| [1] | Spieth, Christian and Streichert, Felix and Speer, Nora and Zell,
Andreas. Multi-Objective Model Optimization for Inferring Gene Regulatory
Networks. In Conference on Evolutionary Multi-Criterion Optimization (EMO 2005), pages 607-620,, Guanajuato, Mexico,mar, 2005. [url]Bibtex@INPROCEEDINGS{2005_33,author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Multi-Objective Model Optimization for Inferring Gene Regulatory Networks}, booktitle = {Conference on Evolutionary Multi-Criterion Optimization (EMO 2005)}, year = {2005}, editor = {Carlos A. Coello Coello and Arturo Hern{\'a}ndez Aguirre and Eckart Zitzler}, volume = {3410}, series = {Lecture Notes in Computer Science}, pages = {607-620}, address = {Guanajuato, Mexico}, month = {mar}, publisher = {Springer}, isbn = {3-540-24983-4}, project = {abt_zell, bioinformatics, javaeva}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05multiobjective.pdf}, } |
| [2] | Streichert, Felix and Ulmer, Holger and Zell, Andreas. Parallelization of multi-objective evolutionary algorithms using
clustering algorithms. In Conference on Evolutionary Multi-Criterion Optimization (EMO 2005), pages 92--107,, Guanajuato, Mexico,mar, 2005. [url]Bibtex@INPROCEEDINGS{2005_118,author = {Streichert, Felix and Ulmer, Holger and Zell, Andreas}, title = {Parallelization of multi-objective evolutionary algorithms using clustering algorithms}, booktitle = {Conference on Evolutionary Multi-Criterion Optimization (EMO 2005)}, year = {2005}, editor = {Carlos A. Coello Coello and Arturo Hern{\'a}ndez Aguirre and Eckart Zitzler}, volume = {3410}, series = {Lecture Notes in Computer Science}, pages = {92--107}, address = {Guanajuato, Mexico}, month = {mar}, publisher = {Springer}, isbn = {3-540-24983-4}, project = {abt_zell, javaeva}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/streichert05parallelization.pdf}, } |
| [3] | Tamimi, Hashem and Halawani, Alaa and Burkhardt, Hans and Zell, Andreas. Using Descriptive Image Features for Global Localization of Mobile
Robots. In 19th Autonomous Mobile Systems (AMS 2005), pages 139-145,, Stuttgart, Germany,mar, 2005. [url]Bibtex@INPROCEEDINGS{2005_125,author = {Tamimi, Hashem and Halawani, Alaa and Burkhardt, Hans and Zell, Andreas}, title = {Using Descriptive Image Features for Global Localization of Mobile Robots}, booktitle = {19th Autonomous Mobile Systems (AMS 2005)}, year = {2005}, series = {Informatik aktuell}, pages = {139-145}, address = {Stuttgart, Germany}, month = {mar}, publisher = {Springer}, abstract = {In this paper descriptive visual features based on integral invariants are proposed to solve the global localization of indoor mobile robots. These descriptive features are locally extracted by applying a set of non-linear kernel functions around a set ofinterest points in the image. To investigate the approach thoroughly, we use a set of Images taken by re-assigning the robot Position many times near a set of reference locations. Also, the presence of Illumination variations is encountered many times inthe Images. Compared to a wellknown approach, our approach has better localization rate with moderate computational overhead.}, doi = {10.1007/3-540-30292-1_18}, isbn = {978-3-540-30291-9}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/tamimi05-ams.pdf}, } |
| [4] | Wegner, Jörg K. and Sieker, Florian and Zell, Andreas. Relevance of feature selection for clustering molecules. , pages U612,, San Diego, CA, USA,mar, 2005. Bibtex@ARTICLE{2005_7,author = {Wegner, Jörg K. and Sieker, Florian and Zell, Andreas}, title = {Relevance of feature selection for clustering molecules}, journal = {Abstracts of Papers American Chemical Society (229th National Meeting of the American-Chemical-Society)}, year = {2005}, volume = {229}, pages = {U612}, number = {Part 1}, month = {mar}, abstract = {We present an extensive study to classify and cluster four different activity classes (5HT1A antagonists, thrombin inhibitors, MAO inhibitors and H2 antagonists) by using four different feature selection algorithms, ten different classification algorithms and three clustering algorithms. We show that depending on the used number of features the generalization ability of the results varies dramatically for clustering compounds. The number of features used was based on the previous feature selection results. The classification rates ranges from 85% up to 97%, which are much better than the clustering confusion matrix results. Finally, we conclude the work with presenting a new approch avoiding the feature selection dilemma.}, address = {San Diego, CA, USA}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?2005_7}, project = {abt_zell, cheminformatics}, } |
| [5] | Wegner, Jörg K. and Zell, Andreas. Difference in vector based and graph based coding for {ADME} prediction. , pages U608,, San Diego, CA, USA,mar, 2005. Bibtex@ARTICLE{2005_6,author = {Wegner, Jörg K. and Zell, Andreas}, title = {Difference in vector based and graph based coding for {ADME} prediction}, journal = {Abstracts of Papers American Chemical Society (229th National Meeting of the American-Chemical-Society)}, year = {2005}, volume = {229}, pages = {U608}, number = {Part 1}, month = {mar}, abstract = {We present an extensive study to build classification and regression models using five different ADMET data sets (HIA, LogP, LogS, BBB, and two toxicological data sets causing cancer in rats and mice). We compare especially the relevance of vector based coding for molecules using descriptors and fingerprints and a coordinate-free coding working directly on the molecular structures avoiding a temporary abstract vector representation. We see that the vector coding can be used for large data sets by loosing accuracy and the coordinate-free approach avoids the feature selection problem, but is only applicable for smaller data sets. Furthermore we discuss shortly the underlying space and time complexities.}, address = {San Diego, CA, USA}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?2005_6}, project = {abt_zell, cheminformatics}, } |
