@inproceedings{3876, abstract = {We consider two-player games played in real time on game structures with clocks and parity objectives. The games are concurrent in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to turn-based (i.e., nonconcurrent) finite-state (i.e., untimed) parity games. The states of the resulting game are pairs of clock regions of the original game. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust strategies. Using a limit-robust strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers.}, author = {Krishnendu Chatterjee and Thomas Henzinger and Prabhu, Vinayak S}, pages = {124 -- 140}, publisher = {Springer}, title = {{Timed parity games: complexity and robustness}}, doi = {10.1007/978-3-540-85778-5_10}, volume = {5215}, year = {2008}, } @inproceedings{3877, abstract = {The synthesis problem asks to construct a reactive finite-state system from an omega-regular specification. Initial specifications are often unrealizable, which means that there is no system that implements the specification. A common reason for unrealizability is that assumptions on the environment of the system are incomplete. We study the problem of correcting an unrealizable specification phi by computing an environment assumption psi such that the new specification psi -> phi is realizable. Our aim is to construct an assumption psi that constrains only the environment and is as weak as possible. We present a two-step algorithm for computing assumptions. The algorithm operates on the game graph that is used to answer the realizability question. First, we compute a safety assumption that removes a minimal set of environment edges from the graph. Second, we compute a liveness assumption that puts fairness conditions on some of the remaining environment edges. We show that the problem of finding a minimal set of fair edges is computationally hard, and we use probabilistic games to compute a locally minimal fairness assumption.}, author = {Krishnendu Chatterjee and Thomas Henzinger and Jobstmann, Barbara}, pages = {147 -- 161}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Environment assumptions for synthesis}}, doi = {10.1007/978-3-540-85361-9_14}, volume = {5201}, year = {2008}, } @inproceedings{3878, abstract = {We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing “reset” action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies.}, author = {Krishnendu Chatterjee and de Alfaro, Luca and Majumdar, Ritankar S}, pages = {91 -- 106}, publisher = {Springer}, title = {{The complexity of coverage}}, doi = {10.1007/978-3-540-89330-1_7}, volume = {5356}, year = {2008}, } @inproceedings{3879, abstract = {Quantitative generalizations of classical languages, which assign to each word a real number instead of a boolean value, have applications in modeling resource-constrained computation. We use weighted automata (finite automata with transition weights) to define several natural classes of quantitative languages over finite and infinite words; in particular, the real value of an infinite run is computed as the maximum, limsup, liminf, limit average, or discounted sum of the transition weights. We define the classical decision problems of automata theory (emptiness, universality, language inclusion, and language equivalence) in the quantitative setting and study their computational complexity. As the decidability of language inclusion remains open for some classes of weighted automata, we introduce a notion of quantitative simulation that is decidable and implies language inclusion. We also give a complete characterization of the expressive power of the various classes of weighted automata. In particular, we show that most classes of weighted automata cannot be determinized.}, author = {Krishnendu Chatterjee and Doyen, Laurent and Thomas Henzinger}, pages = {385 -- 400}, publisher = {Springer}, title = {{Quantitative languages}}, doi = {10.1007/978-3-540-87531-4_28}, volume = {5213}, year = {2008}, } @inproceedings{3880, abstract = {We consider imperfect-information parity games in which strategies rely on observations that provide imperfect information about the history of a play. To solve such games, i.e., to determine the winning regions of players and corresponding winning strategies, one can use the subset construction to build an equivalent perfect-information game. Recently, an algorithm that avoids the inefficient subset construction has been proposed. The algorithm performs a fixed-point computation in a lattice of antichains, thus maintaining a succinct representation of state sets. However, this representation does not allow to recover winning strategies. In this paper, we build on the antichain approach to develop an algorithm for constructing the winning strategies in parity games of imperfect information. We have implemented this algorithm as a prototype. To our knowledge, this is the first implementation of a procedure for solving imperfect-information parity games on graphs.