@article{DandekarGramschHoughtonetal.1985,
  author    = {Dandekar, Thomas and Gramsch, Christian and Houghton, Richard A. and Schultz, R{\"u}diger},
  title     = {Affinity purification of \(\beta\)-endorphin-like material from NG108CC15 cells by means of the monoclonal \(\beta\)-endorphin antibody 3-E7},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29896},
  year      = {1985},
  abstract  = {No abstract available},
  language  = {en}
}
@article{Dandekar1986,
  author    = {Dandekar, Thomas},
  title     = {Offenlegungsschrift ({\"u}ber einen Biosensor)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-31683},
  year      = {1986},
  abstract  = {No abstract available},
  language  = {de}
}
@article{SchultzMetznerDandekaretal.1986,
  author    = {Schultz, R{\"u}diger and Metzner, Katharina and Dandekar, Thomas and Gramsch, Christian},
  title     = {Opiates induce long-term increases in prodynorphin derived peptide levels in the guinea-pig myenteric plexus},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29809},
  year      = {1986},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarSchulz1987,
  author    = {Dandekar, Thomas and Schulz, R.},
  title     = {Evidence for the expression of peptides derived from three opioid precursors in NG 108CC15 hybrid cells},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29909},
  year      = {1987},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarRibesTollervey1989,
  author    = {Dandekar, Thomas and Ribes, V. and Tollervey, David},
  title     = {Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29771},
  year      = {1989},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarTollervey1989,
  author    = {Dandekar, Thomas and Tollervey, David},
  title     = {Cloning of Schizosaccharomyces pombe genes encoding the U1,U2,U3 and U4 snRNAs},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29919},
  year      = {1989},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{Dandekar1990,
  author    = {Dandekar, Thomas},
  title     = {Hefezellen - ein gutes Modell f{\"u}r h{\"o}here Zellen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29726},
  year      = {1990},
  abstract  = {No abstract available},
  language  = {de}
}
@article{DandekarSibbald1990,
  author    = {Dandekar, Thomas and Sibbald, Peter R.},
  title     = {Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29798},
  year      = {1990},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{Dandekar1991,
  author    = {Dandekar, Thomas},
  title     = {Yeast U3 localization and correct sequence (snR17a) and promotor activity (snR17b) identified by homology search},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29781},
  year      = {1991},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarTollervey1991,
  author    = {Dandekar, Thomas and Tollervey, D.},
  title     = {Thirty-three nucleotides of 5' flanking sequence including the TATA box are necessary and sufficient for efficient U2 snRNA transcription in Schizosaccharomycespombe},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29959},
  year      = {1991},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarStripeckeGrayetal.1991,
  author    = {Dandekar, Thomas and Stripecke, Renata and Gray, Nicola K. and Goossen, Britta and Constable, Anne and Johansson, Hans E. and Hentze, Matthias W.},
  title     = {Identification of a novel iron-responsive element in murine and human erythroid \(\delta\)-aminolevulinic acid synthase mRNA},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29929},
  year      = {1991},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{DandekarArgos1991,
  author    = {Dandekar, Thomas and Argos, Patrick},
  title     = {Chaperonin-mediated protein folding at the surface of groEL through a "molten globule" intermediate},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29939},
  year      = {1991},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{Dandekar1991,
  author    = {Dandekar, Thomas},
  title     = {Olbers' Paradox (peer-reviewed scientific correspondence)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-31672},
  year      = {1991},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{DandekarArgos1992,
  author    = {Dandekar, Thomas and Argos, Patrick},
  title     = {A novel heterodimeric cysteine protease is required for interleukin 1ß processing in monocytes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29986},
  year      = {1992},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarTollervey1992,
  author    = {Dandekar, Thomas and Tollervey, David},
  title     = {Mutational analysis of Schizosaccharomyces pombe U4 snRNA by plasmid exchange},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29969},
  year      = {1992},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarArgos1992,
