[{"citation":{"mla":"Alwen, Joel F., et al. <i>On the Complexity of Scrypt and Proofs of Space in the Parallel Random Oracle Model</i>. Vol. 9666, Springer, 2016, pp. 358–87, doi:<a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">10.1007/978-3-662-49896-5_13</a>.","short":"J.F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2016, pp. 358–387.","ama":"Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S. On the complexity of scrypt and proofs of space in the parallel random oracle model. In: Vol 9666. Springer; 2016:358-387. doi:<a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">10.1007/978-3-662-49896-5_13</a>","apa":"Alwen, J. F., Chen, B., Kamath Hosdurg, C., Kolmogorov, V., Pietrzak, K. Z., &#38; Tessaro, S. (2016). On the complexity of scrypt and proofs of space in the parallel random oracle model (Vol. 9666, pp. 358–387). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">https://doi.org/10.1007/978-3-662-49896-5_13</a>","chicago":"Alwen, Joel F, Binyi Chen, Chethan Kamath Hosdurg, Vladimir Kolmogorov, Krzysztof Z Pietrzak, and Stefano Tessaro. “On the Complexity of Scrypt and Proofs of Space in the Parallel Random Oracle Model,” 9666:358–87. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">https://doi.org/10.1007/978-3-662-49896-5_13</a>.","ieee":"J. F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K. Z. Pietrzak, and S. Tessaro, “On the complexity of scrypt and proofs of space in the parallel random oracle model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9666, pp. 358–387.","ista":"Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S. 2016. On the complexity of scrypt and proofs of space in the parallel random oracle model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9666, 358–387."},"conference":{"location":"Vienna, Austria","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","end_date":"2016-05-12","start_date":"2016-05-08"},"type":"conference","volume":9666,"oa":1,"project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"},{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We study the time-and memory-complexities of the problem of computing labels of (multiple) randomly selected challenge-nodes in a directed acyclic graph. The w-bit label of a node is the hash of the labels of its parents, and the hash function is modeled as a random oracle. Specific instances of this problem underlie both proofs of space [Dziembowski et al. CRYPTO’15] as well as popular memory-hard functions like scrypt. As our main tool, we introduce the new notion of a probabilistic parallel entangled pebbling game, a new type of combinatorial pebbling game on a graph, which is closely related to the labeling game on the same graph. As a first application of our framework, we prove that for scrypt, when the underlying hash function is invoked n times, the cumulative memory complexity (CMC) (a notion recently introduced by Alwen and Serbinenko (STOC’15) to capture amortized memory-hardness for parallel adversaries) is at least Ω(w · (n/ log(n))2). This bound holds for adversaries that can store many natural functions of the labels (e.g., linear combinations), but still not arbitrary functions thereof. We then introduce and study a combinatorial quantity, and show how a sufficiently small upper bound on it (which we conjecture) extends our CMC bound for scrypt to hold against arbitrary adversaries. We also show that such an upper bound solves the main open problem for proofs-of-space protocols: namely, establishing that the time complexity of computing the label of a random node in a graph on n nodes (given an initial kw-bit state) reduces tightly to the time complexity for black pebbling on the same graph (given an initial k-node pebbling)."}],"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:22:54Z","page":"358 - 387","_id":"1231","day":"28","publisher":"Springer","oa_version":"Submitted Version","external_id":{"isi":["000389727200013"]},"doi":"10.1007/978-3-662-49896-5_13","title":"On the complexity of scrypt and proofs of space in the parallel random oracle model","quality_controlled":"1","scopus_import":"1","alternative_title":["LNCS"],"article_processing_charge":"No","acknowledgement":"Joël Alwen, Chethan Kamath, and Krzysztof Pietrzak’s research is partially supported by an ERC starting grant (259668-PSPC). Vladimir Kolmogorov is partially supported by an ERC consolidator grant (616160-DOICV). Binyi Chen was partially supported by NSF grants CNS-1423566 and CNS-1514526, and a gift from the Gareatis Foundation. Stefano Tessaro was partially supported by NSF grants CNS-1423566, CNS-1528178, a Hellman Fellowship, and the Glen and Susanne Culler Chair.\r\n\r\nThis work was done in part while the authors were visiting the Simons Institute for the Theory of Computing, supported by the Simons Foundation and by the DIMACS/Simons Collaboration in Cryptography through NSF grant CNS-1523467.","department":[{"_id":"KrPi"},{"_id":"VlKo"}],"publication_status":"published","ec_funded":1,"date_published":"2016-04-28T00:00:00Z","main_file_link":[{"url":"https://eprint.iacr.org/2016/100","open_access":"1"}],"status":"public","month":"04","year":"2016","author":[{"first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"last_name":"Chen","first_name":"Binyi","full_name":"Chen, Binyi"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","first_name":"Chethan"},{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"full_name":"Tessaro, Stefano","last_name":"Tessaro","first_name":"Stefano"}],"publist_id":"6103","intvolume":"      9666","date_created":"2018-12-11T11:50:51Z","isi":1},{"year":"2016","month":"09","status":"public","date_created":"2018-12-11T11:50:51Z","isi":1,"publist_id":"6102","intvolume":"       537","author":[{"last_name":"Letts","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87","full_name":"Letts, James A","orcid":"0000-0002-9864-3586"},{"last_name":"Fiedorczuk","first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov"}],"publication_status":"published","department":[{"_id":"LeSa"}],"date_published":"2016-09-29T00:00:00Z","article_processing_charge":"No","acknowledgement":"We thank the MRC LMB Cambridge for the use of the Titan Krios microscope. Data processing was performed using the IST high-performance computer cluster. J.A.L. holds a long-term fellowship from FEBS. K.F. is partially funded by a MRC UK PhD fellowship.","publication":"Nature","oa_version":"None","external_id":{"isi":["000384331700042"]},"doi":"10.1038/nature19774","scopus_import":"1","quality_controlled":"1","title":"The architecture of respiratory supercomplexes","_id":"1232","day":"29","publisher":"Nature Publishing Group","page":"644 - 648","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes","_id":"2593EBD6-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","volume":537,"date_updated":"2025-09-22T09:22:23Z","language":[{"iso":"eng"}],"abstract":[{"text":"Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII 2 CIV (the respirasome) - a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII 2 at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.","lang":"eng"}],"citation":{"ista":"Letts JA, Fiedorczuk K, Sazanov LA. 2016. The architecture of respiratory supercomplexes. Nature. 537(7622), 644–648.","apa":"Letts, J. A., Fiedorczuk, K., &#38; Sazanov, L. A. (2016). The architecture of respiratory supercomplexes. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature19774\">https://doi.org/10.1038/nature19774</a>","chicago":"Letts, James A, Karol Fiedorczuk, and Leonid A Sazanov. “The Architecture of Respiratory Supercomplexes.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature19774\">https://doi.org/10.1038/nature19774</a>.","ieee":"J. A. Letts, K. Fiedorczuk, and L. A. Sazanov, “The architecture of respiratory supercomplexes,” <i>Nature</i>, vol. 537, no. 7622. Nature Publishing Group, pp. 644–648, 2016.","short":"J.A. Letts, K. Fiedorczuk, L.A. Sazanov, Nature 537 (2016) 644–648.","ama":"Letts JA, Fiedorczuk K, Sazanov LA. The architecture of respiratory supercomplexes. <i>Nature</i>. 