[{"date_created":"2018-12-11T12:01:50Z","publisher":"IEEE","publication_status":"published","extern":1,"citation":{"ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, pp. 1186–1186.","short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 1186–1186.","ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition, 1186–1186.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005). Bi-layer segmentation of binocular stereo video (pp. 1186–1186). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.90\">https://doi.org/10.1109/CVPR.2005.90</a>","chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 1186–1186. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.90\">https://doi.org/10.1109/CVPR.2005.90</a>.","mla":"Kolmogorov, Vladimir, et al. <i>Bi-Layer Segmentation of Binocular Stereo Video</i>. IEEE, 2005, pp. 1186–1186, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.90\">10.1109/CVPR.2005.90</a>.","ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: IEEE; 2005:1186-1186. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.90\">10.1109/CVPR.2005.90</a>"},"_id":"3176","page":"1186 - 1186","doi":"10.1109/CVPR.2005.90","date_updated":"2021-01-12T07:41:35Z","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","year":"2005","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"full_name":"Criminisi, Antonio","last_name":"Criminisi","first_name":"Antonio"},{"last_name":"Blake","full_name":"Blake, Andrew","first_name":"Andrew"},{"first_name":"Geoffrey","full_name":"Cross, Geoffrey","last_name":"Cross"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"month":"01","date_published":"2005-01-01T00:00:00Z","publist_id":"3504","abstract":[{"lang":"eng","text":"This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.\n"}],"status":"public","day":"01","quality_controlled":0,"title":"Bi-layer segmentation of binocular stereo video"},{"year":"2005","author":[{"last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","full_name":"Wainwright, Martin J","last_name":"Wainwright"}],"month":"07","date_published":"2005-07-01T00:00:00Z","publist_id":"3500","abstract":[{"lang":"eng","text":"Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method."}],"day":"01","quality_controlled":0,"title":"On the optimality of tree reweighted max product message passing","status":"public","publisher":"AUAI Press","date_created":"2018-12-11T12:01:51Z","publication_status":"published","main_file_link":[{"url":"http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf","open_access":"0"}],"citation":{"ama":"Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product message passing. In: AUAI Press; 2005:316-323.","mla":"Kolmogorov, Vladimir, and Martin Wainwright. <i>On the Optimality of Tree Reweighted Max Product Message Passing</i>. AUAI Press, 2005, pp. 316–23.","chicago":"Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005.","ista":"Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323.","apa":"Kolmogorov, V., &#38; Wainwright, M. (2005). On the optimality of tree reweighted max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press.","short":"V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323.","ieee":"V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 316–323."},"extern":1,"conference":{"name":"UAI: Uncertainty in Artificial Intelligence"},"type":"conference","_id":"3181","page":"316 - 323","date_updated":"2021-01-12T07:41:38Z"},{"conference":{"name":"ICCV: International Conference on Computer Vision"},"type":"conference","_id":"3182","page":"564 - 571","doi":"10.1109/ICCV.2005.252","date_updated":"2021-01-12T07:41:38Z","citation":{"ieee":"V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts or global optimization of length area and flux,” presented at the ICCV: International Conference on Computer Vision, 2005, vol. 1, pp. 564–571.","mla":"Kolmogorov, Vladimir, and Yuri Boykov. <i>What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux</i>. Vol. 1, IEEE, 2005, pp. 564–71, doi:<a href=\"https://doi.org/10.1109/ICCV.2005.252\">10.1109/ICCV.2005.252</a>.","ama":"Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:<a href=\"https://doi.org/10.1109/ICCV.2005.252\">10.1109/ICCV.2005.252</a>","chicago":"Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005. <a href=\"https://doi.org/10.1109/ICCV.2005.252\">https://doi.org/10.1109/ICCV.2005.252</a>.","apa":"Kolmogorov, V., &#38; Boykov, Y. (2005). What metrics can be approximated by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2005.252\">https://doi.org/10.1109/ICCV.2005.252</a>","ista":"Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts or global optimization of length area and flux. ICCV: International Conference on Computer Vision vol. 1, 564–571.","short":"V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571."},"extern":1,"publication_status":"published","intvolume":"         1","date_created":"2018-12-11T12:01:52Z","publisher":"IEEE","day":"05","quality_controlled":0,"title":"What metrics can be approximated by geo cuts or global optimization of length area and flux","status":"public","publist_id":"3501","date_published":"2005-12-05T00:00:00Z","abstract":[{"lang":"eng","text":"In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such &quot;submodular&quot; metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the &quot;shrinking&quot; problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints."}],"volume":1,"author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"full_name":"Boykov, Yuri","last_name":"Boykov","first_name":"Yuri"}],"month":"12","year":"2005"},{"day":"25","quality_controlled":0,"title":"Bi-layer segmentation of binocular stereo video","status":"public","date_published":"2005-07-25T00:00:00Z","publist_id":"3502","abstract":[{"text":"This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar perfomance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.","lang":"eng"}],"volume":2,"author":[{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"last_name":"Criminisi","full_name":"Criminisi, Antonio","first_name":"Antonio"},{"first_name":"Andrew","full_name":"Blake, Andrew","last_name":"Blake"},{"last_name":"Cross","full_name":"Cross, Geoffrey","first_name":"Geoffrey"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"month":"07","year":"2005","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","_id":"3183","doi":"10.1109/CVPR.2005.91","page":"407 - 414","date_updated":"2021-01-12T07:41:38Z","citation":{"short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 407–414.","ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol. 2, 407–414.