  author    = {Dandekar, Thomas and Argos, P.},
  title     = {Potential of genetic algorithms in protein folding and protein engineering simulations},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29974},
  year      = {1992},
  abstract  = {No abstract available},
  language  = {de}
}
@misc{DandekarArgos1992,
  author    = {Dandekar, Thomas and Argos, Patrick},
  title     = {Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29814},
  year      = {1992},
  abstract  = {No abstract available},
  language  = {en}
}
@inproceedings{DandekarArgos1993,
  author    = {Dandekar, Thomas and Argos, P.},
  title     = {Genetic algorithms as a new tool to study protein stability},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29990},
  year      = {1993},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{DandekarArgos1993,
  author    = {Dandekar, Thomas and Argos, P.},
  title     = {Drug assay using antibody mimics made by molecular imprinting},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-30003},
  year      = {1993},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarTollervey1993,
  author    = {Dandekar, Thomas and Tollervey, David},
  title     = {Identification and functional analysis of a novel yeast small nucleolar RNA},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29850},
  year      = {1993},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{DandekarArgos1993,
  author    = {Dandekar, Thomas and Argos, P.},
  title     = {The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted \(\alpha\)-helices: Crystal structure of the protein DNA-complex},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29866},
  year      = {1993},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarArgos1994,
  author    = {Dandekar, Thomas and Argos, Patrick},
  title     = {Amiloride-sensitive epithelial Na\(^+\) channel is made of three homologous subunits},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29734},
  year      = {1994},
  abstract  = {No abstract available},
  language  = {en}
}
@misc{DandekarDandekar1994,
  author    = {Dandekar, Thomas and Dandekar, G.},
  title     = {Schlange als Attribut des {\"A}skulap},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29822},
  year      = {1994},
  abstract  = {No abstract available},
  language  = {de}
}
@misc{DandekarArgos1994,
  author    = {Dandekar, Thomas and Argos, P.},
  title     = {Three-dimensional structure of the 67k N-terminal Fragment of E.coli DNA Topoisomerase I},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29836},
  year      = {1994},
  abstract  = {No abstract available},
  language  = {en}
}
@article{DandekarArgos1994,
  author    = {Dandekar, Thomas and Argos, P.},
  title     = {Folding the main chain of small proteins with the genetic algorithm},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29847},
  year      = {1994},
  abstract  = {No abstract available},
  language  = {de}
}
@article{ArgosDandekar1994,
  author    = {Argos, P. and Dandekar, Thomas},
  title     = {Delineating the main chain topology of four-helix bundle proteins using the genetic algorithm and knowledge based on the amino acid sequence alone},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33807},
  year      = {1994},
  abstract  = {No abstract available},
  subject      = {Proteine},
  language  = {en}
}
@unpublished{Dandekar2007,
  author    = {Dandekar, Thomas},
  title     = {Some general system properties of a living observer and the environment he explores},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33537},
  year      = {2007},
  abstract  = {In a nice assay published in Nature in 1993 the physicist Richard God III started from a human observer and made a number of witty conclusions about our future prospects giving estimates for the existence of the Berlin Wall, the human race and all the rest of the universe. In the same spirit, we derive implications for "the meaning of life, the universe and all the rest" from few principles. Adams´ absurd answer "42" tells the lesson "garbage in / garbage out" - or suggests that the question is non calculable. We show that experience of "meaning" and to decide fundamental questions which can not be decided by formal systems imply central properties of life: Ever higher levels of internal representation of the world and an escalating tendency to become more complex. An observer, "collecting observations" and three measures for complexity are examined. A theory on living systems is derived focussing on their internal representation of information. Living systems are more complex than Kolmogorov complexity ("life is NOT simple") and overcome decision limits (G{\"o}del theorem) for formal systems as illustrated for cell cycle. Only a world with very fine tuned environments allows life. Such a world is itself rather complex and hence excessive large in its space of different states - a living observer has thus a high probability to reside in a complex and fine tuned universe.},
