[{"title":"A model of substitution trajectories in sequence space and long-term protein evolution","citation":{"ista":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.","ieee":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","chicago":"Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/molbev/msu318\">https://doi.org/10.1093/molbev/msu318</a>.","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:<a href=\"https://doi.org/10.1093/molbev/msu318\">10.1093/molbev/msu318</a>.","short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.","apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., &#38; Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msu318\">https://doi.org/10.1093/molbev/msu318</a>","ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. <i>Molecular Biology and Evolution</i>. 2015;32(2):542-554. doi:<a href=\"https://doi.org/10.1093/molbev/msu318\">10.1093/molbev/msu318</a>"},"oa_version":"None","year":"2015","type":"journal_article","author":[{"first_name":"Dinara","full_name":"Usmanova, Dinara","last_name":"Usmanova"},{"last_name":"Ferretti","full_name":"Ferretti, Luca","first_name":"Luca"},{"full_name":"Povolotskaya, Inna","first_name":"Inna","last_name":"Povolotskaya"},{"first_name":"Peter","full_name":"Vlasov, Peter","last_name":"Vlasov"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"}],"publist_id":"6804","day":"01","doi":"10.1093/molbev/msu318","date_updated":"2021-01-12T08:19:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"issue":"2","page":"542 - 554","date_published":"2015-02-01T00:00:00Z","_id":"848","abstract":[{"lang":"eng","text":"The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution."}],"date_created":"2018-12-11T11:48:49Z","extern":"1","month":"02","publication_status":"published","publisher":"Oxford University Press","volume":32,"status":"public","intvolume":"        32","quality_controlled":"1","publication":"Molecular Biology and Evolution"},{"article_processing_charge":"No","issue":"4","page":"1553-1560","date_created":"2020-09-18T10:46:14Z","_id":"8495","abstract":[{"text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.","lang":"eng"}],"date_published":"2015-12-21T00:00:00Z","month":"12","extern":"1","publisher":"American Mathematical Society","publication_status":"published","intvolume":"       144","status":"public","volume":144,"publication":"Proceedings of the American Mathematical Society","quality_controlled":"1","title":"A note on micro-instability for Hamiltonian systems close to integrable","citation":{"ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2015. <a href=\"https://doi.org/10.1090/proc/12796\">https://doi.org/10.1090/proc/12796</a>.","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:<a href=\"https://doi.org/10.1090/proc/12796\">10.1090/proc/12796</a>.","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","apa":"Bounemoura, A., &#38; Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/12796\">https://doi.org/10.1090/proc/12796</a>","ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. <i>Proceedings of the American Mathematical Society</i>. 2015;144(4):1553-1560. doi:<a href=\"https://doi.org/10.1090/proc/12796\">10.1090/proc/12796</a>"},"author":[{"last_name":"Bounemoura","full_name":"Bounemoura, Abed","first_name":"Abed"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"type":"journal_article","oa_version":"None","year":"2015","article_type":"letter_note","day":"21","publication_identifier":{"issn":["0002-9939","1088-6826"]},"doi":"10.1090/proc/12796","date_updated":"2021-01-12T08:19:40Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2015-06-30T00:00:00Z","_id":"8498","date_created":"2020-09-18T10:46:43Z","abstract":[{"text":"In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$  be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7].","lang":"eng"}],"extern":"1","month":"06","issue":"8","article_processing_charge":"No","page":"2699-2720","volume":28,"status":"public","intvolume":"        28","quality_controlled":"1","publication":"Nonlinearity","publisher":"IOP Publishing","publication_status":"published","year":"2015","oa_version":"None","type":"journal_article","author":[{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"},{"last_name":"Zhang","first_name":"K","full_name":"Zhang, K"}],"day":"30","article_type":"original","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","citation":{"mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” <i>Nonlinearity</i>, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:<a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">10.1088/0951-7715/28/8/2699</a>.","chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” <i>Nonlinearity</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">https://doi.org/10.1088/0951-7715/28/8/2699</a>.","ista":"Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” <i>Nonlinearity</i>, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015.","ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. <i>Nonlinearity</i>. 2015;28(8):2699-2720. doi:<a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">10.1088/0951-7715/28/8/2699</a>","apa":"Kaloshin, V., &#38; Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">https://doi.org/10.1088/0951-7715/28/8/2699</a>","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720."},"doi":"10.1088/0951-7715/28/8/2699","publication_identifier":{"issn":["0951-7715","1361-6544"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:41Z","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"]},{"publisher":"European Mathematical Society Publishing House","publication_status":"published","intvolume":"        17","status":"public","volume":17,"publication":"Journal of the European Mathematical Society","quality_controlled":"1","article_processing_charge":"No","issue":"1","page":"71-149","_id":"8499","date_created":"2020-09-18T10:46:50Z","date_published":"2015-02-05T00:00:00Z","abstract":[{"text":"We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0<T<Kc.","lang":"eng"}],"month":"02","extern":"1","publication_identifier":{"issn":["1435-9855"]},"doi":"10.4171/jems/499","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:41Z","language":[{"iso":"eng"}],"title":"Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation","citation":{"mla":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:<a href=\"https://doi.org/10.4171/jems/499\">10.4171/jems/499</a>.","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.","ista":"Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149.","chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society Publishing House, 2015. <a href=\"https://doi.org/10.4171/jems/499\">https://doi.org/10.4171/jems/499</a>.","apa":"Guardia, M., &#38; Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. <i>Journal of the European Mathematical Society</i>. European Mathematical Society Publishing House. <a href=\"https://doi.org/10.4171/jems/499\">https://doi.org/10.4171/jems/499</a>","ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. <i>Journal of the European Mathematical Society</i>. 