2016;537(7622):644-648. doi:<a href=\"https://doi.org/10.1038/nature19774\">10.1038/nature19774</a>","mla":"Letts, James A., et al. “The Architecture of Respiratory Supercomplexes.” <i>Nature</i>, vol. 537, no. 7622, Nature Publishing Group, 2016, pp. 644–48, doi:<a href=\"https://doi.org/10.1038/nature19774\">10.1038/nature19774</a>."},"issue":"7622"},{"acknowledgement":"G. Fuchsbauer and K. Pietrzak are supported by the European Research Council, ERC Starting Grant (259668-PSPC). F. Heuer is funded by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation and DFG SPP 1736, Algorithms for BIG DATA. E. Kiltz is supported by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation, the German Israel Foundation, and ERC Project ERCC (FP7/615074).","article_processing_charge":"No","alternative_title":["LNCS"],"scopus_import":"1","quality_controlled":"1","title":"Standard security does imply security against selective opening for markov distributions","oa_version":"Submitted Version","doi":"10.1007/978-3-662-49096-9_12","external_id":{"isi":["000376041100012"]},"date_created":"2018-12-11T11:50:51Z","isi":1,"publist_id":"6100","intvolume":"      9562","author":[{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg"},{"full_name":"Heuer, Felix","last_name":"Heuer","first_name":"Felix"},{"last_name":"Kiltz","first_name":"Eike","full_name":"Kiltz, Eike"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"year":"2016","month":"01","status":"public","date_published":"2016-01-01T00:00:00Z","main_file_link":[{"url":"https://eprint.iacr.org/2015/853","open_access":"1"}],"ec_funded":1,"publication_status":"published","department":[{"_id":"KrPi"}],"date_updated":"2025-09-22T09:21:52Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"About three decades ago it was realized that implementing private channels between parties which can be adaptively corrupted requires an encryption scheme that is secure against selective opening attacks. Whether standard (IND-CPA) security implies security against selective opening attacks has been a major open question since. The only known reduction from selective opening to IND-CPA security loses an exponential factor. A polynomial reduction is only known for the very special case where the distribution considered in the selective opening security experiment is a product distribution, i.e., the messages are sampled independently from each other. In this paper we give a reduction whose loss is quantified via the dependence graph (where message dependencies correspond to edges) of the underlying message distribution. In particular, for some concrete distributions including Markov distributions, our reduction is polynomial."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"oa":1,"volume":9562,"type":"conference","conference":{"start_date":"2016-01-10","location":"Tel Aviv, Israel","name":"TCC: Theory of Cryptography Conference","end_date":"2016-01-13"},"citation":{"ieee":"G. Fuchsbauer, F. Heuer, E. Kiltz, and K. Z. Pietrzak, “Standard security does imply security against selective opening for markov distributions,” presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel, 2016, vol. 9562, pp. 282–305.","chicago":"Fuchsbauer, Georg, Felix Heuer, Eike Kiltz, and Krzysztof Z Pietrzak. “Standard Security Does Imply Security against Selective Opening for Markov Distributions,” 9562:282–305. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">https://doi.org/10.1007/978-3-662-49096-9_12</a>.","apa":"Fuchsbauer, G., Heuer, F., Kiltz, E., &#38; Pietrzak, K. Z. (2016). Standard security does imply security against selective opening for markov distributions (Vol. 9562, pp. 282–305). Presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">https://doi.org/10.1007/978-3-662-49096-9_12</a>","ista":"Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. 2016. Standard security does imply security against selective opening for markov distributions. TCC: Theory of Cryptography Conference, LNCS, vol. 9562, 282–305.","mla":"Fuchsbauer, Georg, et al. <i>Standard Security Does Imply Security against Selective Opening for Markov Distributions</i>. Vol. 9562, Springer, 2016, pp. 282–305, doi:<a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">10.1007/978-3-662-49096-9_12</a>.","ama":"Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. Standard security does imply security against selective opening for markov distributions. In: Vol 9562. Springer; 2016:282-305. doi:<a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">10.1007/978-3-662-49096-9_12</a>","short":"G. Fuchsbauer, F. Heuer, E. Kiltz, K.Z. Pietrzak, in:, Springer, 2016, pp. 282–305."},"day":"01","publisher":"Springer","_id":"1233","page":"282 - 305"},{"citation":{"chicago":"Krcál, Marek, and Pawel Pilarczyk. “Computation of Cubical Steenrod Squares,” 9667:140–51. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">https://doi.org/10.1007/978-3-319-39441-1_13</a>.","ieee":"M. Krcál and P. Pilarczyk, “Computation of cubical Steenrod squares,” presented at the CTIC: Computational Topology in Image Context, Marseille, France, 2016, vol. 9667, pp. 140–151.","apa":"Krcál, M., &#38; Pilarczyk, P. (2016). Computation of cubical Steenrod squares (Vol. 9667, pp. 140–151). Presented at the CTIC: Computational Topology in Image Context, Marseille, France: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">https://doi.org/10.1007/978-3-319-39441-1_13</a>","ista":"Krcál M, Pilarczyk P. 2016. Computation of cubical Steenrod squares. CTIC: Computational Topology in Image Context, LNCS, vol. 9667, 140–151.","mla":"Krcál, Marek, and Pawel Pilarczyk. <i>Computation of Cubical Steenrod Squares</i>. Vol. 9667, Springer, 2016, pp. 140–51, doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">10.1007/978-3-319-39441-1_13</a>.","ama":"Krcál M, Pilarczyk P. Computation of cubical Steenrod squares. In: Vol 9667. Springer; 2016:140-151. doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">10.1007/978-3-319-39441-1_13</a>","short":"M. Krcál, P. Pilarczyk, in:, Springer, 2016, pp. 140–151."},"conference":{"start_date":"2016-06-15","location":"Marseille, France","end_date":"2016-06-17","name":"CTIC: Computational Topology in Image Context"},"type":"conference","volume":9667,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"},{"grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps"}],"abstract":[{"lang":"eng","text":"Bitmap images of arbitrary dimension may be formally perceived as unions of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology and homology groups are well known topological invariants of such sets. Cohomological operations, such as the cup product, provide higher-order algebraic topological invariants, especially important for digital images of dimension higher than 3. If such an operation is determined at the level of simplicial chains [see e.g. González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively computable. However, decomposing a cubical complex into a simplicial one deleteriously affects the efficiency of such an approach. In order to avoid this overhead, a direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015, 253-275] for the cup product in cohomology, and implemented in the ChainCon software package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series, 1947, 290-320] directly at the level of cubical chains, and we prove the correctness of this formula. An implementation of this formula is programmed in C++ within the ChainCon software framework. We provide a few examples and discuss the effectiveness of this approach. One specific application follows from the fact that Steenrod squares yield tests for the topological extension problem: Can a given map A → Sd to a sphere Sd be extended to a given super-complex X of A? In particular, the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value r &gt; 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the extension problem."