[{"abstract":[{"text":"Organ formation requires the precise assembly of progenitor cells into a functional unit. Mechanical forces are likely to play a critical role in this process, but it is unclear how these are molecularly controlled during development. Here, we show that Wnt11/ Pk1a-mediated planar cell polarity (PCP) signalling coordinates formation of the zebrafish laterality organ (Kupffer’s vesicle, KV) by regulating adhesion forces between organ progenitor cells (the dorsal forerunner cells, DFCs).","lang":"eng"}],"language":[{"iso":"eng"}],"date_published":"2009-08-05T00:00:00Z","intvolume":"       126","status":"public","date_updated":"2021-01-12T07:54:58Z","date_created":"2018-12-11T12:07:19Z","publication_status":"published","author":[{"full_name":"Oteíza, Pablo","first_name":"Pablo","last_name":"Oteíza"},{"full_name":"Köppen, Mathias","first_name":"Mathias","last_name":"Köppen"},{"last_name":"Krieg","first_name":"Michael","full_name":"Krieg, Michael"},{"last_name":"Preibisch","first_name":"Steffen","full_name":"Preibisch, Steffen"},{"last_name":"Haertel","full_name":"Haertel, Steffen","first_name":"Steffen"},{"last_name":"Müller","full_name":"Müller, Daniel","first_name":"Daniel"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"},{"last_name":"Concha","first_name":"Miguel","full_name":"Concha, Miguel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Oteíza, Pablo, Mathias Köppen, Michael Krieg, Steffen Preibisch, Steffen Haertel, Daniel Müller, Carl-Philipp J Heisenberg, and Miguel Concha. “Wnt11/Pk1a-Mediated Planar Cell Polarity Signalling Orchestrates Epithelial Organ Morphogenesis by Regulating N-Cadherin Dependent Cell Adhesion Forces.” <i>Mechanisms of Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">https://doi.org/10.1016/j.mod.2009.06.098</a>.","ama":"Oteíza P, Köppen M, Krieg M, et al. Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces. <i>Mechanisms of Development</i>. 2009;126(Supplement 1):S80-S80. doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">10.1016/j.mod.2009.06.098</a>","ista":"Oteíza P, Köppen M, Krieg M, Preibisch S, Haertel S, Müller D, Heisenberg C-PJ, Concha M. 2009. Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces. Mechanisms of Development. 126(Supplement 1), S80–S80.","apa":"Oteíza, P., Köppen, M., Krieg, M., Preibisch, S., Haertel, S., Müller, D., … Concha, M. (2009). Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">https://doi.org/10.1016/j.mod.2009.06.098</a>","mla":"Oteíza, Pablo, et al. “Wnt11/Pk1a-Mediated Planar Cell Polarity Signalling Orchestrates Epithelial Organ Morphogenesis by Regulating N-Cadherin Dependent Cell Adhesion Forces.” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1, Elsevier, 2009, pp. S80–S80, doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">10.1016/j.mod.2009.06.098</a>.","ieee":"P. Oteíza <i>et al.</i>, “Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces,” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1. Elsevier, pp. S80–S80, 2009.","short":"P. Oteíza, M. Köppen, M. Krieg, S. Preibisch, S. Haertel, D. Müller, C.-P.J. Heisenberg, M. Concha, Mechanisms of Development 126 (2009) S80–S80."},"_id":"4162","issue":"Supplement 1","year":"2009","oa_version":"None","volume":126,"day":"05","publisher":"Elsevier","doi":"10.1016/j.mod.2009.06.098","page":"S80 - S80","type":"journal_article","title":"Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces","publication":"Mechanisms of Development","article_processing_charge":"No","extern":"1","month":"08","publist_id":"1957"},{"intvolume":"        10","abstract":[{"text":"The tissues of a developing embryo are simultaneously patterned, moved and differentiated according to an exchange of information between their constituent cells. We argue that these complex self-organizing phenomena can only be fully understood with quantitative mathematical frameworks that allow specific hypotheses to be formulated and tested. The quantitative and dynamic imaging of growing embryos at the molecular, cellular and tissue level is the key experimental advance required to achieve this interaction between theory and experiment. Here we describe how mathematical modelling has become an invaluable method to integrate quantitative biological information across temporal and spatial scales, serving to connect the activity of regulatory molecules with the morphological development of organisms.","lang":"eng"}],"date_published":"2009-08-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2021-01-12T07:54:59Z","publication_status":"published","date_created":"2018-12-11T12:07:20Z","author":[{"last_name":"Oates","full_name":"Oates, Andrew","first_name":"Andrew"},{"last_name":"Gorfinkiel","full_name":"Gorfinkiel, Nicole","first_name":"Nicole"},{"full_name":"Gonzalez Gaitan, Marcos","first_name":"Marcos","last_name":"Gonzalez Gaitan"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2009","_id":"4165","citation":{"ieee":"A. Oates, N. Gorfinkiel, M. Gonzalez Gaitan, and C.-P. J. Heisenberg, “Quantitative approaches in developmental biology,” <i>Nature Reviews Genetics</i>, vol. 10, no. 8. Nature Publishing Group, pp. 517–530, 2009.","mla":"Oates, Andrew, et al. “Quantitative Approaches in Developmental Biology.” <i>Nature Reviews Genetics</i>, vol. 10, no. 8, Nature Publishing Group, 2009, pp. 517–30, doi:<a href=\"https://doi.org/10.1038/nrg2548\">10.1038/nrg2548</a>.","apa":"Oates, A., Gorfinkiel, N., Gonzalez Gaitan, M., &#38; Heisenberg, C.-P. J. (2009). Quantitative approaches in developmental biology. <i>Nature Reviews Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrg2548\">https://doi.org/10.1038/nrg2548</a>","ista":"Oates A, Gorfinkiel N, Gonzalez Gaitan M, Heisenberg C-PJ. 2009. Quantitative approaches in developmental biology. Nature Reviews Genetics. 10(8), 517–530.","short":"A. Oates, N. Gorfinkiel, M. Gonzalez Gaitan, C.-P.J. Heisenberg, Nature Reviews Genetics 10 (2009) 517–530.","chicago":"Oates, Andrew, Nicole Gorfinkiel, Marcos Gonzalez Gaitan, and Carl-Philipp J Heisenberg. “Quantitative Approaches in Developmental Biology.” <i>Nature Reviews Genetics</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nrg2548\">https://doi.org/10.1038/nrg2548</a>.","ama":"Oates A, Gorfinkiel N, Gonzalez Gaitan M, Heisenberg C-PJ. Quantitative approaches in developmental biology. <i>Nature Reviews Genetics</i>. 2009;10(8):517-530. doi:<a href=\"https://doi.org/10.1038/nrg2548\">10.1038/nrg2548</a>"},"issue":"8","volume":10,"oa_version":"None","page":"517 - 530","publisher":"Nature Publishing Group","day":"01","doi":"10.1038/nrg2548","title":"Quantitative approaches in developmental biology","type":"journal_article","publication":"Nature Reviews Genetics","article_processing_charge":"No","extern":"1","publist_id":"1953","month":"08"},{"article_processing_charge":"No","publication":"Mechanisms of Development","month":"08","publist_id":"1927","extern":"1","oa_version":"None","volume":126,"_id":"4192","citation":{"ieee":"M. Kai, N. Buchan, C.-P. J. Heisenberg, and M. Tada, “Regulation of planar cell polarity signalling by the prenylation pathway,” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1. Elsevier, pp. S132–S132, 2009.","mla":"Kai, Masatake, et al. “Regulation of Planar Cell Polarity Signalling by the Prenylation Pathway.” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1, Elsevier, 2009, pp. S132–S132, doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">10.1016/j.mod.2009.06.269</a>.","apa":"Kai, M., Buchan, N., Heisenberg, C.-P. J., &#38; Tada, M. (2009). Regulation of planar cell polarity signalling by the prenylation pathway. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">https://doi.org/10.1016/j.mod.2009.06.269</a>","ista":"Kai M, Buchan N, Heisenberg C-PJ, Tada M. 2009. Regulation of planar cell polarity signalling by the prenylation pathway. Mechanisms of Development. 126(Supplement 1), S132–S132.","short":"M. Kai, N. Buchan, C.