| [1] | Dräger, Andreas. Computational Modeling of Biochemical Networks. , Tübingen, Germany,jan, 2011. [url]Bibtex@PHDTHESIS{Draeger2011a,author = {Dräger, Andreas}, title = {Computational Modeling of Biochemical Networks}, school = {University of Tuebingen}, year = {2011}, address = {Tübingen, Germany}, month = {jan}, abstract = {In recent years biology has shifted its focus from the mainly descriptive exploration of individual organisms, cells, or molecules towards a holistic investigation of the complex interactions within living systems. This progress is driven by the development of large-scale measurement techniques, e.g., the timely resolved simultaneous quantification of many cellular components. The exploration of these data sets requires the application of methods from other areas of natural science and the development of novel analysis methods. At this intersection systems biology aims to understand mutual interactions and influences between biological components. Control mechanisms and regulation of processes, which often show a nonlinear behavior, are to be described. Predicting the dynamics of complex interaction systems constitutes its main challenge. Computational modeling methods play a central role to attain this goal. Without loss of generality, we here focus on metabolic systems in preparation for an extension to gene-regulatory systems. Physico-chemical, in particular thermodynamic, constraints restrict the investigated systems and define the domain of plausible and valid models. Setting up such a mathematical description is not only complicated and highly error-prone, it also requires knowledge from many different fields and is therefore not easily applicable for non-experts. This thesis aims at the development of a method that performs the model construction steps to the widest extent automatically, reducing the number of necessary human interactions to a minimum but that still leads to thermodynamically feasible and correct model systems. To this end, it introduces a five-step modeling pipeline that ultimately leads to a mathematical description of a biochemical reaction system. We discuss how to automate each individual step and how to put these steps together: First, we create a topology of interconversion processes and mutual influences between reactive species encoded in the Systems Biology Markup Language (SBML) including semantic information. Second, a procedure is established that generates kinetic equations in a context-sensitive manner. The resulting model can then be combined with already existing models. Third, we estimate the values of all newly introduced parameters in each created rate law. This procedure requires that a time series of quantitative measurements of the reactive species within this system be available, because we calibrate the parameters with the aim that the model will fit these experimental data. The applicability and functioning of these approaches is demonstrated on a model of the valine and leucine biosynthesis in \emph{C.~glutamicum}. In a large-scale benchmark the results of seven modeling techniques are systematically compared when estimating their parameters with a multitude of nature-inspired heuristic optimization processes. This step is crucial for the development of an automatic modeling procedure because it highlights the strength and weaknesses of all these approaches. Fourth, an experimental validation of the resulting model is advisable. Fifth, a model report is generated automatically to document the model with all of its components. In an extension, this computer-aided modeling pipeline is further developed to a fully automatic procedure, the AMUSE algorithm (Automated Modeling Using Specialized Enzyme kinetics). The network topology in form of an SBML file and biological reference data, i.e., at least one time-series of participating metabolite concentrations and some relevant target fluxes, build its only required input. Based on latest estimation methods for standard reaction Gibbs energies, AMUSE determines a thermodynamically feasible, minimal equilibrium configuration of the system, identifies the key reactions and selects kinetic equations describing all reaction velocities. Furthermore, it estimates all remaining parameters with respect to given experimental data. For a better understanding, we begin with an introduction to fundamental modeling and generalized approaches for common rate equations. Subsequently, parameter estimation techniques are introduced and evaluated on the valine and leucine biosynthesis in \emph{C.~glutamicum}. Thereafter, standardization attempts in systems biology will be discussed that are required for the computer-aided modeling pipeline. This pipeline necessitates extending the existing standards. In particular, the development and implementation of JSBML, the Java library for SBML, has been conducted to simplify computation and manipulation of complex models. A discussion of possible further improvements and an extension of the suggested modeling pipeline to gene-regulatory networks completes this thesis.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Draeger2011a}, isbn = {978-3-86853-850-2}, keywords = {automated modeling, AMUSE algorithm, C. glutamicum, enzyme kinetics, evolutionary algorithms, heuristic optimization, JSBML, leucine biosynthesis, metabolic modeling, gene-regulatory network, parameter estimation, rate law, SBML, SBML2LaTeX, SBMLsqueezer, valine biosynthesis}, project = {abt_zell, bioinformatics, NGFNplus, HepatoSys, VLN, NGFN-II, Spher4Sys, metabolic_network_identification, Bioinformatik-Grid, SBML2LaTeX, SBMLsqueezer}, publisher = {Verlag Dr.~Hut, Sternstraße 18, München}, url = {http://www.dr.hut-verlag.de/978-3-86853-850-2.html}, } |
| [2] | Johannes Eichner and Georg Zeller and Sascha Laubinger and Gunnar
Raetsch. {Support vector machines-based identification of alternative splicing
in Arabidopsis thaliana from whole-genome tiling arrays.}. , pages 55,feb, 2011. [url]Bibtex@ARTICLE{Eichner2011,author = {Johannes Eichner and Georg Zeller and Sascha Laubinger and Gunnar Raetsch}, title = {{Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays.}}, journal = {BMC Bioinformatics}, year = {2011}, volume = {12}, pages = {55}, number = {1}, month = {feb}, __markedentry = {[eichner]}, abstract = {ABSTRACT: BACKGROUND: Alternative splicing (AS) is a process which generates several distinct mRNA isoforms from the same gene by splicing different portions out of the precursor transcript. Due to the (patho-)physiological importance of AS, a complete inventory of AS is of great interest. While this is in reach for human and mammalian model organisms, our knowledge of AS in plants has remained more incomplete. Experimental approaches for monitoring AS are either based on transcript sequencing or rely on hybridization to DNA microarrays. Among the microarray platforms facilitating the discovery of AS events, tiling arrays are well-suited for identifying intron retention, the most prevalent type of AS in plants. However, analyzing tiling array data is challenging, because of high noise levels and limited probe coverage. RESULTS: In this work, we present a novel method to detect intron retentions (IR) and exon skips (ES) from tiling arrays. While statistical tests have typically been proposed for this purpose, our method instead utilizes support vector machines (SVMs) which are