  subject      = {Komplex <Algebra>},
  language  = {en}
}
@unpublished{Dandekar2008,
  author    = {Dandekar, Thomas},
  title     = {Why are nature´s constants so fine-tuned? The case for an escalating complex universe},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-34488},
  year      = {2008},
  abstract  = {Why is our universe so fine-tuned? In this preprint we discuss that this is not a strange accident but that fine-tuned universes can be considered to be exceedingly large if one counts the number of observable different states (i.e. one aspect of the more general preprint http://www.opus-bayern.de/uni-wuerzburg/volltexte/2009/3353/). Looking at parameter variation for the same set of physical laws simple and complex processes (including life) and worlds in a multiverse are compared in simple examples. Next the anthropocentric principle is extended as many conditions which are generally interpreted anthropocentric only ensure a large space of different system states. In particular, the observed over-tuning beyond the level for our existence is explainable by these system considerations. More formally, the state space for different systems becomes measurable and comparable looking at their output behaviour. We show that highly interacting processes are more complex then Chaitin complexity, the latter denotes processes not compressible by shorter descriptions (Kolomogorov complexity). The complexity considerations help to better study and compare different processes (programs, living cells, environments and worlds) including dynamic behaviour and can be used for model selection in theoretical physics. Moreover, the large size (in terms of different states) of a world allowing complex processes including life can in a model calculation be determined applying discrete histories from quantum spin-loop theory. Nevertheless there remains a lot to be done - hopefully the preprint stimulates further efforts in this area.},
  subject      = {Natur},
  language  = {en}
}
@article{ShityakovDandekar2010,
  author    = {Shityakov, Sergey and Dandekar, Thomas},
  title     = {Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67824},
  year      = {2010},
  abstract  = {Indinavir (Crivaxan®) is a potent inhibitor of the HIV (human immunodeficiency virus) protease. This enzyme has an important role in viral replication and is considered to be very attractive target for new antiretroviral drugs. However, it becomes less effective due to highly resistant new viral strains of HIV, which have multiple mutations in their proteases. For this reason, we used a lead expansion method to create a new set of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated and screened to determine their ability to interact with protease and establish their QSAR properties. Further computational analyses revealed one unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed in this report.},
  subject      = {Proteasen},
  language  = {en}
}
@article{KellerFoersterMuelleretal.2010,
  author    = {Keller, Alexander and Foerster, Frank and Mueller, Tobias and Dandekar, Thomas and Schultz, Joerg and Wolf, Matthias},
  title     = {Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67832},
  year      = {2010},
  abstract  = {Background: In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results: This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Open peer review: Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.},
  subject      = {Phylogenie},
  language  = {en}
}
@article{VainshteinSanchezBrazmaetal.2010,
  author    = {Vainshtein, Yevhen and Sanchez, Mayka and Brazma, Alvis and Hentze, Matthias W. and Dandekar, Thomas and Muckenthaler, Martina U.},
  title     = {The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67869},
  year      = {2010},
  abstract  = {Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see "Additional Files" section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/},
  subject      = {Microarray},
  language  = {en}
}
@article{FriedrichRahmannWeigeletal.2010,
  author    = {Friedrich, Torben and Rahmann, Sven and Weigel, Wilfried and Rabsch, Wolfgang and Fruth, Angelika and Ron, Eliora and Gunzer, Florian and Dandekar, Thomas and Hacker, Joerg and Mueller, Tobias and Dobrindt, Ulrich},
  title     = {High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67936},
  year      = {2010},
  abstract  = {The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens. Results: We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes. Conclusions: Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.},
  subject      = {Mikroarray},
  language  = {en}
}
@article{WangorschButtMarketal.2011,