}],"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:19:17Z","page":"140 - 151","_id":"1237","day":"02","publisher":"Springer","oa_version":"None","external_id":{"isi":["000389805800013"]},"doi":"10.1007/978-3-319-39441-1_13","title":"Computation of cubical Steenrod squares","quality_controlled":"1","scopus_import":"1","alternative_title":["LNCS"],"article_processing_charge":"No","acknowledgement":"The research conducted by both authors has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreements no. 291734 (for M. K.) and no. 622033 (for P. P.).","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publication_status":"published","ec_funded":1,"date_published":"2016-06-02T00:00:00Z","status":"public","month":"06","year":"2016","author":[{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek","last_name":"Krcál","first_name":"Marek"},{"full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","first_name":"Pawel"}],"publist_id":"6096","intvolume":"      9667","date_created":"2018-12-11T11:50:52Z","isi":1},{"publication_status":"published","department":[{"_id":"JiFr"}],"pubrep_id":"710","date_published":"2016-01-29T00:00:00Z","year":"2016","month":"01","status":"public","isi":1,"date_created":"2018-12-11T11:50:53Z","intvolume":"         6","publist_id":"6094","author":[{"last_name":"Von Wangenheim","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247"},{"full_name":"Rosero, Amparo","last_name":"Rosero","first_name":"Amparo"},{"first_name":"George","last_name":"Komis","full_name":"Komis, George"},{"last_name":"Šamajová","first_name":"Olga","full_name":"Šamajová, Olga"},{"full_name":"Ovečka, Miroslav","first_name":"Miroslav","last_name":"Ovečka"},{"first_name":"Boris","last_name":"Voigt","full_name":"Voigt, Boris"},{"full_name":"Šamaj, Jozef","last_name":"Šamaj","first_name":"Jozef"}],"file":[{"file_name":"IST-2016-710-v1+1_fpls-06-01262.pdf","access_level":"open_access","date_created":"2018-12-12T10:09:36Z","date_updated":"2020-07-14T12:44:41Z","file_id":"4760","content_type":"application/pdf","creator":"system","file_size":1640550,"checksum":"3127eab844d53564bf47e2b6b42f1ca0","relation":"main_file"}],"ddc":["581"],"oa_version":"Published Version","external_id":{"isi":["000368891500001"]},"doi":"10.3389/fpls.2015.01262","file_date_updated":"2020-07-14T12:44:41Z","scopus_import":"1","quality_controlled":"1","title":"Endosomal interactions during root hair growth","article_processing_charge":"No","acknowledgement":"This work was supported by National Program for Sustainability I (grant no. LO1204) provided by the Czech Ministry of Education and by Institutional Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help with the statistics.","publication":"Frontiers in Plant Science","_id":"1238","publisher":"Frontiers Research Foundation","day":"29","citation":{"ieee":"D. von Wangenheim <i>et al.</i>, “Endosomal interactions during root hair growth,” <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016. Frontiers Research Foundation, 2016.","chicago":"Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair Growth.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2016. <a href=\"https://doi.org/10.3389/fpls.2015.01262\">https://doi.org/10.3389/fpls.2015.01262</a>.","apa":"von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt, B., &#38; Šamaj, J. (2016). Endosomal interactions during root hair growth. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2015.01262\">https://doi.org/10.3389/fpls.2015.01262</a>","ista":"von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science. 6(JAN2016), 1262.","mla":"von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.” <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016, 1262, Frontiers Research Foundation, 2016, doi:<a href=\"https://doi.org/10.3389/fpls.2015.01262\">10.3389/fpls.2015.01262</a>.","ama":"von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root hair growth. <i>Frontiers in Plant Science</i>. 2016;6(JAN2016). doi:<a href=\"https://doi.org/10.3389/fpls.2015.01262\">10.3389/fpls.2015.01262</a>","short":"D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt, J. Šamaj, Frontiers in Plant Science 6 (2016)."},"article_number":"1262","issue":"JAN2016","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"license":"https://creativecommons.org/licenses/by/4.0/","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":6,"date_updated":"2025-09-22T09:18:11Z","language":[{"iso":"eng"}],"abstract":[{"text":"The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth.","lang":"eng"}]},{"issue":"2","article_number":"028102","citation":{"apa":"Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., &#38; Voituriez, R. (2016). Cortical flow-driven shapes of nonadherent cells. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">https://doi.org/10.1103/PhysRevLett.116.028102</a>","chicago":"Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Cortical Flow-Driven Shapes of Nonadherent Cells.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">https://doi.org/10.1103/PhysRevLett.116.028102</a>.","ieee":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Cortical flow-driven shapes of nonadherent cells,” <i>Physical Review Letters</i>, vol. 116, no. 2. American Physical Society, 2016.","ista":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 116(2), 028102.","mla":"Callan Jones, Andrew, et al. “Cortical Flow-Driven Shapes of Nonadherent Cells.” <i>Physical Review Letters</i>, vol. 116, no. 2, 028102, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">10.1103/PhysRevLett.116.028102</a>.","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 116 (2016).","ama":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Cortical flow-driven shapes of nonadherent cells. <i>Physical Review Letters</i>. 2016;116(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">10.1103/PhysRevLett.116.028102</a>"},"date_updated":"2025-09-22T09:18:45Z","abstract":[{"text":"Nonadherent polarized cells have been observed to have a pearlike, elongated shape. Using a minimal model that describes the cell cortex as a thin layer of contractile active gel, we show that the anisotropy of active stresses, controlled by cortical viscosity and filament ordering, can account for this morphology. The predicted shapes can be determined from the flow pattern only; they prove to be independent of the mechanism at the origin of the cortical flow, and are only weakly sensitive to the cytoplasmic rheology. In the case of actin flows resulting from a contractile instability, we propose a phase diagram of three-dimensional cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate shapes, all of which have been observed in experiment.","lang":"eng"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":116,"type":"journal_article","publisher":"American Physical Society","day":"15","_id":"1239","scopus_import":"1","title":"Cortical flow-driven shapes of nonadherent cells","quality_controlled":"1","doi":"10.1103/PhysRevLett.116.028102","oa_version":"None","external_id":{"isi":["000368286300022"]},"acknowledgement":"V. R. acknowledges support by the Austrian Science Fund (FWF): (Grant No. T560-B17).","publication":"Physical Review Letters","article_processing_charge":"No","date_published":"2016-01-15T00:00:00Z","publication_status":"published","department":[{"_id":"CaHe"}],"date_created":"2018-12-11T11:50:53Z","isi":1,"author":[{"last_name":"Callan Jones","first_name":"Andrew","full_name":"Callan Jones, Andrew"},{"first_name":"Verena","last_name":"Ruprecht","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wieser, Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","last_name":"Wieser","first_name":"Stefan"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"}],"publist_id":"6095","intvolume":"       116","year":"2016","status":"public","month":"01"},{"external_id":{"isi":["000368904100001"]},"file_date_updated":"2020-07-14T12:44:41Z","oa_version":"Published