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005). Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.91\">https://doi.org/10.1109/CVPR.2005.91</a>","chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.91\">https://doi.org/10.1109/CVPR.2005.91</a>.","ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.91\">10.1109/CVPR.2005.91</a>","mla":"Kolmogorov, Vladimir, et al. <i>Bi-Layer Segmentation of Binocular Stereo Video</i>. Vol. 2, IEEE, 2005, pp. 407–14, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.91\">10.1109/CVPR.2005.91</a>.","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 2, pp. 407–414."},"extern":1,"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf"}],"publication_status":"published","intvolume":"         2","date_created":"2018-12-11T12:01:52Z","publisher":"IEEE"},{"title":"Improved security analyses for CBC MACs","quality_controlled":0,"day":"12","status":"public","abstract":[{"text":"We present an improved bound on the advantage of any q-query adversary at distinguishing between the CBC MAC over a random n-bit permutation and a random function outputting n bits. The result assumes that no message queried is a prefix of any other, as is the case when all messages to be MACed have the same length. We go on to give an improved analysis of the encrypted CBC MAC, where there is no restriction on queried messages. Letting m be the block length of the longest query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate into improved guarantees on the probability of forging these MACs.","lang":"eng"}],"date_published":"2005-09-12T00:00:00Z","publist_id":"3469","acknowledgement":"Pietrzak was supported by the Swiss National Science Foundation, project No. 200020-103847/1.","volume":3621,"month":"09","author":[{"last_name":"Bellare","full_name":"Bellare, Mihir","first_name":"Mihir"},{"last_name":"Pietrzak","full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"first_name":"Phillip","last_name":"Rogaway","full_name":"Rogaway, Phillip"}],"year":"2005","type":"conference","conference":{"name":"CRYPTO: International Cryptology Conference"},"date_updated":"2021-01-12T07:41:50Z","doi":"10.1007/11535218_32","_id":"3211","page":"527 - 545","citation":{"chicago":"Bellare, Mihir, Krzysztof Z Pietrzak, and Phillip Rogaway. “Improved Security Analyses for CBC MACs,” 3621:527–45. Springer, 2005. <a href=\"https://doi.org/10.1007/11535218_32\">https://doi.org/10.1007/11535218_32</a>.","ama":"Bellare M, Pietrzak KZ, Rogaway P. Improved security analyses for CBC MACs. In: Vol 3621. Springer; 2005:527-545. doi:<a href=\"https://doi.org/10.1007/11535218_32\">10.1007/11535218_32</a>","mla":"Bellare, Mihir, et al. <i>Improved Security Analyses for CBC MACs</i>. Vol. 3621, Springer, 2005, pp. 527–45, doi:<a href=\"https://doi.org/10.1007/11535218_32\">10.1007/11535218_32</a>.","short":"M. Bellare, K.Z. Pietrzak, P. Rogaway, in:, Springer, 2005, pp. 527–545.","ista":"Bellare M, Pietrzak KZ, Rogaway P. 2005. Improved security analyses for CBC MACs. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 527–545.","apa":"Bellare, M., Pietrzak, K. Z., &#38; Rogaway, P. (2005). Improved security analyses for CBC MACs (Vol. 3621, pp. 527–545). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/11535218_32\">https://doi.org/10.1007/11535218_32</a>","ieee":"M. Bellare, K. Z. Pietrzak, and P. Rogaway, “Improved security analyses for CBC MACs,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 527–545."},"extern":1,"publication_status":"published","alternative_title":["LNCS"],"intvolume":"      3621","publisher":"Springer","date_created":"2018-12-11T12:02:02Z"},{"volume":3621,"acknowledgement":"Supported by NSF CAREER Award CCR-0133806 and TC Grant No.CCR-0311095. Supported by the Swiss National Science Foundation, project No. 200020-103847/1","date_published":"2005-09-12T00:00:00Z","publist_id":"3470","abstract":[{"lang":"eng","text":"The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use.\nIn this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model."}],"status":"public","day":"12","quality_controlled":0,"title":"On the generic insecurity of the full domain hash","year":"2005","author":[{"first_name":"Yevgeniy","last_name":"Dodis","full_name":"Dodis, Yevgeniy"},{"first_name":"Roberto","last_name":"Oliveira","full_name":"Oliveira, Roberto"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","last_name":"Pietrzak"}],"month":"09","extern":1,"citation":{"short":"Y. Dodis, R. Oliveira, K.Z. Pietrzak, in:, Springer, 2005, pp. 449–466.","apa":"Dodis, Y., Oliveira, R., &#38; Pietrzak, K. Z. (2005). On the generic insecurity of the full domain hash (Vol. 3621, pp. 449–466). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/11535218_27\">https://doi.org/10.1007/11535218_27</a>","ista":"Dodis Y, Oliveira R, Pietrzak KZ. 2005. On the generic insecurity of the full domain hash. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 449–466.","chicago":"Dodis, Yevgeniy, Roberto Oliveira, and Krzysztof Z Pietrzak. “On the Generic Insecurity of the Full Domain Hash,” 3621:449–66. Springer, 2005. <a href=\"https://doi.org/10.1007/11535218_27\">https://doi.org/10.1007/11535218_27</a>.","ama":"Dodis Y, Oliveira R, Pietrzak KZ. On the generic insecurity of the full domain hash. In: Vol 3621. Springer; 2005:449-466. doi:<a href=\"https://doi.org/10.1007/11535218_27\">10.1007/11535218_27</a>","mla":"Dodis, Yevgeniy, et al. <i>On the Generic Insecurity of the Full Domain Hash</i>. Vol. 3621, Springer, 2005, pp. 449–66, doi:<a href=\"https://doi.org/10.1007/11535218_27\">10.1007/11535218_27</a>.","ieee":"Y. Dodis, R. Oliveira, and K. Z. Pietrzak, “On the generic insecurity of the full domain hash,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 449–466."