[{"publisher":"Wiley-Blackwell","date_published":"2009-12-01T00:00:00Z","intvolume":"        31","month":"12","title":"Dorsal closure in Drosophila: cells cannot get out of the tight spot","author":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"12","date_updated":"2021-01-12T07:55:17Z","publist_id":"1911","page":"1284 - 1287","article_processing_charge":"No","year":"2009","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"type":"journal_article","volume":31,"extern":"1","citation":{"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>.","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>","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>.","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>","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.","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."},"day":"01","status":"public","date_created":"2018-12-11T12:07:35Z","_id":"4206","publication":"Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology","doi":"10.1002/bies.200900109","publication_status":"published","oa_version":"None"},{"article_processing_charge":"No","page":"1305 - 1315","publist_id":"1901","language":[{"iso":"eng"}],"year":"2009","month":"04","intvolume":"       136","date_published":"2009-04-15T00:00:00Z","publisher":"Company of Biologists","date_updated":"2021-01-12T07:55:22Z","issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Carvalho, Lara","first_name":"Lara","last_name":"Carvalho"},{"last_name":"Stuehmer","first_name":"Jan","full_name":"Stuehmer, Jan"},{"full_name":"Bois, Justin","first_name":"Justin","last_name":"Bois"},{"last_name":"Kalaidzidis","first_name":"Yannis","full_name":"Kalaidzidis, Yannis"},{"full_name":"Lecaudey, Virginie","first_name":"Virginie","last_name":"Lecaudey"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"title":"Control of convergent yolk syncytial layer nuclear movement in zebrafish","doi":"10.1242/dev.026922","publication_status":"published","publication":"Development","oa_version":"None","citation":{"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>","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.","short":"L. Carvalho, J. Stuehmer, J. Bois, Y. Kalaidzidis, V. Lecaudey, C.-P.J. Heisenberg, Development 136 (2009) 1305–1315.","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.","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>.","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>"},"extern":"1","volume":136,"type":"journal_article","abstract":[{"lang":"eng","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."}],"_id":"4217","date_created":"2018-12-11T12:07:39Z","status":"public","day":"15"},{"publist_id":"1894","article_processing_charge":"No","page":"875 - 883","year":"2009","language":[{"iso":"eng"}],"publisher":"American Chemical Society","month":"08","intvolume":"         4","date_published":"2009-08-18T00:00:00Z","issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus","author":[{"full_name":"Swoboda, Jonathan","first_name":"Jonathan","last_name":"Swoboda"},{"full_name":"Meredith, Timothy","first_name":"Timothy","last_name":"Meredith"},{"full_name":"Campbell, Jennifer","last_name":"Campbell","first_name":"Jennifer"},{"first_name":"Stephanie","last_name":"Brown","full_name":"Brown, Stephanie"},{"full_name":"Suzuki, Takashi","last_name":"Suzuki","first_name":"Takashi"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Malhowski","first_name":"Amy","full_name":"Malhowski, Amy"},{"full_name":"Kishony, Roy","first_name":"Roy","last_name":"Kishony"},{"full_name":"Gilmore, Michael","last_name":"Gilmore","first_name":"Michael"},{"last_name":"Walker","first_name":"Suzanne","full_name":"Walker, Suzanne"}],"date_updated":"2021-01-12T07:55:25Z","publication_status":"published","doi":"10.1021/cb900151k","main_file_link":[{"url":"10.1021/cb900151k [doi]"}],"publication":"ACS Chemical Biology","oa_version":"None","type":"journal_article","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"}],"extern":"1","citation":{"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>.","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>","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.","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.","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.","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>.","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>"},"volume":4,"day":"18","status":"public","_id":"4223","date_created":"2018-12-11T12:07:41Z"},{"publication_status":"published","doi":"10.1016/j.cell.2009.10.025","publication":"Cell","citation":{"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>.","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>","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.","ista":"Bollenbach T, Quan S, Chait RP, Kishony R. 2009. Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. Cell. 139(4), 707–718.","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.","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>"},"extern":1,"volume":139,"type":"journal_article","abstract":[{"lang":"eng","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."}],"date_created":"2018-12-11T12:07:43Z","_id":"4228","status":"public","quality_controlled":0,"day":"01","page":"707 - 718","publist_id":"1890","year":"2009","month":"01","intvolume":"       139","date_published":"2009-01-01T00:00:00Z","publisher":"Cell Press","date_updated":"2021-01-12T07:55:27Z","issue":"4","title":"Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions","author":[{"full_name":"Bollenbach, Tobias","first_name":"Tobias","last_name":"Bollenbach"},{"first_name":"Selwyn","last_name":"Quan","full_name":"Quan, Selwyn"},{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","orcid":"0000-0003-0876-3187","full_name":"Remy Chait"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}]},{"title":"Statistical mechanics and the evolution of polygenic quantitative traits","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"De Vladar","first_name":"Harold","full_name":"De Vladar, Harold"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","date_updated":"2021-01-12T07:55:29Z","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.” ","publisher":"Genetics Society of America","date_published":"2009-03-01T00:00:00Z","month":"03","intvolume":"       181","year":"2009","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"publist_id":"1882","page":"997 - 1011","quality_controlled":"1","day":"01","status":"public","_id":"4231","date_created":"2018-12-11T12:07:44Z","scopus_import":1,"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."}],"type":"journal_article","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>","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.","short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.","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>.","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>."},"oa_version":"None","publication":"Genetics","doi":"10.1534/genetics.108.099309","publication_status":"published"},{"publisher":"Faculty of mathematical and natural sciences, University of Groningen","date_published":"2009-01-01T00:00:00Z","month":"01","author":[{"last_name":"Vladar","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","full_name":"Harold Vladar"}],"title":"Stochasticity and Variability in the dynamics and genetics of populations","date_updated":"2021-01-12T07:55:29Z","publist_id":"1883","year":"2009","type":"dissertation","citation":{"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. <a href=\"https://doi.org/3811\">https://doi.org/3811</a>","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, doi:<a href=\"https://doi.org/3811\">3811</a>.","ama":"de Vladar H. Stochasticity and Variability in the dynamics and genetics of populations. 2009. doi:<a href=\"https://doi.org/3811\">3811</a>","short":"H. de Vladar, Stochasticity and Variability in the Dynamics and Genetics of Populations, Faculty of mathematical and natural sciences, University of Groningen, 2009.","ieee":"H. de Vladar, “Stochasticity and Variability in the dynamics and genetics of populations,” 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.","chicago":"Vladar, Harold de. “Stochasticity and Variability in the Dynamics and Genetics of Populations.” Faculty of mathematical and natural sciences, University of Groningen, 2009. <a href=\"https://doi.org/3811\">https://doi.org/3811</a>."},"extern":1,"status":"public","quality_controlled":0,"day":"01","_id":"4232","date_created":"2018-12-11T12:07:44Z","publication_status":"published","doi":"3811"},{"date_updated":"2021-01-12T07:55:33Z","oa":1,"issue":"5","date_published":"2009-05-01T00:00:00Z","month":"05","intvolume":"        63","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.","year":"2009","page":"1171 - 1190","date_created":"2018-12-11T12:07:48Z","ddc":["570"],"status":"public","day":"01","volume":63,"oa_version":"Submitted Version","publication":"Evolution; International Journal of Organic Evolution","doi":"10.1111/j.1558-5646.2009.00622.x","title":"The evolution of strong reproductive isolation","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"De Cara","first_name":"Maria","full_name":"De