appreciated for their accuracy and robustness to noise. Existing EST and cDNA sequences served for supervised training and evaluation. Analyzing a large collection of publicly available microarray and sequence data for the model plant A. thaliana, we demonstrated that our method is more accurate than existing approaches. The method was applied in a genome-wide screen which resulted in the discovery of 1,355 IR events. A comparison of these IR events to the TAIR annotation and a large set of short-read RNA-seq data showed that 830 of the predicted IR events are novel and that 525 events (39\%) overlap with either the TAIR annotation or the IR events inferred from the RNA-seq data. CONCLUSIONS: The method developed in this work expands the scarce repertoire of analysis tools for the identification of alternative mRNA splicing from whole-genome tiling arrays. Our predictions are highly enriched with known AS events and complement the A. thaliana genome annotation with respect to AS. Since all predicted AS events can be precisely attributed to experimental conditions, our work provides a basis for follow-up studies focused on the elucidation of the regulatory mechanisms underlying tissue-specific and stress-dependent AS in plants.}, doi = {10.1186/1471-2105-12-55}, language = {eng}, pst = {aheadofprint}, owner = {eichner}, pii = {1471-2105-12-55}, pmid = {21324185}, project = {abt_zell, bioinformatics}, timestamp = {2011.02.24}, url = {http://dx.doi.org/10.1186/1471-2105-12-55}, } |
| [3] | Hoeppe, Sibylle and Schreiber, Thomas D. and Planatscher, Hannes
and Zell, Andreas and Templin, Markus F. and Stoll, Dieter and Joos,
Thomas O. and Poetz, Oliver. Targeting peptide termini, a novel immunoaffinity approach to reduce
complexity in mass spectrometric protein identification. , pages M110.002857,feb, 2011. [pdf , url]Bibtex@ARTICLE{Hoeppe2011,author = {Hoeppe, Sibylle and Schreiber, Thomas D. and Planatscher, Hannes and Zell, Andreas and Templin, Markus F. and Stoll, Dieter and Joos, Thomas O. and Poetz, Oliver}, title = {Targeting peptide termini, a novel immunoaffinity approach to reduce complexity in mass spectrometric protein identification}, journal = {Mol Cell Proteomics}, year = {2011}, volume = {10}, pages = {M110.002857}, number = {2}, month = {feb}, abstract = {Mass spectrometry and peptide-centric approaches are powerful techniques for the identification of differentially expressed proteins. Despite enormous improvements in MS technologies, sample preparation and efficient fractionation of target analytes are still major bottlenecks in MS-based protein analysis. The complexity of tryptically digested whole proteomes needs to be considerably reduced before low abundance proteins can be effectively analyzed using MS/MS. Sample preparation strategies that use peptide-specific antibodies are able to reduce the complexity of tryptic digests and lead to a substantial increase in throughput and sensitivity; however, the number of peptide-specific capture reagents is low, and consequently immunoaffinity-based approaches are only capable of detecting small sets of protein-derived peptides. In this proof-of-principle study, special anti-peptide antibodies were used to enrich peptides from a complex mixture. These antibodies recognize short amino acid sequences that are found directly at the termini of the peptides. The recognized epitopes consist of three or four amino acids only and include the terminally charged group of the peptide. Because of its limited length, antibodies recognizing the epitope will enrich not only one peptide but a whole class of peptides that share this terminal epitope. In this study, $\beta$-catenin-derived peptides were used to demonstrate that it is possible (i) to effectively generate antibodies that recognize short C-terminal peptide epitopes and (ii) to enrich and identify peptide classes from a complex mixture using these antibodies in an immunoaffinity MS approach. The expected $\beta$-catenin peptides and a set of 38 epitope-containing peptides were identified from trypsin-digested cell lysates. This might be a first step in the development of proteomics applications that are based on the use of peptide class-specific antibodies.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Hoeppe2011}, doi = {10.1074/mcp.M110.002857}, institution = {NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany}, keywords = {Antibodies, chemistry; Cell Line; Epitopes, chemistry; Gene Library; HEK293 Cells; Humans; Mass Spectrometry, methods; Peptides, chemistry; Protein Binding; Protein Structure, Tertiary; Proteins, chemistry; Proteome; Proteomics, methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Trypsin, chemistry}, language = {eng}, pst = {ppublish}, pdf = {http://www.mcponline.org/content/10/2/M110.002857.pdf}, pii = {M110.002857}, pmid = {20962300}, project = {abt_zell, bioinformatics}, url = {http://dx.doi.org/10.1074/mcp.M110.002857}, } |
| [4] | Henneges, Carsten. Feature Selection and Data Mining for Proteomics and Metabolomics. , Tübingen, Germany,mar, 2011. [url]Bibtex@PHDTHESIS{Henneges2011,author = {Henneges, Carsten}, title = {Feature Selection and Data Mining for Proteomics and Metabolomics}, school = {University of Tuebingen}, year = {2011}, address = {Tübingen, Germany}, month = {mar}, abstract = {The past decades saw a rapid improvement in the technique of biological experiments. While the beginning was coined with long and complex experiments carried out by laboratory staff, automatic high-throughput methods emerged. Especially proteomics profited from advances in mass spectrometry to identify fragments from digested proteins. Mass spectrometry entered the novel field of metabolomics. Metabolomics investigates small molecules from metabolism for their role as disease markers. The goal here is to develop monitoring and screening techniques based on easily obtained body fluids. However, further methods, as IR spectroscopy, are waiting for their advent into metabolomics research. Connected to each area of research is the topic of data mining. Essentially, data mining can be subdivided into the tasks of feature selection and feature construction. Feature selection aims to select relevant features out of a larger pool. A selected combination may aid visualisation and thus understanding of a dataset as well as improve the prediction performance of learning algorithms. To this end, three general approaches exist: wrapper, filter and embedded methods. While wrappers employ an arbitrary learning algorithm for assessing the value of a feature combination, filters rely on statistical criteria. Most recently, embedded methods attracted research interest, wherein feature selection is integrated into a learning algorithm. Feature construction algorithms on the other hand reconstruct the subsignals of an additive superposition. The key approach thereby is matrix factorisation by constraints. Frequent constraints used for this purpose are statistical independence as well as non-negativity and sparsity, leading to problem specific algorithms. This book supports life science researchers with adapted data mining methods from both feature selection and feature construction for proteomics and metabolomics. We describe biomarker identification for breast cancer prediction using a SVM-based wrapper and develop faster wrapper algorithms using surrogate-based optimisation. Applying filters for ranking-specific feature selection, we also design a cost-efficient prediction system for proteotypic peptides. As an application, embedded methods are used to infer energetical interaction patterns in protein 3D structures. Finally, we develop a novel factorisation method for feature construction to decompose IR spectra within a metabolomics context.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Henneges2011}, isbn = {978-3-8439-0122-2}, project = {abt_zell, bioinformatics}, publisher = {Verlag Dr.~Hut,Sternstraße 18, München}, url = {http://www.dr.hut-verlag.de/978-3-8439-0122-2.html}, } |
