[{"author":[{"first_name":"M Pawan","last_name":"Kumar","full_name":"Kumar, M Pawan"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"full_name":"Torr, Philip H","last_name":"Torr","first_name":"Philip"}],"_id":"3197","type":"journal_article","extern":1,"publication":"Journal of Machine Learning Research","citation":{"ama":"Kumar MP, Kolmogorov V, Torr P. An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. 2009;10:71-106.","mla":"Kumar, M. Pawan, et al. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>, vol. 10, Microtome Publishing, 2009, pp. 71–106.","ista":"Kumar MP, Kolmogorov V, Torr P. 2009. An analysis of convex relaxations for MAP estimation of discrete MRFs. Journal of Machine Learning Research. 10, 71–106.","ieee":"M. P. Kumar, V. Kolmogorov, and P. Torr, “An analysis of convex relaxations for MAP estimation of discrete MRFs,” <i>Journal of Machine Learning Research</i>, vol. 10. Microtome Publishing, pp. 71–106, 2009.","chicago":"Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>. Microtome Publishing, 2009.","short":"M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research 10 (2009) 71–106.","apa":"Kumar, M. P., Kolmogorov, V., &#38; Torr, P. (2009). An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. Microtome Publishing."},"quality_controlled":0,"date_created":"2018-12-11T12:01:57Z","intvolume":"        10","status":"public","volume":10,"title":"An analysis of convex relaxations for MAP estimation of discrete MRFs","year":"2009","day":"01","page":"71 - 106","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00773608"}],"publisher":"Microtome Publishing","date_updated":"2021-01-12T07:41:44Z","publist_id":"3484","publication_status":"published","month":"01","date_published":"2009-01-01T00:00:00Z","oa":1,"abstract":[{"lang":"eng","text":"The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.\n\nWe show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches."}]},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1534-5807"]},"year":"2009","intvolume":"        17","pmid":1,"extern":"1","quality_controlled":"1","doi":"10.1016/j.devcel.2009.10.007","citation":{"ama":"Hetzer M, Wente SR. Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes. <i>Developmental Cell</i>. 2009;17(5):606-616. doi:<a href=\"https://doi.org/10.1016/j.devcel.2009.10.007\">10.1016/j.devcel.2009.10.007</a>","mla":"Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis and Organization of the Nuclear Membrane and Pore Complexes.” <i>Developmental Cell</i>, vol. 17, no. 5, Elsevier, 2009, pp. 606–16, doi:<a href=\"https://doi.org/10.1016/j.devcel.2009.10.007\">10.1016/j.devcel.2009.10.007</a>.","ista":"Hetzer M, Wente SR. 2009. Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes. Developmental Cell. 17(5), 606–616.","ieee":"M. Hetzer and S. R. Wente, “Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes,” <i>Developmental Cell</i>, vol. 17, no. 5. Elsevier, pp. 606–616, 2009.","chicago":"Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis and Organization of the Nuclear Membrane and Pore Complexes.” <i>Developmental Cell</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.devcel.2009.10.007\">https://doi.org/10.1016/j.devcel.2009.10.007</a>.","short":"M. Hetzer, S.R. Wente, Developmental Cell 17 (2009) 606–616.","apa":"Hetzer, M., &#38; Wente, S. R. (2009). Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2009.10.007\">https://doi.org/10.1016/j.devcel.2009.10.007</a>"},"abstract":[{"text":"Over the last decade, the nuclear envelope (NE) has emerged as a key component in the organization and function of the nuclear genome. As many as 100 different proteins are thought to specifically localize to this double membrane that separates the cytoplasm and the nucleoplasm of eukaryotic cells. Selective portals through the NE are formed at sites where the inner and outer nuclear membranes are fused, and the coincident assembly of ∼30 proteins into nuclear pore complexes occurs. These nuclear pore complexes are essential for the control of nucleocytoplasmic exchange. Many of the NE and nuclear pore proteins are thought to play crucial roles in gene regulation and thus are increasingly linked to human diseases.","lang":"eng"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"oa":1,"external_id":{"pmid":["19922866"]},"page":"606-616","day":"17","status":"public","volume":17,"title":"Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes","publication":"Developmental Cell","_id":"11103","issue":"5","article_processing_charge":"No","type":"journal_article","oa_version":"Published Version","date_created":"2022-04-07T07:53:45Z","author":[{"last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"},{"last_name":"Wente","first_name":"Susan R.","full_name":"Wente, Susan R."