Publications
2022[ to top ]
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A data-driven semantic segmentation model for direct cardiac functional analysis based on undersampled radial MR cine series. in Magnetic Resonance in Medicine (2022). 87(2) 972–983.
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Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. in Annals of Botany (2022). 130 11–25.
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Critical links between biodiversity, nutrition and health in wild bee conservation. in Trends in Ecology and Evolution (2022). in press.
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Forest landscapes increase diversity of honeybee diets in the tropics. in Forest Ecology and Management (2022). in press.
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In Vitro Rearing Changes Social Task Performance and Physiology in Honeybees. in Insects (2022). 13(1)
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Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus. in Frontiers in Bioinformatics (2022).
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Phylogenetic relatedness of food plants reveals highest insect herbivore specialisation at intermediate temperatures along a broad climatic gradient. in Global Change Biology (2022). in press.
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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. in Preprint (2022).
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Putting vascular epiphytes on the traits map. in Journal of Ecology (2022). 110 340–358.
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Scaling up our understanding of tipping points. in Philosophical Transactions of the Royal Society B (2022). 377 20210386.
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The road to integrate climate change effects on land-use change in regional biodiversity models. in Authorea (2022). Preprint
2021[ to top ]
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(More than) Hitchhikers through the network: The shared microbiome of bees and flowers. in Current Opinion in Insect Science (2021).
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Accuracy of the pneumatic method for estimating xylem vulnerability to embolism in temperate diffuse-porous tree species. in bioRxiv (2021).
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Active zone compaction correlates with presynaptic homeostatic potentiation. in Cell Reports (2021). 37(1)
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Agent-based modeling of the effects of forest dynamics, selective logging, and fragment size on epiphyte communities. in Ecology and Evolution (2021). (11) 2937–2951.
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An integrative environmental pollen diversity assessment and its importance for the Sustainable Development Goals. in Plants, People, Planet (2021). in press.
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Anthropogenic and environmental drivers shape diversity of non-native plants across the Pacific. in Diversity and Distributions (2021). 27 1120–1133.
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B0 shimming of the human heart at 7T. in Magnetic Resonance in Medicine (2021). 85(1) 182–196.
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bioDIVERsity. Ein Computerspiel gegen das Imageproblem von Wasserpflanzen. in Mitteilungen der Fränkischen Geographischen Gesellschaft (2021). (67) 29–36.
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Cryptic species and hidden ecological interactions of halictine bees along an elevational gradient. in Ecology and Evolution (2021).
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Dealing with software complexity in individual-based models. in Methods in Ecology and Evolution (2021). 12 2324–2333.
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Deep learning-based cardiac cine segmentation: Transfer learning application to 7T ultrahigh-field MRI. in Magnetic Resonance in Medicine (2021). 86(4) 2179–2191.
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Defining the {Basis} of {Cyanine} {Phototruncation} {Enables} a {New} {Approach} to {Single}-{Molecule} {Localization} {Microscopy}. in ACS Central Science (2021). 7(7) 1144–1155.
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Depth diversity gradients of macrophytes: shape, drivers and recent shifts. in Ecology and Evolution (2021). 11 13830–13845.
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Depth diversity gradients of macrophytes: Shape, drivers, and recent shifts. in Ecology and Evolution (2021). 11(20) 13830–13845.
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DNA sequence-based biodiversity and interaction ecology. in Basic and Applied Ecology (2021).
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Effects of three flower field types on bumblebees and their pollen diets. in Basic and Applied Ecology (2021). 52 95–108.
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Functional resin use in solitary bees. in Ecological Entomology (2021). in press.
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gen3sis: The GENeral Engine for Eco-Evolutionary SImulationS on the origins of biodiversity. in Plos Biology (2021). 19 e3001340.
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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. in Journal of Applied Ecology (2021). in press.