},"_id":"3212","doi":"10.1007/11535218_27","page":"449 - 466","date_updated":"2021-01-12T07:41:50Z","conference":{"name":"CRYPTO: International Cryptology Conference"},"type":"conference","publisher":"Springer","date_created":"2018-12-11T12:02:03Z","intvolume":"      3621","alternative_title":["LNCS"],"publication_status":"published"},{"author":[{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Krzysztof Pietrzak"}],"month":"09","year":"2005","quality_controlled":0,"day":"12","title":"Composition does not imply adaptive security","status":"public","publist_id":"3468","date_published":"2005-09-12T00:00:00Z","abstract":[{"text":"We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case.\nIn this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.","lang":"eng"}],"volume":3621,"acknowledgement":"Supported by the Swiss National Science Foundation, project No. 200020-103847/1.","publication_status":"published","alternative_title":["LNCS"],"intvolume":"      3621","publisher":"Springer","date_created":"2018-12-11T12:02:03Z","conference":{"name":"CRYPTO: International Cryptology Conference"},"type":"conference","doi":"10.1007/11535218_4","_id":"3213","page":"55 - 65","date_updated":"2021-01-12T07:41:50Z","citation":{"ieee":"K. Z. Pietrzak, “Composition does not imply adaptive security,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 55–65.","ista":"Pietrzak KZ. 2005. Composition does not imply adaptive security. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 55–65.","apa":"Pietrzak, K. Z. (2005). Composition does not imply adaptive security (Vol. 3621, pp. 55–65). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/11535218_4\">https://doi.org/10.1007/11535218_4</a>","short":"K.Z. Pietrzak, in:, Springer, 2005, pp. 55–65.","mla":"Pietrzak, Krzysztof Z. <i>Composition Does Not Imply Adaptive Security</i>. Vol. 3621, Springer, 2005, pp. 55–65, doi:<a href=\"https://doi.org/10.1007/11535218_4\">10.1007/11535218_4</a>.","ama":"Pietrzak KZ. Composition does not imply adaptive security. In: Vol 3621. Springer; 2005:55-65. doi:<a href=\"https://doi.org/10.1007/11535218_4\">10.1007/11535218_4</a>","chicago":"Pietrzak, Krzysztof Z. “Composition Does Not Imply Adaptive Security,” 3621:55–65. Springer, 2005. <a href=\"https://doi.org/10.1007/11535218_4\">https://doi.org/10.1007/11535218_4</a>."},"extern":1},{"type":"journal_article","date_updated":"2021-01-12T07:43:19Z","_id":"3416","page":"37 - 39","doi":"10.1529/biophysj.105.059774","publication":"Biophysical Journal","citation":{"ieee":"H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins explored by forced unfolding experiments,” <i>Biophysical Journal</i>, vol. 88, no. 5. Biophysical Society, pp. 37–39, 2005.","apa":"Janovjak, H. L., Sapra, T., &#38; Mueller, D. (2005). Complex stability of single proteins explored by forced unfolding experiments. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1529/biophysj.105.059774\">https://doi.org/10.1529/biophysj.105.059774</a>","ista":"Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39.","short":"H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39.","ama":"Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored by forced unfolding experiments. <i>Biophysical Journal</i>. 2005;88(5):37-39. doi:<a href=\"https://doi.org/10.1529/biophysj.105.059774\">10.1529/biophysj.105.059774</a>","mla":"Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” <i>Biophysical Journal</i>, vol. 88, no. 5, Biophysical Society, 2005, pp. 37–39, doi:<a href=\"https://doi.org/10.1529/biophysj.105.059774\">10.1529/biophysj.105.059774</a>.","chicago":"Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” <i>Biophysical Journal</i>. Biophysical Society, 2005. <a href=\"https://doi.org/10.1529/biophysj.105.059774\">https://doi.org/10.1529/biophysj.105.059774</a>."},"extern":1,"publication_status":"published","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/","open_access":"1"}],"intvolume":"        88","oa":1,"date_created":"2018-12-11T12:03:13Z","publisher":"Biophysical Society","title":"Complex stability of single proteins explored by forced unfolding experiments","day":"01","quality_controlled":0,"status":"public","abstract":[{"lang":"eng","text":"In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins."}],"date_published":"2005-05-01T00:00:00Z","publist_id":"2985","volume":88,"month":"05","author":[{"full_name":"Harald Janovjak","last_name":"Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"last_name":"Sapra","full_name":"Sapra, Tanuj K","first_name":"Tanuj"},{"last_name":"Mueller","full_name":"Mueller, Daniel J","first_name":"Daniel"}],"year":"2005","issue":"5"},{"_id":"3417","doi":"10.1111/j.1365-2818.2005.01478.x","page":"125 - 132","date_updated":"2021-01-12T07:43:20Z","type":"journal_article","extern":1,"citation":{"mla":"Kuhn, Michael, et al. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” <i>Journal of Microscopy</i>, vol. 218, no. 2, Wiley-Blackwell, 2005, pp. 125–32, doi:<a href=\"https://doi.org/10.1111/j.1365-2818.2005.01478.x\">10.1111/j.1365-2818.2005.01478.x</a>.","ama":"Kuhn M, Janovjak HL, Hubain M, Mueller D. Automated alignment and pattern recognition of single-molecule force spectroscopy data. <i>Journal of Microscopy</i>. 2005;218(2):125-132. doi:<a href=\"https://doi.org/10.1111/j.1365-2818.2005.01478.x\">10.1111/j.1365-2818.2005.01478.x</a>","chicago":"Kuhn, Michael, Harald L Janovjak, Maurice Hubain, and Daniel Mueller. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” <i>Journal of Microscopy</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1111/j.1365-2818.2005.01478.x\">https://doi.org/10.1111/j.1365-2818.2005.01478.x</a>.","ista":"Kuhn M, Janovjak HL, Hubain M, Mueller D. 2005. Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. 218(2), 125–132.","apa":"Kuhn, M., Janovjak, H. L., Hubain, M., &#38; Mueller, D. (2005). Automated alignment and pattern recognition of single-molecule force spectroscopy data. <i>Journal of Microscopy</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-2818.2005.01478.x\">https://doi.org/10.1111/j.1365-2818.2005.01478.x</a>","short":"M. Kuhn, H.L. Janovjak, M. Hubain, D. Mueller, Journal of Microscopy 218 (2005) 125–132.","ieee":"M. Kuhn, H. L. Janovjak, M. Hubain, and D. Mueller, “Automated alignment and pattern recognition of single-molecule force spectroscopy data,” <i>Journal of Microscopy</i>, vol. 218, no. 2. Wiley-Blackwell, pp. 125–132, 2005."