| [5] | Huimin Lu and Shaowu Yang and Hui Zhang and Zhiqiang Zheng. A robust omnidirectional vision sensor for soccer robots. , pages 373-389,mar, 2011. [url]Bibtex@ARTICLE{Yangs2011,author = {Huimin Lu and Shaowu Yang and Hui Zhang and Zhiqiang Zheng}, title = {A robust omnidirectional vision sensor for soccer robots}, journal = {Mechatronics}, year = {2011}, volume = {21}, pages = {373-389}, number = {2}, month = {mar}, issn = {0303-2647}, project = {extern}, publisher = {Elsevier}, timestamp = {2012.05.14}, url = {http://dx.doi.org/10.1016/j.mechatronics.2010.06.007}, } |
| [6] | Schauwecker, Konstantin and van den Hurk, Simon and Yuen, Wallace
and Wünsche, Burkhard. {Sketched Interaction Metaphors for Character Animation}. In International Conference on Computer Graphics Theory and Applications
(GRAPP), pages 247--252,, Vilamoura, Algarve, Portugal,March, 2011. [pdf]Bibtex@INPROCEEDINGS{Schauwecker2011a,author = {Schauwecker, Konstantin and van den Hurk, Simon and Yuen, Wallace and Wünsche, Burkhard}, title = {{Sketched Interaction Metaphors for Character Animation}}, booktitle = {International Conference on Computer Graphics Theory and Applications (GRAPP)}, year = {2011}, pages = {247--252}, address = {Vilamoura, Algarve, Portugal}, month = {March}, publisher = {Springer}, abstract = {The use of 3D virtual worlds is increasing rapidly and new tools are necessary to enable untrained users to create3D content and interact with it. In this paper we present and evaluate sketch-based interaction metaphorsfor specifying complex animations of 3D skeletally animated models. Sketched interactions include bone rotation,motion path translation, sequencing and synchronisation of animations, and an undo-functionality. Thesketches are drawn directly onto a model in a 3D view and are translated into time-dependent joint transformations.We present the design concepts, the implementation of a prototype, and a user study assessing theusability of our animation metaphors. The user study demonstrates that the animation metaphors are intuitive,with the exception of animation ordering. A large variety of animations were successfully created by users.More work is necessary to synchronise animations better. Overall our research demonstrates that sketchedbasedanimations can be useful for applications requiring rapid prototyping containing a limited number ofjoint animations. Examples are the programming of household robots and the creation of simple animatedscenes in education and social network applications.}, owner = {schauwecker}, pdf = {http://www.cs.auckland.ac.nz/~burkhard/Publications/GRAPP2011_SchauweckerEtAl.pdf}, project = {extern}, } |
| [7] | Khan, Yasir Niaz and Komma, Philippe and Bohlmann, Karsten and Zell,
Andreas. Grid-based Visual Terrain Classification for Outdoor Robots using
Local Features. In IEEE Symposium on Computational Intelligence in Vehicles and Transportation
Systems (CIVTS 2011), pages 16 - 22,, Paris, France,apr, 2011. [url]Bibtex@INPROCEEDINGS{khan11a,author = {Khan, Yasir Niaz and Komma, Philippe and Bohlmann, Karsten and Zell, Andreas}, title = {Grid-based Visual Terrain Classification for Outdoor Robots using Local Features}, booktitle = {IEEE Symposium on Computational Intelligence in Vehicles and Transportation Systems (CIVTS 2011)}, year = {2011}, pages = {16 - 22}, address = {Paris, France}, month = {apr}, abstract = {In this paper we present a comparison of multiple approaches to visual terrain classification for outdoor mobile robots based on local features. We compare the more traditional texture classification approaches, such as Local Binary Patterns, Local Ternary Patterns and a newer extension Local Adaptive Ternary Patterns, and also modify and test three non-traditional approaches called SURF, DAISY and CCH. We drove our robot under different weather and ground conditions and captured images of five different terrain types for our experiments. We did not filter out blurred images which are due to robot motion and other artifacts caused by rain, etc.We used Random Forests for classification, and cross-validation for the verification of our results. The results show that most of the approaches work well for terrain classification in a fast moving mobile robot, despite image blur and other artifacts induced due to extremely variant weather conditions.}, comment = {http://ieeexplore.ieee.org/search/freesrchabstract.jsp?tp=&arnumber=5949534&queryText%3DGrid-based+Visual+Terrain+Classification+for+Outdoor+Robots+using+Local+Features%26openedRefinements%3D*%26filter%3DAND%28NOT%284283010803%29%29%26searchField%3DSearch+All&abstractAccess=no&userType=inst}, doi = {10.1109/CIVTS.2011.5949534}, keywords = {CCH;DAISY;SURF;artifacts;blurred images filtering;local features;outdoor mobile robots;random forests;robot motion;texture classification;visual terrain classification;feature extraction;image restoration;image texture;mobile robots;pattern classification}, owner = {khan}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/khan2011civts.pdf}, } |
| [8] | Klette, Reinhard and Ahn, Je and Haeusler, Ralf and Herman, Simon
and Huang, Jinsheng and Khan, Waqar and Manoharan, Sathiamoorthy
and Morales, Sandino and Morris, John and Nicolescu, Radu and Ren,
FeiXiang and Schauwecker, Konstantin and Yang, Xi. {Advance in Vision-Based Driver Assistance}. In Electric Technology and Civil Engineering (ICETCE), pages 987--990,, Lushan, China,April, 2011. [url]Bibtex@INPROCEEDINGS{Schauwecker2011c,author = {Klette, Reinhard and Ahn, Je and Haeusler, Ralf and Herman, Simon and Huang, Jinsheng and Khan, Waqar and Manoharan, Sathiamoorthy and Morales, Sandino and Morris, John and Nicolescu, Radu and Ren, FeiXiang and Schauwecker, Konstantin and Yang, Xi}, title = {{Advance in Vision-Based Driver Assistance}}, booktitle = {Electric Technology and Civil Engineering (ICETCE)}, year = {2011}, pages = {987--990}, address = {Lushan, China}, month = {April}, publisher = {IEEE}, abstract = {Vision-based driver assistance is an active safety measure currently under development in various car companies and research institutes worldwide. The paper informs about related activities at The University of Auckland, focussing on stereo vision, performance evaluation, provided test data, and currently developed components.}, owner = {schauwecker}, project = {extern}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5775884}, } |
| [9] | Hofmeister, Marius and Kronfeld, Marcel and Zell, Andreas. Cooperative Visual Mapping in a Heterogeneous Team of Mobile Robots. In IEEE International Conference on Robotics and Automation (ICRA), pages 1491--1496,, Shanghai, China,may, 2011. [url]Bibtex@INPROCEEDINGS{hofmeistICRA,author = {Hofmeister, Marius and Kronfeld, Marcel and Zell, Andreas}, title = {Cooperative Visual Mapping in a Heterogeneous Team of Mobile Robots}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2011}, pages = {1491--1496}, address = {Shanghai, China}, month = {may}, project = {abt_zell, robotics, ctbots, hetTeam}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/hofmeister2011icra.pdf}, } |
