| [1] | D\"{o}rr, Alexander and Rosenbaum, Lars and Zell, Andreas. A Ranking Method for the Concurrent Learning of Compounds with Various
Activity Profiles. jan, 2015. Bibtex@ARTICLE{Doerr2014b,author = {D\"{o}rr, Alexander and Rosenbaum, Lars and Zell, Andreas}, title = {A Ranking Method for the Concurrent Learning of Compounds with Various Activity Profiles}, journal = {J. Cheminf.}, year = {2015}, volume = {7}, number = {1}, month = {jan}, project = {abt_zell, cheminformatics}, timestamp = {2014.12.16}, } |
| [2] | Ohrnberger, Stefan and Thavamani, Abhishek and Braeuning, Albert
and Lipka, Daniel B and Kirilov, Milen and Geffers, Robert and Authenrieth,
Stella E and Römer, Michael and Zell, Andreas and Bonin, Michael
and Schwarz, Michael and Sch\"{u}tz, G\"{u}nther and Schirmacher,
Peter and Plass, Christoph and Longerich, Thomas and Nordheim, Alfred. {Dysregulated serum response factor triggers formation of hepatocellular carcinoma}. mar, 2015. [pdf , url]Bibtex@ARTICLE{Ohrnberger2014,author = {Ohrnberger, Stefan and Thavamani, Abhishek and Braeuning, Albert and Lipka, Daniel B and Kirilov, Milen and Geffers, Robert and Authenrieth, Stella E and Römer, Michael and Zell, Andreas and Bonin, Michael and Schwarz, Michael and Sch\"{u}tz, G\"{u}nther and Schirmacher, Peter and Plass, Christoph and Longerich, Thomas and Nordheim, Alfred}, title = {{Dysregulated serum response factor triggers formation of hepatocellular carcinoma}}, journal = {Hepatology}, year = {2015}, month = {mar}, doi = {10.1002/hep.27539}, issn = {1527-3350}, pmid = {25266280}, abstract = {The ubiquitously expressed transcriptional regulator serum response factor (SRF) is controlled by both Ras/MAPK (mitogen-activated protein kinase) and Rho/actin signaling pathways, which are frequently activated in hepatocellular carcinoma (HCC). We generated \emph{SRF-VP16\textsuperscript{iHep}} mice, which conditionally express constitutively active SRF-VP16 in hepatocytes, thereby controlling subsets of both Ras/MAPK- and Rho/actin-stimulated target genes. All \emph{SRF-VP16\textsuperscript{iHep}} mice develop hyperproliferative liver nodules that progresses to lethal HCC. Some murine (m)HCCs acquire \emph{Ctnnb1} mutations equivalent to those in human (h)HCC. The resulting transcript signatures mirror those of a distinct subgroup of hHCCs, with shared activation of oncofetal genes including \emph{Igf2}, correlating with CpG hypomethylation at the imprinted \emph{Igf2/H19} locus. \emph{Conclusion:} \emph{SRF-VP16\textsuperscript{iHep}} mHCC reveal convergent Ras/MAPK and Rho/actin signaling as a highly oncogenic driver mechanism for hepatocarcinogenesis. This suggests simultaneous inhibition of Ras/MAPK and Rho/actin signaling as a treatment strategy in hHCC therapy.}, project = {abt_zell, bioinformatics, VLN}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365683/}, pdf = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365683/pdf/hep0061-0979.pdf}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Ohrnberger2014}, } |
| [3] | Grasl-Kraupp, Bettina and Riegler, Teresa and Nejabat, Marzieh and Paur, Jakob and Eichner, Johannes and Römer, Michael and Zell, Andreas and Schulte-Hermann, Rolf and Huber, Wolfgang. Abstract 810: Non-genotoxic hepatocarcinogens induce growth and anti-apoptotic pathways in hepatocytes via mesenchymal cytokines. , pages 810,April, 2015. [url]Bibtex@article{GraslKraupp2015,author = {Grasl-Kraupp, Bettina and Riegler, Teresa and Nejabat, Marzieh and Paur, Jakob and Eichner, Johannes and Römer, Michael and Zell, Andreas and Schulte-Hermann, Rolf and Huber, Wolfgang}, title = {Abstract 810: Non-genotoxic hepatocarcinogens induce growth and anti-apoptotic pathways in hepatocytes via mesenchymal cytokines}, volume = {75}, month = {April}, number = {15 Supplement}, pages = {810}, year = {2015}, doi = {10.1158/1538-7445.AM2015-810}, abstract = {Purpose of study. Chemical carcinogens are categorized as either genotoxic or non-genotoxic. While most genotoxic carcinogens are known to interfere with DNA, the mode of action of non-genotoxic carcinogens (NGC) is far from being understood. Many steroid hormones act as NGC and account for cancer of the breast, prostate, or other organs. As ligands of nuclear receptors hormones induce growth in target tissues and support the outgrowth of mutated cells to malignancy. An almost identical principle is underlying the action of NGC producing liver tumors in