| [1] | Wrzodek, Clemens and Büchel, Finja and Ruff, Manuel and Dräger,
Andreas and Zell, Andreas. Precise generation of systems biology models from {KEGG} pathways.. , pages 15,jan, 2013. [pdf , url]Bibtex@ARTICLE{Wrzodek2013a,author = {Wrzodek, Clemens and Büchel, Finja and Ruff, Manuel and Dräger, Andreas and Zell, Andreas}, title = {Precise generation of systems biology models from {KEGG} pathways.}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {15}, number = {1}, month = {jan}, abstract = {Background: The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with an enormous amount of information and provide a foundation for initial structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries. Thus, a direct conversion into systems biology models would produce incomplete and erroneous models. Results: Here, we present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded in the standardized community pathway formats SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3). This method involves correcting invalid or incomplete KGML content, creating complete and valid stoichiometric reactions, translating relations to signaling models and augmenting the pathway content with various information, such as cross-references to Entrez Gene, OMIM, UniProt ChEBI, and many more. Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can only be performed using SBML Level 3, including its recently proposed qualitative models and groups extension packages. Conclusions: Building correct BioPAX and SBML signaling models from the KEGG database is a unique characteristic of the proposed method. Further, there is no other approach that is able to appropriately construct metabolic models from KEGG pathways, including correct reactions with stoichiometry. The resulting initial models, which contain valid and comprehensive SBML or BioPAX code and a multitude of cross-references, lay the foundation to facilitate further modeling steps.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Wrzodek2013a.html}, doi = {10.1186/1752-0509-7-15}, issn = {1752-0509}, keywords = {KEGG, KGML, SBML, BioPAX, modeling, systems biology, qualitative modeling, quantitative modeling, converter, comparison}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-15.pdf}, project = {abt_zell, bioinformatics, kegg_translator, NGFNplus, VLN}, url = {http://www.biomedcentral.com/1752-0509/7/15}, } |
| [2] | Shaowu Yang and Sebastian A. Scherer and Andreas Zell. An Onboard Monocular Vision System for Autonomous Takeoff, Hovering
and Landing of a Micro Aerial Vehicle. , pages 499--515,jan, 2013. [pdf , url]Bibtex@ARTICLE{YangsJINT12,author = {Shaowu Yang and Sebastian A. Scherer and Andreas Zell}, title = {An Onboard Monocular Vision System for Autonomous Takeoff, Hovering and Landing of a Micro Aerial Vehicle}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2013}, volume = {69}, pages = {499--515}, number = {1--4}, month = {jan}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?YangsJINT12}, owner = {yangs}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/yang_JINT.pdf}, project = {abt_zell, multicamSLAM, uav}, publisher = {Springer}, url = {http://link.springer.com/article/10.1007/s10846-012-9749-7}, } |
| [3] | Jimenez Lugo, Jacobo and Andreas Zell. Framework for Autonomous Onboard Navigation with the AR.Drone. In International Conference on Unmanned Aircraft Systems (ICUAS'13), Atlanta, Georgia, USA,April, 2013. [url]Bibtex@INPROCEEDINGS{jimenez2013ICUAS,author = {Jimenez Lugo, Jacobo and Andreas Zell}, title = {Framework for Autonomous Onboard Navigation with the AR.Drone}, booktitle = {International Conference on Unmanned Aircraft Systems (ICUAS'13)}, year = {2013}, address = {Atlanta, Georgia, USA}, month = {April}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?jimenez2013ecmr}, owner = {jimenez}, project = {abt_zell, robotics, uav}, timestamp = {2013.06.24}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/jimenez_icuas_final.pdf}, } |
| [4] | Andreas Masselli and Shaowu Yang and Karl Engelbert Wenzel and Andreas
Zell. A Cross-Platform Comparison of Visual Marker Based Approaches for
Autonomous Flight of Quadrocopters. In Proceedings of International Conference on Unmanned Aircraft Systems, pages 1-9,, Atlanta, Georgia, USA,may, 2013. [url]Bibtex@INPROCEEDINGS{Masselli2013,author = {Andreas Masselli and Shaowu Yang and Karl Engelbert Wenzel and Andreas Zell}, title = {A Cross-Platform Comparison of Visual Marker Based Approaches for Autonomous Flight of Quadrocopters}, booktitle = {Proceedings of International Conference on Unmanned Aircraft Systems}, year = {2013}, pages = {1-9}, address = {Atlanta, Georgia, USA}, month = {may}, abstract = {In this paper, we compare three different marker based approaches for six degrees of freedom (6DOF) pose estimation, which can be used for position and attitude control of micro aerial vehicles (MAV). All methods are able to achieve real time pose estimation onboard without assistance of any external metric sensor. Since these methods can be used in various working environments, we compare their performance by carrying out experiments across two different platforms: An AscTec Hummingbird and a Pixhawk quadrocopter. We evaluate each method's accuracy by using an external tracking system and compare the methods with respect to their operating ranges and processing time. We finally compare each method's performance during autonomous takeoff, hovering and landing of a quadrocopter.}, days = {28-31}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Masselli2013}, owner = {masselli}, project = {abt_zell, robotics, uav, passivemarkers}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/masselli2013icuas.pdf}, } |
| [5] | Schauwecker, Konstantin and Zell, Andreas. {On-Board Dual-Stereo-Vision for Autonomous Quadrotor Navigation}. In International Conference on Unmanned Aircraft Systems (ICUAS), pages 332--341,, Atlanta, GA, USA,May, 2013. [pdf , url]Bibtex@INPROCEEDINGS{Schauwecker2013a,author = {Schauwecker, Konstantin and Zell, Andreas}, title = {{On-Board Dual-Stereo-Vision for Autonomous Quadrotor Navigation}}, booktitle = {International Conference on Unmanned Aircraft Systems (ICUAS)}, year = {2013}, pages = {332--341}, address = {Atlanta, GA, USA}, month = {May}, publisher = {IEEE}, abstract = {We present a quadrotor Micro Aerial Vehicle (MAV) capable of autonomous indoor navigation. The MAV is equipped with four cameras arranged in two stereo configurations. One camera pair is facing forward and serves as input for a reduced stereo SLAM system. The other camera pair is facing downwards and is used for ground plane detection and tracking. All processing, including sparse stereo matching, is run on-board in real-time and at high processing rates. We demonstrate the capabilities of this MAV design in several flight experiments. Our MAV is able to recover from pose estimation errors and can cope with processing failures for one camera pair. We show that by using two camera pairs instead of one, we are able to significantly increase navigation accuracy and robustness.}, owner = {schauwecker}, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2013/schauwecker_icuas2013.pdf}, project = {abt_zell, robotics, stereo_mav, uav}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6564706}, } |