2015;17(1):71-149. doi:<a href=\"https://doi.org/10.4171/jems/499\">10.4171/jems/499</a>","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149."},"author":[{"full_name":"Guardia, Marcel","first_name":"Marcel","last_name":"Guardia"},{"last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"type":"journal_article","year":"2015","oa_version":"None","article_type":"original","day":"05"},{"_id":"866","date_published":"2015-07-28T00:00:00Z","date_created":"2018-12-11T11:48:55Z","abstract":[{"text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF.","lang":"eng"}],"month":"07","extern":1,"issue":"30","page":"9328 - 9333","status":"public","intvolume":"       112","volume":112,"publication":"PNAS","quality_controlled":0,"publisher":"National Academy of Sciences","publication_status":"published","type":"journal_article","author":[{"last_name":"Kretz","first_name":"Colin","full_name":"Kretz, Colin A"},{"full_name":"Dai, Manhong","first_name":"Manhong","last_name":"Dai"},{"last_name":"Soylemez","full_name":"Soylemez, Onuralp","first_name":"Onuralp"},{"full_name":"Yee, Andrew","first_name":"Andrew","last_name":"Yee"},{"last_name":"Desch","first_name":"Karl","full_name":"Desch, Karl C"},{"first_name":"David","full_name":"Siemieniak, David R","last_name":"Siemieniak"},{"last_name":"Tomberg","first_name":"Kärt","full_name":"Tomberg, Kärt"},{"last_name":"Kondrashov","full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Meng, Fan","first_name":"Fan","last_name":"Meng"},{"full_name":"Ginsburg, David B","first_name":"David","last_name":"Ginsburg"}],"year":"2015","day":"28","publist_id":"6783","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","citation":{"ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","ieee":"C. Kretz <i>et al.</i>, “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” <i>PNAS</i>, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>.","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>","ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. 2015;112(30):9328-9333. doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>"},"doi":"10.1073/pnas.1511328112","date_updated":"2021-01-12T08:20:26Z","acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\n"},{"publication":"Trends in Genetics","quality_controlled":0,"intvolume":"        31","status":"public","volume":31,"publisher":"Elsevier","publication_status":"published","month":"01","extern":1,"date_published":"2015-01-01T00:00:00Z","_id":"886","date_created":"2018-12-11T11:49:01Z","abstract":[{"lang":"eng","text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space."}],"page":"24 - 33","issue":"1","date_updated":"2021-01-12T08:21:16Z","doi":"10.1016/j.tig.2014.09.009","acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.","publist_id":"6764","day":"01","type":"journal_article","author":[{"last_name":"Kondrashov","full_name":"Kondrashov, Dmitry A","first_name":"Dmitry"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"}],"year":"2015","citation":{"short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. <i>Trends in Genetics</i>. 2015;31(1):24-33. doi:<a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">10.1016/j.tig.2014.09.009</a>","apa":"Kondrashov, D., &#38; Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">https://doi.org/10.1016/j.tig.2014.09.009</a>","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” <i>Trends in Genetics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">https://doi.org/10.1016/j.tig.2014.09.009</a>.","ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” <i>Trends in Genetics</i>, vol. 31, no. 1. Elsevier, pp. 24–33, 2015.","ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” <i>Trends in Genetics</i>, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:<a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">10.1016/j.tig.2014.09.009</a>."},"title":"Topological features of rugged fitness landscapes in sequence space"},{"publist_id":"5551","year":"2015","has_accepted_license":"1","oa_version":"Published Version","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:01Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"5005","date_created":"2018-12-12T10:13:23Z","file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf","creator":"system","file_size":2314406,"checksum":"44d30fbb543774b076b4938bd36af9d7","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access"}],"_id":"1615","abstract":[{"text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches.","lang":"eng"}],"date_published":"2015-10-20T00:00:00Z","issue":"3","file_date_updated":"2020-07-14T12:45:07Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"470","volume":13,"publication_status":"published","oa":1,"day":"20","author":[{"last_name":"Hammer","first_name":"Matthieu","full_name":"Hammer, Matthieu"},{"first_name":"Dilja","full_name":"Krueger Burg, Dilja","last_name":"Krueger Burg"},{"full_name":"Tuffy, Liam","first_name":"Liam","last_name":"Tuffy"},{"last_name":"Cooper","full_name":"Cooper, Benjamin","first_name":"Benjamin"},{"last_name":"Taschenberger","full_name":"Taschenberger, Holger","first_name":"Holger"},{"last_name":"Goswami","first_name":"Sarit","full_name":"Goswami, Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ehrenreich, Hannelore","first_name":"Hannelore","last_name":"Ehrenreich"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"},{"full_name":"Varoqueaux, Frederique","first_name":"Frederique","last_name":"Varoqueaux"},{"full_name":"Rhee, Jeong","first_name":"Jeong","last_name":"Rhee"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"}],"type":"journal_article","citation":{"mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>.","ieee":"M. Hammer <i>et al.