| [6] | Bronni, Jan and Hofmann, Stefanie and Kronfeld, Marcel and Monger,
Andreas. {Eine strategieorientierte, modulare Simulationsumgebung für mobile
Ad-Hoc-Szenarien}. In Informatiktage 2005, Bonn, Germany,apr, 2005. Bibtex@INPROCEEDINGS{Kron05GI,author = {Bronni, Jan and Hofmann, Stefanie and Kronfeld, Marcel and Monger, Andreas}, title = {{Eine strategieorientierte, modulare Simulationsumgebung für mobile Ad-Hoc-Szenarien}}, booktitle = {Informatiktage 2005}, year = {2005}, address = {Bonn, Germany}, month = {apr}, publisher = {Gesellschaft für Informatik (GI)}, owner = {mkron}, project = {extern}, timestamp = {2010.03.17}, } |
| [7] | Streichert, Felix and Ulmer, Holger. {JavaEvA}: a {Java} based framework for Evolutionary Algorithms. apr, 2005. [url]Bibtex@TECHREPORT{2005_70,author = {Streichert, Felix and Ulmer, Holger}, title = {{JavaEvA}: a {Java} based framework for Evolutionary Algorithms}, institution = {Center for Bioinformatics Tuebingen (ZBIT) of the Eberhard Karls University, Tuebingen, Germany}, year = {2005}, number = {WSI-2005-06}, month = {apr}, abstract = {The package JavaEvA (a Java implementation of Evolutionary Algorithms) is a general modular framework with an inherent client server structure to solve practical optimization problems. This package was especially designed to test and develop new approaches for Evolutionary Algorithms and to utilize them in real-world applications. JavaEvA already provides implementations of the most common Evolutionary Algorithms, like Genetic Algorithms, CHC Adaptive Search, Population Based Incremental Learning, Evolution Strategies, Model-Assisted Evolution Strategies, Genetic Programming and Grammatical Evolution. In addition the modular framework of JavaEvA allows everyone to add their own optimization modules to meet their specific requirements. The JavaEvA package uses a generic GUI framework that allows GUI access to any member of a class if get and set methods are provided and an editor is defined for the given data type. This approach allows very fast development cycles, since hardly any additional effort is necessary for implementing GUI elements, while still at the same time user specific GUI elements can be developed and integrated to increase usability. Since we cannot anticipate specific optimization problem and requirements, it is necessary for users to define their optimization problem. Therefore, we provide an additional framework and explain how one can include JavaEvA in an existing Java project or how one can implement ones own optimization problem and optimize it by using JavaEvA. This gives users total control of the optimization algorithms used.}, project = {abt_zell, optimization, javaeva}, url = {http://w210.ub.uni-tuebingen.de/dbt/volltexte/2005/1702/}, } |
| [8] | Wang, Maosen and Tamimi, Hashem and Zell, Andreas. {Robot Navigation Using Biosonar for Natural Landmark Tracking}. In IEEE International Symposium on Computational Intelligence in Robotics
and Automation (CIRA 2005), pages 3--7,, Espoo, Finland,jun, 2005. [url]Bibtex@INPROCEEDINGS{2005_121,author = {Wang, Maosen and Tamimi, Hashem and Zell, Andreas}, title = {{Robot Navigation Using Biosonar for Natural Landmark Tracking}}, booktitle = {IEEE International Symposium on Computational Intelligence in Robotics and Automation (CIRA 2005)}, year = {2005}, pages = {3--7}, address = {Espoo, Finland}, month = {jun}, publisher = {IEEE Press}, abstract = {A biosonar based mobile robot navigation system is presented for the natural landmark classification using acoustic image matching. The aim of this approach is to take advantage of the perceived properties of bats' prey and landmark identification mechanisms for mobile robots' tracking of natural landmarks. Recognizing natural landmarks like trees through sequential echolocation and acoustic image analyzing allows mobile robot to update its location in the natural environment. In this work, a working implementation of the biosonar system on a mobile robot is shown. It collects sequential echoes to produce acoustic images through digital signal processing (DSP), then compresses images with discrete cosine transform or pyramid algorithm. Fast normalized cross correlation (FNCC) and kernel principal component analysis (KPCA) are respectively used to make the final classification. Experimental result indicates that a mobile robot can achieve the ability of natural landmark classification only based on biomemetic sonar, the topological congruency of the relational structure with cross correlation in acoustic images is reliable in time domain, while the kernel principle component analysis based classification is robust in frequency domain and demands fewer echolocation for landmark classification.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?2005_121}, doi = {10.1109/CIRA.2005.1554246}, isbn = {0-7803-9355-4}, keywords = {image classification, mobile robots, path planning, robot vision, sonar detection, sonar target recognition, sonar tracking}, project = {abt_zell, robotics}, url = {http://dx.doi.org/10.1109/CIRA.2005.1554246}, } |