| [6] | Shaowu Yang and Sebastian A. Scherer and Konstantin Schauwecker and
Andreas Zell. {Onboard Monocular Vision for Landing of an MAV on a Landing Site
Specified by a Single Reference Image}. In 2013 International Conference on Unmanned Aircraft Systems (ICUAS'13), pages 317--324,, Atlanta, GA, USA,May, 2013. [pdf , url]Bibtex@INPROCEEDINGS{YangsICUAS13,author = {Shaowu Yang and Sebastian A. Scherer and Konstantin Schauwecker and Andreas Zell}, title = {{Onboard Monocular Vision for Landing of an MAV on a Landing Site Specified by a Single Reference Image}}, booktitle = {2013 International Conference on Unmanned Aircraft Systems (ICUAS'13)}, year = {2013}, pages = {317--324}, address = {Atlanta, GA, USA}, month = {May}, abstract = {This paper presents a real-time monocular vision solution for MAVs to autonomously search for and land on an arbitrary landing site. The autonomous MAV is provided with only one single reference image of the landing site with an unknown size before initiating this task. To search for such landing sites, we extend a well-known visual SLAM algorithm that enables autonomous navigation of the MAV in unknown environments. A multi-scale ORB feature based method is implemented and integrated into the SLAM framework for landing site detection. We use a RANSAC-based method to locate the landing site within the map of the SLAM system, taking advantage of those map points associated with the detected landing site. We demonstrate the efficiency of the presented vision system in autonomous flight, and compare its accuracy with ground truth data provided by an external tracking system.}, days = {28-31}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?YangsICUAS13}, owner = {yangs}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/ICUAS13_yangs_final.pdf}, project = {abt_zell, autoLanding, uav}, timestamp = {2013.04.15}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6564704}, } |
| [7] | Yin, Peiyuan and Peter, Andreas and Franken, Holger and Zhao, Xinjie
and Neukamm, Sabine Sarah and Rosenbaum, Lars and Lucio, Marianna
and Zell, Andreas and Häring, Hans-Ulrich and Xu, Guowang and Lehmann,
Rainer. Pre-analytical aspects and sample quality assessment in metabolomics
studies of human blood. , pages 833-845,May, 2013. Bibtex@ARTICLE{Yin2013,author = {Yin, Peiyuan and Peter, Andreas and Franken, Holger and Zhao, Xinjie and Neukamm, Sabine Sarah and Rosenbaum, Lars and Lucio, Marianna and Zell, Andreas and Häring, Hans-Ulrich and Xu, Guowang and Lehmann, Rainer}, title = {Pre-analytical aspects and sample quality assessment in metabolomics studies of human blood}, journal = {Clinical Chemistry}, year = {2013}, volume = {59}, pages = {833-845}, number = {5}, month = {May}, project = {diabetes, abt_zell, bioinformatics}, } |
| [8] | Vlaic, Sebastian and Hoffmann, Bianca and Kupfer, Peter and Weber,
Michael and Dräger, Andreas. {GRN2SBML: Automated encoding and annotation of inferred gene regulatory
networks complying with SBML}. , pages 2216--2217,jun, 2013. [pdf , url]Bibtex@ARTICLE{Vlaic26062013,author = {Vlaic, Sebastian and Hoffmann, Bianca and Kupfer, Peter and Weber, Michael and Dräger, Andreas}, title = {{GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML}}, journal = {Bioinformatics}, year = {2013}, volume = {29}, pages = {2216--2217}, month = {jun}, abstract = {Summary: GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and \emph{minimum information required in the annotation of models} registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage. Availability: GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from \url{http://www.hki-jena.de/index.php/0/2/490}. Supplementary information: General information on GRN2SBML, examples and tutorials are available at the tool's web page. Contact: \url{mailto:Sebastian.Vlaic@hki-jena.de} or \url{mailto:andraeger@eng.ucsd.edu}}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Vlaic26062013.html}, doi = {10.1093/bioinformatics/btt370}, pdf = {http://bioinformatics.oxfordjournals.org/content/29/17/2216.full.pdf}, project = {extern, bioinformatics, VLN, biochemical_reaction_systems}, url = {http://bioinformatics.oxfordjournals.org/content/29/17/2216.abstract}, } |
| [9] | Wrzodek, Clemens. Inference and integration of biochemical networks with multilayered
omics data. , Tübingen, Germany,jun, 2013. [url]Bibtex@PHDTHESIS{Wrzodek2013PhD,author = {Wrzodek, Clemens}, title = {Inference and integration of biochemical networks with multilayered omics data}, school = {University of Tuebingen}, year = {2013}, address = {Tübingen, Germany}, month = {jun}, abstract = {The technological advances of the last decade have led to numerous studies focusing on genome-wide transcriptomic changes. This is also reflected in a great number of publications that compare the gene expression levels of healthy and other samples. However, the detailed molecular mechanisms that cause these changes remain largely unknown. The different types of cancer are popular examples, for which altered transcriptomic expression profiles are known for a long time, and researchers nowadays focus on identifying causes and treatments against these alterations. Epigenetic effects, such as DNA methylation, have been identified as associated to most types of cancer. The integration of both omics layers---transcriptomic and epigenomic---allowed for explaining varied gene expression levels for some genes. Despite these promising results, automated methods for an integration of multiple omics datasets are still in an early stage of development. More omics layers need to be analyzed integratively and more approaches need to be developed that help researchers finding causes for varied expression levels. For this purpose, systems biology methods are required that interpret biological coherences as an overall system and help to identify complex interactions. However, the biochemical networks that underly those systems must be reconstructed before most systems biology methods can be applied or interactions can be identified. Thus, approaches for the reconstruction of biochemical networks and novel methods, which help identifying complex coherences between different omics layers are firstly described in