[{"_id":"3220","author":[{"last_name":"Dziembowski","first_name":"Stefan","full_name":"Dziembowski, Stefan"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:02:05Z","publication_status":"published","month":"10","title":"Intrusion resilient secret sharing","quality_controlled":0,"page":"227 - 237","publisher":"IEEE","conference":{"name":"FOCS: Foundations of Computer Science"},"year":"2007","citation":{"ieee":"S. Dziembowski and K. Z. Pietrzak, “Intrusion resilient secret sharing,” presented at the FOCS: Foundations of Computer Science, 2007, pp. 227–237.","chicago":"Dziembowski, Stefan, and Krzysztof Z Pietrzak. “Intrusion Resilient Secret Sharing,” 227–37. IEEE, 2007. <a href=\"https://doi.org/10.1109/FOCS.2007.63\">https://doi.org/10.1109/FOCS.2007.63</a>.","ama":"Dziembowski S, Pietrzak KZ. Intrusion resilient secret sharing. In: IEEE; 2007:227-237. doi:<a href=\"https://doi.org/10.1109/FOCS.2007.63\">10.1109/FOCS.2007.63</a>","apa":"Dziembowski, S., &#38; Pietrzak, K. Z. (2007). Intrusion resilient secret sharing (pp. 227–237). Presented at the FOCS: Foundations of Computer Science, IEEE. <a href=\"https://doi.org/10.1109/FOCS.2007.63\">https://doi.org/10.1109/FOCS.2007.63</a>","ista":"Dziembowski S, Pietrzak KZ. 2007. Intrusion resilient secret sharing. FOCS: Foundations of Computer Science, 227–237.","short":"S. Dziembowski, K.Z. Pietrzak, in:, IEEE, 2007, pp. 227–237.","mla":"Dziembowski, Stefan, and Krzysztof Z. Pietrzak. <i>Intrusion Resilient Secret Sharing</i>. IEEE, 2007, pp. 227–37, doi:<a href=\"https://doi.org/10.1109/FOCS.2007.63\">10.1109/FOCS.2007.63</a>."},"date_updated":"2021-01-12T07:41:54Z","type":"conference","date_published":"2007-10-23T00:00:00Z","day":"23","doi":"10.1109/FOCS.2007.63","publist_id":"3459","abstract":[{"text":"We introduce a new primitive called intrusion-resilient secret sharing (IRSS), whose security proof exploits the fact that there exist functions which can be efficiently computed interactively using low communication complexity in k, but not in k-1 rounds. IRSS is a means of sharing a secret message amongst a set of players which comes with a very strong security guarantee. The shares in an IRSS are made artificially large so that it is hard to retrieve them completely, and the reconstruction procedure is interactive requiring the players to exchange k short messages. The adversaries considered can attack the scheme in rounds, where in each round the adversary chooses some player to corrupt and some function, and retrieves the output of that function applied to the share of the corrupted player. This model captures for example computers connected to a network which can occasionally he infected by malicious software like viruses, which can compute any function on the infected machine, but cannot sent out a huge amount of data. Using methods from the bounded-retrieval model, we construct an IRSS scheme which is secure against any computationally unbounded adversary as long as the total amount of information retrieved by the adversary is somewhat less than the length of the shares, and the adversary makes at most k-1 corruption rounds (as described above, where k rounds are necessary for reconstruction). We extend our basic scheme in several ways in order to allow the shares sent by the dealer to be short (the players then blow them up locally) and to handle even stronger adversaries who can learn some of the shares completely. As mentioned, there is an obvious connection between IRSS schemes and the fact that there exist functions with an exponential gap in their communication complexity for k and k-1 rounds. Our scheme implies such a separation which is in several aspects stronger than the previously known ones.","lang":"eng"}],"status":"public","extern":1},{"abstract":[{"text":"We investigate a general class of (black-box) constructions for range extension of weak pseudorandom functions: a construction based on m independent functions F 1,...,F m is given by a set of strings over {1,...,m}*, where for example {〈2〉, 〈1,2〉} corresponds to the function X ↦[F 2(X),F 2(F 1(X))]. All efficient constructions for range expansion of weak pseudorandom functions that we are aware of are of this form.\nWe completely classify such constructions as good, bad or ugly, where the good constructions are those whose security can be proven via a black-box reduction, the bad constructions are those whose insecurity can be proven via a black-box reduction, and the ugly constructions are those which are neither good nor bad.\nOur classification shows that the range expansion from [10] is optimal, in the sense that it achieves the best possible expansion (2 m  − 1 when using m keys).\nAlong the way we show that for weak quasirandom functions (i.e. in the information theoretic setting), all constructions which are not bad – in particular all the ugly ones – are secure.","lang":"eng"}],"publist_id":"3460","doi":"10.1007/978-3-540-72540-4_30","day":"12","date_published":"2007-06-12T00:00:00Z","type":"conference","date_updated":"2021-01-12T07:41:54Z","citation":{"short":"K.Z. Pietrzak, J. Sjödin, in:, Springer, 2007, pp. 517–533.","mla":"Pietrzak, Krzysztof Z., and Johan Sjödin. <i>Range Extension for Weak PRFs the Good the Bad and the Ugly</i>. Vol. 4515, Springer, 2007, pp. 517–33, doi:<a href=\"https://doi.org/10.1007/978-3-540-72540-4_30\">10.1007/978-3-540-72540-4_30</a>.","ista":"Pietrzak KZ, Sjödin J. 2007. Range extension for weak PRFs the good the bad and the ugly. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4515, 517–533.","ama":"Pietrzak KZ, Sjödin J. Range extension for weak PRFs the good the bad and the ugly. In: Vol 4515. Springer; 2007:517-533. doi:<a href=\"https://doi.org/10.1007/978-3-540-72540-4_30\">10.1007/978-3-540-72540-4_30</a>","apa":"Pietrzak, K. Z., &#38; Sjödin, J. (2007). Range extension for weak PRFs the good the bad and the ugly (Vol. 4515, pp. 517–533). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. <a href=\"https://doi.org/10.1007/978-3-540-72540-4_30\">https://doi.org/10.1007/978-3-540-72540-4_30</a>","chicago":"Pietrzak, Krzysztof Z, and Johan Sjödin. “Range Extension for Weak PRFs the Good the Bad and the Ugly,” 4515:517–33. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-72540-4_30\">https://doi.org/10.1007/978-3-540-72540-4_30</a>.","ieee":"K. Z. Pietrzak and J. Sjödin, “Range extension for weak PRFs the good the bad and the ugly,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2007, vol. 4515, pp. 517–533."},"year":"2007","extern":1,"status":"public","volume":4515,"acknowledgement":"This work was partially supported by the Zurich Information Security Center. It represents the views of the authors.","title":"Range extension for weak PRFs the good the bad and the ugly","alternative_title":["LNCS"],"month":"06","intvolume":"      4515","publication_status":"published","date_created":"2018-12-11T12:02:06Z","author":[{"orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sjödin","first_name":"Johan","full_name":"Sjödin,  Johan"}],"_id":"3221","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"publisher":"Springer","page":"517 - 533","quality_controlled":0},{"quality_controlled":0,"page":"86 - 102","conference":{"name":"TCC: Theory of Cryptography Conference"},"publisher":"Springer","author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"full_name":"Wikström, Douglas","last_name":"Wikström","first_name":"Douglas"}],"_id":"3222","intvolume":"      4392","month":"03","alternative_title":["LNCS"],"title":"Parallel repetition of computationally sound protocols revisited","date_created":"2018-12-11T12:02:06Z","publication_status":"published","status":"public","extern":1,"volume":4392,"type":"conference","date_published":"2007-03-22T00:00:00Z","citation":{"chicago":"Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited,” 4392:86–102. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-70936-7_5\">https://doi.org/10.1007/978-3-540-70936-7_5</a>.","ieee":"K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound protocols revisited,” presented at the TCC: Theory of Cryptography Conference, 2007, vol. 4392, pp. 86–102.","apa":"Pietrzak, K. Z., &#38; Wikström, D. (2007). Parallel repetition of computationally sound protocols revisited (Vol. 4392, pp. 86–102). Presented at the TCC: Theory of Cryptography Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-540-70936-7_5\">https://doi.org/10.1007/978-3-540-70936-7_5</a>","ama":"Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols revisited. In: Vol 4392. Springer; 2007:86-102. doi:<a href=\"https://doi.org/10.1007/978-3-540-70936-7_5\">10.1007/978-3-540-70936-7_5</a>","ista":"Pietrzak KZ, Wikström D. 2007. Parallel repetition of computationally sound protocols revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 4392, 86–102.","mla":"Pietrzak, Krzysztof Z., and Douglas Wikström. <i>Parallel Repetition of Computationally Sound Protocols Revisited</i>. Vol. 4392, Springer, 2007, pp. 86–102, doi:<a href=\"https://doi.org/10.1007/978-3-540-70936-7_5\">10.1007/978-3-540-70936-7_5</a>.","short":"K.Z. Pietrzak, D. Wikström, in:, Springer, 2007, pp. 86–102."