</i>, “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” <i>Cell Reports</i>, vol. 13, no. 3. Cell Press, pp. 516–523, 2015.","ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>.","apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. 2015;13(3):516-523. doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523."},"title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1016/j.celrep.2015.09.011","acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","month":"10","date_created":"2018-12-11T11:53:02Z","page":"516 - 523","publication":"Cell Reports","quality_controlled":"1","department":[{"_id":"PeJo"}],"intvolume":"        13","status":"public","publisher":"Cell Press"},{"citation":{"apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>","ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. 2015;54(27):4163-4166. doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>","short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.","mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>.","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166.","ieee":"C. Veldkamp <i>et al.</i>, “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” <i>Biochemistry</i>, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>."},"ec_funded":1,"title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","day":"26","author":[{"full_name":"Veldkamp, Christopher","first_name":"Christopher","last_name":"Veldkamp"},{"id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6165-5738","last_name":"Kiermaier","full_name":"Kiermaier, Eva","first_name":"Eva"},{"last_name":"Gabel Eissens","first_name":"Skylar","full_name":"Gabel Eissens, Skylar"},{"first_name":"Miranda","full_name":"Gillitzer, Miranda","last_name":"Gillitzer"},{"last_name":"Lippner","full_name":"Lippner, David","first_name":"David"},{"last_name":"Disilvio","full_name":"Disilvio, Frank","first_name":"Frank"},{"last_name":"Mueller","first_name":"Casey","full_name":"Mueller, Casey"},{"last_name":"Wantuch","full_name":"Wantuch, Paeton","first_name":"Paeton"},{"full_name":"Chaffee, Gary","first_name":"Gary","last_name":"Chaffee"},{"last_name":"Famiglietti","first_name":"Michael","full_name":"Famiglietti, Michael"},{"first_name":"Danielle","full_name":"Zgoba, Danielle","last_name":"Zgoba"},{"first_name":"Asha","full_name":"Bailey, Asha","last_name":"Bailey"},{"last_name":"Bah","first_name":"Yaya","full_name":"Bah, Yaya"},{"last_name":"Engebretson","first_name":"Samantha","full_name":"Engebretson, Samantha"},{"last_name":"Graupner","first_name":"David","full_name":"Graupner, David"},{"first_name":"Emily","full_name":"Lackner, Emily","last_name":"Lackner"},{"last_name":"Larosa","first_name":"Vincent","full_name":"Larosa, Vincent"},{"last_name":"Medeiros","full_name":"Medeiros, Tysha","first_name":"Tysha"},{"first_name":"Michael","full_name":"Olson, Michael","last_name":"Olson"},{"full_name":"Phillips, Andrew","first_name":"Andrew","last_name":"Phillips"},{"first_name":"Harley","full_name":"Pyles, Harley","last_name":"Pyles"},{"last_name":"Richard","full_name":"Richard, Amanda","first_name":"Amanda"},{"first_name":"Scott","full_name":"Schoeller, Scott","last_name":"Schoeller"},{"first_name":"Boris","full_name":"Touzeau, Boris","last_name":"Touzeau"},{"full_name":"Williams, Larry","first_name":"Larry","last_name":"Williams"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"},{"last_name":"Peterson","full_name":"Peterson, Francis","first_name":"Francis"}],"type":"journal_article","pmid":1,"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"}],"language":[{"iso":"eng"}],"doi":"10.1021/acs.biochem.5b00560","page":"4163 - 4166","month":"06","date_created":"2018-12-11T11:53:03Z","publisher":"American Chemical Society","publication":"Biochemistry","quality_controlled":"1","department":[{"_id":"MiSi"}],"intvolume":"        54","status":"public","publist_id":"5548","oa_version":"Submitted Version","year":"2015","scopus_import":"1","external_id":{"pmid":["26115234"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-03-30T11:32:57Z","article_processing_charge":"No","issue":"27","date_published":"2015-06-26T00:00:00Z","_id":"1618","abstract":[{"text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed.","lang":"eng"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/"}],"oa":1,"volume":54},{"quality_controlled":"1","department":[{"_id":"ToBo"}],"publication":"PLoS Biology","status":"public","intvolume":"        13","publisher":"Public Library of Science","month":"11","date_created":"2018-12-11T11:53:04Z","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1371/journal.pbio.1002299","project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"},{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9711"},{"status":"public","relation":"research_data","id":"9765"},{"status":"public","id":"6263","relation":"dissertation_contains"}]},"day":"18","type":"journal_article","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","first_name":"Guillaume","full_name":"Chevereau, Guillaume"},{"last_name":"Dravecka","first_name":"Marta","full_name":"Dravecka, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"full_name":"Batur, Tugce","first_name":"Tugce","last_name":"Batur"},{"last_name":"Guvenek","first_name":"Aysegul","full_name":"Guvenek, Aysegul"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay","first_name":"Dilay"},{"full_name":"Toprak, Erdal","first_name":"Erdal","last_name":"Toprak"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"ec_funded":1,"citation":{"short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., &#38; Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. 2015;13(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>","ieee":"G. Chevereau <i>et al.</i>, “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” <i>PLoS Biology</i>, vol. 13, no. 11. Public Library of Science, 2015.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>.","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>."