| [10] | Dräger, Andreas and Rodriguez, Nicolas and Dumousseau, Marine and
Dörr, Alexander and Wrzodek, Clemens and {Le Nov\`{e}re}, Nicolas
and Zell, Andreas and Hucka, Michael. {JSBML: a flexible Java library for working with SBML}. , pages 2167--2168,jun, 2011. [pdf , url]Bibtex@ARTICLE{Draeger2011b,author = {Dräger, Andreas and Rodriguez, Nicolas and Dumousseau, Marine and Dörr, Alexander and Wrzodek, Clemens and {Le Nov\`{e}re}, Nicolas and Zell, Andreas and Hucka, Michael}, title = {{JSBML: a flexible Java library for working with SBML}}, journal = {Bioinformatics}, year = {2011}, volume = {27}, pages = {2167--2168}, number = {15}, month = {jun}, abstract = {Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations, and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java\texttrademark{} programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level~3 Version~1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end-user applications, as well as ease migration from a libSBML-based backend. Availability: Source code, binaries, and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website \url{http://sbml.org/Software/JSBML}.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Draeger2011b.html}, doi = {10.1093/bioinformatics/btr361}, pdf = {http://bioinformatics.oxfordjournals.org/content/27/15/2167.full.pdf}, project = {abt_zell, bioinformatics, VLN, Spher4Sys}, url = {http://bioinformatics.oxfordjournals.org/content/27/15/2167}, } |
| [11] | Schauwecker, Konstantin and Morales, Sandino and Hermann, Simon and
Klette, Reinhard. {A Comparative Study of Stereo-Matching Algorithms for Road-Modeling
in the Presence of Windscreen Wipers}. In IEEE Intelligent Vehicles Symposium (IV), pages 7--12,, Baden-Baden, Germany,June, 2011. [url]Bibtex@INPROCEEDINGS{Schauwecker2011b,author = {Schauwecker, Konstantin and Morales, Sandino and Hermann, Simon and Klette, Reinhard}, title = {{A Comparative Study of Stereo-Matching Algorithms for Road-Modeling in the Presence of Windscreen Wipers}}, booktitle = {IEEE Intelligent Vehicles Symposium (IV)}, year = {2011}, pages = {7--12}, address = {Baden-Baden, Germany}, month = {June}, publisher = {IEEE}, abstract = {In this study we examine three road-modeling methods, which weevaluate on seven stereo matching algorithms. The road-modeling methods weconsider are a B-spline modeling technique based on region-growing and twoversions of the popular v-disparity approach. The used stereo algorithms arevariations or different parameterizations of belief propagation, graph cutand semi-global matching. We examine the performance of the possiblecombinations of modeling methods and stereo algorithms by comparing thedeviation towards a reference road profile. Two evaluation sequences areused, of which one features switched on windscreen wipers that are visiblein the the recorded imagery. Our findings are that the examined B-splinemodeling method provides the best results in most cases. In terms of themodeled distance, belief propagation is the most suitable stereo matchingmethod, which also performs best with the wiper sequence. Semi globalmatching achieves smaller model deviations, but with drastically reducedmodeled distances.}, owner = {schauwecker}, project = {extern}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5940392}, } |
| [12] | Schröder, Adrian and Wrzodek, Clemens and Wollnik, Johannes and
Dräger, Andreas and Wanke, Dierk and Berendzen, Kenneth W. and
Zell, Andreas. Inferring transcriptional regulators for sets of co-expressed genes
by multi-objective evolutionary optimization. In IEEE Congress on Evolutionary Computation (CEC 2011), New Orleans, USA,jun, 2011. [pdf , url]Bibtex@INPROCEEDINGS{Schroeder2011a,author = {Schröder, Adrian and Wrzodek, Clemens and Wollnik, Johannes and Dräger, Andreas and Wanke, Dierk and Berendzen, Kenneth W. and Zell, Andreas}, title = {Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2011)}, year = {2011}, address = {New Orleans, USA}, month = {jun}, publisher = {IEEE}, abstract = {Higher organisms are able to respond to continuously changing external conditions by transducing cellular signals into specific regulatory programs, which control gene expression states of thousands of different genes. One of the central problems in understanding gene regulation is to decipher how combinations of transcription factors control sets of coexpressed genes under specific experimental conditions. Existing methods in this field mainly focus on sequence aspects and pattern recognition, e.g., by detecting \emph{cis}-regulatory modules (CRMs) based on gene expression profiling data. We propose a novel approach by combining experimental data with a priori knowledge of respective experimental conditions. These various sources of evidence are likewise considered using multi-objective evolutionary optimization. In this work, we present three objective functions that are especially designed for stimulus-response experiments and can be used to integrate a priori knowledge into the detection of gene regulatory modules. This method was tested and evaluated on whole-genome microarray measurements of drug-response in human hepatocytes.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Schroeder2011a.html}, doi = {10.1109/CEC.2011.5949899}, isbn = {978-1-4244-7833-0}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/Schroeder2011cec.pdf}, project = {abt_zell, bioinformatics, VLN}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5949899}, } |
| [13] | Wrzodek, Clemens and Dräger, Andreas and Zell, Andreas. {KEGGtranslator: visualizing and converting the KEGG PATHWAY database
to various formats}. , pages 2314--2315,jun, 2011. [pdf , url]Bibtex@ARTICLE{Wrzodek2011,author = {Wrzodek, Clemens and Dräger, Andreas and Zell, Andreas}, title = {{KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats}}, journal = {Bioinformatics}, year = {2011}, volume = {27}, pages = {2314--2315}, number = {16}, month = {jun}, abstract = {Summary: The KEGG PATHWAY database provides a widely used service for metabolic and non-metabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. Availability: KEGGtranslator is freely available as a Java\texttrademark{} Web Start application and for download at \url{http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/}. KGML files can be downloaded within the application.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Wrzodek2011.html}, doi = {10.1093/bioinformatics/btr377}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/wrzodek/publications/2011-08-04-KEGGtranslator-with-color.pdf}, project = {abt_zell, bioinformatics, kegg_translator, NGFNplus, Spher4Sys}, url = {http://bioinformatics.oxfordjournals.org/content/27/16/2314}, } |
| [14] | Hofmeister, Marius. Self-Localization, Mapping and Coverage with Resource-Limited Mobile
Robots. , Tübingen, Germany,July, 2011. Bibtex@PHDTHESIS{hofmeistDiss,author = {Hofmeister, Marius}, title = {Self-Localization, Mapping and Coverage with Resource-Limited Mobile Robots}, school = {University of Tuebingen}, year = {2011}, address = {Tübingen, Germany}, month = {July}, isbn = {978-3-8325-2887-4}, owner = {hofmeister}, project = {abt_zell, robotics, ctbots}, publisher = {Logos Verlag Berlin GmbH, Comeniushof, Gubener Str. 47, 10243 Berlin}, timestamp = {2011.07.07}, } |