long-term rodent bioassays. This group of compounds comprises drugs prescribed to hundred-thousands of humans, like hypolipidemic and antidiabetic drugs, or synthetic steroid hormones. A thorough knowledge of the mode of action of NGC is of utmost importance in order to estimate the risk of exposed humans.Conventional notion regards the action of NGC an autonomous process largely confined to parenchymal cells. Here, we aim to elucidate the role of the hepatic mesenchyme for the action of two prototypical NGC, phenobarbital (PB), an anti-epileptic drug, and cyproterone acetate (CPA), a gestagen used in contraceptive pills.Experimental procedures. Mesenchymal liver cells (MC) and hepatocytes (HC) were isolated from control and PB/CPA-treated rat livers by collagenase perfusion and subsequent low-speed centrifugation. Transcriptomics was performed by oligo-array analyses (Affymetrix). Cytokine levels were determined by ELISA. Nuclear translocation of NFkB was shown by immunoblotts of nuclear extracts and by reporter gene assay.Results: Analyses by oligo-arrays revealed that PB and CPA altered the transcriptome profiles of HC and MC. In PB-treated MC, there were deregulations of pro-inflammatory cytokines and chemokines of the TNF-, CCL- and CXCL-family. PB treatment in vivo or in vitro elevated the production and release of tumor necrosis factor alpha (TNFalpha)from MC. The secretome of PB-treated MC induced in HC a pro-inflammatory reaction and nuclear translocation of nuclear factor-kB (NFkB), an effect also observed with recombinant TNFalpha. Both, TNFalpha and the secretome of PB-treated MC, protected HC from pro-apoptotic stimuli.Transcriptome analyses of CPA-treated MC revealed enhanced expression not only of pro-inflammatory cytokines but also of several potent growth factors. Accordingly, the supernatant of CPA-treated MC enhanced considerably the DNA replication of preneoplastic hepatocytes.Conclusion: PB and CPA appear to alter considerably the function of the hepatic mesenchyme. The resulting release of cytokines induces growth and/or activates anti-apoptotic pathways in HC which may contribute to the tumor promoting activity of these compounds. Thus, epithelial-mesenchymal interactions appear crucial in NGC-driven hepatocarcinogenesis.Project MARCAR, funded by IMI JU under grant agreement Nr 115001.Citation Format: Bettina Grasl-Kraupp, Teresa Riegler, Marzieh Nejabat, Jakob Paur, Johannes Eichner, Michael Roemer, Andreas Zell, Rolf Schulte-Hermann, Wolfgang Huber. Non-genotoxic hepatocarcinogens induce growth and anti-apoptotic pathways in hepatocytes via mesenchymal cytokines. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 810. doi:10.1158/1538-7445.AM2015-810}, url = {http://cancerres.aacrjournals.org/content/75/15_Supplement/810.abstract}, journal = {Cancer Research}, project = {abt_zell, bioinformatics, MARCAR}, } |
| [4] | Otte, Sebastian and Becker, Fabian and Butz, Martin V. and Liwicki, Marcus and Zell, Andreas. {Learning} {Recurrent} {Dynamics} {using} {Differential} {Evolution}. In European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN), pages 65--70,, Bruges, Belgium,apr, 2015. Bibtex@INPROCEEDINGS{otte_esann_2015a,title = {{Learning} {Recurrent} {Dynamics} {using} {Differential} {Evolution}}, booktitle = {European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN)}, author = {Otte, Sebastian and Becker, Fabian and Butz, Martin V. and Liwicki, Marcus and Zell, Andreas}, address = {Bruges, Belgium}, year = {2015}, month = {apr}, pages = {65--70}, project = {abt_zell, rnn}, } |
| [5] | Otte, Sebastian and Laible, Stefan and Hanten, Richard and Liwicki, Marcus and Zell, Andreas. {Robust} {Visual} {Terrain} {Classification} {with} {Recurrent} {Neural} {Networks}. In European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN), pages 451--456,, Bruges, Belgium,apr, 2015. Bibtex@INPROCEEDINGS{otte_esann_2015b,title = {{Robust} {Visual} {Terrain} {Classification} {with} {Recurrent} {Neural} {Networks}}, booktitle = {European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN)}, author = {Otte, Sebastian and Laible, Stefan and Hanten, Richard and Liwicki, Marcus and Zell, Andreas}, address = {Bruges, Belgium}, year = {2015}, month = {apr}, pages = {451--456}, project = {abt_zell, rnn}, } |
