[{"date_published":"2010-03-26T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:02:10Z","intvolume":"      5978","volume":5978,"extern":1,"page":"343 - 360","date_updated":"2021-01-12T07:41:59Z","abstract":[{"lang":"eng","text":"The strongest standard security notion for digital signature schemes is unforgeability under chosen message attacks. In practice, however, this notion can be insufficient due to &quot;side-channel attacks&quot; which exploit leakage of information about the secret internal state. In this work we put forward the notion of &quot;leakage-resilient signatures,&quot; which strengthens the standard security notion by giving the adversary the additional power to learn a bounded amount of arbitrary information about the secret state that was accessed during every signature generation. This notion naturally implies security against all side-channel attacks as long as the amount of information leaked on each invocation is bounded and &quot;only computation leaks information.&quot; The main result of this paper is a construction which gives a (tree-based, stateful) leakage-resilient signature scheme based on any 3-time signature scheme. The amount of information that our scheme can safely leak per signature generation is 1/3 of the information the underlying 3-time signature scheme can leak in total. Signature schemes that remain secure even if a bounded total amount of information is leaked were recently constructed, hence instantiating our construction with these schemes gives the first constructions of provably secure leakage-resilient signature schemes. The above construction assumes that the signing algorithm can sample truly random bits, and thus an implementation would need some special hardware (randomness gates). Simply generating this randomness using a leakage-resilient stream-cipher will in general not work. Our second contribution is a sound general principle to replace uniform random bits in any leakage-resilient construction with pseudorandom ones: run two leakage-resilient stream-ciphers (with independent keys) in parallel and then apply a two-source extractor to their outputs. "}],"month":"03","publication_status":"published","_id":"3234","publist_id":"3447","citation":{"apa":"Faust, S., Kiltz, E., Pietrzak, K. Z., &#38; Rothblum, G. (2010). Leakage resilient signatures (Vol. 5978, pp. 343–360). Presented at the TCC: Theory of Cryptography Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">https://doi.org/10.1007/978-3-642-11799-2_21</a>","ieee":"S. Faust, E. Kiltz, K. Z. Pietrzak, and G. Rothblum, “Leakage resilient signatures,” presented at the TCC: Theory of Cryptography Conference, 2010, vol. 5978, pp. 343–360.","mla":"Faust, Sebastian, et al. <i>Leakage Resilient Signatures</i>. Vol. 5978, Springer, 2010, pp. 343–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">10.1007/978-3-642-11799-2_21</a>.","chicago":"Faust, Sebastian, Eike Kiltz, Krzysztof Z Pietrzak, and Guy Rothblum. “Leakage Resilient Signatures,” 5978:343–60. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">https://doi.org/10.1007/978-3-642-11799-2_21</a>.","short":"S. Faust, E. Kiltz, K.Z. Pietrzak, G. Rothblum, in:, Springer, 2010, pp. 343–360.","ama":"Faust S, Kiltz E, Pietrzak KZ, Rothblum G. Leakage resilient signatures. In: Vol 5978. Springer; 2010:343-360. doi:<a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">10.1007/978-3-642-11799-2_21</a>","ista":"Faust S, Kiltz E, Pietrzak KZ, Rothblum G. 2010. Leakage resilient signatures. TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 343–360."},"doi":"10.1007/978-3-642-11799-2_21","publisher":"Springer","title":"Leakage resilient signatures","year":"2010","status":"public","author":[{"last_name":"Faust","first_name":"Sebastian","full_name":"Faust, Sebastian"},{"last_name":"Kiltz","first_name":"Eike","full_name":"Kiltz, Eike"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guy","last_name":"Rothblum","full_name":"Rothblum, Guy N"}],"type":"conference","conference":{"name":"TCC: Theory of Cryptography Conference"},"alternative_title":["LNCS"],"day":"26"},{"quality_controlled":0,"date_created":"2018-12-11T12:02:10Z","date_published":"2010-09-30T00:00:00Z","volume":6223,"intvolume":"      6223","page":"21 - 40","extern":1,"date_updated":"2021-01-12T07:42:00Z","abstract":[{"text":"A cryptographic primitive is leakage-resilient, if it remains secure even if an adversary can learn a bounded amount of arbitrary information about the computation with every invocation. As a consequence, the physical implementation of a leakage-resilient primitive is secure against every side-channel as long as the amount of information leaked per invocation is bounded. In this paper we prove positive and negative results about the feasibility of constructing leakage-resilient pseudorandom functions and permutations (i.e. block-ciphers). Our results are three fold: 1. We construct (from any standard PRF) a PRF which satisfies a relaxed notion of leakage-resilience where (1) the leakage function is fixed (and not adaptively chosen with each query.) and (2) the computation is split into several steps which leak individually (a &quot;step&quot; will be the invocation of the underlying PRF.) 2. We prove that a Feistel network with a super-logarithmic number of rounds, each instantiated with a leakage-resilient PRF, is a leakage resilient PRP. This reduction also holds for the non-adaptive notion just discussed, we thus get a block-cipher which is leakage-resilient (against non-adaptive leakage). 3. We propose generic side-channel attacks against Feistel networks. The attacks are generic in the sense that they work for any round functions (e.g. uniformly random functions) and only require some simple leakage from the inputs to the round functions. For example we show how to invert an r round Feistel network over 2n bits making 4•(n+1) r-2 forward queries, if with each query we are also given as leakage the Hamming weight of the inputs to the r round functions. This complements the result from the previous item showing that a super-constant number of rounds is necessary.","lang":"eng"}],"publication_status":"published","month":"09","_id":"3235","publist_id":"3445","publisher":"Springer","doi":"10.1007/978-3-642-14623-7_2","citation":{"ama":"Dodis Y, Pietrzak KZ. Leakage resilient pseudorandom functions and side channel attacks on feistel networks. In: Vol 6223. Springer; 2010:21-40. doi:<a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">10.1007/978-3-642-14623-7_2</a>","ista":"Dodis Y, Pietrzak KZ. 2010. Leakage resilient pseudorandom functions and side channel attacks on feistel networks. CRYPTO: International Cryptology Conference, LNCS, vol. 6223, 21–40.","short":"Y. Dodis, K.Z. Pietrzak, in:, Springer, 2010, pp. 21–40.","chicago":"Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Leakage Resilient Pseudorandom Functions and Side Channel Attacks on Feistel Networks,” 6223:21–40. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">https://doi.org/10.1007/978-3-642-14623-7_2</a>.","mla":"Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. <i>Leakage Resilient Pseudorandom Functions and Side Channel Attacks on Feistel Networks</i>. Vol. 6223, Springer, 2010, pp. 21–40, doi:<a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">10.1007/978-3-642-14623-7_2</a>.","apa":"Dodis, Y., &#38; Pietrzak, K. Z. (2010). Leakage resilient pseudorandom functions and side channel attacks on feistel networks (Vol. 6223, pp. 21–40). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">https://doi.org/10.1007/978-3-642-14623-7_2</a>","ieee":"Y. Dodis and K. Z. Pietrzak, “Leakage resilient pseudorandom functions and side channel attacks on feistel networks,” presented at the CRYPTO: International Cryptology Conference, 2010, vol. 6223, pp. 21–40."