Version","doi":"10.1186/s13059-016-0873-8","ddc":["576"],"file":[{"relation":"main_file","content_type":"application/pdf","file_id":"4789","creator":"system","checksum":"a268beee1a690801c83ec6729f9ebc5b","file_size":2914601,"access_level":"open_access","file_name":"IST-2016-709-v1+1_s13059-016-0873-8.pdf","date_created":"2018-12-12T10:10:05Z","date_updated":"2020-07-14T12:44:41Z"}],"title":"Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","publication":"Genome Biology","acknowledgement":"This study was partly funded by the Austrian Science Fund (FWF F43-B09, FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions, Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript.","pubrep_id":"709","department":[{"_id":"GaNo"}],"publication_status":"published","date_published":"2016-01-29T00:00:00Z","status":"public","month":"01","year":"2016","author":[{"last_name":"Kornienko","first_name":"Aleksandra","full_name":"Kornienko, Aleksandra"},{"last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"full_name":"Guenzl, Philipp","first_name":"Philipp","last_name":"Guenzl"},{"first_name":"Heinz","last_name":"Gisslinger","full_name":"Gisslinger, Heinz"},{"last_name":"Gisslinger","first_name":"Bettina","full_name":"Gisslinger, Bettina"},{"last_name":"Cleary","first_name":"Ciara","full_name":"Cleary, Ciara"},{"full_name":"Kralovics, Robert","last_name":"Kralovics","first_name":"Robert"},{"first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barlow","first_name":"Denise","full_name":"Barlow, Denise"}],"intvolume":"        17","publist_id":"6093","date_created":"2018-12-11T11:50:53Z","isi":1,"citation":{"ama":"Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. 2016;17(1). doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>","short":"A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary, R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016).","mla":"Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>, vol. 17, no. 1, 14, BioMed Central, 2016, doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>.","ista":"Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 17(1), 14.","chicago":"Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger, Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>. BioMed Central, 2016. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>.","ieee":"A. Kornienko <i>et al.</i>, “Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans,” <i>Genome Biology</i>, vol. 17, no. 1. BioMed Central, 2016.","apa":"Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary, C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>"},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"1","article_number":"14","volume":17,"type":"journal_article","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:17:40Z","_id":"1240","publisher":"BioMed Central","day":"29"},{"date_updated":"2025-09-22T09:17:06Z","language":[{"iso":"eng"}],"abstract":[{"text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"Evolutionary rescue"}],"oa":1,"volume":202,"type":"journal_article","issue":"2","citation":{"mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>. 2016;202(2):721-732. doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>","apa":"Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary rescue. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732."},"day":"01","publisher":"Genetics Society of America","_id":"1241","page":"721 - 732","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","publication":"Genetics","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","title":"The role of recombination in evolutionary rescue","oa_version":"Preprint","doi":"10.1534/genetics.115.180299","external_id":{"isi":["000371304600028"]},"isi":1,"date_created":"2018-12-11T11:50:54Z","intvolume":"       202","publist_id":"6091","author":[{"first_name":"Hildegard","last_name":"Uecker","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"year":"2016","month":"02","status":"public","date_published":"2016-02-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract"}],"ec_funded":1,"publication_status":"published","department":[{"_id":"NiBa"}]},{"_id":"1242","publisher":"American Institute of Physics","day":"04","citation":{"ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>.","ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2. American Institute of Physics, 2016.","apa":"Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>."},"issue":"2","article_number":"022404","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"type":"journal_article","volume":93,"date_updated":"2025-09-22T09:16:30Z","abstract":[{"text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"GaTk"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.02562"}],"date_published":"2016-02-04T00:00:00Z","year":"2016","status":"public","month":"02","isi":1,"date_created":"2018-12-11T11:50:54Z","arxiv":1,"author":[{"first_name":"Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R"},{"last_name":"Walczak","first_name":"Aleksandra","full_name":"Walczak, Aleksandra"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publist_id":"6088","intvolume":"        93","external_id":{"isi":["000369439100005"],"arxiv":["1507.02562"]},"doi":"10.1103/PhysRevE.93.022404","oa_version":"Preprint","scopus_import":"1","title":"Extending the dynamic range of transcription factor action by translational regulation","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics"},{"article_processing_charge":"No","publication":"PNAS","acknowledgement":"We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”","external_id":{"isi":["000370220000046"]},"doi":"10.1073/pnas.1419248113","oa_version":"Submitted Version","title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","quality_controlled":"1","scopus_import":"1","status":"public","month":"02","year":"2016","author":[{"last_name":"Recouvreux","first_name":"Pierre","full_name":"Recouvreux, Pierre"},{"last_name":"Sokolowski","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779"},{"full_name":"Grammoustianou, Aristea","first_name":"Aristea","last_name":"Grammoustianou"},{"full_name":"Tenwolde, Pieter","last_name":"Tenwolde","first_name":"Pieter"},{"full_name":"Dogterom, Marileen","first_name":"Marileen","last_name":"Dogterom"}],"intvolume":"       113","publist_id":"6085","date_created":"2018-12-11T11:50:55Z","isi":1,"department":[{"_id":"GaTk"}],"publication_status":"published","date_published":"2016-02-16T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/"}],"type":"journal_article","volume":113,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:15:17Z","citation":{"mla":"Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>.","short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","ama":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. 2016;113(7):1811-1816. doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>","apa":"Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &#38; Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>","ieee":"P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” <i>PNAS</i>, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.","chicago":"Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>.","ista":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816."},"issue":"7","_id":"1244","publisher":"National Academy of Sciences","day":"16","page":"1811 - 1816"},{"department":[{"_id":"KrCh"}],"publication_status":"published","date_published":"2016-02-27T00:00:00Z","ec_funded":1,"month":"02","status":"public","year":"2016","publist_id":"6083","intvolume":"        26","author":[{"full_name":"Pandey, Vineet","first_name":"Vineet","last_name":"Pandey"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"isi":1,"date_created":"2018-12-11T11:50:55Z","doi":"10.1145/2818052.2869122","oa_version":"None","external_id":{"isi":["000468137600088"]},"quality_controlled":"1","title":"Game-theoretic models identify useful principles for peer collaboration in online learning platforms","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the ACM Conference on Computer Supported Cooperative Work","acknowledgement":"ERC Start Grant Graph Games 279307 supported this  research. ","page":"365 - 368","_id":"1245","day":"27","publisher":"ACM","citation":{"ista":"Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. Proceedings of the ACM Conference on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work and Social Computing vol. 26, 365–368.","apa":"Pandey, V., &#38; Chatterjee, K. (2016). Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i> (Vol. 26, pp. 365–368). San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2818052.2869122\">https://doi.org/10.1145/2818052.2869122</a>","chicago":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” In <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, 26:365–68. ACM, 2016. <a href=\"https://doi.org/10.1145/2818052.2869122\">https://doi.org/10.1145/2818052.2869122</a>.","ieee":"V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles for peer collaboration in online learning platforms,” in <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, San Francisco, CA, USA, 2016, vol. 26, no. Februar-2016, pp. 365–368.","short":"V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer Supported Cooperative Work, ACM, 2016, pp. 365–368.","ama":"Pandey V, Chatterjee K. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In: <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>. Vol 26. ACM; 2016:365-368. doi:<a href=\"https://doi.org/10.1145/2818052.2869122\">10.1145/2818052.2869122</a>","mla":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, vol. 26, no. Februar-2016, ACM, 2016, pp. 365–68, doi:<a href=\"https://doi.org/10.1145/2818052.2869122\">10.1145/2818052.2869122</a>."},"conference":{"start_date":"2016-02-26","name":"CSCW: Computer Supported Cooperative Work and Social Computing","end_date":"2016-03-02","location":"San Francisco, CA, USA"},"issue":"Februar-2016","type":"conference","volume":26,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"To facilitate collaboration in massive online classrooms, instructors must make many decisions. For instance, the following parameters need to be decided when designing a peer-feedback system where students review each others' essays: the number of students each student must provide feedback to, an algorithm to map feedback providers to receivers, constraints that ensure students do not become free-riders (receiving feedback but not providing it), the best times to receive feedback to improve learning etc. While instructors can answer these questions by running experiments or invoking past experience, game-theoretic models with data from online learning platforms can identify better initial designs for further improvements. As an example, we explore the design space of a peer feedback system by modeling it using game theory. Our simulations show that incentivizing students to provide feedback requires the value obtained from receiving a feedback to exceed the cost of providing it by a large factor (greater than 7). Furthermore, hiding feedback from low-effort students incentivizes them to provide more feedback."}],"date_updated":"2025-09-22T09:14:46Z"},{"language":[{"iso":"eng"}],"abstract":[{"text":"Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire's evanescent field and the probe's response function. As a result, we find that the probe's sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments.","lang":"eng"}],"date_updated":"2025-09-22T09:14:06Z","type":"journal_article","volume":6,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","article_number":"22665","citation":{"ista":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 6, 22665.","apa":"Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., &#38; Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep22665\">https://doi.org/10.1038/srep22665</a>","ieee":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers, “Imaging of electric and magnetic fields near plasmonic nanowires,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","chicago":"Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep22665\">https://doi.org/10.1038/srep22665</a>.","short":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers, Scientific Reports 6 (2016).","ama":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging of electric and magnetic fields near plasmonic nanowires. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep22665\">10.1038/srep22665</a>","mla":"Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” <i>Scientific Reports</i>, vol. 6, 22665, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep22665\">10.1038/srep22665</a>."},"publisher":"Nature Publishing Group","day":"07","_id":"1246","publication":"Scientific Reports","acknowledgement":"This work is supported part of the research program of the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO), and part of this work has been funded by the project ‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging Technologies (FET) program within the Seventh Framework Programme for Research of the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).","article_processing_charge":"No","quality_controlled":"1","title":"Imaging of electric and magnetic fields near plasmonic nanowires","scopus_import":"1","ddc":["539"],"external_id":{"isi":["000371407500001"]},"doi":"10.1038/srep22665","file_date_updated":"2020-07-14T12:44:41Z","oa_version":"Published Version","file":[{"relation":"main_file","date_created":"2018-12-12T10:14:11Z","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-707-v1+1_srep22665.pdf","access_level":"open_access","file_size":1425165,"checksum":"ca76236cb1aae22cb90c65313e2c5e98","content_type":"application/pdf","file_id":"5061","creator":"system"}],"intvolume":"         6","publist_id":"6082","author":[{"last_name":"Kabakova","first_name":"Irina","full_name":"Kabakova, Irina"},{"first_name":"Anouk","last_name":"De Hoogh","full_name":"De Hoogh, Anouk"},{"first_name":"Ruben","last_name":"Van Der Wel","full_name":"Van Der Wel, Ruben"},{"last_name":"Wulf","first_name":"Matthias","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378"},{"full_name":"Le Feber, Boris","first_name":"Boris","last_name":"Le Feber"},{"full_name":"Kuipers, Laurens","last_name":"Kuipers","first_name":"Laurens"}],"date_created":"2018-12-11T11:50:55Z","isi":1,"month":"03","status":"public","year":"2016","date_published":"2016-03-07T00:00:00Z","department":[{"_id":"JoFi"}],"pubrep_id":"707","publication_status":"published"},{"citation":{"short":"M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík, L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol, J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.","ama":"Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>. 2016;113(10):2768-2773. doi:<a href=\"https://doi.org/10.1073/pnas.1501343112\">10.1073/pnas.1501343112</a>","mla":"Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>, vol. 113, no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:<a href=\"https://doi.org/10.1073/pnas.1501343112\">10.1073/pnas.1501343112</a>.","ista":"Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10), 2768–2773.","apa":"Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík, J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1501343112\">https://doi.org/10.1073/pnas.1501343112</a>","chicago":"Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1501343112\">https://doi.org/10.1073/pnas.1501343112</a>.","ieee":"M. Karampelias <i>et al.</i>, “ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling,” <i>PNAS</i>, vol. 113, no. 10. National Academy of Sciences, pp. 2768–2773, 2016."},"issue":"10","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"type":"journal_article","volume":113,"date_updated":"2025-09-22T09:13:28Z","abstract":[{"lang":"eng","text":"The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity."}],"language":[{"iso":"eng"}],"page":"2768 - 2773","_id":"1247","day":"08","publisher":"National Academy of Sciences","external_id":{"isi":["000372013300055"]},"doi":"10.1073/pnas.1501343112","oa_version":"Submitted Version","scopus_import":"1","title":"ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"This work was supported by the Ghent University Special Research Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP) (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted to the Agency for Science and Technology for\r\na predoctoral fellowship.","publication":"PNAS","publication_status":"published","department":[{"_id":"JiFr"}],"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/"}],"date_published":"2016-03-08T00:00:00Z","year":"2016","status":"public","month":"03","isi":1,"date_created":"2018-12-11T11:50:56Z","author":[{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"full_name":"Neyt, Pia","last_name":"Neyt","first_name":"Pia"},{"first_name":"Steven","last_name":"De Groeve","full_name":"De Groeve, Steven"},{"full_name":"Aesaert, Stijn","last_name":"Aesaert","first_name":"Stijn"},{"full_name":"Coussens, Griet","first_name":"Griet","last_name":"Coussens"},{"full_name":"Rolčík, Jakub","first_name":"Jakub","last_name":"Rolčík"},{"full_name":"Bruno, Leonardo","first_name":"Leonardo","last_name":"Bruno"},{"full_name":"De Winne, Nancy","first_name":"Nancy","last_name":"De Winne"},{"full_name":"Van Minnebruggen, Annemie","last_name":"Van Minnebruggen","first_name":"Annemie"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc"},{"full_name":"Ponce, Maria","first_name":"Maria","last_name":"Ponce"},{"first_name":"José","last_name":"Micol","full_name":"Micol, José"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"full_name":"Van Lijsebettens, Mieke","first_name":"Mieke","last_name":"Van Lijsebettens"}],"intvolume":"       113","publist_id":"6081"},{"acknowledgement":"Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations.","publication":"Annual Review of Condensed Matter Physics","article_processing_charge":"No","scopus_import":"1","title":"Information processing in living systems","quality_controlled":"1","external_id":{"arxiv":["1412.8752"],"isi":["000372188500005"]},"oa_version":"Preprint","doi":"10.1146/annurev-conmatphys-031214-014803","isi":1,"date_created":"2018-12-11T11:50:56Z","arxiv":1,"author":[{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"}],"publist_id":"6080","intvolume":"         7","year":"2016","status":"public","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1412.8752","open_access":"1"}],"date_published":"2016-03-10T00:00:00Z","publication_status":"published","department":[{"_id":"GaTk"}],"date_updated":"2025-09-22T09:12:56Z","abstract":[{"text":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"volume":7,"type":"journal_article","citation":{"mla":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>.","ama":"Tkačik G, Bialek W. Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. 2016;7:89-117. doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","ieee":"G. Tkačik and W. Bialek, “Information processing in living systems,” <i>Annual Review of Condensed Matter Physics</i>, vol. 7. Annual Reviews, pp. 89–117, 2016.","chicago":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>.","apa":"Tkačik, G., &#38; Bialek, W. (2016). Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117."},"publisher":"Annual Reviews","day":"10","_id":"1248","page":"89 - 117"},{"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"Control of Epithelial Cell Layer Spreading in Zebrafish","call_identifier":"FWF","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","grant_number":"I930-B20"}],"volume":110,"type":"journal_article","date_updated":"2025-09-22T09:12:06Z","abstract":[{"lang":"eng","text":"Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell- and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example, the characteristic time of stress relaxation (the Maxwell time τM) in the actomyosin sets the timescale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length λ) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer in vivo directly from laser ablation experiments. For this we investigate the cortical response to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained physical description of the cortex in terms of a two-dimensional thin film of an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated the response to laser ablation in two different ways: by quantifying flow and density fields as a function of space and time, and by determining the time evolution of the shape of the ablated region. Importantly, both methods provide best-fit physical parameters that are in close agreement with each other and that are similar to previous estimates in the two systems. Our method provides an accurate and robust means for measuring physical parameters of the actomyosin cortical layer. It can be useful for investigations of actomyosin mechanics at the cellular-scale, but also for providing insights into the active mechanics processes that govern tissue-scale morphogenesis."}],"language":[{"iso":"eng"}],"citation":{"mla":"Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” <i>Biophysical Journal</i>, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">10.1016/j.bpj.2016.02.013</a>.","short":"A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill, Biophysical Journal 110 (2016) 1421–1429.","ama":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining physical properties of the cell cortex. <i>Biophysical Journal</i>. 2016;110(6):1421-1429. doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">10.1016/j.bpj.2016.02.013</a>","apa":"Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., &#38; Grill, S. (2016). Determining physical properties of the cell cortex. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">https://doi.org/10.1016/j.bpj.2016.02.013</a>","ieee":"A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S. Grill, “Determining physical properties of the cell cortex,” <i>Biophysical Journal</i>, vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016.","chicago":"Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg, Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell Cortex.” <i>Biophysical Journal</i>. Biophysical Society, 2016. <a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">https://doi.org/10.1016/j.bpj.2016.02.013</a>.","ista":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016. Determining physical properties of the cell cortex. Biophysical Journal. 110(6), 1421–1429."},"issue":"6","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","_id":"1249","publisher":"Biophysical Society","day":"29","page":"1421 - 1429","article_processing_charge":"No","acknowledgement":"S.W.G. acknowledges support by grant no. 281903 from the European Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft. S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20). We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.","publication":"Biophysical Journal","file":[{"file_size":1965645,"checksum":"c408cf2e25a25c8d711cffea524bda55","file_id":"4845","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:10:54Z","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf","access_level":"open_access","relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:41Z","oa_version":"Published Version","external_id":{"isi":["000373487200023"]},"doi":"10.1016/j.bpj.2016.02.013","ddc":["572","576"],"scopus_import":"1","title":"Determining physical properties of the cell cortex","quality_controlled":"1","year":"2016","status":"public","month":"03","date_created":"2018-12-11T11:50:56Z","isi":1,"author":[{"full_name":"Saha, Arnab","first_name":"Arnab","last_name":"Saha"},{"full_name":"Nishikawa, Masatoshi","last_name":"Nishikawa","first_name":"Masatoshi"},{"first_name":"Martin","last_name":"Behrndt","full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"full_name":"Grill, Stephan","last_name":"Grill","first_name":"Stephan"}],"intvolume":"       110","publist_id":"6079","publication_status":"published","pubrep_id":"706","department":[{"_id":"CaHe"}],"date_published":"2016-03-29T00:00:00Z"},{"_id":"1250","related_material":{"record":[{"relation":"research_data","status":"public","id":"9873"}]},"publisher":"Public Library of Science","day":"19","citation":{"mla":"Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” <i>PLoS Genetics</i>, vol. 12, no. 4, e1005974, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974\">10.1371/journal.pgen.1005974</a>.