| [9] | Wang, Maosen and Zell, Andreas. {Sequential sensing with Biosonar for natural landmark classification}. In Safety, Security and Rescue Robotics, Workshop, 2005 IEEE International, pages 137--142,, Kobe, Japan,jun, 2005. [pdf , url]Bibtex@INPROCEEDINGS{2005_261,author = {Wang, Maosen and Zell, Andreas}, title = {{Sequential sensing with Biosonar for natural landmark classification}}, booktitle = {Safety, Security and Rescue Robotics, Workshop, 2005 IEEE International}, year = {2005}, pages = {137--142}, address = {Kobe, Japan}, month = {jun}, publisher = {IEEE Press}, abstract = {Echolocating bats can make nocturnal flights in acoustically cluttered environments with the use of echolocation. Their ability to evaluate targets in complete darkness provides mobile robots an opportunity to learn target detection, classification and identification with similar biomimetic platforms. In this work, natural landmark classification with a binaural system, a sequential sensing strategy and a frequency after reconstruction algorithm were developed and tested. The aim of the work is to overcome some inherent shortcomings of airborne sonar and take advantage of bats' perceived properties for mobile robots' navigation in natural environments. Experimental results suggest considerable improvements in classification accuracy can be achieved by the use of this sequential classification method.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?2005_261}, doi = {10.1109/SSRR.2005.1501230}, isbn = {0-7803-8945-x}, keywords = {mobile robots, mobile robots, navigation, remote sensing, signal reconstruction, sonar detection}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/wang_1006.pdf}, project = {abt_zell, robotics}, url = {http://dx.doi.org/10.1109/SSRR.2005.1501230}, } |
| [10] | Felix Streichert and Holger Ulmer and Andreas Zell. Hybrid Representations for Composition Optimization and Parallelizing
MOEAs. In Practical Approaches to Multi-Objective Optimizationaug, 2005. [url]Bibtex@INPROCEEDINGS{Streichert05Hybrid,author = {Felix Streichert and Holger Ulmer and Andreas Zell}, title = {Hybrid Representations for Composition Optimization and Parallelizing MOEAs}, booktitle = {Practical Approaches to Multi-Objective Optimization}, year = {2005}, editor = {Jürgen Branke and Kalyanmoy Deb and Kaisa Miettinen and Ralph E. Steuer}, number = {04461}, series = {Dagstuhl Seminar Proceedings}, month = {aug}, publisher = {Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany}, abstract = {In many real-world optimization problems sparse solution vectors are often preferred. Unfortunately, evolutionary algorithms can have problems to eliminate certain components completely, especially in multi-modal or neutral search spaces. A simple extension of the real-valued representation enables evolutionary algorithms to solve these types of optimization problems more efficiently. In case of multi-objective optimization some of these compositional optimization problems show most peculiar structures on the Pareto front. Here, the Pareto front is often non-convex and consists of multiple local segments. This feature invites parallelization based on the 'divide and conquer' principle, since subdivision into multiple local multi-objective optimization problems seems to be feasible. Therefore, we introduce a new parallelization scheme for multi-objective evolutionary algorithms based on clustering.}, project = {abt_zell, optimization}, url = {http://drops.dagstuhl.de/opus/volltexte/2005/251}, } |
| [11] | Speer, Nora and Spieth, Christian and Zell, Andreas. Spectral Clustering Gene Ontology Terms to Group Genes by Function. In Algorithms in Bioinformatics, 5th InternationalWorkshop, WABI 2005,
Mallorca, Spain, October 3-6, 2005, Proceedings, pages 1-12,, Palma, Spain,oct, 2005. [url]Bibtex@INPROCEEDINGS{2005_25,author = {Speer, Nora and Spieth, Christian and Zell, Andreas}, title = {Spectral Clustering Gene Ontology Terms to Group Genes by Function}, booktitle = {Algorithms in Bioinformatics, 5th InternationalWorkshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings}, year = {2005}, editor = {Rita Casadio and Gene Myers}, volume = {3692}, series = {Lecture Note in Computer Science}, pages = {1-12}, address = {Palma, Spain}, month = {oct}, publisher = {Springer}, abstract = {With the invention of biotechnological high throughput methods like DNA microarrays, biologists are capable of producing huge amounts of data. During the analysis of such data the need for a grouping of the genes according to their biological function arises. In this paper, we propose a method that provides such a grouping. As functional information, we use Gene Ontology terms. Our method clusters all GO terms present in a data set using a Spectral Clustering method. Then, mapping the genes back to their annotation, genes can be associated to one or more clusters of defined biological processes. We show that our Spectral Clustering method is capable of finding clusters with high inner cluster similarity.}, doi = {10.1007/11557067_1}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/speer05-wabi.pdf}, } |
| [12] | Spieth, Christian and Streichert, Felix and Speer, Nora and Zell,
Andreas. Inferring Regulatory Systems with Noisy Pathway Information. In Proceedings of the German Conference on Bioinformatics (GCB 2005), pages 193-203,, Hamburg, Germany,oct, 2005. [url]Bibtex@INPROCEEDINGS{2005_23,author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Inferring Regulatory Systems with Noisy Pathway Information}, booktitle = {Proceedings of the German Conference on Bioinformatics (GCB 2005)}, year = {2005}, volume = {71}, series = {LNI}, pages = {193-203}, address = {Hamburg, Germany}, month = {oct}, publisher = {GI}, isbn = {3-88579-400-4}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05inferring.pdf}, } |
| [13] | Spieth, Christian and Streichert, Felix and Speer, Nora and Sinzger,
Christian and Eberhard, Kathrin and Zell, Andreas. Predicting Single Genes Related to Immune-Relevant Processes. In IEEE Symposium on Computational Intelligence and Computational Biology, pages 461-468,, San Diego, USA,nov, 2005. [url]Bibtex@INPROCEEDINGS{2005_19,author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Sinzger, Christian and Eberhard, Kathrin and Zell, Andreas}, title = {Predicting Single Genes Related to Immune-Relevant Processes}, booktitle = {IEEE Symposium on Computational Intelligence and Computational Biology}, year = {2005}, pages = {461-468}, address = {San Diego, USA}, month = {nov}, publisher = {IEEE Press}, abstract = {In this paper we address the problem of predicting gene activities by finding gene regulatory dependencies in experimental DNA microarray data. Only few approaches to infer the dependencies of complete gene interconnectivity networks can be found in the literature. Due to the limited number of available data, the inferring problem is under-determined and ambiguous. Therefore, we introduce a new algorithm to infer relationships only between selected genes and the unknown gene network. This method is able to predict gene activation by mathematical modeling of the network and its simulation. The parameters of the mathematical model are determined by optimization with evolutionary algorithms. In this paper we will show that our approach is able to correctly predict gene responses in immune related regulatory processes and correctly identify some of the true genomic relationships of these genes.}, isbn = {0-7803-9387-2}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05single.pdf}, } |