},"year":"2010","status":"public","title":"Leakage resilient pseudorandom functions and side channel attacks on feistel networks","author":[{"full_name":"Dodis, Yevgeniy","first_name":"Yevgeniy","last_name":"Dodis"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"type":"conference","conference":{"name":"CRYPTO: International Cryptology Conference"},"alternative_title":["LNCS"],"day":"30"},{"date_published":"2010-01-14T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:02:11Z","intvolume":"      6477","volume":6477,"page":"595 - 612","extern":1,"date_updated":"2021-01-12T07:42:01Z","abstract":[{"lang":"eng","text":"Blinding is a popular and well-known countermeasure to protect public-key cryptosystems against side-channel attacks. The high level idea is to randomize an exponentiation in order to prevent multiple measurements of the same operation on different data, as such measurements might allow the adversary to learn the secret exponent. Several variants of blinding have been proposed in the literature, using additive or multiplicative secret-sharing to blind either the base or the exponent. These countermeasures usually aim at preventing particular side-channel attacks (mostly power analysis) and come without any formal security guarantee. In this work we investigate to which extend blinding can provide provable security against a general class of side-channel attacks. Surprisingly, it turns out that in the context of public-key encryption some blinding techniques are more suited than others. In particular, we consider a multiplicatively blinded version of ElGamal public-key encryption where - we prove that the scheme, instantiated over bilinear groups of prime order p (where p - 1 is not smooth) is leakage resilient in the generic-group model. Here we consider the model of chosen-ciphertext security in the presence of continuous leakage, i.e., the scheme remains chosen-ciphertext secure even if with every decryption query the adversary can learn a bounded amount (roughly log(p)/2 bits) of arbitrary, adversarially chosen information about the computation. - we conjecture that the scheme, instantiated over arbitrary groups of prime order p (where p - 1 is not smooth) is leakage resilient. Previous to this work no encryption scheme secure against continuous leakage was known. Constructing a scheme that can be proven secure in the standard model remains an interesting open problem. "}],"month":"01","publication_status":"published","_id":"3237","publist_id":"3444","doi":"10.1007/978-3-642-17373-8_34","citation":{"ieee":"E. Kiltz and K. Z. Pietrzak, “Leakage resilient ElGamal encryption,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, 2010, vol. 6477, pp. 595–612.","apa":"Kiltz, E., &#38; Pietrzak, K. Z. (2010). Leakage resilient ElGamal encryption (Vol. 6477, pp. 595–612). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Springer. <a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">https://doi.org/10.1007/978-3-642-17373-8_34</a>","chicago":"Kiltz, Eike, and Krzysztof Z Pietrzak. “Leakage Resilient ElGamal Encryption,” 6477:595–612. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">https://doi.org/10.1007/978-3-642-17373-8_34</a>.","mla":"Kiltz, Eike, and Krzysztof Z. Pietrzak. <i>Leakage Resilient ElGamal Encryption</i>. Vol. 6477, Springer, 2010, pp. 595–612, doi:<a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">10.1007/978-3-642-17373-8_34</a>.","ista":"Kiltz E, Pietrzak KZ. 2010. Leakage resilient ElGamal encryption. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 6477, 595–612.","ama":"Kiltz E, Pietrzak KZ. Leakage resilient ElGamal encryption. In: Vol 6477. Springer; 2010:595-612. doi:<a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">10.1007/978-3-642-17373-8_34</a>","short":"E. Kiltz, K.Z. Pietrzak, in:, Springer, 2010, pp. 595–612."},"publisher":"Springer","title":"Leakage resilient ElGamal encryption","status":"public","year":"2010","author":[{"full_name":"Kiltz, Eike","first_name":"Eike","last_name":"Kiltz"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"conference":{"name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"type":"conference","day":"14","alternative_title":["LNCS"]},{"quality_controlled":0,"date_created":"2018-12-11T12:02:31Z","date_published":"2010-01-01T00:00:00Z","intvolume":"       107","volume":107,"page":"9855 - 60","issue":"21","extern":1,"date_updated":"2021-01-12T07:42:27Z","publication_status":"published","abstract":[{"lang":"eng","text":"Olfactory responses of Drosophila undergo pronounced changes after eclosion. The flies develop attraction to odors to which they are exposed and aversion to other odors. Behavioral adaptation is correlated with changes in the firing pattern of olfactory receptor neurons (ORNs). In this article, we present an information-theoretic analysis of the firing pattern of ORNs. Flies reared in a synthetic odorless medium were transferred after eclosion to three different media: (i) a synthetic medium relatively devoid of odor cues, (ii) synthetic medium infused with a single odorant, and (iii) complex cornmeal medium rich in odors. Recordings were made from an identified sensillum (type II), and the Jensen-Shannon divergence (D(JS)) was used to assess quantitatively the differences between ensemble spike responses to different odors. Analysis shows that prolonged exposure to ethyl acetate and several related esters increases sensitivity to these esters but does not improve the ability of the fly to distinguish between them. Flies exposed to cornmeal display varied sensitivity to these odorants and at the same time develop greater capacity to distinguish between odors. Deprivation of odor experience on an odorless synthetic medium leads to a loss of both sensitivity and acuity. Rich olfactory experience thus helps to shape the ORNs response and enhances its discriminative power. The experiments presented here demonstrate an experience-dependent adaptation at the level of the receptor neuron."}],"month":"01","_id":"3294","publist_id":"3347","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1003856107","citation":{"ista":"Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. 2010. Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. PNAS. 107(21), 9855–60.","ama":"Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. <i>PNAS</i>. 2010;107(21):9855-9860. doi:<a href=\"https://doi.org/10.1073/pnas.1003856107\">10.1073/pnas.1003856107</a>","short":"A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, O. Siddiqi, PNAS 107 (2010) 9855–60.","apa":"Iyengar, A., Chakraborty Tuhin, S., Goswami, S., Wu, C., &#38; Siddiqi, O. (2010). Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1003856107\">https://doi.org/10.1073/pnas.1003856107</a>","ieee":"A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, and O. Siddiqi, “Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila,” <i>PNAS</i>, vol. 107, no. 21. National Academy of Sciences, pp. 9855–60, 2010.","chicago":"Iyengar, Atulya, Subhra Chakraborty Tuhin, Sarit Goswami, Chun Wu, and Obaid Siddiqi. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron Coding in Drosophila.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1003856107\">https://doi.org/10.1073/pnas.1003856107</a>.","mla":"Iyengar, Atulya, et al. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron Coding in Drosophila.” <i>PNAS</i>, vol. 107, no. 21, National Academy of Sciences, 2010, pp. 9855–60, doi:<a href=\"https://doi.org/10.1073/pnas.1003856107\">10.1073/pnas.1003856107</a>."},"publication":"PNAS","title":"Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila","status":"public","year":"2010","author":[{"full_name":"Iyengar, Atulya","last_name":"Iyengar","first_name":"Atulya"},{"full_name":"Chakraborty Tuhin, Subhra","last_name":"Chakraborty Tuhin","first_name":"Subhra"},{"id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Sarit Goswami","first_name":"Sarit","last_name":"Goswami"},{"last_name":"Wu","first_name":"Chun","full_name":"Wu, Chun Fang"},{"last_name":"Siddiqi","first_name":"Obaid","full_name":"Siddiqi, Obaid"}],"type":"journal_article","day":"01"},{"_id":"3296","month":"11","publication_status":"published","abstract":[{"text":"Accurate computational representations of highly deformable surfaces are indispensable in the fields of computer animation, medical simulation, computer vision, digital modeling, and computational physics. The focus of this dissertation is on the animation of physics-based phenomena with highly detailed deformable surfaces represented by triangle meshes.