  author    = {Wangorsch, Gaby and Butt, Elke and Mark, Regina and Hubertus, Katharina and Geiger, J{\"o}rg and Dandekar, Thomas and Dittrich, Marcus},
  title     = {Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69145},
  year      = {2011},
  abstract  = {Background: Hemostasis is a critical and active function of the blood mediated by platelets. Therefore, the prevention of pathological platelet aggregation is of great importance as well as of pharmaceutical and medical interest. Endogenous platelet inhibition is predominantly based on cyclic nucleotides (cAMP, cGMP) elevation and subsequent cyclic nucleotide-dependent protein kinase (PKA, PKG) activation. In turn, platelet phosphodiesterases (PDEs) and protein phosphatases counterbalance their activity. This main inhibitory pathway in human platelets is crucial for countervailing unwanted platelet activation. Consequently, the regulators of cyclic nucleotide signaling are of particular interest to pharmacology and therapeutics of atherothrombosis. Modeling of pharmacodynamics allows understanding this intricate signaling and supports the precise description of these pivotal targets for pharmacological modulation. Results: We modeled dynamically concentration-dependent responses of pathway effectors (inhibitors, activators, drug combinations) to cyclic nucleotide signaling as well as to downstream signaling events and verified resulting model predictions by experimental data. Experiments with various cAMP affecting compounds including antiplatelet drugs and their combinations revealed a high fidelity, fine-tuned cAMP signaling in platelets without crosstalk to the cGMP pathway. The model and the data provide evidence for two independent feedback loops: PKA, which is activated by elevated cAMP levels in the platelet, subsequently inhibits adenylyl cyclase (AC) but as well activates PDE3. By multi-experiment fitting, we established a comprehensive dynamic model with one predictive, optimized and validated set of parameters. Different pharmacological conditions (inhibition, activation, drug combinations, permanent and transient perturbations) are successfully tested and simulated, including statistical validation and sensitivity analysis. Downstream cyclic nucleotide signaling events target different phosphorylation sites for cAMP- and cGMP-dependent protein kinases (PKA, PKG) in the vasodilator-stimulated phosphoprotein (VASP). VASP phosphorylation as well as cAMP levels resulting from different drug strengths and combined stimulants were quantitatively modeled. These predictions were again experimentally validated. High sensitivity of the signaling pathway at low concentrations is involved in a fine-tuned balance as well as stable activation of this inhibitory cyclic nucleotide pathway. Conclusions: On the basis of experimental data, literature mining and database screening we established a dynamic in silico model of cyclic nucleotide signaling and probed its signaling sensitivity. Thoroughly validated, it successfully predicts drug combination effects on platelet function, including synergism, antagonism and regulatory loops.},
  subject      = {Vasodilatator-stimuliertes Phosphoprotein},
  language  = {en}
}
@article{BeisserGrohmeKopkaetal.2012,
  author    = {Beisser, Daniela and Grohme, Markus A. and Kopka, Joachim and Frohme, Marcus and Schill, Ralph O. and Hengherr, Steffen and Dandekar, Thomas and Klau, Gunnar W. and Dittrich, Marcus and M{\"u}ller, Tobias},
  title     = {Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-75241},
  year      = {2012},
  abstract  = {Background: Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. Results: In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurablemetabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration. Conclusions: The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner.},
  subject      = {Milnesium tardigradum},
  language  = {en}
}
@article{KruegerFriedrichFoersteretal.2012,
  author    = {Krueger, Beate and Friedrich, Torben and F{\"o}rster, Frank and Bernhardt, J{\"o}rg and Gross, Roy and Dandekar, Thomas},
  title     = {Different evolutionary modifications as a guide to rewire two-component systems},
  series = {Bioinformatics and Biology Insights},
  volume    = {6},
  journal   = {Bioinformatics and Biology Insights},
  doi       = {10.4137/BBI.S9356},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123647},
  pages     = {97-128},
  year      = {2012},
  abstract  = {Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases.},
  language  = {en}
}
@article{MergetKoetschanHackletal.2012,
  author    = {Merget, Benjamin and Koetschan, Christian and Hackl, Thomas and F{\"o}rster, Frank and Dandekar, Thomas and M{\"u}ller, Tobias and Schultz, J{\"o}rg and Wolf, Matthias},
  title     = {The ITS2 Database},
  series = {Journal of Visual Expression},
  volume    = {61},
