(8), p. e77. 2016.
  • 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. consortium, The 1001 genomes. In Cell, 166(2), pp. 481–491. 2016.
  • Leaf growth response to mild drought: natural variation in Arabidopsis sheds light on trait architecture. Clauw, Pieter; Coppens, Frederik; Korte, Arthur; Herman, Dorota; Slabbinck, Bram; Dhondt, Stijn; Van Daele, Twiggy; De Milde, Liesbeth; Vermeersch, Mattias; Maleux, Katrien; others. In The Plant Cell, 28(10), pp. 2417–2434. American Society of Plant Biologists, 2016.
  • {{W}{H}{A}{M}{Y} is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in {D}rosophila}. Brinkmann, K.; Winterhoff, M.; Onel, S. F.; Schultz, J.; Faix, J.; Bogdan, S. In J. Cell. Sci., 129(3), pp. 604–620. 2016.
  • {{G}enome of a tardigrade: {H}orizontal gene transfer or bacterial contamination?}. Bemm, F.; Weiss, C. L.; Schultz, J.; Forster, F. In Proc. Natl. Acad. Sci. U.S.A. 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), pp. 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.
  • {{G}ating of the two-pore cation channel {A}t{T}{P}{C}1 in the plant vacuole is based on a single voltage-sensing domain}. Ja?lan, D.; Mueller, T. D.; Becker, D.; Schultz, J.; Cuin, T. A.; Marten, I.; Dreyer, I.; Schonknecht, G.; Hedrich, R. In Plant Biol (Stuttg), 18(5), pp. 750–760. 2016.
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., 32(11), pp. 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), pp. 3030–3032. 2015.
2014[ to top ]
  • Evolutionary Multiplayer Games. Gokhale, Chaitanya S.; Traulsen, Arne. In Dyn. Games Appl., 4(4), C. S. Gokhale; A. Traulsen (eds.), pp. 468–488. Center for Computational and Theoretical Biology (CCTB), 2014.
2013[ to top ]
  • {Dynamic Properties of Evolutionary Multi-player Games in Finite Populations}. Wu, Bin; Traulsen, Arne; Gokhale, Chaitanya. In Games, 4(2), pp. 182–199. Center for Computational and Theoretical Biology (CCTB), 2013.
2009[ to top ]
  • MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease. Bhardwaj, Anshu; Mukerji, Mitali; Sharma, Shipra; Paul, Jinny; Gokhale, Chaitanya S.; Srivastava, Achal K.; Tiwari, Shrish. In BMC Bioinform., 10(S-8), p. 7. 2009.