\r\n \r\nWe first present results from an algorithm that generates continuum mechanics animations with intricate surface features. This method combines a finite element method with a tetrahedral mesh generator and a high resolution surface mesh, and it is orders of magnitude more efficient than previous approaches. Next, we present an efficient solution for the challenging problem of computing topological changes in detailed dynamic surface meshes. We then introduce a new physics-inspired surface tracking algorithm that is capable of preserving arbitrarily thin features and reproducing realistic fine-scale topological changes like Rayleigh-Plateau instabilities. This physics-inspired surface tracking technique also opens the door for a unique coupling between surficial finite element methods and volumetric finite difference methods, in order to simulate liquid surface tension phenomena more efficiently than any previous method. Due to its dramatic increase in computational resolution and efficiency, this method yielded the first computer simulations of a fully developed crown splash with droplet pinch off.","lang":"eng"}],"article_processing_charge":"No","supervisor":[{"full_name":"Essa, Irfan","first_name":"Irfan","last_name":"Essa"},{"full_name":"Liu, Karen","first_name":"Karen","last_name":"Liu"},{"last_name":"Mucha","first_name":"Peter","full_name":"Mucha, Peter"},{"full_name":"Rossignac, Jarek","last_name":"Rossignac","first_name":"Jarek"}],"date_updated":"2023-02-23T11:21:00Z","page":"1 - 175","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_published":"2010-11-17T00:00:00Z","date_created":"2018-12-11T12:02:31Z","day":"17","type":"dissertation","main_file_link":[{"url":"http://hdl.handle.net/1853/37256"}],"author":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546"}],"status":"public","title":"Animating physical phenomena with embedded surface meshes","year":"2010","citation":{"apa":"Wojtan, C. (2010). <i>Animating physical phenomena with embedded surface meshes</i>. Georgia Institute of Technology.","ieee":"C. Wojtan, “Animating physical phenomena with embedded surface meshes,” Georgia Institute of Technology, 2010.","mla":"Wojtan, Chris. <i>Animating Physical Phenomena with Embedded Surface Meshes</i>. Georgia Institute of Technology, 2010, pp. 1–175.","chicago":"Wojtan, Chris. “Animating Physical Phenomena with Embedded Surface Meshes.” Georgia Institute of Technology, 2010.","short":"C. Wojtan, Animating Physical Phenomena with Embedded Surface Meshes, Georgia Institute of Technology, 2010.","ama":"Wojtan C. Animating physical phenomena with embedded surface meshes. 2010:1-175.","ista":"Wojtan C. 2010. Animating physical phenomena with embedded surface meshes. Georgia Institute of Technology."},"publisher":"Georgia Institute of Technology","oa_version":"None","publist_id":"3345"},{"status":"public","year":"2010","title":"The rate of fitness-valley crossing in sexual populations","acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","publisher":"Genetics Society of America","doi":"10.1534/genetics.110.123240","oa_version":"Submitted Version","publist_id":"3337","type":"journal_article","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/","open_access":"1"}],"author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel","last_name":"Weissman","first_name":"Daniel"},{"full_name":"Feldman, Marcus","last_name":"Feldman","first_name":"Marcus"},{"full_name":"Fisher, Daniel","first_name":"Daniel","last_name":"Fisher"}],"date_updated":"2021-01-12T07:42:31Z","issue":"4","page":"1389 - 1410","language":[{"iso":"eng"}],"date_published":"2010-12-01T00:00:00Z","quality_controlled":"1","_id":"3303","month":"12","publication":"Genetics","department":[{"_id":"NiBa"}],"citation":{"ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. 2010;186(4):1389-1410. doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410.","short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","apa":"Weissman, D., Feldman, M., &#38; Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>","ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” <i>Genetics</i>, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010.","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>. Genetics Society of America, 2010. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>.","mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>."},"oa":1,"ec_funded":1,"day":"01","scopus_import":1,"volume":186,"intvolume":"       186","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:02:33Z","abstract":[{"lang":"eng","text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. "}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}]},{"extern":1,"page":"238 - 266","date_updated":"2021-01-12T07:42:32Z","date_created":"2018-12-11T12:02:35Z","quality_controlled":0,"date_published":"2010-01-01T00:00:00Z","intvolume":"        20","volume":20,"abstract":[{"text":"We use methods from combinatorics and algebraic statistics to study analogues of birth-and-death processes that have as their state space a finite subset of the m-dimensional lattice and for which the m matrices that record the transition probabilities in each of the lattice directions commute pairwise. One reason such processes are of interest is that the transition matrix is straightforward to diagonalize, and hence it is easy to compute n step transition probabilities. The set of commuting birth-and-death processes decomposes as a union of toric varieties, with the main component being the closure of all processes whose nearest neighbor transition probabilities are positive. We exhibit an explicit monomial parametrization for this main component, and we explore the boundary components using primary decomposition.","lang":"eng"}],"publication_status":"published","month":"01","_id":"3306","citation":{"ista":"Evans S, Sturmfels B, Uhler C. 2010. Commuting birth and death processes. The Annals of Applied Probability. 20, 238–266.","ama":"Evans S, Sturmfels B, Uhler C. Commuting birth and death processes. <i>The Annals of Applied Probability</i>. 2010;20:238-266. doi:<a href=\"https://doi.org/10.1214/09-AAP615\">10.1214/09-AAP615</a>","short":"S. Evans, B. Sturmfels, C. Uhler, The Annals of Applied Probability 20 (2010) 238–266.","chicago":"Evans, Steven, Bernd Sturmfels, and Caroline Uhler. “Commuting Birth and Death Processes.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2010. <a href=\"https://doi.org/10.1214/09-AAP615\">https://doi.org/10.1214/09-AAP615</a>.","mla":"Evans, Steven, et al. “Commuting Birth and Death Processes.” <i>The Annals of Applied Probability</i>, vol. 20, Institute of Mathematical Statistics, 2010, pp. 238–66, doi:<a href=\"https://doi.org/10.1214/09-AAP615\">10.1214/09-AAP615</a>.","ieee":"S. Evans, B. Sturmfels, and C. Uhler, “Commuting birth and death processes,” <i>The Annals of Applied Probability</i>, vol. 20. Institute of Mathematical Statistics, pp. 238–266, 2010.","apa":"Evans, S., Sturmfels, B., &#38; Uhler, C. (2010). Commuting birth and death processes. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/09-AAP615\">https://doi.org/10.1214/09-AAP615</a>"},"doi":"10.1214/09-AAP615","publisher":"Institute of Mathematical Statistics","acknowledgement":"Steven N. Evans was supported in part by NSF Grants DMS-04-05778 and DMS-09-07630. Bernd Sturmfels was supported in part by NSF Grants DMS-04-56960 and DMS-07-57236. Caroline Uhler was supported by an International Fulbright Science and Technology Fellowship.","publication":"The Annals of Applied Probability","status":"public","year":"2010","title":"Commuting birth and death processes","publist_id":"3334","oa":1,"type":"journal_article","day":"01","author":[{"last_name":"Evans","first_name":"Steven","full_name":"Evans, Steven N"},{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Uhler","full_name":"Caroline Uhler","orcid":"0000-0002-7008-0216"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0812.2724"}]},{"date_created":"2018-12-11T12:02:35Z","quality_controlled":0,"date_published":"2010-08-01T00:00:00Z","intvolume":"        62","volume":62,"issue":"4","page":"603 - 638","extern":1,"date_updated":"2021-01-12T07:42:33Z","abstract":[{"text":"We study multivariate normal models that are described by linear constraints on the inverse of the covariance matrix. Maximum likelihood estimation for such models leads to the problem of maximizing the determinant function over a spectrahedron, and to the problem of characterizing the image of the positive definite cone under an arbitrary linear projection. These problems at the interface of statistics and optimization are here examined from the perspective of convex algebraic geometry.","lang":"eng"}],"month":"08","publication_status":"published","_id":"3308","publist_id":"3332","oa":1,"publisher":"Springer","doi":"10.1007/s10463-010-0295-4","citation":{"apa":"Sturmfels, B., &#38; Uhler, C. (2010). Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry. <i>Annals of the Institute of Statistical Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10463-010-0295-4\">https://doi.org/10.1007/s10463-010-0295-4</a>","ieee":"B. Sturmfels and C. Uhler, “Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry,” <i>Annals of the Institute of Statistical Mathematics</i>, vol. 62, no. 4. Springer, pp. 603–638, 2010.","chicago":"Sturmfels, Bernd, and Caroline Uhler. “Multivariate Gaussians, Semidefinite Matrix Completion, and Convex Algebraic Geometry.” <i>Annals of the Institute of Statistical Mathematics</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s10463-010-0295-4\">https://doi.org/10.1007/s10463-010-0295-4</a>.","mla":"Sturmfels, Bernd, and Caroline Uhler. “Multivariate Gaussians, Semidefinite Matrix Completion, and Convex Algebraic Geometry.” <i>Annals of the Institute of Statistical Mathematics</i>, vol. 62, no. 4, Springer, 2010, pp. 603–38, doi:<a href=\"https://doi.org/10.1007/s10463-010-0295-4\">10.1007/s10463-010-0295-4</a>.","ista":"Sturmfels B, Uhler C. 2010. Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry. Annals of the Institute of Statistical Mathematics. 62(4), 603–638.","ama":"Sturmfels B, Uhler C. Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry. <i>Annals of the Institute of Statistical Mathematics</i>. 2010;62(4):603-638. doi:<a href=\"https://doi.org/10.1007/s10463-010-0295-4\">10.1007/s10463-010-0295-4</a>","short":"B. Sturmfels, C. Uhler, Annals of the Institute of Statistical Mathematics 62 (2010) 603–638."},"year":"2010","title":"Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry","publication":"Annals of the Institute of Statistical Mathematics","status":"public","acknowledgement":"B. Sturmfels is supported in part by NSF grants DMS-0456960 and DMS-0757236. C. Uhler is supported by an International Fulbright Science and Technology Fellowship.","author":[{"last_name":"Sturmfels","first_name":"Bernd","full_name":"Sturmfels, Bernd"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Caroline Uhler","first_name":"Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0906.3529"}],"type":"journal_article","day":"01"},{"_id":"10908","month":"05","article_processing_charge":"No","publication_identifier":{"eisbn":["9783642175114"],"isbn":["9783642175107"],"eissn":["1611-3349"],"issn":["0302-9743"]},"date_updated":"2022-06-13T07:44:21Z","series_title":"LNCS","page":"103-118","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2010-05-01T00:00:00Z","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","end_date":"2010-05-01","start_date":"2010-04-25","location":"Dakar, Senegal"},"type":"conference","main_file_link":[{"url":"https://infoscience.epfl.ch/record/186096","open_access":"1"}],"author":[{"full_name":"Blanc, Régis","last_name":"Blanc","first_name":"Régis"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hottelier, Thibaud","last_name":"Hottelier","first_name":"Thibaud"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"}],"acknowledgement":"This work was supported in part by the Swiss NSF. The fourth author is supported by an FWF Hertha Firnberg Research grant (T425-N23).","place":"Berlin, Heidelberg","year":"2010","status":"public","title":"ABC: Algebraic Bound Computation for loops","doi":"10.1007/978-3-642-17511-4_7","publisher":"Springer Nature","oa_version":"Submitted Version","abstract":[{"text":"We present ABC, a software tool for automatically computing symbolic upper bounds on the number of iterations of nested program loops. The system combines static analysis of programs with symbolic summation techniques to derive loop invariant relations between program variables. Iteration bounds are obtained from the inferred invariants, by replacing variables with bounds on their greatest values. We have successfully applied ABC to a large number of examples. The derived symbolic bounds express non-trivial polynomial relations over loop variables. We also report on results to automatically infer symbolic expressions over harmonic numbers as upper bounds on loop iteration counts.","lang":"eng"}],"publication_status":"published","editor":[{"full_name":"Clarke, Edmund M","last_name":"Clarke","first_name":"Edmund M"},{"full_name":"Voronkov, Andrei","first_name":"Andrei","last_name":"Voronkov"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      6355","volume":6355,"date_created":"2022-03-21T08:14:35Z","day":"01","scopus_import":"1","publication":"Logic for Programming, Artificial Intelligence, and Reasoning","department":[{"_id":"ToHe"}],"citation":{"chicago":"Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács. “ABC: Algebraic Bound Computation for Loops.” In <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, 6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>.","mla":"Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>.","ieee":"R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound Computation for loops,” in <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.","apa":"Blanc, R., Henzinger, T. A., Hottelier, T., &#38; Kovács, L. (2010). ABC: Algebraic Bound Computation for loops. In E. M. Clarke &#38; A. Voronkov (Eds.), <i>Logic for Programming, Artificial Intelligence, and Reasoning</i> (Vol. 6355, pp. 103–118). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>","ista":"Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355, 103–118.","ama":"Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation for loops. In: Clarke EM, Voronkov A, eds. <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>. Vol 6355. LNCS. Berlin, Heidelberg: Springer Nature; 2010:103-118. doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>","short":"R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov (Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer Nature, Berlin, Heidelberg, 2010, pp. 103–118."},"oa":1},{"acknowledgement":"Partially supported by the Austrian Science Fund under grantFSP-S9103-N04 and P20134-N13.","status":"public","year":"2010","publication":"Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms","title":"Hardness results for homology localization","doi":"10.1137/1.9781611973075.129","citation":{"chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1594–1604. Society for Industrial and Applied Mathematics, 2010. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>.","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>.","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” in <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Austin, TX, United States, 2010, pp. 1594–1604.","apa":"Chen, C., &#38; Freedman, D. (2010). Hardness results for homology localization. In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>","ama":"Chen C, Freedman D. Hardness results for homology localization. In: <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2010:1594-1604. doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>","ista":"Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1594–1604.","short":"C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–1604."