-P.J. Heisenberg, M. Tada, Mechanisms of Development 126 (2009) S132–S132.","chicago":"Kai, Masatake, Nina Buchan, Carl-Philipp J Heisenberg, and Masazumi Tada. “Regulation of Planar Cell Polarity Signalling by the Prenylation Pathway.” <i>Mechanisms of Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">https://doi.org/10.1016/j.mod.2009.06.269</a>.","ama":"Kai M, Buchan N, Heisenberg C-PJ, Tada M. Regulation of planar cell polarity signalling by the prenylation pathway. <i>Mechanisms of Development</i>. 2009;126(Supplement 1):S132-S132. doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">10.1016/j.mod.2009.06.269</a>"},"issue":"Supplement 1","year":"2009","type":"journal_article","title":"Regulation of planar cell polarity signalling by the prenylation pathway","publisher":"Elsevier","doi":"10.1016/j.mod.2009.06.269","day":"05","page":"S132 - S132","author":[{"full_name":"Kai, Masatake","first_name":"Masatake","last_name":"Kai"},{"last_name":"Buchan","full_name":"Buchan, Nina","first_name":"Nina"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tada, Masazumi","first_name":"Masazumi","last_name":"Tada"}],"publication_status":"published","date_created":"2018-12-11T12:07:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","abstract":[{"text":"During vertebrate gastrulation, the body axis is established by a variety of co-ordinated and directed movements of cells. One of these movements is convergence and extension (CE), which is regulated by a non-canonical Wnt/planar cell polarity (PCP) pathway. From our forward genetic screen, we have identified 3-hydroxy-3-methyglutaryl-coenzyme A reductase 1b (hmgcr1b) gene as a dominant enhancer of the silberblick (slb)/wnt11 CE phenotype. hmgcr1b mutant embryos exhibit only very mild CE phenotype during gastrulation while showing a thicker yolk extension at pharyngula stages. Notably, abrogation of hmgcr1b also enhances the CE defects of other core PCP mutants/morphants. The prenylation pathway is one of branches downstream of HMGCR, and has been implicated for lipid modification at the C-terminus of proteins. To test the possibility that the prenylation pathway regulates activities of the PCP pathway, we abrogated farnesyl transferase (FT) or geranylgeranyl transferase (GGT) function using morpholinos on PCP mutant/morphant backgrounds. Consistent with the notion that FT preferentially performs lipid modification on to proteins with the CAAX motif including the core PCP protein Prickle (Pk), abrogation of FT, but not GGT, enhances the pk1a or pk1b morphant CE phenotype, suggesting the specif icity for targets of the prenylation enzymes.\r\n","lang":"eng"}],"language":[{"iso":"eng"}],"date_published":"2009-08-05T00:00:00Z","intvolume":"       126","date_updated":"2021-01-12T07:55:11Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:07:35Z","publication_status":"published","author":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:55:17Z","abstract":[{"lang":"eng","text":"Dorsal closure (DC), the closure of a hole in the dorsal epidermis of Drosophila embryos by the joining of opposing epithelial cell sheets, has been used as a model process to study the molecular and cellular mechanisms underlying epithelial spreading and wound healing. Recent studies have provided novel insights into how different tissues function cooperatively in this process. Specifically, they demonstrate a critical function of the epidermis surrounding the hole in modulating the behavior of the amnioserosa cells inside. These findings shed light not only on the mechanisms by which the behavior of different tissues is coordinated during DC, but also on the general mechanisms by which tissues interact to trigger global morphogenesis, an essential but yet poorly explored aspect of embryogenesis."}],"language":[{"iso":"eng"}],"date_published":"2009-12-01T00:00:00Z","intvolume":"        31","status":"public","extern":"1","month":"12","publist_id":"1911","publication":"Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology","article_processing_charge":"No","publisher":"Wiley-Blackwell","doi":"10.1002/bies.200900109","day":"01","page":"1284 - 1287","type":"journal_article","title":"Dorsal closure in Drosophila: cells cannot get out of the tight spot","issue":"12","_id":"4206","citation":{"short":"C.-P.J. Heisenberg, Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology 31 (2009) 1284–1287.","ieee":"C.-P. J. Heisenberg, “Dorsal closure in Drosophila: cells cannot get out of the tight spot,” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 31, no. 12. Wiley-Blackwell, pp. 1284–1287, 2009.","apa":"Heisenberg, C.-P. J. (2009). Dorsal closure in Drosophila: cells cannot get out of the tight spot. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/bies.200900109\">https://doi.org/10.1002/bies.200900109</a>","mla":"Heisenberg, Carl-Philipp J. “Dorsal Closure in Drosophila: Cells Cannot Get out of the Tight Spot.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 31, no. 12, Wiley-Blackwell, 2009, pp. 1284–87, doi:<a href=\"https://doi.org/10.1002/bies.200900109\">10.1002/bies.200900109</a>.","ista":"Heisenberg C-PJ. 2009. Dorsal closure in Drosophila: cells cannot get out of the tight spot. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 31(12), 1284–1287.","ama":"Heisenberg C-PJ. Dorsal closure in Drosophila: cells cannot get out of the tight spot. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. 2009;31(12):1284-1287. doi:<a href=\"https://doi.org/10.1002/bies.200900109\">10.1002/bies.200900109</a>","chicago":"Heisenberg, Carl-Philipp J. “Dorsal Closure in Drosophila: Cells Cannot Get out of the Tight Spot.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell, 2009. <a href=\"https://doi.org/10.1002/bies.200900109\">https://doi.org/10.1002/bies.200900109</a>."},"year":"2009","oa_version":"None","volume":31},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Carvalho","full_name":"Carvalho, Lara","first_name":"Lara"},{"first_name":"Jan","full_name":"Stuehmer, Jan","last_name":"Stuehmer"},{"last_name":"Bois","full_name":"Bois, Justin","first_name":"Justin"},{"full_name":"Kalaidzidis, Yannis","first_name":"Yannis","last_name":"Kalaidzidis"},{"full_name":"Lecaudey, Virginie","first_name":"Virginie","last_name":"Lecaudey"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"publication_status":"published","date_created":"2018-12-11T12:07:39Z","date_updated":"2021-01-12T07:55:22Z","status":"public","intvolume":"       136","abstract":[{"text":"Nuclear movements play an essential role in metazoan development. Although the intracellular transport mechanisms underlying nuclear movements have been studied in detail, relatively little is known about signals from surrounding cells and tissues controlling these movements. Here, we show that, in gastrulating zebrafish embryos, convergence movements of nuclei within the yolk syncytial layer (YSL) are guided by mesoderm and endoderm progenitors migrating along the surface of the yolk towards the dorsal side of the developing gastrula. Progenitor cells direct the convergence movements of internal yolk syncytial nuclei (iYSN) by modulating cortical flow within the YSL in which the iYSN are entrained. The effect of mesoderm and endoderm progenitors on the convergence movement of iYSN depends on the expression of E-cadherin, indicating that adhesive contact between the cells and the YSL is required for the mesendoderm-modulated YSL cortical flow mediating nuclear convergence. In summary, our data reveal a crucial function for cortical flow in the coordination of syncytial nuclear movements with surrounding cells and tissues during zebrafish gastrulation.","lang":"eng"}],"date_published":"2009-04-15T00:00:00Z","language":[{"iso":"eng"}],"publist_id":"1901","month":"04","extern":"1","article_processing_charge":"No","publication":"Development","title":"Control of convergent yolk syncytial layer nuclear movement in zebrafish","type":"journal_article","page":"1305 - 1315","publisher":"Company of Biologists","day":"15","doi":"10.1242/dev.026922","volume":136,"oa_version":"None","year":"2009","issue":"8","_id":"4217","citation":{"ieee":"L. Carvalho, J. Stuehmer, J. Bois, Y. Kalaidzidis, V. Lecaudey, and C.