}, author = {Berwanger, Dietmar and Krishnendu Chatterjee and Doyen, Laurent and Thomas Henzinger and Raje, Sangram}, pages = {325 -- 339}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Strategy construction for parity games with imperfect information}}, doi = {10.1007/978-3-540-85361-9}, volume = {5201}, year = {2008}, } @article{3903, abstract = {Background The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations. Results Three clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression between populations could be predicted from their genetic and chemical distance, and two major clusters of non-aggressive groups of populations were found. However, populations of L. neglectus did not separate into clear supercolonial associations, as is typical for other invasive ants. Conclusion The three methodological approaches gave consistent and complementary results. All joint evidence supports the inference that the 14 introduced populations of L. neglectus in Europe likely arose from only very few independent introductions from the native range, and that new infestations were typically started through introductions from other invasive populations. This indicates that existing introduced populations have a very high invasive potential when the ants are inadvertently spread by human transport. }, author = {Ugelvig, Line V and Drijfhout, Falko and Kronauer, Daniel and Boomsma, Jacobus and Pedersen, Jes and Cremer, Sylvia}, journal = {BMC Biology}, number = {11}, publisher = {BioMed Central}, title = {{The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches}}, doi = {10.1186/1741-7007-6-11}, volume = {6}, year = {2008}, } @article{3905, abstract = {Winged and wingless males coexist in the ant Cardiocondyla obscurior. Wingless (“ergatoid”) males never leave their maternal colony and fight remorselessly among each other for the access to emerging females. The peaceful winged males disperse after about 10 days, but beforehand also mate in the nest. In the first 5 days of their life, winged males perform a chemical female mimicry that protects them against attack and even makes them sexually attractive to ergatoid males. When older, the chemical profile of winged males no longer matches that of virgin females; nevertheless, they are still tolerated, which so far has been puzzling. Contrasting this general pattern, we have identified a single aberrant colony in which all winged males were attacked and killed by the ergatoid males. A comparative analysis of the morphology and chemical profile of these untypical attacked winged males and the tolerated males from several normal colonies revealed that normal old males are still performing some chemical mimicry to the virgin queens, though less perfect than in their young ages. The anomalous attacked winged males, on the other hand, had a very different odour to the females. Our study thus exemplifies that the analysis of rare malfunctioning can add valuable insight on functioning under normal conditions and allows the conclusion that older winged males from normal colonies of the ant C. obscurior are guarded through an imperfect chemical female mimicry, still close enough to protect against attacks by the wingless fighters yet dissimilar enough not to elicit their sexual interest.}, author = {Cremer, Sylvia and D'Ettorre, Patrizia and Drijfhout, Falko and Sledge, Matthew and Turillazzi, Stefano and Heinze, Jürgen}, journal = {Naturwissenschaften}, number = {11}, pages = {1101 -- 1105}, publisher = {Springer}, title = {{Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior}}, doi = {10.1007/s00114-008-0430-8}, volume = {95}, year = {2008}, } @article{3906, author = {Cremer, Sylvia and Ugelvig, Line V and Drijfhout, Falko and Schlick Steiner, Birgit and Steiner, Florian and Seifert, Bernhard and Hughes, David and Schulz, Andreas and Petersen, Klaus and Konrad, Heino and Stauffer, Christian and Kiran, Kadri and Espadaler, Xavier and D'Ettorre, Patrizia and Aktaç, Nihat and Eilenberg, Jørgen and Jones, Graeme and Nash, David and Pedersen, Jes and Boomsma, Jacobus}, journal = {PLoS One}, number = {12}, publisher = {Public Library of Science}, title = {{The evolution of invasiveness in garden ants}}, doi = {10.1371/journal.pone.0003838}, volume = {3}, year = {2008}, } @article{3907, abstract = {Wingless males of the ant genus Cardiocondyla engage in fatal fighting for access to female sexual nestmates. Older, heavily sclerotized males are usually capable of eliminating all younger rivals, whose cuticle is still soft. In Cardiocondyla sp. A, this type of local mate competition (LMC) has turned the standard pattern of brood production of social insects upside down, in that mother queens in multi-queen colonies produce extremely long-lived sons very early in the life cycle of the colony. Here, we investigated the emergence pattern of sexuals in two species with LMC, in which males are much less long-lived. Queens of Cardiocondyla obscurior and Cardiocondyla minutior reared their first sons significantly earlier in multi-queen than in single-queen societies. In addition, first female sexuals also emerged earlier in multi-queen colonies, so that early males had mating opportunities. Hence, the timing