},"title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","file_date_updated":"2020-07-14T12:45:07Z","volume":13,"pubrep_id":"468","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"article_number":"e1002299","file":[{"date_created":"2018-12-12T10:09:00Z","content_type":"application/pdf","file_id":"4723","relation":"main_file","checksum":"0e82e3279f50b15c6c170c042627802b","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","file_size":1387760,"creator":"system"}],"date_published":"2015-11-18T00:00:00Z","_id":"1619","abstract":[{"text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.","lang":"eng"}],"issue":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-25T23:30:14Z","scopus_import":1,"publist_id":"5547","year":"2015","has_accepted_license":"1","oa_version":"Published Version"},{"issue":"1","_id":"1623","abstract":[{"lang":"eng","text":"Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n"}],"date_published":"2015-11-25T00:00:00Z","article_number":"193","file":[{"file_name":"IST-2016-467-v1+1_s13068-015-0380-2.pdf","file_size":2914089,"creator":"system","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","checksum":"172b0b6f4eb2e5c22b7cec1d57dc0107","content_type":"application/pdf","file_id":"4796","relation":"main_file","date_created":"2018-12-12T10:10:11Z"}],"oa":1,"publication_status":"published","pubrep_id":"467","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":8,"file_date_updated":"2020-07-14T12:45:07Z","year":"2015","oa_version":"Published Version","has_accepted_license":"1","publist_id":"5537","scopus_import":1,"date_updated":"2021-01-12T06:52:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:53:05Z","month":"11","publisher":"BioMed Central","intvolume":"         8","status":"public","publication":"Biotechnology for Biofuels","department":[{"_id":"ToBo"}],"quality_controlled":"1","title":"Single-cell screening of photosynthetic growth and lactate production by cyanobacteria","citation":{"mla":"Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” <i>Biotechnology for Biofuels</i>, vol. 8, no. 1, 193, BioMed Central, 2015, doi:<a href=\"https://doi.org/10.1186/s13068-015-0380-2\">10.1186/s13068-015-0380-2</a>.","chicago":"Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” <i>Biotechnology for Biofuels</i>. BioMed Central, 2015. <a href=\"https://doi.org/10.1186/s13068-015-0380-2\">https://doi.org/10.1186/s13068-015-0380-2</a>.","ista":"Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.","ieee":"P. Hammar <i>et al.</i>, “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” <i>Biotechnology for Biofuels</i>, vol. 8, no. 1. BioMed Central, 2015.","ama":"Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. <i>Biotechnology for Biofuels</i>. 2015;8(1). doi:<a href=\"https://doi.org/10.1186/s13068-015-0380-2\">10.1186/s13068-015-0380-2</a>","apa":"Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., &#38; Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. <i>Biotechnology for Biofuels</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13068-015-0380-2\">https://doi.org/10.1186/s13068-015-0380-2</a>","short":"P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015)."},"type":"journal_article","author":[{"last_name":"Hammar","full_name":"Hammar, Petter","first_name":"Petter"},{"id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","last_name":"Angermayr","full_name":"Angermayr, Andreas","first_name":"Andreas"},{"first_name":"Staffan","full_name":"Sjostrom, Staffan","last_name":"Sjostrom"},{"full_name":"Van Der Meer, Josefin","first_name":"Josefin","last_name":"Van Der Meer"},{"last_name":"Hellingwerf","full_name":"Hellingwerf, Klaas","first_name":"Klaas"},{"last_name":"Hudson","first_name":"Elton","full_name":"Hudson, Elton"},{"full_name":"Joensson, Hakaan","first_name":"Hakaan","last_name":"Joensson"}],"day":"25","ddc":["570"],"doi":"10.1186/s13068-015-0380-2","language":[{"iso":"eng"}]},{"volume":5,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"466","file_date_updated":"2020-07-14T12:45:07Z","oa":1,"publication_status":"published","_id":"1624","abstract":[{"lang":"eng","text":"Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions."}],"date_published":"2015-11-25T00:00:00Z","article_number":"17147","file":[{"creator":"system","file_size":1021931,"file_name":"IST-2016-466-v1+1_srep17147.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","checksum":"38e06d8310d2087cae5f6d4d4bfe082b","file_id":"4947","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:29Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:05Z","scopus_import":1,"oa_version":"Published Version","year":"2015","has_accepted_license":"1","publist_id":"5536","status":"public","intvolume":"         5","department":[{"_id":"KrCh"}],"quality_controlled":"1","publication":"Scientific Reports","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:53:06Z","month":"11","doi":"10.1038/srep17147","ddc":["000"],"language":[{"iso":"eng"}],"acknowledgement":"The research was supported by the Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton foundation is gratefully acknowledged.","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Adlam","full_name":"Adlam, Ben","first_name":"Ben"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"type":"journal_article","day":"25","title":"Cellular cooperation with shift updating and repulsion","ec_funded":1,"citation":{"mla":"Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and Repulsion.” <i>Scientific Reports</i>, vol. 5, 17147, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep17147\">10.1038/srep17147</a>.","ieee":"A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation with shift updating and repulsion,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015.","ista":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation with shift updating and repulsion. Scientific Reports. 5, 17147.","chicago":"Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak. “Cellular Cooperation with Shift Updating and Repulsion.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep17147\">https://doi.org/10.1038/srep17147</a>.","apa":"Pavlogiannis, A., Chatterjee, K., Adlam, B., &#38; Nowak, M. (2015). Cellular cooperation with shift updating and repulsion. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep17147\">https://doi.org/10.1038/srep17147</a>","ama":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift updating and repulsion. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep17147\">10.1038/srep17147</a>","short":"A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5 (2015)."}},{"oa_version":"None","year":"2015","author":[{"full_name":"Bermano, Amit","first_name":"Amit","last_name":"Bermano"},{"last_name":"Beeler","first_name":"Thabo","full_name":"Beeler, Thabo"},{"last_name":"Kozlov","first_name":"Yeara","full_name":"Kozlov, Yeara"},{"first_name":"Derek","full_name":"Bradley, Derek","last_name":"Bradley"},{"first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gross","full_name":"Gross, Markus","first_name":"Markus"}],"type":"conference","publist_id":"5535","day":"27","conference":{"location":"Los Angeles, CA, United States","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","end_date":"2015-08-13"},"title":"Detailed spatio-temporal reconstruction of eyelids","citation":{"ista":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. 2015. Detailed spatio-temporal reconstruction of eyelids. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 44.","ieee":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, and M. Gross, “Detailed spatio-temporal reconstruction of eyelids,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","chicago":"Bermano, Amit, Thabo Beeler, Yeara Kozlov, Derek Bradley, Bernd Bickel, and Markus Gross. “Detailed Spatio-Temporal Reconstruction of Eyelids,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766924\">https://doi.org/10.1145/2766924</a>.","mla":"Bermano, Amit, et al. <i>Detailed Spatio-Temporal Reconstruction of Eyelids</i>. Vol. 34, no. 4, 44, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766924\">10.1145/2766924</a>.","short":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, M. Gross, in:, ACM, 2015.","apa":"Bermano, A., Beeler, T., Kozlov, Y., Bradley, D., Bickel, B., &#38; Gross, M. (2015). Detailed spatio-temporal reconstruction of eyelids (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766924\">https://doi.org/10.1145/2766924</a>","ama":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. Detailed spatio-temporal reconstruction of eyelids. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766924\">10.1145/2766924</a>"},"doi":"10.1145/2766924","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:05Z","language":[{"iso":"eng"}],"scopus_import":1,"date_published":"2015-07-27T00:00:00Z","_id":"1625","date_created":"2018-12-11T11:53:06Z","abstract":[{"lang":"eng","text":"In recent years we have seen numerous improvements on 3D scanning and tracking of human faces, greatly advancing the creation of digital doubles for film and video games. However, despite the high-resolution quality of the reconstruction approaches available, current methods are unable to capture one of the most important regions of the face - the eye region. In this work we present the first method for detailed spatio-temporal reconstruction of eyelids. Tracking and reconstructing eyelids is extremely challenging, as this region exhibits very complex and unique skin deformation where skin is folded under while opening the eye. Furthermore, eyelids are often only partially visible and obstructed due to selfocclusion and eyelashes. Our approach is to combine a geometric deformation model with image data, leveraging multi-view stereo, optical flow, contour tracking and wrinkle detection from local skin appearance. Our deformation model serves as a prior that enables reconstruction of eyelids even under strong self-occlusions caused by rolling and folding skin as the eye opens and closes. The output is a person-specific, time-varying eyelid reconstruction with anatomically plausible deformations. Our high-resolution detailed eyelids couple naturally with current facial performance capture approaches. As a result, our method can largely increase the fidelity of facial capture and the creation of digital doubles."}],"article_number":"44","month":"07","issue":"4","volume":34,"status":"public","intvolume":"        34","quality_controlled":"1","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published"},{"title":"OmniAD: Data-driven omni-directional aerodynamics","conference":{"location":"Los Angeles, CA, United States","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","end_date":"2015-08-13"},"citation":{"mla":"Martin, Tobias, et al. <i>OmniAD: Data-Driven Omni-Directional Aerodynamics</i>. Vol. 34, no. 4, 113, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766919\">10.1145/2766919</a>.","chicago":"Martin, Tobias, Nobuyuki Umetani, and Bernd Bickel. “OmniAD: Data-Driven Omni-Directional Aerodynamics,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766919\">https://doi.org/10.1145/2766919</a>.","ista":"Martin T, Umetani N, Bickel B. 2015. OmniAD: Data-driven omni-directional aerodynamics. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 113.","ieee":"T. Martin, N. Umetani, and B. Bickel, “OmniAD: Data-driven omni-directional aerodynamics,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ama":"Martin T, Umetani N, Bickel B. OmniAD: Data-driven omni-directional aerodynamics. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766919\">10.1145/2766919</a>","apa":"Martin, T., Umetani, N., &#38; Bickel, B. (2015). OmniAD: Data-driven omni-directional aerodynamics (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766919\">https://doi.org/10.1145/2766919</a>","short":"T. Martin, N. Umetani, B. Bickel, in:, ACM, 2015."