-P. J. Heisenberg, “Control of convergent yolk syncytial layer nuclear movement in zebrafish,” <i>Development</i>, vol. 136, no. 8. Company of Biologists, pp. 1305–1315, 2009.","ista":"Carvalho L, Stuehmer J, Bois J, Kalaidzidis Y, Lecaudey V, Heisenberg C-PJ. 2009. Control of convergent yolk syncytial layer nuclear movement in zebrafish. Development. 136(8), 1305–1315.","apa":"Carvalho, L., Stuehmer, J., Bois, J., Kalaidzidis, Y., Lecaudey, V., &#38; Heisenberg, C.-P. J. (2009). Control of convergent yolk syncytial layer nuclear movement in zebrafish. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.026922\">https://doi.org/10.1242/dev.026922</a>","mla":"Carvalho, Lara, et al. “Control of Convergent Yolk Syncytial Layer Nuclear Movement in Zebrafish.” <i>Development</i>, vol. 136, no. 8, Company of Biologists, 2009, pp. 1305–15, doi:<a href=\"https://doi.org/10.1242/dev.026922\">10.1242/dev.026922</a>.","short":"L. Carvalho, J. Stuehmer, J. Bois, Y. Kalaidzidis, V. Lecaudey, C.-P.J. Heisenberg, Development 136 (2009) 1305–1315.","chicago":"Carvalho, Lara, Jan Stuehmer, Justin Bois, Yannis Kalaidzidis, Virginie Lecaudey, and Carl-Philipp J Heisenberg. “Control of Convergent Yolk Syncytial Layer Nuclear Movement in Zebrafish.” <i>Development</i>. Company of Biologists, 2009. <a href=\"https://doi.org/10.1242/dev.026922\">https://doi.org/10.1242/dev.026922</a>.","ama":"Carvalho L, Stuehmer J, Bois J, Kalaidzidis Y, Lecaudey V, Heisenberg C-PJ. Control of convergent yolk syncytial layer nuclear movement in zebrafish. <i>Development</i>. 2009;136(8):1305-1315. doi:<a href=\"https://doi.org/10.1242/dev.026922\">10.1242/dev.026922</a>"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:07:41Z","publication_status":"published","author":[{"first_name":"Jonathan","full_name":"Swoboda, Jonathan","last_name":"Swoboda"},{"last_name":"Meredith","first_name":"Timothy","full_name":"Meredith, Timothy"},{"full_name":"Campbell, Jennifer","first_name":"Jennifer","last_name":"Campbell"},{"full_name":"Brown, Stephanie","first_name":"Stephanie","last_name":"Brown"},{"full_name":"Suzuki, Takashi","first_name":"Takashi","last_name":"Suzuki"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"},{"first_name":"Amy","full_name":"Malhowski, Amy","last_name":"Malhowski"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"},{"full_name":"Gilmore, Michael","first_name":"Michael","last_name":"Gilmore"},{"last_name":"Walker","first_name":"Suzanne","full_name":"Walker, Suzanne"}],"date_updated":"2021-01-12T07:55:25Z","date_published":"2009-08-18T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"text":"Both Gram-positive and Gram-negative bacteria contain bactoprenol-dependent biosynthetic pathways expressing non-essential cell surface polysaccharides that function as virulence factors. Although these polymers are not required for bacterial viability in vitro, genes in many of the biosynthetic pathways are conditionally essential: they cannot be deleted except in strains incapable of initiating polymer synthesis. We report a cell-based, pathway-specific strategy to screen for small molecule inhibitors of conditionally essential enzymes. The screen identifies molecules that prevent the growth of a wildtype bacterial strain but do not affect the growth of a mutant strain incapable of initiating polymer synthesis. We have applied this approach to discover inhibitors of wall teichoic acid (WTA) biosynthesis in Staphylococcus aureus. WTAs are anionic cell surface polysaccharides required for host colonization that have been suggested as targets for new antimicrobials. We have identified a small molecule, 7-chloro-N,N-diethyl-3-(phenylsulfonyl)-[1,2,3]triazolo[1,5-a]quinolin-5-amine (1835F03), that inhibits the growth of a panel of S. aureus strains (MIC = 1−3 μg mL−1), including clinical methicillin-resistant S. aureus (MRSA) isolates. Using a combination of biochemistry and genetics, we have identified the molecular target as TarG, the transmembrane component of the ABC transporter that exports WTAs to the cell surface. We also show that preventing the completion of WTA biosynthesis once it has been initiated triggers growth arrest. The discovery of 1835F03 validates our chemical genetics strategy for identifying inhibitors of conditionally essential enzymes, and the strategy should be applicable to many other bactoprenol-dependent biosynthetic pathways in the pursuit of novel antibacterials and probes of bacterial stress responses.","lang":"eng"}],"intvolume":"         4","status":"public","main_file_link":[{"url":"10.1021/cb900151k [doi]"}],"extern":"1","publist_id":"1894","month":"08","publication":"ACS Chemical Biology","article_processing_charge":"No","doi":"10.1021/cb900151k","day":"18","publisher":"American Chemical Society","page":"875 - 883","type":"journal_article","title":"Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus","_id":"4223","issue":"10","citation":{"ama":"Swoboda J, Meredith T, Campbell J, et al. Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. <i>ACS Chemical Biology</i>. 2009;4(10):875-883. doi:<a href=\"https://doi.org/10.1021/cb900151k\">10.1021/cb900151k</a>","chicago":"Swoboda, Jonathan, Timothy Meredith, Jennifer Campbell, Stephanie Brown, Takashi Suzuki, Mark Tobias Bollenbach, Amy Malhowski, Roy Kishony, Michael Gilmore, and Suzanne Walker. “Discovery of a Small Molecule That Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus Aureus.” <i>ACS Chemical Biology</i>. American Chemical Society, 2009. <a href=\"https://doi.org/10.1021/cb900151k\">https://doi.org/10.1021/cb900151k</a>.","short":"J. Swoboda, T. Meredith, J. Campbell, S. Brown, T. Suzuki, M.T. Bollenbach, A. Malhowski, R. Kishony, M. Gilmore, S. Walker, ACS Chemical Biology 4 (2009) 875–883.","ieee":"J. Swoboda <i>et al.</i>, “Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus,” <i>ACS Chemical Biology</i>, vol. 4, no. 10. American Chemical Society, pp. 875–883, 2009.","mla":"Swoboda, Jonathan, et al. “Discovery of a Small Molecule That Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus Aureus.” <i>ACS Chemical Biology</i>, vol. 4, no. 10, American Chemical Society, 2009, pp. 875–83, doi:<a href=\"https://doi.org/10.1021/cb900151k\">10.1021/cb900151k</a>.","ista":"Swoboda J, Meredith T, Campbell J, Brown S, Suzuki T, Bollenbach MT, Malhowski A, Kishony R, Gilmore M, Walker S. 2009. Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. ACS Chemical Biology. 4(10), 875–883.","apa":"Swoboda, J., Meredith, T., Campbell, J., Brown, S., Suzuki, T., Bollenbach, M. T., … Walker, S. (2009). Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. <i>ACS Chemical Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/cb900151k\">https://doi.org/10.1021/cb900151k</a>"},"year":"2009","oa_version":"None","volume":4},{"type":"journal_article","title":"Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions","day":"01","publisher":"Cell Press","doi":"10.1016/j.cell.2009.10.025","page":"707 - 718","volume":139,"_id":"4228","citation":{"ama":"Bollenbach T, Quan S, Chait RP, Kishony R. Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. <i>Cell</i>. 2009;139(4):707-718. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">10.1016/j.cell.2009.10.025</a>","chicago":"Bollenbach, Tobias, Selwyn Quan, Remy P Chait, and Roy Kishony. “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions.” <i>Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">https://doi.org/10.1016/j.cell.2009.10.025</a>.","short":"T. Bollenbach, S. Quan, R.P. Chait, R. Kishony, Cell 139 (2009) 707–718.","apa":"Bollenbach, T., Quan, S., Chait, R. P., &#38; Kishony, R. (2009). Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">https://doi.org/10.1016/j.cell.2009.10.025</a>","ista":"Bollenbach T, Quan S, Chait RP, Kishony R. 2009. Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. Cell. 139(4), 707–718.","mla":"Bollenbach, Tobias, et al. “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions.” <i>Cell</i>, vol. 139, no. 4, Cell Press, 2009, pp. 707–18, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">10.1016/j.cell.2009.10.025</a>.","ieee":"T. Bollenbach, S. Quan, R. P. Chait, and R. Kishony, “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions,” <i>Cell</i>, vol. 139, no. 4. Cell Press, pp. 707–718, 2009."