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Identifying {New} {Potential} {Biomarkers} in {Adrenocortical} {Tumors} {Based} on {mRNA} {Expression} {Data} {Using} {Machine} {Learning}. in Cancers (2021). 13(18) 4671.
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Inferring core genome phylogenies for bacteria. in Bacterial Pangenomics (in press), A. Mengoni, M. Fondi, G. Bacci (eds.) (2021).
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Many small rather than few large sources identified in long-term bee pollen diets in agroecosystems. in Agriculture, Ecosystems and Environment (2021).
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Niche evolution reveals disparate signatures of speciation in the ‘great speciator‘ (White-eyes, Aves: genus Zosterops). in Journal of Biogeography (2021). 48 1981–1993.
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On the way to routine cardiac MRI at 7 Tesla - a pilot study on consecutive 84 examinations. in PLOS ONE (2021). 16(7) 1–18.
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Open Science principles for accelerating trait-based science across the Tree of Life. in Nature Ecology \& Evolution (2021). 294–303.
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Osmotic adaptation and compatible solute biosynthesis of phototrophic bacteria as revealed from genome analyses. in Microorganisms (2021). 9(1) 46.
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Pollen diets and niche overlap of honey bees and native bees in protected areas. in Basic and Applied Ecology (2021). Special issue: Sequence based molecular ecology
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Preservation methods of honey-bee collected pollen are not a source of bias in ITS2 metabarcoding. in Environmental Monitoring and Assessment (2021). in press.
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Propagule pressure and an invasion syndrome determine invasion success in a plant community model. in Ecology and Evolution (2021). 11 17106–17116.
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Putative roles of bacteria in the carbon and nitrogen cycles in a tropical peat swamp forest. in Basic and Applied Ecology (2021). Special issue: Predictors of microbiomes
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Self-configuring nnU-net pipeline enables fully automatic infarct segmentation in late enhancement MRI after myocardial infarction. in European Journal of Radiology (2021). 141 109817.
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Sensitivity analysis for interpretation of machine learning based segmentation models in cardiac {MRI}. in BMC Medical Imaging (2021). 21(1) 27.
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Species richness is more important for ecosystem functioning than species turnover along an elevational gradient. in Nature Ecology and Evolution (2021). in press.
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Standard methods for pollen research. in Journal of Apicultural Research (2021). 60(4) 1–109.
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Subgroup-{Independent} {Mapping} of {Renal} {Cell} {Carcinoma}—{Machine} {Learning} {Reveals} {Prognostic} {Mitochondrial} {Gene} {Signature} {Beyond} {Histopathologic} {Boundaries}. in Frontiers in Oncology (2021). 11
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Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections. in Communications Biology (2021). 4(1) 1–13.
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Temporal environmental variation imposes differential selection on both genomic and ecological traits. in Oikos (2021). 130 1100–1115.
2020[ to top ]
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A systematic comparison of chloroplast genome assembly tools. in Genome Biology (2020). 21(1) 254.
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BCdatabaser: on-the-fly reference database creation for DNA (meta-)barcoding. in Bioinformatics (2020). in press.
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Biological network growth in complex environments – a computational framework. in PLOS Computational Biology (2020). 16(11) e1008003.
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Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach. in Scientific Reports (2020). 10(1) 22405-.
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Changes amid constancy: flower and leaf microbiomes along land use gradients and between bioregions. in Basic and Applied Ecology (2020). 50 1–15.
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Chronic exposure to the pesticide flupyradifurone can lead to premature onset of foraging in honeybees (Apis mellifera). in Journal of Applied Ecology (2020). 57 609–618.
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CRISPR/Cas 9 mediated mutations as a new tool for studying taste in honeybees. in Chemical Senses (2020). bjaa063.
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DeepCLEM: automated registration for correlative light and electron microscopy using deep learning [version 1; peer review: awaiting peer review]. in F1000Research (2020). 9(1275)
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Disentangling the drivers of local species richness using probabilistic species pools. in Journal of Biogeography (2020). (47) 879–889.