},"publication":"Journal of Microscopy","publication_status":"published","publisher":"Wiley-Blackwell","date_created":"2018-12-11T12:03:13Z","intvolume":"       218","status":"public","day":"01","quality_controlled":0,"title":"Automated alignment and pattern recognition of single-molecule force spectroscopy data","volume":218,"publist_id":"2984","date_published":"2005-05-01T00:00:00Z","abstract":[{"text":"Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.","lang":"eng"}],"author":[{"last_name":"Kuhn","full_name":"Kuhn, Michael","first_name":"Michael"},{"last_name":"Janovjak","full_name":"Harald Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"full_name":"Hubain, Maurice","last_name":"Hubain","first_name":"Maurice"},{"last_name":"Mueller","full_name":"Mueller, Daniel J","first_name":"Daniel"}],"month":"05","issue":"2","year":"2005"},{"intvolume":"        34","date_created":"2018-12-11T12:03:14Z","publisher":"Springer","publication_status":"published","publication":"European Biophysics Journal","citation":{"ieee":"H. L. Janovjak, J. Struckmeier, and D. Mueller, “Hydrodynamic effects in fast AFM single molecule force measurements,” <i>European Biophysics Journal</i>, vol. 34, no. 1. Springer, pp. 91–96, 2005.","apa":"Janovjak, H. L., Struckmeier, J., &#38; Mueller, D. (2005). Hydrodynamic effects in fast AFM single molecule force measurements. <i>European Biophysics Journal</i>. Springer. <a href=\"https://doi.org/10.1007/s00249-004-0430-3\">https://doi.org/10.1007/s00249-004-0430-3</a>","ista":"Janovjak HL, Struckmeier J, Mueller D. 2005. Hydrodynamic effects in fast AFM single molecule force measurements. European Biophysics Journal. 34(1), 91–96.","short":"H.L. Janovjak, J. Struckmeier, D. Mueller, European Biophysics Journal 34 (2005) 91–96.","ama":"Janovjak HL, Struckmeier J, Mueller D. Hydrodynamic effects in fast AFM single molecule force measurements. <i>European Biophysics Journal</i>. 2005;34(1):91-96. doi:<a href=\"https://doi.org/10.1007/s00249-004-0430-3\">10.1007/s00249-004-0430-3</a>","mla":"Janovjak, Harald L., et al. “Hydrodynamic Effects in Fast AFM Single Molecule Force Measurements.” <i>European Biophysics Journal</i>, vol. 34, no. 1, Springer, 2005, pp. 91–96, doi:<a href=\"https://doi.org/10.1007/s00249-004-0430-3\">10.1007/s00249-004-0430-3</a>.","chicago":"Janovjak, Harald L, Jens Struckmeier, and Daniel Mueller. “Hydrodynamic Effects in Fast AFM Single Molecule Force Measurements.” <i>European Biophysics Journal</i>. Springer, 2005. <a href=\"https://doi.org/10.1007/s00249-004-0430-3\">https://doi.org/10.1007/s00249-004-0430-3</a>."},"extern":1,"type":"journal_article","date_updated":"2021-01-12T07:43:20Z","doi":"10.1007/s00249-004-0430-3","_id":"3418","page":"91 - 96","year":"2005","issue":"1","month":"02","author":[{"full_name":"Harald Janovjak","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L"},{"full_name":"Struckmeier, Jens","last_name":"Struckmeier","first_name":"Jens"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"abstract":[{"lang":"eng","text":"Atomic force microscopy (AFM) allows the critical forces that unfold single proteins and rupture individual receptor–ligand bonds to be measured. To derive the shape of the energy landscape, the dynamic strength of the system is probed at different force loading rates. This is usually achieved by varying the pulling speed between a few nm/s and a few mgrm/s, although for a more complete investigation of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic drag force acting on the AFM cantilever reaches the same order of magnitude as the molecular forces. This has limited the maximum pulling speed in AFM single-molecule force spectroscopy experiments. Here, we present an approach for considering these hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements recorded over an extended range of pulling speeds (and thus loading rates). To support and illustrate our theoretical considerations, we experimentally evaluated the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling speed."}],"publist_id":"2983","date_published":"2005-02-01T00:00:00Z","volume":34,"title":"Hydrodynamic effects in fast AFM single molecule force measurements","day":"01","quality_controlled":0,"status":"public"},{"main_file_link":[{"url":"http://arxiv.org/abs/q-bio/0412014","open_access":"1"}],"publication_status":"published","oa":1,"publisher":"American Physical Society","date_created":"2018-12-11T12:03:16Z","intvolume":"        94","date_updated":"2021-01-12T07:43:23Z","doi":"10.1103/PhysRevLett.94.018103","_id":"3426","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","publication":"Physical Review Letters","arxiv":1,"citation":{"short":"M.T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, F. Jülicher, Physical Review Letters 94 (2005).","apa":"Bollenbach, M. T., Kruse, K., Pantazis, P., González Gaitán, M., &#38; Jülicher, F. (2005). Robust formation of morphogen gradients. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">https://doi.org/10.1103/PhysRevLett.94.018103</a>","ista":"Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. 2005. Robust formation of morphogen gradients. Physical Review Letters. 94(1).","chicago":"Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos González Gaitán, and Frank Jülicher. “Robust Formation of Morphogen Gradients.” <i>Physical Review Letters</i>. American Physical Society, 2005. <a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">https://doi.org/10.1103/PhysRevLett.94.018103</a>.","mla":"Bollenbach, Mark Tobias, et al. “Robust Formation of Morphogen Gradients.” <i>Physical Review Letters</i>, vol. 94, no. 1, American Physical Society, 2005, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">10.1103/PhysRevLett.94.018103</a>.","ama":"Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. Robust formation of morphogen gradients. <i>Physical Review Letters</i>. 2005;94(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">10.1103/PhysRevLett.94.018103</a>","ieee":"M. T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, and F. Jülicher, “Robust formation of morphogen gradients,” <i>Physical Review Letters</i>, vol. 94, no. 1. American Physical Society, 2005."