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    Center for Computational and Theoretical Biology

    Publications

    [ 2018 ] [ 2017 ] [ 2016 ] [ 2015 ] [ 2013 ] [ 2011 ]

    2018[ to top ]

    • 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-Förster, Charlotte in Scientific Reports (2018). 8(1) 816.
       
    • 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 (2018). 4(1) eaao4881.
       
    • 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 (2018). 27 2-13.
       
    • reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome.Terhoeven, Niklas; Schultz, Jörg; Hackl, Thomas in The Journal of Open Source Software (2018). 3(22) 527.
       
    • 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).
       
    • 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 (2018). 14(4) 1-23.
       
    • 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 (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 (2018). 21 167–180.
       
    • 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.
       
    • 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 (2018). 7(12) e01083--18.
       
    • 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 (2018). 6(25) e00459--18.
       
    • chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data.Ankenbrand, Markus J; Pfaff, Simon; Terhoeven, Niklas; Qureischi, Musga; Gündel, Maik; Weiß, Clemens L.; Hackl, Thomas; Förster, Frank in The Journal of Open Source Software (2018). 3(21) 464.
       
    • 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 (2018). 13(10) e0205348.
       

    2017[ to top ]

    • 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 (2017). 19 073019.
       
    • 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 (2017). gkx954.
       
    • 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 (2017). 6 101-108.
       
    • 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 (2017). in press
       
    • Mechanistic models in macroecology and biogeography: state-of-art and prospects.Cabral, Juliano Sarmento; Valente, Luis; Hartig, Florian in Ecography (2017). 40(267-280)
       
    • 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 (2017). 19 298-308.
       
    • Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of island biodiversity.Cabral, J.S.; Wiegand, K.; Kreft, H. in bioRxiv (2017). (099978)
       
    • Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen.Danner, Nadja; Keller, Alexander; Härtel, Stephan; Steffan-Dewenter, Ingolf in PloS one (2017). 12(8) e0183716.
       
    • 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 (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 (2017). 31 481-485.
       
    • 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 (2017). 13(1) 1-21.
       
    • 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 (2017). (100289)
       
    • 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 (2017). 199 177-186.
       
    • 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 (2017). 5 2348.
       
    • Biodiversity dynamics on islands: explicitly accounting for causality in mechanistic models.Leidinger, Ludwig; Cabral, Juliano Sarmento in Diversity (2017). 9(30)
       
    • Biodiversity dynamics on islands: explicitly accounting for causality in mechanistic models.Leidinger, Ludwig; Cabral, Juliano Sarmento in Diversity (2017). 9(3)
       
    • AraPheno: a public database for Arabidopsis thaliana phenotypes.Seren, Ümit; Grimm, Dominik; Fitz, Joffrey; Weigel, Detlef; Nordborg, Magnus; Borgwardt, Karsten; Korte, Arthur in Nucleic acids research (2017). 45(D1) D1054--D1059.
       
    • 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.; Müller, B.F.; Depner, S.; Klingmüller, U.; Breuhahn, K.; Matthäus, F. in NPJ Systems Biology and Applications (2017). 3 Art. no. 5.
       

    2016[ to top ]

    • WHAMY is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in Drosophila.Brinkmann, K.; Winterhoff, M.; Onel, S. F.; Schultz, J.; Faix, J.; Bogdan, S. in J. Cell. Sci. (2016). 129(3) 604--620.
       
    • Venus 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
       
    • 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 (2016). 28(10) 2417--2434.
       
    • Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?Bemm, F.; Weiss, C. L.; Schultz, J.; Forster, F. in Proc. Natl. Acad. Sci. U.S.A. (2016).
       
    • Gating of the two-pore cation channel AtTPC1 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) (2016). 18(5) 750--760.
       
    • 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.
       
    • ALVIS: 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. (2016). 44(8) e77.
       
    • 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana.consortium, The 1001 genomes in Cell (2016). 166(2) 481--491.
       

    2015[ to top ]

    • 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.
       
    • ITS2 Database V: Twice as Much.Ankenbrand, M. J.; Keller, A.; Wolf, M.; Schultz, J.; Forster, F. in Mol. Biol. Evol. (2015). 32(11) 3030--3032.
       

    2013[ to top ]

    • The bilaterian roots of cordon-bleu.Schultz, J.; Terhoeven, N. in BMC Res Notes (2013). 6(1) 393.
       

    2011[ to top ]

    • Hawaiian ant-flower networks: nectar-thieving ants prefer undefended native over introduced plants with floral defenses.Junker, Robert R; Daehler, Curtis C; Dötterl, Stefan; Keller, Alexander; Blüthgen, Nico in Ecological Monographs (2011). 81(2) 295--311.
       
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