},"year":"2007","date_updated":"2021-01-12T07:41:54Z","publist_id":"3457","abstract":[{"text":"Parallel repetition is well known to reduce the error probability at an exponential rate for single- and multi-prover interactive proofs.\nBellare, Impagliazzo and Naor (1997) show that this is also true for protocols where the soundness only holds against computationally bounded provers (e.g. interactive arguments) if the protocol has at most three rounds.\nOn the other hand, for four rounds they give a protocol where this is no longer the case: the error probability does not decrease below some constant even if the protocol is repeated a polynomial number of times. Unfortunately, this protocol is not very convincing as the communication complexity of each instance of the protocol grows linearly with the number of repetitions, and for such protocols the error does not even decrease for some types of interactive proofs. Noticing this, Bellare et al. construct (a quite artificial) oracle relative to which a four round protocol exists whose communication complexity does not depend on the number of parallel repetitions. This shows that there is no “black-box” error reduction theorem for four round protocols.\nIn this paper we give the first computationally sound protocol where k-fold parallel repetition does not decrease the error probability below some constant for any polynomial k (and where the communication complexity does not depend on k). The protocol has eight rounds and uses the universal arguments of Barak and Goldreich (2001). We also give another four round protocol relative to an oracle, unlike the artificial oracle of Bellare et al., we just need a generic group. This group can then potentially be instantiated with some real group satisfying some well defined hardness assumptions (we do not know of any candidate for such a group at the moment).","lang":"eng"}],"day":"22","doi":"10.1007/978-3-540-70936-7_5"},{"type":"conference","date_published":"2007-10-11T00:00:00Z","year":"2007","citation":{"short":"Y. Dodis, K.Z. Pietrzak, in:, Springer, 2007, pp. 414–433.","mla":"Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. <i>Improving the Security of MACs via Randomized Message Preprocessing</i>. Vol. 4593, Springer, 2007, pp. 414–33, doi:<a href=\"https://doi.org/10.1007/978-3-540-74619-5_26\">10.1007/978-3-540-74619-5_26</a>.","ista":"Dodis Y, Pietrzak KZ. 2007. Improving the security of MACs via randomized message preprocessing. FSE: Fast Software Encryption, LNCS, vol. 4593, 414–433.","apa":"Dodis, Y., &#38; Pietrzak, K. Z. (2007). Improving the security of MACs via randomized message preprocessing (Vol. 4593, pp. 414–433). Presented at the FSE: Fast Software Encryption, Springer. <a href=\"https://doi.org/10.1007/978-3-540-74619-5_26\">https://doi.org/10.1007/978-3-540-74619-5_26</a>","ama":"Dodis Y, Pietrzak KZ. Improving the security of MACs via randomized message preprocessing. In: Vol 4593. Springer; 2007:414-433. doi:<a href=\"https://doi.org/10.1007/978-3-540-74619-5_26\">10.1007/978-3-540-74619-5_26</a>","ieee":"Y. Dodis and K. Z. Pietrzak, “Improving the security of MACs via randomized message preprocessing,” presented at the FSE: Fast Software Encryption, 2007, vol. 4593, pp. 414–433.","chicago":"Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Improving the Security of MACs via Randomized Message Preprocessing,” 4593:414–33. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-74619-5_26\">https://doi.org/10.1007/978-3-540-74619-5_26</a>."},"date_updated":"2021-01-12T07:41:55Z","publist_id":"3458","abstract":[{"text":"“Hash then encrypt” is an approach to message authentication, where first the message is hashed down using an ε-universal hash function, and then the resulting k-bit value is encrypted, say with a block-cipher. The security of this scheme is proportional to εq2, where q is the number of MACs the adversary can request. As ε is at least 2−k, the best one can hope for is O(q2/2k) security. Unfortunately, such small ε is not achieved by simple hash functions used in practice, such as the polynomial evaluation or the Merkle-Damg ̊ard construction, where ε grows with the message length L.\nThe main insight of this work comes from the fact that, by using ran- domized message preprocessing via a short random salt p (which must then be sent as part of the authentication tag), we can use the “hash then encrypt” paradigm with suboptimal “practical” ε-universal hash func- tions, and still improve its exact security to optimal O(q2/2k). Specif- ically, by using at most an O(logL)-bit salt p, one can always regain the optimal exact security O(q2/2k), even in situations where ε grows polynomially with L. We also give very simple preprocessing maps for popular “suboptimal” hash functions, namely polynomial evaluation and the Merkle-Damg ̊ard construction.\nOur results come from a general extension of the classical Carter- Wegman paradigm, which we believe is of independent interest. On a high level, it shows that public randomization allows one to use the potentially much smaller “average-case” collision probability in place of the “worst-case” collision probability ε.","lang":"eng"}],"day":"11","doi":"10.1007/978-3-540-74619-5_26","status":"public","extern":1,"volume":4593,"author":[{"last_name":"Dodis","first_name":"Yevgeniy","full_name":"Dodis, Yevgeniy"},{"full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3223","intvolume":"      4593","alternative_title":["LNCS"],"month":"10","title":"Improving the security of MACs via randomized message preprocessing","date_created":"2018-12-11T12:02:06Z","publication_status":"published","quality_controlled":0,"page":"414 - 433","conference":{"name":"FSE: Fast Software Encryption"},"publisher":"Springer"},{"publisher":"Genetics Society of America","page":"1001 - 10","quality_controlled":0,"publication_status":"published","date_created":"2018-12-11T12:02:34Z","month":"01","title":"Evolution can favor antagonistic epistasis","intvolume":"       177","publication":"Genetics","_id":"3305","author":[{"first_name":"Michael","last_name":"Desai","full_name":"Desai, Michael M"},{"full_name":"Daniel Weissman","last_name":"Weissman","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcus","last_name":"Feldman","full_name":"Feldman, Marcus W"}],"issue":"2","volume":177,"extern":1,"status":"public","doi":"10.1534/genetics.107.075812","day":"01","abstract":[{"text":"The accumulation of deleterious mutations plays a major role in evolution, and key to this are the interactions between their fitness effects, known as epistasis. Whether mutations tend to interact synergistically (with multiple mutations being more deleterious than would be expected from their individual fitness effects) or antagonistically is important for a variety of evolutionary questions, particularly the evolution of sex. Unfortunately, the experimental evidence on the prevalence and strength of epistasis is mixed and inconclusive. Here we study theoretically whether synergistic or antagonistic epistasis is likely to be favored by evolution and by how much. We find that in the presence of recombination, evolution favors less synergistic or more antagonistic epistasis whenever mutations that change the epistasis in this direction are possible. This is because evolution favors increased buffering against the effects of deleterious mutations. This suggests that we should not expect synergistic epistasis to be widespread in nature and hence that the mutational deterministic hypothesis for the advantage of sex may not apply widely.","lang":"eng"}],"publist_id":"3335","date_updated":"2021-01-12T07:42:32Z","citation":{"ama":"Desai M, Weissman D, Feldman M. Evolution can favor antagonistic epistasis. <i>Genetics</i>. 