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Efficient {Classification} of {White} {Blood} {Cell} {Leukemia} with {Improved} {Swarm} {Optimization} of {Deep} {Features}. in Scientific Reports (2020). 10(1) 2536.
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Exploring Ensemble Applications for Multi-sequence Myocardial Pathology Segmentation. in Myocardial Pathology Segmentation Combining Multi-Sequence Cardiac Magnetic Resonance Images, X. Zhuang, L. Li (eds.) (2020). 60–67.
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Floral Species Richness Correlates with Changes in the Nutritional Quality of Larval Diets in a Stingless Bee. in Insects (2020). 11(2)
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Haruspex: {A} {Neural} {Network} for the {Automatic} {Identification} of {Oligonucleotides} and {Protein} {Secondary} {Structure} in {Cryo}-{Electron} {Microscopy} {Maps}. in Angewandte Chemie International Edition (2020). n/a(n/a)
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Integrating the underlying structure of stochasticity into community ecology. in Ecology (2020). 101 e02922.
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Introduced bees (Osmia cornifrons) collect pollen from both coevolved and novel host-plant species within their family-level phylogenetic preferences. in Royal Society Open Science (2020). in press.
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Macroecology in the age of big data – where to go from here?. in Journal of Biogeography (2020). 47 1–12.
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Mapping human pressures on biodiversity across the planet uncovers anthropogenic threat complexes. in People and Nature (2020). 2 380–394.
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Modeling how community assembly alters the functioning of ecosystems. in bioRxiv (2020).
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Strong phylogenetic constraint on transition metal incorporation in the mandibles of the hyper-diverse Hymenoptera (Insecta). in Organisms, Diversity and Evolution (2020). in press.
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Susceptibility of red mason bee larvae to bacterial threats due to microbiome exchange with imported pollen provisions. in Insects (2020). 11(6)
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The effect of species extinctions on island biogeographic patterns. in Ecological Research (2020). 35 372–381.
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The genus Micromonospora as a model microorganism for bioactive natural product discovery. in Royal Society of Chemistry Advances (2020). 10(35) 20939–20959.
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The transition from local to global patterns governs the differentiation of mouse blastocysts. in PLOS ONE (2020). 15(5) 1–29.
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Tracking beekeepers in floristic regions of Iran: employing DNA metabarcoding to determine the geographical origin of honey. in Heliyon (2020).
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{{G}enomes of the {V}enus {F}lytrap and {C}lose {R}elatives {U}nveil the {R}oots of {P}lant {C}arnivory}. in Curr Biol (2020). 30(12) 2312–2320.
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{{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}. in Trends Plant Sci (2020).
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{{T}he {V}enus flytrap trigger hair-specific potassium channel {K}{D}{M}1 can reestablish the {K}+ gradient required for hapto-electric signaling}. in PLoS Biol (2020). 18(12) e3000964.
2019[ to top ]
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A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics. in Nature Communications (2019). 10(4095)
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A minimal model for the latitudinal diversity gradient suggests a dominant role for ecological limits. in The American Naturalist (2019). (194) E122-E133.
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Active zone compaction for presynaptic strength. in bioRxiv (2019).
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An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians. in Computational Biology, H. Husi (ed.) (2019).
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Assessing predicted isolation effects from the general dynamic model of island biogeography with an eco-evolutionary model for plants. in Journal of Biogeography (2019). 46 1569–1581.
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Bacterial community structure and succession in nests of two megachilid bee genera. in FEMS Microbiology Ecology (2019). 95(1) fiy218.
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Climate–land-use interactions shape tropical mountain biodiversity and ecosystem functions. in Nature (2019).
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Cold-adaptation of Subtercola vilae DB165T, an isolate from a high-altitude cold volcano lake, as revealed by its genome analysis. (2019).
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Drivers, diversity and functions of solitary bee microbiota. in Trends in Microbiology (2019). in press.
