[{"month":"06","publication_identifier":{"issn":["00335606"]},"quality_controlled":"1","project":[{"name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.7172"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/qmath/haw053","publist_id":"7022","ec_funded":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"TaHa"}],"year":"2017","date_updated":"2021-01-12T08:09:24Z","date_created":"2018-12-11T11:47:55Z","volume":68,"author":[{"full_name":"Davison, Ben","last_name":"Davison","first_name":"Ben","orcid":"0000-0002-8944-4390","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"day":"01","page":"635 - 703","publication":"Quarterly Journal of Mathematics","citation":{"mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053.","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703.","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053.","ama":"Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053"},"date_published":"2017-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs."}],"issue":"2","title":"The critical CoHA of a quiver with potential","status":"public","intvolume":" 68","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"687","oa_version":"Submitted Version"},{"publication_status":"published","status":"public","title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","department":[{"_id":"CaHe"}],"intvolume":" 145","publisher":"Elsevier","_id":"686","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:09:23Z","date_created":"2018-12-11T11:47:55Z","volume":145,"oa_version":"None","author":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology."}],"publist_id":"7024","quality_controlled":"1","page":"32 - 37","publication":"Mechanisms of Development","citation":{"mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.","short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37.","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006.","ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006","ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.","apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006"},"language":[{"iso":"eng"}],"doi":"10.1016/j.mod.2017.03.006","date_published":"2017-06-01T00:00:00Z","scopus_import":1,"month":"06","day":"01","publication_identifier":{"issn":["09254773"]}},{"date_created":"2018-12-11T11:47:56Z","date_updated":"2021-01-12T08:09:29Z","volume":9,"oa_version":"None","author":[{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"status":"public","title":"Rett syndrome modeling goes simian","publication_status":"published","intvolume":" 9","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","_id":"689","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","abstract":[{"lang":"eng","text":"Rett syndrome modeling in monkey mirrors the human disorder."}],"issue":"393","publist_id":"7019","article_number":"eaan8196","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aan8196","date_published":"2017-06-07T00:00:00Z","quality_controlled":"1","publication":"Science Translational Medicine","citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196.","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196.","ama":"Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196."},"month":"06","day":"07","publication_identifier":{"issn":["19466234"]},"scopus_import":1},{"quality_controlled":"1","external_id":{"pmid":["28607047"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1704470114","month":"06","publication_identifier":{"issn":["00278424"]},"publication_status":"published","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1,"date_created":"2018-12-11T11:47:57Z","date_updated":"2023-02-23T12:54:57Z","volume":114,"author":[{"first_name":"Takafumi","last_name":"Miki","full_name":"Miki, Takafumi"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"first_name":"Gerardo","last_name":"Malagon","full_name":"Malagon, Gerardo"},{"full_name":"Gomez, Laura","first_name":"Laura","last_name":"Gomez"},{"last_name":"Tabuchi","first_name":"Katsuhiko","full_name":"Tabuchi, Katsuhiko"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"full_name":"Marty, Alain","last_name":"Marty","first_name":"Alain"}],"file_date_updated":"2020-07-14T12:47:44Z","publist_id":"7013","page":"E5246 - E5255","publication":"PNAS","citation":{"chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114","ieee":"T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114"},"date_published":"2017-06-27T00:00:00Z","scopus_import":1,"day":"27","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","ddc":["570"],"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","status":"public","intvolume":" 114","_id":"693","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_PNAS_Miki.pdf","content_type":"application/pdf","file_size":2721544,"creator":"kschuh","relation":"main_file","file_id":"7223","checksum":"2ab75d554f3df4a34d20fa8040589b7e","date_created":"2020-01-03T13:27:29Z","date_updated":"2020-07-14T12:47:44Z"}],"type":"journal_article","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"issue":"26"},{"publist_id":"7008","file_date_updated":"2020-07-14T12:47:45Z","volume":130,"date_updated":"2021-01-12T08:09:41Z","date_created":"2018-12-11T11:47:58Z","author":[{"full_name":"Veß, Astrid","last_name":"Veß","first_name":"Astrid"},{"full_name":"Blache, Ulrich","last_name":"Blache","first_name":"Ulrich"},{"last_name":"Leitner","first_name":"Laura","full_name":"Leitner, Laura"},{"last_name":"Kurz","first_name":"Angela","full_name":"Kurz, Angela"},{"full_name":"Ehrenpfordt, Anja","first_name":"Anja","last_name":"Ehrenpfordt"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Posern, Guido","first_name":"Guido","last_name":"Posern"}],"publisher":"Company of Biologists","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2017","publication_identifier":{"issn":["00219533"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1242/jcs.200899","quality_controlled":"1","oa":1,"external_id":{"pmid":["28515231"]},"issue":"13","abstract":[{"lang":"eng","text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells."}],"type":"journal_article","file":[{"creator":"dernst","file_size":10847596,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_CellScience_Vess.pdf","checksum":"42c81a0a4fc3128883b391c3af3f74bc","date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-24T09:43:56Z","file_id":"6966","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 130","title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","ddc":["570"],"status":"public","_id":"694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-07-01T00:00:00Z","page":"2172 - 2184","article_type":"original","citation":{"apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899","ieee":"A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899."