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. <i>PLoS Genetics</i>. 2016;12(4). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974\">10.1371/journal.pgen.1005974</a>","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” <i>PLoS Genetics</i>, vol. 12, no. 4. Public Library of Science, 2016.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” <i>PLoS Genetics</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1005974\">https://doi.org/10.1371/journal.pgen.1005974</a>.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &#38; Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005974\">https://doi.org/10.1371/journal.pgen.1005974</a>","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 12(4), e1005974."},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"e1005974","issue":"4","volume":12,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported.","lang":"eng"}],"date_updated":"2025-09-22T09:10:03Z","department":[{"_id":"CaGu"}],"pubrep_id":"705","publication_status":"published","date_published":"2016-04-19T00:00:00Z","month":"04","status":"public","year":"2016","intvolume":"        12","publist_id":"6077","author":[{"last_name":"Boehm","first_name":"Alex","full_name":"Boehm, Alex"},{"full_name":"Arnoldini, Markus","last_name":"Arnoldini","first_name":"Markus"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller"},{"full_name":"Röösli, Thomas","first_name":"Thomas","last_name":"Röösli"},{"full_name":"Bigosch, Colette","last_name":"Bigosch","first_name":"Colette"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"date_created":"2018-12-11T11:50:56Z","isi":1,"ddc":["576","579"],"doi":"10.1371/journal.pgen.1005974","external_id":{"isi":["000375231900025"]},"file_date_updated":"2020-07-14T12:44:41Z","oa_version":"Published Version","file":[{"checksum":"53d22b2b39e5adc243d34f18b2615a85","file_size":6273249,"content_type":"application/pdf","creator":"system","file_id":"5067","date_created":"2018-12-12T10:14:17Z","date_updated":"2020-07-14T12:44:41Z","access_level":"open_access","file_name":"IST-2016-705-v1+1_journal.pgen.1005974.PDF","relation":"main_file"}],"quality_controlled":"1","title":"Genetic manipulation of glycogen allocation affects replicative lifespan in E coli","scopus_import":"1","article_processing_charge":"No","publication":"PLoS Genetics","acknowledgement":"This manuscript is dedicated to the memory of Alex Böhm, who was a great friend and a passionate biologist. Alex passed away after the initial submission of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and Nela Nikolic for helpful discussions. This work was supported by the Swiss National Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB)."},{"publisher":"American Society of Plant Biologists","day":"01","_id":"1251","page":"930 - 948","date_updated":"2025-09-22T09:10:52Z","abstract":[{"text":"Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":28,"type":"journal_article","issue":"4","citation":{"mla":"Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>, vol. 28, no. 4, American Society of Plant Biologists, 2016, pp. 930–48, doi:<a href=\"https://doi.org/10.1105/tpc.15.00726\">10.1105/tpc.15.00726</a>.","short":"J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri, B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O. Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann, R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948.","ama":"Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. <i>Plant Cell</i>. 2016;28(4):930-948. doi:<a href=\"https://doi.org/10.1105/tpc.15.00726\">10.1105/tpc.15.00726</a>","apa":"Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler, M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00726\">https://doi.org/10.1105/tpc.15.00726</a>","chicago":"Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00726\">https://doi.org/10.1105/tpc.15.00726</a>.","ieee":"J. Zhu <i>et al.</i>, “TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics,” <i>Plant Cell</i>, vol. 28, no. 4. American Society of Plant Biologists, pp. 930–948, 2016.","ista":"Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B, Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948."},"date_created":"2018-12-11T11:50:57Z","isi":1,"author":[{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Sovero, Valpuri","first_name":"Valpuri","last_name":"Sovero"},{"full_name":"Di Donato, Martin","first_name":"Martin","last_name":"Di Donato"},{"full_name":"Ge, Pei","first_name":"Pei","last_name":"Ge"},{"last_name":"Oehri","first_name":"Jacqueline","full_name":"Oehri, Jacqueline"},{"full_name":"Aryal, Bibek","last_name":"Aryal","first_name":"Bibek"},{"first_name":"Pengchao","last_name":"Hao","full_name":"Hao, Pengchao"},{"first_name":"Miriam","last_name":"Linnert","full_name":"Linnert, Miriam"},{"full_name":"Burgardt, Noelia","last_name":"Burgardt","first_name":"Noelia"},{"full_name":"Lücke, Christian","last_name":"Lücke","first_name":"Christian"},{"full_name":"Weiwad, Matthias","first_name":"Matthias","last_name":"Weiwad"},{"full_name":"Michel, Max","first_name":"Max","last_name":"Michel"},{"full_name":"Weiergräber, Oliver","last_name":"Weiergräber","first_name":"Oliver"},{"last_name":"Pollmann","first_name":"Stephan","full_name":"Pollmann, Stephan"},{"last_name":"Azzarello","first_name":"Elisa","full_name":"Azzarello, Elisa"},{"full_name":"Mancuso, Stefano","first_name":"Stefano","last_name":"Mancuso"},{"full_name":"Ferro, Noel","first_name":"Noel","last_name":"Ferro"},{"full_name":"Fukao, Yoichiro","last_name":"Fukao","first_name":"Yoichiro"},{"first_name":"Céline","last_name":"Hoffmann","full_name":"Hoffmann, Céline"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"Thomas","first_name":"Clément","full_name":"Thomas, Clément"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"}],"intvolume":"        28","publist_id":"6078","year":"2016","status":"public","month":"04","date_published":"2016-04-01T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/","open_access":"1"}],"publication_status":"published","department":[{"_id":"JiFr"}],"acknowledgement":" This work was supported by grants from the European Social Fund (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F. and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all to M.G.). ","publication":"Plant Cell","article_processing_charge":"No","scopus_import":"1","title":"TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics","quality_controlled":"1","oa_version":"Submitted Version","external_id":{"isi":["000375416000012"]},"doi":"10.1105/tpc.15.00726"},{"day":"01","publisher":"American Mathematical Society","article_type":"original","_id":"1252","page":"1787 - 1801","abstract":[{"lang":"eng","text":"We study the homomorphism induced in homology by a closed correspondence between topological spaces, using projections from the graph of the correspondence to its domain and codomain. We provide assumptions under which the homomorphism induced by an outer approximation of a continuous map coincides with the homomorphism induced in homology by the map. In contrast to more classical results we do not require that the projection to the domain have acyclic preimages. Moreover, we show that it is possible to retrieve correct homological information from a correspondence even if some data is missing or perturbed. Finally, we describe an application to combinatorial maps that are either outer approximations of continuous maps or reconstructions of such maps from a finite set of data points."