this thesis. It thereby focuses on the inference of biochemical networks and their subsequent integration with multilayered omics data. A widely-used source for biochemical networks are biological pathways. Unfortunately, they are mostly stored as inaccurate and incomplete qualitative descriptions in proprietary formats and thus, cannot be used directly with systems biology methods. This thesis presents a method that automatically fixes those issues and translates pathways to well-defined computational models. As a result of this work, 142,050 revised models of metabolic and non-metabolic pathways have been generated and put into the popular BioModels repository for the systems biology modeling language (SBML). The ModuleMaster method is a second approach for the generation of biochemical networks. More specifically, transcriptional regulatory networks are inferred from combinations of experimental gene expression data and a priori knowledge. To this end, gene expression data is clustered and regulatory transcription factors are determined. The inferred interactions between both span the final network. The established biochemical networks are used for a joint visualization of multilayered omics data. For this purpose, it is discussed how different omics layers can be integrated into a single dataset. On this basis, a methodology has been developed that integratively depicts messenger RNA, microRNA, DNA methylation and protein data in a single network. Besides this integration technique, several further integrated omics data analysis methods are presented in this thesis. The concept of gene-set enrichment analysis is extended to multilayered omics data and methods that ease a joint inspection of these high-dimensional datasets are presented. Finally, a machine learning approach is described that links epigenetic profiles to genetic features. This is used to discover the mechanisms and features that induce changes in the epigenome.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Wrzodek2013PhD}, isbn = {978-3-8439-1116-0}, keywords = {Integrator, InCroMAP, integration of omics data, machine learning, omics data, JSBML, MARCAR, metabolic modeling, gene-regulatory network, ModuleMaster, path2models, SBML, BioPAX, KEGG, KEGGtranslator, CpG island}, project = {abt_zell, bioinformatics, NGFNplus, VLN, kegg_translator, comp_epigenetics, InCroMAP, HepatoSys, MARCAR, NGFN-II, Spher4Sys}, publisher = {Verlag Dr.~Hut, Sternstraße 18, München}, url = {http://www.dr.hut-verlag.de/978-3-8439-1116-0.html}, } |
| [10] | Gispert, Suzana and Parganlija, Dajana and Klinkenberg, Michael and
Dröse, Stefan and Wittig, Ilka and Mittelbronn, Michel and Grzmil,
Pawel and Koob, Sebastian and Hamann, Andrea and Walter, Michael
and Büchel, Finja and Adler, Thure and de Angelis, Martin Hrab\'{e}
and Busch, Dirk H. and Zell, Andreas and Reichert, Andreas S. and
Brandt, Ulrich and Osiewacz, Heinz D. and Jendrach, Marina and Auburger,
Georg. Loss of mitochondrial peptidase Clpp leads to infertility, hearing
loss plus growth retardation via accumulation of {CLPX, mtDNA,} and
inflammatory factors. July, 2013. [url]Bibtex@ARTICLE{Gispert12072013,author = {Gispert, Suzana and Parganlija, Dajana and Klinkenberg, Michael and Dröse, Stefan and Wittig, Ilka and Mittelbronn, Michel and Grzmil, Pawel and Koob, Sebastian and Hamann, Andrea and Walter, Michael and Büchel, Finja and Adler, Thure and de Angelis, Martin Hrab\'{e} and Busch, Dirk H. and Zell, Andreas and Reichert, Andreas S. and Brandt, Ulrich and Osiewacz, Heinz D. and Jendrach, Marina and Auburger, Georg}, title = {Loss of mitochondrial peptidase Clpp leads to infertility, hearing loss plus growth retardation via accumulation of {CLPX, mtDNA,} and inflammatory factors}, journal = {Human Molecular Genetics}, year = {2013}, month = {July}, abstract = {The peptidase {CLPP} is conserved from bacteria to humans. In the mitochondrial matrix, it multimerizes and forms a macromolecular proteasome-like cylinder together with the chaperone CLPX. In spite of a known relevance for the mitochondrial unfolded protein response, its substrates and tissue-specific roles are unclear in mammals. Recessive CLPP mutations were recently observed in the human Perrault variant of ovarian failure and sensorineural hearing loss. Here, a first characterization of Clpp null mice demonstrated complete female and male infertility and auditory deficits. Disrupted spermatogenesis already at the spermatid stage and ovarian follicular differentiation failure were evident. Reduced pre-/post-natal survival and marked ubiquitous growth retardation contrasted with only light impairment of movement and respiratory activities. Interestingly, the mice showed resistance to ulcerative dermatitis. Systematic expression studies detected up-regulation of other mitochondrial chaperones, accumulation of CLPX and mtDNA as well as inflammatory factors throughout tissues. T-lymphocytes in the spleen were activated. Thus, murine Clpp deletion represents a faithful Perrault model. The disease mechanism probably involves deficient clearance of mitochondrial components and inflammatory tissue destruction.}, doi = {10.1093/hmg/ddt338}, eprint = {http://hmg.oxfordjournals.org/content/early/2013/07/12/hmg.ddt338.full.pdf+html}, project = {abt_zell, bioinformatics}, url = {http://hmg.oxfordjournals.org/content/early/2013/07/12/hmg.ddt338.abstract}, } |
| [11] | Keller, Roland and Dörr, Alexander and Tabira, Akito and Funahashi,
Akira and Ziller, Michael J. and Adams, Richard and Rodriguez, Nicolas
and {Le Nov\`{e}re}, Nicolas and Hiroi, Noriko and Planatscher, Hannes
and Zell, Andreas and Dräger, Andreas. The systems biology simulation core algorithm. , pages 55,jul, 2013. [pdf , url]Bibtex@ARTICLE{Keller2013,author = {Keller, Roland and Dörr, Alexander and Tabira, Akito and Funahashi, Akira and Ziller, Michael J. and Adams, Richard and Rodriguez, Nicolas and {Le Nov\`{e}re}, Nicolas and Hiroi, Noriko and Planatscher, Hannes and Zell, Andreas and Dräger, Andreas}, title = {The systems biology simulation core algorithm}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {55}, month = {jul}, abstract = {Background: With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases. Results: This article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database. Conclusions: The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from \url{http://simulation-core.sourceforge.net}. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list \url{mailto:simulation-core-development@lists.sourceforge.net}.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Keller2013.html}, doi = {10.1186/1752-0509-7-55}, keywords = {Systems biology; Biological networks; Mathematical modeling; Simulation; Algorithms; Ordinary differential equation systems; Numerical integration; Software engineering}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-55.pdf}, project = {abt_zell, VLN, SBMLsimulator, bioinformatics, biochemical_reaction_systems, PHH}, url = {http://www.biomedcentral.com/1752-0509/7/55}, } |