}],"article_type":"review","month":"11","date_published":"2009-11-17T00:00:00Z","date_updated":"2022-07-18T08:55:01Z","publisher":"Elsevier","publication_status":"published","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2009.10.007"}],"scopus_import":"1"},{"author":[{"first_name":"Maya","last_name":"Capelson","full_name":"Capelson, Maya"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER"}],"date_created":"2022-04-07T07:54:06Z","oa_version":"Published Version","issue":"7","_id":"11105","article_processing_charge":"No","type":"journal_article","publication":"EMBO reports","title":"The role of nuclear pores in gene regulation, development and disease","volume":10,"status":"public","day":"01","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/embor.2009.147","open_access":"1"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published","publisher":"EMBO","date_updated":"2022-07-18T08:42:44Z","date_published":"2009-07-01T00:00:00Z","month":"07","article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1038/embor.2009.176","relation":"erratum"}]},"citation":{"ama":"Capelson M, Hetzer M. The role of nuclear pores in gene regulation, development and disease. <i>EMBO reports</i>. 2009;10(7):697-705. doi:<a href=\"https://doi.org/10.1038/embor.2009.147\">10.1038/embor.2009.147</a>","mla":"Capelson, Maya, and Martin Hetzer. “The Role of Nuclear Pores in Gene Regulation, Development and Disease.” <i>EMBO Reports</i>, vol. 10, no. 7, EMBO, 2009, pp. 697–705, doi:<a href=\"https://doi.org/10.1038/embor.2009.147\">10.1038/embor.2009.147</a>.","ista":"Capelson M, Hetzer M. 2009. The role of nuclear pores in gene regulation, development and disease. EMBO reports. 10(7), 697–705.","ieee":"M. Capelson and M. Hetzer, “The role of nuclear pores in gene regulation, development and disease,” <i>EMBO reports</i>, vol. 10, no. 7. EMBO, pp. 697–705, 2009.","short":"M. Capelson, M. Hetzer, EMBO Reports 10 (2009) 697–705.","chicago":"Capelson, Maya, and Martin Hetzer. “The Role of Nuclear Pores in Gene Regulation, Development and Disease.” <i>EMBO Reports</i>. EMBO, 2009. <a href=\"https://doi.org/10.1038/embor.2009.147\">https://doi.org/10.1038/embor.2009.147</a>.","apa":"Capelson, M., &#38; Hetzer, M. (2009). The role of nuclear pores in gene regulation, development and disease. <i>EMBO Reports</i>. EMBO. <a href=\"https://doi.org/10.1038/embor.2009.147\">https://doi.org/10.1038/embor.2009.147</a>"},"doi":"10.1038/embor.2009.147","quality_controlled":"1","extern":"1","pmid":1,"intvolume":"        10","year":"2009","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"page":"697-705","external_id":{"pmid":["19543230"]},"oa":1,"keyword":["Genetics","Molecular Biology","Biochemistry"],"abstract":[{"text":"Nuclear-pore complexes (NPCs) are large protein channels that span the nuclear envelope (NE), which is a double membrane that encloses the nuclear genome of eukaryotes. Each of the typically 2,000–4,000 pores in the NE of vertebrate cells is composed of multiple copies of 30 different proteins known as nucleoporins. The evolutionarily conserved NPC proteins have the well-characterized function of mediating the transport of molecules between the nucleoplasm and the cytoplasm. Mutations in nucleoporins are often linked to specific developmental defects and disease, and the resulting phenotypes are usually interpreted as the consequences of perturbed nuclear transport activity. However, recent evidence suggests that NPCs have additional functions in chromatin organization and gene regulation, some of which might be independent of nuclear transport. Here, we review the transport-dependent and transport-independent roles of NPCs in the regulation of nuclear function and gene expression.","lang":"eng"}]},{"main_file_link":[{"url":"https://doi.org/10.1083/jcb.200901106","open_access":"1"}],"scopus_import":"1","article_type":"original","month":"07","date_published":"2009-07-20T00:00:00Z","date_updated":"2022-07-18T08:58:35Z","publisher":"Rockefeller University Press","publication_status":"published","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication":"Journal of Cell Biology","issue":"2","_id":"11106","type":"journal_article","article_processing_charge":"No","oa_version":"Published Version","date_created":"2022-04-07T07:54:18Z","author":[{"full_name":"Anderson, Daniel J.","last_name":"Anderson","first_name":"Daniel J."},{"full_name":"Vargas, Jesse D.","first_name":"Jesse D.","last_name":"Vargas"},{"last_name":"Hsiao","first_name":"Joshua P.","full_name":"Hsiao, Joshua P."