| [15] | Schröder, Adrian and Wollnik, Johannes and Wrzodek, Clemens and
Dräger, Andreas and Bonin, Michael and Burk, Oliver and Thomas,
Maria and Thasler, Wolfgang E. and Zanger, Ulrich M. and Zell, Andreas. Inferring statin-induced gene regulatory relationships in primary
human hepatocytes. , pages 2473--2477,jul, 2011. [pdf , url]Bibtex@ARTICLE{Schroeder2011b,author = {Schröder, Adrian and Wollnik, Johannes and Wrzodek, Clemens and Dräger, Andreas and Bonin, Michael and Burk, Oliver and Thomas, Maria and Thasler, Wolfgang E. and Zanger, Ulrich M. and Zell, Andreas}, title = {Inferring statin-induced gene regulatory relationships in primary human hepatocytes}, journal = {Bioinformatics}, year = {2011}, volume = {27}, pages = {2473--2477}, number = {18}, month = {jul}, abstract = {Motivation: Statins are the most widely used cholesterol-lowering drugs. The primary target of statins is HMG-CoA reductase, a key enzyme in cholesterol synthesis. However, statins elicit pleitropic responses including beneficial as well as adverse effects in the liver or other organs. Today, the regulatory mechanisms that cause these pleiotropic effects are not sufficiently understood. Results: In this work, genome-wide RNA expression changes in primary human hepatocytes of six individuals were measured at up to six time points upon atorvastatin treatment. A computational analysis workflow was applied to reconstruct regulatory mechanisms based on these drug-response data and available knowledge about TF binding specificities, and protein-drug interactions. Several previously unknown transcription factors were predicted to be involved in atorvastatin-responsive gene expression. The novel relationships of nuclear receptors NR2C2 and PPARA on CYP3A4 were successfully validated in wet-lab experiments. Availability: Microarray data are available at the Gene Expression Omnibus (GEO) database at \url{http://www.ncbi.nlm.nih.gov/geo/}, under accession number GSE29868.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Schroeder2011b.html}, doi = {10.1093/bioinformatics/btr416}, pdf = {http://bioinformatics.oxfordjournals.org/content/27/18/2473.full.pdf}, project = {abt_zell, bioinformatics, VLN}, url = {http://bioinformatics.oxfordjournals.org/content/27/18/2473.abstract}, } |
| [16] | Büchel, Finja and Wrzodek, Clemens and Mittag, Florian and Dräger,
Andreas and Schröder, Adrian and Zell, Andreas. {ProDGe: investigating protein-protein interactions at the domain
level}. aug, 2011. [pdf , url]Bibtex@TECHREPORT{Buechel2011a,author = {Büchel, Finja and Wrzodek, Clemens and Mittag, Florian and Dräger, Andreas and Schröder, Adrian and Zell, Andreas}, title = {{ProDGe: investigating protein-protein interactions at the domain level}}, institution = {Nature Precedings}, year = {2011}, month = {aug}, abstract = {An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the Java\texttrademark{} program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domain-domain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confidence classes, depending on the reliability of the underlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly helpful when investigating poorly annotated species. We further evaluated and compared experimentally identified protein interactions from IntAct with domain interactions from DOMINE for six species and noticed that 31.13% of all IntAct protein interactions in all six species can be mapped to the actual interacting domains. ProDGe and a comprehensive documentation are freely available at \url{http://www.cogsys.cs.uni-tuebingen.de/software/ProDGe}.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Buechel2011a.html}, doi = {10.1038/npre.2011.6188.1}, keywords = {protein, domain, interaction, domain-domain interaction, interaction visualization, protein-protein interaction}, pdf = {http://precedings.nature.com/documents/6188/version/1/files/npre20116188-1.pdf}, project = {abt_zell, bioinformatics, NGFNplus}, url = {http://precedings.nature.com/documents/6188/version/1}, } |
| [17] | Vorst, Philipp. Mapping, Localization, and Trajectory Estimation with Mobile Robots
Using Long-Range Passive {RFID}. aug, 2011. [pdf , url]Bibtex@PHDTHESIS{vorst2011thesis,author = {Vorst, Philipp}, title = {Mapping, Localization, and Trajectory Estimation with Mobile Robots Using Long-Range Passive {RFID}}, school = {University of Tuebingen, Tübingen, Germany}, year = {2011}, month = {aug}, abstract = {This thesis addresses the use of radio-frequency identification (RFID) for three fundamental tasks in mobile robotics: mapping, self-localization, and trajectory estimation. These topics have widely been studied in recent years, because they are regarded as key ingredients to autonomous robots. In particular, we investigate the application of long-range passive RFID in the work at hand. This RFID standard is expected to play a major role in the automation of identification processes in industry and commerce. We present solutions to the automated inventory of RFID-tagged goods, which we interpret as mapping the locations of RFID transponders. In order to quickly provide the required model of the detection behavior of the RFID reader on board the mobile robot, we devise a semi-autonomous learning method for probabilistic sensor models. Moreover, we compare different techniques to self-localize in an RFID-tagged environment. In the last part, we show how the trajectory of the robot can be estimated in previously unknown surroundings by tailoring approaches from the field of simultaneous localization and mapping (SLAM).}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?vorst2011thesis}, isbn = {978-3-8439-0060-7}, keywords = {radio-frequency identification (RFID), passive UHF RFID, mobile robot, self-localization, mapping, trajectory estimation, simultaneous localization and mapping, SLAM, sensor model, location fingerprinting}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/vorst/publications/Dissertation_Philipp_Vorst.pdf}, project = {abt_zell, robotics, ambisense, rfid}, publisher = {Verlag Dr.~Hut}, series = {Robotik und Automation}, url = {http://www.dr.hut-verlag.de/978-3-8439-0060-7.html}, } |
| [18] | Courtot, M\'{e}lanie and Juty, Nick and Knüpfer, Christian and
Waltemath, Dagmar and Zhukova, Anna and Dräger, Andreas and Dumontier,
Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna
and Hoops, Stefan and Keating, Sarah M. and Kell, Douglas B. and Kerrien,
Samuel and Lawson, James and Lister, Allyson and Lu, James and Machne,
Rainer and Mendes, Pedro and Pocock, Matthew and Rodriguez, Nicolas
and Vill\'{e}ger, Alice and Wilkinson, Darren J. and Wimalaratne,