},"type":"conference","author":[{"first_name":"Tobias","full_name":"Martin, Tobias","last_name":"Martin"},{"last_name":"Umetani","first_name":"Nobuyuki","full_name":"Umetani, Nobuyuki"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel"}],"year":"2015","alternative_title":["ACM Transactions on Graphics"],"oa_version":"None","publist_id":"5532","day":"27","doi":"10.1145/2766919","scopus_import":1,"date_updated":"2021-01-12T06:52:05Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","_id":"1626","date_created":"2018-12-11T11:53:06Z","date_published":"2015-07-27T00:00:00Z","abstract":[{"text":"This paper introduces &quot;OmniAD,&quot; a novel data-driven pipeline to model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally, aerodynamics are examined through elaborate wind tunnel experiments or expensive fluid dynamics computations, and are only measured for a small number of discrete wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag and lift, for any incoming wind direction using a novel representation based on spherical harmonics. Our datadriven technique acquires the aerodynamic properties of an object simply by capturing its falling motion using a single camera. Once model parameters are estimated, OmniAD enables realistic realtime simulation of rigid bodies, such as the tumbling and gliding of leaves, without simulating the surrounding air. In addition, we propose an intuitive user interface based on OmniAD to interactively design three-dimensional kites that actually fly. Various nontraditional kites were designed to demonstrate the physical validity of our model.","lang":"eng"}],"month":"07","article_number":"113","publication_status":"published","publisher":"ACM","intvolume":"        34","status":"public","volume":34,"department":[{"_id":"BeBi"}],"quality_controlled":"1"},{"status":"public","intvolume":"        34","volume":34,"quality_controlled":"1","department":[{"_id":"BeBi"}],"publication_status":"published","publisher":"ACM","date_created":"2018-12-11T11:53:07Z","_id":"1627","date_published":"2015-07-27T00:00:00Z","abstract":[{"lang":"eng","text":"We present a computational tool for fabrication-oriented design of flexible rod meshes. Given a deformable surface and a set of deformed poses as input, our method automatically computes a printable rod mesh that, once manufactured, closely matches the input poses under the same boundary conditions. The core of our method is formed by an optimization scheme that adjusts the cross-sectional profiles of the rods and their rest centerline in order to best approximate the target deformations. This approach allows us to locally control the bending and stretching resistance of the surface with a single material, yielding high design flexibility and low fabrication cost."}],"month":"07","article_number":"138","issue":"4","doi":"10.1145/2766998","scopus_import":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:06Z","acknowledgement":"This work was supported in part by grants from the Spanish Ministry of Economy (TIN2012-35840), and the European Research Council (ERC Starting Grant no. 280135 Animetrics).","type":"conference","author":[{"last_name":"Pérez","full_name":"Pérez, Jesús","first_name":"Jesús"},{"full_name":"Thomaszewski, Bernhard","first_name":"Bernhard","last_name":"Thomaszewski"},{"full_name":"Coros, Stelian","first_name":"Stelian","last_name":"Coros"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"},{"first_name":"José","full_name":"Canabal, José","last_name":"Canabal"},{"full_name":"Sumner, Robert","first_name":"Robert","last_name":"Sumner"},{"full_name":"Otaduy, Miguel","first_name":"Miguel","last_name":"Otaduy"}],"year":"2015","oa_version":"None","day":"27","publist_id":"5530","title":"Design and fabrication of flexible rod meshes","conference":{"end_date":"2015-08-13","start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Los Angeles, CA, United States"},"citation":{"mla":"Pérez, Jesús, et al. <i>Design and Fabrication of Flexible Rod Meshes</i>. Vol. 34, no. 4, 138, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766998\">10.1145/2766998</a>.","chicago":"Pérez, Jesús, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, José Canabal, Robert Sumner, and Miguel Otaduy. “Design and Fabrication of Flexible Rod Meshes,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766998\">https://doi.org/10.1145/2766998</a>.","ieee":"J. Pérez <i>et al.</i>, “Design and fabrication of flexible rod meshes,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ista":"Pérez J, Thomaszewski B, Coros S, Bickel B, Canabal J, Sumner R, Otaduy M. 2015. Design and fabrication of flexible rod meshes. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 138.","ama":"Pérez J, Thomaszewski B, Coros S, et al. Design and fabrication of flexible rod meshes. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766998\">10.1145/2766998</a>","apa":"Pérez, J., Thomaszewski, B., Coros, S., Bickel, B., Canabal, J., Sumner, R., &#38; Otaduy, M. (2015). Design and fabrication of flexible rod meshes (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766998\">https://doi.org/10.1145/2766998</a>","short":"J. Pérez, B. Thomaszewski, S. Coros, B. Bickel, J. Canabal, R. Sumner, M. Otaduy, in:, ACM, 2015."}},{"article_processing_charge":"No","issue":"4","article_number":"136","abstract":[{"lang":"eng","text":"We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications."}],"_id":"1628","date_published":"2015-08-01T00:00:00Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/2766926"}],"oa":1,"volume":34,"publist_id":"5529","year":"2015","oa_version":"Published Version","scopus_import":1,"date_updated":"2021-01-12T06:52:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","date_created":"2018-12-11T11:53:07Z","publisher":"ACM","department":[{"_id":"BeBi"}],"quality_controlled":"1","intvolume":"        34","status":"public","citation":{"ieee":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross, “Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","ista":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 136.","chicago":"Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio, and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766926\">https://doi.org/10.1145/2766926</a>.","mla":"Schumacher, Christian, et al. <i>Microstructures to Control Elasticity in 3D Printing</i>. Vol. 34, no. 4, 136, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766926\">10.1145/2766926</a>.","short":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:, ACM, 2015.","apa":"Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., &#38; Gross, M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2766926\">https://doi.org/10.1145/2766926</a>","ama":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766926\">10.1145/2766926</a>"},"title":"Microstructures to control elasticity in 3D printing","conference":{"location":"Los