},"article_processing_charge":"No","month":"01","author":[{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"},{"first_name":"Karsten","last_name":"Kruse","full_name":"Kruse, Karsten"},{"full_name":"Pantazis, Periklis","last_name":"Pantazis","first_name":"Periklis"},{"full_name":"González Gaitán, Marcos","last_name":"González Gaitán","first_name":"Marcos"},{"full_name":"Jülicher, Frank","last_name":"Jülicher","first_name":"Frank"}],"year":"2005","issue":"1","external_id":{"arxiv":["q-bio/0412014"]},"status":"public","title":"Robust formation of morphogen gradients","day":"01","volume":94,"abstract":[{"lang":"eng","text":"We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from the binding of ligands to receptors on the cell surface, incorporation into the cell, and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production."}],"publist_id":"2975","date_published":"2005-01-01T00:00:00Z"},{"publisher":"Springer","date_created":"2018-12-11T12:03:18Z","publication_status":"published","publication":"Statistical methods in Molecular Evolution","citation":{"ama":"Bollback JP. Posterior mapping and posterior predictive distributions. In: Nielsen R, ed. <i>Statistical Methods in Molecular Evolution</i>. Springer; 2005:439-462. doi:<a href=\"https://doi.org/10.1007/0-387-27733-1\">10.1007/0-387-27733-1</a>","mla":"Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” <i>Statistical Methods in Molecular Evolution</i>, edited by Rasmus Nielsen, Springer, 2005, pp. 439–62, doi:<a href=\"https://doi.org/10.1007/0-387-27733-1\">10.1007/0-387-27733-1</a>.","chicago":"Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” In <i>Statistical Methods in Molecular Evolution</i>, edited by Rasmus Nielsen, 439–62. Springer, 2005. <a href=\"https://doi.org/10.1007/0-387-27733-1\">https://doi.org/10.1007/0-387-27733-1</a>.","ista":"Bollback JP. 2005.Posterior mapping and posterior predictive distributions. In: Statistical methods in Molecular Evolution. , 439–462.","apa":"Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions. In R. Nielsen (Ed.), <i>Statistical methods in Molecular Evolution</i> (pp. 439–462). Springer. <a href=\"https://doi.org/10.1007/0-387-27733-1\">https://doi.org/10.1007/0-387-27733-1</a>","short":"J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution, Springer, 2005, pp. 439–462.","ieee":"J. P. Bollback, “Posterior mapping and posterior predictive distributions,” in <i>Statistical methods in Molecular Evolution</i>, R. Nielsen, Ed. Springer, 2005, pp. 439–462."},"extern":1,"type":"book_chapter","date_updated":"2021-01-12T07:43:26Z","page":"439 - 462","_id":"3433","doi":"10.1007/0-387-27733-1","editor":[{"first_name":"Rasmus","last_name":"Nielsen","full_name":"Nielsen, Rasmus"}],"year":"2005","month":"04","author":[{"last_name":"Bollback","full_name":"Jonathan Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"}],"date_published":"2005-04-21T00:00:00Z","publist_id":"2967","title":"Posterior mapping and posterior predictive distributions","quality_controlled":0,"day":"21","status":"public"},{"issue":"42","year":"2005","author":[{"first_name":"Thomas","full_name":"Klausberger,Thomas","last_name":"Klausberger"},{"last_name":"Marton","full_name":"Marton,Laszlo F","first_name":"Laszlo"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","full_name":"Joseph O'Neill","last_name":"O'Neill"},{"first_name":"Jojanneke","last_name":"Huck","full_name":"Huck, Jojanneke H"},{"first_name":"Yannis","last_name":"Dalezios","full_name":"Dalezios, Yannis"},{"first_name":"Pablo","last_name":"Fuentealba","full_name":"Fuentealba,Pablo"},{"full_name":"Suen, Wai Yee","last_name":"Suen","first_name":"Wai"},{"full_name":"Papp, Edit Cs","last_name":"Papp","first_name":"Edit"},{"first_name":"Takeshi","last_name":"Kaneko","full_name":"Kaneko, Takeshi"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"full_name":"Jozsef Csicsvari","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"},{"last_name":"Somogyi","full_name":"Somogyi, Péter","first_name":"Péter"}],"month":"10","publist_id":"2944","date_published":"2005-10-19T00:00:00Z","abstract":[{"lang":"eng","text":"In the hippocampal CA1 area, a relatively homogenous population of pyramidal cells is accompanied by a diversity of GABAergic interneurons. Previously, we found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum moleculare cells, innervating different domains of pyramidal cells, have distinct firing patterns during network oscillations in vivo. A second family of interneurons, expressing cholecystokinin but not parvalbumin, is known to target the same domains of pyramidal cells as do the parvalbumin cells. To test the temporal activity of these independent and parallel GABAergic inputs, we recorded the precise spike timing of identified cholecystokinin interneurons during hippocampal network oscillations in anesthetized rats and determined their molecular expression profiles and synaptic targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz during high-frequency ripple oscillations in an episode-dependent manner. During theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3 Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°), when place cells start firing in freely moving animals. The firing patterns of some interneurons recorded in drug-free behaving rats were similar to cholecystokinin cells in anesthetized animals. Our results demonstrate that cholecystokinin- and parvalbumin-expressing interneurons make different contributions to network oscillations and play distinct roles in different brain states. We suggest that the specific spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids might contribute to differentiate subgroups of pyramidal cells forming neuronal assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire network. Copyright © 2005 Society for Neuroscience."}],"volume":25,"day":"19","quality_controlled":0,"title":"Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations","status":"public","intvolume":"        25","publisher":"Society for Neuroscience","date_created":"2018-12-11T12:03:21Z","publication_status":"published","publication":"Journal of Neuroscience","citation":{"ieee":"T. Klausberger <i>et al.