Sarala and Laibe, Camille and Hucka, Michael and {Le Nov\`{e}re}, Nicolas. Controlled vocabularies and semantics in systems biology. , pages 543,sep, 2011. [pdf , url]Bibtex@ARTICLE{Courtot2011a,author = {Courtot, M\'{e}lanie and Juty, Nick and Knüpfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Dräger, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and Hoops, Stefan and Keating, Sarah M. and Kell, Douglas B. and Kerrien, Samuel and Lawson, James and Lister, Allyson and Lu, James and Machne, Rainer and Mendes, Pedro and Pocock, Matthew and Rodriguez, Nicolas and Vill\'{e}ger, Alice and Wilkinson, Darren J. and Wimalaratne, Sarala and Laibe, Camille and Hucka, Michael and {Le Nov\`{e}re}, Nicolas}, title = {Controlled vocabularies and semantics in systems biology}, journal = {Molecular Systems Biology}, year = {2011}, volume = {7}, pages = {543}, number = {1}, month = {sep}, abstract = {The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the Systems Biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of Systems Biology models, their characterization, and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Courtot2011a.html}, doi = {10.1038/msb.2011.77}, keywords = {dynamics; kinetics; model; ontology; simulation}, pdf = {http://msb.embopress.org/content/7/1/543.full.pdf}, project = {extern, bioinformatics, VLN}, url = {http://dx.doi.org/10.1038/msb.2011.77}, } |
| [19] | Ran Liu and Philipp Vorst and Artur Koch and Andreas Zell. Path Following for Indoor Robots with {RFID} Received Signal Strength. In The 19th International Conference on Software, Telecommunications
and Computer Networks (SoftCOM 2011), Split, Hvar, and Dubrovnik, Croatia,September, 2011. [url]Bibtex@INPROCEEDINGS{liu1109:Path,author = {Ran Liu and Philipp Vorst and Artur Koch and Andreas Zell}, title = {Path Following for Indoor Robots with {RFID} Received Signal Strength}, booktitle = {The 19th International Conference on Software, Telecommunications and Computer Networks (SoftCOM 2011)}, year = {2011}, address = {Split, Hvar, and Dubrovnik, Croatia}, month = {September}, note = {(Best paper award at the Symposium on RFID Technologies and Internet of Things)}, abstract = {We present a novel method for robot path following in an RFID-equipped corridor using received signal strength (RSS). RSS measurements are recorded as reference fingerprints during the exploration phase. These data are used to guide the robot through the corridor in the navigation phase. Distance and orientation that the robot derivates from the expected trajectory are approximated through the RSS differences and the index differences of two antennas. The RSS differences are calculated by comparing the current fingerprint to reference fingerprints, and the index differences are estimated by a particle filter. Finally, a P-controller is used for the navigation of the robot. This enables the robot to follow a certain path, which may be defined in the first phase of our approach. The actual experiments with a SCITOS G5 service robot confirm the validity and robustness of our approach.}, days = {15}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?liu1109:Path}, keywords = {RFID-based Navigation, Particle Filter, Fingerprints, Received Signal Strength (RSS)}, project = {abt_zell, robotics, ambisense, rfid}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/ranliu2011-path-following-rss.pdf}, } |
| [20] | Timo Schairer and Benjamin Huhle and Philipp Vorst and Andreas Schilling
and Wolfgang Strasser. Visual Mapping with Uncertainty for Correspondence-free Localization
using {Gaussian} Process Regression. In Proceedings of the 2011 IEEE/RSJ International Conference on Intelligent
Robots and Systems (IROS 2011), San Francisco, California, USA,September, 2011. Bibtex@INPROCEEDINGS{schairer2011iros,author = {Timo Schairer and Benjamin Huhle and Philipp Vorst and Andreas Schilling and Wolfgang Strasser}, title = {Visual Mapping with Uncertainty for Correspondence-free Localization using {Gaussian} Process Regression}, booktitle = {Proceedings of the 2011 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2011)}, year = {2011}, address = {San Francisco, California, USA}, month = {September}, note = {Accepted for publication}, project = {extern, robotics, ambisense}, } |
| [21] | Scherer, Sebastian A. and Daniel Dube and Philippe Komma and Andreas
Masselli and Andreas Zell. {Robust Real-Time Number Sign Detection on a Mobile Outdoor Robot}. In Proceedings of the 6th European Conference on Mobile Robots (ECMR
2011), Örebro, Sweden,sep, 2011. [url]Bibtex@INPROCEEDINGS{scherer2011ecmr,author = {Scherer, Sebastian A. and Daniel Dube and Philippe Komma and Andreas Masselli and Andreas Zell}, title = {{Robust Real-Time Number Sign Detection on a Mobile Outdoor Robot}}, booktitle = {Proceedings of the 6th European Conference on Mobile Robots (ECMR 2011)}, year = {2011}, address = {Örebro, Sweden}, month = {sep}, abstract = {We present the evolution of a highly-efficient system for visually detecting number signs in real-time on a mobile robot with limited computational power. The system was designed for use on a robot participating in the 2010 ``SICK robot day'' robotics challenge, in which the robot needed to autonomously find 10 number signs and drive to all of them in a given order as fast as possible. Our most efficient method has proven to be robust and successful, since our robot won the competition using the final vision systems described in this paper.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Scherer2011ecmr}, owner = {scherer}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/scherer11.pdf}, } |
| [22] | Schröder, Adrian and Klein, Kathrin and Winter, Stefan and Schwab,
Matthias and Bonin, Michael and Zell, Andreas and Zanger, Ulrich
M.. {Genomics of ADME gene expression: mapping expression quantitative
trait loci relevant for absorption, distribution, metabolism and
excretion of drugs in human liver}. , pages 1473--1150,sep, 2011. [pdf , url]Bibtex@ARTICLE{Schroeder2011c,author = {Schröder, Adrian and Klein, Kathrin and Winter, Stefan and Schwab, Matthias and Bonin, Michael and Zell, Andreas and Zanger, Ulrich M.}, title = {{Genomics of ADME gene expression: mapping expression quantitative trait loci relevant for absorption, distribution, metabolism and excretion of drugs in human liver}}, journal = {The Pharmacogenomics Journal}, year = {2011}, pages = {1473--1150}, month = {sep}, abstract = {Expression quantitative trait loci (eQTL) analysis is a powerful approach toward identifying genetic loci associated with quantitative changes in gene expression. We applied genome-wide association analysis to a data set of 4300\,000 single-nucleotide polymorphisms and 48 000 mRNA expression phenotypes obtained by Illumina microarray profiling of 149 human surgical liver samples obtained from Caucasian donors with detailed medical documentation. Of 1\,226 significant associations, only 200 were validated when comparing with a previously published similar study. Potential explanations for low replication rate include differences in microarray platforms, statistical modeling, covariates considered and origin and collection procedures of tissues. Focused analysis revealed a subset of 95 associations related to absorption, distribution, metabolism and excretion of drugs. Of these, 21 were true replications and 74 were newly discovered associations in enzymes, transporters, transcriptional regulators and other genes. This study extends our knowledge about the genetics of interindividual variability of gene expression with particular emphasis on pharmacogenomics.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Schroeder2011c}, doi = {10.1038/tpj.2011.44}, keywords = {ADME, eQTL, gene expression, pharmacogenetics, quantitative trait loci, SNP}, pdf = {http://www.nature.com/tpj/journal/vaop/ncurrent/pdf/tpj201144a.pdf}, project = {abt_zell, bioinformatics, VLN}, url = {http://dx.doi.org/10.1038/tpj.2011.44}, } |