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"day":"20","status":"public","volume":186,"title":"Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo","external_id":{"pmid":["19620630"]},"page":"183-191","keyword":["Cell Biology"],"abstract":[{"text":"Formation of the nuclear envelope (NE) around segregated chromosomes occurs by the reshaping of the endoplasmic reticulum (ER), a reservoir for disassembled nuclear membrane components during mitosis. In this study, we show that inner nuclear membrane proteins such as lamin B receptor (LBR), MAN1, Lap2β, and the trans-membrane nucleoporins Ndc1 and POM121 drive the spreading of ER membranes into the emerging NE via their capacity to bind chromatin in a collaborative manner. Despite their redundant functions, decreasing the levels of any of these trans-membrane proteins by RNAi-mediated knockdown delayed NE formation, whereas increasing the levels of any of them had the opposite effect. Furthermore, acceleration of NE formation interferes with chromosome separation during mitosis, indicating that the time frame over which chromatin becomes membrane enclosed is physiologically relevant and regulated. These data suggest that functionally distinct classes of chromatin-interacting membrane proteins, which are present at nonsaturating levels, collaborate to rapidly reestablish the nuclear compartment at the end of mitosis.","lang":"eng"}],"oa":1,"extern":"1","quality_controlled":"1","doi":"10.1083/jcb.200901106","citation":{"mla":"Anderson, Daniel J., et al. “Recruitment of Functionally Distinct Membrane Proteins to Chromatin Mediates Nuclear Envelope Formation in Vivo.” <i>Journal of Cell Biology</i>, vol. 186, no. 2, Rockefeller University Press, 2009, pp. 183–91, doi:<a href=\"https://doi.org/10.1083/jcb.200901106\">10.1083/jcb.200901106</a>.","ista":"Anderson DJ, Vargas JD, Hsiao JP, Hetzer M. 2009. Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. Journal of Cell Biology. 186(2), 183–191.","ieee":"D. J. Anderson, J. D. Vargas, J. P. Hsiao, and M. Hetzer, “Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo,” <i>Journal of Cell Biology</i>, vol. 186, no. 2. Rockefeller University Press, pp. 183–191, 2009.","chicago":"Anderson, Daniel J., Jesse D. Vargas, Joshua P. Hsiao, and Martin Hetzer. “Recruitment of Functionally Distinct Membrane Proteins to Chromatin Mediates Nuclear Envelope Formation in Vivo.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2009. <a href=\"https://doi.org/10.1083/jcb.200901106\">https://doi.org/10.1083/jcb.200901106</a>.","short":"D.J. Anderson, J.D. Vargas, J.P. Hsiao, M. Hetzer, Journal of Cell Biology 186 (2009) 183–191.","apa":"Anderson, D. J., Vargas, J. D., Hsiao, J. P., &#38; Hetzer, M. (2009). Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.200901106\">https://doi.org/10.1083/jcb.200901106</a>","ama":"Anderson DJ, Vargas JD, Hsiao JP, Hetzer M. Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. <i>Journal of Cell Biology</i>. 2009;186(2):183-191. doi:<a href=\"https://doi.org/10.1083/jcb.200901106\">10.1083/jcb.200901106</a>"},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1083/jcb.20090110620090903c"}]},"publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"language":[{"iso":"eng"}],"year":"2009","intvolume":"       186","pmid":1},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1083/jcb.200806174"}],"date_updated":"2022-07-18T08:55:05Z","publisher":"Rockefeller University Press","publication_status":"published","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_type":"original","month":"03","date_published":"2009-03-09T00:00:00Z","author":[{"full_name":"Dawson, T. Renee","first_name":"T. Renee","last_name":"Dawson"},{"first_name":"Michelle D.","last_name":"Lazarus","full_name":"Lazarus, Michelle D."},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"},{"full_name":"Wente, Susan R.","first_name":"Susan R.","last_name":"Wente"}],"publication":"Journal of Cell Biology","issue":"5","_id":"11107","article_processing_charge":"No","type":"journal_article","oa_version":"Published Version","date_created":"2022-04-07T07:54:44Z","status":"public","title":"ER membrane–bending proteins are necessary for de novo nuclear pore formation","volume":184,"day":"09","external_id":{"pmid":["19273614"]},"page":"659-675","abstract":[{"text":"Nucleocytoplasmic transport occurs exclusively through nuclear pore complexes (NPCs) embedded in pores formed by inner and outer nuclear membrane fusion. The mechanism for de novo pore and NPC biogenesis remains unclear. Reticulons (RTNs) and Yop1/DP1 are conserved membrane protein families required to form and maintain the tubular endoplasmic reticulum (ER) and the postmitotic nuclear envelope. In this study, we report that members of the RTN and Yop1/DP1 families are required for nuclear pore formation. Analysis of Saccharomyces cerevisiae prp20-G282S and nup133Δ NPC assembly mutants revealed perturbations in Rtn1–green fluorescent protein (GFP) and Yop1-GFP ER distribution and colocalization to NPC clusters. Combined deletion of RTN1 and YOP1 resulted in NPC clustering, nuclear import defects, and synthetic lethality with the additional absence of Pom34, Pom152, and Nup84 subcomplex members. We tested for a direct role in NPC biogenesis using Xenopus laevis in vitro assays and found that anti-Rtn4a antibodies specifically inhibited de novo nuclear pore formation. We hypothesize that these ER membrane–bending proteins mediate early NPC assembly steps.","lang":"eng"}],"keyword":["Cell Biology"],"oa":1,"extern":"1","quality_controlled":"1","doi":"10.1083/jcb.200806174","citation":{"ieee":"T. R. Dawson, M. D. Lazarus, M. Hetzer, and S. R. Wente, “ER membrane–bending proteins are necessary for de novo nuclear pore formation,” <i>Journal of Cell Biology</i>, vol. 184, no. 5. Rockefeller University Press, pp. 659–675, 2009.","ista":"Dawson TR, Lazarus MD, Hetzer M, Wente SR. 2009. ER membrane–bending proteins are necessary for de novo nuclear pore formation. Journal of Cell Biology. 