@article{HempelKoseskaKurthsetal.2011,
  author    = {Hempel, Stefan and Koseska, Aneta and Kurths, J{\"u}rgen and Nikoloski, Zoran},
  title     = {Inner composition alignment for inferring directed networks from short time series},
  series = {Physical review letters},
  volume    = {107},
  journal   = {Physical review letters},
  number    = {5},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {0031-9007},
  doi       = {10.1103/PhysRevLett.107.054101},
  pages     = {4},
  year      = {2011},
  abstract  = {Identifying causal links (couplings) is a fundamental problem that facilitates the understanding of emerging structures in complex networks. We propose and analyze inner composition alignment-a novel, permutation-based asymmetric association measure to detect regulatory links from very short time series, currently applied to gene expression. The measure can be used to infer the direction of couplings, detect indirect (superfluous) links, and account for autoregulation. Applications to the gene regulatory network of E. coli are presented.},
  language  = {en}
}
@article{HornHempelRistowetal.2015,
  author    = {Horn, Sebastian and Hempel, Stefan and Ristow, Michael and Rillig, Matthias C. and Kowarik, Ingo and Caruso, Tancredi},
  title     = {Plant community assembly at small scales: Spatial vs. environmental factors in a European grassland},
  series = {Acta oecologica : international journal of ecology},
  volume    = {63},
  journal   = {Acta oecologica : international journal of ecology},
  publisher = {Elsevier},
  address   = {Paris},
  issn      = {1146-609X},
  doi       = {10.1016/j.actao.2015.01.004},
  pages     = {56 -- 62},
  year      = {2015},
  abstract  = {Dispersal limitation and environmental conditions are crucial drivers of plant species distribution and establishment. As these factors operate at different spatial scales, we asked: Do the environmental factors known to determine community assembly at broad scales operate at fine scales (few meters)? How much do these factors account for community variation at fine scales? In which way do biotic and abiotic interactions drive changes in species composition? We surveyed the plant community within a dry grassland along a very steep gradient of soil characteristics like pH and nutrients. We used a spatially explicit sampling design, based on three replicated macroplots of 15 x 15, 12 x 12 and 12 x 12 m in extent. Soil samples were taken to quantify several soil properties (carbon, nitrogen, plant available phosphorus, pH, water content and dehydrogenase activity as a proxy for overall microbial activity). We performed variance partitioning to assess the effect of these variables on plant composition and statistically controlled for spatial autocorrelation via eigenvector mapping. We also applied null model analysis to test for non-random patterns in species co-occurrence using randomization schemes that account for patterns expected under species interactions. At a fine spatial scale, environmental factors explained 18\% of variation when controlling for spatial autocorrelation in the distribution of plant species, whereas purely spatial processes accounted for 14\% variation. Null model analysis showed that species spatially segregated in a non-random way and these spatial patterns could be due to a combination of environmental filtering and biotic interactions. Our grassland study suggests that environmental factors found to be directly relevant in broad scale studies are present also at small scales, but are supplemented by spatial processes and more direct interactions like competition. (C) 2015 Elsevier Masson SAS. All rights reserved.},
  language  = {en}
}
@article{SteinRissmannHempeletal.2009,
  author    = {Stein, Claudia and Rißmann, Cornelia and Hempel, Stefan and Renker, Carsten and Buscot, Francois and Prati, Daniel and Auge, Harald},
  title     = {Interactive effects of mycorrhizae and a root hemiparasite on plant community productivity and diversity},
  issn      = {0029-8549},
  doi       = {10.1007/s00442-008-1192-x},
  year      = {2009},
  abstract  = {Plant communities can be affected both by arbuscular mycorrhizal fungi (AMF) and hemiparasitic plants. However, little is known about the interactive effects of these two biotic factors on the productivity and diversity of plant communities. To address this question, we set up a greenhouse study in which different AMF inocula and a hemiparasitic plant (Rhinanthus minor) were added to experimental grassland communities in a fully factorial design. In addition, single plants of each species in the grassland community were grown with the same treatments to distinguish direct AMF effects from indirect effects via plant competition. We found that AMF changed plant community structure by influencing the plant species differently. At the community level, AMF decreased the productivity by 15-24\%, depending on the particular AMF treatment, mainly because two dominant species, Holcus lanatus and Plantago lanceolata, showed a negative mycorrhizal dependency. Concomitantly, plant diversity increased due to AMF inoculation and was highest in the treatment with a combination of two commercial AM strains. AMF had a positive effect on growth of the hemiparasite, and thereby induced a negative impact of the hemiparasite on host plant biomass which was not found in non-inoculated communities. However, the hemiparasite did not increase plant diversity. Our results highlight the importance of interactions with soil microbes for plant community structure and that these indirect effects can vary among AMF treatments. We conclude that mutualistic interactions with AMF, but not antagonistic interactions with a root hemiparasite, promote plant diversity in this grassland community.},
  language  = {en}
}