| [6] | Lixing Jiang and Artur Koch and Andreas Zell. Salient Regions Detection for Indoor Robots using {RGB-D} Data. In IEEE International Conference on Robotics and Automation (ICRA), Seattle, USA,May, 2015. [url]Bibtex@INPROCEEDINGS{Jiang2015icra,author = {Lixing Jiang and Artur Koch and Andreas Zell}, title = {Salient Regions Detection for Indoor Robots using {RGB-D} Data}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2015}, address = {Seattle, USA}, month = {May}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Jiang2015icra}, owner = {jiang}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Jiang_ICRA15.pdf}, } |
| [7] | Rodriguez, Nicolas and Thomas, Alex and Watanabe, Leandro and
Vazirabad, Ibrahim Y. and Kofia, Victor and G\'{o}mez, Harold F. and Mittag,
Florian and Matthes, Jakob and Rudolph, Jan D. and Wrzodek, Finja and Netz,
Eugen and Diamantikos, Alexander and Eichner, Johannes and Keller, Roland
and Wrzodek, Clemens and Fröhlich, Sebastian and Lewis, Nathan E. and
Myers, Chris J. and {Le Nov\`{e}re}, Nicolas and Palsson, Bernhard {\O}. and
Hucka, Michael and Dräger, Andreas. {JSBML 1.0: providing a smorgasbord of options to encode systems biology models}. jun, 2015. [pdf , url]Bibtex@ARTICLE{Rodriguez2015,author = {Rodriguez, Nicolas and Thomas, Alex and Watanabe, Leandro and Vazirabad, Ibrahim Y. and Kofia, Victor and G\'{o}mez, Harold F. and Mittag, Florian and Matthes, Jakob and Rudolph, Jan D. and Wrzodek, Finja and Netz, Eugen and Diamantikos, Alexander and Eichner, Johannes and Keller, Roland and Wrzodek, Clemens and Fröhlich, Sebastian and Lewis, Nathan E. and Myers, Chris J. and {Le Nov\`{e}re}, Nicolas and Palsson, Bernhard {\O}. and Hucka, Michael and Dräger, Andreas}, title = {{JSBML 1.0: providing a smorgasbord of options to encode systems biology models}}, journal = {Bioinformatics}, year = {2015}, month = {jun}, doi = {10.1093/bioinformatics/btv341}, abstract = {Summary: JSBML, the official pure Java programming library for the SBML format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. 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}. Supplementary Information: More information about JSBML can be found in the user guide at \url{http://sbml.org/Software/JSBML/docs/}. Contact: \url{mailto:jsbml-development@googlegroups.com}}, url = {http://bioinformatics.oxfordjournals.org/content/31/20/3383}, eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/30/bioinformatics.btv341.full.pdf+html}, pdf = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/30/bioinformatics.btv341.full.pdf}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Rodriguez2015.html}, project = {extern, bioinformatics, AMBiCon, NIH_JSBML, VLN}, } |
| [8] | Sebastian A. Scherer and Shaowu Yang and Andreas Zell. DCTAM: Drift-corrected tracking and mapping for autonomous micro aerial vehicles. In Unmanned Aircraft Systems (ICUAS), 2015 International Conference on, pages 1094-1101,, Denver, CO, USA,June, 2015. [pdf , url]Bibtex@INPROCEEDINGS{scherer2015,title = {DCTAM: Drift-corrected tracking and mapping for autonomous micro aerial vehicles}, author = {Sebastian A. Scherer and Shaowu Yang and Andreas Zell}, booktitle = {Unmanned Aircraft Systems (ICUAS), 2015 International Conference on}, year = {2015}, address = {Denver, CO, USA}, month = {June}, pages = {1094-1101}, abstract = {Visual odometry, especially using a forward-looking camera only, can be challenging: It is doomed to fail from time to time and will inevitably drift in the long run. We accept this fact and present methods to cope with and correct the effects for an autonomous MAV using an RGBD camera as its main sensor. We propose correcting drift and failure in visual odometry by combining its pose estimates with information about efficiently detected ground planes in the short term and running a full SLAM back-end incorporating loop closures and ground plane measurements in pose graph optimization. We show that the system presented here achieves accurate results on several instances of the TUM RGB-D benchmark dataset while being computationally efficient enough to enable autonomous flight of an MAV.}, days = {9-12}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?scherer2015}, owner = {scherer}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/scherer2015.pdf}, project = {abt_zell, robotics, rgbd_slam, uav}, timestamp = {2015.07.24}, url = {http://dx.doi.org/10.1109/ICUAS.2015.7152401}, } |
| [9] | Buck, Sebastian and Hanten, Richard and Huski\'{c}, Goran and Rauscher, Gerald and
