@misc{AndorfGaertnerSteinfathetal.2008,
  author    = {Andorf, Sandra and G{\"a}rtner, Tanja and Steinfath, Matthias and Witucka-Wall, Hanna and Altmann, Thomas and Repsilber, Dirk},
  title     = {Towards systems biology of heterosis},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {949},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43627},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436274},
  pages     = {14},
  year      = {2008},
  abstract  = {We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature.},
  language  = {en}
}
@misc{BoeckmannOsterloh2014,
  author    = {B{\"o}ckmann, Christine and Osterloh, Lukas},
  title     = {Runge-Kutta type regularization method for inversion of spheroidal particle distribution from limited optical data},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {907},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44120},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441200},
  pages     = {150 -- 165},
  year      = {2014},
  abstract  = {The Runge-Kutta type regularization method was recently proposed as a potent tool for the iterative solution of nonlinear ill-posed problems. In this paper we analyze the applicability of this regularization method for solving inverse problems arising in atmospheric remote sensing, particularly for the retrieval of spheroidal particle distribution. Our numerical simulations reveal that the Runge-Kutta type regularization method is able to retrieve two-dimensional particle distributions using optical backscatter and extinction coefficient profiles, as well as depolarization information.},
  language  = {en}
}
@misc{ArvidssonKwasniewskiRianoPachonetal.2008,
  author    = {Arvidsson, Samuel Janne and Kwasniewski, Miroslaw and Ria{\~n}o- Pach{\´o}n, Diego Mauricio and Mueller-Roeber, Bernd},
  title     = {QuantPrime},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {943},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43153},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431531},
  pages     = {17},
  year      = {2008},
  abstract  = {Background Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. Results Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96\%. Conclusion QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.},
  language  = {en}
}
@misc{GebserLeeLierler2011,
  author    = {Gebser, Martin and Lee, Joohyung and Lierler, Yuliya},
  title     = {On elementary loops of logic programs},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {566},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41309},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413091},
  pages     = {36},
  year      = {2011},
  abstract  = {Using the notion of an elementary loop, Gebser and Schaub (2005. Proceedings of the Eighth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR'05 ), 53-65) refined the theorem on loop formulas attributable to Lin and Zhao (2004) by considering loop formulas of elementary loops only. In this paper, we reformulate the definition of an elementary loop, extend it to disjunctive programs, and study several properties of elementary loops, including how maximal elementary loops are related to minimal unfounded sets. The results provide useful insights into the stable model semantics in terms of elementary loops. For a nondisjunctive program, using a graph-theoretic characterization of an elementary loop, we show that the problem of recognizing an elementary loop is tractable. On the other hand, we also show that the corresponding problem is coNP-complete for a disjunctive program. Based on the notion of an elementary loop, we present the class of Head-Elementary-loop-Free (HEF) programs, which strictly generalizes the class of Head-Cycle-Free (HCF) programs attributable to Ben-Eliyahu and Dechter (1994. Annals of Mathematics and Artificial Intelligence 12, 53-87). Like an HCF program, an HEF program can be turned into an equivalent nondisjunctive program in polynomial time by shifting head atoms into the body.},
  language  = {en}
}
@misc{GebserKaufmannSchaub2012,
  author    = {Gebser, Martin and Kaufmann, Benjamin and Schaub, Torsten H.},
  title     = {Multi-threaded ASP solving with clasp},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {586},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41397},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413977},
  pages     = {21},
  year      = {2012},
  abstract  = {We present the new multi-threaded version of the state-of-the-art answer set solver clasp. We detail its component and communication architecture and illustrate how they support the principal functionalities of clasp. Also, we provide some insights into the data representation used for different constraint types handled by clasp. All this is accompanied by an extensive experimental analysis of the major features related to multi-threading in clasp.},
  language  = {en}
}
@misc{DworschakGrellNikiforovaetal.2008,
  author    = {Dworschak, Steve and Grell, Susanne and Nikiforova, Victoria J. and Schaub, Torsten H. and Selbig, Joachim},
  title     = {Modeling biological networks by action languages via answer set programming},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {843},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42984},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429846},
  pages     = {47},
  year      = {2008},
  abstract  = {We describe an approach to modeling biological networks by action languages via answer set programming. To this end, we propose an action language for modeling biological networks, building on previous work by Baral et al. We introduce its syntax and semantics along with a translation into answer set programming, an efficient Boolean Constraint Programming Paradigm. Finally, we describe one of its applications, namely, the sulfur starvation response-pathway of the model plant Arabidopsis thaliana and sketch the functionality of our system and its usage.},
  language  = {en}
}
@misc{KaminskiSchaubSiegeletal.2013,
  author    = {Kaminski, Roland and Schaub, Torsten H. and Siegel, Anne and Videla, Santiago},
  title     = {Minimal intervention strategies in logical signaling networks with ASP},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {4-5},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41570},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415704},
  pages     = {675 -- 690},
  year      = {2013},
  abstract  = {Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms.},
  language  = {en}
}
@unpublished{PrasseGrubenMachlikaetal.2016,
  author    = {Prasse, Paul and Gruben, Gerrit and Machlika, Lukas and Pevny, Tomas and Sofka, Michal and Scheffer, Tobias},
  title     = {Malware Detection by HTTPS Traffic Analysis},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100942},
  pages     = {10},
  year      = {2016},
  abstract  = {In order to evade detection by network-traffic analysis, a growing proportion of malware uses the encrypted HTTPS protocol. We explore the problem of detecting malware on client computers based on HTTPS traffic analysis. In this setting, malware has to be detected based on the host IP address, ports, timestamp, and data volume information of TCP/IP packets that are sent and received by all the applications on the client. We develop a scalable protocol that allows us to collect network flows of known malicious and benign applications as training data and derive a malware-detection method based on a neural networks and sequence classification. We study the method's ability to detect known and new, unknown malware in a large-scale empirical study.},
  language  = {en}
}
@misc{LamprechtMargariaSteffenetal.2008,
  author    = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard and Sczyrba, Alexander and Hartmeier, Sven and Giegerich, Robert},
  title     = {GeneFisher-P},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {868},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43424},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434241},
  pages     = {17},
  year      = {2008},
  abstract  = {Background: PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility. Results: Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology. The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI). Conclusions: The resulting service-and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.},
  language  = {en}
}
@misc{LarhlimiDavidSelbigetal.2012,
  author    = {Larhlimi, Abdelhalim and David, Laszlo and Selbig, Joachim and Bockmayr, Alexander},
  title     = {F2C2},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {921},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43243},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432431},
  pages     = {11},
  year      = {2012},
  abstract  = {Background: Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions. Results: We present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. Conclusions: We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/.},
  language  = {en}
}