  journal   = {Journal of Visual Expression},
  number    = {e3806},
  doi       = {10.3791/3806},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124600},
  year      = {2012},
  abstract  = {The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation. The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold. The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure. In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.},
  language  = {en}
}
@article{FoersterBeisserGrohmeetal.2012,
  author    = {F{\"o}rster, Frank and Beisser, Daniela and Grohme, Markus A. and Liang, Chunguang and Mali, Brahim and Siegl, Alexander Matthias and Engelmann, Julia C. and Shkumatov, Alexander V. and Schokraie, Elham and M{\"u}ller, Tobias and Schn{\"o}lzer, Martina and Schill, Ralph O. and Frohme, Marcus and Dandekar, Thomas},
  title     = {Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations},
  series = {Bioinformatics and biology insights},
  volume    = {6},
  journal   = {Bioinformatics and biology insights},
  doi       = {10.4137/BBI.S9150},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123089},
  pages     = {69-96},
  year      = {2012},
  abstract  = {Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade \(Milnesium\) \(tardigradum\) were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from \(Hypsibius\) \(dujardini\), revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for \(M.\) \(tardigradum\) are different from typical motifs known from higher animals. \(M.\) \(tardigradum\) and \(H.\) \(dujardini\) protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of \(M.\) \(tardigradum\). These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and \(M.\) \(tardigradum\) in particular so highly stress resistant.},
  language  = {en}
}
@article{DandekarFieselmannPoppetal.2012,
  author    = {Dandekar, Thomas and Fieselmann, Astrid and Popp, Jasmin and Hensel, Michael},
  title     = {Salmonella enterica: a surprisingly well-adapted intracellular lifestyle},
  series = {Frontiers in Microbiology},
  journal   = {Frontiers in Microbiology},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123135},
  year      = {2012},
  abstract  = {The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole (SCV) in host cells. We summarize latest results on metabolic requirements for Salmonella during infection. This includes intracellular phenotypes of mutant strains based on metabolic modeling and experimental tests, isotopolog profiling using (13)C-compounds in intracellular Salmonella, and complementation of metabolic defects for attenuated mutant strains towards a comprehensive understanding of the metabolic requirements of the intracellular lifestyle of Salmonella. Helpful for this are also genomic comparisons. We outline further recent studies and which analyses of intracellular phenotypes and improved metabolic simulations were done and comment on technical required steps as well as progress involved in the iterative refinement of metabolic flux models, analyses of mutant phenotypes, and isotopolog analyses. Salmonella lifestyle is well-adapted to the SCV and its specific metabolic requirements. Salmonella metabolism adapts rapidly to SCV conditions, the metabolic generalist Salmonella is quite successful in host infection.},
  language  = {en}
}
@article{NaseemDandekar2012,
  author    = {Naseem, Muhammad and Dandekar, Thomas},
  title     = {The Role of Auxin-Cytokinin Antagonism in Plant-Pathogen Interactions},
  series = {PLOS Pathogens},
  volume    = {8},
  journal   = {PLOS Pathogens},
  number    = {11},
  doi       = {10.1371/journal.ppat.1003026},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131901},
  pages     = {e1003026},
  year      = {2012},
  abstract  = {No abstract available.},
  language  = {en}
}
@article{SchokraieWarnkenHotzWagenblattetal.2012,
  author    = {Schokraie, Elham and Warnken, Uwe and Hotz-Wagenblatt, Agnes and Grohme, Markus A. and Hengherr, Steffen and F{\"o}rster, Frank and Schill, Ralph O. and Frohme, Marcus and Dandekar, Thomas and Schn{\"o}lzer, Martina},
  title     = {Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state},
  series = {PLoS One},
  volume    = {7},
  journal   = {PLoS One},
  number    = {9},
  doi       = {10.1371/journal.pone.0045682},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134447},
  pages     = {e45682},
  year      = {2012},
  abstract  = {Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.},
  language  = {en}
}
@article{BugaScholzKumaretal.2012,
  author    = {Buga, Ana-Maria and Scholz, Claus J{\"u}rgen and Kumar, Senthil and Herndon, James G. and Alexandru, Dragos and Cojocaru, Gabriel Radu and Dandekar, Thomas and Popa-Wagner, Aurel},
  title     = {Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke},
  series = {PLoS One},
  volume    = {7},
  journal   = {PLoS One},
  number    = {12},