},"department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics","oa_version":"None","scopus_import":"1","day":"01","type":"conference","conference":{"end_date":"2010-01-19","name":"SODA: Symposium on Discrete Algorithms","start_date":"2010-01-17","location":"Austin, TX, United States"},"author":[{"last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"3267"}]},"date_updated":"2023-02-23T11:19:46Z","page":"1594-1604","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2022-03-21T08:24:07Z","date_published":"2010-02-01T00:00:00Z","_id":"10909","abstract":[{"lang":"eng","text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field."}],"publication_status":"published","month":"02","article_processing_charge":"No","publication_identifier":{"eisbn":["9781611973075"]}},{"quality_controlled":"1","date_published":"2010-02-03T00:00:00Z","language":[{"iso":"eng"}],"page":"a000539-a000539","issue":"3","external_id":{"pmid":["20300205"]},"date_updated":"2022-07-18T08:53:50Z","article_type":"original","publication_identifier":{"issn":["1943-0264"]},"article_processing_charge":"No","month":"02","_id":"11097","oa_version":"None","publisher":"Cold Spring Harbor Laboratory","doi":"10.1101/cshperspect.a000539","title":"The nuclear envelope","status":"public","year":"2010","author":[{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"type":"journal_article","date_created":"2022-04-07T07:52:49Z","volume":2,"intvolume":"         2","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","pmid":1,"extern":"1","publication_status":"published","abstract":[{"text":"The nuclear envelope (NE) is a highly regulated membrane barrier that separates the nucleus from the cytoplasm in eukaryotic cells. It contains a large number of different proteins that have been implicated in chromatin organization and gene regulation. Although the nuclear membrane enables complex levels of gene expression, it also poses a challenge when it comes to cell division. To allow access of the mitotic spindle to chromatin, the nucleus of metazoans must completely disassemble during mitosis, generating the need to re-establish the nuclear compartment at the end of each cell division. Here, I summarize our current understanding of the dynamic remodeling of the NE during the cell cycle.","lang":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"citation":{"ama":"Hetzer M. The nuclear envelope. <i>Cold Spring Harbor Perspectives in Biology</i>. 2010;2(3):a000539-a000539. doi:<a href=\"https://doi.org/10.1101/cshperspect.a000539\">10.1101/cshperspect.a000539</a>","ista":"Hetzer M. 2010. The nuclear envelope. Cold Spring Harbor Perspectives in Biology. 2(3), a000539–a000539.","short":"M. Hetzer, Cold Spring Harbor Perspectives in Biology 2 (2010) a000539–a000539.","chicago":"Hetzer, Martin. “The Nuclear Envelope.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory, 2010. <a href=\"https://doi.org/10.1101/cshperspect.a000539\">https://doi.org/10.1101/cshperspect.a000539</a>.","mla":"Hetzer, Martin. “The Nuclear Envelope.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 2, no. 3, Cold Spring Harbor Laboratory, 2010, pp. a000539–a000539, doi:<a href=\"https://doi.org/10.1101/cshperspect.a000539\">10.1101/cshperspect.a000539</a>.","apa":"Hetzer, M. (2010). The nuclear envelope. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/cshperspect.a000539\">https://doi.org/10.1101/cshperspect.a000539</a>","ieee":"M. Hetzer, “The nuclear envelope,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 2, no. 3. Cold Spring Harbor Laboratory, pp. a000539–a000539, 2010."},"publication":"Cold Spring Harbor Perspectives in Biology","scopus_import":"1","day":"03"},{"publication_status":"published","extern":"1","pmid":1,"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":"         2","volume":2,"date_created":"2022-04-07T07:52:58Z","scopus_import":"1","day":"01","publication":"Aging","citation":{"mla":"Hetzer, Martin. “The Role of the Nuclear Pore Complex in Aging of Post-Mitotic Cells.” <i>Aging</i>, vol. 2, no. 2, Impact Journals, 2010, pp. 74–75, doi:<a href=\"https://doi.org/10.18632/aging.100125\">10.18632/aging.100125</a>.","chicago":"Hetzer, Martin. “The Role of the Nuclear Pore Complex in Aging of Post-Mitotic Cells.” <i>Aging</i>. Impact Journals, 2010. <a href=\"https://doi.org/10.18632/aging.100125\">https://doi.org/10.18632/aging.100125</a>.","apa":"Hetzer, M. (2010). The role of the nuclear pore complex in aging of post-mitotic cells. <i>Aging</i>. Impact Journals. <a href=\"https://doi.org/10.18632/aging.100125\">https://doi.org/10.18632/aging.100125</a>","ieee":"M. Hetzer, “The role of the nuclear pore complex in aging of post-mitotic cells,” <i>Aging</i>, vol. 2, no. 2. Impact Journals, pp. 74–75, 2010.","short":"M. Hetzer, Aging 2 (2010) 74–75.","ama":"Hetzer M. The role of the nuclear pore complex in aging of post-mitotic cells. <i>Aging</i>. 2010;2(2):74-75. doi:<a href=\"https://doi.org/10.18632/aging.100125\">10.18632/aging.100125</a>","ista":"Hetzer M. 2010. The role of the nuclear pore complex in aging of post-mitotic cells. Aging. 2(2), 74–75."},"keyword":["Cell Biology","Aging"],"oa":1,"_id":"11098","month":"02","article_processing_charge":"No","publication_identifier":{"issn":["1945-4589"]},"article_type":"original","external_id":{"pmid":["20354266"]},"date_updated":"2022-07-18T08:54:15Z","page":"74-75","issue":"2","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2010-02-01T00:00:00Z","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.18632/aging.100125","open_access":"1"}],"author":[{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"year":"2010","status":"public","title":"The role of the nuclear pore complex in aging of post-mitotic cells","doi":"10.18632/aging.100125","publisher":"Impact Journals","oa_version":"Published Version"},{"pmid":1,"extern":"1","volume":119,"intvolume":"       119","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","date_created":"2022-04-07T07:53:12Z","publication_status":"published","abstract":[{"text":"Nuclear pore complexes (NPCs) serve as transport channels across the nuclear membrane, a double lipid bilayer that physically separates the nucleoplasm and cytoplasm of eukaryotic cells. New evidence suggests that the multiprotein nuclear pores also play a role in chromatin organization and gene expression. Given the importance of NPC function, it is not surprising that a growing list of human diseases and developmental defects have been linked to its malfunction. In order to fully understand the functional repertoire of NPCs and their essential role for nuclear organization, it is critical to determine the sequence of events that lead to the formation of nuclear pores. This is particularly relevant since NPC number, and possibly composition, are tightly linked to metabolic activity. Most of our knowledge is derived from NPC formation that occurs in dividing cells at the end of mitosis when the nuclear envelope (NE) and NPCs reform from disassembled precursors. However, NPC assembly also takes place during interphase into an intact NE. Importantly, this process is not restricted to dividing cells but also occurs during cell differentiation. Here, we will review aspects unique to this process, namely the regulation of nuclear expansion and the mechanisms of fusion between the outer and inner nuclear membranes. We will then discuss conserved and diverging mechanisms between post-mitotic and interphase assembly of the proteinaceous structure in light of recently published data.","lang":"eng"}],"publication":"Chromosoma","keyword":["Genetics (clinical)","Genetics"],"citation":{"apa":"Doucet, C. M., &#38; Hetzer, M. (2010). Nuclear pore biogenesis into an intact nuclear envelope. <i>Chromosoma</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00412-010-0289-2\">https://doi.org/10.1007/s00412-010-0289-2</a>","ieee":"C. M. Doucet and M. Hetzer, “Nuclear pore biogenesis into an intact nuclear envelope,” <i>Chromosoma</i>, vol. 119. Springer Nature, pp. 469–477, 2010.","mla":"Doucet, Christine M., and Martin Hetzer. “Nuclear Pore Biogenesis into an Intact Nuclear Envelope.” <i>Chromosoma</i>, vol. 119, Springer Nature, 2010, pp. 469–77, doi:<a href=\"https://doi.org/10.1007/s00412-010-0289-2\">10.1007/s00412-010-0289-2</a>.","chicago":"Doucet, Christine M., and Martin Hetzer. “Nuclear Pore Biogenesis into an Intact Nuclear Envelope.” <i>Chromosoma</i>. Springer Nature, 2010. <a href=\"https://doi.org/10.1007/s00412-010-0289-2\">https://doi.org/10.1007/s00412-010-0289-2</a>.","short":"C.M. Doucet, M. Hetzer, Chromosoma 119 (2010) 469–477.","ista":"Doucet CM, Hetzer M. 2010. Nuclear pore biogenesis into an intact nuclear envelope. Chromosoma. 