</i>, “Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations,” <i>Journal of Neuroscience</i>, vol. 25, no. 42. Society for Neuroscience, pp. 9782–9793, 2005.","ama":"Klausberger T, Marton L, O’Neill J, et al. Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. <i>Journal of Neuroscience</i>. 2005;25(42):9782-9793. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">10.1523/JNEUROSCI.3269-05.2005</a>","mla":"Klausberger, Thomas, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.” <i>Journal of Neuroscience</i>, vol. 25, no. 42, Society for Neuroscience, 2005, pp. 9782–93, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">10.1523/JNEUROSCI.3269-05.2005</a>.","chicago":"Klausberger, Thomas, Laszlo Marton, Joseph O’Neill, Jojanneke Huck, Yannis Dalezios, Pablo Fuentealba, Wai Suen, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2005. <a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">https://doi.org/10.1523/JNEUROSCI.3269-05.2005</a>.","apa":"Klausberger, T., Marton, L., O’Neill, J., Huck, J., Dalezios, Y., Fuentealba, P., … Somogyi, P. (2005). Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">https://doi.org/10.1523/JNEUROSCI.3269-05.2005</a>","ista":"Klausberger T, Marton L, O’Neill J, Huck J, Dalezios Y, Fuentealba P, Suen W, Papp E, Kaneko T, Watanabe M, Csicsvari JL, Somogyi P. 2005. Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. Journal of Neuroscience. 25(42), 9782–9793.","short":"T. Klausberger, L. Marton, J. O’Neill, J. Huck, Y. Dalezios, P. Fuentealba, W. Suen, E. Papp, T. Kaneko, M. Watanabe, J.L. Csicsvari, P. Somogyi, Journal of Neuroscience 25 (2005) 9782–9793."},"extern":1,"type":"journal_article","doi":"10.1523/JNEUROSCI.3269-05.2005","_id":"3443","page":"9782 - 9793","date_updated":"2021-01-12T07:43:30Z"},{"status":"public","title":"Methods, apparatus and computer program products for modeling three-dimensional colored objects","day":"08","abstract":[{"text":"Methods, apparatus and computer program products can generate light weight but highly realistic and accurate colored models of three-dimensional colored objects. The colored model may be generated from a second plurality of points that define a coarse digital representation of the surface and at least one texture map containing information derived from a first plurality of colored points that define a fine digital representation of the surface. This derivation is achieved by mapping points within the texture map to the fine digital representation of the three-dimensional surface. Colored scan data may be used to construct the fine digital representation as a triangulated surface (i.e., triangulation) using a wrapping operation.","lang":"eng"}],"publist_id":"2878","date_published":"2005-02-08T00:00:00Z","article_processing_charge":"No","applicant":["Raindrop Geomagic, Inc."],"month":"02","author":[{"last_name":"Williams","full_name":"Williams, Steven","first_name":"Steven"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"full_name":"Fu, Ping","last_name":"Fu","first_name":"Ping"}],"year":"2005","date_updated":"2022-01-05T13:59:09Z","_id":"3509","ipc":"G06T17/20 ; G06T15/04","type":"patent","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","citation":{"ama":"Williams S, Edelsbrunner H, Fu P. Methods, apparatus and computer program products for modeling three-dimensional colored objects. 2005.","mla":"Williams, Steven, et al. <i>Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects</i>. 2005.","chicago":"Williams, Steven, Herbert Edelsbrunner, and Ping Fu. “Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects,” 2005.","apa":"Williams, S., Edelsbrunner, H., &#38; Fu, P. (2005). Methods, apparatus and computer program products for modeling three-dimensional colored objects.","ista":"Williams S, Edelsbrunner H, Fu P. 2005. Methods, apparatus and computer program products for modeling three-dimensional colored objects.","short":"S. Williams, H. Edelsbrunner, P. Fu, (2005).","ieee":"S. Williams, H. Edelsbrunner, and P. Fu, “Methods, apparatus and computer program products for modeling three-dimensional colored objects.” 2005."},"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/US6853373B2/"}],"ipn":"US6853373B2","publication_date":"2005-02-08","oa":1,"date_created":"2018-12-11T12:03:42Z"},{"citation":{"mla":"Edelsbrunner, Herbert. <i>Surface Tiling with Differential Topology</i>. ACM, 2005, pp. 9–11, doi:<a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>.","ama":"Edelsbrunner H. Surface tiling with differential topology. In: ACM; 2005:9-11. doi:<a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>","chicago":"Edelsbrunner, Herbert. “Surface Tiling with Differential Topology,” 9–11. ACM, 2005. <a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>.","ista":"Edelsbrunner H. 2005. Surface tiling with differential topology. SGP: Eurographics Symposium on Geometry processing, 9–11.","apa":"Edelsbrunner, H. (2005). Surface tiling with differential topology (pp. 9–11). Presented at the SGP: Eurographics Symposium on Geometry processing, ACM. <a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>","short":"H. Edelsbrunner, in:, ACM, 2005, pp. 9–11.","ieee":"H. Edelsbrunner, “Surface tiling with differential topology,” presented at the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 9–11."