TY - JOUR
A1 - Wolff, Alexander
A1 - Rutter, Iganz
T1 - Augmenting the Connectivity of Planar and Geometric Graphs
JF - Journal of Graph Algorithms and Applications
N2 - In this paper we study connectivity augmentation problems. Given a connected graph G with some desirable property, we want to make G 2-vertex connected (or 2-edge connected) by adding edges such that the resulting graph keeps the property. The aim is to add as few edges as possible. The property that we consider is planarity, both in an abstract graph-theoretic and in a geometric setting, where vertices correspond to points in the plane and edges to straight-line segments.
We show that it is NP-hard to � nd a minimum-cardinality augmentation that makes a planar graph 2-edge connected. For making a planar graph 2-vertex connected this was known. We further show that both problems are hard in the geometric setting, even when restricted to trees. The problems remain hard for higher degrees of connectivity. On the other hand we give polynomial-time algorithms for the special case of convex geometric graphs.
We also study the following related problem. Given a planar (plane geometric) graph G, two vertices s and t of G, and an integer c, how many edges have to be added to G such that G is still planar (plane geometric) and contains c edge- (or vertex-) disjoint s{t paths? For the planar case we give a linear-time algorithm for c = 2. For the plane geometric case we give optimal worst-case bounds for c = 2; for c = 3 we characterize the cases that have a solution.
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-97587
ER -
TY - THES
A1 - Baunach, Marcel
T1 - Advances in Distributed Real-Time Sensor/Actuator Systems Operation - Operating Systems, Communication, and Application Design Concepts -
T1 - Fortschritte im Betrieb drahtloser Sensor/Aktuator Netzwerke
N2 - This work takes a close look at several quite different research areas related to the design of networked embedded sensor/actuator systems. The variety of the topics illustrates the potential complexity of current sensor network applications; especially when enriched with actuators for proactivity and environmental interaction. Besides their conception, development, installation and long-term operation, we'll mainly focus on more "low-level" aspects: Compositional hardware and software design, task cooperation and collaboration, memory management, and real-time operation will be addressed from a local node perspective. In contrast, inter-node synchronization, communication, as well as sensor data acquisition, aggregation, and fusion will be discussed from a rather global network view. The diversity in the concepts was intentionally accepted to finally facilitate the reliable implementation of truly complex systems. In particular, these should go beyond the usual "sense and transmit of sensor data", but show how powerful today's networked sensor/actuator systems can be despite of their low computational performance and constrained hardware: If their resources are only coordinated efficiently!
N2 - Diese Arbeit behandelt einige sehr unterschiedliche Forschungsbereiche bezüglich des Designs vernetzter und eingebetteter Sensor/Aktuator-Systeme. Die Vielfalt der Themen zeigt die potenzielle Komplexität aktueller Sensornetzwerk-Anwendungen, insbesondere wenn sie mit Aktuatoren zur Interaktion mit der Umwelt ausgestattet sind. Neben deren Konzeption, Entwicklung, Installation und dem langfristigen Betrieb wird besonders auf diverse "low-level" Aspekte eingegangen: Kompositionelles Hardware- und Software-Design, Task Kooperation und Kollaboration, Speicher-Verwaltung und Echtzeit-Betrieb werden aus lokaler Sicht der Sensorknoten betrachtet. Im Kontrast werden Knoten-Synchronisation, Kommunikation, sowie Sensordatenerfassung, -aggregation und -fusion aus globaler Netzwerk-Sicht diskutiert. Die Vielfalt der behandelten Konzepte wurde bewusst in Kauf genommen, um letztlich die zuverlässige Umsetzung sehr komplexer Systeme zu erleichtern. Insbesondere sollte dies über das übliche "Erfassen und Übertragen von Sensordaten" hinausgehen, und zeigen, wie mächtig heutige vernetzte Sensor/Aktuator-Systeme trotz ihrer geringen Rechenleistung und eingeschränkten Hardware sein können: Wenn ihre Ressourcen effizient koordiniert werden!