119, 469–477.","ama":"Doucet CM, Hetzer M. Nuclear pore biogenesis into an intact nuclear envelope. <i>Chromosoma</i>. 2010;119:469-477. doi:<a href=\"https://doi.org/10.1007/s00412-010-0289-2\">10.1007/s00412-010-0289-2</a>"},"day":"01","scopus_import":"1","date_updated":"2022-07-18T08:54:20Z","external_id":{"pmid":["20721671"]},"article_type":"review","page":"469-477","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2010-10-01T00:00:00Z","_id":"11099","article_processing_charge":"No","month":"10","publication_identifier":{"eissn":["1432-0886"],"issn":["0009-5915"]},"status":"public","title":"Nuclear pore biogenesis into an intact nuclear envelope","year":"2010","publisher":"Springer Nature","doi":"10.1007/s00412-010-0289-2","oa_version":"None","type":"journal_article","author":[{"full_name":"Doucet, Christine M.","last_name":"Doucet","first_name":"Christine M."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}]},{"author":[{"last_name":"Doucet","first_name":"Christine M.","full_name":"Doucet, Christine M."},{"first_name":"Jessica A.","last_name":"Talamas","full_name":"Talamas, Jessica A."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2010.04.036"}],"type":"journal_article","oa_version":"Published Version","doi":"10.1016/j.cell.2010.04.036","publisher":"Elsevier","status":"public","title":"Cell cycle-dependent differences in nuclear pore complex assembly in metazoa","year":"2010","publication_identifier":{"issn":["0092-8674"]},"month":"06","article_processing_charge":"No","_id":"11101","quality_controlled":"1","date_published":"2010-06-11T00:00:00Z","language":[{"iso":"eng"}],"page":"1030-1041","issue":"6","article_type":"original","external_id":{"pmid":["20550937"]},"date_updated":"2022-07-18T08:54:52Z","day":"11","scopus_import":"1","oa":1,"citation":{"ama":"Doucet CM, Talamas JA, Hetzer M. Cell cycle-dependent differences in nuclear pore complex assembly in metazoa. <i>Cell</i>. 2010;141(6):1030-1041. doi:<a href=\"https://doi.org/10.1016/j.cell.2010.04.036\">10.1016/j.cell.2010.04.036</a>","ista":"Doucet CM, Talamas JA, Hetzer M. 2010. Cell cycle-dependent differences in nuclear pore complex assembly in metazoa. Cell. 141(6), 1030–1041.","short":"C.M. Doucet, J.A. Talamas, M. Hetzer, Cell 141 (2010) 1030–1041.","apa":"Doucet, C. M., Talamas, J. A., &#38; Hetzer, M. (2010). Cell cycle-dependent differences in nuclear pore complex assembly in metazoa. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2010.04.036\">https://doi.org/10.1016/j.cell.2010.04.036</a>","ieee":"C. M. Doucet, J. A. Talamas, and M. Hetzer, “Cell cycle-dependent differences in nuclear pore complex assembly in metazoa,” <i>Cell</i>, vol. 141, no. 6. Elsevier, pp. 1030–1041, 2010.","chicago":"Doucet, Christine M., Jessica A. Talamas, and Martin Hetzer. “Cell Cycle-Dependent Differences in Nuclear Pore Complex Assembly in Metazoa.” <i>Cell</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cell.2010.04.036\">https://doi.org/10.1016/j.cell.2010.04.036</a>.","mla":"Doucet, Christine M., et al. “Cell Cycle-Dependent Differences in Nuclear Pore Complex Assembly in Metazoa.” <i>Cell</i>, vol. 141, no. 6, Elsevier, 2010, pp. 1030–41, doi:<a href=\"https://doi.org/10.1016/j.cell.2010.04.036\">10.1016/j.cell.2010.04.036</a>."},"keyword":["General Biochemistry","Genetics and Molecular Biology"],"publication":"Cell","publication_status":"published","abstract":[{"lang":"eng","text":"In metazoa, nuclear pore complexes (NPCs) assemble from disassembled precursors into a reforming nuclear envelope (NE) at the end of mitosis and into growing intact NEs during interphase. Here, we show via RNAi-mediated knockdown that ELYS, a nucleoporin critical for the recruitment of the essential Nup107/160 complex to chromatin, is required for NPC assembly at the end of mitosis but not during interphase. Conversely, the transmembrane nucleoporin POM121 is critical for the incorporation of the Nup107/160 complex into new assembly sites specifically during interphase. Strikingly, recruitment of the Nup107/160 complex to an intact NE involves a membrane curvature-sensing domain of its constituent Nup133, which is not required for postmitotic NPC formation. Our results suggest that in organisms with open mitosis, NPCs assemble via two distinct mechanisms to accommodate cell cycle-dependent differences in NE topology."}],"date_created":"2022-04-07T07:53:29Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","volume":141,"intvolume":"       141","pmid":1,"extern":"1"},{"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2009.12.054","open_access":"1"}],"author":[{"full_name":"Capelson, Maya","first_name":"Maya","last_name":"Capelson"},{"full_name":"Liang, Yun","first_name":"Yun","last_name":"Liang"},{"full_name":"Schulte, Roberta","last_name":"Schulte","first_name":"Roberta"},{"last_name":"Mair","first_name":"William","full_name":"Mair, William"},{"first_name":"Ulrich","last_name":"Wagner","full_name":"Wagner, Ulrich"},{"orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W"}],"year":"2010","status":"public","title":"Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes","doi":"10.1016/j.cell.2009.12.054","publisher":"Elsevier","oa_version":"Published Version","_id":"11102","month":"02","article_processing_charge":"No","publication_identifier":{"issn":["0092-8674"]},"article_type":"original","date_updated":"2022-07-18T08:55:03Z","external_id":{"pmid":["20144761"]},"issue":"3","page":"372-383","language":[{"iso":"eng"}],"date_published":"2010-02-05T00:00:00Z","quality_controlled":"1","day":"05","scopus_import":"1","publication":"Cell","citation":{"chicago":"Capelson, Maya, Yun Liang, Roberta Schulte, William Mair, Ulrich Wagner, and Martin Hetzer. “Chromatin-Bound Nuclear Pore Components Regulate Gene Expression in Higher Eukaryotes.” <i>Cell</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cell.2009.12.054\">https://doi.org/10.1016/j.cell.2009.12.054</a>.","mla":"Capelson, Maya, et al. “Chromatin-Bound Nuclear Pore Components Regulate Gene Expression in Higher Eukaryotes.” <i>Cell</i>, vol. 140, no. 3, Elsevier, 2010, pp. 372–83, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.12.054\">10.1016/j.cell.2009.12.054</a>.","ieee":"M. Capelson, Y. Liang, R. Schulte, W. Mair, U. Wagner, and M. Hetzer, “Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes,” <i>Cell</i>, vol. 140, no. 3. Elsevier, pp. 372–383, 2010.","apa":"Capelson, M., Liang, Y., Schulte, R., Mair, W., Wagner, U., &#38; Hetzer, M. (2010). Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2009.12.054\">https://doi.org/10.1016/j.cell.2009.12.054</a>","ama":"Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer M. Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. <i>Cell</i>. 2010;140(3):372-383. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.12.054\">10.1016/j.cell.2009.12.054</a>","ista":"Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer M. 2010. Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell. 140(3), 372–383.","short":"M. Capelson, Y. Liang, R. Schulte, W. Mair, U. Wagner, M. Hetzer, Cell 140 (2010) 372–383."