Angeles, CA, USA","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","end_date":"2015-08-13"},"day":"01","type":"conference","author":[{"first_name":"Christian","full_name":"Schumacher, Christian","last_name":"Schumacher"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rys, Jan","first_name":"Jan","last_name":"Rys"},{"last_name":"Marschner","full_name":"Marschner, Steve","first_name":"Steve"},{"first_name":"Chiara","full_name":"Daraio, Chiara","last_name":"Daraio"},{"last_name":"Gross","first_name":"Markus","full_name":"Gross, Markus"}],"language":[{"iso":"eng"}],"doi":"10.1145/2766926"},{"quality_controlled":"1","department":[{"_id":"ChWo"}],"intvolume":"        34","status":"public","publisher":"ACM","month":"07","date_created":"2018-12-11T11:53:08Z","language":[{"iso":"eng"}],"doi":"10.1145/2766933","ddc":["000"],"project":[{"name":"Deep Pictures: Creating Visual and Haptic Vector Images","grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledgement":"This publication is based upon work supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no. P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23).","day":"27","type":"conference","author":[{"last_name":"Guerrero","full_name":"Guerrero, Paul","first_name":"Paul"},{"last_name":"Jeschke","first_name":"Stefan","full_name":"Jeschke, Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wimmer","full_name":"Wimmer, Michael","first_name":"Michael"},{"last_name":"Wonka","first_name":"Peter","full_name":"Wonka, Peter"}],"citation":{"mla":"Guerrero, Paul, et al. <i>Learning Shape Placements by Example</i>. Vol. 34, no. 4, 108, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766933\">10.1145/2766933</a>.","ista":"Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 108.","ieee":"P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","chicago":"Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning Shape Placements by Example,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766933\">https://doi.org/10.1145/2766933</a>.","apa":"Guerrero, P., Jeschke, S., Wimmer, M., &#38; Wonka, P. (2015). Learning shape placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766933\">https://doi.org/10.1145/2766933</a>","ama":"Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766933\">10.1145/2766933</a>","short":"P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015."},"title":"Learning shape placements by example","conference":{"location":"Los Angeles, CA, United States","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","end_date":"2015-08-13"},"file_date_updated":"2020-07-14T12:45:07Z","pubrep_id":"576","volume":34,"publication_status":"published","oa":1,"file":[{"date_created":"2018-12-12T10:07:49Z","file_id":"4647","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","checksum":"8b05a51e372c9b0b5af9a00098a9538b","file_size":11902290,"creator":"system","file_name":"IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf"}],"article_number":"108","abstract":[{"text":"We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D    scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction.","lang":"eng"}],"_id":"1630","date_published":"2015-07-27T00:00:00Z","issue":"4","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:07Z","publist_id":"5525","oa_version":"Submitted Version","has_accepted_license":"1","year":"2015"},{"day":"27","type":"conference","author":[{"last_name":"Ando","first_name":"Ryoichi","full_name":"Ando, Ryoichi"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"alternative_title":["ACM Transactions on Graphics"],"citation":{"mla":"Ando, Ryoichi, et al. <i>A Stream Function Solver for Liquid Simulations</i>. Vol. 34, no. 4, 53, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766935\">10.1145/2766935</a>.","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","ista":"Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 53.","chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver for Liquid Simulations,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766935\">https://doi.org/10.1145/2766935</a>.","apa":"Ando, R., Thuerey, N., &#38; Wojtan, C. (2015). A stream function solver for liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2766935\">https://doi.org/10.1145/2766935</a>","ama":"Ando R, Thuerey N, Wojtan C. A stream function solver for liquid simulations. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766935\">10.1145/2766935</a>","short":"R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015."},"title":"A stream function solver for liquid simulations","conference":{"location":"Los Angeles, CA, USA","start_date":"2015-08-09","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"language":[{"iso":"eng"}],"doi":"10.1145/2766935","ddc":["000"],"acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014 realFlow and ERC-2014- StG-638176 BigSplash.","month":"07","date_created":"2018-12-11T11:53:09Z","quality_controlled":"1","department":[{"_id":"ChWo"}],"status":"public","intvolume":"        34","publisher":"ACM","publist_id":"5523","year":"2015","oa_version":"Submitted Version","has_accepted_license":"1","scopus_import":1,"date_updated":"2023-02-23T10:07:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:11:52Z","content_type":"application/pdf","file_id":"4909","relation":"main_file","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","checksum":"7a9afdfaba9209157ce19376e15bc90b","file_name":"IST-2016-610-v1+1_vecpotential.pdf","file_size":21831121,"creator":"system"}],"article_number":"53","abstract":[{"text":"This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling.","lang":"eng"}],"_id":"1632","date_published":"2015-07-27T00:00:00Z","issue":"4","file_date_updated":"2020-07-14T12:45:07Z","pubrep_id":"610","volume":34,"publication_status":"published","oa":1},{"ec_funded":1,"citation":{"short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","apa":"Hahn, D., &#38; Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766896\">https://doi.org/10.1145/2766896</a>","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766896\">10.1145/2766896</a>","ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766896\">https://doi.org/10.1145/2766896</a>.","mla":"Hahn, David, and Chris Wojtan. <i>High-Resolution Brittle Fracture Simulation with Boundary Elements</i>. Vol. 34, no. 4, 151, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766896\">10.1145/2766896</a>."