KW - Eingebettetes System
KW - Drahtloses Sensorsystem
KW - Echtzeitsystem
KW - Dynamische Speicherverwaltung
KW - Ressourcenallokation
KW - Fernwartung
KW - Betriebssystem
KW - Verteiltes System
KW - Lokalisation
KW - Embedded Systems
KW - Real-Time Operating Systems
KW - Localization
KW - Wireless Sensor/Actuator Systems
KW - Dynamic Memory Management
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-76489
ER -
TY - JOUR
A1 - Atienza, Nieves
A1 - de Castro, Natalia
A1 - Cortés, Carmen
A1 - Garrido, M. Ángeles
A1 - Grima, Clara I.
A1 - Hernández, Gregorio
A1 - Márquez, Alberto
A1 - Moreno-González, Auxiliadora
A1 - Nöllenburg, Martin
A1 - Portillo, José Ramón
A1 - Reyes, Pedro
A1 - Valenzuela, Jesús
A1 - Trinidad Villar, Maria
A1 - Wolff, Alexander
T1 - Cover contact graphs
N2 - We study problems that arise in the context of covering certain geometric objects called seeds (e.g., points or disks) by a set of other geometric objects called cover (e.g., a set of disks or homothetic triangles). We insist that the interiors of the seeds and the cover elements are pairwise disjoint, respectively, but they can touch. We call the contact graph of a cover a cover contact graph (CCG). We are interested in three types of tasks, both in the general case and in the special case of seeds on a line: (a) deciding whether a given seed set has a connected CCG, (b) deciding whether a given graph has a realization as a CCG on a given seed set, and (c) bounding the sizes of certain classes of CCG’s. Concerning (a) we give efficient algorithms for the case that seeds are points and show that the problem becomes hard if seeds and covers are disks. Concerning (b) we show that this problem is hard even for point seeds and disk covers (given a fixed correspondence between graph vertices and seeds). Concerning (c) we obtain upper and lower bounds on the number of CCG’s for point seeds.
KW - Informatik
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-78845
ER -
TY - JOUR
A1 - Zirkel, J.
A1 - Cecil, A.
A1 - Schäfer, F.
A1 - Rahlfs, S.
A1 - Ouedraogo, A.
A1 - Xiao, K.
A1 - Sawadogo, S.
A1 - Coulibaly, B.
A1 - Becker, K.
A1 - Dandekar, T.
T1 - Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling
JF - Bioinformatics and Biology Insights
N2 - BACKGROUND: In the face of growing resistance in malaria parasites to drugs, pharmacological combination therapies are important. There is accumulating evidence that methylene blue (MB) is an effective drug against malaria. Here we explore the biological effects of both MB alone and in combination therapy using modeling and experimental data.
RESULTS: We built a model of the central metabolic pathways in P. falciparum. Metabolic flux modes and their changes under MB were calculated by integrating experimental data (RT-PCR data on mRNAs for redox enzymes) as constraints and results from the YANA software package for metabolic pathway calculations. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, chloroquine resistance based on pfmdr/and pfcrt transporters, as well as pyrimethamine/sulfadoxine resistance (by mutations in DHF/DHPS), were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs.
CONCLUSIONS: Theoretical and experimental results support that methylene blue should, because of its resistance-breaking potential, be further tested as a key component in drug combination therapy efforts in holoendemic areas.
KW - methylene blue
KW - malaria
KW - elementary mode analysis
KW - drug
KW - resistance
KW - combination therapy
KW - pathway
KW - metabolic flux
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123751
N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.
VL - 6
ER -
TY - JOUR
A1 - Krueger, Beate
A1 - Friedrich, Torben
A1 - Förster, Frank
A1 - Bernhardt, Jörg
A1 - Gross, Roy
A1 - Dandekar, Thomas
T1 - Different evolutionary modifications as a guide to rewire two-component systems
JF - Bioinformatics and Biology Insights
N2 - Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases.
KW - histidine kinase
KW - connector
KW - Mycoplasma
KW - engineering
KW - promoter
KW - sensor
KW - response regulator
KW - synthetic biology
KW - sequence alignment
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123647
N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.