2007;177(2):1001-1010. doi:<a href=\"https://doi.org/10.1534/genetics.107.075812\">10.1534/genetics.107.075812</a>","apa":"Desai, M., Weissman, D., &#38; Feldman, M. (2007). Evolution can favor antagonistic epistasis. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.107.075812\">https://doi.org/10.1534/genetics.107.075812</a>","ieee":"M. Desai, D. Weissman, and M. Feldman, “Evolution can favor antagonistic epistasis,” <i>Genetics</i>, vol. 177, no. 2. Genetics Society of America, pp. 1001–10, 2007.","chicago":"Desai, Michael, Daniel Weissman, and Marcus Feldman. “Evolution Can Favor Antagonistic Epistasis.” <i>Genetics</i>. Genetics Society of America, 2007. <a href=\"https://doi.org/10.1534/genetics.107.075812\">https://doi.org/10.1534/genetics.107.075812</a>.","short":"M. Desai, D. Weissman, M. Feldman, Genetics 177 (2007) 1001–10.","mla":"Desai, Michael, et al. “Evolution Can Favor Antagonistic Epistasis.” <i>Genetics</i>, vol. 177, no. 2, Genetics Society of America, 2007, pp. 1001–10, doi:<a href=\"https://doi.org/10.1534/genetics.107.075812\">10.1534/genetics.107.075812</a>.","ista":"Desai M, Weissman D, Feldman M. 2007. Evolution can favor antagonistic epistasis. Genetics. 177(2), 1001–10."},"year":"2007","date_published":"2007-01-01T00:00:00Z","type":"journal_article"},{"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"type":"journal_article","date_published":"2007-09-09T00:00:00Z","keyword":["Cell Biology"],"language":[{"iso":"eng"}],"oa_version":"None","month":"09","publication":"Nature Cell Biology","volume":9,"extern":"1","day":"09","doi":"10.1038/ncb1636","abstract":[{"text":"The formation of the nuclear envelope (NE) around chromatin is a major membrane-remodelling event that occurs during cell division of metazoa. It is unclear whether the nuclear membrane reforms by the fusion of NE fragments or if it re-emerges from an intact tubular network of the endoplasmic reticulum (ER). Here, we show that NE formation and expansion requires a tubular ER network and occurs efficiently in the presence of the membrane fusion inhibitor GTPγS. Chromatin recruitment of membranes, which is initiated by tubule-end binding, followed by the formation, expansion and sealing of flat membrane sheets, is mediated by DNA-binding proteins residing in the ER. Thus, chromatin plays an active role in reshaping of the ER during NE formation.","lang":"eng"}],"citation":{"apa":"Anderson, D. J., &#38; Hetzer, M. (2007). Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ncb1636\">https://doi.org/10.1038/ncb1636</a>","ama":"Anderson DJ, Hetzer M. Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. <i>Nature Cell Biology</i>. 2007;9(10):1160-1166. doi:<a href=\"https://doi.org/10.1038/ncb1636\">10.1038/ncb1636</a>","ieee":"D. J. Anderson and M. Hetzer, “Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum,” <i>Nature Cell Biology</i>, vol. 9, no. 10. Springer Nature, pp. 1160–1166, 2007.","chicago":"Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” <i>Nature Cell Biology</i>. Springer Nature, 2007. <a href=\"https://doi.org/10.1038/ncb1636\">https://doi.org/10.1038/ncb1636</a>.","mla":"Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” <i>Nature Cell Biology</i>, vol. 9, no. 10, Springer Nature, 2007, pp. 1160–66, doi:<a href=\"https://doi.org/10.1038/ncb1636\">10.1038/ncb1636</a>.","short":"D.J. Anderson, M. Hetzer, Nature Cell Biology 9 (2007) 1160–1166.","ista":"Anderson DJ, Hetzer M. 2007. Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology. 9(10), 1160–1166."},"year":"2007","date_updated":"2022-07-18T08:56:38Z","external_id":{"pmid":["17828249"]},"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","page":"1160-1166","date_created":"2022-04-07T07:56:04Z","article_processing_charge":"No","publication_status":"published","intvolume":"         9","title":"Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum","scopus_import":"1","_id":"11115","pmid":1,"issue":"10","author":[{"full_name":"Anderson, Daniel J.","first_name":"Daniel J.","last_name":"Anderson"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}]},{"title":"MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly","intvolume":"         8","publication_status":"published","article_processing_charge":"No","date_created":"2022-04-07T07:56:13Z","author":[{"first_name":"Cerstin","last_name":"Franz","full_name":"Franz, Cerstin"},{"first_name":"Rudolf","last_name":"Walczak","full_name":"Walczak, Rudolf"},{"first_name":"Sevil","last_name":"Yavuz","full_name":"Yavuz, Sevil"},{"last_name":"Santarella","first_name":"Rachel","full_name":"Santarella, Rachel"},{"full_name":"Gentzel, Marc","first_name":"Marc","last_name":"Gentzel"},{"full_name":"Askjaer, Peter","last_name":"Askjaer","first_name":"Peter"},{"first_name":"Vincent","last_name":"Galy","full_name":"Galy, Vincent"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"},{"first_name":"Iain W","last_name":"Mattaj","full_name":"Mattaj, Iain W"},{"first_name":"Wolfram","last_name":"Antonin","full_name":"Antonin, Wolfram"}],"issue":"2","_id":"11116","pmid":1,"scopus_import":"1","article_type":"original","publisher":"EMBO","page":"165-172","quality_controlled":"1","abstract":[{"text":"The metazoan nuclear envelope (NE) breaks down and re-forms during each cell cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport during interphase, assemble into the re-forming NE at the end of mitosis. Using in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal effect lethal), a recently discovered NE component in Caenorhabditis elegans, functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex (Nup for nucleoporin), an important building block of the NPC, and is essential for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28 acts as a seeding point for NPC assembly.","lang":"eng"}],"doi":"10.1038/sj.embor.7400889","day":"19","external_id":{"pmid":["17235358"]},"date_updated":"2022-07-18T08:56:40Z","year":"2007","citation":{"chicago":"Franz, Cerstin, Rudolf Walczak, Sevil Yavuz, Rachel Santarella, Marc Gentzel, Peter Askjaer, Vincent Galy, Martin Hetzer, Iain W Mattaj, and Wolfram Antonin. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” <i>EMBO Reports</i>. EMBO, 2007. <a href=\"https://doi.org/10.1038/sj.embor.7400889\">https://doi.org/10.1038/sj.embor.7400889</a>.","ieee":"C. Franz <i>et al.</i>, “MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly,” <i>EMBO reports</i>, vol. 8, no. 2. EMBO, pp. 165–172, 2007.","ama":"Franz C, Walczak R, Yavuz S, et al. MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. <i>EMBO reports</i>. 2007;8(2):165-172. doi:<a href=\"https://doi.org/10.1038/sj.embor.7400889\">10.1038/sj.embor.7400889</a>","apa":"Franz, C., Walczak, R., Yavuz, S., Santarella, R., Gentzel, M., Askjaer, P., … Antonin, W. (2007). MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. <i>EMBO Reports</i>. EMBO. <a href=\"https://doi.org/10.1038/sj.embor.7400889\">https://doi.org/10.1038/sj.embor.7400889</a>","ista":"Franz C, Walczak R, Yavuz S, Santarella R, Gentzel M, Askjaer P, Galy V, Hetzer M, Mattaj IW, Antonin W. 2007. MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO reports. 8(2), 165–172.","short":"C. Franz, R. Walczak, S. Yavuz, R. Santarella, M. Gentzel, P. Askjaer, V. Galy, M. Hetzer, I.W. Mattaj, W. Antonin, EMBO Reports 8 (2007) 165–172.","mla":"Franz, Cerstin, et al. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” <i>EMBO Reports</i>, vol. 8, no. 2, EMBO, 2007, pp. 165–72, doi:<a href=\"https://doi.org/10.1038/sj.embor.7400889\">10.1038/sj.embor.7400889</a>."},"extern":"1","volume":8,"month":"01","oa_version":"Published Version","publication":"EMBO reports","language":[{"iso":"eng"}],"keyword":["Genetics","Molecular Biology","Biochemistry"],"oa":1,"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"date_published":"2007-01-19T00:00:00Z","type":"journal_article","status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","main_file_link":[{"url":"https://doi.org/10.1038/sj.embor.7400889","open_access":"1"}]},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":111,"abstract":[{"text":"We used single-channel electrical recordings and Langevin molecular dynamics simulations to explore the electrophoretic translocation of various β-hairpin peptides across the staphylococcal α-hemolysin (αHL) protein pore at single-molecule resolution. The β-hairpin peptides, which varied in their folding properties, corresponded to the C terminal residues of the B1 domain of protein G. The translocation time was strongly dependent on the electric force and was correlated with the folding features of the β-hairpin peptides. Highly unfolded peptides entered the pore in an extended conformation, resulting in fast single-file translocation events. In contrast, the translocation of the folded β-hairpin peptides occurred more slowly. In this case, the β-hairpin peptides traversed the αHL pore in a misfolded or fully folded conformation. This study demonstrates that the interaction between a polypeptide and a β-barrel protein pore is dependent on the folding features of the polypeptide. ","lang":"eng"}],"doi":"10.1021/jp071364h","day":"13","publication_identifier":{"issn":["1520-6106","1520-5207"]},"date_published":"2007-03-13T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T08:15:29Z","citation":{"ista":"Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, Zhu A, Scholtz JM, Makarov DE, Movileanu L. 2007. Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations. The Journal of Physical Chemistry B. 111(13), 3332–3335.","short":"C.P. Goodrich, S. Kirmizialtin, B.M. Huyghues-Despointes, A. Zhu, J.M. Scholtz, D.E. Makarov, L. Movileanu, The Journal of Physical Chemistry B 111 (2007) 3332–3335.","mla":"Goodrich, Carl Peter, et al. “Single-Molecule Electrophoresis of β-Hairpin Peptides by Electrical Recordings and Langevin Dynamics Simulations.” <i>The Journal of Physical Chemistry B</i>, vol. 111, no. 13, American Chemical Society, 2007, pp. 3332–35, doi:<a href=\"https://doi.org/10.1021/jp071364h\">10.1021/jp071364h</a>.","chicago":"Goodrich, Carl Peter, Serdal Kirmizialtin, Beatrice M. Huyghues-Despointes, Aiping Zhu, J. Martin Scholtz, Dmitrii E. Makarov, and Liviu Movileanu. “Single-Molecule Electrophoresis of β-Hairpin Peptides by Electrical Recordings and Langevin Dynamics Simulations.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/jp071364h\">https://doi.org/10.1021/jp071364h</a>.","ieee":"C. P. Goodrich <i>et al.</i>, “Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations,” <i>The Journal of Physical Chemistry B</i>, vol. 111, no. 13. American Chemical Society, pp. 3332–3335, 2007.","apa":"Goodrich, C. P., Kirmizialtin, S., Huyghues-Despointes, B. M., Zhu, A., Scholtz, J. M., Makarov, D. E., &#38; Movileanu, L. (2007). Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jp071364h\">https://doi.org/10.1021/jp071364h</a>","ama":"Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, et al. Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations. <i>The Journal of Physical Chemistry B</i>. 2007;111(13):3332-3335. doi:<a href=\"https://doi.org/10.1021/jp071364h\">10.1021/jp071364h</a>"},"year":"2007","article_type":"original","publisher":"American Chemical Society","language":[{"iso":"eng"}],"page":"3332-3335","quality_controlled":"1","title":"Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations","month":"03","intvolume":"       111","oa_version":"None","publication_status":"published","article_processing_charge":"No","date_created":"2020-04-30T12:19:15Z","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich"},{"first_name":"Serdal","last_name":"Kirmizialtin","full_name":"Kirmizialtin, Serdal"},{"first_name":"Beatrice M.","last_name":"Huyghues-Despointes","full_name":"Huyghues-Despointes, Beatrice M."},{"full_name":"Zhu, Aiping","last_name":"Zhu","first_name":"Aiping"},{"last_name":"Scholtz","first_name":"J. Martin","full_name":"Scholtz, J. Martin"},{"full_name":"Makarov, Dmitrii E.","first_name":"Dmitrii E.","last_name":"Makarov"},{"last_name":"Movileanu","first_name":"Liviu","full_name":"Movileanu, Liviu"}],"issue":"13","_id":"7780","publication":"The Journal of Physical Chemistry B"},{"page":"2168-2181","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Wiley","article_type":"original","publication":"Evolution","_id":"7781","author":[{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Pilkington","first_name":"Jill G.","full_name":"Pilkington, Jill G."},{"last_name":"Clutton-Brock","first_name":"Tim H.","full_name":"Clutton-Brock, Tim H."},{"full_name":"Pemberton, Josephine M.","first_name":"Josephine M.","last_name":"Pemberton"},{"full_name":"Kruuk, Loeske E.B.","last_name":"Kruuk","first_name":"Loeske E.B."}],"issue":"10","publication_status":"published","oa_version":"None","date_created":"2020-04-30T13:01:47Z","article_processing_charge":"No","title":"Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep","month":"05","intvolume":"        60","volume":60,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2021-01-12T08:15:30Z","year":"2007","citation":{"ista":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2007. Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep. Evolution. 60(10), 2168–2181.","mla":"Robinson, Matthew Richard, et al. “Live Fast, Die Young: Trade-Offs between Fitness Components and Sexually Antagonistic Selection on Weaponry in Soay Sheep.” <i>Evolution</i>, vol. 60, no. 10, Wiley, 2007, pp. 2168–81, doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">10.1111/j.0014-3820.2006.tb01854.x</a>.","short":"M.R. Robinson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B. Kruuk, Evolution 60 (2007) 2168–2181.","ieee":"M. R. Robinson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and L. E. B. Kruuk, “Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep,” <i>Evolution</i>, vol. 60, no. 10. Wiley, pp. 2168–2181, 2007.","chicago":"Robinson, Matthew Richard, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine M. Pemberton, and Loeske E.B. Kruuk. “Live Fast, Die Young: Trade-Offs between Fitness Components and Sexually Antagonistic Selection on Weaponry in Soay Sheep.” <i>Evolution</i>. Wiley, 2007. <a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">https://doi.org/10.1111/j.0014-3820.2006.tb01854.x</a>.","apa":"Robinson, M. R., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M., &#38; Kruuk, L. E. B. (2007). Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">https://doi.org/10.1111/j.0014-3820.2006.tb01854.x</a>","ama":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep. <i>Evolution</i>. 2007;60(10):2168-2181. doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2006.tb01854.x\">10.1111/j.0014-3820.2006.tb01854.x</a>"},"date_published":"2007-05-08T00:00:00Z","type":"journal_article","doi":"10.1111/j.0014-3820.2006.tb01854.x","publication_identifier":{"issn":["0014-3820"]},"day":"08","abstract":[{"text":"Males are predicted to compete for reproductive opportunities, with sexual selection driving the evolution of large body size and weaponry through the advantage they confer for access to females. Few studies have explored potential trade‐offs of investment in secondary sexual traits between different components of fitness or tested for sexually antagonistic selection pressures. These factors may provide explanations for observed polymorphisms in both form and quality of secondary sexual traits. We report here an analysis of selection on horn phenotype in a feral population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, Scotland. Soay sheep display a phenotypic polymorphism for horn type with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred, or no (polled) horns; further variation in size exists within horn morphs. We show that horn phenotype and the size of the trait displayed is subject to different selection pressures in males and females, generating sexually antagonistic selection. Furthermore, there was evidence of a trade‐off between breeding success and longevity in normal‐horned males, with both the normal horn type and larger horn size being associated with greater annual breeding success but reduced longevity. Therefore, selection through lifetime breeding success was not found to act upon horn phenotype in males. In females, a negative association of annual breeding success within the normal‐horned phenotype did not result in a significant difference in lifetime fitness when compared to scurred individuals, as no significant difference in longevity was found. However, increased horn size within this group was negatively associated with breeding success and longevity. Females without horns (polled) suffered reduced longevity and thus reduced lifetime breeding success relative the other horn morphs. Our results therefore suggest that trade‐offs between different components of fitness and antagonistic selection between the sexes may maintain genetic variation for secondary sexual traits within a population.","lang":"eng"}]},{"volume":40,"extern":"1","doi":"10.1055/s-2007-992130","day":"01","abstract":[{"lang":"eng","text":"Gating deficits and hallucinatory sensations are prominent symptoms of schizophrenia. Comparing these abnormalities with the failure modes of network models is an interesting way to explore how they arise. We present a network model that can both propagate and gate signals. The model exhibits effects reminiscent of clinically observed pathologies when the balance between excitation and inhibition that it requires is not properly maintained."