Kloss, Alina and Leininger, Jan and Ruff, Eugen and Widmaier, Felix and Zell, Andreas. Conclusions from an Object-Delivery Robotic Competition: SICK Robot Day 2014. In Advanced Robotics (ICAR), The 17th International Conference on, pages 137-143,, Istanbul, TR,July, 2015. [pdf , url]Bibtex@INPROCEEDINGS{BuckICAR2015,title = {Conclusions from an Object-Delivery Robotic Competition: SICK Robot Day 2014}, author = {Buck, Sebastian and Hanten, Richard and Huski\'{c}, Goran and Rauscher, Gerald and Kloss, Alina and Leininger, Jan and Ruff, Eugen and Widmaier, Felix and Zell, Andreas}, booktitle = {Advanced Robotics (ICAR), The 17th International Conference on}, year = {2015}, address = {Istanbul, TR}, month = {July}, pages = {137-143}, abstract = {Contrary to controlled experiments in a laboratory, robotics competitions pose a real challenge to an intelligent autonomous system. To allow a good performance, robotic systems have to be very robust to unforeseen circumstances in a highly constrained time frame. In this paper we present the design, implementation and performance of the robotic system we developed for participation in the SICK robot day 2014, with which we achieved very good results, placing second, with the same maximum score as the first. The task of this competition was to alternately fetch and deliver objects in a simplified warehouse scenario. Participating robots had to be able to carry out different tasks, such as detecting filling and delivery stations, receiving and analysing bar-code labelled objects as well as navigating in an arena among three other robots.}, days = {27-31}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?BuckICAR2015}, owner = {buck}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/BuckICAR2015.pdf}, project = {abt_zell, robotics, sick_robot_day_2014, competition, csapex, csnavigation}, timestamp = {2015.07.29}, url = {http://dx.doi.org/10.1109/ICAR.2015.7251446}, doi = {10.1109/ICAR.2015.7251446}, } |
| [10] | Radouane Ait Jellal and Andreas Zell. A fast dense stereo matching algorithm with an application to 3D occupancy mapping using quadrocopters. In The 17th International Conference on Advanced Robotics (ICAR), pages 587 - 592,, Istanbul, TR,jul, 2015. [pdf , url]Bibtex@INPROCEEDINGS{Ait_JellalICAR2015,title = {A fast dense stereo matching algorithm with an application to 3D occupancy mapping using quadrocopters}, author = {Radouane Ait Jellal and Andreas Zell}, booktitle = {The 17th International Conference on Advanced Robotics (ICAR)}, year = {2015}, address = {Istanbul, TR}, month = {jul}, pages = {587 - 592}, abstract = {We propose a fast algorithm for computing stereo correspondences and correcting the mismatches. The correspondences are computed using stereo block matching and refined with a depth-aware method. We compute 16 disparities at the same time using SSE instructions. We evaluated our method on the Middlebury benchmark and obtained promosing results for practical realtime applications. The use of SSE instructions allows us to reduce the time needed to process the Tsukuba stereo pair to 8 milliseconds (125 fps) on a Core i5 CPU with 2X3.3 GHz. Our disparity refinement method has corrected 40\% of the wrong matches with an additional computational time of 5.2\% (0.41ms). The algorithm has been used to build 3D occupancy grid maps from stereo images. We used the datasets provided by the EuRoC Robotic Challenge. The reconstruction was accurate enough to perform realtime safe navigation.}, days = {27-31}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Ait_JellalICAR2015}, owner = {buck}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Ait_JellalICAR2015.pdf}, project = {abt_zell, robotics, miniGRK_FlyingRobots, Stereo}, timestamp = {2015.07.30}, url = {http://ieeexplore.ieee.org/Xplore/defdeny.jsp?url=http\%3A\%2F\%2Fieeexplore.ieee.org\%2Fstamp\%2Fstamp.jsp\%3Ftp\%3D\%26arnumber\%3D7251515\%26userType\%3Dinst&denyReason=-134&arnumber=7251515&productsMatched=null&userType=inst}, } |
| [11] | Otte, Sebastian and Liwicki, Marcus and Zell, Andreas. {An} {Analysis} {of} {Dynamic} {Cortex} {Memory} {Networks}. In International Joint Conference on Neural Networks (IJCNN), pages 3338--3345,, Killarney, Ireland,jul, 2015. Bibtex@INPROCEEDINGS{otte_ijcnn_2015,title = {{An} {Analysis} {of} {Dynamic} {Cortex} {Memory} {Networks}}, booktitle = {International Joint Conference on Neural Networks (IJCNN)}, author = {Otte, Sebastian and Liwicki, Marcus and Zell, Andreas}, address = {Killarney, Ireland}, pages = {3338--3345}, isbn = {978-1-4799-1959-8}, year = {2015}, month = {jul}, project = {abt_zell, rnn}, } |