Cara, Maria"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-12T10:11:46Z","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf","access_level":"open_access","relation":"main_file","checksum":"1920d2e25ef335833764256c1a47bbfb","creator":"system","file_size":720913,"file_id":"4903","content_type":"application/pdf"},{"file_size":290160,"creator":"system","file_id":"4904","content_type":"application/pdf","checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","access_level":"open_access","relation":"main_file","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-12T10:11:47Z"}],"has_accepted_license":"1","publisher":"Wiley","language":[{"iso":"eng"}],"pubrep_id":"551","department":[{"_id":"NiBa"}],"publist_id":"1866","_id":"4242","quality_controlled":"1","citation":{"short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 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.","ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","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>","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>.","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>","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>."},"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."}],"file_date_updated":"2020-07-14T12:46:25Z","type":"journal_article","publication_status":"published"},{"year":"2009","publist_id":"1101","page":"225 - 234","author":[{"full_name":"Jonathan Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","last_name":"Bollback"},{"last_name":"Huelsenbeck","first_name":"John","full_name":"Huelsenbeck, John P"}],"title":"Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence","issue":"1","date_updated":"2021-01-12T07:56:22Z","publisher":"Genetics Society of America","date_published":"2009-01-01T00:00:00Z","month":"01","intvolume":"       181","publication":"Genetics","publication_status":"published","doi":"10.1534/genetics.107.085225","status":"public","day":"01","quality_controlled":0,"_id":"4357","date_created":"2018-12-11T12:08:26Z","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."}],"type":"journal_article","volume":181,"citation":{"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>.","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.","short":"J.P. Bollback, J. Huelsenbeck, Genetics 181 (2009) 225–234.","ista":"Bollback JP, Huelsenbeck J. 2009. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics. 181(1), 225–234.","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>","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>."},"extern":1},{"doi":"1558","publication_status":"published","date_created":"2018-12-11T12:08:27Z","_id":"4360","quality_controlled":0,"status":"public","day":"01","extern":1,"citation":{"apa":"Wies, T., Piskac, R., &#38; Kuncak, V. (2009). Combining Theories with Shared Set Operations (pp. 366–382). Presented at the FroCoS: Frontiers of Combining Systems, Springer. <a href=\"https://doi.org/1558\">https://doi.org/1558</a>","mla":"Wies, Thomas, et al. <i>Combining Theories with Shared Set Operations</i>. Springer, 2009, pp. 366–82, doi:<a href=\"https://doi.org/1558\">1558</a>.","ieee":"T. Wies, R. Piskac, and V. Kuncak, “Combining Theories with Shared Set Operations,” presented at the FroCoS: Frontiers of Combining Systems, 2009, pp. 366–382.","short":"T. Wies, R. Piskac, V. Kuncak, in:, Springer, 2009, pp. 366–382.","ista":"Wies T, Piskac R, Kuncak V. 2009. Combining Theories with Shared Set Operations. FroCoS: Frontiers of Combining Systems, LNCS 5749, , 366–382.","ama":"Wies T, Piskac R, Kuncak V. Combining Theories with Shared Set Operations. In: Springer; 2009:366-382. doi:<a href=\"https://doi.org/1558\">1558</a>","chicago":"Wies, Thomas, Ruzica Piskac, and Viktor Kuncak. “Combining Theories with Shared Set Operations,” 366–82. Springer, 2009. <a href=\"https://doi.org/1558\">https://doi.org/1558</a>."},"type":"conference","year":"2009","page":"366 - 382","publist_id":"1098","conference":{"name":"FroCoS: Frontiers of Combining Systems"},"date_updated":"2021-01-12T07:56:24Z","author":[{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Wies"},{"first_name":"Ruzica","last_name":"Piskac","full_name":"Piskac, Ruzica"},{"full_name":"Kuncak, Viktor","first_name":"Viktor","last_name":"Kuncak"}],"title":"Combining Theories with Shared Set Operations","month":"01","date_published":"2009-01-01T00:00:00Z","alternative_title":["LNCS 5749"],"publisher":"Springer"},{"publication_status":"published","publication":"Formalizing and Verifying Transactional Memories","status":"public","day":"01","quality_controlled":0,"_id":"4363","date_created":"2018-12-11T12:08:28Z","type":"dissertation","citation":{"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.","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.","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."