of sexual production appears to be well predicted by evolutionary theory, in particular by local mate and queen–queen competition. }, author = {Suefuji, Masaki and Cremer, Sylvia and Oettler, Jan and Heinze, Jürgen}, journal = {Biology Letters}, number = {6}, pages = {670 -- 673}, publisher = {Royal Society, The}, title = {{Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants}}, doi = {10.1098/rsbl.2008.0355}, volume = {4}, year = {2008}, } @article{3939, abstract = {The priming of a T cell results from its physical interaction with a dendritic cell (DC) that presents the cognate antigenic peptide. The success rate of such interactions is extremely low, because the precursor frequency of a naive T cell recognizing a specific antigen is in the range of 1:10(5)-10(6). To make this principle practicable, encounter frequencies between DCs and T cells are maximized within lymph nodes (LNs) that are compact immunological projections of the peripheral tissue they drain. But LNs are more than passive meeting places for DCs that immigrated from the tissue and lymphocytes that recirculated via the blood. The microanatomy of the LN stroma actively organizes the cellular encounters by providing preformed migration tracks that create dynamic but highly ordered movement patterns. LN architecture further acts as a sophisticated filtration system that sieves the incoming interstitial fluid at different levels and guarantees that immunologically relevant antigens are loaded on DCs or B cells while inert substances are channeled back into the blood circulation. This review focuses on the non-hematopoietic infrastructure of the lymph node. We describe the association between fibroblastic reticular cell, conduit, DC, and T cell as the essential functional unit of the T-cell cortex.}, author = {Lämmermann, Tim and Sixt, Michael K}, journal = {Immunological Reviews}, number = {1}, pages = {26 -- 43}, publisher = {Wiley-Blackwell}, title = {{The microanatomy of T-cell responses}}, doi = {10.1111/j.1600-065X.2008.00592.x}, volume = {221}, year = {2008}, } @article{3940, abstract = {Until recently little information was available on the molecular details of the extracellular matrix (ECM) of secondary lymphoid tissues. There is now growing evidence that these ECMs are unique structures, combining characteristics of basement membranes and interstitial or fibrillar matrices, resulting in scaffolds that are strong and highly flexible and, in certain secondary lymphoid compartments, also forming conduit networks for rapid fluid transport. This review will address the structural characteristics of the ECM of the murine spleen and its potential role as an organizer of immune cell compartments, with reference to the lymph node where relevant.}, author = {Lokmic, Zerina and Lämmermann, Tim and Michael Sixt and Cardell, Susanna and Hallmann, Rupert and Sorokin, Lydia}, journal = {Seminars in Immunology}, number = {1}, pages = {4 -- 13}, publisher = {Academic Press}, title = {{The extracellular matrix of the spleen as a potential organizer of immune cell compartments}}, doi = {10.1016/j.smim.2007.12.009}, volume = {20}, year = {2008}, } @article{3941, abstract = {All metazoan cells carry transmembrane receptors of the integrin family, which couple the contractile force of the actomyosin cytoskeleton to the extracellular environment. In agreement with this principle, rapidly migrating leukocytes use integrin-mediated adhesion when moving over two-dimensional surfaces. As migration on two-dimensional substrates naturally overemphasizes the role of adhesion, the contribution of integrins during three-dimensional movement of leukocytes within tissues has remained controversial. We studied the interplay between adhesive, contractile and protrusive forces during interstitial leukocyte chemotaxis in vivo and in vitro. We ablated all integrin heterodimers from murine leukocytes, and show here that functional integrins do not contribute to migration in three-dimensional environments. Instead, these cells migrate by the sole force of actin-network expansion, which promotes protrusive flowing of the leading edge. Myosin II-dependent contraction is only required on passage through narrow gaps, where a squeezing contraction of the trailing edge propels the rigid nucleus.}, author = {Lämmermann, Tim and Bader, Bernhard L and Monkley, Susan J and Worbs, Tim and Wedlich-Söldner, Roland and Hirsch, Karin and Keller, Markus and Förster, Reinhold and Critchley, David R and Fässler, Reinhard and Michael Sixt}, journal = {Nature}, number = {7191}, pages = {51 -- 55}, publisher = {Nature Publishing Group}, title = {{Rapid leukocyte migration by integrin-independent flowing and squeezing}}, doi = {10.1038/nature06887}, volume = {453}, year = {2008}, } @article{3942, abstract = {Recent in vitro studies have suggested a role for sialylation in chemokine receptor binding to its ligand (Bannert, N., S. Craig, M. Farzan, D. Sogah, N.V. Santo, H. Choe, and J. Sodroski. 