| [12] | Mittag, Florian and Römer, Michael and Zell, Andreas. {Influence of Feature Encoding and Choice of Classifier on Disease Risk Prediction in Genome-Wide Association Studies}. , pages e0135832,aug, 2015. [url]Bibtex@article{Mittag2015,abstract = {Various attempts have been made to predict the individual disease risk based on genotype data from genome-wide association studies (GWAS). However, most studies only investigated one or two classification algorithms and feature encoding schemes. In this study, we applied seven different classification algorithms on GWAS case-control data sets for seven different diseases to create models for disease risk prediction. Further, we used three different encoding schemes for the genotypes of single nucleotide polymorphisms (SNPs) and investigated their influence on the predictive performance of these models. Our study suggests that an additive encoding of the SNP data should be the preferred encoding scheme, as it proved to yield the best predictive performances for all algorithms and data sets. Furthermore, our results showed that the differences between most state-of-the-art classification algorithms are not statistically significant. Consequently, we recommend to prefer algorithms with simple models like the linear support vector machine (SVM) as they allow for better subsequent interpretation without significant loss of accuracy.}, author = {Mittag, Florian and Römer, Michael and Zell, Andreas}, doi = {10.1371/journal.pone.0135832}, editor = {Raghava, Gajendra P. S.}, issn = {1932-6203}, journal = {PLoS ONE}, publisher = {Public Library of Science}, month = {aug}, number = {8}, pages = {e0135832}, pmid = {26285210}, title = {{Influence of Feature Encoding and Choice of Classifier on Disease Risk Prediction in Genome-Wide Association Studies}}, url = {http://dx.doi.org/10.1371/journal.pone.0135832 http://dx.plos.org/10.1371/journal.pone.0135832}, volume = {10}, year = {2015}, project = {abt_zell, bioinformatics}, } |
| [13] | Yang, Laurence and Tan, Justin and O'Brien, Edward J. and
Monk, Jonathan and Kim, Donghyuk and Lia, Howard J. and Charusantia, Pep
and Ebrahim, Ali and Lloyd, Colton J. and Yurkovich, James T. and Du, Bin
and Dräger, Andreas and Thomas, Alex and Sun, Yuekai and Saunders, Michael A.
and Palsson, Bernhard O.. Systems biology definition of the core proteome of metabolism and
expression is consistent with high-throughput data. aug, 2015. [pdf , url]Bibtex@ARTICLE{Yang2015,author = {Yang, Laurence and Tan, Justin and O'Brien, Edward J. and Monk, Jonathan and Kim, Donghyuk and Lia, Howard J. and Charusantia, Pep and Ebrahim, Ali and Lloyd, Colton J. and Yurkovich, James T. and Du, Bin and Dräger, Andreas and Thomas, Alex and Sun, Yuekai and Saunders, Michael A. and Palsson, Bernhard O.}, title = {Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data}, journal = {Proceedings of the National Academy of Sciences}, abstract = {Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44\% of the \emph{Escherichia coli} proteome by mass based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65\% of known essential genes in \emph{E.~coli}, and has 78\% gene function overlap with minimal genomes (\emph{Buchnera aphidicola} and \emph{Mycoplasma genitalium}). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in non-differentially expressed genes, and depleted in differentially expressed genes. Compared to the non-core, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation), and exhibit significantly more complex transcriptional and post-transcriptional regulatory features (40\% more transcription start sites per gene, 22\% longer 5'UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it \emph{de facto} defines a paleome.}, year = {2015}, month = {aug}, url = {http://www.pnas.org/content/early/2015/08/05/1501384112}, pdf = {http://www.pnas.org/content/early/2015/08/05/1501384112.full.pdf}, doi = {10.1073/pnas.1501384112}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Yang2015.html}, project = {extern, AMBiCon}, } |
| [14] | King, Zachary A. and Dräger, Andreas and Ebrahim, Ali and
Sonnenschein, Nikolaus and Lewis, Nathan E. and Palsson, Bernhard O.. Escher: A web application for building, sharing, and embedding