},"extern":1,"year":"2009","publist_id":"1095","title":"Formalizing and Verifying Transactional Memories","author":[{"full_name":"Vasu Singh","last_name":"Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:56:25Z","publisher":"EPFL Lausanne","month":"01","date_published":"2009-01-01T00:00:00Z"},{"publication_status":"published","doi":"1556","type":"conference","extern":1,"citation":{"chicago":"Seghir, Mohamed, Andreas Podelski, and Thomas Wies. “Abstraction Refinement for Quantified Array Assertions,” 3–18. Springer, 2009. <a href=\"https://doi.org/1556\">https://doi.org/1556</a>.","ieee":"M. Seghir, A. Podelski, and T. Wies, “Abstraction Refinement for Quantified Array Assertions,” presented at the SAS: Static Analysis Symposium, 2009, pp. 3–18.","short":"M. Seghir, A. Podelski, T. Wies, in:, Springer, 2009, pp. 3–18.","ista":"Seghir M, Podelski A, Wies T. 2009. Abstraction Refinement for Quantified Array Assertions. SAS: Static Analysis Symposium, LNCS 5673, , 3–18.","ama":"Seghir M, Podelski A, Wies T. Abstraction Refinement for Quantified Array Assertions. In: Springer; 2009:3-18. doi:<a href=\"https://doi.org/1556\">1556</a>","mla":"Seghir, Mohamed, et al. <i>Abstraction Refinement for Quantified Array Assertions</i>. Springer, 2009, pp. 3–18, doi:<a href=\"https://doi.org/1556\">1556</a>.","apa":"Seghir, M., Podelski, A., &#38; Wies, T. (2009). Abstraction Refinement for Quantified Array Assertions (pp. 3–18). Presented at the SAS: Static Analysis Symposium, Springer. <a href=\"https://doi.org/1556\">https://doi.org/1556</a>"},"quality_controlled":0,"status":"public","day":"01","date_created":"2018-12-11T12:08:29Z","_id":"4365","conference":{"name":"SAS: Static Analysis Symposium"},"publist_id":"1094","page":"3 - 18","year":"2009","publisher":"Springer","date_published":"2009-01-01T00:00:00Z","alternative_title":["LNCS 5673"],"month":"01","title":"Abstraction Refinement for Quantified Array Assertions","author":[{"full_name":"Seghir,Mohamed Nassim","first_name":"Mohamed","last_name":"Seghir"},{"full_name":"Podelski,Andreas","first_name":"Andreas","last_name":"Podelski"},{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Wies"}],"date_updated":"2021-01-12T07:56:26Z"},{"doi":"1555","publication_status":"published","status":"public","day":"01","quality_controlled":0,"date_created":"2018-12-11T12:08:32Z","_id":"4375","type":"conference","extern":1,"citation":{"chicago":"Lahiri, Shuvendu, Shaz Qadeer, Juan Galeotti, Jan Voung, and Thomas Wies. “Intra-Module Inference,” 493–508. Springer, 2009. <a href=\"https://doi.org/1555\">https://doi.org/1555</a>.","short":"S. Lahiri, S. Qadeer, J. Galeotti, J. Voung, T. Wies, in:, Springer, 2009, pp. 493–508.","ieee":"S. Lahiri, S. Qadeer, J. Galeotti, J. Voung, and T. Wies, “Intra-module Inference,” presented at the CAV: Computer Aided Verification, 2009, pp. 493–508.","ista":"Lahiri S, Qadeer S, Galeotti J, Voung J, Wies T. 2009. Intra-module Inference. CAV: Computer Aided Verification, LNCS 5643, , 493–508.","ama":"Lahiri S, Qadeer S, Galeotti J, Voung J, Wies T. Intra-module Inference. In: Springer; 2009:493-508. doi:<a href=\"https://doi.org/1555\">1555</a>","mla":"Lahiri, Shuvendu, et al. <i>Intra-Module Inference</i>. Springer, 2009, pp. 493–508, doi:<a href=\"https://doi.org/1555\">1555</a>.","apa":"Lahiri, S., Qadeer, S., Galeotti, J., Voung, J., &#38; Wies, T. (2009). Intra-module Inference (pp. 493–508). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/1555\">https://doi.org/1555</a>"},"year":"2009","publist_id":"1082","conference":{"name":"CAV: Computer Aided Verification"},"page":"493 - 508","title":"Intra-module Inference","author":[{"full_name":"Lahiri,Shuvendu K.","first_name":"Shuvendu","last_name":"Lahiri"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer,Shaz"},{"full_name":"Galeotti,Juan P.","first_name":"Juan","last_name":"Galeotti"},{"first_name":"Jan","last_name":"Voung","full_name":"Voung,Jan W."},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Thomas Wies"}],"date_updated":"2021-01-12T07:56:30Z","publisher":"Springer","alternative_title":["LNCS 5643"],"date_published":"2009-01-01T00:00:00Z","month":"01"},{"publication_status":"published","doi":"1546","type":"conference","extern":1,"citation":{"mla":"Lublinerman, Roberto, et al. <i>Parallel Programming with Object Assemblies</i>. ACM, 2009, pp. 61–80, doi:<a href=\"https://doi.org/1546\">1546</a>.","apa":"Lublinerman, R., Chaudhuri, S., &#38; Cerny, P. (2009). Parallel programming with object assemblies (pp. 61–80). Presented at the Oopsla Object Oriented Programming Systems Languages and Applications, ACM. <a href=\"https://doi.org/1546\">https://doi.org/1546</a>","chicago":"Lublinerman, Roberto, Swarat Chaudhuri, and Pavol Cerny. “Parallel Programming with Object Assemblies,” 61–80. ACM, 2009. <a