}],"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:09:31Z","type":"journal_article","volume":144,"oa":1,"project":[{"name":"Persistent Homology - Images, Data and Maps","grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"4","citation":{"ista":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 144(4), 1787–1801.","ieee":"S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on homology from a correspondence,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016.","chicago":"Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk. “Inducing a Map on Homology from a Correspondence.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/proc/12812\">https://doi.org/10.1090/proc/12812</a>.","apa":"Harker, S., Kokubu, H., Mischaikow, K., &#38; Pilarczyk, P. (2016). Inducing a map on homology from a correspondence. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/12812\">https://doi.org/10.1090/proc/12812</a>","ama":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from a correspondence. <i>Proceedings of the American Mathematical Society</i>. 2016;144(4):1787-1801. doi:<a href=\"https://doi.org/10.1090/proc/12812\">10.1090/proc/12812</a>","short":"S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American Mathematical Society 144 (2016) 1787–1801.","mla":"Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1787–801, doi:<a href=\"https://doi.org/10.1090/proc/12812\">10.1090/proc/12812</a>."},"author":[{"full_name":"Harker, Shaun","first_name":"Shaun","last_name":"Harker"},{"full_name":"Kokubu, Hiroshi","last_name":"Kokubu","first_name":"Hiroshi"},{"full_name":"Mischaikow, Konstantin","first_name":"Konstantin","last_name":"Mischaikow"},{"last_name":"Pilarczyk","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel"}],"intvolume":"       144","publication_identifier":{"issn":["1088-6826"]},"publist_id":"6075","isi":1,"date_created":"2018-12-11T11:50:57Z","arxiv":1,"status":"public","month":"04","year":"2016","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1411.7563","open_access":"1"}],"date_published":"2016-04-01T00:00:00Z","corr_author":"1","department":[{"_id":"HeEd"}],"publication_status":"published","publication":"Proceedings of the American Mathematical Society","acknowledgement":"The authors gratefully acknowledge the support of the Lorenz Center which\r\nprovided an opportunity for us to discuss in depth the work of this paper. Research leading to these results has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033 (supporting PP). The work of the first and third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019, 1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029), Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan.","article_processing_charge":"No","title":"Inducing a map on homology from a correspondence","quality_controlled":"1","scopus_import":"1","doi":"10.1090/proc/12812","external_id":{"isi":["000369298400038"],"arxiv":["1411.7563"]},"oa_version":"Preprint"},{"_id":"1253","day":"01","publisher":"American Medical Association","page":"409 - 410","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":73,"type":"journal_article","date_updated":"2025-09-22T09:08:34Z","language":[{"iso":"eng"}],"abstract":[{"text":"This article provides an introduction to the role of microRNAs in the nervous system and outlines their potential involvement in the pathophysiology of schizophrenia, which is hypothesized to arise owing to environmental factors and genetic predisposition.","lang":"eng"}],"citation":{"ama":"Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. <i>JAMA Psychiatry</i>. 2016;73(4):409-410. doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">10.1001/jamapsychiatry.2015.3144</a>","short":"L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.","mla":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” <i>JAMA Psychiatry</i>, vol. 73, no. 4, American Medical Association, 2016, pp. 409–10, doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">10.1001/jamapsychiatry.2015.3144</a>.","ista":"Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 73(4), 409–410.","chicago":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” <i>JAMA Psychiatry</i>. American Medical Association, 2016. <a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>.","ieee":"L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,” <i>JAMA Psychiatry</i>, vol. 73, no. 4. American Medical Association, pp. 409–410, 2016.","apa":"Tsai, L., &#38; Siegert, S. (2016). How MicroRNAs Are involved in splitting the mind. <i>JAMA Psychiatry</i>. American Medical Association. <a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>"},"issue":"4","has_accepted_license":"1","year":"2016","month":"04","status":"public","isi":1,"date_created":"2018-12-11T11:50:58Z","publist_id":"6074","intvolume":"        73","publication_identifier":{"issn":["2168-622X"]},"author":[{"first_name":"Lihuei","last_name":"Tsai","full_name":"Tsai, Lihuei"},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"}],"publication_status":"published","department":[{"_id":"SaSi"}],"pubrep_id":"981","date_published":"2016-04-01T00:00:00Z","article_processing_charge":"No","publication":"JAMA Psychiatry","pmid":1,"file":[{"relation":"main_file","date_created":"2018-12-12T10:17:24Z","date_updated":"2020-07-14T12:44:41Z","access_level":"open_access","file_name":"IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf","checksum":"649aee381f30f7ef7e9efa912d41c2e3","file_size":601679,"content_type":"application/pdf","creator":"system","file_id":"5278"}],"ddc":["576","610"],"external_id":{"isi":["000373444700017"],"pmid":["26963490"]},"file_date_updated":"2020-07-14T12:44:41Z","doi":"10.1001/jamapsychiatry.2015.3144","oa_version":"Submitted Version","scopus_import":"1","quality_controlled":"1","title":"How MicroRNAs Are involved in splitting the mind"},{"issue":"2","citation":{"ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” <i>Experimental Mathematics</i>, vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.","chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>. Taylor and Francis, 2016. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>.","apa":"Golmakani, A., Luzzatto, S., &#38; Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>","ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124.","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>, vol. 25, no. 2, Taylor and Francis, 2016, pp. 116–24, doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>.","ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. 2016;25(2):116-124. doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>","short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124."},"date_updated":"2025-09-22T09:07:52Z","language":[{"iso":"eng"}],"abstract":[{"text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.","lang":"eng"}],"project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":25,"page":"116 - 124","publisher":"Taylor and Francis","day":"02","_id":"1254","scopus_import":"1","quality_controlled":"1","title":"Uniform expansivity outside a critical neighborhood in the quadratic family","oa_version":"Preprint","doi":"10.1080/10586458.2015.1048011","external_id":{"arxiv":["1504.00116"],"isi":["000372490500002"]},"acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The  authors  gratefully  acknowledge  the  Department  of\r\nMathematics  of  Kyoto  University  for  providing  access\r\nto  their  server  for  conducting  computations  for  this\r\nproject.","publication":"Experimental Mathematics","article_processing_charge":"No","corr_author":"1","date_published":"2016-04-02T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1504.00116","open_access":"1"}],"ec_funded":1,"publication_status":"published","department":[{"_id":"HeEd"}],"arxiv":1,"isi":1,"date_created":"2018-12-11T11:50:58Z","publist_id":"6071","intvolume":"        25","author":[{"first_name":"Ali","last_name":"Golmakani","full_name":"Golmakani, Ali"},{"last_name":"Luzzatto","first_name":"Stefano","full_name":"Luzzatto, Stefano"},{"last_name":"Pilarczyk","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel"}],"year":"2016","month":"04","status":"public"}]