184(5), 659–675.","mla":"Dawson, T. Renee, et al. “ER Membrane–Bending Proteins Are Necessary for de Novo Nuclear Pore Formation.” <i>Journal of Cell Biology</i>, vol. 184, no. 5, Rockefeller University Press, 2009, pp. 659–75, doi:<a href=\"https://doi.org/10.1083/jcb.200806174\">10.1083/jcb.200806174</a>.","apa":"Dawson, T. R., Lazarus, M. D., Hetzer, M., &#38; Wente, S. R. (2009). ER membrane–bending proteins are necessary for de novo nuclear pore formation. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.200806174\">https://doi.org/10.1083/jcb.200806174</a>","short":"T.R. Dawson, M.D. Lazarus, M. Hetzer, S.R. Wente, Journal of Cell Biology 184 (2009) 659–675.","chicago":"Dawson, T. Renee, Michelle D. Lazarus, Martin Hetzer, and Susan R. Wente. “ER Membrane–Bending Proteins Are Necessary for de Novo Nuclear Pore Formation.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2009. <a href=\"https://doi.org/10.1083/jcb.200806174\">https://doi.org/10.1083/jcb.200806174</a>.","ama":"Dawson TR, Lazarus MD, Hetzer M, Wente SR. ER membrane–bending proteins are necessary for de novo nuclear pore formation. <i>Journal of Cell Biology</i>. 2009;184(5):659-675. doi:<a href=\"https://doi.org/10.1083/jcb.200806174\">10.1083/jcb.200806174</a>"},"intvolume":"       184","pmid":1,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"language":[{"iso":"eng"}],"year":"2009"},{"external_id":{"pmid":["19167330"]},"page":"284-295","oa":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"abstract":[{"lang":"eng","text":"In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis and reassemble into the newly forming nuclei. However, the fate of nuclear pores in postmitotic cells is unknown. Here, we show that NPCs, unlike other nuclear structures, do not turn over in differentiated cells. While a subset of NPC components, like Nup153 and Nup50, are continuously exchanged, scaffold nucleoporins, like the Nup107/160 complex, are extremely long-lived and remain incorporated in the nuclear membrane during the entire cellular life span. Besides the lack of nucleoporin expression and NPC turnover, we discovered an age-related deterioration of NPCs, leading to an increase in nuclear permeability and the leaking of cytoplasmic proteins into the nucleus. Our finding that nuclear “leakiness” is dramatically accelerated during aging and that a subset of nucleoporins is oxidatively damaged in old cells suggests that the accumulation of damage at the NPC might be a crucial aging event."}],"extern":"1","citation":{"apa":"D’Angelo, M. A., Raices, M., Panowski, S. H., &#38; Hetzer, M. (2009). Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2008.11.037\">https://doi.org/10.1016/j.cell.2008.11.037</a>","chicago":"D’Angelo, Maximiliano A., Marcela Raices, Siler H. Panowski, and Martin Hetzer. “Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells.” <i>Cell</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.cell.2008.11.037\">https://doi.org/10.1016/j.cell.2008.11.037</a>.","short":"M.A. D’Angelo, M. Raices, S.H. Panowski, M. Hetzer, Cell 136 (2009) 284–295.","ista":"D’Angelo MA, Raices M, Panowski SH, Hetzer M. 2009. Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell. 136(2), 284–295.","ieee":"M. A. D’Angelo, M. Raices, S. H. Panowski, and M. Hetzer, “Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells,” <i>Cell</i>, vol. 136, no. 2. Elsevier, pp. 284–295, 2009.","mla":"D’Angelo, Maximiliano A., et al. “Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells.” <i>Cell</i>, vol. 136, no. 2, Elsevier, 2009, pp. 284–95, doi:<a href=\"https://doi.org/10.1016/j.cell.2008.11.037\">10.1016/j.cell.2008.11.037</a>.","ama":"D’Angelo MA, Raices M, Panowski SH, Hetzer M. Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. <i>Cell</i>. 2009;136(2):284-295. doi:<a href=\"https://doi.org/10.1016/j.cell.2008.11.037\">10.1016/j.cell.2008.11.037</a>"},"doi":"10.1016/j.cell.2008.11.037","quality_controlled":"1","pmid":1,"intvolume":"       136","publication_identifier":{"issn":["0092-8674"]},"language":[{"iso":"eng"}],"year":"2009","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2008.11.037"}],"publisher":"Elsevier","date_updated":"2022-07-18T08:55:29Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published","date_published":"2009-01-23T00:00:00Z","month":"01","article_type":"original","author":[{"full_name":"D'Angelo, Maximiliano A.","first_name":"Maximiliano A.","last_name":"D'Angelo"},{"full_name":"Raices, Marcela","first_name":"Marcela","last_name":"Raices"},{"full_name":"Panowski, Siler H.","last_name":"Panowski","first_name":"Siler H."