  doi       = {10.1371/journal.pone.0050985},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-130657},
  pages     = {e50985},
  year      = {2012},
  abstract  = {Background: Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions. Methodology/Principal Findings: We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. Overall, the pattern of gene expression strongly suggests that the response of the aged rat brain is qualitatively rather than quantitatively different from the young, i.e. the total number of regulated genes is comparable in the two age groups, but the aged rats had great difficulty in mounting a timely response to stroke. Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. New therapeutic options in aged rats may also include Calcrl, Cyp11b1, Prcp, Cebpa, Cfd, Gpnmb, Fcgr2b, Fcgr3a, Tnfrsf26, Adam 17 and Mmp14. An unexpected target is the enzyme 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 in aged rats, a key enzyme in the cholesterol synthesis pathway. Post-stroke axonal growth was compromised in both age groups. Conclusion/Significance: We suggest that a multi-stage, multimodal treatment in aged animals may be more likely to produce positive results. Such a therapeutic approach should be focused on tissue restoration but should also address other aspects of patient post-stroke therapy such as neuropathic syndrome, stress, anxiety disorders, depression, neurotransmission and blood pressure.},
  language  = {en}
}
@article{RatzkaFoersterLiangetal.2012,
  author    = {Ratzka, Carolin and F{\"o}rster, Frank and Liang, Chunguang and Kupper, Maria and Dandekar, Thomas and Feldhaar, Heike and Gross, Roy},
  title     = {Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-75985},
  year      = {2012},
  abstract  = {The production of antimicrobial peptides (AMPs) is a major defense mechanism against pathogen infestation and of particular importance for insects relying exclusively on an innate immune system. Here, we report on the characterization of three AMPs from the carpenter ant Camponotus floridanus. Due to sequence similarities and amino acid composition these peptides can be classified into the cysteine-rich (e.g. defensin) and glycine-rich (e.g. hymenoptaecin) AMP groups, respectively. The gene and cDNA sequences of these AMPs were established and their expression was shown to be induced by microbial challenge. We characterized two different defensin genes. The defensin-2 gene has a single intron, whereas the defensin-1 gene has two introns. The deduced amino acid sequence of the C. floridanus defensins is very similar to other known ant defensins with the exception of a short C-terminal extension of defensin-1. The hymenoptaecin gene has a single intron and a very peculiar domain structure. The corresponding precursor protein consists of a signal- and a pro-sequence followed by a hymenoptaecin-like domain and six directly repeated hymenoptaecin domains. Each of the hymenoptaecin domains is flanked by an EAEP-spacer sequence and a RR-site known to be a proteolytic processing site. Thus, proteolytic processing of the multipeptide precursor may generate several mature AMPs leading to an amplification of the immune response. Bioinformatical analyses revealed the presence of hymenoptaecin genes with similar multipeptide precursor structure in genomes of other ant species suggesting an evolutionary conserved important role of this gene in ant immunity.},
  subject      = {Biologie},
  language  = {en}
}
@article{KarlDandekar2013,
  author    = {Karl, Stefan and Dandekar, Thomas},
  title     = {Jimena: Efficient computing and system state identification for genetic regulatory networks},
  series = {BMC Bioinformatics},
  volume    = {14},
  journal   = {BMC Bioinformatics},
  doi       = {10.1186/1471-2105-14-306},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-128671},
  year      = {2013},
  abstract  = {Background: Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. Results: (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Conclusions: Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior.},
  language  = {en}
}
@article{SchulzeTillichDandekaretal.2013,
  author    = {Schulze, Katja and Tillich, Ulrich M. and Dandekar, Thomas and Frohme, Marcus},
  title     = {PlanktoVision - an automated analysis system for the identification of phytoplankton},
  series = {BMC Bioinformatics},
  journal   = {BMC Bioinformatics},
  doi       = {10.1186/1471-2105-14-115},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96395},
  year      = {2013},