| [12] | Dräger, Andreas and Planatscher, Hannes. {Encyclopedia of Systems Biology}. , pages 1249--1251,, Springer New York Heidelberg Dorodrecht London,aug, 2013. [url]Bibtex@INBOOK{Draeger2013a,chapter = {Metabolic Networks}, pages = {1249--1251}, title = {{Encyclopedia of Systems Biology}}, publisher = {Springer-Verlag}, year = {2013}, editor = {Dubitzky, Werner and Wolkenhauer, Olaf and Yokota, Hiroki and Cho, Kwang-Hyun}, author = {Dräger, Andreas and Planatscher, Hannes}, address = {Springer New York Heidelberg Dorodrecht London}, month = {aug}, abstract = {Metabolic networks are interconnected pathways of biochemical reactions within living cells through which building blocks or compounds necessary for cellular functioning are assembled (anabolism) or energy and matter are produced by breaking down biomolecules (catabolism). These pathways are often organized as cycles or chains of coupled reactions, in which the product of one reaction serves as the substrate of the succeeding reaction. Although all reactions are reversible in principle, thermodynamic gradients within metabolic reactions often promote one direction, yielding a flux through the metabolic pathways. In many cases distinct pathways or reactions exist for contrary flows of matter. All processes within a metabolic network are temporally and spatially organized. Often cells contain several compartments which separate parts of its reaction network into subnetworks. The reacting compounds are called metabolites or species. Additionally, modifiers can activate, inhibit or catalyze a reaction. Enzymes play a central role in metabolic networks, because they act as catalysts in the vast majority of the reactions. The interplay of its components determines the dynamic behavior of the overall network.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Draeger2013a.html}, doi = {10.1007/978-1-4419-9863-7_1277}, isbn = {978-1441998644}, keywords = {Biochemical network; Metabolic pathways; Pathway map; Pathways; Reaction network; Reaction pathways}, language = {eng}, project = {extern, bioinformatics, VLN}, url = {http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_100849}, } |
| [13] | Dräger, Andreas and Planatscher, Hannes. {Encyclopedia of Systems Biology}. , pages 1627--1631,, Springer New York Heidelberg Dorodrecht London,aug, 2013. [url]Bibtex@INBOOK{Draeger2013b,chapter = {{Parameter Estimation, Metabolic Network Modeling}}, pages = {1627--1631}, title = {{Encyclopedia of Systems Biology}}, publisher = {Springer-Verlag}, year = {2013}, editor = {Dubitzky, Werner and Wolkenhauer, Olaf and Yokota, Hiroki and Cho, Kwang-Hyun}, author = {Dräger, Andreas and Planatscher, Hannes}, address = {Springer New York Heidelberg Dorodrecht London}, month = {aug}, abstract = {Metabolic networks can mathematically be modeled as a differential equation system. These models consist of a stoichiometric matrix, a modulation matrix, and a vector of reaction rates. The mathematical structure of the differential equation system is usually assumed to be known, its parameters, however, in general are not. Here the term ``parameter'' denotes all quantities within the model whose values are uncertain or difficult to obtain experimentally. In the most common case, these comprise kinetic constants, concentrations of external metabolites, enzyme concentrations or activities, and compartment sizes. The parameter estimation problem aims at estimating meaningful values for these targets by trying to coincide given experimental data with the predictions of the model. Bayesian methods, maximum likelihood estimates, and (biologically inspired) optimization procedures are frequently used estimation approaches. Experimental data usually contain a time-course or steady state of concentration values of the reacting species (compounds) within the network. Before estimating their values, a parameter identifiability analysis should be conducted. Estimated values should be analyzed regarding their thermodynamic plausibility.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Draeger2013b.html}, doi = {10.1007/978-1-4419-9863-7_1174}, isbn = {978-1441998644}, keywords = {Model calibration, Model fitting, Parameter fitting, Parameter identification, Regression}, language = {eng}, project = {extern, bioinformatics, VLN}, url = {http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_1174}, } |
| [14] | Büchel, Finja and Mittag, Florian and Wrzodek, Clemens and Zell,
Andreas and Gasser, Thomas and Sharma, Manu. {Integrative pathway-based approach for genome-wide association studies:
identification of new pathways for rheumatoid arthritis and type
1 diabetes}. , pages e78577,sep, 2013. [url]Bibtex@ARTICLE{Buechel2013a,author = {Büchel, Finja and Mittag, Florian and Wrzodek, Clemens and Zell, Andreas and Gasser, Thomas and Sharma, Manu}, title = {{Integrative pathway-based approach for genome-wide association studies: identification of new pathways for rheumatoid arthritis and type 1 diabetes}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2013}, volume = {8}, pages = {e78577}, number = {10}, month = {sep}, doi = {10.1371/journal.pone.0078577}, project = {abt_zell, bioinformatics, NGFNplus}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078577}, } |
| [15] | My Vo Duc and Andreas Zell. Real Time Face Tracking and Pose Estimation Using an Adaptive Correlation
Filter for Human-Robot Interaction. In European Conference on Mobile Robots (ECMR 2013) (Oral), Barcelona, Catalonia, Spain,September, 2013. [url]Bibtex@INPROCEEDINGS{voduc2013,author = {My Vo Duc and Andreas Zell}, title = {Real Time Face Tracking and Pose Estimation Using an Adaptive Correlation Filter for Human-Robot Interaction}, booktitle = {European Conference on Mobile Robots (ECMR 2013) (Oral)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = {September}, abstract = {In this paper, we present a real time algorithm for mobile robots to track human faces and estimate face poses accurately, even when humans move freely and far away from the camera or go through different illumination conditions in uncontrolled environments. We combine the algorithm of an adaptive correlation filter with a Viola-Jones object detection to track the face as well as the facial features including the two external eye corners and the nose. These facial features provide geometric cues to estimate the face pose robustly. In our method, the depth information from a Microsoft Kinect camera is used to estimate the face size and improve the performance of tracking facial features. Our method is shown to be robust and fast in uncontrolled environments.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?voduc2013}, owner = {my}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/voduc2013.pdf}, } |