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Electron tomography of mouse LINC complexes at meiotic telomere attachment sites with and without microtubules. in Communications Biology (2019). 2(1) 376-.
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Honey bee waggle dance communication increases diversity of pollen diets in intensively managed agricultural landscapes. in Molecular Ecology (2019). in press.
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Immersive Analysis of 3D Multi-cellular In-Vitro and In-Silico Cell Cultures. in 2019 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR) (2019). 82–89.
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Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of insular plant diversity. in Journal of Biogeography (2019). 46 1582–1597.
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Linking the foraging patterns of megachilid bee species to nest bacteria. in Ecology and Evolution (2019). in press.
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Mouse ICM organoids reveal three-dimensional cell fate clustering. in Biophysical Journal (2019). 116 127–141.
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Species richness change across spatial scales. in Oikos (2019).
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Surface tension determines tissue shape and growth kinetics. in Science Advances (2019). 5(9) eaav9394.
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The dimensionality of stability depends on disturbance type. in Ecology Letters (2019). 22 674–684.
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The latitudinal diversity gradient - novel understanding through mechanistic eco-evolutionary models. in Trends in Ecology & Evolution (2019). 34 211–223.
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Towards a {Connectomic} {Description} of the {Osteocyte} {Lacunocanalicular} {Network} in {Bone}. in Current Osteoporosis Reports (2019).
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Understanding extinction debts: spatio-temporal scales, mechanisms and a roadmap for future research. in Ecography (2019). 42 1973–1990.
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Venus flytrap microbiota withstand harsh conditions during prey digestion. in FEMS Microbiology Ecology (2019). fiz010.
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{{A}cquiring {C}ontrol: {T}he {E}volution of {S}tomatal {S}ignalling {P}athways}. in Trends Plant Sci. (2019). 24(4) 342–351.
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{{V}enus flytrap microbiotas withstand harsh conditions during prey digestion}. in FEMS Microbiol. Ecol. (2019). 95(3)
2018[ to top ]
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Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning. in PLoS one (2018). 13(10) e0205348.
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Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest. in Genome announcements (2018). 6(25) e00459–18.
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Draft Genome Sequence of Dyella sp. Strain C9, Isolated from a Malaysian Tropical Peat Swamp Forest. in Microbiol Res Announc (2018). 7(12) e01083–18.
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Draft Genome Sequence of Klebsiella sp. Strain C31 Isolated from a Malaysian Tropical Peat Swamp Forest. in Genome announcements (2018). 6(25) e00560–18.
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Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest. in Genome announcements (2018). 6(25) e00561–18.
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Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest. in Genome Announcements (2018). 6(25)
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FENNEC - Functional Exploration of Natural Networks and Ecological Communities. in Methods in Ecology and Evolution (2018). 2028–2033.
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Integrating community assembly and biodiversity reveals new dimensions of ecosystem functions: the Community Assembly and the Functioning of Ecosystems (CAFE) approach. in Ecology Letters (2018). 21 167–180.
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Microbial community structure in a Malaysian tropical peat swamp forest: the influence of tree species and depth. in Frontiers in Microbiology (2018). 9 2859.
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Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition. in PLOS Genetics (2018). 14(4) 1–23.
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Physical contact between mesenchymal stem cells and endothelial precursors induces distinct signatures with relevance to the very early phase of regeneration. in Journal of Cellular Biochemistry (2018).
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reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. in The Journal of Open Source Software (2018). 3(22) 527.
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reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. in Journal of Open Source Software (2018). 3(22) 527.
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Spatial scaling of extinction rates: theory and data reveal non-linearity, and a major upscaling and downscaling challenge. in Global Ecology and Biogeography (2018). 27 2–13.
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Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts. in Science Advances (2018). 4(1) eaao4881.
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The characterization of the circadian clock in the olive fly Bactrocera oleae (Diptera: Tephritidae) reveals a Drosophila-like organization. in Scientific Reports (2018). 8(1) 816.