| [14] | Spieth, Christian and Streichert, Felix and Supper, Jochen and Speer,
Nora and Zell, Andreas. Feedback Memetic Algorithms for Modelling Gene Regulatory Networks. In IEEE Symposium on Computational Intelligence and Computational Biology, pages 61-67,, San Diego, USA,nov, 2005. [url]Bibtex@INPROCEEDINGS{2005_20,author = {Spieth, Christian and Streichert, Felix and Supper, Jochen and Speer, Nora and Zell, Andreas}, title = {Feedback Memetic Algorithms for Modelling Gene Regulatory Networks}, booktitle = {IEEE Symposium on Computational Intelligence and Computational Biology}, year = {2005}, pages = {61-67}, address = {San Diego, USA}, month = {nov}, publisher = {IEEE Press}, abstract = {In this paper we address the problem of finding gene regulatory networks from experimental DNA microarray data. We focus on the evaluation of the performance of memetic algorithms on the inference problem. These algorithms are used to evolve an underlying quantitative mathematical model. The dynamics of the regulatory system are modeled with two commonly used approaches, namely linear weight matrices and S-systems. Due to the complexity of the inference problem, some researchers suggested evolutionary algorithms for this purpose. We introduce memetic enhancements to this optimization process to infer the parameters of sparsely connected nonlinear systems from the observed data. Due to the limited number of available data, the inferring problem is underdetermined and ambiguous. Further on, the problem often is multimodal and therefore appropriate optimization strategies become necessary. We propose a memetic method, which separates the overall inference problem into two subproblems to find the correct network: first, the search for a valid topology, and secondly, the optimization of the parameters of the mathematical model. The performance and the properties of the proposed methods are evaluated and compared to standard algorithms found in the literature.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?2005_20}, isbn = {0-7803-9387-2}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05feedback.pdf}, } |
| [15] | Stefan, Norbert and Machicao, Fausto and Staiger, Harald and Machann,
J. and Schick, F. and Tschritter, Otto and Spieth, Christian and
Weigert, Cora and Fritsche, Andreas and Stumvoll, M. and Häring,
Hans-Ulrich. Polymorphisms in the gene encoding adiponectin receptor 1 are associated
with insulin resistance and high liver fat. , pages 2282-2291,nov, 2005. Bibtex@ARTICLE{2005_18,author = {Stefan, Norbert and Machicao, Fausto and Staiger, Harald and Machann, J. and Schick, F. and Tschritter, Otto and Spieth, Christian and Weigert, Cora and Fritsche, Andreas and Stumvoll, M. and Häring, Hans-Ulrich}, title = {Polymorphisms in the gene encoding adiponectin receptor 1 are associated with insulin resistance and high liver fat}, journal = {Diabetologia}, year = {2005}, volume = {48}, pages = {2282-2291}, number = {11}, month = {nov}, abstract = {AIMS/HYPOTHESIS: The adipokine adiponectin has insulin-sensitising, anti-atherogenic and anti-inflammatory properties. Recently, the genes for mouse and human adiponectin receptor-1 (ADIPOR1) and -2 (ADIPOR2) have been cloned. The aim of this study was to investigate whether genetic variants of the genes encoding ADIPOR1 and ADIPOR2 play a role in human metabolism. MATERIALS AND METHODS: We screened ADIPOR1 and ADIPOR2 for polymorphisms and determined their association with glucose metabolism, lipid metabolism, an atherogenic lipid profile and inflammatory markers in 502 non-diabetic subjects. A subgroup participated in a longitudinal study; these subjects received diet counselling and increased their physical activity. RESULTS: We identified six variants of ADIPOR1 and seven variants of ADIPOR2. A single-nucleotide polymorphism (SNP) in the putative promoter region 8503 bp upstream of the translational start codon (-8503 G/A) of ADIPOR1 (frequency of allele A=0.31) was in almost complete linkage disequilibrium with another SNP (-1927 T/C) in intron 1. Subjects carrying the -8503 A and -1927 C alleles had lower insulin sensitivity, as estimated from a 75 g OGTT (p=0.04) and determined during a euglycaemic clamp (n=295, p=0.04); they also had higher HbA(1)c levels (p=0.02) and, although the difference was not statistically significant, higher liver fat (n=85, determined by proton magnetic resonance spectroscopy, p=0.056) (all p values are adjusted for age, sex and percentage of body fat). In the longitudinal study (n=45), the -8503 A and -1927 C alleles were associated with lower insulin sensitivity (p=0.03) and higher liver fat (p=0.02) at follow-up compared with the -8503 G and -1927 T alleles, independently of basal measurements, sex and baseline and follow-up percentage of body fat. CONCLUSIONS/INTERPRETATION: The present findings suggest that the -8503 G/A SNP in the promoter or the -1927 T/C SNP in intron 1 of ADIPOR1 may affect insulin sensitivity and liver fat in humans.}, doi = {10.1007/s00125-005-1948-3}, keywords = {Adipose Tissue/pathology Adult Body Fat Distribution Cross-Sectional Studies Diabetes Mellitus, Type 2/*genetics/pathology Female Gene Frequency Genetic Predisposition to Disease Germany Humans Insulin Resistance/*genetics Introns Lipids/chemistry Liver/*pathology Longitudinal Studies Male Middle Aged *Polymorphism, Single Nucleotide Promoter Regions, Genetic Receptors, Adiponectin Receptors, Cell Surface/*genetics}, project = {abt_zell, bioinformatics}, } |