VL - 6
ER -
TY - JOUR
A1 - Merget, Benjamin
A1 - Koetschan, Christian
A1 - Hackl, Thomas
A1 - Förster, Frank
A1 - Dandekar, Thomas
A1 - Müller, Tobias
A1 - Schultz, Jörg
A1 - Wolf, Matthias
T1 - The ITS2 Database
JF - Journal of Visual Expression
N2 - The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation.
The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold.
The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure.
In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.
KW - homology modeling
KW - molecular systematics
KW - internal transcribed spacer 2
KW - alignment
KW - genetics
KW - secondary structure
KW - ribosomal RNA
KW - phylogenetic tree
KW - phylogeny
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124600
VL - 61
IS - e3806
ER -
TY - JOUR
A1 - Buchin, Kevin
A1 - Buchin, Maike
A1 - Byrka, Jaroslaw
A1 - Nöllenburg, Martin
A1 - Okamoto, Yoshio
A1 - Silveira, Rodrigo I.
A1 - Wolff, Alexander
T1 - Drawing (Complete) Binary Tanglegrams
JF - Algorithmica
N2 - A binary tanglegram is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential that both trees are drawn without edge crossings and that the inter-tree edges have as few crossings as possible. It is known that finding a tanglegram with the minimum number of crossings is NP-hard and that the problem is fixed-parameter tractable with respect to that number.
We prove that under the Unique Games Conjecture there is no constant-factor approximation for binary trees. We show that the problem is NP-hard even if both trees are complete binary trees. For this case we give an O(n 3)-time 2-approximation and a new, simple fixed-parameter algorithm. We show that the maximization version of the dual problem for binary trees can be reduced to a version of MaxCut for which the algorithm of Goemans and Williamson yields a 0.878-approximation.
KW - NP-hardness
KW - crossing minimization
KW - binary tanglegram
KW - approximation algorithm
KW - fixed-parameter tractability
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124622
VL - 62
ER -
TY - JOUR
A1 - Staiger, Christine
A1 - Cadot, Sidney
A1 - Kooter, Raul
A1 - Dittrich, Marcus
A1 - Müller, Tobias
A1 - Klau, Gunnar W.
A1 - Wessels, Lodewyk F. A.
T1 - A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer
JF - PLoS One
N2 - Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer.
KW - modules
KW - protein-interaction networks
KW - expression signature
KW - classification
KW - set
KW - metastasis
KW - stability
KW - survival
KW - database
KW - markers
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131323
VL - 7
IS - 4
ER -
TY - JOUR
A1 - Böhler, Elmar
A1 - Creignou, Nadia
A1 - Galota, Matthias
A1 - Reith, Steffen
A1 - Schnoor, Henning
A1 - Vollmer, Heribert
T1 - Complexity Classifications for Different Equivalence and Audit Problems for Boolean Circuits
JF - Logical Methods in Computer Science
N2 - We study Boolean circuits as a representation of Boolean functions and conskier different equivalence, audit, and enumeration problems. For a number of restricted sets of gate types (bases) we obtain efficient algorithms, while for all other gate types we show these problems are at least NP-hard.
KW - hierarchy
KW - satisfiability problems
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131121
VL - 8
IS - 3:27
SP - 1
EP - 25
ER -
TY - JOUR
A1 - Schokraie, Elham
A1 - Warnken, Uwe
A1 - Hotz-Wagenblatt, Agnes
A1 - Grohme, Markus A.
A1 - Hengherr, Steffen
A1 - Förster, Frank
A1 - Schill, Ralph O.
A1 - Frohme, Marcus
A1 - Dandekar, Thomas
A1 - Schnölzer, Martina
T1 - Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state
JF - PLoS One
N2 - Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
KW - life-span regulation
KW - genes
KW - Yolk protein
KW - water stress
KW - expression
KW - tolerance
KW - richtersius coronifer
KW - superoxide-dismutase
KW - caenorhabditis elegans
KW - arabidopsis thaliana
KW - vitellogenin
Y1 - 2012
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134447
VL - 7
IS - 9
ER -