},"conference":{"end_date":"2015-08-13","start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Los Angeles, CA, United States"},"title":"High-resolution brittle fracture simulation with boundary elements","day":"27","author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David","first_name":"David","last_name":"Hahn"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"type":"conference","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"839","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"ddc":["000"],"doi":"10.1145/2766896","month":"07","date_created":"2018-12-11T11:53:09Z","publisher":"ACM","quality_controlled":"1","department":[{"_id":"ChWo"}],"intvolume":"        34","status":"public","publist_id":"5522","has_accepted_license":"1","year":"2015","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T12:02:56Z","scopus_import":1,"issue":"4","file":[{"checksum":"955aee971983f6b6152bcc1c9b4a7c20","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","file_size":20154270,"creator":"system","date_created":"2018-12-12T10:15:13Z","content_type":"application/pdf","file_id":"5131","relation":"main_file"}],"article_number":"151","abstract":[{"lang":"eng","text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix."}],"_id":"1633","date_published":"2015-07-27T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:45:07Z","volume":34,"pubrep_id":"609"},{"title":"Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams","conference":{"location":"Los Angeles, CA, United States","end_date":"2015-08-13","start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"citation":{"ista":"Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 149.","ieee":"F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","chicago":"Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2767003\">https://doi.org/10.1145/2767003</a>.","mla":"Da, Fang, et al. <i>Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams</i>. Vol. 34, no. 4, 149, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2767003\">10.1145/2767003</a>.","short":"F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015.","apa":"Da, F., Batty, C., Wojtan, C., &#38; Grinspun, E. (2015). Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2767003\">https://doi.org/10.1145/2767003</a>","ama":"Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2767003\">10.1145/2767003</a>"},"ec_funded":1,"author":[{"last_name":"Da","full_name":"Da, Fang","first_name":"Fang"},{"last_name":"Batty","first_name":"Christopher","full_name":"Batty, Christopher"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"},{"last_name":"Grinspun","first_name":"Eitan","full_name":"Grinspun, Eitan"}],"type":"conference","day":"27","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ddc":["000"],"doi":"10.1145/2767003","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:53:09Z","month":"07","publisher":"ACM","intvolume":"        34","status":"public","quality_controlled":"1","department":[{"_id":"ChWo"}],"oa_version":"Submitted Version","year":"2015","has_accepted_license":"1","publist_id":"5521","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:07:42Z","issue":"4","date_published":"2015-07-27T00:00:00Z","_id":"1634","abstract":[{"text":"Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart.","lang":"eng"}],"file":[{"date_created":"2018-12-12T10:11:14Z","content_type":"application/pdf","file_id":"4867","relation":"main_file","checksum":"57b07d78d2d612a8052744b37d4a71fa","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","file_name":"IST-2016-608-v1+1_doublebubbles.pdf","creator":"system","file_size":8973215}],"article_number":"149","oa":1,"publication_status":"published","pubrep_id":"608","volume":34,"file_date_updated":"2020-07-14T12:45:07Z"},{"citation":{"mla":"Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” <i>Annales de La Faculté Des Sciences de Toulouse</i>, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:<a href=\"https://doi.org/10.5802/afst.1464\">10.5802/afst.1464</a>.","ista":"Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800.","ieee":"M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” <i>Annales de la faculté des sciences de Toulouse</i>, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.","chicago":"Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” <i>Annales de La Faculté Des Sciences de Toulouse</i>. Faculté des sciences de Toulouse, 2015. <a href=\"https://doi.org/10.5802/afst.1464\">https://doi.org/10.5802/afst.1464</a>.","apa":"Erbar, M., Maas, J., &#38; Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. <i>Annales de La Faculté Des Sciences de Toulouse</i>. Faculté des sciences de Toulouse. <a href=\"https://doi.org/10.5802/afst.1464\">https://doi.org/10.5802/afst.1464</a>","ama":"Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. <i>Annales de la faculté des sciences de Toulouse</i>. 2015;24(4):781-800. doi:<a href=\"https://doi.org/10.5802/afst.1464\">10.5802/afst.1464</a>","short":"M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800."},"title":"Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models","day":"01","author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","first_name":"Jan"},{"last_name":"Tetali","full_name":"Tetali, Prasad","first_name":"Prasad"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.5802/afst.1464","page":"781 - 800","month":"01","date_created":"2018-12-11T11:53:10Z","publisher":"Faculté des sciences de Toulouse","publication":"Annales de la faculté des sciences de Toulouse","quality_controlled":"1","department":[{"_id":"JaMa"}],"intvolume":"        24","status":"public","article_type":"original","publist_id":"5520","year":"2015","oa_version":"Preprint","external_id":{"arxiv":["1409.8605"]},"date_updated":"2023-10-18T07:48:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"article_processing_charge":"No","issue":"4","date_published":"2015-01-01T00:00:00Z","_id":"1635","abstract":[{"text":"We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.","lang":"eng"}],"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.8605"}],"volume":24}]