| [16] | Johannes Eichner and Nadine Kossler and Clemens Wrzodek and Arno
Kalkuhl and Dorthe Bach Toft and Nina Ostenfeldt and Virgile Richard
and Andreas Zell. {A Toxicogenomic Approach for the Prediction of Murine Hepatocarcinogenesis
Using Ensemble Feature Selection}. , pages e73938,sep, 2013. [url]Bibtex@ARTICLE{Eichner2013a,author = {Johannes Eichner and Nadine Kossler and Clemens Wrzodek and Arno Kalkuhl and Dorthe Bach Toft and Nina Ostenfeldt and Virgile Richard and Andreas Zell}, title = {{A Toxicogenomic Approach for the Prediction of Murine Hepatocarcinogenesis Using Ensemble Feature Selection}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2013}, volume = {8}, pages = {e73938}, number = {9}, month = {sep}, doi = {10.1371/journal.pone.0073938}, project = {abt_zell, bioinformatics, MARCAR}, timestamp = {2013.07.25}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073938}, } |
| [17] | Jimenez Lugo, Jacobo and Andreas Masselli and Andreas Zell. Following a quadrotor with another quadrotor using computer vision. In European Conference on Mobile Robots (ECMR 2013), Barcelona, Catalonia, Spain,September, 2013. [url]Bibtex@INPROCEEDINGS{jimenez2013ecmr,author = {Jimenez Lugo, Jacobo and Andreas Masselli and Andreas Zell}, title = {Following a quadrotor with another quadrotor using computer vision}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = {September}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?jimenez2013ecmr}, owner = {jimenez}, project = {abt_zell, robotics, uav, passivemarkers}, timestamp = {2013.06.24}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/JimeMassECMR13.pdf}, } |
| [18] | Stefan Laible and Yasir Niaz Khan and Andreas Zell. Terrain Classification With Conditional Random Fields on Fused 3D
LIDAR and Camera Data. In European Conference on Mobile Robots (ECMR 2013), pages 172--177,, Barcelona, Catalonia, Spain,September, 2013. [pdf]Bibtex@INPROCEEDINGS{laible2013ecmr,author = {Stefan Laible and Yasir Niaz Khan and Andreas Zell}, title = {Terrain Classification With Conditional Random Fields on Fused 3D LIDAR and Camera Data}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, pages = {172--177}, address = {Barcelona, Catalonia, Spain}, month = {September}, publisher = {IEEE}, abstract = {For a mobile robot to navigate safely and efficiently in an outdoor environment, it has to recognize its surrounding terrain. Our robot is equipped with a low-resolution 3D LIDAR and a color camera. The data from both sensors are fused to classify the terrain in front of the robot. Therefore, the ground plane is divided into a grid and each cell is classified as either asphalt, cobblestones, grass or gravel. We use height and intensity features for the LIDAR data and Local ternary patterns for the image data. By additionally taking into account the context-sensitive nature of the terrain, the results can be improved significantly. We present a method based on Conditional Random Fields and compare it with a Markov Random Field based approach. We show that the Conditional Random Field model is better suited for our task. We achieve an average true positive rate of 94.2% for classifying the grid cells into the four terrain classes.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?laible2013ecmr}, doi = {10.1109/ECMR.2013.6698838}, owner = {laible}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/laible2013ecmr.pdf}, project = {abt_zell, robotics, terrain_classification}, timestamp = {2013.06.24}, } |
| [19] | Andreas Masselli and Richard Hanten and Andreas Zell. {Robust Real-Time Detection of Multiple Balls on a Mobile Robot}. In European Conference on Mobile Robots (ECMR 2013), Barcelona, Catalonia, Spain,September, 2013. [url]Bibtex@INPROCEEDINGS{Masselli2013ecmr,author = {Andreas Masselli and Richard Hanten and Andreas Zell}, title = {{Robust Real-Time Detection of Multiple Balls on a Mobile Robot}}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = {September}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Masselli2013ecmr}, owner = {masselli}, project = {abt_zell, robotics}, timestamp = {2013.07.19}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/masselli2013ecmr.pdf}, } |
| [20] | Scherer, Sebastian A. and Alina Kloss and Andreas Zell. {Loop Closure Detection using Depth Images}. In European Conference on Mobile Robots (ECMR 2013), Barcelona, Catalonia, Spain,September, 2013. [pdf]Bibtex@INPROCEEDINGS{scherer2013ecmr,author = {Scherer, Sebastian A. and Alina Kloss and Andreas Zell}, title = {{Loop Closure Detection using Depth Images}}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = {September}, abstract = {We investigate the question whether loop closure detection using depth images is feasible using currently available depth features. For this reason, we collected a benchmark dataset consisting of a total number of 15 logfiles with several loops in various environments, implemented a modular and easily extensible loop closure detector and used this to evaluate the adequacy of state-of-the art depth features on our benchmark dataset. To allow for a fair comparison, we determined the best values for the sometimes large number of user-chosen parameters using a large-scale grid search. Since our benchmark dataset contains both depth and RGB images, we can compare the performance relying on depth features with the performance achieved when using intensity image features.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?scherer2013ecmr}, owner = {scherer}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/scherer2013ecmr.pdf}, project = {abt_zell, robotics, rgbd_slam, uav}, timestamp = {2013.06.24}, } |
| [21] | Johannes Eichner. {Inference of Alternative Splicing from Tiling Array Data}. In Tiling Arrays, pages 143-164,oct, 2013. [url]Bibtex@INBOOK{Eichner2013b,pages = {143-164}, title = {{Inference of Alternative Splicing from Tiling Array Data}}, publisher = {Humana Press}, year = {2013}, editor = {Lee, Tin-Lap and Luk, Shui and Chun, Alfred}, author = {Johannes Eichner}, volume = {1067}, series = {Methods in Molecular Biology}, month = {oct}, booktitle = {Tiling Arrays}, project = {abt_zell, bioinformatics}, url = {http://dx.doi.org/10.1007/978-1-62703-607-8_10}, } |
| [22] | Büchel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek,
Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian
and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and
{van Iersel}, Martijn and Keating, Sarah M. and Rall, Matthias and Wybrow,