2001. J. Exp. Med. 194:1661-1673). This prompted us to investigate chemokine-induced leukocyte adhesion in inflamed cremaster muscle venules of alpha2,3 sialyltransferase (ST3Gal-IV)-deficient mice. We found a marked reduction in leukocyte adhesion to inflamed microvessels upon injection of the CXCR2 ligands CXCL1 (keratinocyte-derived chemokine) or CXCL8 (interleukin 8). In addition, extravasation of ST3Gal-IV(-/-) neutrophils into thioglycollate-pretreated peritoneal cavities was significantly decreased. In vitro assays revealed that CXCL8 binding to isolated ST3Gal-IV(-/-) neutrophils was markedly impaired. Furthermore, CXCL1-mediated adhesion of ST3Gal-IV(-/-) leukocytes at physiological flow conditions, as well as transendothelial migration of ST3Gal-IV(-/-) leukocytes in response to CXCL1, was significantly reduced. In human neutrophils, enzymatic desialylation decreased binding of CXCR2 ligands to the neutrophil surface and diminished neutrophil degranulation in response to these chemokines. In addition, binding of alpha2,3-linked sialic acid-specific Maackia amurensis lectin II to purified CXCR2 from neuraminidase-treated CXCR2-transfected HEK293 cells was markedly impaired. Collectively, we provide substantial evidence that sialylation by ST3Gal-IV significantly contributes to CXCR2-mediated leukocyte adhesion during inflammation in vivo.}, author = {Frommhold, David and Ludwig, Andreas and Bixel, M Gabriele and Zarbock, Alexander and Babushkina, Inna and Weissinger, Melitta and Cauwenberghs, Sandra and Ellies, Lesley G and Marth, Jamey D and Beck-Sickinger, Annette G and Michael Sixt and Lange-Sperandio, Bärbel and Zernecke, Alma and Brandt, Ernst and Weber, Christian and Vestweber, Dietmar and Ley, Klaus and Sperandio, Markus}, journal = {The Journal of Experimental Medicine}, number = {6}, pages = {1435 -- 1446}, publisher = {Rockefeller University Press}, title = {{Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation}}, doi = {10.1084/jem.20070846}, volume = {205}, year = {2008}, } @article{3943, abstract = {Neutrophil granulocytes form the body's first line of antibacterial defense, but they also contribute to tissue injury and noninfectious, chronic inflammation. Proteinase 3 (PR3) and neutrophil elastase (NE) are 2 abundant neutrophil serine proteases implicated in antimicrobial defense with overlapping and potentially redundant substrate specificity. Here, we unraveled a cooperative role for PR3 and NE in neutrophil activation and noninfectious inflammation in vivo, which we believe to be novel. Mice lacking both PR3 and NE demonstrated strongly diminished immune complex-mediated (IC-mediated) neutrophil infiltration in vivo as well as reduced activation of isolated neutrophils by ICs in vitro. In contrast, in mice lacking just NE, neutrophil recruitment to ICs was only marginally impaired. The defects in mice lacking both PR3 and NE were directly linked to the accumulation of antiinflammatory progranulin (PGRN). Both PR3 and NE cleaved PGRN in vitro and during neutrophil activation and inflammation in vivo. Local administration of recombinant PGRN potently inhibited neutrophilic inflammation in vivo, demonstrating that PGRN represents a crucial inflammation-suppressing mediator. We conclude that PR3 and NE enhance neutrophil-dependent inflammation by eliminating the local antiinflammatory activity of PGRN. Our results support the use of serine protease inhibitors as antiinflammatory agents.}, author = {Kessenbrock, Kai and Fröhlich, Leopold and Michael Sixt and Lämmermann, Tim and Pfister, Heiko and Bateman, Andrew and Belaaouaj, Azzaq and Ring, Johannes and Ollert, Markus and Fässler, Reinhard and Jenne, Dieter E}, journal = {The Journal of Clinical Investigation}, number = {7}, pages = {2438 -- 2447}, publisher = {American Society for Clinical Investigation}, title = {{Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin}}, doi = {10.1172/JCI34694}, volume = {118}, year = {2008}, } @article{3944, abstract = {Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches to visualize actin have several limitations. Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin (F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere with actin dynamics in vitro and in vivo and in its chemically modified peptide form allowed visualization of actin dynamics in nontransfectable cells.}, author = {Riedl, Julia and Crevenna, Alvaro H and Kessenbrock, Kai and Yu, Jerry Haochen and Neukirchen, Dorothee and Bista, Michal and Bradke, Frank and Jenne, Dieter and Holak, Tad A and Werb, Zena and Michael Sixt and Wedlich-Soldner, Roland}, journal = {Nature Methods}, number = {7}, pages = {605 -- 607}, publisher = {Nature Publishing Group}, title = {{Lifeact: a versatile marker to visualize F-actin}}, doi = {10.1038/nmeth.1220}, volume = {5}, year = {2008}, } @article{3945, abstract = {Langerhans cells and dermal dendritic cells migrate to the draining lymph nodes through dermal lymphatic vessels. They do so in the steady-state and under inflammatory conditions. Peripheral T cell tolerance or T cell priming, respectively, are the consequences of migration. The nature of dendritic cell-containing vessels was mostly defined by