},"issue":"4","year":"2009","month":"01","publist_id":"1890","extern":1,"publication":"Cell","date_updated":"2021-01-12T07:55:27Z","status":"public","abstract":[{"text":"Suppressive drug interactions, in which one antibiotic can actually help bacterial cells to grow faster in the presence of another, occur between protein and DNA synthesis inhibitors. Here, we show that this suppression results from nonoptimal regulation of ribosomal genes in the presence of DNA stress. Using GFP-tagged transcription reporters in Escherichia coli, we find that ribosomal genes are not directly regulated by DNA stress, leading to an imbalance between cellular DNA and protein content. To test whether ribosomal gene expression under DNA stress is nonoptimal for growth rate, we sequentially deleted up to six of the seven ribosomal RNA operons. These synthetic manipulations of ribosomal gene expression correct the protein-DNA imbalance, lead to improved survival and growth, and completely remove the suppressive drug interaction. A simple mathematical model explains the nonoptimal regulation in different nutrient environments. These results reveal the genetic mechanism underlying an important class of suppressive drug interactions.","lang":"eng"}],"date_published":"2009-01-01T00:00:00Z","quality_controlled":0,"intvolume":"       139","author":[{"full_name":"Bollenbach, Tobias","first_name":"Tobias","last_name":"Bollenbach"},{"first_name":"Selwyn","full_name":"Quan, Selwyn","last_name":"Quan"},{"orcid":"0000-0003-0876-3187","last_name":"Chait","full_name":"Remy Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"publication_status":"published","date_created":"2018-12-11T12:07:43Z"},{"article_processing_charge":"No","month":"03","oa_version":"None","year":"2009","_id":"4231","issue":"3","title":"Statistical mechanics and the evolution of polygenic quantitative traits","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"full_name":"De Vladar, Harold","first_name":"Harold","last_name":"De Vladar"}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"status":"public","date_published":"2009-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ &gt; 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection."}],"scopus_import":"1","acknowledgement":"N.B. was supported by the Engineering and Physical Sciences Research Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to Ellen Baake for helping to initiate this project and for her comments on this manuscript. We also thank Michael Turelli for his comments on the manuscript and I. Pen for discussions and support in this project. This project was a result of a collaboration supported by the European Science Foundation grant “Integrating population genetics and conservation biology.” ","publication":"Genetics","publist_id":"1882","volume":181,"citation":{"ama":"Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. 2009;181(3):997-1011. doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>","chicago":"Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>.","short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.","ieee":"N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of polygenic quantitative traits,” <i>Genetics</i>, vol. 181, no. 3. Genetics Society of America, pp. 997–1011, 2009.","ista":"Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011.","apa":"Barton, N. H., &#38; De Vladar, H. (2009). Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>","mla":"Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>, vol. 181, no. 3, Genetics Society of America, 2009, pp. 997–1011, doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>."},"type":"journal_article","page":"997 - 1011","day":"01","publisher":"Genetics Society of America","doi":"10.1534/genetics.108.099309","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T12:07:44Z","intvolume":"       181","language":[{"iso":"eng"}],"quality_controlled":"1","external_id":{"isi":["000270213500018"]},"corr_author":"1","date_updated":"2025-09-30T09:52:35Z"},{"date_updated":"2025-07-02T06:46:07Z","status":"public","language":[{"iso":"eng"}],"date_published":"2009-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Vladar","orcid":"0000-0002-5985-7653","first_name":"Harold","full_name":"Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:07:44Z","publication_status":"published","title":"Stochasticity and Variability in the dynamics and genetics of populations","type":"dissertation","day":"01","publisher":"Faculty of mathematical and natural sciences, University of Groningen","oa_version":"None","year":"2009","_id":"4232","citation":{"ama":"de Vladar H. Stochasticity and Variability in the dynamics and genetics of populations. 2009.","chicago":"Vladar, Harold de. “Stochasticity and Variability in the Dynamics and Genetics of Populations.” Faculty of mathematical and natural sciences, University of Groningen, 2009.","short":"H. de Vladar, Stochasticity and Variability in the Dynamics and Genetics of Populations, Faculty of mathematical and natural sciences, University of Groningen, 2009.","apa":"de Vladar, H. (2009). <i>Stochasticity and Variability in the dynamics and genetics of populations</i>. Faculty of mathematical and natural sciences, University of Groningen.","mla":"de Vladar, Harold. <i>Stochasticity and Variability in the Dynamics and Genetics of Populations</i>. Faculty of mathematical and natural sciences, University of Groningen, 2009.","ista":"de Vladar H. 2009. Stochasticity and Variability in the dynamics and genetics of populations. Faculty of mathematical and natural sciences, University of Groningen.","ieee":"H. de Vladar, “Stochasticity and Variability in the dynamics and genetics of populations,” Faculty of mathematical and natural sciences, University of Groningen, 2009."},"publist_id":"1883","month":"01","extern":"1","article_processing_charge":"No"},{"external_id":{"isi":["000265145800006"]},"corr_author":"1","date_updated":"2025-09-30T09:52:11Z","has_accepted_license":"1","intvolume":"        63","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-11T12:07:48Z","type":"journal_article","page":"1171 - 1190","pubrep_id":"551","publisher":"Wiley","doi":"10.1111/j.1558-5646.2009.00622.x","day":"01","volume":63,"citation":{"chicago":"Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>.","ama":"Barton NH, De Cara M. The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. 2009;63(5):1171-1190. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>","mla":"Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5, Wiley, 2009, pp. 1171–90, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>.","apa":"Barton, N. H., &#38; De Cara, M. (2009). The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>","ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","ieee":"N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009.","short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190."},"publist_id":"1866","publication":"Evolution; International Journal of Organic Evolution","acknowledgement":"This work was supported by a Royal Society/Wolfson Research Merit award, and by a grant from the Natural Environment Research Council.\r\nWe are very grateful for insightful comments from S. P. Otto, and for helpful suggestions from the referees and the Associate Editor, Maria Servedio.","ddc":["570"],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation."}],"date_published":"2009-05-01T00:00:00Z","oa":1,"file":[{"content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:11:46Z","creator":"system","file_id":"4903","relation":"main_file","file_size":720913,"checksum":"1920d2e25ef335833764256c1a47bbfb","date_updated":"2020-07-14T12:46:25Z","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf"},{"content_type":"application/pdf","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:11:47Z","file_id":"4904","file_size":290160,"relation":"main_file","checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","date_updated":"2020-07-14T12:46:25Z","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"De Cara","full_name":"De Cara, Maria","first_name":"Maria"}],"publication_status":"published","title":"The evolution of strong reproductive isolation","oa_version":"Submitted Version","year":"2009","issue":"5","_id":"4242","month":"05","article_processing_charge":"No"},{"type":"journal_article","title":"Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence","day":"01","doi":"10.1534/genetics.107.085225","publisher":"Genetics Society of America","page":"225 - 234","volume":181,"_id":"4357","citation":{"chicago":"Bollback, Jonathan P, and John Huelsenbeck. “Parallel Genetic Evolution within and between Bacteriophage Species of Varying Degrees of Divergence.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.107.085225\">https://doi.org/10.1534/genetics.107.085225</a>.","ama":"Bollback JP, Huelsenbeck J. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. <i>Genetics</i>. 2009;181(1):225-234. doi:<a href=\"https://doi.org/10.1534/genetics.107.085225\">10.1534/genetics.107.085225</a>","ieee":"J. P. Bollback and J. Huelsenbeck, “Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence,” <i>Genetics</i>, vol. 181, no. 1. Genetics Society of America, pp. 225–234, 2009.","ista":"Bollback JP, Huelsenbeck J. 2009. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics. 181(1), 225–234.","apa":"Bollback, J. P., &#38; Huelsenbeck, J. (2009). Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.107.085225\">https://doi.org/10.1534/genetics.107.085225</a>","mla":"Bollback, Jonathan P., and John Huelsenbeck. “Parallel Genetic Evolution within and between Bacteriophage Species of Varying Degrees of Divergence.” <i>Genetics</i>, vol. 181, no. 1, Genetics Society of America, 2009, pp. 225–34, doi:<a href=\"https://doi.org/10.1534/genetics.107.085225\">10.1534/genetics.107.085225</a>.","short":"J.P. Bollback, J. Huelsenbeck, Genetics 181 (2009) 225–234."},"issue":"1","year":"2009","month":"01","publist_id":"1101","extern":1,"publication":"Genetics","date_updated":"2021-01-12T07:56:22Z","status":"public","date_published":"2009-01-01T00:00:00Z","quality_controlled":0,"abstract":[{"lang":"eng","text":"Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions-if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives-which likely overlap more in the details of their adaptive solutions-will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence."}],"intvolume":"       181","author":[{"last_name":"Bollback","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Jonathan Bollback"},{"last_name":"Huelsenbeck","first_name":"John","full_name":"Huelsenbeck, John P"}],"date_created":"2018-12-11T12:08:26Z","publication_status":"published"},{"status":"public","date_published":"2009-01-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","abstract":[{"text":"Motivated by applications in software verification, we explore automated reasoning about the non-disjoint combination of theories of infinitely many finite structures, where the theories share set variables and set operations. We prove a combination theorem and apply it to show the decidability of the satisfiability problem for a class of formulas obtained by applying propositional connectives to formulas belonging to: 1) Boolean Algebra with Presburger Arithmetic (with quantifiers over sets and integers), 2) weak monadic second-order logic over trees (with monadic second-order quantifiers), 3) two-variable logic with counting quantifiers (ranging over elements), 4) the Bernays-Schönfinkel-Ramsey class of first-order logic with equality (with ∃ * ∀ * quantifier prefix), and 5) the quantifier-free logic of multisets with cardinality constraints.","lang":"eng"}],"intvolume":"      5749","conference":{"start_date":"2009-09-16","end_date":"2009-09-18","name":"FroCoS: Frontiers of Combining Systems","location":"Trento, Italy"},"date_updated":"2025-07-02T06:21:09Z","author":[{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas"},{"first_name":"Ruzica","full_name":"Piskac, Ruzica","last_name":"Piskac"},{"full_name":"Kuncak, Viktor","first_name":"Viktor","last_name":"Kuncak"}],"date_created":"2018-12-11T12:08:27Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":5749,"citation":{"ama":"Wies T, Piskac R, Kuncak V. Combining theories with shared set operations. In: <i>7th International Symposium on Frontiers of Combining Systems</i>. Vol 5749. Springer; 2009:366-382. doi:<a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">10.1007/978-3-642-04222-5_23</a>","chicago":"Wies, Thomas, Ruzica Piskac, and Viktor Kuncak. “Combining Theories with Shared Set Operations.” In <i>7th International Symposium on Frontiers of Combining Systems</i>, 5749:366–82. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">https://doi.org/10.1007/978-3-642-04222-5_23</a>.","short":"T. Wies, R. Piskac, V. Kuncak, in:, 7th International Symposium on Frontiers of Combining Systems, Springer, 2009, pp. 366–382.","ieee":"T. Wies, R. Piskac, and V. Kuncak, “Combining theories with shared set operations,” in <i>7th International Symposium on Frontiers of Combining Systems</i>, Trento, Italy, 2009, vol. 5749, pp. 366–382.","ista":"Wies T, Piskac R, Kuncak V. 2009. Combining theories with shared set operations. 7th International Symposium on Frontiers of Combining Systems. FroCoS: Frontiers of Combining Systems, LNCS, vol. 5749, 366–382.","apa":"Wies, T., Piskac, R., &#38; Kuncak, V. (2009). Combining theories with shared set operations. In <i>7th International Symposium on Frontiers of Combining Systems</i> (Vol. 5749, pp. 366–382). Trento, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">https://doi.org/10.1007/978-3-642-04222-5_23</a>","mla":"Wies, Thomas, et al. “Combining Theories with Shared Set Operations.” <i>7th International Symposium on Frontiers of Combining Systems</i>, vol. 5749, Springer, 2009, pp. 366–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">10.1007/978-3-642-04222-5_23</a>."},"_id":"4360","year":"2009","type":"conference","title":"Combining theories with shared set operations","doi":"10.1007/978-3-642-04222-5_23","day":"01","publisher":"Springer","page":"366 - 382","article_processing_charge":"No","alternative_title":["LNCS"],"publication":"7th International Symposium on Frontiers of Combining Systems","publist_id":"1098","month":"01","extern":"1"},{"year":"2009","citation":{"chicago":"Singh, Vasu. “Formalizing and Verifying Transactional Memories.” <i>Formalizing and Verifying Transactional Memories</i>. EPFL Lausanne, 2009.","ama":"Singh V. Formalizing and Verifying Transactional Memories. <i>Formalizing and Verifying Transactional Memories</i>. 2009.","mla":"Singh, Vasu. “Formalizing and Verifying Transactional Memories.” <i>Formalizing and Verifying Transactional Memories</i>, EPFL Lausanne, 2009.","apa":"Singh, V. (2009). <i>Formalizing and Verifying Transactional Memories</i>. <i>Formalizing and Verifying Transactional Memories</i>. EPFL Lausanne.","ista":"Singh V. 2009. Formalizing and Verifying Transactional Memories. EPFL Lausanne.","ieee":"V. Singh, “Formalizing and Verifying Transactional Memories,” EPFL Lausanne, 2009.","short":"V. Singh, Formalizing and Verifying Transactional Memories, EPFL Lausanne, 2009."