Michael and Hermjakob, Henning and Hucka, Michael and {B Kell}, Douglas
and Müller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya,
Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe,
Camille and Dräger, Andreas and {Le Nov\`{e}re}, Nicolas. {Path2Models: large-scale generation of computational models from
biochemical pathway maps}. , pages 116,nov, 2013. [pdf , url]Bibtex@ARTICLE{Buechel2013b,author = {Büchel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek, Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and {van Iersel}, Martijn and Keating, Sarah M. and Rall, Matthias and Wybrow, Michael and Hermjakob, Henning and Hucka, Michael and {B Kell}, Douglas and Müller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya, Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe, Camille and Dräger, Andreas and {Le Nov\`{e}re}, Nicolas}, title = {{Path2Models: large-scale generation of computational models from biochemical pathway maps}}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {116}, number = {1}, month = {nov}, abstract = {Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data. Results: To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2~600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at \url{http://www.ebi.ac.uk/biomodels-main/path2models}. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps. Conclusions: To date, the project has resulted in more than 140~000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Buechel2013b.html}, doi = {10.1186/1752-0509-7-116}, keywords = {Modular rate law, Constraint based models, Logical models, SBGN, SBML}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-116.pdf}, project = {abt_zell, bioinformatics, NGFNplus, VLN, AMBiCon}, url = {http://www.biomedcentral.com/1752-0509/7/116}, } |
| [23] | Büchel, Finja and Saliger, Sandra and Dräger, Andreas and Hoffmann,
Stephanie and Wrzodek, Clemens and Zell, Andreas and Kahle, Philipp
J.. {Parkinson's disease: dopaminergic nerve cell model is consistent
with experimental finding of increased extracellular transport of
$\alpha$-synuclein}. nov, 2013. [pdf , url]Bibtex@ARTICLE{Buechel2013c,author = {Büchel, Finja and Saliger, Sandra and Dräger, Andreas and Hoffmann, Stephanie and Wrzodek, Clemens and Zell, Andreas and Kahle, Philipp J.}, title = {{Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of $\alpha$-synuclein}}, journal = {BMC Neuroscience}, year = {2013}, volume = {14}, number = {136}, month = {nov}, abstract = {Background: Parkinson's disease is an age-related disease, whose pathogenesis is not completely known. Animal models exist for investigating the disease but not all results can be easily transferred to humans. Therefore, mathematical or probabilistic models for the human disease are to be constructed \emph{in-silico} in order to predict specific processes within a cell, such as the dopamine metabolism and transport processes in a neuron. Results: We present an SBML model of a whole dopaminergic nerve cell consisting of 139 reactions and 111 metabolites which includes, among others, the dopamine metabolism and transport, oxidative stress, aggregation of $\alpha$-synuclein ($\alpha$SYN), lysosomal and proteasomal degradation, and mitophagy. The predictive power of the model was investigated using flux balance analysis for the identification of steady model states. To this end, we performed six experiments: (i) investigation of the normal cell behavior, (ii) increase of O\textsubscript{2}, (iii) increase of ATP, (iv) influence of neurotoxins, (v) increase of $\alpha$SYN the cell and (vi) increase of dopamine synthesis. The SBML model is available in BioModels database with identifier MODEL1302200000. Conclusion: It is possible to simulate the normal behavior of an \emph{in-vivo} nerve cell with the developed model. We show that the model is sensitive for neurotoxins and oxidative stress. Further, an increased level of $\alhpa$SYN induces apoptosis and we observed an increased flux of $\alpha$SYN to the extracellular space.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Buechel2013c.html}, doi = {10.1186/1471-2202-14-136}, issn = {1471-2202}, keywords = {Parkinson's disease, Dopaminergic nerve cell model, SBML model, Flux balance analysis}, pdf = {http://www.biomedcentral.com/content/pdf/1471-2202-14-136.pdf}, project = {abt_zell, bioinformatics, NGFNplus, AMBiCon}, url = {http://www.biomedcentral.com/1471-2202/14/136}, } |
| [24] | Ran Liu and Artur Koch and Andreas Zell. {Mapping UHF RFID Tags with a Mobile Robot using 3D Sensor Model}. In IEEE/RSJ International Conference on Intelligent Robots and Systems
(IROS 2013), Big Sight, Tokyo, Japan,November, 2013. [url]Bibtex@INPROCEEDINGS{RanArtur_IROS_2013,author = {Ran Liu and Artur Koch and Andreas Zell}, title = {{Mapping UHF RFID Tags with a Mobile Robot using 3D Sensor Model}}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2013)}, year = {2013}, address = {Big Sight, Tokyo, Japan}, month = {November}, abstract = {Recently, researchers showed growing interest in utilizing UHF Radio-Frequency Identification (RFID) technology for localizing tagged items with mobile robots in industrial scenarios. In this paper we present a novel three-dimensional (3D) probability sensor model of RFID antennas in the context of mapping passive RFID tags with mobile robots. The proposed 3D sensor model characterizes both detection rates and received signal strength (RSS). Compared to 2D-sensor model based approaches, the 3D model gains a higher mapping accuracy for 2D position estimation. Specially, with this sensor model, we are able to localize the tags in 3D by integrating the measurements from a pair of RFID antennas mounted at different heights of the robot. Furthermore, by integrating negative information (i.e., non-detections), the 3D mapping accuracy can be improved. Additionally, we utilize KLD-sampling to reduce the number of particles for our specific application, so that our algorithm can be performed online. Indoor experiments with a Scitos G5 robot demonstrate the effectiveness of our approach.}, days = {3-8}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?RanArtur_IROS_2013}, project = {abt_zell, robotics, rfid, iros2013}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/ran_iros_2013.pdf}, } |
| [25] | Scherer, Sebastian A. and Andreas Zell. {Efficient Onboard RGBD-SLAM for Fully Autonomous MAVs}. In IEEE/RSJ International Conference on Intelligent Robots and Systems