},"extern":1,"conference":{"name":"SGP: Eurographics Symposium on Geometry processing"},"type":"conference","page":"9 - 11","_id":"3557","doi":"http://dx.doi.org/10.2312/SGP/SGP05/009-011","date_updated":"2021-01-12T07:44:17Z","date_created":"2018-12-11T12:03:57Z","publisher":"ACM","publication_status":"published","main_file_link":[{"url":"http://www.cs.duke.edu/~edels/Papers/2005-P-03-SurfaceTiling.pdf","open_access":"0"}],"date_published":"2005-07-01T00:00:00Z","publist_id":"2828","abstract":[{"text":"A challenging problem in computer-aided geometric design is the decomposition of a surface into four-sided regions that are then represented by NURBS patches. There are various approaches published in the literature and implemented as commercially available software, but all fall short in either automation or quality of the result. At Raindrop Geomagic, we have recently taken a fresh approach based on concepts from Morse theory. This by itself is not a new idea, but we have some novel ingredients that make this work, one being a rational notion of hierarchy that guides the construction of a simplified decomposition sensitive to only the major critical points.","lang":"eng"}],"quality_controlled":0,"day":"01","title":"Surface tiling with differential topology","status":"public","year":"2005","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner"}],"month":"07"},{"extern":1,"citation":{"ieee":"D. Attali, D. Cohen Steiner, and H. Edelsbrunner, “Extraction and simplification of iso-surfaces in tandem,” presented at the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 139–148.","apa":"Attali, D., Cohen Steiner, D., &#38; Edelsbrunner, H. (2005). Extraction and simplification of iso-surfaces in tandem (pp. 139–148). Presented at the SGP: Eurographics Symposium on Geometry processing, ACM.","ista":"Attali D, Cohen Steiner D, Edelsbrunner H. 2005. Extraction and simplification of iso-surfaces in tandem. SGP: Eurographics Symposium on Geometry processing, 139–148.","short":"D. Attali, D. Cohen Steiner, H. Edelsbrunner, in:, ACM, 2005, pp. 139–148.","ama":"Attali D, Cohen Steiner D, Edelsbrunner H. Extraction and simplification of iso-surfaces in tandem. In: ACM; 2005:139-148.","mla":"Attali, Dominique, et al. <i>Extraction and Simplification of Iso-Surfaces in Tandem</i>. ACM, 2005, pp. 139–48.","chicago":"Attali, Dominique, David Cohen Steiner, and Herbert Edelsbrunner. “Extraction and Simplification of Iso-Surfaces in Tandem,” 139–48. ACM, 2005."},"page":"139 - 148","_id":"3558","date_updated":"2021-01-12T07:44:18Z","conference":{"name":"SGP: Eurographics Symposium on Geometry processing"},"type":"conference","publisher":"ACM","date_created":"2018-12-11T12:03:57Z","main_file_link":[{"url":"http://dl.acm.org/citation.cfm?id=1281943","open_access":"0"}],"publication_status":"published","acknowledgement":"Partially supported the generated triangulations. Two questions arise: “how do by NSF grant CCR-00-86013 (BioGeometry).","publist_id":"2827","date_published":"2005-01-01T00:00:00Z","abstract":[{"text":"The tandem algorithm combines the marching cube algorithm for surface extraction and the edge contraction algorithm for surface simplification in lock-step to avoid the costly intermediate step of storing the entire extracted surface triangulation. Beyond this basic strategy, we introduce refinements to prevent artifacts in the resulting triangulation, first, by carefully monitoring the amount of simplification during the process and, second, by driving the simplification toward a compromise between shape approximation and mesh quality. We have implemented the algorithm and used extensive computational experiments to document the effects of various design options and to further fine-tune the algorithm.","lang":"eng"}],"status":"public","quality_controlled":0,"day":"01","title":"Extraction and simplification of iso-surfaces in tandem","year":"2005","author":[{"full_name":"Attali, Dominique","last_name":"Attali","first_name":"Dominique"},{"full_name":"Cohen-Steiner, David","last_name":"Cohen Steiner","first_name":"David"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner"}],"month":"01"},{"title":"The geometry of biomolecular solvation","day":"08","quality_controlled":0,"status":"public","abstract":[{"text":"ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes.\nHere we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics.\nIn parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.","lang":"eng"}],"publist_id":"2809","date_published":"2005-08-08T00:00:00Z","volume":52,"month":"08","author":[{"full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"full_name":"Koehl, Patrice","last_name":"Koehl","first_name":"Patrice"}],"year":"2005","type":"book_chapter","date_updated":"2021-01-12T07:44:25Z","_id":"3576","page":"243 - 275","citation":{"apa":"Edelsbrunner, H., &#38; Koehl, P. (2005). The geometry of biomolecular solvation. In <i>Combinatorial and Computational Geometry</i> (Vol. 52, pp. 243–275). Cambridge University Press.","ista":"Edelsbrunner H, Koehl P. 2005.The geometry of biomolecular solvation. In: Combinatorial and Computational Geometry. Mathematical Sciences Research Institute Publications, vol. 52, 243–275.","short":"H. Edelsbrunner, P. Koehl, in:, Combinatorial and Computational Geometry, Cambridge University Press, 2005, pp. 243–275.","mla":"Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.” <i>Combinatorial and Computational Geometry</i>, vol. 52, Cambridge University Press, 2005, pp. 243–75.","ama":"Edelsbrunner H, Koehl P. The geometry of biomolecular solvation. In: <i>Combinatorial and Computational Geometry</i>. Vol 52. Cambridge University Press; 2005:243-275.","chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.” In <i>Combinatorial and Computational Geometry</i>, 52:243–75. Cambridge University Press, 2005.","ieee":"H. Edelsbrunner and P. Koehl, “The geometry of biomolecular solvation,” in <i>Combinatorial and Computational Geometry</i>, vol. 52, Cambridge University Press, 2005, pp. 243–275."},"publication":"Combinatorial and Computational Geometry","extern":1,"publication_status":"published","main_file_link":[{"open_access":"0","url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.117.3732"}],"alternative_title":["Mathematical Sciences Research Institute Publications"],"intvolume":"        52","date_created":"2018-12-11T12:04:03Z","publisher":"Cambridge University Press"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","page":"71 - 105","_id":"3588","doi":"10.1002/3527604669","date_updated":"2021-01-12T07:44:29Z","oa_version":"None","publication":"Cell Migration in Development and Disease","citation":{"short":"I. Castanon Ortega, C.-P.J. Heisenberg, in:, D. Wedlich (Ed.), Cell Migration in Development and Disease, Wiley-VCH, 2005, pp. 71–105.","ista":"Castanon Ortega I, Heisenberg C-PJ. 2005.Cell migration during zebrafish gastrulation. In: Cell Migration in Development and Disease. , 71–105.","apa":"Castanon Ortega, I., &#38; Heisenberg, C.