},"keyword":["General Biochemistry","Genetics and Molecular Biology"],"oa":1,"abstract":[{"lang":"eng","text":"Nuclear pore complexes have recently been shown to play roles in gene activation; however their potential involvement in metazoan transcription remains unclear. Here we show that the nucleoporins Sec13, Nup98, and Nup88, as well as a group of FG-repeat nucleoporins, bind to the Drosophila genome at functionally distinct loci that often do not represent nuclear envelope contact sites. Whereas Nup88 localizes to silent loci, Sec13, Nup98, and a subset of FG-repeat nucleoporins bind to developmentally regulated genes undergoing transcription induction. Strikingly, RNAi-mediated knockdown of intranuclear Sec13 and Nup98 specifically inhibits transcription of their target genes and prevents efficient reactivation of transcription after heat shock, suggesting an essential role of NPC components in regulating complex gene expression programs of multicellular organisms."}],"publication_status":"published","pmid":1,"extern":"1","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","volume":140,"intvolume":"       140","date_created":"2022-04-07T07:53:36Z"},{"day":"01","scopus_import":"1","type":"conference","conference":{"location":"Potsdam, Germany","end_date":"2010-06-09","name":"ICSD: International Conference on Solid Dielectrics","start_date":"2010-06-04"},"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"11754"}]},"author":[{"last_name":"Lang","first_name":"S. B.","full_name":"Lang, S. B."},{"full_name":"Lashley, J. C.","first_name":"J. C.","last_name":"Lashley"},{"orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A","first_name":"Kimberly A","last_name":"Modic"},{"first_name":"R. A.","last_name":"Fisher","full_name":"Fisher, R. A."},{"full_name":"Zhu, W. M.","last_name":"Zhu","first_name":"W. M."},{"full_name":"Ye, Z. G.","first_name":"Z. G.","last_name":"Ye"}],"title":"Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary","publication":"Proceedings of the 2010 IEEE International Conference on Solid Dielectrics","year":"2010","status":"public","citation":{"ieee":"S. B. Lang, J. C. Lashley, K. A. Modic, R. A. Fisher, W. M. Zhu, and Z. G. Ye, “Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary,” in <i>Proceedings of the 2010 IEEE International Conference on Solid Dielectrics</i>, Potsdam, Germany, 2010.","apa":"Lang, S. B., Lashley, J. C., Modic, K. A., Fisher, R. A., Zhu, W. M., &#38; Ye, Z. G. (2010). Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary. In <i>Proceedings of the 2010 IEEE International Conference on Solid Dielectrics</i>. Potsdam, Germany: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/icsd.2010.5568033\">https://doi.org/10.1109/icsd.2010.5568033</a>","chicago":"Lang, S. B., J. C. Lashley, Kimberly A Modic, R. A. Fisher, W. M. Zhu, and Z. G. Ye. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic Phase Boundary.” In <i>Proceedings of the 2010 IEEE International Conference on Solid Dielectrics</i>. Institute of Electrical and Electronics Engineers, 2010. <a href=\"https://doi.org/10.1109/icsd.2010.5568033\">https://doi.org/10.1109/icsd.2010.5568033</a>.","mla":"Lang, S. B., et al. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic Phase Boundary.” <i>Proceedings of the 2010 IEEE International Conference on Solid Dielectrics</i>, 5568033, Institute of Electrical and Electronics Engineers, 2010, doi:<a href=\"https://doi.org/10.1109/icsd.2010.5568033\">10.1109/icsd.2010.5568033</a>.","ista":"Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. 2010. Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary. Proceedings of the 2010 IEEE International Conference on Solid Dielectrics. ICSD: International Conference on Solid Dielectrics, 5568033.","ama":"Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary. In: <i>Proceedings of the 2010 IEEE International Conference on Solid Dielectrics</i>. Institute of Electrical and Electronics Engineers; 2010. doi:<a href=\"https://doi.org/10.1109/icsd.2010.5568033\">10.1109/icsd.2010.5568033</a>","short":"S.B. Lang, J.C. Lashley, K.A. Modic, R.A. Fisher, W.M. Zhu, Z.G. Ye, in:, Proceedings of the 2010 IEEE International Conference on Solid Dielectrics, Institute of Electrical and Electronics Engineers, 2010."},"doi":"10.1109/icsd.2010.5568033","publisher":"Institute of Electrical and Electronics Engineers","oa_version":"None","_id":"11753","publication_status":"published","month":"06","abstract":[{"lang":"eng","text":"Ferroelectric ceramic materials have a wide range of applications because of their piezoelectric and pyroelectric properties. One of their most important physical properties is the specific heat. In this study, the specific heats of a series of lead-zirconate-titanate (PZT) compositions in the vicinity of the morphotropic phase boundary (MPB) were measured. The temperature range was from 1.8 to 300 K. It is believed that these are the lowest temperature measurements ever made on PZT. Differences between the specific heats of the different compositions were very small. However, the calculated Debye temperatures were slightly different. The results are useful in computing design parameters for technical devices."}],"article_processing_charge":"No","publication_identifier":{"eissn":["2159-1687"],"issn":["1553-5282"]},"article_number":"5568033","date_updated":"2023-02-21T16:26:58Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2010-06-01T00:00:00Z","date_created":"2022-08-08T09:00:17Z"},{"author":[{"full_name":"Lang, S.B.","first_name":"S.B.","last_name":"Lang"},{"last_name":"Lashley","first_name":"J.C.","full_name":"Lashley, J.C."},{"full_name":"Modic, Kimberly A","first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147"},{"full_name":"Fisher, R.A.","last_name":"Fisher","first_name":"R.A."},{"full_name":"Zhu, W.M.","last_name":"Zhu","first_name":"W.M."},{"full_name":"Ye, Z.G.","last_name":"Ye","first_name":"Z.G."}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"11753"}]},"conference":{"end_date":"2010-04-28","name":"MELECON: Mediterranean Electrotechnical Conference","start_date":"2010-04-26","location":"Valletta, Malta"},"type":"conference","scopus_import":"1","day":"26","oa_version":"None","doi":"10.1109/melcon.2010.5476345","citation":{"short":"S.B. Lang, J.C. Lashley, K.A. Modic, R.A. Fisher, W.M. Zhu, Z.G. Ye, in:, 15th IEEE Mediterranean Electrotechnical Conference, Institute of Electrical and Electronics Engineers, 2010.","ama":"Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary. In: <i>15th IEEE Mediterranean Electrotechnical Conference</i>. Institute of Electrical and Electronics Engineers; 2010. doi:<a href=\"https://doi.org/10.1109/melcon.2010.5476345\">10.1109/melcon.2010.5476345</a>","ista":"Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. 2010. Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary. 15th IEEE Mediterranean Electrotechnical Conference. MELECON: Mediterranean Electrotechnical Conference, 5476345.","mla":"Lang, S. B., et al. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic Phase Boundary.” <i>15th IEEE Mediterranean Electrotechnical Conference</i>, 5476345, Institute of Electrical and Electronics Engineers, 2010, doi:<a href=\"https://doi.org/10.1109/melcon.2010.5476345\">10.1109/melcon.2010.5476345</a>.","chicago":"Lang, S.B., J.C. Lashley, Kimberly A Modic, R.A. Fisher, W.M. Zhu, and Z.G. Ye. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic Phase Boundary.” In <i>15th IEEE Mediterranean Electrotechnical Conference</i>. Institute of Electrical and Electronics Engineers, 2010. <a href=\"https://doi.org/10.1109/melcon.2010.5476345\">https://doi.org/10.1109/melcon.2010.5476345</a>.","apa":"Lang, S. B., Lashley, J. C., Modic, K. A., Fisher, R. A., Zhu, W. M., &#38; Ye, Z. G. (2010). Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary. In <i>15th IEEE Mediterranean Electrotechnical Conference</i>. Valletta, Malta: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/melcon.2010.5476345\">https://doi.org/10.1109/melcon.2010.5476345</a>","ieee":"S. B. Lang, J. C. Lashley, K. A. Modic, R. A. Fisher, W. M. Zhu, and Z. G. Ye, “Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary,” in <i>15th IEEE Mediterranean Electrotechnical Conference</i>, Valletta, Malta, 2010."