| [23] | Philipp Vorst and Artur Koch and Andreas Zell. Efficient Self-Adjusting, Similarity-based Location Fingerprinting
with Passive {UHF} {RFID}. In IEEE International Conference on RFID-Technology and Applications
(RFID-TA2011), pages 160--167,, Sitges, Barcelona, Spain,September 15-16, 2011. [url]Bibtex@INPROCEEDINGS{vorst2011rfidta,author = {Philipp Vorst and Artur Koch and Andreas Zell}, title = {Efficient Self-Adjusting, Similarity-based Location Fingerprinting with Passive {UHF} {RFID}}, booktitle = {IEEE International Conference on RFID-Technology and Applications (RFID-TA2011)}, year = {2011}, pages = {160--167}, address = {Sitges, Barcelona, Spain}, month = {September 15-16}, publisher = {IEEE}, abstract = {In this paper we present extensive experimental results of location fingerprinting with passive UHF radio-frequency identification (RFID). As recent passive RFID hardware provides information about received signal strength (RSS), we evaluate its usefulness in the context of fingerprinting based on classical vector similarity measures. We analyze the impact of decisive parameters of the applied approach and also select them automatically via cross-validation, including the most appropriate similarity measure. A further novelty is an RSS thresholding mechanism which reduces the computational demands of comparing fingerprints. This technique is especially useful in surroundings which are densely equipped with RFID tags, such as future supermarkets or logistic centers. We conducted realworld experiments with a mobile robot and two different RFID readers. Results are reported both for global localization in each time frame and for time-filtered position tracking. We provide the experimental data of this work for download. Details on the experimental setup as well as downloadable datasets can be obtained at \url{http://www.cogsys.cs.uni-tuebingen.de/datasets/rfid-ta2011/}.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?vorst2011rfidta}, doi = {10.1109/RFID-TA.2011.6068632}, ee = {http://dx.doi.org/10.1109/RFID-TA.2011.6068632}, isbn = {978-1-4577-0028-6}, project = {abt_zell, robotics, ambisense, rfid}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/vorstkoch2011rfidta.pdf}, } |
| [24] | Dube, Daniel and Zell, Andreas. Real-Time Plane Extraction from Depth Images with the Randomized
Hough Transform. In IEEE ICCV Workshop on Challenges and Opportunities in Robot Perception, pages 1084 -1091,, Barcelona, Spain,nov, 2011. Bibtex@INPROCEEDINGS{dube2011,author = {Dube, Daniel and Zell, Andreas}, title = {Real-Time Plane Extraction from Depth Images with the Randomized Hough Transform}, booktitle = {IEEE ICCV Workshop on Challenges and Opportunities in Robot Perception}, year = {2011}, pages = {1084 -1091}, address = {Barcelona, Spain}, month = {nov}, doi = {10.1109/ICCVW.2011.6130371}, owner = {dube}, project = {abt_zell, robotics}, } |
| [25] | Khan, Yasir Niaz and Komma, Philippe and Zell, Andreas. High Resolution Visual Terrain Classification for Outdoor Robots. In Computer Vision Workshops (ICCV Workshops), 2011 IEEE International
Conference on, pages 1014 -1021,, Barcelona, Spain,nov, 2011. [url]Bibtex@INPROCEEDINGS{khan11b,author = {Khan, Yasir Niaz and Komma, Philippe and Zell, Andreas}, title = {High Resolution Visual Terrain Classification for Outdoor Robots}, booktitle = {Computer Vision Workshops (ICCV Workshops), 2011 IEEE International Conference on}, year = {2011}, pages = {1014 -1021}, address = {Barcelona, Spain}, month = {nov}, abstract = {In this paper we investigate SURF features for visual terrain classification for outdoor mobile robots. The image is divided into a grid and SURF features are calculated on the intersections of this grid. These features are then used to train a classifier that can differentiate between different terrain classes. Images of five different terrain types are taken using a single camera mounted on a mobile outdoor robot. We further introduce another descriptor, which is a modified form of the dense Daisy descriptor. Random forests are used for classification on each descriptor. Classification results of SURF and Daisy descriptors are compared with the results from traditional texture descriptors like LBP, LTP and LATP. It is shown that SURF features perform better than other descriptors at higher resolutions. Daisy features, although not better than SURF features, also perform better than the three texture descriptors at high resolution.}, doi = {10.1109/ICCVW.2011.6130362}, keywords = {SURF;artifacts;blurred images filtering;local features;outdoor mobile robots;random forests;robot motion;texture classification;visual terrain classification;feature extraction;image restoration;image texture;mobile robots;pattern classification}, owner = {khan}, project = {abt_zell, robotics, terrain_classification}, timestamp = {2011.09.22}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/khan2011iccvworkshop.pdf}, } |
| [26] | Schröder, Adrian. Inference of gene-regulatory networks in primary human hepatocytes. , Tübingen, Germany,nov, 2011. [url]Bibtex@PHDTHESIS{Schroeder2011d,author = {Schröder, Adrian}, title = {Inference of gene-regulatory networks in primary human hepatocytes}, school = {University of Tuebingen}, year = {2011}, address = {Tübingen, Germany}, month = {nov}, abstract = {The liver is among the largest and most complex organs in the human body. It is responsible for the detoxification, metabolization, and elimination of thousands of chemically diverse substances. This essential functionality is mainly accomplished by hepatocytes, the most abundant cell type in human liver tissue. An arsenal of liver proteins that are sensitive to chemical compounds, orchestrates the activation of genes and thus the production of specific enzymes, transporters, and other proteins. These proteins transform endogenous and exogenous chemical substances into less toxic and more water soluble metabolites and promote the efflux of these compounds. The complex architecture of these regulatory programs in human liver cells is widely unknown. Defects in the regulatory mechanisms are known to be involved in the development of a variety of liver diseases. Understanding the structure and functionality of gene-regulatory networks in human liver cells is, therefore, of high medical relevance. The work at hand presents several new approaches to the reconstruction of gene-regulatory networks in primary human hepatocytes. The main building blocks of this kind of networks are transcription factors, which are able to activate genes by recognizing and binding to specific DNA sequence elements in the regulatory region of these genes. In this work, first, a new approach for the prediction of transcription factor binding specificities is proposed. Next, a new method for the reconstruction of transcriptional regulatory networks is presented that mines for patterns of transcription factor binding sites in sets of co-expressed genes. The application of this method to drug-response gene expression data revealed several new regulatory relationships that were successfully validated in wet lab experiments. Finally, genome-wide association analyses are performed to identify new associations between genetic markers and quantitative gene expression levels based on a cohort of 150 human liver samples.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Schroeder2011d}, isbn = {978-3-8439-0256-4}, project = {abt_zell, bioinformatics, VLN, HepatoSys, Spher4Sys}, publisher = {Verlag Dr.~Hut, Sternstraße 18, München}, url = {http://www.dr.hut-verlag.de/978-3-8439-0256-4.html}, } |