data-rich visualizations of biological pathways. , pages e1004321,aug, 2015. [url]Bibtex@ARTICLE{King2015a,author = {King, Zachary A. and Dräger, Andreas and Ebrahim, Ali and Sonnenschein, Nikolaus and Lewis, Nathan E. and Palsson, Bernhard O.}, title = {Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways}, abstract = {Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzmyes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g., RNA-Seq, proteomics, ChIP) in conjunction with metabolite- and reaction-oriented data types (e.g., metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.}, doi = {10.1371/journal.pcbi.1004321}, publisher = {Public Library of Science}, journal = {PLoS Computational Biology}, month = {aug}, pages = {e1004321}, volume = {11}, number = {8}, url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1004321}, year = {2015}, keywords = {Data visualization; Metabolites; Web-based application; Genomic databases; Genome analysis; Enzymes; Protein metabolism; Genomic libraries}, project = {extern, bioinformatics, AMBiCon}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/King2015a.html}, } |
| [15] | Dräger, Andreas and Zielinski, Daniel C. and Keller, Roland and
Rall, Matthias and Eichner, Johannes and Palsson, Bernhard O. and Zell, Andreas. {SBMLsqueezer~2: Context-sensitive creation of kinetic equations in biochemical networks}. , pages 1--17,sep, 2015. [pdf , url]Bibtex@article{Draeger2015,author = {Dräger, Andreas and Zielinski, Daniel C. and Keller, Roland and Rall, Matthias and Eichner, Johannes and Palsson, Bernhard O. and Zell, Andreas}, title = {{SBMLsqueezer~2: Context-sensitive creation of kinetic equations in biochemical networks}}, journal = {BMC Systems Biology}, volume = {9}, number = {1}, pages = {1--17}, issn = {1752-0509}, month = {sep}, year = {2015}, doi = {10.1186/s12918-015-0212-9}, url = {http://dx.doi.org/10.1186/s12918-015-0212-9}, abstract = {Background: The size and complexity of published biochemical network reconstructions are steadily increasing, expanding the potential scale of derived computational models. However, the construction of large biochemical network models is a laborious and error-prone task. Automated methods have simplified the network reconstruction process, but building kinetic models for these systems is still a manually intensive task. Appropriate kinetic equations, based upon reaction rate laws, must be constructed and parameterized for each reaction. The complex test-and-evaluation cycles that can be involved during kinetic model construction would thus benefit from automated methods for rate law assignment. Results: We present a high-throughput algorithm to automatically suggest and create suitable rate laws based upon reaction type according to several criteria. The criteria for choices made by the algorithm can be influenced in order to assign the desired type of rate law to each reaction. This algorithm is implemented in the software package SBMLsqueezer~2. In addition, this program contains an integrated connection to the kinetics database SABIO-RK to obtain experimentally-derived rate laws when desired. Conclusions: The described approach fills a heretofore absent niche in workflows for large-scale biochemical kinetic model construction. In several applications the algorithm has already been demonstrated to be useful and scalable. SBMLsqueezer is platform independent and can be used as a stand-alone package, as an integrated plugin, or through a web interface, enabling flexible solutions and use-case scenarios.}, pdf = {http://www.biomedcentral.com/content/pdf/s12918-015-0212-9.pdf}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Draeger2015.html}, project = {abt_zell, bioinformatics, VLN, AMBiCon, SBMLsqueezer}, } |
| [16] | Hucka, Michael and Bergmann, Frank T. and Dräger, Andreas and
Hoops, Stefan and Keating, Sarah M. and {Le Nov\`{e}re}, Nicolas and Myers,
Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and
Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J.. {Systems Biology Markup Language (SBML) Level 2 Version 5: Structures