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Wild bees and their nests host Paenibacillus bacteria with functional potential of avail. in Microbiome (2018). (6) 229.
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{chloroExtractor}: extraction and assembly of the chloroplast genome from whole genome shotgun data. in The Journal of Open Source Software (2018). 3(21) 464.
2017[ to top ]
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AliTV - interactive visualization of whole genome comparisons. in PeerJ Comput. Sci. (2017). 3 e116.
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An individual-based model for the collective cancer cell migration explains speed dynamics and phenotype variability in response to growth factors. in NPJ Systems Biology and Applications (2017). 3 Art. no. 5.
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AraPheno: a public database for Arabidopsis thaliana phenotypes. in Nucleic acids research (2017). 45(D1) D1054-D1059.
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Biodiversity dynamics on islands: explicitly accounting for causality in mechanistic models. in Diversity (2017). 9(30)
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Biodiversity dynamics on islands: explicitly accounting for causality in mechanistic models. in Diversity (2017). 9(3)
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biojs-io-biom, a {BioJS} component for handling data in Biological Observation Matrix ({BIOM}) format. in F1000Research (2017). 5 2348.
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Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone. in Journal of Stuctural Biology (2017). 199 177–186.
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Effects of time and isolation on plant diversity: testing island biogeography theory with an eco-evolutionary model. in bioRxiv (2017). (100289)
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FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. in PLOS Computational Biology (2017). 13(1) 1–21.
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Flagship umbrella species needed for conservation of overlooked biodiversity. in Conservation Biology (2017). 31 481–485.
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Genetic Components of Root Architecture Remodeling in Response to Salt Stress. in The Plant Cell (2017).
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Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. in PloS one (2017). 12(8) e0183716.
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Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of island biodiversity. in bioRxiv (2017). (099978)
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Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. in Plant Biology (2017). 19 298–308.
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Mechanistic models in macroecology and biogeography: state-of-art and prospects. in Ecography (2017). 40(267-280)
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Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps. in Evolution (2017). in press
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Spatial heterogeneity in the canalicular density of the osteocyte network in human osteons. in Bone Reports (2017). 6 101–108.
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The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. in Nucleic Acids Research (2017). gkx954.
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The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone. in New Journal of Physics (2017). 19 073019.
2016[ to top ]
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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. in Cell (2016). 166(2) 481–491.
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biojs-io-biom, a {BioJS} component for handling data in Biological Observation Matrix ({BIOM}) format. in F1000Research (2016). 5 2348.
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Leaf growth response to mild drought: natural variation in Arabidopsis sheds light on trait architecture. in The Plant Cell (2016). 28(10) 2417–2434.
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TBro: visualization and management of de novo transcriptomes. in Database (2016). 2016
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{{A}{L}{V}{I}{S}: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments}. in Nucleic Acids Res. (2016). 44(8) e77.
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{{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}. in Plant Biol (Stuttg) (2016). 18(5) 750–760.
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{{G}enome of a tardigrade: {H}orizontal gene transfer or bacterial contamination?}. in Proc. Natl. Acad. Sci. U.S.A. (2016).
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{{V}enus flytrap carnivorous lifestyle builds on herbivore defense strategies}. in Genome Res. (2016). 26(6) 812–825.
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{{W}{H}{A}{M}{Y} is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in {D}rosophila}. in J. Cell. Sci. (2016). 129(3) 604–620.
2015[ to top ]
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ITS2 Database V: Twice as Much. in Molecular Biology and Evolution (2015). 32(11) 3030–3032.
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{{I}{T}{S}2 {D}atabase {V}: {T}wice as {M}uch}. in Mol. Biol. Evol. (2015). 32(11) 3030–3032.
2013[ to top ]
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{{T}he bilaterian roots of cordon-bleu}. in BMC Res Notes (2013). 6(1) 393.