(IROS 2013), Tokyo Big Sight, Japan,November, 2013. [pdf]Bibtex@INPROCEEDINGS{scherer2013iros,author = {Scherer, Sebastian A. and Andreas Zell}, title = {{Efficient Onboard RGBD-SLAM for Fully Autonomous MAVs}}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2013)}, year = {2013}, address = {Tokyo Big Sight, Japan}, month = {November}, abstract = {We present a computationally inexpensive RGBD-SLAM solution taylored to the application on autonomous MAVs, which enables our MAV to fly in an unknown environment and create a map of its surroundings completely autonomously, with all computations running on its onboard computer. We achieve this by implementing efficient methods for both tracking its current location with respect to a heavily processed previously seen RGBD image (keyframe) and efficient relative registration of a set of keyframes using bundle adjustment with depth constraints as a front-end for pose graph optimization. We prove the accuracy and efficiency of our system based on a public benchmark dataset and demonstrate that the proposed method enables our quadrotor to fly autonomously.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?scherer2013iros}, owner = {scherer}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/scherer2013iros.pdf}, project = {abt_zell, robotics, rgbd_slam, uav}, timestamp = {2013.07.02}, } |
| [26] | Chaouiya, Claudine and B\'{e}renguier, Duncan and Keating, Sarah M. and
Naldi, Aur\'{e}lien and van Iersel, Martijn P. and Rodriguez, Nicolas
and Dräger, Andreas and Büchel, Finja and Cokelaer, Thomas and
Kowal, Bryan and Wicks, Benjamin and Gon\c{c}alves, Emanuel and Dorier,
Julien and Page, Michel and Monteiro, Pedro T. and von Kamp, Axel
and Xenarios, Ioannis and de Jong, Hidde and Hucka, Michael and Klamt,
Steffen and Thierffry, Dennis and {Le Nov\`{e}re}, Nicolas and Saez-Rodriguez,
Julio and Helikar, Tom\'{a}\v{s}. {SBML Qualitative Models: a model representation format and infrastructure
to foster interactions between qualitative modelling formalisms and
tools}. , pages 135,dec, 2013. [pdf , url]Bibtex@ARTICLE{Chaouiya2013,author = {Chaouiya, Claudine and B\'{e}renguier, Duncan and Keating, Sarah M. and Naldi, Aur\'{e}lien and van Iersel, Martijn P. and Rodriguez, Nicolas and Dräger, Andreas and Büchel, Finja and Cokelaer, Thomas and Kowal, Bryan and Wicks, Benjamin and Gon\c{c}alves, Emanuel and Dorier, Julien and Page, Michel and Monteiro, Pedro T. and von Kamp, Axel and Xenarios, Ioannis and de Jong, Hidde and Hucka, Michael and Klamt, Steffen and Thierffry, Dennis and {Le Nov\`{e}re}, Nicolas and Saez-Rodriguez, Julio and Helikar, Tom\'{a}\v{s}}, title = {{SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools}}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {135}, number = {1}, month = {dec}, abstract = {Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. Results: We present the System Biology Markup Language (SBML) Qualitative Models Package (``qual''), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the cooperative development of the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyze qualitative models. Conclusion: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Chaouiya2013.html}, doi = {10.1186/1752-0509-7-135}, eprint = {1309.1910}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-135.pdf}, project = {extern, bioinformatics, VLN, AMBiCon}, publisher = {Springer (Biomed Central Ltd.)}, url = {http://www.biomedcentral.com/1752-0509/7/135}, } |
| [27] | Eichner, Johannes and Topf, Florian and Dräger, Andreas and Wrzodek,
Clemens and Wanke, Dierk and Zell, Andreas. {TFpredict and SABINE: Sequence-Based Prediction of Structural and
Functional Characteristics of Transcription Factors}. , pages e82238,dec, 2013. [pdf , url]Bibtex@ARTICLE{Eichner2013c,author = {Eichner, Johannes and Topf, Florian and Dräger, Andreas and Wrzodek, Clemens and Wanke, Dierk and Zell, Andreas}, title = {{TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2013}, volume = {8}, pages = {e82238}, number = {12}, month = {dec}, abstract = {One of the key mechanisms of transcriptional control are the specific connections between transcription factors (TF) and \emph{cis}-regulatory elements in gene promoters. The elucidation of these specific protein-DNA interactions is crucial to gain insights into the complex regulatory mechanisms and networks underlying the adaptation of organisms to dynamically changing environmental conditions. As experimental techniques for determining TF binding sites are expensive and mostly performed for selected TFs only, accurate computational approaches are needed to analyze transcriptional regulation in eukaryotes on a genome-wide level. We implemented a four-step classification workflow which for a given protein sequence (1) discriminates TFs from other proteins, (2) determines the structural superclass of TFs, (3) identifies the DNA-binding domains of TFs and (4) predicts their \emph{cis}-acting DNA motif. While existing tools were extended and adapted for performing the latter two prediction steps, the first two steps are based on a novel numeric sequence representation which allows for combining existing knowledge from a BLAST scan with robust machine learning-based classification. By evaluation on a set of experimentally confirmed TFs and non-TFs, we demonstrate that our new protein sequence representation facilitates more reliable identification and structural classification of TFs than previously proposed sequence-derived features. The algorithms underlying our proposed methodology are implemented in the two complementary tools TFpredict and SABINE. The online and stand-alone versions of TFpredict and SABINE are freely available to academics at \url{http://www.cogsys.cs.uni-tuebingen.de/software/TFpredict/} and \url{http://www.cogsys.cs.uni-tuebingen.de/software/SABINE/}.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Eichner2013c.html}, doi = {10.1371/journal.pone.0082238}, pdf = {http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0082238&representation=PDF}, project = {abt_zell, bioinformatics, VLN, AMBiCon, Spher4Sys}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0082238}, } |
| [28] | Jiang, Lixing and Koch, Artur and Scherer, Sebastian A. and Zell,
Andreas. Multi-class Fruit Classification using {RGB-D} Data for Indoor Robots. In IEEE International Conference on Robotics and Biomimetics (ROBIO), Shenzhen, China,December, 2013. [url]Bibtex@INPROCEEDINGS{jiang_ROBIO2013,author = {Jiang, Lixing and Koch, Artur and Scherer, Sebastian A. and Zell, Andreas}, title = {Multi-class Fruit Classification using {RGB-D} Data for Indoor Robots}, booktitle = {IEEE International Conference on Robotics and Biomimetics (ROBIO)}, year = {2013}, address = {Shenzhen, China}, month = {December}, abstract = {In this paper we present an effective and robust system to classify fruits under varying pose and lighting conditions tailored for an object recognition system on a mobile platform. Therefore, we present results on the effectiveness of our underlying segmentation method using RGB as well as depth cues for the specific technical setup of our robot. A combination of RGB low-level visual feature descriptors and 3D geometric properties is used to retrieve complementary object information for the classification task. The unified approach is validated using two multi-class RGB-D fruit categorization datasets. Experimental results compare different feature sets and classification methods and highlight the effectiveness of the proposed features using a Random Forest classifier.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?jiang_ROBIO2013}, owner = {jiang}, project = {abt_zell, robotics}, timestamp = {2013.12.12}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/jiang_robio2013.pdf}, } |