and Facilities for Model Definitions}. , pages 271,sep, 2015. [pdf , url]Bibtex@article{Hucka2015,author = {Hucka, Michael and Bergmann, Frank T. and Dräger, Andreas and Hoops, Stefan and Keating, Sarah M. and {Le Nov\`{e}re}, Nicolas and Myers, Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J.}, title = {{Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions}}, journal = {Journal of Integrative Bioinformatics}, volume = {12}, number = {2}, pages = {271}, month = {sep}, year = {2015}, doi = {10.2390/biecoll-jib-2015-271}, abstract = {Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, \url{http://sbml.org}}, url = {http://journal.imbio.de/article.php?aid=271}, pdf = {http://journal.imbio.de/articles/pdf/jib-271.pdf}, project = {extern, bioinformatics, NIH_JSBML}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Hucka2015.html}, } |
| [17] | Huimin Lu and Lixing Jiang and Andreas Zell. Long Range Traversable Region Detection Based on Superpixels Clustering for Mobile Robots. In IEEE/RSJ International Conference on Intelligent Robots and Systems
({IROS}), Hamburg, Germany,Sept., 2015. [url]Bibtex@INPROCEEDINGS{Lu2015iros,author = {Huimin Lu and Lixing Jiang and Andreas Zell}, title = {Long Range Traversable Region Detection Based on Superpixels Clustering for Mobile Robots}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems ({IROS})}, year = {2015}, address = {Hamburg, Germany}, month = {Sept.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Lu2015iros}, owner = {Lu}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Lu_IROS15.pdf}, } |
| [18] | King, Zachary A. and Lu, Justin S. and Dräger, Andreas and Miller,
Philip C. and Federowicz, Stephen and Lerman, Joshua A and Ebrahim, Ali and
Palsson, Bernhard O. and Lewis, Nathan E.. {BiGG Models: A platform for integrating, standardizing, and sharing
genome-scale models}. oct, 2015. [pdf , url]Bibtex@article{King2015b,author = {King, Zachary A. and Lu, Justin S. and Dräger, Andreas and Miller, Philip C. and Federowicz, Stephen and Lerman, Joshua A and Ebrahim, Ali and Palsson, Bernhard O. and Lewis, Nathan E.}, title = {{BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models}}, journal = {Nucleic Acids Research}, abstract = {Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards, and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (\url{http://bigg.ucsd.edu}), a completely redesigned Biochemical, Genetic, and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search, and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface (API) for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized, and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.}, keywords = {genome-scale model, knowledge base, omics data}, month = {oct}, year = {2015}, doi = {10.1093/nar/gkv1049}, url = {http://nar.oxfordjournals.org/content/44/D1/D515}, pdf = {http://nar.oxfordjournals.org/content/early/2015/10/15/nar.gkv1049.full.pdf}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/King2015b.html}, project = {extern, bioinformatics, AMBiCon}, } |
| [19] | Ebrahim, Ali and Almaas, Eivind and Bauer, Eugen and Bordbar, Aarash
and Burgard, Anthony P. and Chang, Roger L. and Dräger, Andreas and
Famili, Iman and Feist, Adam M. and Fleming, Ronan M.~T. and Fong, Stephen S.
and Hatzimanikatis, Vassily and Herrg\r{a}rd, Markus J. and Holder, Allen
and Hucka, Michael and Hyduke, Daniel and Jamshidi, Neema and Lee, Sang Yup
and {Le Nov\`{e}re}, Nicolas and Lerman, Joshua A. and Lewis, Nathan E. and
Ma, Ding and Mahadevan, Radhakrishnan and Maranas, Costas and Nagarajan, Harish
and Navid, Ali and Nielsen, Jens and Nielsen, Lars K. and Nogales, Juan and
Noronha, Alberto and Pal, Csaba and Palsson, Bernhard O. and Papin, Jason A.
and Patil, Kiran R. and Price, Nathan D. and Reed, Jennifer L. and Saunders,
Michael and Senger, Ryan S. and Sonnenschein, Nikolaus and Sun, Yuekai and
Thiele, Ines. {Do Genome-scale Models Need Exact Solvers or Clearer Standards?}. , pages 831,oct, 2015. [pdf , url]Bibtex@ARTICLE{Ebrahim2015,author = {Ebrahim, Ali and Almaas, Eivind and Bauer, Eugen and Bordbar, Aarash and Burgard, Anthony P. and Chang, Roger L. and Dräger, Andreas and Famili, Iman and Feist, Adam M. and Fleming, Ronan M.~T. and Fong, Stephen S. and Hatzimanikatis, Vassily and Herrg\r{a}rd, Markus J. and Holder, Allen and Hucka, Michael and Hyduke, Daniel and Jamshidi, Neema and Lee, Sang Yup and {Le Nov\`{e}re}, Nicolas and Lerman, Joshua A. and Lewis, Nathan E. and Ma, Ding and Mahadevan, Radhakrishnan and Maranas, Costas and Nagarajan, Harish and Navid, Ali and Nielsen, Jens and Nielsen, Lars K. and Nogales, Juan and Noronha, Alberto and Pal, Csaba and Palsson, Bernhard O. and Papin, Jason A. and Patil, Kiran R. and Price, Nathan D. and Reed, Jennifer L. and Saunders, Michael and Senger, Ryan S. and Sonnenschein, Nikolaus and Sun, Yuekai and Thiele, Ines}, title = {{Do Genome-scale Models Need Exact Solvers or Clearer Standards?}}, journal = {Molecular Systems Biology}, year = {2015}, month = {oct}, volume = {11}, number = {10}, pages = {831}, issn = {1744-4292}, url = {http://dx.doi.org/10.15252/msb.20156157}, doi = {10.15252/msb.20156157}, pdf = {http://msb.embopress.org/content/11/10/831.full.pdf}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Ebrahim2015.html}, project = {extern, bioinformatics, AMBiCon}, } |