href=\"https://doi.org/1546\">https://doi.org/1546</a>.","ista":"Lublinerman R, Chaudhuri S, Cerny P. 2009. Parallel programming with object assemblies. Oopsla Object Oriented Programming Systems Languages and Applications, 61–80.","short":"R. Lublinerman, S. Chaudhuri, P. Cerny, in:, ACM, 2009, pp. 61–80.","ieee":"R. Lublinerman, S. Chaudhuri, and P. Cerny, “Parallel programming with object assemblies,” presented at the Oopsla Object Oriented Programming Systems Languages and Applications, 2009, pp. 61–80.","ama":"Lublinerman R, Chaudhuri S, Cerny P. Parallel programming with object assemblies. In: ACM; 2009:61-80. doi:<a href=\"https://doi.org/1546\">1546</a>"},"status":"public","quality_controlled":0,"day":"01","date_created":"2018-12-11T12:08:32Z","_id":"4376","conference":{"name":"Oopsla Object Oriented Programming Systems Languages and Applications"},"publist_id":"1083","page":"61 - 80","year":"2009","publisher":"ACM","month":"01","date_published":"2009-01-01T00:00:00Z","author":[{"full_name":"Lublinerman,Roberto","last_name":"Lublinerman","first_name":"Roberto"},{"full_name":"Chaudhuri,Swarat","last_name":"Chaudhuri","first_name":"Swarat"},{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny","full_name":"Pavol Cerny"}],"title":"Parallel programming with object assemblies","date_updated":"2021-01-12T07:56:30Z"},{"publisher":"Springer","alternative_title":["LNCS 5850"],"date_published":"2009-01-01T00:00:00Z","month":"01","author":[{"last_name":"Hoenicke","first_name":"Jochen","full_name":"Hoenicke,Jochen"},{"full_name":"Leino, K Rustan","first_name":"K Rustan","last_name":"Leino"},{"full_name":"Podelski,Andreas","last_name":"Podelski","first_name":"Andreas"},{"full_name":"Schäf,Martin","first_name":"Martin","last_name":"Schäf"},{"first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","full_name":"Thomas Wies"}],"title":"It's Doomed; We Can Prove It","date_updated":"2021-01-12T07:56:31Z","conference":{"name":"FM: Formal Methods"},"publist_id":"1079","page":"338 - 353","year":"2009","type":"conference","citation":{"apa":"Hoenicke, J., Leino, K. R., Podelski, A., Schäf, M., &#38; Wies, T. (2009). It’s Doomed; We Can Prove It (pp. 338–353). Presented at the FM: Formal Methods, Springer. <a href=\"https://doi.org/1557\">https://doi.org/1557</a>","mla":"Hoenicke, Jochen, et al. <i>It’s Doomed; We Can Prove It</i>. Springer, 2009, pp. 338–53, doi:<a href=\"https://doi.org/1557\">1557</a>.","ama":"Hoenicke J, Leino KR, Podelski A, Schäf M, Wies T. It’s Doomed; We Can Prove It. In: Springer; 2009:338-353. doi:<a href=\"https://doi.org/1557\">1557</a>","ieee":"J. Hoenicke, K. R. Leino, A. Podelski, M. Schäf, and T. Wies, “It’s Doomed; We Can Prove It,” presented at the FM: Formal Methods, 2009, pp. 338–353.","short":"J. Hoenicke, K.R. Leino, A. Podelski, M. Schäf, T. Wies, in:, Springer, 2009, pp. 338–353.","ista":"Hoenicke J, Leino KR, Podelski A, Schäf M, Wies T. 2009. It’s Doomed; We Can Prove It. FM: Formal Methods, LNCS 5850, , 338–353.","chicago":"Hoenicke, Jochen, K Rustan Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “It’s Doomed; We Can Prove It,” 338–53. Springer, 2009. <a href=\"https://doi.org/1557\">https://doi.org/1557</a>."},"extern":1,"status":"public","day":"01","quality_controlled":0,"date_created":"2018-12-11T12:08:32Z","_id":"4377","publication_status":"published","doi":"1557"},{"date_created":"2018-12-11T12:08:34Z","_id":"4383","status":"public","quality_controlled":0,"day":"19","volume":5643,"citation":{"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>.","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>","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.","ista":"Guerraoui R, Henzinger TA, Singh V. 2009. Software transactional memory on relaxed memory models. CAV: Computer Aided Verification, LNCS, vol. 5643, 321–336.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2009, pp. 321–336.","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>.","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>"},"extern":1,"abstract":[{"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.","lang":"eng"}],"type":"conference","file_date_updated":"2020-07-14T12:46:28Z","doi":"10.1007/978-3-642-02658-4_26","publication_status":"published","date_updated":"2021-01-12T07:56:34Z","oa":1,"title":"Software transactional memory on relaxed memory models","author":[{"full_name":"Guerraoui, Rachid","first_name":"Rachid","last_name":"Guerraoui"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Thomas Henzinger"},{"full_name":"Vasu