| [29] | Markus Beck and Peter Bayer and Michael de Paly and Jozsef Hecht-Mendez
and Andreas Zell. Geometric Arrangement and Operation Mode Adjustment in Low Enthalpy
Geothermal Borehole Fields for Heating. , pages 434-443,2013. Bibtex@ARTICLE{Beck13_1,author = {Markus Beck and Peter Bayer and Michael de Paly and Jozsef Hecht-Mendez and Andreas Zell}, title = {Geometric Arrangement and Operation Mode Adjustment in Low Enthalpy Geothermal Borehole Fields for Heating}, journal = {Energy}, year = {2013}, volume = {49}, pages = {434-443}, abstract = {The efficient operation of ground source heat pump (GSHP) systems with multiple borehole heat exchangers (BHEs) over a lifetime of decades implies an optimized performance of the BHEs and a mitigation of the environmental impact of the system. This paper introduces a new combined optimization approach, which optimizes the BHE positions as well as the individually regulated energy extraction for each single BHE within a given BHE field in conduction dominated media for a given seasonal changing load profile. The optimization of only the BHE positions without optimizing the individual BHE loads nearly produces the same improvement of the underground temperature change of approximately 12% as an optimization of the BHE loads without optimized positioning. The combination of both optimization approaches result in only slightly better results compared to a result achieved by only one of the optimization approaches. Thus for homogeneous fields without groundwater flow, an optimal load assignment can be replaced by an optimal BHE placement, which leads to a considerably reduced complexity of the BHE field.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Beck12_2}, keywords = {shallow geothermal energy; multiple BHEs; BHE positioning; optimization; evolutionary algorithms; linear programming}, owner = {beck}, project = {optimization, hydrogeo, abt_zell, eva2}, } |
| [30] | Jozsef Hecht-Mendez and Michael de Paly and Markus Beck and Peter
Bayer. Optimization of energy extraction for vertical closed-loop geothermal
systems considering groundwater flow. , pages 1-10,2013. Bibtex@ARTICLE{hecht_mendez13,author = {Jozsef Hecht-Mendez and Michael de Paly and Markus Beck and Peter Bayer}, title = {Optimization of energy extraction for vertical closed-loop geothermal systems considering groundwater flow}, journal = {Energy Conversion and Management}, year = {2013}, volume = {66}, pages = {1-10}, abstract = {A combined simulation-optimization procedure is presented to regulate the operation of borehole heat exchangers (BHEs) in a multiple BHE field when groundwater flow exists. Such fields are of increasing interest for large-scale geothermal heating energy supply of buildings, but so far strategic adjustment of energy extraction rates (loads) of the individual BHEs has not been considered in practice. Groundwater flow means an additional advective energy supply, which is advantageous but also complicates proper BHE adjustment. In the presented procedure, the field is simulated by temporally and spatially superimposed moving line source equations. The optimization goal is formulated in an objective function to minimize the thermal impact in the ground, to avoid extreme temperature anomalies, and by this, ultimately improve heat pump performance. For a given seasonal energy demand and total operation time, linear programming efficiently delivers optimized BHE operation patterns. For an examined square lattice of 25 BHEs, the optimized radial load patterns characteristic for conduction dominated conditions change to patterns that are oriented at the groundwater flow when advection dominates. Through this, optimization always levels the temperature distribution in the ground. Also, in comparison to routine practice, mean BHE outlet temperatures can be increased. For the small study case, numerical simulation reveals that already more than 1 K can be achieved, given a seasonal energy demand oriented at common conditions in central Europe. However, for a fixed energy demand, advective heat supply towards the BHEs increases with groundwater flow velocity and thus mitigates the benefits from optimization.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?hecht_mendez13}, project = {optimization, hydrogeo, extern, abt_zell, eva2}, } |
| [31] | Lehmann, R. and Franken, H. and Dammeier, S. and Rosenbaum, L. and
Kantartzis, K. and Peter, A. and Zell, A. and Adam, P. and Li, J.
and Xu, G. and Königsrainer, A. and Machann, J. and Schick, F.
and Hrabe de Angelis, M. and Schwab, M. and Staiger, H. and Schleicher,
E. and Gastaldelli, A. and Fritsche, A. and Häring, H.-U. and Stefan,
N.. Circulating lyso-phosphatidylcholines are markers of ametabolically
benign nonalcoholic fatty liver. , pages 2331--2338,2013. Bibtex@ARTICLE{Lehmann2013,author = {Lehmann, R. and Franken, H. and Dammeier, S. and Rosenbaum, L. and Kantartzis, K. and Peter, A. and Zell, A. and Adam, P. and Li, J. and Xu, G. and Königsrainer, A. and Machann, J. and Schick, F. and Hrabe de Angelis, M. and Schwab, M. and Staiger, H. and Schleicher, E. and Gastaldelli, A. and Fritsche, A. and Häring, H.-U. and Stefan, N.}, title = {Circulating lyso-phosphatidylcholines are markers of ametabolically benign nonalcoholic fatty liver}, journal = {Diabetes Care}, year = {2013}, volume = {36}, pages = {2331--2338}, number = {8}, owner = {rosenbaum}, project = {diabetes, abt_zell, bioinformatics}, timestamp = {2013.02.15}, } |
| [32] | Liu, Yuyi and Longo, Stefano and Kerrigan, Eric C.. Nonlinear Predictive Control of Autonomous Soaring {UAVs} Using {3DOF}
Models. In Proc. of European Control Conference ({ECC 13}), pages 1365-1370,2013. Bibtex@INPROCEEDINGS{yuyiliu13,author = {Liu, Yuyi and Longo, Stefano and Kerrigan, Eric C.}, title = {Nonlinear Predictive Control of Autonomous Soaring {UAVs} Using {3DOF} Models}, booktitle = {Proc. of European Control Conference ({ECC 13})}, year = {2013}, pages = {1365-1370}, project = {extern, robotics, uav}, } |
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