| [27] | Franken, Holger and Lehmann, Rainer and Häring, Hans-Ulrich and
Fritsche, Andreas and Stefan, Norbert and Zell, Andreas. Wrapper- and Ensemble-Based Feature Subset Selection Methods for
Biomarker Discovery in Targeted Metabolomics. In Pattern Recognition in Bioinformatics, pages 121-132,2011. [url]Bibtex@INCOLLECTION{Franken2011,author = {Franken, Holger and Lehmann, Rainer and Häring, Hans-Ulrich and Fritsche, Andreas and Stefan, Norbert and Zell, Andreas}, title = {Wrapper- and Ensemble-Based Feature Subset Selection Methods for Biomarker Discovery in Targeted Metabolomics}, booktitle = {Pattern Recognition in Bioinformatics}, publisher = {Springer Berlin / Heidelberg}, year = {2011}, editor = {Loog, Marco and Wessels, Lodewyk and Reinders, Marcel and de Ridder, Dick}, volume = {7036}, series = {Lecture Notes in Computer Science}, pages = {121-132}, note = {10.1007/978-3-642-24855-9_11}, abstract = {The discovery of markers allowing for accurate classification of metabolically very similar proband groups constitutes a challenging problem. We apply several search heuristics combined with different classifier types to targeted metabolomics data to identify compound subsets that classify plasma samples of insulin sensitive and -resistant subjects, both suffering from non-alcoholic fatty liver disease. Additionally, we integrate these methods into an ensemble and screen selected subsets for common features. We investigate, which methods appear the most suitable for the task, and test feature subsets for robustness and reproducibility. Furthermore, we consider the predictive potential of different compound classes. We find that classifiers fail in discriminating the non-selected data accurately, but benefit considerably from feature subset selection. Especially, a Pareto-based multi-objective genetic algorithm detects highly discriminative subsets and outperforms widely used heuristics. When transferred to new data, feature sets assembled by the ensemble approach show greater robustness than those selected by single methods.}, affiliation = {Center for Bioinformatics (ZBIT), University of Tübingen, D-72076 Tübingen, Germany}, isbn = {978-3-642-24854-2}, keyword = {Computer Science}, project = {diabetes, abt_zell, bioinformatics}, url = {http://dx.doi.org/10.1007/978-3-642-24855-9_11}, } |
| [28] | Hinselmann, Georg and Jahn, Andreas and Fechner, Nikolas and Rosenbaum,
Lars and Zell, Andreas. Approximation of Graph Kernel Similarities for Chemical Graphs by
Kernel Principal Component Analysis. In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, pages 123--134,2011. Bibtex@INCOLLECTION{Hinselmann2011evostar,author = {Hinselmann, Georg and Jahn, Andreas and Fechner, Nikolas and Rosenbaum, Lars and Zell, Andreas}, title = {Approximation of Graph Kernel Similarities for Chemical Graphs by Kernel Principal Component Analysis}, booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics}, publisher = {Springer Berlin Heidelberg}, year = {2011}, editor = {Pizzuti, Clara and Ritchie, Marylyn D. and Giacobini, Mario}, volume = {6623}, series = {Lecture Notes in Computer Science}, pages = {123--134}, editors = {C. Pizzuti and M.D. Ritchie and M. Giacobini}, owner = {rosenbaum}, project = {abt_zell, cheminformatics}, timestamp = {2013.05.07}, } |
| [29] | Georg Hinselmann and Andreas Jahn and Lars Rosenbaum and Andreas
Zell. Fast Data Mining with Sparse Chemical Graph Fingerprints by Estimating
the Probability of Unique Patterns. In Proceedings of 19th European Symposium on Artificial Neural Networks
(ESANN 2011), pages 417-422,, Bruges, Belgium,2011. Bibtex@INPROCEEDINGS{HinselmannESANN2011,author = {Georg Hinselmann and Andreas Jahn and Lars Rosenbaum and Andreas Zell}, title = {Fast Data Mining with Sparse Chemical Graph Fingerprints by Estimating the Probability of Unique Patterns}, booktitle = {Proceedings of 19th European Symposium on Artificial Neural Networks (ESANN 2011)}, year = {2011}, editor = {Michel Verleysen}, pages = {417-422}, address = {Bruges, Belgium}, project = {abt_zell, cheminformatics}, } |
| [30] | Hinselmann, Georg and Rosenbaum, Lars and Jahn, Andreas and Fechner,
Nikolas and Ostermann, Claude and Zell, Andreas. Large-Scale Learning of Structure-Activity Relationships Using a
Linear Support Vector Machine and Problem-specific Metrics. , pages 203--213,2011. Bibtex@ARTICLE{Hinselmann2010a,author = {Hinselmann, Georg and Rosenbaum, Lars and Jahn, Andreas and Fechner, Nikolas and Ostermann, Claude and Zell, Andreas}, title = {Large-Scale Learning of Structure-Activity Relationships Using a Linear Support Vector Machine and Problem-specific Metrics}, journal = {Journal of Chemical Information and Modeling}, year = {2011}, volume = {52}, pages = {203--213}, issue = {2}, owner = {hinselma}, project = {abt_zell, cheminformatics}, timestamp = {2010.12.07}, } |
| [31] | Georg Hinselmann and Lars Rosenbaum and Andreas Jahn and Nikolas
Fechner and Andreas Zell. jCompoundMapper: An Open Source Java Library and Command-Line Tool
for Chemical Fingerprints. 2011. Bibtex@ARTICLE{Hinselmann2010c,author = {Georg Hinselmann and Lars Rosenbaum and Andreas Jahn and Nikolas Fechner and Andreas Zell}, title = {jCompoundMapper: An Open Source Java Library and Command-Line Tool for Chemical Fingerprints}, journal = {Journal of Cheminformatics}, year = {2011}, volume = {3}, number = {3}, project = {abt_zell, cheminformatics}, } |
| [32] | Andreas Jahn and Georg Hinselmann and Lars Rosenbaum and Nikolas
Fechner and Andreas Zell. Boltzmann-enhanced Flexible Atom-Pair Kernel with Dynamic Dimension
Reduction. , pages 307--315,2011. Bibtex@ARTICLE{Jahn2011a,author = {Andreas Jahn and Georg Hinselmann and Lars Rosenbaum and Nikolas Fechner and Andreas Zell}, title = {Boltzmann-enhanced Flexible Atom-Pair Kernel with Dynamic Dimension Reduction}, journal = {Molecular Informatics}, year = {2011}, volume = {30}, pages = {307--315}, number = {4}, project = {abt_zell, cheminformatics}, } |
| [33] | Andreas Jahn and Lars Rosenbaum and Georg Hinselmann and Andreas
Zell. {4D Flexible Atom-Pairs: An efficient probabilistic conformational
space comparison for ligand-based virtual screening}. 2011. Bibtex@ARTICLE{Jahn2011b,author = {Andreas Jahn and Lars Rosenbaum and Georg Hinselmann and Andreas Zell}, title = {{4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening}}, journal = {Journal of Cheminformatics}, year = {2011}, volume = {3}, number = {23}, owner = {jahn}, project = {abt_zell, cheminformatics}, timestamp = {2011.06.22}, } |
| [34] | Andreas Masselli and Karl Engelbert Wenzel and Andreas Zell. {Verfahren zur Bestimmung der relativen Lage eines Objektes im Raum
sowie optisches Eingabesystem}. 2011. Bibtex@MISC{MasselliWenzel2011,author = {Andreas Masselli and Karl Engelbert Wenzel and Andreas Zell}, title = {{Verfahren zur Bestimmung der relativen Lage eines Objektes im Raum sowie optisches Eingabesystem}}, year = {2011}, note = {Patent, DE 10 2011 075 253.6, Submitted 2011.05.04}, project = {abt_zell, robotics, p3p}, } |
| [35] | Lars Rosenbaum and Georg Hinselmann and Andreas Jahn and Andreas
Zell. Interpreting linear support vector machine models with heat map atom
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