  abstract  = {Background Phytoplankton communities are often used as a marker for the determination of fresh water quality. The routine analysis, however, is very time consuming and expensive as it is carried out manually by trained personnel. The goal of this work is to develop a system for an automated analysis. Results A novel open source system for the automated recognition of phytoplankton by the use of microscopy and image analysis was developed. It integrates the segmentation of the organisms from the background, the calculation of a large range of features, and a neural network for the classification of imaged organisms into different groups of plankton taxa. The analysis of samples containing 10 different taxa showed an average recognition rate of 94.7\% and an average error rate of 5.5\%. The presented system has a flexible framework which easily allows expanding it to include additional taxa in the future. Conclusions The implemented automated microscopy and the new open source image analysis system - PlanktoVision - showed classification results that were comparable or better than existing systems and the exclusion of non-plankton particles could be greatly improved. The software package is published as free software and is available to anyone to help make the analysis of water quality more reproducible and cost effective.},
  language  = {en}
}
@article{DandekarLiangKrueger2013,
  author    = {Dandekar, Thomas and Liang, Chunguang and Kr{\"u}ger, Beate},
  title     = {GoSynthetic database tool to analyse natural and engineered molecular processes},
  series = {Database},
  journal   = {Database},
  doi       = {10.1093/database/bat043},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-97023},
  year      = {2013},
  abstract  = {An essential topic for synthetic biologists is to understand the structure and function of biological processes and involved proteins and plan experiments accordingly. Remarkable progress has been made in recent years towards this goal. However, efforts to collect and present all information on processes and functions are still cumbersome. The database tool GoSynthetic provides a new, simple and fast way to analyse biological processes applying a hierarchical database. Four different search modes are implemented. Furthermore, protein interaction data, cross-links to organism-specific databases (17 organisms including six model organisms and their interactions), COG/KOG, GO and IntAct are warehoused. The built in connection to technical and engineering terms enables a simple switching between biological concepts and concepts from engineering, electronics and synthetic biology. The current version of GoSynthetic covers more than one million processes, proteins, COGs and GOs. It is illustrated by various application examples probing process differences and designing modifications.},
  language  = {en}
}
@article{DandekarAhmedSamanetal.2013,
  author    = {Dandekar, Thomas and Ahmed, Zeeshan and Saman, Zeeshan and Huber, Claudia and Hensel, Michael and Schomburg, Dietmar and M{\"u}nch, Richard and Eisenreich, Wolfgang},
  title     = {Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling},
  series = {BMC Bioinformatics},
  journal   = {BMC Bioinformatics},
  doi       = {10.1186/1471-2334-13-266},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-95882},
  year      = {2013},
  abstract  = {Background The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. Results The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. Conclusions The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.},
  language  = {en}
}
@article{DandekarFieselmannFischeretal.2014,
  author    = {Dandekar, Thomas and Fieselmann, Astrid and Fischer, Eva and Popp, Jasmin and Hensel, Michael and Noster, Janina},
  title     = {Salmonella—how a metabolic generalist adopts an intracellular lifestyle during infection},
  series = {Frontiers in Cellular and Infection Microbiology},
  volume    = {4},
  journal   = {Frontiers in Cellular and Infection Microbiology},
  number    = {191},
  issn      = {2235-2988},
  doi       = {10.3389/fcimb.2014.00191},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120686},
  year      = {2014},
  abstract  = {The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, "-omics" data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology.},
  language  = {en}
}
@article{WirthGlushakovaScheuermayeretal.2014,
  author    = {Wirth, Christine C. and Glushakova, Svetlana and Scheuermayer, Matthias and Repnik, Urska and Garg, Swatl and Schaack, Dominik and Kachman, Marika M. and Weißbach, Tim and Zimmerberg, Joshua and Dandekar, Thomas and Griffiths, Gareth and Chitnis, Chetan E. and Singh, Shallja and Fischer, Rainer and Pradel, Gabriele},
  title     = {Perforin-like protein PPLP2 permeabilizes the red blood cell membrane during egress of Plasmodium falciparum gametocytes},
  series = {Cellular Microbiology},
  volume    = {16},
  journal   = {Cellular Microbiology},
  number    = {5},
  doi       = {10.1111/cmi.12288},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120895},
  pages     = {709-33},
  year      = {2014},
