Stefan Wuchty

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An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities, such as the partition function or measures for structural(More)
We have used 19.9 million papers over 5 decades and 2.1 million patents to demonstrate that teams increasingly dominate solo authors in the production of knowledge. Research is increasingly done in teams across nearly all fields. Teams typically produce more frequently cited research than individuals do, and this advantage has been increasing over time.(More)
Several technical, social, and biological networks were recently found to demonstrate scale-free and small-world behavior instead of random graph characteristics. In this work, the topology of protein domain networks generated with data from the ProDom, Pfam, and Prosite domain databases was studied. It was found that these networks exhibited small-world(More)
This paper demonstrates that teamwork in science increasingly spans university boundaries, a dramatic shift in knowledge production that generalizes across virtually all fields of science, engineering, and social science. Moreover, elite universities play a dominant role in this shift. By examining 4.2 million papers published over three decades, we found(More)
Understanding why some cellular components are conserved across species but others evolve rapidly is a key question of modern biology. Here we show that in Saccharomyces cerevisiae, proteins organized in cohesive patterns of interactions are conserved to a substantially higher degree than those that do not participate in such motifs. We find that the(More)
To obtain candidates of interactions between proteins of the malaria parasite Plasmodium falciparum and the human host, homologous and conserved interactions were inferred from various sources of interaction data. Such candidate interactions were assessed by applying a machine learning approach and further filtered according to expression and molecular(More)
  • Stefan Wuchty
  • Proceedings of the National Academy of Sciences…
  • 2014
Recently, the focus of network research shifted to network controllability, prompting us to determine proteins that are important for the control of the underlying interaction webs. In particular, we determined minimum dominating sets of proteins (MDSets) in human and yeast protein interaction networks. Such groups of proteins were defined as optimized(More)
The modeling of complex systems, as disparate as the World Wide Web and the cellular metabolism, as networks has recently uncovered a set of generic organizing principles: Most of these systems are scale-free while at the same time modular, resulting in a hierarchical architecture. The structure of the protein domain network, where individual domains(More)
A set of highly connected proteins (or hubs) plays an important role for the integrity of the protein interaction network of Saccharomyces cerevisae by connecting the network's intrinsic modules. The importance of the hubs' central placement is further confirmed by their propensity to be lethal. However, although highly emphasized, little is known about the(More)
One goal of contemporary proteome research is the elucidation of cellular protein interactions. Based on currently available protein-protein interaction and domain data, we introduce a novel method, Maximum Specificity Set Cover (MSSC), for the prediction of protein-protein interactions. In our approach, we map the relationship between interactions of(More)