electron microscopy or by their lack of blood endothelial markers. Selective markers for murine lymph endothelium were hitherto rare or not available. Here, we utilised recently developed antibodies against the murine hyaluronan receptor, LYVE-1, to study the lymph vessel network in mouse skin in more detail. In hairless skin from the ears, lymph vessels were spread out in a horizontal plane. They formed anastomoses, and they possessed frequent blind endings that were occasionally open. Lymph vessels were wider than blood vessels, which were identified by their strong CD31 expression. In body wall skin LYVE-1 reactive vessels did not extend laterally but they dived straight down into the deeper dermis. There, they are connected to each other and formed a network similar to ear skin. The number and width of lymph vessels did not grossly change upon inflammatory stimuli such as skin explant culture or tape stripping. There were also no marked changes in caliber in response to the TLR 7/8 ligand Imiquimod. Double-labelling experiments of cultured skin showed that most of the strongly cell surface MHC II-expressing (i.e. activated) dendritic cells were confined to the lymph vessels. Langerin/CD207(+) cells within this population appeared later than dermal dendritic cells, i.e. langerin-negative cells. Comparable results were obtained after stimulating the skin in vivo with the TLR 7/8 ligand Imiquimod or by tape stripping. In untreated skin (i.e. steady state) a few MHC II(+) and Langerin/CD207(+) cells, presumably migrating skin dendritic cells including epidermal Langerhans cells, were consistently observed within the lymph vessels. The novel antibody reagents may serve as important tools to further study the dendritic cell traffic in the skin under physiological conditions as well as in conditions of adoptive dendritic cell transfer in immunotherapy.}, author = {Tripp, Christoph H and Haid, Bernhard and Flacher, Vincent and Michael Sixt and Peter, Hannes and Farkas, Julia and Gschwentner, Robert and Sorokin, Lydia and Romani, Nikolaus and Stoitzner, Patrizia}, journal = {Immunobiology}, number = {9-10}, pages = {715 -- 28}, publisher = {Elsevier}, title = {{The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1}}, doi = {10.1016/j.imbio.2008.07.025}, volume = {213}, year = {2008}, } @inbook{3969, abstract = {Persistent homology is an algebraic tool for measuring topological features of shapes and functions. It casts the multi-scale organization we frequently observe in nature into a mathematical formalism. Here we give a record of the short history of persistent homology and present its basic concepts. Besides the mathematics we focus on algorithms and mention the various connections to applications, including to biomolecules, biological networks, data analysis, and geometric modeling.}, author = {Herbert Edelsbrunner and Harer, John}, booktitle = {Surveys on Discrete and Computational Geometry: Twenty Years Later}, pages = {257 -- 282}, publisher = {American Mathematical Society}, title = {{Persistent homology - a survey}}, year = {2008}, } @article{3970, abstract = {While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.}, author = {Dequéant, Mary-Lee and Ahnert, Sebastian and Herbert Edelsbrunner and Fink, Thomas M and Glynn, Earl F and Hattem, Gaye and Kudlicki, Andrzej and Mileyko, Yuriy and Morton, Jason and Mushegian, Arcady R and Pachter, Lior and Rowicka, Maga and Shiu, Anne and Sturmfels, Bernd and Pourquie, Olivier}, journal = {PLoS One}, number = {8}, publisher = {Public Library of Science}, title = {{Comparison of pattern detection methods in microarray time series of the segmentation clock}}, doi = {10.1371/journal.pone.0002856}, volume = {3}, year = {2008}, } @article{3971, abstract = {The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimensional space. We show how to maintain the Reeb graph over time and compress the entire sequence of Reeb graphs into a single, partially persistent data structure, and augment this data structure with Betti numbers to describe the topology of level sets and with path seeds to assist in the fast extraction of level sets for visualization.}, author = {Herbert Edelsbrunner and Harer, John and Mascarenhas, Ajith and Pascucci, Valerio and Snoeyink, Jack}, journal = {Computational Geometry: Theory and Applications}, number = {3}, pages = {149 -- 166}, publisher = {Elsevier}, title = {{Time-varying Reeb graphs for continuous space-time data}}, doi = {10.1016/j.comgeo.2007.11.001}, volume = {41}, year = {2008}, } @inproceedings{3974, abstract = {Generalizing the concept of a Reeb graph, the Reeb space of a multivariate continuous mapping identifies points of the domain that belong to a common component of the preimage of a point in the range. We study the local and global structure of this space for generic, piecewise linear mappings on a combinatorial manifold.}, author = {Herbert Edelsbrunner and Harer, John and Amit Patel}, pages = {242 -- 250}, publisher = {ACM}, title = {{Reeb spaces of piecewise linear mappings}}, doi = {10.1145/1377676.1377720}, year = {2008}, }