-P. J. (2005). Cell migration during zebrafish gastrulation. In D. Wedlich (Ed.), <i>Cell Migration in Development and Disease</i> (pp. 71–105). Wiley-VCH. <a href=\"https://doi.org/10.1002/3527604669\">https://doi.org/10.1002/3527604669</a>","chicago":"Castanon Ortega, Irinka, and Carl-Philipp J Heisenberg. “Cell Migration during Zebrafish Gastrulation.” In <i>Cell Migration in Development and Disease</i>, edited by Doris Wedlich, 71–105. Wiley-VCH, 2005. <a href=\"https://doi.org/10.1002/3527604669\">https://doi.org/10.1002/3527604669</a>.","ama":"Castanon Ortega I, Heisenberg C-PJ. Cell migration during zebrafish gastrulation. In: Wedlich D, ed. <i>Cell Migration in Development and Disease</i>. Wiley-VCH; 2005:71-105. doi:<a href=\"https://doi.org/10.1002/3527604669\">10.1002/3527604669</a>","mla":"Castanon Ortega, Irinka, and Carl-Philipp J. Heisenberg. “Cell Migration during Zebrafish Gastrulation.” <i>Cell Migration in Development and Disease</i>, edited by Doris Wedlich, Wiley-VCH, 2005, pp. 71–105, doi:<a href=\"https://doi.org/10.1002/3527604669\">10.1002/3527604669</a>.","ieee":"I. Castanon Ortega and C.-P. J. Heisenberg, “Cell migration during zebrafish gastrulation,” in <i>Cell Migration in Development and Disease</i>, D. Wedlich, Ed. Wiley-VCH, 2005, pp. 71–105."},"language":[{"iso":"eng"}],"extern":"1","publication_status":"published","date_created":"2018-12-11T12:04:07Z","publisher":"Wiley-VCH","day":"14","title":"Cell migration during zebrafish gastrulation","status":"public","date_published":"2005-03-14T00:00:00Z","publist_id":"2795","author":[{"last_name":"Castanon Ortega","full_name":"Castanon Ortega, Irinka","first_name":"Irinka"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"month":"03","article_processing_charge":"No","editor":[{"first_name":"Doris","full_name":"Wedlich, Doris","last_name":"Wedlich"}],"year":"2005"},{"publication_status":"published","date_created":"2018-12-11T12:04:07Z","publisher":"Wiley-Blackwell","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:44:30Z","doi":"10.1038/npg.els.0001072","_id":"3589","language":[{"iso":"eng"}],"oa_version":"None","citation":{"ieee":"M. Köppen and C.-P. J. Heisenberg, “Cleavage and gastrulation in zebrafish embryos,” in <i>Encyclopedia of Life Sciences</i>, Wiley-Blackwell, 2005.","ista":"Köppen M, Heisenberg C-PJ. 2005.Cleavage and gastrulation in zebrafish embryos. In: Encyclopedia of Life Sciences. .","apa":"Köppen, M., &#38; Heisenberg, C.-P. J. (2005). Cleavage and gastrulation in zebrafish embryos. In <i>Encyclopedia of Life Sciences</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/npg.els.0001072\">https://doi.org/10.1038/npg.els.0001072</a>","short":"M. Köppen, C.-P.J. Heisenberg, in:, Encyclopedia of Life Sciences, Wiley-Blackwell, 2005.","ama":"Köppen M, Heisenberg C-PJ. Cleavage and gastrulation in zebrafish embryos. In: <i>Encyclopedia of Life Sciences</i>. Wiley-Blackwell; 2005. doi:<a href=\"https://doi.org/10.1038/npg.els.0001072\">10.1038/npg.els.0001072</a>","mla":"Köppen, Mathias, and Carl-Philipp J. Heisenberg. “Cleavage and Gastrulation in Zebrafish Embryos.” <i>Encyclopedia of Life Sciences</i>, Wiley-Blackwell, 2005, doi:<a href=\"https://doi.org/10.1038/npg.els.0001072\">10.1038/npg.els.0001072</a>.","chicago":"Köppen, Mathias, and Carl-Philipp J Heisenberg. “Cleavage and Gastrulation in Zebrafish Embryos.” In <i>Encyclopedia of Life Sciences</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1038/npg.els.0001072\">https://doi.org/10.1038/npg.els.0001072</a>."},"publication":"Encyclopedia of Life Sciences","extern":"1","month":"09","author":[{"last_name":"Köppen","full_name":"Köppen, Mathias","first_name":"Mathias"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_processing_charge":"No","year":"2005","title":"Cleavage and gastrulation in zebrafish embryos","day":"23","status":"public","abstract":[{"lang":"eng","text":"During zebrafish gastrulation, the interplay between patterning events and morphogenesis creates an embryo out of a seemingly unstructured blastula stage embryo, an embryo with distinct polarities along its anterior–posterior, dorsoventral and left–right axes at the end of gastrulation."}],"publist_id":"2794","date_published":"2005-09-23T00:00:00Z"},{"publication_status":"published","date_created":"2018-12-11T12:04:07Z","publisher":"Nature Publishing Group","intvolume":"         7","date_updated":"2020-10-07T06:26:47Z","_id":"3590","page":"19 - 19","doi":"10.1038/ncb0105-19","type":"review","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","language":[{"iso":"eng"}],"oa_version":"None","citation":{"short":"I. Castanon Ortega, C.-P.J. Heisenberg, Nature Cell Biology 7 (2005) 19–19.","apa":"Castanon Ortega, I., &#38; Heisenberg, C.-P. J. (2005). A stern view of gastrulation. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb0105-19\">https://doi.org/10.1038/ncb0105-19</a>","ista":"Castanon Ortega I, Heisenberg C-PJ. 2005. A stern view of gastrulation. Nature Cell Biology. 7(1), 19–19.","chicago":"Castanon Ortega, Irinka, and Carl-Philipp J Heisenberg. “A Stern View of Gastrulation.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/ncb0105-19\">https://doi.org/10.1038/ncb0105-19</a>.","mla":"Castanon Ortega, Irinka, and Carl-Philipp J. Heisenberg. “A Stern View of Gastrulation.” <i>Nature Cell Biology</i>, vol. 7, no. 1, Nature Publishing Group, 2005, pp. 19–19, doi:<a href=\"https://doi.org/10.1038/ncb0105-19\">10.1038/ncb0105-19</a>.","ama":"Castanon Ortega I, Heisenberg C-PJ. A stern view of gastrulation. <i>Nature Cell Biology</i>. 2005;7(1):19-19. doi:<a href=\"https://doi.org/10.1038/ncb0105-19\">10.1038/ncb0105-19</a>","ieee":"I. Castanon Ortega and C.-P. J. Heisenberg, “A stern view of gastrulation,” <i>Nature Cell Biology</i>, vol. 7, no. 1. Nature Publishing Group, pp. 19–19, 2005."},"publication":"Nature Cell Biology","article_processing_charge":"No","month":"01","author":[{"first_name":"Irinka","full_name":"Castanon Ortega, Irinka","last_name":"Castanon Ortega"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"year":"2005","issue":"1","status":"public","title":"A stern view of gastrulation","day":"01","acknowledgement":"BOOK REVIEWED - Gastrulation: From Cells to Embryo, Edited by Claudio Stern. Published by Cold Spring Harbor Laboratory Press: 2004. ","volume":7,"publist_id":"2793","date_published":"2005-01-01T00:00:00Z"}]