}],"date_updated":"2021-01-12T08:16:36Z","year":"2007","citation":{"ama":"Vogels TP, Abbott L. Gating deficits in model networks: A path to schizophrenia? <i>Pharmacopsychiatry</i>. 2007;40(S 1):S73-S77. doi:<a href=\"https://doi.org/10.1055/s-2007-992130\">10.1055/s-2007-992130</a>","apa":"Vogels, T. P., &#38; Abbott, L. (2007). Gating deficits in model networks: A path to schizophrenia? <i>Pharmacopsychiatry</i>. Thieme. <a href=\"https://doi.org/10.1055/s-2007-992130\">https://doi.org/10.1055/s-2007-992130</a>","ieee":"T. P. Vogels and L. Abbott, “Gating deficits in model networks: A path to schizophrenia?,” <i>Pharmacopsychiatry</i>, vol. 40, no. S 1. Thieme, pp. S73–S77, 2007.","chicago":"Vogels, Tim P, and L. Abbott. “Gating Deficits in Model Networks: A Path to Schizophrenia?” <i>Pharmacopsychiatry</i>. Thieme, 2007. <a href=\"https://doi.org/10.1055/s-2007-992130\">https://doi.org/10.1055/s-2007-992130</a>.","mla":"Vogels, Tim P., and L. Abbott. “Gating Deficits in Model Networks: A Path to Schizophrenia?” <i>Pharmacopsychiatry</i>, vol. 40, no. S 1, Thieme, 2007, pp. S73–77, doi:<a href=\"https://doi.org/10.1055/s-2007-992130\">10.1055/s-2007-992130</a>.","short":"T.P. Vogels, L. Abbott, Pharmacopsychiatry 40 (2007) S73–S77.","ista":"Vogels TP, Abbott L. 2007. Gating deficits in model networks: A path to schizophrenia? Pharmacopsychiatry. 40(S 1), S73–S77."},"external_id":{"pmid":["18080946"]},"publisher":"Thieme","article_type":"original","page":"S73-S77","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","date_created":"2020-06-25T13:11:37Z","title":"Gating deficits in model networks: A path to schizophrenia?","intvolume":"        40","pmid":1,"_id":"8027","author":[{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"first_name":"L.","last_name":"Abbott","full_name":"Abbott, L."}],"issue":"S 1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","publication_identifier":{"issn":["0176-3679","1439-0795"]},"date_published":"2007-12-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"None","month":"12","publication":"Pharmacopsychiatry"},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":104,"type":"journal_article","date_published":"2007-07-03T00:00:00Z","citation":{"ista":"Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National Academy of Sciences. 104(27), 11257–11262.","short":"P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of Sciences 104 (2007) 11257–11262.","mla":"Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62, doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>.","chicago":"Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>.","ieee":"P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27. National Academy of Sciences, pp. 11257–11262, 2007.","apa":"Schanda, P., Forge, V., &#38; Brutscher, B. (2007). Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>","ama":"Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(27):11257-11262. doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>"},"year":"2007","date_updated":"2021-01-12T08:19:35Z","abstract":[{"text":"Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.","lang":"eng"}],"day":"03","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.0702069104","keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"quality_controlled":"1","page":"11257-11262","article_type":"original","publisher":"National Academy of Sciences","issue":"27","author":[{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"V.","last_name":"Forge","full_name":"Forge, V."},{"last_name":"Brutscher","first_name":"B.","full_name":"Brutscher, B."}],"_id":"8483","publication":"Proceedings of the National Academy of Sciences","intvolume":"       104","title":"Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy","month":"07","article_processing_charge":"No","date_created":"2020-09-18T10:12:54Z","publication_status":"published","oa_version":"None"},{"volume":187,"extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:35Z","year":"2007","citation":{"ista":"Lescop E, Schanda P, Brutscher B. 2007. A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. Journal of Magnetic Resonance. 187(1), 163–169.","mla":"Lescop, Ewen, et al. “A Set of BEST Triple-Resonance Experiments for Time-Optimized Protein Resonance Assignment.” <i>Journal of Magnetic Resonance</i>, vol. 187, no. 1, Elsevier, 2007, pp. 163–69, doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">10.1016/j.jmr.2007.04.002</a>.","short":"E. Lescop, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 187 (2007) 163–169.","chicago":"Lescop, Ewen, Paul Schanda, and Bernhard Brutscher. “A Set of BEST Triple-Resonance Experiments for Time-Optimized Protein Resonance Assignment.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">https://doi.org/10.1016/j.jmr.2007.04.002</a>.","ieee":"E. Lescop, P. Schanda, and B. Brutscher, “A set of BEST triple-resonance experiments for time-optimized protein resonance assignment,” <i>Journal of Magnetic Resonance</i>, vol. 187, no. 1. Elsevier, pp. 163–169, 2007.","ama":"Lescop E, Schanda P, Brutscher B. A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. <i>Journal of Magnetic Resonance</i>. 2007;187(1):163-169. doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">10.1016/j.jmr.2007.04.002</a>","apa":"Lescop, E., Schanda, P., &#38; Brutscher, B. (2007). A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">https://doi.org/10.1016/j.jmr.2007.04.002</a>"},"date_published":"2007-07-01T00:00:00Z","type":"journal_article","doi":"10.1016/j.jmr.2007.04.002","day":"01","publication_identifier":{"issn":["1090-7807"]},"abstract":[{"lang":"eng","text":"A series of sequential, intra-residue, and bi-directional BEST H–N–CA, H–N–CO, and H–N–CB pulse sequences is presented that extends the BEST concept introduced recently for fast multidimensional protein NMR [Schanda et al., J. Am. Chem. Soc. 128 (2006) 9042] to the complete set of experiments required for sequential resonance assignment. We demonstrate for the protein ubiquitin that 3D BEST H–N–C correlation spectra can be recorded on a 600 MHz NMR spectrometer equipped with a cryogenic probe in only a few minutes of acquisition time with sufficient sensitivity to detect all expected cross peaks."}],"page":"163-169","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Elsevier","article_type":"letter_note","publication":"Journal of Magnetic Resonance","_id":"8484","author":[{"last_name":"Lescop","first_name":"Ewen","full_name":"Lescop, Ewen"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"issue":"1","oa_version":"None","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-18T10:13:02Z","title":"A set of BEST triple-resonance experiments for time-optimized protein resonance assignment","month":"07","intvolume":"       187"},{"volume":38,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.1007/s10858-006-9138-2","publication_identifier":{"issn":["0925-2738","1573-5001"]},"day":"08","abstract":[{"lang":"eng","text":"High signal to noise is a necessity for the quantification of NMR spectral parameters to be translated into accurate and precise restraints on protein structure and dynamics. An important source of long-range structural information is obtained from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules. For sensitivity reasons, such measurements are generally performed on highly deuterated protein samples. Here we show that high sensitivity is also obtained for protonated protein samples if the pulse schemes are optimized in terms of longitudinal relaxation efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized quantitative J-correlation experiment yields important signal gains reaching factors of 1.5 to 8 for individual correlation peaks when compared to previously proposed pulse schemes."}],"date_updated":"2021-01-12T08:19:36Z","citation":{"ista":"Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. 2007. Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. Journal of Biomolecular NMR. 38, 47–55.","mla":"Schanda, Paul, et al. “Sensitivity-Optimized Experiment for the Measurement of Residual Dipolar Couplings between Amide Protons.” <i>Journal of Biomolecular NMR</i>, vol. 38, Springer Nature, 2007, pp. 47–55, doi:<a href=\"https://doi.org/10.1007/s10858-006-9138-2\">10.1007/s10858-006-9138-2</a>.","short":"P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, B. Brutscher, Journal of Biomolecular NMR 38 (2007) 47–55.","ieee":"P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, and B. Brutscher, “Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons,” <i>Journal of Biomolecular NMR</i>, vol. 38. Springer Nature, pp. 47–55, 2007.","chicago":"Schanda, Paul, Ewen Lescop, Mirjam Falge, Rémy Sounier, Jérôme Boisbouvier, and Bernhard Brutscher. “Sensitivity-Optimized Experiment for the Measurement of Residual Dipolar Couplings between Amide Protons.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2007. <a href=\"https://doi.org/10.1007/s10858-006-9138-2\">https://doi.org/10.1007/s10858-006-9138-2</a>.","ama":"Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. <i>Journal of Biomolecular NMR</i>. 2007;38:47-55. doi:<a href=\"https://doi.org/10.1007/s10858-006-9138-2\">10.1007/s10858-006-9138-2</a>","apa":"Schanda, P., Lescop, E., Falge, M., Sounier, R., Boisbouvier, J., &#38; Brutscher, B. (2007). Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-006-9138-2\">https://doi.org/10.1007/s10858-006-9138-2</a>"},"year":"2007","date_published":"2007-03-08T00:00:00Z","type":"journal_article","publisher":"Springer Nature","article_type":"original","page":"47-55","quality_controlled":"1","language":[{"iso":"eng"}],"keyword":["Spectroscopy","Biochemistry"],"publication_status":"published","oa_version":"None","article_processing_charge":"No","date_created":"2020-09-18T10:13:12Z","month":"03","title":"Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons","intvolume":"        38","_id":"8485","publication":"Journal of Biomolecular NMR","author":[{"last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Lescop","first_name":"Ewen","full_name":"Lescop, Ewen"},{"last_name":"Falge","first_name":"Mirjam","full_name":"Falge, Mirjam"},{"full_name":"Sounier, Rémy","first_name":"Rémy","last_name":"Sounier"},{"last_name":"Boisbouvier","first_name":"Jérôme","full_name":"Boisbouvier, Jérôme"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"}]},{"abstract":[{"lang":"eng","text":"A technique is described that allows reducing acquisition times of multidimensional NMR experiments by extensive spectral folding. The method is simple and has many interesting applications for NMR studies of molecular structure, dynamics, and kinetics."}],"doi":"10.1021/ja068949u","publication_identifier":{"issn":["0002-7863","1520-5126"]},"day":"17","date_published":"2007-02-17T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T08:19:36Z","citation":{"mla":"Lescop, Ewen, et al. “Automated Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 129, no. 10, American Chemical Society, 2007, pp. 2756–57, doi:<a href=\"https://doi.org/10.1021/ja068949u\">10.1021/ja068949u</a>.","short":"E. Lescop, P. Schanda, R. Rasia, B. Brutscher, Journal of the American Chemical Society 129 (2007) 2756–2757.","ista":"Lescop E, Schanda P, Rasia R, Brutscher B. 2007. Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. Journal of the American Chemical Society. 129(10), 2756–2757.","apa":"Lescop, E., Schanda, P., Rasia, R., &#38; Brutscher, B. (2007). Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja068949u\">https://doi.org/10.1021/ja068949u</a>","ama":"Lescop E, Schanda P, Rasia R, Brutscher B. Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2007;129(10):2756-2757. doi:<a href=\"https://doi.org/10.1021/ja068949u\">10.1021/ja068949u</a>","ieee":"E. Lescop, P. Schanda, R. Rasia, and B. Brutscher, “Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 129, no. 10. American Chemical Society, pp. 2756–2757, 2007.","chicago":"Lescop, Ewen, Paul Schanda, Rodolfo Rasia, and Bernhard Brutscher. “Automated Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/ja068949u\">https://doi.org/10.1021/ja068949u</a>."},"year":"2007","extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":129,"title":"Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy","month":"02","intvolume":"       129","publication_status":"published","oa_version":"None","article_processing_charge":"No","date_created":"2020-09-18T10:13:21Z","author":[{"full_name":"Lescop, Ewen","last_name":"Lescop","first_name":"Ewen"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"},{"full_name":"Rasia, Rodolfo","last_name":"Rasia","first_name":"Rodolfo"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"issue":"10","publication":"Journal of the American Chemical Society","_id":"8486","article_type":"original","publisher":"American Chemical Society","language":[{"iso":"eng"}],"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"page":"2756-2757","quality_controlled":"1"},{"abstract":[{"text":"Following unidirectional biophysical events such as the folding of proteins or the equilibration of binding interactions, requires experimental methods that yield information at both atomic-level resolution and at high repetition rates. Toward this end a number of different approaches enabling the rapid acquisition of 2D NMR spectra have been recently introduced, including spatially encoded “ultrafast” 2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions by reducing the number of scans that are necessary for completing arbitrary 2D NMR experiments, the latter operates by reducing the delay between consecutive scans while preserving sensitivity. Given the complementarities between these two approaches it seems natural to combine them into a single tool, enabling the acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate here this capability with the introduction of “ultraSOFAST” HMQC NMR, a spatially encoded and relaxation-optimized approach that can provide 2D protein correlation spectra at ∼1 s repetition rates for samples in the ∼2 mM concentration range. The principles, relative advantages, and current limitations of this new approach are discussed, and its application is exemplified with a study of the fast hydrogen−deuterium exchange characterizing amide sites in Ubiquitin.","lang":"eng"}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"day":"10","doi":"10.1021/ja066915g","type":"journal_article","date_published":"2007-01-10T00:00:00Z","citation":{"short":"M. Gal, P. Schanda, B. Brutscher, L. Frydman, Journal of the American Chemical Society 129 (2007) 1372–1377.","mla":"Gal, Maayan, et al. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” <i>Journal of the American Chemical Society</i>, vol. 129, no. 5, American Chemical Society, 2007, pp. 1372–77, doi:<a href=\"https://doi.org/10.1021/ja066915g\">10.1021/ja066915g</a>.","ista":"Gal M, Schanda P, Brutscher B, Frydman L. 2007. UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. Journal of the American Chemical Society. 129(5), 1372–1377.","ama":"Gal M, Schanda P, Brutscher B, Frydman L. UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. <i>Journal of the American Chemical Society</i>. 2007;129(5):1372-1377. doi:<a href=\"https://doi.org/10.1021/ja066915g\">10.1021/ja066915g</a>","apa":"Gal, M., Schanda, P., Brutscher, B., &#38; Frydman, L. (2007). UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja066915g\">https://doi.org/10.1021/ja066915g</a>","chicago":"Gal, Maayan, Paul Schanda, Bernhard Brutscher, and Lucio Frydman. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/ja066915g\">https://doi.org/10.1021/ja066915g</a>.","ieee":"M. Gal, P. Schanda, B. Brutscher, and L. Frydman, “UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates,” <i>Journal of the American Chemical Society</i>, vol. 129, no. 5. American Chemical Society, pp. 1372–1377, 2007."},"year":"2007","date_updated":"2021-01-12T08:19:37Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":129,"intvolume":"       129","month":"01","title":"UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates","article_processing_charge":"No","date_created":"2020-09-18T10:13:27Z","publication_status":"published","oa_version":"None","issue":"5","author":[{"full_name":"Gal, Maayan","last_name":"Gal","first_name":"Maayan"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"},{"first_name":"Lucio","last_name":"Frydman","full_name":"Frydman, Lucio"}],"publication":"Journal of the American Chemical Society","_id":"8487","article_type":"original","publisher":"American Chemical Society","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"quality_controlled":"1","page":"1372-1377"},{"date_updated":"2021-01-12T08:19:47Z","citation":{"apa":"Gorodetski, A., &#38; Kaloshin, V. (2007). How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">https://doi.org/10.1016/j.aim.2006.03.012</a>","ama":"Gorodetski A, Kaloshin V. How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. <i>Advances in Mathematics</i>. 