Singh","last_name":"Singh","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu"}],"file":[{"file_name":"IST-2012-45-v1+1_Software_transactional_memory_on_relaxed_memory_models.pdf","date_updated":"2020-07-14T12:46:28Z","date_created":"2018-12-12T10:14:50Z","creator":"system","file_size":265763,"content_type":"application/pdf","file_id":"5105","relation":"main_file","access_level":"open_access","checksum":"df3c3e6306afd3f630a9146f91642f0a"}],"date_published":"2009-06-19T00:00:00Z","alternative_title":["LNCS"],"month":"06","intvolume":"      5643","acknowledgement":"This research was supported by the Swiss National Science Foundation.","publisher":"Springer","pubrep_id":"45","year":"2009","page":"321 - 336","publist_id":"1074","conference":{"name":"CAV: Computer Aided Verification"}},{"year":"2009","publist_id":"1070","conference":{"name":"POPL: Principles of Programming Languages"},"page":"7 - 16","author":[{"full_name":"Dragojevic,Aleksandar","last_name":"Dragojevic","first_name":"Aleksandar"},{"last_name":"Guerraoui","first_name":"Rachid","full_name":"Guerraoui, Rachid"},{"full_name":"Singh, Anmol V","first_name":"Anmol","last_name":"Singh"},{"id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu","last_name":"Singh","full_name":"Vasu Singh"}],"title":"Preventing versus curing: avoiding conflicts in transactional memories","date_updated":"2021-01-12T07:56:34Z","publisher":"ACM","month":"01","date_published":"2009-01-01T00:00:00Z","doi":"1533","publication_status":"published","status":"public","quality_controlled":0,"day":"01","_id":"4385","date_created":"2018-12-11T12:08:35Z","type":"conference","citation":{"apa":"Dragojevic, A., Guerraoui, R., Singh, A., &#38; Singh, V. (2009). Preventing versus curing: avoiding conflicts in transactional memories (pp. 7–16). Presented at the POPL: Principles of Programming Languages, ACM. <a href=\"https://doi.org/1533\">https://doi.org/1533</a>","mla":"Dragojevic, Aleksandar, et al. <i>Preventing versus Curing: Avoiding Conflicts in Transactional Memories</i>. ACM, 2009, pp. 7–16, doi:<a href=\"https://doi.org/1533\">1533</a>.","short":"A. Dragojevic, R. Guerraoui, A. Singh, V. Singh, in:, ACM, 2009, pp. 7–16.","ista":"Dragojevic A, Guerraoui R, Singh A, Singh V. 2009. Preventing versus curing: avoiding conflicts in transactional memories. 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,” presented at the POPL: Principles of Programming Languages, 2009, pp. 7–16.","ama":"Dragojevic A, Guerraoui R, Singh A, Singh V. Preventing versus curing: avoiding conflicts in transactional memories. In: ACM; 2009:7-16. doi:<a href=\"https://doi.org/1533\">1533</a>","chicago":"Dragojevic, Aleksandar, Rachid Guerraoui, Anmol Singh, and Vasu Singh. “Preventing versus Curing: Avoiding Conflicts in Transactional Memories,” 7–16. ACM, 2009. <a href=\"https://doi.org/1533\">https://doi.org/1533</a>."},"extern":1},{"date_updated":"2021-01-12T07:56:37Z","author":[{"full_name":"Pavol Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"full_name":"Alur, Rajeev","last_name":"Alur","first_name":"Rajeev"}],"title":"Automated Analysis of Java Methods for Confidentiality","alternative_title":["LNCS"],"date_published":"2009-07-01T00:00:00Z","month":"07","publisher":"Springer","year":"2009","page":"173 - 187","publist_id":"1067","conference":{"name":"CAV: Computer Aided Verification"},"_id":"4391","date_created":"2018-12-11T12:08:36Z","quality_controlled":0,"day":"01","status":"public","citation":{"chicago":"Cerny, Pavol, and Rajeev Alur. “Automated Analysis of Java Methods for Confidentiality,” 173–87. Springer, 2009. <a href=\"https://doi.org/1548\">https://doi.org/1548</a>.","ama":"Cerny P, Alur R. Automated Analysis of Java Methods for Confidentiality. In: Springer; 2009:173-187. doi:<a href=\"https://doi.org/1548\">1548</a>","ista":"Cerny P, Alur R. 2009. Automated Analysis of Java Methods for Confidentiality. CAV: Computer Aided Verification, LNCS, , 173–187.","ieee":"P. Cerny and R. Alur, “Automated Analysis of Java Methods for Confidentiality,” presented at the CAV: Computer Aided Verification, 2009, pp. 173–187.","short":"P. Cerny, R. Alur, in:, Springer, 2009, pp. 173–187.","mla":"Cerny, Pavol, and Rajeev Alur. <i>Automated Analysis of Java Methods for Confidentiality</i>. Springer, 2009, pp. 173–87, doi:<a href=\"https://doi.org/1548\">1548</a>.","apa":"Cerny, P., &#38; Alur, R. (2009). Automated Analysis of Java Methods for Confidentiality (pp. 173–187). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/1548\">https://doi.org/1548</a>"},"extern":1,"type":"conference","doi":"1548","publication_status":"published"},{"date_updated":"2023-02-23T11:06:20Z","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Algorithmic analysis of array-accessing programs","author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"full_name":"Weinstein, Scott","last_name":"Weinstein","first_name":"Scott"}],"intvolume":"      5771","month":"09","alternative_title":["LNCS"],"date_published":"2009-09-01T00:00:00Z","publisher":"Springer","language":[{"iso":"eng"}],"year":"2009","page":"86 - 101","publist_id":"1056","conference":{"start_date":"2009-09-07","end_date":"2009-09-11","name":"CSL: Computer Science Logic","location":"Coimbra, Portugal"},"_id":"4403","date_created":"2018-12-11T12:08:40Z","quality_controlled":"1","status":"public","day":"01","citation":{"mla":"Alur, Rajeev, et al. <i>Algorithmic Analysis of Array-Accessing Programs</i>. Vol. 5771, Springer, 2009, pp. 86–101, doi:<a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">10.1007/978-3-642-04027-6_9</a>.","apa":"Alur, R., Cerny, P., &#38; Weinstein, S. (2009). Algorithmic analysis of array-accessing programs (Vol. 5771, pp. 86–101). Presented at the CSL: Computer Science Logic, Coimbra, Portugal: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">https://doi.org/10.1007/978-3-642-04027-6_9</a>","chicago":"Alur, Rajeev, Pavol Cerny, and Scott Weinstein. “Algorithmic Analysis of Array-Accessing Programs,” 5771:86–101. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">https://doi.org/10.1007/978-3-642-04027-6_9</a>.","short":"R. Alur, P. Cerny, S. Weinstein, in:, Springer, 2009, pp. 86–101.","ieee":"R. Alur, P. Cerny, and S. Weinstein, “Algorithmic analysis of array-accessing programs,” presented at the CSL: Computer Science Logic, Coimbra, Portugal, 2009, vol. 5771, pp. 86–101.","ista":"Alur R, Cerny P, Weinstein S. 2009. Algorithmic analysis of array-accessing programs. CSL: Computer Science Logic, LNCS, vol. 5771, 86–101.","ama":"Alur R, Cerny P, Weinstein S. Algorithmic analysis of array-accessing programs. In: Vol 5771. Springer; 2009:86-101. doi:<a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">10.1007/978-3-642-04027-6_9</a>"},"extern":"1","volume":5771,"type":"conference","abstract":[{"lang":"eng","text":"For programs whose data variables range over boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this paper, we consider algorithmic verification of programs that use boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over a potentially unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) Pspace-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly-nested loops. The second result establishes connections to automata and logics defining languages over data words."}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"2967"}]},"oa_version":"Submitted Version","main_file_link":[{"url":"http://repository.upenn.edu/cis_reports/894/","open_access":"1"}],"publication_status":"published","doi":"10.1007/978-3-642-04027-6_9"},{"main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/sliding-window_abstraction_for_infinite_markov_chains.pdf"}],"publication_status":"published","doi":"10.1007/978-3-642-02658-4_27","_id":"4453","date_created":"2018-12-11T12:08:55Z","day":"01","quality_controlled":0,"status":"public","extern":1,"citation":{"chicago":"Henzinger, Thomas A, Maria Mateescu, and Verena Wolf. “Sliding-Window Abstraction for Infinite Markov Chains,” 5643:337–52. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">https://doi.org/10.1007/978-3-642-02658-4_27</a>.","ista":"Henzinger TA, Mateescu M, Wolf V. 2009. Sliding-window abstraction for infinite Markov chains. CAV: Computer Aided Verification, LNCS, vol. 5643, 337–352.","short":"T.A. Henzinger, M. Mateescu, V. Wolf, in:, Springer, 2009, pp. 337–352.","ieee":"T. A. Henzinger, M. Mateescu, and V. Wolf, “Sliding-window abstraction for infinite Markov chains,” presented at the CAV: Computer Aided Verification, 2009, vol. 5643, pp. 337–352.","ama":"Henzinger TA, Mateescu M, Wolf V. Sliding-window abstraction for infinite Markov chains. In: Vol 5643. Springer; 2009:337-352. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">10.1007/978-3-642-02658-4_27</a>","mla":"Henzinger, Thomas A., et al. <i>Sliding-Window Abstraction for Infinite Markov Chains</i>. Vol. 5643, Springer, 2009, pp. 337–52, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">10.1007/978-3-642-02658-4_27</a>.","apa":"Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Sliding-window abstraction for infinite Markov chains (Vol. 5643, pp. 337–352). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">https://doi.org/10.1007/978-3-642-02658-4_27</a>"},"volume":5643,"type":"conference","file_date_updated":"2020-07-14T12:46:30Z","abstract":[{"lang":"eng","text":"We present an on-the-fly abstraction technique for infinite-state continuous -time Markov chains. We consider Markov chains that are specified by a finite set of transition classes. Such models naturally represent biochemical reactions and therefore play an important role in the stochastic modeling of biological systems. We approximate the transient probability distributions at various time instances by solving a sequence of dynamically constructed abstract models, each depending on the previous one. Each abstract model is a finite Markov chain that represents the behavior of the original, infinite chain during a specific time interval. Our approach provides complete information about probability distributions, not just about individual parameters like the mean. The error of each abstraction can be computed, and the precision of the abstraction refined when desired. We implemented the algorithm and demonstrate its usefulness and efficiency on several case studies from systems biology."}],"pubrep_id":"40","year":"2009","page":"337 - 352","conference":{"name":"CAV: Computer Aided Verification"},"publist_id":"278","date_updated":"2021-01-12T07:57:04Z","file":[{"file_name":"IST-2012-40-v1+1_Sliding-window_abstraction_for_infinite_markov_chains.pdf","date_updated":"2020-07-14T12:46:30Z","date_created":"2018-12-12T10:12:20Z","file_id":"4938","content_type":"application/pdf","creator":"system","file_size":804295,"checksum":"36b974111521ea534aae294166e93a63","access_level":"open_access","relation":"main_file"}],"oa":1,"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"},{"full_name":"Maria Mateescu","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Mateescu"},{"first_name":"Verena","last_name":"Wolf","full_name":"Wolf, Verena"}],"title":"Sliding-window abstraction for infinite Markov chains","intvolume":"      5643","month":"01","alternative_title":["LNCS"],"date_published":"2009-01-01T00:00:00Z","acknowledgement":"The research has been partially funded by the Swiss National Science Foundation under grant 205321-111840.","publisher":"Springer"},{"publication_status":"published","doi":"10.1007/978-3-642-03845-7_12","related_material":{"record":[{"relation":"later_version","status":"public","id":"3364"}]},"citation":{"chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Approximation of Event Probabilities in Noisy Cellular Processes,” 5688:173–88. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-03845-7_12\">https://doi.org/10.1007/978-3-642-03845-7_12</a>.","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, Springer, 2009, pp. 173–188.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Approximation of event probabilities in noisy cellular processes. CMSB: Computational Methods in Systems Biology, LNCS, vol. 5688, 173–188.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Approximation of event probabilities in noisy cellular processes,” presented at the CMSB: Computational Methods in Systems Biology, 2009, vol. 5688, pp. 173–188.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Approximation of event probabilities in noisy cellular processes. In: Vol 5688. Springer; 2009:173-188. doi:<a href=\"https://doi.org/10.1007/978-3-642-03845-7_12\">10.1007/978-3-642-03845-7_12</a>","mla":"Didier, Frédéric, et al. <i>Approximation of Event Probabilities in Noisy Cellular Processes</i>. Vol. 5688, Springer, 2009, pp. 173–88, doi:<a href=\"https://doi.org/10.1007/978-3-642-03845-7_12\">10.1007/978-3-642-03845-7_12</a>.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Approximation of event probabilities in noisy cellular processes (Vol. 5688, pp. 173–188). Presented at the CMSB: Computational Methods in Systems Biology, Springer. <a href=\"https://doi.org/10.1007/978-3-642-03845-7_12\">https://doi.org/10.1007/978-3-642-03845-7_12</a>"},"extern":1,"volume":5688,"type":"conference","abstract":[{"text":"Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete -state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive.\nWe present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required.","lang":"eng"}],"date_created":"2018-12-11T12:09:21Z","_id":"4535","day":"17","quality_controlled":0,"status":"public","page":"173 - 188","publist_id":"189","conference":{"name":"CMSB: Computational Methods in Systems Biology"},"year":"2009","intvolume":"      5688","month":"08","alternative_title":["LNCS"],"date_published":"2009-08-17T00:00:00Z","publisher":"Springer","acknowledgement":"This research was supported in part by the Swiss National Science Foundation under grant 205321-111840 and by the Excellence Cluster on Multimodal Computing and Interaction.","date_updated":"2023-02-23T11:24:03Z","title":"Approximation of event probabilities in noisy cellular processes","author":[{"full_name":"Didier, Frédéric","last_name":"Didier","first_name":"Frédéric"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Thomas Henzinger"},{"full_name":"Maria Mateescu","last_name":"Mateescu","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}]}]