@article{SchudomaLarhlimiWalther2011,
  author    = {Schudoma, Christian and Larhlimi, Abdelhalim and Walther, Dirk},
  title     = {The influence of the local sequence environment on RNA loop structures},
  series = {RNA : a publication of the RNA Society},
  volume    = {17},
  journal   = {RNA : a publication of the RNA Society},
  number    = {7},
  publisher = {Cold Spring Harbor Laboratory Press},
  address   = {Cold Spring Harbor, NY},
  issn      = {1355-8382},
  doi       = {10.1261/rna.2550211},
  pages     = {1247 -- 1257},
  year      = {2011},
  abstract  = {RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized eta/theta-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55\%, thus significantly better than expected by chance (17\%-25\%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.},
  language  = {en}
}
@misc{DurekSchudomaWeckwerthetal.2009,
  author    = {Durek, Pawel and Schudoma, Christian and Weckwerth, Wolfram and Selbig, Joachim and Walther, Dirk},
  title     = {Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45129},
  year      = {2009},
  abstract  = {Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results: We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion: While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structurebased P-site prediction method has been made available at http://phos3d.mpimp-golm.mpg.de.},
  language  = {en}
}
@phdthesis{Schudoma2011,
  author    = {Schudoma, Christian},
  title     = {Bioinformatic approaches to sequence-structure relationships in RNA loops},
  address   = {Potsdam},
  pages     = {114},
  year      = {2011},
  language  = {en}
}
@article{SprengerRudackSchudomaetal.2015,
  author    = {Sprenger, Heike and Rudack, Katharina and Schudoma, Christian and Neumann, Arne and Seddig, Sylvia and Peters, Rolf and Zuther, Ellen and Kopka, Joachim and Hincha, Dirk K. and Walther, Dirk and Koehl, Karin},
  title     = {Assessment of drought tolerance and its potential yield penalty in potato},
  series = {Functional plant biology : an international journal of plant function},
  volume    = {42},
  journal   = {Functional plant biology : an international journal of plant function},
  number    = {7},
  publisher = {CSIRO},
  address   = {Clayton},
  issn      = {1445-4408},
  doi       = {10.1071/FP15013},
  pages     = {655 -- 667},
  year      = {2015},
  abstract  = {Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied the genetic variance, predictability of field performance and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit of water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial dataset, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified the deviation of relative starch yield from the experimental median (DRYM) as the most efficient index. DRYM corresponded qualitatively to the partial least square model-based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.},
  language  = {en}
}