| [20] | Ibrahim, Tamer M. and Bauer, Matthias R. and Dörr, Alexander and Veyisoglu, Erdem and Boeckler, Frank M.. pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening. October, 2015. [url]Bibtex@article{Ibrahim2015,title = {pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening}, author = {Ibrahim, Tamer M. and Bauer, Matthias R. and Dörr, Alexander and Veyisoglu, Erdem and Boeckler, Frank M.}, journal = {Journal of Chemical Information and Modeling}, year = {2015}, month = {October}, publisher = {ACS Publications}, doi = {10.1021/acs.jcim.5b00475}, project = {abt_zell, cheminformatics}, url = {http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00475}, } |
| [21] | Jiang, Lixing and Lu, Huimin and Duc, My Vo and Koch, Artur and Zell, Andreas. Superpixel Segmentation Based Gradient Maps on {RGB-D} Dataset. In IEEE International Conference on Robotics and Biomimetics (ROBIO), Zhuhai, China,December, 2015. [url]Bibtex@INPROCEEDINGS{jiang_ROBIO2015,author = {Jiang, Lixing and Lu, Huimin and Duc, My Vo and Koch, Artur and Zell, Andreas}, title = {Superpixel Segmentation Based Gradient Maps on {RGB-D} Dataset}, booktitle = {IEEE International Conference on Robotics and Biomimetics (ROBIO)}, year = {2015}, address = {Zhuhai, China}, month = {December}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?jiang_ROBIO2015}, owner = {jiang}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Jiang_ROBIO15.pdf}, } |
| [22] | Binz, Marcel and Otte, Sebastian and Zell, Andreas. {On} the {Applicability} of {Recurrent} {Neural} {Networks} for {Pattern} {Recognition} in {Electroencephalography} {Signals}. In Machine Learning Reports 03/2015, Workshop New Challenges in Neural Computation, pages 85--92,2015. Bibtex@inproceedings{2015_nc2_eegrnn,title = {{On} the {Applicability} of {Recurrent} {Neural} {Networks} for {Pattern} {Recognition} in {Electroencephalography} {Signals}}, author = {Binz, Marcel and Otte, Sebastian and Zell, Andreas}, booktitle = {Machine Learning Reports 03/2015, Workshop New Challenges in Neural Computation}, year = {2015}, pages = {85--92}, project = {abt_zell, rnn}, } |
| [23] | Ran Liu and Goran Huski\'{c} and Andreas Zell. {On Tracking Dynamic Objects with Long Range Passive UHF RFID Using a Mobile Robot}. 2015. [url]Bibtex@ARTICLE{Ran_IJDSN_2015,author = {Ran Liu and Goran Huski\'{c} and Andreas Zell}, title = {{On Tracking Dynamic Objects with Long Range Passive UHF RFID Using a Mobile Robot}}, journal = {International Journal of Distributed Sensor Networks (IJDSN)}, year = {2015}, volume = {Article ID 781380}, project = {abt_zell, robotics}, issn = {781380}, publisher = {Hindawi}, url = {http://dx.doi.org/10.1155/2015/781380}, } |
| [24] | Liu, Yuyi and {van Schijndel}, Jos and Longo, Stefano and Kerrigan, Eric C.. {UAV} Energy Extraction with Incomplete Atmospheric Data Using {MPC}. , pages 1203-1215,2015. Bibtex@ARTICLE{yuyiliu14,author = {Liu, Yuyi and {van Schijndel}, Jos and Longo, Stefano and Kerrigan, Eric C.}, title = {{UAV} Energy Extraction with Incomplete Atmospheric Data Using {MPC}}, journal = {{IEEE} Transactions on Aerospace and Electronic Systems}, year = {2015}, volume = {51}, number = {2}, pages = {1203-1215}, project = {extern, robotics, uav}, } |
| [25] | Liu, Yuyi and Montenbruck, Jan Maximilian and Stegagno, Paolo and Allgöwer, Frank and Zell, Andreas. A Robust Nonlinear Controller for Nontrivial Quadrotor Maneuvers: Approach and Verification. In Proc. 2015 {IEEE/RSJ} International Conference on Intelligent Robots and Systems, pages 5410-5416,2015. Bibtex@INPROCEEDINGS{yuyiliu15,author = {Liu, Yuyi and Montenbruck, Jan Maximilian and Stegagno, Paolo and Allgöwer, Frank and Zell, Andreas}, title = {A Robust Nonlinear Controller for Nontrivial Quadrotor Maneuvers: Approach and Verification}, booktitle = {Proc. 2015 {IEEE/RSJ} International Conference on Intelligent Robots and Systems}, year = {2015}, pages = {5410-5416}, project = {abt_zell, robotics, uav}, } |