| [16] | Supper, Jochen and Spieth, Christian and Zell, Andreas. Reverse Engineering Non-Linear Gene Regulatory Networks Based on
the Bacteriophage lambda cI Circuit. In Proceedings of the 2005 IEEE Symposium on Computational Intelligence
and Computational Biology (CIBCB '05), pages 325-332,, San Diego, USA,nov, 2005. [url]Bibtex@INPROCEEDINGS{2005_22,author = {Supper, Jochen and Spieth, Christian and Zell, Andreas}, title = {Reverse Engineering Non-Linear Gene Regulatory Networks Based on the Bacteriophage lambda cI Circuit}, booktitle = {Proceedings of the 2005 IEEE Symposium on Computational Intelligence and Computational Biology (CIBCB '05)}, year = {2005}, pages = {325-332}, address = {San Diego, USA}, month = {nov}, publisher = {IEEE}, abstract = {The ability to measure the transcriptional response of cells has drawn much attention to the underlying transcriptional networks. To untangle the network, numerous models with corresponding reverse engineering methods have been applied. In this work, we propose a non-linear model with adjustable degrees of complexity. The corresponding reverse engineering method uses a probabilistic scheme to reduce the reconstruction problem to subnetworks. Adequate models for gene regulatory networks must be anchored on sufficient biological knowledge. Here, the cI auto-inhibition circuit (cI circuit) is used to validate our reverse engineering method. Simulations of the cI circuit are used for the reconstruction, whereas a simplified cI circuit model assists the modeling phase. Several levels of complexity are evaluated, subsequently the reconstructed models show different properties. As a result, we reconstruct an abstract model, capturing the dynamic behavior of the cI circuit to a high degree.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?2005_22}, doi = {10.1109/CIBCB.2005.1594936}, isbn = {0-7803-9387-2}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/Supper05reveng.pdf}, } |
| [17] | Tamimi, Hashem and Zell, Andreas. Global Robot localization using Iterative Scale Invariant Feature
Transform. In 36th International Symposium Robotics (ISR 2005), pages 142-149,, Tokyo, Japan,nov, 2005. [url]Bibtex@INPROCEEDINGS{2005_123,author = {Tamimi, Hashem and Zell, Andreas}, title = {Global Robot localization using Iterative Scale Invariant Feature Transform}, booktitle = {36th International Symposium Robotics (ISR 2005)}, year = {2005}, volume = {36}, pages = {142-149}, address = {Tokyo, Japan}, month = {nov}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/tamimi05-isr2.pdf}, } |
| [18] | Tamimi, Hashem and Zell, Andreas. Using Scale Space Image Histograms for Global Localization of Mobile
Robots. In 36th International Symposium Robotics (ISR 2005), pages 143-150,, Tokyo, Japan,nov, 2005. [url]Bibtex@INPROCEEDINGS{2005_124,author = {Tamimi, Hashem and Zell, Andreas}, title = {Using Scale Space Image Histograms for Global Localization of Mobile Robots}, booktitle = {36th International Symposium Robotics (ISR 2005)}, year = {2005}, volume = {36}, pages = {143-150}, address = {Tokyo, Japan}, month = {nov}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/tamimi05-isr1.pdf}, } |
| [19] | Dräger, Andreas. {Automatische und vergleichende Analyse bakterieller Genome mit Schwerpunkt
auf \emph{Ralstonia}/\emph{Cupriavidus}-Arten sowie verwandten Proteobakerien}. , von-Seckendorff-Platz 1, 06120 Halle (Saale),dec, 2005. [pdf]Bibtex@Diplomarbeit{Draeger2005,author = {Dräger, Andreas}, title = {{Automatische und vergleichende Analyse bakterieller Genome mit Schwerpunkt auf \emph{Ralstonia}/\emph{Cupriavidus}-Arten sowie verwandten Proteobakerien}}, school = {Martin-Luther-Universität Halle-Wittenberg}, year = {2005}, address = {von-Seckendorff-Platz 1, 06120 Halle (Saale)}, month = {dec}, abstract = {Knowledge generation by comparative genomics become more and more meaningful due to the increased availability of genomic sequence data. This thesis compares the genomes of $\beta$-proteobacteria, a taxonomic group of bacteria showing a high degree of diversity. Sequenced species of this group inhabit various ecological niches. Therefore, they need special features to surviving toxic heavy metal concentrations, to act as pathogens of plants or animals or to degrade organic substances, which are normally difficult to break down. These characteristic features are mediated by special proteins, leading to the question, if characteristic proteins can be detected automatically by comparing the sequences of related proteins of different species. By comparison of highly conserved proteins with essential life functions in a taxonomic context a measurement should be developed to normalize later on comparison of these specialized proteins. The taxonomic context of different bacterial species can be derived from comparisons of the highly conserved genes for the 16 S rRNA, which is involved in the protein synthesis of bacteria. To perform those comparisons different algorithms have been released. For global alignments the Needleman-Wunsch algorithm or a special Hidden Markov Model can be used. Local alignments can be done by the Smith-Waterman algorithm or its heuristic approximation BLAST. Global alignments compare whole sequences, whereas local alignments find longest conserved regions in two sequences. Proteins contain functional regions (domains) surrounded by less important regions, so that these can be compared by local alignments. The complete 16 S rRNA sequence is essential for its functionality, so that for taxonomic analysis global alignments are needed. To evaluate the quality of alignments different substitutions matrices like BLOSUM, PAM, NUC contain scores for the substitution of a