  abstract  = {Egress of malaria parasites from the host cell requires the concerted rupture of its enveloping membranes. Hence, we investigated the role of the plasmodial perforin-like protein PPLP2 in the egress of Plasmodium falciparum from erythrocytes. PPLP2 is expressed in blood stage schizonts and mature gametocytes. The protein localizes in vesicular structures, which in activated gametocytes discharge PPLP2 in a calcium-dependent manner. PPLP2 comprises a MACPF domain and recombinant PPLP2 has haemolytic activities towards erythrocytes. PPLP2-deficient [PPLP2(-)] merozoites show normal egress dynamics during the erythrocytic replication cycle, but activated PPLP2(-) gametocytes were unable to leave erythrocytes and stayed trapped within these cells. While the parasitophorous vacuole membrane ruptured normally, the activated PPLP2(-) gametocytes were unable to permeabilize the erythrocyte membrane and to release the erythrocyte cytoplasm. In consequence, transmission of PPLP2(-) parasites to the Anopheles vector was reduced. Pore-forming equinatoxin II rescued both PPLP2(-) gametocyte exflagellation and parasite transmission. The pore sealant Tetronic 90R4, on the other hand, caused trapping of activated wild-type gametocytes within the enveloping erythrocytes, thus mimicking the PPLP2(-) loss-of-function phenotype. We propose that the haemolytic activity of PPLP2 is essential for gametocyte egress due to permeabilization of the erythrocyte membrane and depletion of the erythrocyte cytoplasm.},
  language  = {en}
}
@article{NaseemKunzDandekar2014,
  author    = {Naseem, Muhammad and Kunz, Meik and Dandekar, Thomas},
  title     = {Probing the unknowns in cytokinin-mediated immune defense in Arabidopsis with systems biology approaches},
  series = {Bioinformatics and Biology Insights},
  volume    = {8},
  journal   = {Bioinformatics and Biology Insights},
  issn      = {1177-9322},
  doi       = {10.4137/bbi.s13462},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120199},
  pages     = {35-44},
  year      = {2014},
  abstract  = {Plant hormones involving salicylic acid (SA), jasmonic acid (JA), ethylene (Et), and auxin, gibberellins, and abscisic acid (ABA) are known to regulate host immune responses. However, plant hormone cytokinin has the potential to modulate defense signaling including SA and JA. It promotes plant pathogen and herbivore resistance; underlying mechanisms are still unknown. Using systems biology approaches, we unravel hub points of immune interaction mediated by cytokinin signaling in Arabidopsis. High-confidence Arabidopsis protein-protein interactions (PPI) are coupled to changes in cytokinin-mediated gene expression. Nodes of the cellular interactome that are enriched in immune functions also reconstitute sub-networks. Topological analyses and their specific immunological relevance lead to the identification of functional hubs in cellular interactome. We discuss our identified immune hubs in light of an emerging model of cytokinin-mediated immune defense against pathogen infection in plants.},
  language  = {en}
}
@article{NaseemSrivastavaDandekar2014,
  author    = {Naseem, Muhammad and Srivastava, Mugdha and Dandekar, Thomas},
  title     = {Stem-cell-triggered immunity safeguards cytokinin enriched plant shoot apexes from pathogen infection},
  series = {Frontiers in Plant Science},
  volume    = {5},
  journal   = {Frontiers in Plant Science},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2014.00588},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-118247},
  pages     = {588},
  year      = {2014},
  abstract  = {Intricate mechanisms discriminate between friends and foes in plants. Plant organs deploy overlapping and distinct protection strategies. Despite vulnerability to a plethora of pathogens, the growing tips of plants grow bacteria free. The shoot apical meristem (SAM) is among three stem cells niches, a self-renewable reservoir for the future organogenesis of leaf, stem, and flowers. How plants safeguard this high value growth target from infections was not known until now. Recent reports find the stem cell secreted 12-amino acid peptide CLV3p (CLAVATA3 peptide) is perceived by FLS2 (FLAGELLIN SENSING 2) receptor and activates the transcription of immunity and defense marker genes. No infection in the SAM of wild type plants and bacterial infection in clv3 and fls2 mutants illustrate this natural protection against infections. Cytokinins (CKs) are enriched in the SAM and regulate meristem activities by their involvement in stem cell signaling networks. Auxin mediates plant susceptibility to pathogen infections while CKs boost plant immunity. Here, in addition to the stem-cell-triggered immunity we also highlight a potential link between CK signaling and CLV3p mediated immune response in the SAM.},
  language  = {en}
}