},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER"}],"article_processing_charge":"No","_id":"11108","type":"journal_article","issue":"2","publication":"Cell","date_created":"2022-04-07T07:54:52Z","oa_version":"Published Version","status":"public","title":"Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells","volume":136,"day":"23"},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-17T08:57:16Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2009-02-01T00:00:00Z","month":"02","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.STACS.2009.1809","open_access":"1"}],"title":"A comparison of techniques for sampling web pages","volume":3,"status":"public","day":"01","author":[{"full_name":"Baykan,  Eda","first_name":" Eda","last_name":"Baykan"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Keller, Stefan F.","last_name":"Keller","first_name":"Stefan F."},{"full_name":"de Castelberg, Sebastian","first_name":"Sebastian","last_name":"de Castelberg"},{"full_name":"Kinzler, Markus","first_name":"Markus","last_name":"Kinzler"}],"date_created":"2022-08-18T06:57:25Z","oa_version":"Published Version","publication":"26th International Symposium on Theoretical Aspects of Computer Science","_id":"11912","type":"conference","article_processing_charge":"No","abstract":[{"text":"As the World Wide Web is growing rapidly, it is getting increasingly challenging to gather representative information about it. Instead of crawling the web exhaustively one has to resort to other techniques like sampling to determine the properties of the web. A uniform random sample of the web would be useful to determine the percentage of web pages in a specific language, on a topic or in a top level domain. Unfortunately, no approach has been shown to sample the web pages in an unbiased way. Three promising web sampling algorithms are based on random walks. They each have been evaluated individually, but making a comparison on different data sets is not possible. We directly compare these algorithms in this paper. We performed three random walks on the web under the same conditions and analyzed their outcomes in detail. We discuss the strengths and the weaknesses of each algorithm and propose improvements based on experimental results.","lang":"eng"}],"oa":1,"alternative_title":["LIPIcs"],"page":"13-30","external_id":{"arxiv":["0902.1604"]},"intvolume":"         3","arxiv":1,"year":"2009","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-939897-09-5"]},"language":[{"iso":"eng"}],"conference":{"location":"Freiburg, Germany","end_date":"2009-02-28","start_date":"2009-02-26","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"quality_controlled":"1","citation":{"apa":"Baykan,  Eda, Henzinger, M. H., Keller, S. F., de Castelberg, S., &#38; Kinzler, M. (2009). A comparison of techniques for sampling web pages. In <i>26th International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 3, pp. 13–30). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.STACS.2009.1809\">https://doi.org/10.4230/LIPICS.STACS.2009.1809</a>","short":"Eda Baykan, M.H. Henzinger, S.F. Keller, S. de Castelberg, M. Kinzler, in:, 26th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30.","chicago":"Baykan,  Eda, Monika H Henzinger, Stefan F. Keller, Sebastian de Castelberg, and Markus Kinzler. “A Comparison of Techniques for Sampling Web Pages.” In <i>26th International Symposium on Theoretical Aspects of Computer Science</i>, 3:13–30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009. <a href=\"https://doi.org/10.4230/LIPICS.STACS.2009.1809\">https://doi.org/10.4230/LIPICS.STACS.2009.1809</a>.","ieee":"Eda Baykan, M. H. Henzinger, S. F. Keller, S. de Castelberg, and M. Kinzler, “A comparison of techniques for sampling web pages,” in <i>26th International Symposium on Theoretical Aspects of Computer Science</i>, Freiburg, Germany, 2009, vol. 3, pp. 13–30.","ista":"Baykan  Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. 2009. A comparison of techniques for sampling web pages. 26th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 3, 13–30.","mla":"Baykan,  Eda, et al. “A Comparison of Techniques for Sampling Web Pages.” <i>26th International Symposium on Theoretical Aspects of Computer Science</i>, vol. 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30, doi:<a href=\"https://doi.org/10.4230/LIPICS.STACS.2009.1809\">10.4230/LIPICS.STACS.2009.1809</a>.","ama":"Baykan  Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. A comparison of techniques for sampling web pages. In: <i>26th International Symposium on Theoretical Aspects of Computer Science</i>. Vol 3. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2009:13-30. doi:<a href=\"https://doi.org/10.4230/LIPICS.STACS.2009.1809\">10.4230/LIPICS.STACS.2009.1809</a>"},"doi":"10.4230/LIPICS.STACS.2009.1809","extern":"1"},{"extern":1,"publication":"Nature","type":"journal_article","_id":"1763","issue":"7202","quality_controlled":0,"date_created":"2018-12-11T11:53:53Z","doi":"10.1038/nature07112","citation":{"mla":"Fink, Johannes M., et al. “Climbing the Jaynes-Cummings Ladder and Observing Its √n Nonlinearity in a Cavity QED System.” <i>Nature</i>, vol. 454, no. 7202, Nature Publishing Group, 2008, pp. 315–18, doi:<a href=\"https://doi.org/10.1038/nature07112\">10.1038/nature07112</a>.","ista":"Fink JM, Göppl M, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008. Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. Nature. 454(7202), 315–318.","ieee":"J. M. Fink <i>et al.</i>, “Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system,” <i>Nature</i>, vol. 454, no. 7202. Nature Publishing Group, pp. 315–318, 2008.","short":"J.M. Fink, M. Göppl, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff, Nature 454 (2008) 315–318.","chicago":"Fink, Johannes M, M Göppl, Matthias Baur, R Bianchetti, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Climbing the Jaynes-Cummings Ladder and Observing Its √n Nonlinearity in a Cavity QED System.” <i>Nature</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/nature07112\">https://doi.org/10.1038/nature07112</a>.","apa":"Fink, J. M., Göppl, M., Baur, M., Bianchetti, R., Leek, P., Blais, A., &#38; Wallraff, A. (2008). Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature07112\">https://doi.org/10.1038/nature07112</a>","ama":"Fink JM, Göppl M, Baur M, et al. Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. <i>Nature</i>. 2008;454(7202):315-318. doi:<a href=\"https://doi.org/10.1038/nature07112\">10.1038/nature07112</a>"},"acknowledgement":"This work was supported by SNF and ETHZ. P.J.L. was supported by the EU with an MC-EIF. A.B. was supported by NSERC, CIFAR and FQRNT","author":[{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X"},{"full_name":"Göppl, M","first_name":"M","last_name":"Göppl"},{"full_name":"Baur, Matthias P","first_name":"Matthias","last_name":"Baur"},{"first_name":"R","last_name":"Bianchetti","full_name":"Bianchetti, R"},{"full_name":"Leek, Peter J","first_name":"Peter","last_name":"Leek"},{"first_name":"Alexandre","last_name":"Blais","full_name":"Blais, Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"year":"2008","day":"17","intvolume":"       454","status":"public","volume":454,"title":"Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0902.1827"}],"page":"315 - 318","month":"07","date_published":"2008-07-17T00:00:00Z","abstract":[{"text":"The field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has gained new momentum by recent reports of quantum optical experiments with solid-state semiconducting and superconducting systems. In cavity QED, the observation of the vacuum Rabi mode splitting is used to investigate the nature of matter-light interaction at a quantum-mechanical level. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED set-up, in which very strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems also provide a natural quantum interface between flying qubits (photons) and stationary qubits for applications in quantum information processing and communication.","lang":"eng"}],"oa":1,"publist_id":"5358","date_updated":"2021-01-12T06:53:03Z","publisher":"Nature Publishing Group","publication_status":"published"},{"oa":1,"abstract":[{"text":"High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits.","lang":"eng"}],"month":"01","date_published":"2008-01-01T00:00:00Z","publication_status":"published","publisher":"American Institute of Physics","date_updated":"2021-01-12T06:53:03Z","publist_id":"5355","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0807.4094"}],"day":"01","year":"2008","title":"Coplanar waveguide resonators for circuit quantum electrodynamics","volume":104,"status":"public","intvolume":"       104","citation":{"ama":"Göppl M, Fragner A, Baur M, et al. Coplanar waveguide resonators for circuit quantum electrodynamics. <i>Journal of Applied Physics</i>. 2008;104(11). doi:<a href=\"https://doi.org/10.1063/1.3010859\">10.1063/1.3010859</a>","apa":"Göppl, M., Fragner, A., Baur, M., Bianchetti, R., Filipp, S., Fink, J. M., … Wallraff, A. (2008). Coplanar waveguide resonators for circuit quantum electrodynamics. <i>Journal of Applied Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.3010859\">https://doi.org/10.1063/1.3010859</a>","short":"M. Göppl, A. Fragner, M. Baur, R. Bianchetti, S. Filipp, J.M. Fink, P. Leek, G. Puebla, L. Steffen, A. Wallraff, Journal of Applied Physics 104 (2008).","chicago":"Göppl, M, A Fragner, Matthias Baur, R Bianchetti, Stefan Filipp, Johannes M Fink, Peter Leek, G Puebla, L. Steffen, and Andreas Wallraff. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.” <i>Journal of Applied Physics</i>. American Institute of Physics, 2008. <a href=\"https://doi.org/10.1063/1.3010859\">https://doi.org/10.1063/1.3010859</a>.","ieee":"M. Göppl <i>et al.</i>, “Coplanar waveguide resonators for circuit quantum electrodynamics,” <i>Journal of Applied Physics</i>, vol. 104, no. 11. American Institute of Physics, 2008.","ista":"Göppl M, Fragner A, Baur M, Bianchetti R, Filipp S, Fink JM, Leek P, Puebla G, Steffen L, Wallraff A. 2008. Coplanar waveguide resonators for circuit quantum electrodynamics. Journal of Applied Physics. 104(11).","mla":"Göppl, M., et al. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.” <i>Journal of Applied Physics</i>, vol. 104, no. 11, American Institute of Physics, 2008, doi:<a href=\"https://doi.org/10.1063/1.3010859\">10.1063/1.3010859</a>."},"doi":"10.1063/1.3010859","quality_controlled":0,"date_created":"2018-12-11T11:53:53Z","issue":"11","_id":"1765","type":"journal_article","publication":"Journal of Applied Physics","extern":1,"author":[{"last_name":"Göppl","first_name":"M","full_name":"Göppl, M"},{"full_name":"Fragner, A","first_name":"A","last_name":"Fragner"},{"last_name":"Baur","first_name":"Matthias","full_name":"Baur, Matthias P"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Johannes Fink"},{"first_name":"Peter","last_name":"Leek","full_name":"Leek, Peter J"},{"last_name":"Puebla","first_name":"G","full_name":"Puebla, G"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"}],"acknowledgement":"This work was supported by Swiss National Fund (SNF) and ETH Zürich. P.J.L. was supported by the EC with a MC-EIF"},{"main_file_link":[{"url":"http://arxiv.org/abs/math/0612668","open_access":"1"}],"page":"555 - 624","month":"12","date_published":"2008-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"We calculate the E-polynomials of certain twisted GL(n,ℂ)-character varieties Mn of Riemann surfaces by counting points over finite fields using the character table of the finite group of Lie-type GL(n, q) and a theorem proved in the appendix by N. Katz. We deduce from this calculation several geometric results, for example, the value of the topological Euler characteristic of the associated PGL(n,ℂ)-character variety. The calculation also leads to several conjectures about the cohomology of Mn: an explicit conjecture for its mixed Hodge polynomial; a conjectured curious hard Lefschetz theorem and a conjecture relating the pure part to absolutely indecomposable representations of a certain quiver. We prove these conjectures for n=2."}],"oa":1,"date_updated":"2021-01-12T06:50:54Z","publist_id":"5732","publisher":"Springer","publication_status":"published","publication":"Inventiones Mathematicae","extern":1,"type":"journal_article","_id":"1460","issue":"3","date_created":"2018-12-11T11:52:09Z","quality_controlled":0,"citation":{"ama":"Hausel T, Rodríguez Villegas F. Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz. <i>Inventiones Mathematicae</i>. 2008;174(3):555-624. doi:<a href=\"https://doi.org/10.1007/s00222-008-0142-x\">10.1007/s00222-008-0142-x</a>","mla":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Mixed Hodge Polynomials of Character Varieties: With an Appendix by Nicholas M. Katz.” <i>Inventiones Mathematicae</i>, vol. 174, no. 3, Springer, 2008, pp. 555–624, doi:<a href=\"https://doi.org/10.1007/s00222-008-0142-x\">10.1007/s00222-008-0142-x</a>.","ieee":"T. Hausel and F. Rodríguez Villegas, “Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz,” <i>Inventiones Mathematicae</i>, vol. 174, no. 3. Springer, pp. 555–624, 2008.","ista":"Hausel T, Rodríguez Villegas F. 2008. Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz. Inventiones Mathematicae. 174(3), 555–624.","short":"T. Hausel, F. Rodríguez Villegas, Inventiones Mathematicae 174 (2008) 555–624.","chicago":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Mixed Hodge Polynomials of Character Varieties: With an Appendix by Nicholas M. Katz.” <i>Inventiones Mathematicae</i>. Springer, 2008. <a href=\"https://doi.org/10.1007/s00222-008-0142-x\">https://doi.org/10.1007/s00222-008-0142-x</a>.","apa":"Hausel, T., &#38; Rodríguez Villegas, F. (2008). Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz. <i>Inventiones Mathematicae</i>. Springer. <a href=\"https://doi.org/10.1007/s00222-008-0142-x\">https://doi.org/10.1007/s00222-008-0142-x</a>"},"doi":"10.1007/s00222-008-0142-x","acknowledgement":"The first author was supported by NSF grants DMS-0305505 and DMS- 0604775 an Alfred Sloan Fellowship and a Royal Society University Research Fellowship. The second author was supported by an NSF grant DMS-0200605.","author":[{"full_name":"Tamas Hausel","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"},{"first_name":"Fernando","last_name":"Rodríguez Villegas","full_name":"Rodríguez Villegas, Fernando"}],"year":"2008","day":"01","status":"public","intvolume":"       174","volume":174,"title":"Mixed Hodge polynomials of character varieties: With an appendix by Nicholas M. Katz"},{"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:21Z","publisher":"Proceedings of the National Academy of Sciences","month":"06","date_published":"2008-06-10T00:00:00Z","title":"A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans","volume":105,"status":"public","day":"10","author":[{"first_name":"A. J.","last_name":"Bretscher","full_name":"Bretscher, A. J."