symbol with another one. The sum of these scores is the score of the alignment. Several online database servers like NCBI, RDP, EMBL, JGI, SwissProt, Tigr and many others provide genomic and proteomic sequence data of different species. These databases grow at an exponential rate, because new techniques of sequencing proteins and genetic elements in high throughput analysis are used and data can be uploaded by individual authors, laboratories or other scientific institutions. However, to use these data to perform comparative local analysis, an efficient way of storage has to be found. Problems of data storage occur due to the different naming conventions of species, genes, proteins and other biological data. To maintain the data consistently without redundancy, a database server was installed using MySQL. As a relation scheme BioSQL was used. To integrate downloaded data into the local database different pre-processing steps (data cleaning) were necessary. A client program to compare the locally stored data was implemented in Java, using the open source library BioJava. The resulting database application also provides interactive visualizations of the data in the database such as the taxonomic tree and genetic annotations. It contains a graphical user interface to interact with BioSQL without knowledge of databases. In addition, different file formats of biological sequence data can be converted into each other. With a special dialog global and local sequence alignments can be performed interactively. The BioJava library had to be extended to provide the full functionality of that program. This application was used on a selection of essential proteins (involved in DNA transcription and translation) of 15 $\beta$-proteobacteria and 7 $\gamma$-proteobacteria and non essential proteins (involved in heavy metal resistance) and the 16 S rRNA genes. All comparisons are relative to the well investigated species \emph{Escherichia coli} K12. Plotting the protein similarity against the taxonomic neighborhood shows an almost linear increase for essential proteins with taxonomic nearness. The other proteins show higher variability. This leads to the conclusion that proteins with special features are less conserved than highly essential proteins, so that these can be detected from the taxonomic context by normalization with essential proteins.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Draeger2005}, pdf = {https://nirvana.informatik.uni-halle.de/~molitor/Diplomarbeiten/2005/draeger_andreas.pdf}, project = {extern, bioinformatics}, } |
| [20] | Fröhlich, Holger and Wegner, Jörg K. and Sieker, Florian and
Zell, Andreas. Kernel Functions for Attributed Molecular Graphs - A New Similarity
Based Approach To {ADME} Prediction in Classification and Regression. , pages 317-326,2005. [url]Bibtex@ARTICLE{2005_27,author = {Fröhlich, Holger and Wegner, Jörg K. and Sieker, Florian and Zell, Andreas}, title = {Kernel Functions for Attributed Molecular Graphs - A New Similarity Based Approach To {ADME} Prediction in Classification and Regression}, journal = {QSAR \& Combinatorial Science}, year = {2005}, volume = {25}, pages = {317-326}, number = {4}, abstract = {Kernel methods, like the well-known Support Vector Machine (SVM), have received growing attention in recent years for designing QSAR models that have a high predictive strength. One of the key concepts of SVMs is the usage of a so-called kernel function, which can be thought of as a special similarity measure. In this paper we consider kernels for molecular structures, which are based on a graph representation of chemical compounds. The similarity score is calculated by computing an optimal assignment of the atoms from one molecule to those of another one, including information on specific chemical properties, membership to a substructure (e.g., aromatic ring, carbonyl group, etc.) and neighborhood for each atom. We show that by using this kernel we can achieve a generalization performance comparable to a classical model with a few descriptors, which are a-priori known to be relevant for the problem, and significantly better results than with and without performing an automatic descriptor selection. For this purpose we investigate ADME classification and regression datasets for predicting bioavailability (Yoshida), Human Intestinal Absorption (HIA), Blood-Brain-Barrier (BBB) penetration and a dataset consisting of four different inhibitor classes (SOL). We further explore the effect of combining our kernel with a problem-dependent descriptor set. We also demonstrate the usefulness of an extension of our method to a reduced graph representation of molecules, in which certain structural features, like, e.g., rings, donors or acceptors, are represented as a single node in the molecular graph.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?2005_27}, doi = {10.1002/qsar.200510135}, issn = {1611020X}, project = {abt_zell, cheminformatics}, publisher = {Wiley}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05QSAR&CombSci.pdf}, } |
| [21] | Fröhlich, Holger and Wegner, Jörg K. and Sieker, Florian and
Zell, Andreas. Optimal Assignment Kernels For Attributed Molecular Graphs. In International Conference on Machine Learning (ICML 2005), pages 252-232,, Bonn, Germany,2005. [url]Bibtex@INPROCEEDINGS{2005_28,author = {Fröhlich, Holger and Wegner, Jörg K. and Sieker, Florian and Zell, Andreas}, title = {Optimal Assignment Kernels For Attributed Molecular Graphs}, booktitle = {International Conference on Machine Learning (ICML 2005)}, year = {2005}, pages = {252-232}, address = {Bonn, Germany}, publisher = {ACM Press}, project = {abt_zell, cheminformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05OAKernels.pdf}, } |
