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Center for Computational and Theoretical Biology

Publications

[ 2021 ] [ 2020 ] [ 2019 ] [ 2018 ] [ 2017 ] [ 2016 ] [ 2015 ] [ 2013 ]

2021 [ to top ]

  • 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 (2021). 37(1)
     
  • 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 (2021). 7(7) 1144–1155.
     
  • 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 (2021). 13(18) 4671.
     
  • Inferring core genome phylogenies for bacteria. Keller, Alexander; Ankenbrand, Markus J in Bacterial Pangenomics (in press), A. Mengoni, M. Fondi, G. Bacci (eds.) (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 (2021). 11
     
  • 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 (2021). 4(1) 1–13.
     

2020 [ to top ]

  • (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 (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 (2020). in press.
     
  • Biological network growth in complex environments – a computational framework. Paul, Torsten Johann; Kollmannsberger, Philip in PLOS Computational Biology (2020). 16(11) e1008003.
     
  • 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 (2020). 50 1–15.
     
  • 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 (2020). bjaa063.
     
  • 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 (2020). 9(1275)
     
  • 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 (2020). (47) 879–889.
     
  • 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 (2020). 10(1) 2536.
     
  • 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 (2020). 11(2)
     
  • Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory. 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 (2020). 30(12) 2312–2320.
     
  • 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 (2020). n/a(n/a)
     
  • How to Grow a Tree: Plant Voltage-Dependent Cation Channels in the Spotlight of Evolution. Dreyer, I.; Sussmilch, F. C.; Fukushima, K.; Riadi, G.; Becker, D.; Schultz, J.; Hedrich, R. in Trends Plant Sci (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 (2020). 101 e02922.
     
  • 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 (2020). in press.
     
  • 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 (2020). 47 1–12.
     
  • 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 (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 (2020). 2 380–394.
     
  • 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 (2020). 294–303.
     
  • 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 (2020). Special issue: Sequence based molecular ecology
     
  • 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 (2020). Special issue: Predictors of microbiomes
     
  • 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 (2020). in press.
     
  • 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 (2020). 11(6)
     
  • The effect of species extinctions on island biogeographic patterns. Matthews, Tom; Leidinger, Ludwig; Cabral, Juliano in Ecological Research (2020). 35 372–381.
     
  • 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 (2020). 10(35) 20939–20959.
     
  • 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 (2020). 15(5) 1–29.
     
  • The Venus flytrap trigger hair-specific potassium channel KDM1 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 (2020). 18(12) e3000964.
     
  • 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).
     

2019 [ to top ]

  • 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 (2019). 10(4095)
     
  • 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 (2019). (194) E122-E133.
     
  • Acquiring Control: The Evolution of Stomatal Signalling Pathways. Sussmilch, F. C.; Schultz, J.; Hedrich, R.; Roelfsema, M. R. G. in Trends Plant Sci. (2019). 24(4) 342–351.
     
  • Active zone compaction for presynaptic strength. Mrestani, Achmed; Kollmannsberger, Philip; Pauli, Martin; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, Sören; Sauer, Markus; Sirén, Anna-Leena; Heckmann, Manfred; Paul, Mila M. in bioRxiv (2019).
     
  • An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians. Fischer, Sabine C. in Computational Biology, H. Husi (ed.) (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 (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 (2019). 95(1) fiy218.
     
  • 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).
     
  • 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).
     
  • Drivers, diversity and functions of solitary bee microbiota. Voulgari-Kokota, Anna; McFrederick, Quinn; Steffan-Dewenter, Ingolf; Keller, Alexander in Trends in Microbiology (2019). in press.
     
  • 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 (2019). 2(1) 376-.
     
  • 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 (2019). in press.
     
  • 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) (2019). 82–89.
     
  • 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 (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 (2019). in press.
     
  • 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 (2019). 116 127–141.
     
  • 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).
     
  • 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 (2019). 5(9) eaav9394.
     
  • 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 (2019). 22 674–684.
     
  • 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 (2019). 34 211–223.
     
  • Towards a Connectomic Description of the Osteocyte Lacunocanalicular Network in Bone. Weinkamer, Richard; Kollmannsberger, Philip; Fratzl, Peter in Current Osteoporosis Reports (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 (2019). 42 1973–1990.
     
  • 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 (2019). fiz010.
     
  • Venus 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. (2019). 95(3)
     

2018 [ to top ]

  • 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.
     
  • 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.
     
  • 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.
     
  • 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 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 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)
     
  • 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.
     
  • 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.
     
  • 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.
     
  • 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 (2018). 9 2859.
     
  • 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.
     
  • 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).
     
  • 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.
     
  • 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 (2018). 3(22) 527.
     
  • 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.
     
  • 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.
     
  • 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.
     
  • 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.
     

2017 [ to top ]

  • 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.
     
  • 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.
     
  • 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)
     
  • 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.
     
  • 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.
     
  • 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)
     
  • 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.
     
  • 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.
     
  • 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).
     
  • 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.
     
  • Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of island biodiversity. Cabral, J.S.; Wiegand, K.; Kreft, H. in bioRxiv (2017). (099978)
     
  • 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.
     
  • Mechanistic models in macroecology and biogeography: state-of-art and prospects. Cabral, Juliano Sarmento; Valente, Luis; Hartig, Florian in Ecography (2017). 40(267-280)
     
  • 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
     
  • 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.
     
  • 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.
     
  • 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.
     

2016 [ to top ]

  • 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. consortium, The 1001 genomes in Cell (2016). 166(2) 481–491.
     
  • 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.
     
  • 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.
     
  • 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.
     
  • 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).
     
  • 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.
     
  • TBro: visualization and management of de novo transcriptomes. Ankenbrand, Markus J.; Weber, Lorenz; Becker, Dirk; Förster, Frank; Bemm, Felix in Database (2016). 2016
     
  • 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.
     
  • 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.
     

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.