},"_id":"4363","title":"Formalizing and Verifying Transactional Memories","type":"dissertation","day":"01","publisher":"EPFL Lausanne","publication":"Formalizing and Verifying Transactional Memories","month":"01","publist_id":"1095","extern":1,"status":"public","quality_controlled":0,"date_published":"2009-01-01T00:00:00Z","date_updated":"2021-01-12T07:56:25Z","author":[{"last_name":"Singh","first_name":"Vasu","full_name":"Vasu Singh","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:08:28Z","publication_status":"published"},{"extern":"1","publist_id":"1094","month":"01","publication":"16th International Symposium on Static Analysis","article_processing_charge":"No","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-03237-0_3","publisher":"Springer","day":"01","page":"3 - 18","type":"conference","title":"Abstraction refinement for quantified array assertions","citation":{"short":"M. Seghir, A. Podelski, T. Wies, in:, 16th International Symposium on Static Analysis, Springer, 2009, pp. 3–18.","ieee":"M. Seghir, A. Podelski, and T. Wies, “Abstraction refinement for quantified array assertions,” in <i>16th International Symposium on Static Analysis</i>, Los Angeles, CA, United States, 2009, vol. 5673, pp. 3–18.","mla":"Seghir, Mohamed, et al. “Abstraction Refinement for Quantified Array Assertions.” <i>16th International Symposium on Static Analysis</i>, vol. 5673, Springer, 2009, pp. 3–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-03237-0_3\">10.1007/978-3-642-03237-0_3</a>.","apa":"Seghir, M., Podelski, A., &#38; Wies, T. (2009). Abstraction refinement for quantified array assertions. In <i>16th International Symposium on Static Analysis</i> (Vol. 5673, pp. 3–18). Los Angeles, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-642-03237-0_3\">https://doi.org/10.1007/978-3-642-03237-0_3</a>","ista":"Seghir M, Podelski A, Wies T. 2009. Abstraction refinement for quantified array assertions. 16th International Symposium on Static Analysis. SAS: Static Analysis Symposium, LNCS, vol. 5673, 3–18.","ama":"Seghir M, Podelski A, Wies T. Abstraction refinement for quantified array assertions. In: <i>16th International Symposium on Static Analysis</i>. Vol 5673. Springer; 2009:3-18. doi:<a href=\"https://doi.org/10.1007/978-3-642-03237-0_3\">10.1007/978-3-642-03237-0_3</a>","chicago":"Seghir, Mohamed, Andreas Podelski, and Thomas Wies. “Abstraction Refinement for Quantified Array Assertions.” In <i>16th International Symposium on Static Analysis</i>, 5673:3–18. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-03237-0_3\">https://doi.org/10.1007/978-3-642-03237-0_3</a>."},"_id":"4365","year":"2009","oa_version":"None","volume":5673,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:08:29Z","publication_status":"published","author":[{"last_name":"Seghir","full_name":"Seghir, Mohamed","first_name":"Mohamed"},{"last_name":"Podelski","first_name":"Andreas","full_name":"Podelski, Andreas"},{"last_name":"Wies","first_name":"Thomas","full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-07-02T06:45:01Z","conference":{"location":"Los Angeles, CA, United States","start_date":"2009-08-09","end_date":"2009-08-11","name":"SAS: Static Analysis Symposium"},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present an abstraction refinement technique for the verification of universally quantified array assertions such as “all elements in the array are sorted”. Our technique can be seamlessly combined with existing software model checking algorithms. We implemented our technique in the ACSAR software model checker and successfully verified quantified array assertions for both text book examples and real-life examples taken from the Linux operating system kernel."}],"date_published":"2009-01-01T00:00:00Z","intvolume":"      5673","status":"public"},{"date_updated":"2025-07-02T06:41:41Z","conference":{"location":"Grenoble, France","start_date":"2009-06-26","name":"CAV: Computer Aided Verification","end_date":"2009-07-02"},"intvolume":"      5643","date_published":"2009-01-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-3-642-02658-4"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T12:08:32Z","author":[{"first_name":"Shuvendu","full_name":"Lahiri, Shuvendu","last_name":"Lahiri"},{"full_name":"Qadeer, Shaz","first_name":"Shaz","last_name":"Qadeer"},{"last_name":"Galeotti","first_name":"Juan","full_name":"Galeotti, Juan"},{"last_name":"Voung","full_name":"Voung, Jan","first_name":"Jan"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas","first_name":"Thomas","last_name":"Wies"}],"page":"493 - 508","day":"01","doi":"10.1007/978-3-642-02658-4_37","publisher":"Springer","title":"Intra-module inference","type":"conference","year":"2009","_id":"4375","citation":{"short":"S. Lahiri, S. Qadeer, J. Galeotti, J. Voung, T. Wies, in:, 21st International Conference on Computer Aided Verification, Springer, 2009, pp. 493–508.","ista":"Lahiri S, Qadeer S, Galeotti J, Voung J, Wies T. 2009. Intra-module inference. 21st International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 5643, 493–508.","apa":"Lahiri, S., Qadeer, S., Galeotti, J., Voung, J., &#38; Wies, T. (2009). Intra-module inference. In <i>21st International Conference on Computer Aided Verification</i> (Vol. 5643, pp. 493–508). Grenoble, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_37\">https://doi.org/10.1007/978-3-642-02658-4_37</a>","mla":"Lahiri, Shuvendu, et al. “Intra-Module Inference.” <i>21st International Conference on Computer Aided Verification</i>, vol. 5643, Springer, 2009, pp. 493–508, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_37\">10.1007/978-3-642-02658-4_37</a>.","ieee":"S. Lahiri, S. Qadeer, J. Galeotti, J. Voung, and T. Wies, “Intra-module inference,” in <i>21st International Conference on Computer Aided Verification</i>, Grenoble, France, 2009, vol. 5643, pp. 493–508.","ama":"Lahiri S, Qadeer S, Galeotti J, Voung J, Wies T. Intra-module inference. In: <i>21st International Conference on Computer Aided Verification</i>. Vol 5643. Springer; 2009:493-508. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_37\">10.1007/978-3-642-02658-4_37</a>","chicago":"Lahiri, Shuvendu, Shaz Qadeer, Juan Galeotti, Jan Voung, and Thomas Wies. “Intra-Module Inference.” In <i>21st International Conference on Computer Aided Verification</i>, 5643:493–508. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_37\">https://doi.org/10.1007/978-3-642-02658-4_37</a>."},"volume":5643,"oa_version":"None","extern":"1","publist_id":"1082","month":"01","publication":"21st International Conference on Computer Aided Verification","article_processing_charge":"No","alternative_title":["LNCS"]},{"extern":"1","month":"10","publist_id":"1083","publication":"ACM SIGPLAN Notices","article_processing_charge":"No","page":"61 - 80","publisher":"ACM","doi":"10.1145/1639949.164009","day":"25","title":"Parallel programming with object assemblies","type":"journal_article","year":"2009","citation":{"ieee":"R. Lublinerman, S. Chaudhuri, and P. Cerny, “Parallel programming with object assemblies,” <i>ACM SIGPLAN Notices</i>, vol. 44, no. 10. ACM, pp. 61–80, 2009.","ista":"Lublinerman R, Chaudhuri S, Cerny P. 2009. Parallel programming with object assemblies. ACM SIGPLAN Notices. 44(10), 61–80.","mla":"Lublinerman, Roberto, et al. “Parallel Programming with Object Assemblies.” <i>ACM SIGPLAN Notices</i>, vol. 44, no. 10, ACM, 2009, pp. 61–80, doi:<a href=\"https://doi.org/10.1145/1639949.164009\">10.1145/1639949.164009</a>.","apa":"Lublinerman, R., Chaudhuri, S., &#38; Cerny, P. (2009). Parallel programming with object assemblies. <i>ACM SIGPLAN Notices</i>. ACM. <a href=\"https://doi.org/10.1145/1639949.164009\">https://doi.org/10.1145/1639949.164009</a>","short":"R. Lublinerman, S. Chaudhuri, P. Cerny, ACM SIGPLAN Notices 44 (2009) 61–80.","chicago":"Lublinerman, Roberto, Swarat Chaudhuri, and Pavol Cerny. “Parallel Programming with Object Assemblies.” <i>ACM SIGPLAN Notices</i>. ACM, 2009. <a href=\"https://doi.org/10.1145/1639949.164009\">https://doi.org/10.1145/1639949.164009</a>.","ama":"Lublinerman R, Chaudhuri S, Cerny P. Parallel programming with object assemblies. <i>ACM SIGPLAN Notices</i>. 2009;44(10):61-80. doi:<a href=\"https://doi.org/10.1145/1639949.164009\">10.1145/1639949.164009</a>"},"_id":"4376","issue":"10","volume":44,"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:08:32Z","publication_status":"published","author":[{"last_name":"Lublinerman","full_name":"Lublinerman, Roberto","first_name":"Roberto"},{"full_name":"Chaudhuri, Swarat","first_name":"Swarat","last_name":"Chaudhuri"},{"first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"}],"date_updated":"2025-07-02T06:17:51Z","intvolume":"        44","quality_controlled":"1","scopus_import":"1","date_published":"2009-10-25T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"text":"We present Chorus, a high-level parallel programming model suitable for irregular, heap-manipulating applications like mesh refinement and epidemic simulations, and JChorus, an implementation of the model on top of Java. One goal of Chorus is to express the dynamic and instance-dependent patterns of memory access that are common in typical irregular applications. Its other focus is locality of effects: the property that in many of the same applications, typical imperative commands only affect small, local regions in the shared heap.