| [22] | Fröhlich, Holger and Wegner, Jörg K. and Zell, Andreas. Assignment Kernels For Chemical Compounds. In International Joint Conference on Neural Networks (IJCNN 2005), pages 913-918,, Montreal, Canada,2005. [url]Bibtex@INPROCEEDINGS{2005_29,author = {Fröhlich, Holger and Wegner, Jörg K. and Zell, Andreas}, title = {Assignment Kernels For Chemical Compounds}, booktitle = {International Joint Conference on Neural Networks (IJCNN 2005)}, year = {2005}, pages = {913-918}, address = {Montreal, Canada}, publisher = {IEEE Press}, project = {abt_zell, cheminformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05ChemKernels.pdf}, } |
| [23] | Fröhlich, Holger and Wegner, Jörg K. and Zell, Andreas. Efficient Parameter Selection for Support Vector Machines in Classification
and Regression via Model-Based Global Optimization. In International Joint Conference on Neural Networks (IJCNN 2005), pages 1431-1438,, Montreal, Canada,2005. [url]Bibtex@INPROCEEDINGS{2005_31,author = {Fröhlich, Holger and Wegner, Jörg K. and Zell, Andreas}, title = {Efficient Parameter Selection for Support Vector Machines in Classification and Regression via Model-Based Global Optimization}, booktitle = {International Joint Conference on Neural Networks (IJCNN 2005)}, year = {2005}, pages = {1431-1438}, address = {Montreal, Canada}, publisher = {IEEE Press}, project = {abt_zell, optimization, cheminformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05ParamSelSVM.pdf}, } |
| [24] | Heinemann, Patrick and Haase, Jürgen and Zell, Andreas. {Verbesserte Effizienz der Monte-Carlo-Lokalisierung im RoboCup}. In Autonome Mobile Systeme: 19. Fachgespräch Stuttgart, 8./9. Dezember
2005, pages 19-24,2005. [url]Bibtex@INPROCEEDINGS{2005_127,author = {Heinemann, Patrick and Haase, Jürgen and Zell, Andreas}, title = {{Verbesserte Effizienz der Monte-Carlo-Lokalisierung im RoboCup}}, booktitle = {Autonome Mobile Systeme: 19. Fachgespräch Stuttgart, 8./9. Dezember 2005}, year = {2005}, pages = {19-24}, project = {abt_zell, robotics, robocup}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/heinemann05verbesserte.pdf}, } |
| [25] | Heinemann, Patrick and Treptow, Andr\'{e} and Zell, Andreas. The {Attempto} {Tübingen} Robot Soccer Team. In RoboCup-2004: Robot Soccer World Cup VIII2005. [url]Bibtex@INPROCEEDINGS{2005_260,author = {Heinemann, Patrick and Treptow, Andr\'{e} and Zell, Andreas}, title = {The {Attempto} {Tübingen} Robot Soccer Team}, booktitle = {RoboCup-2004: Robot Soccer World Cup VIII}, year = {2005}, editor = {Nardi, D. and Riedmiller, M. and Sammut, C. and Santos-Victor, J}, volume = {3276 (CD supplement)}, series = {Lecture Notes in Computer Science}, publisher = {Springer}, project = {abt_zell, robotics, robocup}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/heinemann05attempto.pdf}, } |
| [26] | Lilienthal, Achim and Streichert, Felix and Zell, Andreas. Model-based shape analysis of gas concentration gridmaps for improved
gas source localisation. In IEEE International Conference on Robotics and Automation (ICRA 2005), pages 3575-3580,, Barcelona, Spain,2005. Bibtex@INPROCEEDINGS{2005_119,author = {Lilienthal, Achim and Streichert, Felix and Zell, Andreas}, title = {Model-based shape analysis of gas concentration gridmaps for improved gas source localisation}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA 2005)}, year = {2005}, pages = {3575-3580}, address = {Barcelona, Spain}, publisher = {IEEE}, project = {abt_zell, robotics}, } |
| [27] | Sch\"{u}tze, Niels and de Paly, Michael and W\"{o}hling, Thomas and
Schmitz, Gerd. Global optimisation of deficit irrigation systems using evolutionary
algorithms and neural networks. In Proceedings of the ICID 21st European Regional Conference 2005, Integrated
Land and Water Resources Management Towards Sustainable Rural Development, Frankfurt (Oder), Germany and Slubice, Poland,2005. Bibtex@INPROCEEDINGS{Schuetze05,author = {Sch\"{u}tze, Niels and de Paly, Michael and W\"{o}hling, Thomas and Schmitz, Gerd}, title = {Global optimisation of deficit irrigation systems using evolutionary algorithms and neural networks}, booktitle = {Proceedings of the ICID 21st European Regional Conference 2005, Integrated Land and Water Resources Management Towards Sustainable Rural Development}, year = {2005}, address = {Frankfurt (Oder), Germany and Slubice, Poland}, project = {extern, irrigation, hydrogeo, optimization}, timestamp = {2010.01.25}, } |
| [28] | Speer, Nora and Fröhlich, Holger and Spieth, Christian and Zell,
Andreas. Functional Distances for Genes Based on {GO} Feature Maps and their
Application to Clustering. In IEEE Symposium on Computational Intelligence and Computational Biology, pages 142-149,, San Diego, USA,2005. [url]Bibtex@INPROCEEDINGS{2005_21,author = {Speer, Nora and Fröhlich, Holger and Spieth, Christian and Zell, Andreas}, title = {Functional Distances for Genes Based on {GO} Feature Maps and their Application to Clustering}, booktitle = {IEEE Symposium on Computational Intelligence and Computational Biology}, year = {2005}, pages = {142-149}, address = {San Diego, USA}, publisher = {IEEE Press}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/Speer05goclust.pdf}, } |
| [29] | Speer, Nora and Fröhlich, Holger and Spieth, Christian and Zell,
Andreas. Functional Grouping of Genes Using Spectral Clustering and Gene Ontology. In International Joint Conference on Neural Networks (IJCNN 2005), pages 298-303,, Montreal, Canada,2005. [url]Bibtex@INPROCEEDINGS{2005_32,author = {Speer, Nora and Fröhlich, Holger and Spieth, Christian and Zell, Andreas}, title = {Functional Grouping of Genes Using Spectral Clustering and Gene Ontology}, booktitle = {International Joint Conference on Neural Networks (IJCNN 2005)}, year = {2005}, pages = {298-303}, address = {Montreal, Canada}, publisher = {IEEE Press}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/speer05-ijcnn.pdf}, } |
| [30] | Speer, Nora and Spieth, Christian and Zell, Andreas. Biological Cluster Validity Indices Based on the Gene Ontology. In Advances in Intelligent Data Analysis VI, 6th International Symposium
on Intelligent Data Analysis, IDA 2005, Madrid, Spain, September