},"publisher":"Institute of Electrical and Electronics Engineers","year":"2010","title":"Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary","publication":"15th IEEE Mediterranean Electrotechnical Conference","status":"public","article_number":"5476345","publication_identifier":{"isbn":["978-142445795-3"]},"month":"04","publication_status":"published","abstract":[{"lang":"eng","text":"Ferroelectric ceramic materials have a wide range of applications because of their piezoelectric and pyroelectric properties. One of their most important physical properties is the specific heat. In this study, the specific heats of a series of lead-zirconate-titanate (PZT) compositions in the vicinity of the morphotropic phase boundary (MPB) were measured. The temperature range was from 1.8 to 300 K. It is believed that these are the lowest temperature measurements ever made on PZT. Differences between the specific heats of the different compositions were very small. However, the calculated Debye temperatures were slightly different. The results are useful in computing design parameters for technical devices."}],"article_processing_charge":"No","_id":"11754","date_published":"2010-04-26T00:00:00Z","date_created":"2022-08-08T09:11:43Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"extern":"1","date_updated":"2023-02-21T16:26:55Z"},{"oa_version":"None","status":"public","publication":"Journal of the American Chemical Society","title":"Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy","year":"2010","citation":{"apa":"Schanda, P., Meier, B. H., &#38; Ernst, M. (2010). Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>","ieee":"P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45. American Chemical Society, pp. 15957–15967, 2010.","mla":"Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45, American Chemical Society, 2010, pp. 15957–67, doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>.","chicago":"Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>.","short":"P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society 132 (2010) 15957–15967.","ista":"Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal of the American Chemical Society. 132(45), 15957–15967.","ama":"Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2010;132(45):15957-15967. doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>"},"doi":"10.1021/ja100726a","publisher":"American Chemical Society","author":[{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Beat H.","last_name":"Meier","full_name":"Meier, Beat H."},{"first_name":"Matthias","last_name":"Ernst","full_name":"Ernst, Matthias"}],"day":"26","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":132,"intvolume":"       132","quality_controlled":"1","date_published":"2010-10-26T00:00:00Z","date_created":"2020-09-18T10:11:13Z","article_type":"original","date_updated":"2021-01-12T08:19:30Z","page":"15957-15967","issue":"45","extern":"1","publication_identifier":{"issn":["0002-7863","1520-5126"]},"_id":"8472","abstract":[{"text":"Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure 1H−15N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated 15N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins.","lang":"eng"}],"month":"10","publication_status":"published","article_processing_charge":"No"},{"publication_identifier":{"issn":["0021-9258","1083-351X"]},"_id":"8473","abstract":[{"text":"β2-microglobulin (β2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified β2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the β2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type β2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G β2m mutant.","lang":"eng"}],"month":"02","publication_status":"published","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":285,"language":[{"iso":"eng"}],"intvolume":"       285","quality_controlled":"1","date_created":"2020-09-18T10:11:23Z","date_published":"2010-02-19T00:00:00Z","article_type":"original","date_updated":"2021-01-12T08:19:31Z","extern":"1","issue":"8","page":"5827-5835","author":[{"first_name":"Alessandra","last_name":"Corazza","full_name":"Corazza, Alessandra"},{"last_name":"Rennella","first_name":"Enrico","full_name":"Rennella, Enrico"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"full_name":"Mimmi, Maria Chiara","first_name":"Maria Chiara","last_name":"Mimmi"},{"full_name":"Cutuil, Thomas","first_name":"Thomas","last_name":"Cutuil"},{"last_name":"Raimondi","first_name":"Sara","full_name":"Raimondi, Sara"},{"full_name":"Giorgetti, Sofia","last_name":"Giorgetti","first_name":"Sofia"},{"last_name":"Fogolari","first_name":"Federico","full_name":"Fogolari, Federico"},{"full_name":"Viglino, Paolo","last_name":"Viglino","first_name":"Paolo"},{"first_name":"Lucio","last_name":"Frydman","full_name":"Frydman, Lucio"},{"full_name":"Gal, Maayan","first_name":"Maayan","last_name":"Gal"},{"full_name":"Bellotti, Vittorio","last_name":"Bellotti","first_name":"Vittorio"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"},{"full_name":"Esposito, Gennaro","first_name":"Gennaro","last_name":"Esposito"}],"day":"19","type":"journal_article","oa_version":"None","title":"Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR","status":"public","publication":"Journal of Biological Chemistry","year":"2010","citation":{"ama":"Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. 2010;285(8):5827-5835. doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>","ista":"Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito G. 2010. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. Journal of Biological Chemistry. 285(8), 5827–5835.","short":"A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi, S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher, G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.","chicago":"Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi, Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2010. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>.","mla":"Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8, American Society for Biochemistry &#38; Molecular Biology, 2010, pp. 5827–35, doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>.","apa":"Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi, S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>","ieee":"A. Corazza <i>et al.</i>, “Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR,” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8. American Society for Biochemistry &#38; Molecular Biology, pp. 5827–5835, 2010."},"doi":"10.1074/jbc.m109.061168","publisher":"American Society for Biochemistry & Molecular Biology","keyword":["Cell Biology","Biochemistry","Molecular Biology"]},{"publisher":"Elsevier","citation":{"mla":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87, doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>.","chicago":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In <i>Handbook of Dynamical Systems</i>, 3:43–87. Elsevier, 2010. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>.","ieee":"B. R. Hunt and V. Kaloshin, “Prevalence,” in <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87.","apa":"Hunt, B. R., &#38; Kaloshin, V. (2010). Prevalence. In <i>Handbook of Dynamical Systems</i> (Vol. 3, pp. 43–87). Elsevier. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>","short":"B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010, pp. 43–87.","ama":"Hunt BR, Kaloshin V. Prevalence. In: <i>Handbook of Dynamical Systems</i>. Vol 3. Elsevier; 2010:43-87. doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>","ista":"Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems. vol. 3, 43–87."},"doi":"10.1016/s1874-575x(10)00310-3","title":"Prevalence","status":"public","publication":"Handbook of Dynamical Systems","year":"2010","oa_version":"None","type":"book_chapter","day":"01","author":[{"first_name":"Brian R.","last_name":"Hunt","full_name":"Hunt, Brian R."},{"orcid":"0000-0002-6051-2628","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"extern":"1","page":"43-87","date_updated":"2021-01-12T08:19:45Z","date_created":"2020-09-18T10:47:48Z","quality_controlled":"1","date_published":"2010-01-01T00:00:00Z","language":[{"iso":"eng"}],"intvolume":"         3","volume":3,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"01","publication_status":"published","_id":"8506","publication_identifier":{"isbn":["9780444531414"],"issn":["1874-575X"]}}]