2007;208(2):710-797. doi:<a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">10.1016/j.aim.2006.03.012</a>","ieee":"A. Gorodetski and V. Kaloshin, “How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency,” <i>Advances in Mathematics</i>, vol. 208, no. 2. Elsevier, pp. 710–797, 2007.","chicago":"Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.” <i>Advances in Mathematics</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">https://doi.org/10.1016/j.aim.2006.03.012</a>.","short":"A. Gorodetski, V. Kaloshin, Advances in Mathematics 208 (2007) 710–797.","mla":"Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.” <i>Advances in Mathematics</i>, vol. 208, no. 2, Elsevier, 2007, pp. 710–97, doi:<a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">10.1016/j.aim.2006.03.012</a>.","ista":"Gorodetski A, Kaloshin V. 2007. How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. Advances in Mathematics. 208(2), 710–797."},"year":"2007","date_published":"2007-01-30T00:00:00Z","type":"journal_article","doi":"10.1016/j.aim.2006.03.012","day":"30","publication_identifier":{"issn":["0001-8708"]},"abstract":[{"lang":"eng","text":"Here we study an amazing phenomenon discovered by Newhouse [S. Newhouse, Non-density of Axiom A(a) on S2, in: Proc. Sympos. Pure Math., vol. 14, Amer. Math. Soc., 1970, pp. 191–202; S. Newhouse,\r\nDiffeomorphisms with infinitely many sinks, Topology 13 (1974) 9–18; S. Newhouse, The abundance of\r\nwild hyperbolic sets and nonsmooth stable sets of diffeomorphisms, Publ. Math. Inst. Hautes Études Sci.\r\n50 (1979) 101–151]. It turns out that in the space of Cr smooth diffeomorphisms Diffr(M) of a compact\r\nsurface M there is an open set U such that a Baire generic diffeomorphism f ∈ U has infinitely many coexisting sinks. In this paper we make a step towards understanding “how often does a surface diffeomorphism\r\nhave infinitely many sinks.” Our main result roughly says that with probability one for any positive D a\r\nsurface diffeomorphism has only finitely many localized sinks either of cyclicity bounded by D or those\r\nwhose period is relatively large compared to its cyclicity. It verifies a particular case of Palis’ Conjecture\r\nsaying that even though diffeomorphisms with infinitely many coexisting sinks are Baire generic, they have\r\nprobability zero.\r\nOne of the key points of the proof is an application of Newton Interpolation Polynomials to study the dynamics initiated in [V. Kaloshin, B. Hunt, A stretched exponential bound on the rate of growth of the number\r\nof periodic points for prevalent diffeomorphisms I, Ann. of Math., in press, 92 pp.; V. Kaloshin, A stretched\r\nexponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II,\r\npreprint, 85 pp.]."}],"volume":208,"extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Advances in Mathematics","_id":"8511","author":[{"first_name":"A.","last_name":"Gorodetski","full_name":"Gorodetski, A."},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628"}],"issue":"2","oa_version":"None","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-18T10:48:27Z","month":"01","title":"How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency","intvolume":"       208","page":"710-797","quality_controlled":"1","language":[{"iso":"eng"}],"keyword":["General Mathematics"],"publisher":"Elsevier","article_type":"original"},{"publication":"Annals of Mathematics","_id":"8512","issue":"1","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"last_name":"Hunt","first_name":"Brian","full_name":"Hunt, Brian"}],"date_created":"2020-09-18T10:48:33Z","article_processing_charge":"No","publication_status":"published","oa_version":"None","intvolume":"       165","title":"Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I","month":"01","quality_controlled":"1","page":"89-170","language":[{"iso":"eng"}],"publisher":"Princeton University Press","article_type":"original","citation":{"apa":"Kaloshin, V., &#38; Hunt, B. (2007). Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. <i>Annals of Mathematics</i>. Princeton University Press. <a href=\"https://doi.org/10.4007/annals.2007.165.89\">https://doi.org/10.4007/annals.2007.165.89</a>","ama":"Kaloshin V, Hunt B. Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. <i>Annals of Mathematics</i>. 2007;165(1):89-170. doi:<a href=\"https://doi.org/10.4007/annals.2007.165.89\">10.4007/annals.2007.165.89</a>","ieee":"V. Kaloshin and B. Hunt, “Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I,” <i>Annals of Mathematics</i>, vol. 165, no. 1. Princeton University Press, pp. 89–170, 2007.","chicago":"Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” <i>Annals of Mathematics</i>. Princeton University Press, 2007. <a href=\"https://doi.org/10.4007/annals.2007.165.89\">https://doi.org/10.4007/annals.2007.165.89</a>.","mla":"Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” <i>Annals of Mathematics</i>, vol. 165, no. 1, Princeton University Press, 2007, pp. 89–170, doi:<a href=\"https://doi.org/10.4007/annals.2007.165.89\">10.4007/annals.2007.165.89</a>.","short":"V. Kaloshin, B. Hunt, Annals of Mathematics 165 (2007) 89–170.","ista":"Kaloshin V, Hunt B. 2007. Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. Annals of Mathematics. 165(1), 89–170."},"year":"2007","date_updated":"2021-01-12T08:19:48Z","type":"journal_article","date_published":"2007-01-01T00:00:00Z","publication_identifier":{"issn":["0003-486X"]},"day":"01","doi":"10.4007/annals.2007.165.89","abstract":[{"text":"For diffeomorphisms of smooth compact finite-dimensional manifolds, we consider the problem of how fast the number of periodic points with period n grows as a function of n. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for C2 or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call “prevalence”, the growth is not much faster than exponential. Specifically, we show that for each ρ,δ>0, there is a prevalent set of C1+ρ (or smoother) diffeomorphisms for which the number of periodic n points is bounded above by exp(Cn1+δ) for some C independent of n. We also obtain a related bound on the decay of hyperbolicity of the periodic points as a function of n, and obtain the same results for 1-dimensional endomorphisms. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity show this to be a subtle and complex phenomenon, reminiscent of KAM theory. Here in Part I we state our results and describe the methods we use. We complete most of the proof in the 1-dimensional C2-smooth case and outline the remaining steps, deferred to Part II, that are needed to establish the general case.\r\n\r\nThe novel feature of the approach we develop in this paper is the introduction of Newton Interpolation Polynomials as a tool for perturbing trajectories of iterated maps.","lang":"eng"}],"volume":165,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"intvolume":"        81","title":"Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state","month":"07","date_created":"2018-12-11T11:48:53Z","publication_status":"published","issue":"1","author":[{"last_name":"Plotnikova","first_name":"Olga","full_name":"Plotnikova, Olga V"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"},{"full_name":"Vlasov, Peter K","first_name":"Peter","last_name":"Vlasov"},{"first_name":"Anastasia","last_name":"Grigorenko","full_name":"Grigorenko, Anastasia P"},{"full_name":"Ginter, Evgeny K","first_name":"Evgeny","last_name":"Ginter"},{"full_name":"Rogaev, Evgeny I","last_name":"Rogaev","first_name":"Evgeny"}],"publication":"American Journal of Human Genetics","_id":"860","publisher":"Cell Press","quality_controlled":0,"page":"32 - 43","publist_id":"6788","abstract":[{"text":"We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene cluster that is associated with a polymorphic congenital cataract that occurs with frequency of ∼0.3% in a human population. To gain insight into the molecular mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary analysis of the available mammalian and newly obtained primate sequences of the γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the ancestral state, since it was found in CRYGD of a lower primate and all the surveyed nonprimate mammals. Crystallin proteins include two structurally similar domains, and substitutions in mammalian CRYGD protein at site 23 of the first domain were always associated with substitutions in the structurally reciprocal sites 109 and 136 of the second domain. These data suggest that the cataractogenic effect of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly by amino acid changes in a distal domain. We also found that gene conversion was a factor in the evolution of the γ-crystallin gene cluster throughout different mammalian clades. The high rate of gene conversion observed between the functional CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled with a surprising finding of apparent negative selection in primate pseudogenes suggest a deleterious impact of recently derived pseudogenes involved in gene conversion in the γ-crystallin gene cluster.","lang":"eng"}],"day":"01","doi":"10.1086/518616","type":"journal_article","date_published":"2007-07-01T00:00:00Z","citation":{"chicago":"Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko, Evgeny Ginter, and Evgeny Rogaev. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” <i>American Journal of Human Genetics</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1086/518616\">https://doi.org/10.1086/518616</a>.","ieee":"O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” <i>American Journal of Human Genetics</i>, vol. 81, no. 1. Cell Press, pp. 32–43, 2007.","ama":"Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. <i>American Journal of Human Genetics</i>. 2007;81(1):32-43. doi:<a href=\"https://doi.org/10.1086/518616\">10.1086/518616</a>","apa":"Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., &#38; Rogaev, E. (2007). Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. <i>American Journal of Human Genetics</i>. Cell Press. <a href=\"https://doi.org/10.1086/518616\">https://doi.org/10.1086/518616</a>","ista":"Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. 81(1), 32–43.","mla":"Plotnikova, Olga, et al. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” <i>American Journal of Human Genetics</i>, vol. 81, no. 1, Cell Press, 2007, pp. 32–43, doi:<a href=\"https://doi.org/10.1086/518616\">10.1086/518616</a>.","short":"O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev, American Journal of Human Genetics 81 (2007) 32–43."},"year":"2007","date_updated":"2021-01-12T08:20:14Z","status":"public","extern":1,"volume":81,"acknowledgement":"This study was supported by the Biodiversity and Dynamics of Gene Pools program of the Presidium of the Russian Academy of Sciences (support to E.I.R.). E.I.R. is also supported in part by the National Institute of Diabetes and Digestive and Kidney Diseases and National Institute of Neurological Disorders and Stroke (National Institutes of Health), and F.A.K. is supported by a National Science Foundation graduate research fellowship."},{"publication_status":"published","date_created":"2018-12-11T11:48:54Z","month":"11","title":"A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures","intvolume":"         8","publication":"BMC Bioinformatics","_id":"861","author":[{"first_name":"Konstantin","last_name":"Popadin","full_name":"Popadin, Konstantin Yu"},{"full_name":"Mamirova, Leila A","last_name":"Mamirova","first_name":"Leila"},{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"publisher":"BioMed Central","quality_controlled":0,"doi":"10.1186/1471-2105-8-441","day":"14","abstract":[{"text":"Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.","lang":"eng"}],"publist_id":"6789","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2021-01-12T08:20:18Z","year":"2007","citation":{"apa":"Popadin, K., Mamirova, L., &#38; Kondrashov, F. (2007). A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. <i>BMC Bioinformatics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2105-8-441\">https://doi.org/10.1186/1471-2105-8-441</a>","ama":"Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. <i>BMC Bioinformatics</i>. 2007;8. doi:<a href=\"https://doi.org/10.1186/1471-2105-8-441\">10.1186/1471-2105-8-441</a>","ieee":"K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures,” <i>BMC Bioinformatics</i>, vol. 8. BioMed Central, 2007.","chicago":"Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” <i>BMC Bioinformatics</i>. BioMed Central, 2007. <a href=\"https://doi.org/10.1186/1471-2105-8-441\">https://doi.org/10.1186/1471-2105-8-441</a>.","mla":"Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” <i>BMC Bioinformatics</i>, vol. 8, BioMed Central, 2007, doi:<a href=\"https://doi.org/10.1186/1471-2105-8-441\">10.1186/1471-2105-8-441</a>.","short":"K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).","ista":"Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 8."},"date_published":"2007-11-14T00:00:00Z","type":"journal_article","acknowledgement":"KYuP and LAM were supported by the Molecular and Cellular Biology Program of the Russian Academy of Science. KYuP was supported by the Russian Fund of Basic Research (grant 04-04-49623). LAM was partially supported by grants from the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is a National Science Foundation Graduate Research Fellow.","volume":8,"extern":1,"status":"public"},{"intvolume":"        23","month":"05","title":"Selection for functional uniformity of tuf duplicates in γ-proteobacteria","date_created":"2018-12-11T11:48:59Z","publication_status":"published","issue":"5","author":[{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gurbich, Tatiana A","first_name":"Tatiana","last_name":"Gurbich"},{"full_name":"Vlasov, Peter K","first_name":"Peter","last_name":"Vlasov"}],"_id":"879","publication":"Trends in Genetics","publisher":"Elsevier","quality_controlled":0,"page":"215 - 218","publist_id":"6771","abstract":[{"lang":"eng","text":"Having an extra copy of a gene is thought to provide some functional redundancy, which results in a higher rate of evolution in duplicated genes. In this article, we estimate the impact of gene duplication on the selection of tuf paralogs, and we find that in the absence of gene conversion, tuf paralogs have evolved significantly slower than when gene conversion has been a factor in their evolution. Thus, tuf gene copies evolve under a selective pressure that ensures their functional uniformity, and gene conversion reduces selection against amino acid substitutions that affect the function of the encoded protein, EF-Tu."}],"day":"01","doi":"10.1016/j.tig.2007.03.002","type":"journal_article","date_published":"2007-05-01T00:00:00Z","year":"2007","citation":{"apa":"Kondrashov, F., Gurbich, T., &#38; Vlasov, P. (2007). Selection for functional uniformity of tuf duplicates in γ-proteobacteria. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">https://doi.org/10.1016/j.tig.2007.03.002</a>","ama":"Kondrashov F, Gurbich T, Vlasov P. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. <i>Trends in Genetics</i>. 2007;23(5):215-218. doi:<a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">10.1016/j.tig.2007.03.002</a>","ieee":"F. Kondrashov, T. Gurbich, and P. Vlasov, “Selection for functional uniformity of tuf duplicates in γ-proteobacteria,” <i>Trends in Genetics</i>, vol. 23, no. 5. Elsevier, pp. 215–218, 2007.","chicago":"Kondrashov, Fyodor, Tatiana Gurbich, and Peter Vlasov. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” <i>Trends in Genetics</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">https://doi.org/10.1016/j.tig.2007.03.002</a>.","mla":"Kondrashov, Fyodor, et al. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” <i>Trends in Genetics</i>, vol. 23, no. 5, Elsevier, 2007, pp. 215–18, doi:<a href=\"https://doi.org/10.1016/j.tig.2007.03.002\">10.1016/j.tig.2007.03.002</a>.","short":"F. Kondrashov, T. Gurbich, P. Vlasov, Trends in Genetics 23 (2007) 215–218.","ista":"Kondrashov F, Gurbich T, Vlasov P. 2007. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. 23(5), 215–218."},"date_updated":"2021-01-12T08:21:04Z","status":"public","extern":1,"acknowledgement":"We thank Peter Andolfatto, Doris Bachtrog, Robert Cutler, Hideki Innan, Eugene Koonin, Alexey Kondrashov and Martin Lercher for comments on the manuscript and for discussions on the interplay between gene conversion and selection. This work was supported by a National Science Foundation Graduate Research Fellowship (F.A.K.) and a Molecular and Cellular Biology RAS (Program No 10) grant (P.K.V.).","volume":23}]