8-10, 2005, Proceedings, pages 429-439,, Madrid, Spain,2005. [url]Bibtex@INPROCEEDINGS{2005_26,author = {Speer, Nora and Spieth, Christian and Zell, Andreas}, title = {Biological Cluster Validity Indices Based on the Gene Ontology}, booktitle = {Advances in Intelligent Data Analysis VI, 6th International Symposium on Intelligent Data Analysis, IDA 2005, Madrid, Spain, September 8-10, 2005, Proceedings}, year = {2005}, editor = {A. Fazel Famili and Joost N. Kok and Jos{\'e} Mar\'{\i}a Pe{\~n}a and Arno Siebes and A. J. Feelders}, volume = {3646}, series = {Lecture Notes in Computer Science}, pages = {429-439}, address = {Madrid, Spain}, publisher = {Springer}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/speer05-ida.pdf}, } |
| [31] | Spieth, Christian and Streichert, Felix and Speer, Nora and Zell,
Andreas. Identifying Valid Solutions for the Inference of Regulatory Networks. In Genetic and Evolutionary Computation Conference (GECCO 2005), pages 469-471,, Washington, USA,2005. [url]Bibtex@INPROCEEDINGS{2005_30,author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Identifying Valid Solutions for the Inference of Regulatory Networks}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO 2005)}, year = {2005}, pages = {469-471}, address = {Washington, USA}, publisher = {ACM Press}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05identifying.pdf}, } |
| [32] | Spieth, Christian and Streichert, Felix and Speer, Nora and Zell,
Andreas. Clustering-based Approach to Identify Solutions for the Inference
of Regulatory Networks. In IEEE Congress on Evolutionary Computation (CEC 2005), pages 660-667,, Edinburgh, UK,2005. [url]Bibtex@INPROCEEDINGS{Spieth2005ClusteringApproach,author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Clustering-based Approach to Identify Solutions for the Inference of Regulatory Networks}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2005)}, year = {2005}, pages = {660-667}, address = {Edinburgh, UK}, publisher = {IEEE Press}, project = {abt_zell, bioinformatics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05clustering.pdf}, } |
| [33] | Tschritter, Otto and Machicao, Fausto and Stefan, Norbert and Schäfer,
Silke and Weigert, Cora and Staiger, Harald and Spieth, Christian
and Häring, Hans-Ulrich and Fritsche, Andreas. A new variant in the human {Kv1.3} gene is associated with low insulin
sensitivity and impaired glucose tolerance. , pages 654-658,2005. Bibtex@ARTICLE{2005_17,author = {Tschritter, Otto and Machicao, Fausto and Stefan, Norbert and Schäfer, Silke and Weigert, Cora and Staiger, Harald and Spieth, Christian and Häring, Hans-Ulrich and Fritsche, Andreas}, title = {A new variant in the human {Kv1.3} gene is associated with low insulin sensitivity and impaired glucose tolerance}, journal = {Journal of Clinical Endocrinology \& Metabolism}, year = {2005}, volume = {91}, pages = {654-658}, number = {2}, abstract = {CONTEXT: The voltage-gated potassium channel Kv1.3 (KCNA3) is expressed in a variety of tissues including liver and skeletal muscle. In animal models, knockout of Kv1.3 has been found to improve insulin sensitivity and glucose tolerance. OBJECTIVE: We examined whether mutations in the Kv1.3 gene exist in humans and whether they are associated with alterations of glucose homeostasis. DESIGN AND SETTING: We conducted a genotype-phenotype association study at a university hospital. PARTICIPANTS AND METHODS: In 50 nondiabetic subjects, we screened approximately 4.5 kb of chromosome 1 comprising the single exon, the promoter/5'-untranslated region, and the 3'-untranslated region of the human Kv1.3 gene for mutations by direct sequencing. Subsequently, all identified single-nucleotide polymorphisms were analyzed in 552 nondiabetic subjects who underwent an oral glucose tolerance test (OGTT). Of these, 304 had undergone an additional hyperinsulinemic euglycemic clamp. MAIN OUTCOME MEASURES: We assessed postprandial blood glucose during OGTT and insulin sensitivity measured by hyperinsulinemic euglycemic clamp. RESULTS: We identified five single-nucleotide polymorphisms in the promoter region (T-548C, G-697T, A-845G, T-1645C, and G-2069A) with allelic frequencies of the minor allele of 26, 23, 9, 41, and 16%, respectively. The -1645C allele was associated with higher plasma glucose concentrations in the 2-h OGTT (P = 0.03) even after adjustment for sex, age, and body mass index (P = 0.002). In addition, it was associated with lower insulin sensitivity (P = 0.01, adjusted for sex, age, and body mass index). Functional in vitro analysis using EMSA showed differential transcription factor binding to the T-1645C polymorphism. CONCLUSIONS: We show that a variant in the promoter of the Kv1.3 gene is associated with impaired glucose tolerance and lower insulin sensitivity. Therefore, the Kv1.3 channel represents a candidate gene for type 2 diabetes.}, keywords = {3' Untranslated Regions/chemistry/genetics 5' Untranslated Regions/chemistry/genetics Adult Blood Glucose/metabolism DNA/chemistry/genetics Electrophoretic Mobility Shift Assay Female Glucose Intolerance/*genetics/physiopathology Glucose Tolerance Test Humans Insulin Resistance/*genetics/physiology Kv1.3 Potassium Channel/*genetics/physiology Male Polymerase Chain Reaction Polymorphism, Single Nucleotide Promoter Regions, Genetic/genetics/physiology Sequence Analysis, DNA}, project = {abt_zell, bioinformatics}, } |
| [34] | Weiss, Christian and Zell, Andreas. Automatic Generation of Indoor {VR}-Models by a Mobile Robot with
a Laser Range Finder and a Color Camera. In Autonome Mobile Systeme (AMS 2005), pages 107-113,, Stuttgart, Germany,2005. [url]Bibtex@INPROCEEDINGS{2005_126,author = {Weiss, Christian and Zell, Andreas}, title = {Automatic Generation of Indoor {VR}-Models by a Mobile Robot with a Laser Range Finder and a Color Camera}, booktitle = {Autonome Mobile Systeme (AMS 2005)}, year = {2005}, pages = {107-113}, address = {Stuttgart, Germany}, publisher = {Springer}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/weiss05ams.pdf}, } |