},"publication":"Journal of Cell Science"},{"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-07-01T00:00:00Z","citation":{"ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39","apa":"Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39."},"abstract":[{"text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","file":[{"creator":"system","content_type":"application/pdf","file_size":601004,"file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:08:40Z","checksum":"e95618a001692f1af2d68f5fde43bc1f","file_id":"4701","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"893","status":"public","title":"Non uniform attacks against pseudoentropy","ddc":["005"],"intvolume":" 80","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"697","month":"07","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Warsaw, Poland","start_date":"2017-07-10","end_date":"2017-07-14"},"doi":"10.4230/LIPIcs.ICALP.2017.39","quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:46Z","ec_funded":1,"publist_id":"7003","article_number":"39","date_created":"2018-12-11T11:47:59Z","date_updated":"2021-01-12T08:11:15Z","volume":80,"author":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"year":"2017"},{"page":"1997 - 2009","citation":{"ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","apa":"Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825.","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825."},"publication":"Molecular Biology of the Cell","date_published":"2017-07-07T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"07","intvolume":" 28","title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","ddc":["519"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"698","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","content_type":"application/pdf","file_size":1086097,"creator":"system","relation":"main_file","file_id":"4844","checksum":"de01dac9e30970cfa6ae902480a4e04d","date_created":"2018-12-12T10:10:53Z","date_updated":"2020-07-14T12:47:46Z"}],"pubrep_id":"892","type":"journal_article","issue":"14","abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"project":[{"name":"Gaussian Graphical Models: Theory and Applications","call_identifier":"FWF","_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1091/mbc.E16-12-0825","publication_identifier":{"issn":["10591524"]},"month":"07","department":[{"_id":"CaUh"}],"publisher":"American Society for Cell Biology","publication_status":"published","year":"2017","volume":28,"date_updated":"2021-01-12T08:11:17Z","date_created":"2018-12-11T11:47:59Z","author":[{"last_name":"Wang","first_name":"Yejun","full_name":"Wang, Yejun"},{"first_name":"Mallika","last_name":"Nagarajan","full_name":"Nagarajan, Mallika"},{"last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline"},{"last_name":"Shivashankar","first_name":"Gv","full_name":"Shivashankar, Gv"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publist_id":"7001","file_date_updated":"2020-07-14T12:47:46Z"},{"publist_id":"7002","date_created":"2018-12-11T11:48:00Z","date_updated":"2021-01-12T08:11:21Z","volume":114,"author":[{"full_name":"Veller, Carl","first_name":"Carl","last_name":"Veller"},{"full_name":"Hayward, Laura","first_name":"Laura","last_name":"Hayward"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1,"month":"07","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1702020114","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"oa":1,"external_id":{"pmid":["28630336"]},"abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"issue":"27","type":"journal_article","oa_version":"Submitted Version","title":"The red queen and king in finite populations","status":"public","intvolume":" 114","_id":"699","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"03","scopus_import":1,"date_published":"2017-07-03T00:00:00Z","page":"E5396 - E5405","publication":"PNAS","citation":{"ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","apa":"Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114."}},{"day":"12","scopus_import":1,"date_published":"2017-07-12T00:00:00Z","citation":{"chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404.","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404.","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404"},"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","issue":"1","abstract":[{"lang":"eng","text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs."}],"type":"journal_article","oa_version":"Submitted Version","_id":"700","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 96","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","status":"public","publication_identifier":{"issn":["24700045"]},"month":"07","doi":"10.1103/PhysRevE.96.012404","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1612.07061.pdf"}],"project":[{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","call_identifier":"H2020"}],"quality_controlled":"1","publist_id":"6997","ec_funded":1,"article_number":"012404","author":[{"last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"last_name":"Salari","first_name":"Vahid","full_name":"Salari, Vahid"},{"last_name":"Tuszynski","first_name":"Jack","full_name":"Tuszynski, Jack"},{"first_name":"Michal","last_name":"Cifra","full_name":"Cifra, Michal"},{"full_name":"Simon, Christoph","last_name":"Simon","first_name":"Christoph"}],"volume":96,"date_created":"2018-12-11T11:48:00Z","date_updated":"2023-02-23T12:56:35Z","year":"2017","publisher":"American Institute of Physics","department":[{"_id":"JoFi"}],"publication_status":"published"},{"page":"1-44","publication":"The Electronic Journal of Combinatorics","citation":{"chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44.","apa":"Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44."},"date_published":"2017-07-14T00:00:00Z","day":"14","has_accepted_license":"1","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","status":"public","ddc":["500"],"intvolume":" 24","_id":"701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"checksum":"a431e573e31df13bc0f66de3061006ec","date_created":"2018-12-12T10:14:25Z","date_updated":"2020-07-14T12:47:47Z","file_id":"5077","relation":"main_file","creator":"system","file_size":544042,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf"}],"pubrep_id":"984","type":"journal_article","abstract":[{"lang":"eng","text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2."}],"issue":"3","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["10778926"]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"International Press","year":"2017","date_updated":"2021-01-12T08:11:28Z","date_created":"2018-12-11T11:48:00Z","volume":24,"author":[{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"}],"file_date_updated":"2020-07-14T12:47:47Z","publist_id":"6996"}]