\r\nChorus addresses dynamism and locality through the unifying abstraction of an object assembly: a local region in a shared data structure equipped with a short-lived, speculative thread of control. The thread of control in an assembly can only access objects within the assembly. While objects can migrate from assembly to assembly, such migration is local--i.e., objects only move from one assembly to a neighboring one--and does not lead to aliasing. Programming primitives include a merge operation, by which an assembly merges with an adjacent assembly, and a split operation, which splits an assembly into smaller ones. Our abstractions are race and deadlock-free, and inherently data-centric.\r\nWe demonstrate that Chorus and JChorus allow natural programming of several important applications exhibiting irregular data-parallelism. We also present an implementation of JChorus based on a many-to-one mapping of assemblies to lower-level threads, and report on preliminary performance numbers.","lang":"eng"}],"status":"public"},{"extern":"1","publist_id":"1079","month":"01","publication":"Second World Congress on Formal Methods","article_processing_charge":"No","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-05089-3_22","day":"01","publisher":"Springer","page":"338 - 353","type":"conference","title":"It's doomed; we can prove it","citation":{"mla":"Hoenicke, Jochen, et al. “It’s Doomed; We Can Prove It.” <i>Second World Congress on Formal Methods</i>, vol. 5850, Springer, 2009, pp. 338–53, doi:<a href=\"https://doi.org/10.1007/978-3-642-05089-3_22\">10.1007/978-3-642-05089-3_22</a>.","apa":"Hoenicke, J., Leino, K. R., Podelski, A., Schäf, M., &#38; Wies, T. (2009). It’s doomed; we can prove it. In <i>Second World Congress on Formal Methods</i> (Vol. 5850, pp. 338–353). Eindhoven, The Netherlands: Springer. <a href=\"https://doi.org/10.1007/978-3-642-05089-3_22\">https://doi.org/10.1007/978-3-642-05089-3_22</a>","ista":"Hoenicke J, Leino KR, Podelski A, Schäf M, Wies T. 2009. It’s doomed; we can prove it. Second World Congress on Formal Methods. FM: Formal Methods, LNCS, vol. 5850, 338–353.","ieee":"J. Hoenicke, K. R. Leino, A. Podelski, M. Schäf, and T. Wies, “It’s doomed; we can prove it,” in <i>Second World Congress on Formal Methods</i>, Eindhoven, The Netherlands, 2009, vol. 5850, pp. 338–353.","short":"J. Hoenicke, K.R. Leino, A. Podelski, M. Schäf, T. Wies, in:, Second World Congress on Formal Methods, Springer, 2009, pp. 338–353.","chicago":"Hoenicke, Jochen, K Rustan Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “It’s Doomed; We Can Prove It.” In <i>Second World Congress on Formal Methods</i>, 5850:338–53. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-05089-3_22\">https://doi.org/10.1007/978-3-642-05089-3_22</a>.","ama":"Hoenicke J, Leino KR, Podelski A, Schäf M, Wies T. It’s doomed; we can prove it. In: <i>Second World Congress on Formal Methods</i>. Vol 5850. Springer; 2009:338-353. doi:<a href=\"https://doi.org/10.1007/978-3-642-05089-3_22\">10.1007/978-3-642-05089-3_22</a>"},"_id":"4377","year":"2009","oa_version":"None","volume":5850,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T12:08:32Z","author":[{"first_name":"Jochen","full_name":"Hoenicke, Jochen","last_name":"Hoenicke"},{"first_name":"K Rustan","full_name":"Leino, K Rustan","last_name":"Leino"},{"last_name":"Podelski","full_name":"Podelski, Andreas","first_name":"Andreas"},{"full_name":"Schäf, Martin","first_name":"Martin","last_name":"Schäf"},{"last_name":"Wies","first_name":"Thomas","full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-07-02T06:38:22Z","conference":{"start_date":"2009-11-02","end_date":"2009-11-06","name":"FM: Formal Methods","location":"Eindhoven, The Netherlands"},"abstract":[{"lang":"eng","text":"Programming errors found early are the cheapest. Tools applying to the early stage of code development exist but either they suffer from false positives (“noise”) or they require strong user interaction. We propose to avoid this deficiency by defining a new class of errors. A program fragment is doomed if its execution will inevitably fail, in whatever state it is started. We use a formal verification method to identify such errors fully automatically and, most significantly, without producing noise. We report on preliminary experiments with a prototype tool."}],"quality_controlled":"1","date_published":"2009-01-01T00:00:00Z","scopus_import":"1","language":[{"iso":"eng"}],"intvolume":"      5850","status":"public"},{"file":[{"checksum":"df3c3e6306afd3f630a9146f91642f0a","date_updated":"2020-07-14T12:46:28Z","file_name":"IST-2012-45-v1+1_Software_transactional_memory_on_relaxed_memory_models.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:14:50Z","creator":"system","file_id":"5105","file_size":265763,"relation":"main_file"}],"oa":1,"file_date_updated":"2020-07-14T12:46:28Z","publication_status":"published","date_created":"2018-12-11T12:08:34Z","author":[{"first_name":"Rachid","full_name":"Guerraoui, Rachid","last_name":"Guerraoui"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger"},{"id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","full_name":"Vasu Singh","first_name":"Vasu","last_name":"Singh"}],"date_updated":"2021-01-12T07:56:34Z","conference":{"name":"CAV: Computer Aided Verification"},"acknowledgement":"This research was supported by the Swiss National Science Foundation.","quality_controlled":0,"abstract":[{"lang":"eng","text":"Pseudo-code descriptions of STMs assume sequentially consistent program execution and atomicity of high-level STM operations like read, write, and commit. These assumptions are often violated in realistic settings, as STM implementations run on relaxed memory models, with the atomicity of operations as provided by the hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We present RML, a new high-level language for expressing concurrent algorithms with a hardware-level atomicity of instructions, and whose semantics is parametrized by various relaxed memory models. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order."}],"date_published":"2009-06-19T00:00:00Z","intvolume":"      5643","status":"public","extern":1,"publist_id":"1074","month":"06","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-02658-4_26","day":"19","publisher":"Springer","page":"321 - 336","pubrep_id":"45","type":"conference","title":"Software transactional memory on relaxed memory models","_id":"4383","citation":{"short":"R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2009, pp. 321–336.","apa":"Guerraoui, R., Henzinger, T. A., &#38; Singh, V. (2009). Software transactional memory on relaxed memory models (Vol. 5643, pp. 321–336). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">https://doi.org/10.1007/978-3-642-02658-4_26</a>","mla":"Guerraoui, Rachid, et al. <i>Software Transactional Memory on Relaxed Memory Models</i>. Vol. 5643, Springer, 2009, pp. 321–36, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">10.1007/978-3-642-02658-4_26</a>.","ista":"Guerraoui R, Henzinger TA, Singh V. 2009. Software transactional memory on relaxed memory models. CAV: Computer Aided Verification, LNCS, vol. 5643, 321–336.","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Software transactional memory on relaxed memory models,” presented at the CAV: Computer Aided Verification, 2009, vol. 5643, pp. 321–336.","ama":"Guerraoui R, Henzinger TA, Singh V. Software transactional memory on relaxed memory models. In: Vol 5643. Springer; 2009:321-336. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">10.1007/978-3-642-02658-4_26</a>","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Software Transactional Memory on Relaxed Memory Models,” 5643:321–36. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">https://doi.org/10.1007/978-3-642-02658-4_26</a>."},"year":"2009","volume":5643},{"author":[{"last_name":"Dragojevic","full_name":"Dragojevic, Aleksandar","first_name":"Aleksandar"},{"last_name":"Guerraoui","full_name":"Guerraoui, Rachid","first_name":"Rachid"},{"first_name":"Anmol","full_name":"Singh, Anmol","last_name":"Singh"},{"last_name":"Singh","full_name":"Singh, Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu"}],"publication_status":"published","date_created":"2018-12-11T12:08:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","abstract":[{"lang":"eng","text":"Transactional memories are typically speculative and rely on contention managers to cure conflicts. This paper explores a complementary approach that prevents conflicts by scheduling transactions according to predictions on their access sets.\r\nWe first explore the theoretical boundaries of this approach and prove that (1) a TM scheduler with an accurate prediction can be 2-competitive with an optimal offline TM scheduler, but (2) even a slight inaccuracy in prediction makes the competitive ratio of the TM scheduler in the order of the number of transactions.\r\nWe then show that, in practice, there is room for a pragmatic approach with good average case performance. We present Shrink, a scheduler that (1) bases its prediction of transactional accesses on the access patterns of the past transactions from the same thread, and (2) uses a novel heuristic, which we call serialization affinity, to schedule transactions with a probability proportional to the current amount of contention. Shrink obtains roughly 70% accurate read and write access predictions on STMBench7 and STAMP. In our experimental evaluation, Shrink significantly improves STM performance in cases the number of executing threads is higher than the number of available CPU cores. For SwissTM, Shrink improves the performance by up to 55% on STMBench7, and up to 120% on STAMP. For TinySTM, Shrink drastically improves the performance on STMBench7 and STAMP benchmarks."}],"date_published":"2009-08-10T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","conference":{"location":"Calgary, Canada","start_date":"2009-08-10","end_date":"2009-08-12","name":"POPL: Principles of Programming Languages"},"date_updated":"2025-07-02T06:35:49Z","article_processing_charge":"No","publication":"Proceedings of the 28th ACM symposium on Principles of distributed computing","month":"08","publist_id":"1070","extern":"1","oa_version":"None","year":"2009","_id":"4385","citation":{"short":"A. Dragojevic, R. Guerraoui, A. Singh, V. Singh, in:, Proceedings of the 28th ACM Symposium on Principles of Distributed Computing, ACM, 2009, pp. 7–16.","apa":"Dragojevic, A., Guerraoui, R., Singh, A., &#38; Singh, V. (2009). Preventing versus curing: Avoiding conflicts in transactional memories. In <i>Proceedings of the 28th ACM symposium on Principles of distributed computing</i> (pp. 7–16). Calgary, Canada: ACM. <a href=\"https://doi.org/10.1145/1582716.1582725\">https://doi.org/10.1145/1582716.1582725</a>","mla":"Dragojevic, Aleksandar, et al. “Preventing versus Curing: Avoiding Conflicts in Transactional Memories.” <i>Proceedings of the 28th ACM Symposium on Principles of Distributed Computing</i>, ACM, 2009, pp. 7–16, doi:<a href=\"https://doi.org/10.1145/1582716.1582725\">10.1145/1582716.1582725</a>.","ista":"Dragojevic A, Guerraoui R, Singh A, Singh V. 2009. Preventing versus curing: Avoiding conflicts in transactional memories. Proceedings of the 28th ACM symposium on Principles of distributed computing. POPL: Principles of Programming Languages, 7–16.","ieee":"A. Dragojevic, R. Guerraoui, A. Singh, and V. Singh, “Preventing versus curing: Avoiding conflicts in transactional memories,” in <i>Proceedings of the 28th ACM symposium on Principles of distributed computing</i>, Calgary, Canada, 2009, pp. 7–16.","ama":"Dragojevic A, Guerraoui R, Singh A, Singh V. Preventing versus curing: Avoiding conflicts in transactional memories. In: <i>Proceedings of the 28th ACM Symposium on Principles of Distributed Computing</i>. ACM; 2009:7-16. doi:<a href=\"https://doi.org/10.1145/1582716.1582725\">10.1145/1582716.1582725</a>","chicago":"Dragojevic, Aleksandar, Rachid Guerraoui, Anmol Singh, and Vasu Singh. “Preventing versus Curing: Avoiding Conflicts in Transactional Memories.” In <i>Proceedings of the 28th ACM Symposium on Principles of Distributed Computing</i>, 7–16. ACM, 2009. <a href=\"https://doi.org/10.1145/1582716.1582725\">https://doi.org/10.1145/1582716.1582725</a>."},"title":"Preventing versus curing: Avoiding conflicts in transactional memories","type":"conference","page":"7 - 16","doi":"10.1145/1582716.1582725","day":"10","publisher":"ACM"},{"type":"conference","title":"Automated analysis of Java methods for confidentiality","publisher":"Springer","doi":"10.1007/978-3-642-02658-4_16","day":"01","page":"173 - 187","oa_version":"None","volume":5643,"citation":{"short":"P. Cerny, R. Alur, in:, 21st International Conference on Computer Aided Verification, Springer, 2009, pp. 173–187.","apa":"Cerny, P., &#38; Alur, R. (2009). Automated analysis of Java methods for confidentiality. In <i>21st International Conference on Computer Aided Verification</i> (Vol. 5643, pp. 173–187). Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_16\">https://doi.org/10.1007/978-3-642-02658-4_16</a>","ista":"Cerny P, Alur R. 2009. Automated analysis of Java methods for confidentiality. 21st International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 5643, 173–187.","mla":"Cerny, Pavol, and Rajeev Alur. “Automated Analysis of Java Methods for Confidentiality.” <i>21st International Conference on Computer Aided Verification</i>, vol. 5643, Springer, 2009, pp. 173–87, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_16\">10.1007/978-3-642-02658-4_16</a>.","ieee":"P. Cerny and R. Alur, “Automated analysis of Java methods for confidentiality,” in <i>21st International Conference on Computer Aided Verification</i>, 2009, vol. 5643, pp. 173–187.","ama":"Cerny P, Alur R. Automated analysis of Java methods for confidentiality. In: <i>21st International Conference on Computer Aided Verification</i>. Vol 5643. Springer; 2009:173-187. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_16\">10.1007/978-3-642-02658-4_16</a>","chicago":"Cerny, Pavol, and Rajeev Alur. “Automated Analysis of Java Methods for Confidentiality.” In <i>21st International Conference on Computer Aided Verification</i>, 5643:173–87. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_16\">https://doi.org/10.1007/978-3-642-02658-4_16</a>."},"_id":"4391","year":"2009","publist_id":"1067","month":"07","extern":"1","alternative_title":["LNCS"],"article_processing_charge":"No","publication":"21st International Conference on Computer Aided Verification","conference":{"name":"CAV: Computer Aided Verification"},"date_updated":"2025-07-02T06:32:32Z","status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"We address the problem of analyzing programs such as J2ME midlets for mobile devices, where a central correctness requirement concerns confidentiality of data that the user wants to keep secret. Existing software model checking tools analyze individual program executions, and are not applicable to checking confidentiality properties that require reasoning about equivalence among executions. We develop an automated analysis technique for such properties. We show that both over- and under- approximation is needed for sound analysis. Given a program and a confidentiality requirement, our technique produces a formula that is satisfiable if the requirement holds. We evaluate the approach by analyzing bytecode of a set of Java (J2ME) methods."}],"date_published":"2009-07-01T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"      5643","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"first_name":"Rajeev","full_name":"Alur, Rajeev","last_name":"Alur"}],"publication_status":"published","date_created":"2018-12-11T12:08:36Z"}]