},{"first_name":"K. E.","last_name":"Busch","full_name":"Busch, K. E."},{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"}],"date_created":"2019-03-21T08:10:15Z","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:20Z","publication":"Proceedings of the National Academy of Sciences","issue":"23","_id":"6146","type":"journal_article","abstract":[{"lang":"eng","text":"Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental to all animals. Here we examine the CO2 response of the nematode Caenorhabditis elegans. This species inhabits rotting material, which typically has a broad CO2 concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%. Animals can respond to both absolute CO2 concentrations and changes in CO2 levels within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16, strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1. The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1, besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs so that one response dominates. Food and allelic variation at NPR-1 regulate which response prevails. Our results suggest that multiple sensory inputs are coordinated by C. elegans to generate different coherent foraging strategies."}],"oa":1,"ddc":["570"],"file":[{"date_updated":"2020-07-14T12:47:20Z","creator":"kschuh","checksum":"eac0413064b022c1489f7b6719e7228c","file_size":501506,"relation":"main_file","file_name":"2008_PNAS_Bretscher.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2019-03-21T08:14:54Z","file_id":"6147"}],"page":"8044-8049","external_id":{"pmid":["18524954"]},"has_accepted_license":"1","intvolume":"       105","pmid":1,"year":"2008","publication_identifier":{"issn":["0027-8424","1091-6490"]},"language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1073/pnas.0707607105","citation":{"ama":"Bretscher AJ, Busch KE, de Bono M. A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2008;105(23):8044-8049. doi:<a href=\"https://doi.org/10.1073/pnas.0707607105\">10.1073/pnas.0707607105</a>","mla":"Bretscher, A. J., et al. “A Carbon Dioxide Avoidance Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 105, no. 23, Proceedings of the National Academy of Sciences, 2008, pp. 8044–49, doi:<a href=\"https://doi.org/10.1073/pnas.0707607105\">10.1073/pnas.0707607105</a>.","ista":"Bretscher AJ, Busch KE, de Bono M. 2008. A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 105(23), 8044–8049.","ieee":"A. J. Bretscher, K. E. Busch, and M. de Bono, “A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 105, no. 23. Proceedings of the National Academy of Sciences, pp. 8044–8049, 2008.","chicago":"Bretscher, A. J., K. E. Busch, and Mario de Bono. “A Carbon Dioxide Avoidance Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2008. <a href=\"https://doi.org/10.1073/pnas.0707607105\">https://doi.org/10.1073/pnas.0707607105</a>.","short":"A.J. Bretscher, K.E. Busch, M. de Bono, Proceedings of the National Academy of Sciences 105 (2008) 8044–8049.","apa":"Bretscher, A. J., Busch, K. E., &#38; de Bono, M. (2008). A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0707607105\">https://doi.org/10.1073/pnas.0707607105</a>"},"extern":"1"},{"extern":"1","citation":{"ama":"Gustavsson M, Haller E, Mark M, Danzl JG, Rojas Kopeinig G, Nägerl H. Control of interaction-induced dephasing of bloch oscillations. <i>Physical Review Letters</i>. 2008;100(8). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.100.080404\">10.1103/PhysRevLett.100.080404</a>","apa":"Gustavsson, M., Haller, E., Mark, M., Danzl, J. G., Rojas Kopeinig, G., &#38; Nägerl, H. (2008). Control of interaction-induced dephasing of bloch oscillations. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.100.080404\">https://doi.org/10.1103/PhysRevLett.100.080404</a>","chicago":"Gustavsson, Mattias, Elmar Haller, Manfred Mark, Johann G Danzl, Gabriel Rojas Kopeinig, and Hanns Nägerl. “Control of Interaction-Induced Dephasing of Bloch Oscillations.” <i>Physical Review Letters</i>. American Physical Society, 2008. <a href=\"https://doi.org/10.1103/PhysRevLett.100.080404\">https://doi.org/10.1103/PhysRevLett.100.080404</a>.","short":"M. Gustavsson, E. Haller, M. Mark, J.G. Danzl, G. Rojas Kopeinig, H. Nägerl, Physical Review Letters 100 (2008).","ieee":"M. Gustavsson, E. Haller, M. Mark, J. G. Danzl, G. Rojas Kopeinig, and H. Nägerl, “Control of interaction-induced dephasing of bloch oscillations,” <i>Physical Review Letters</i>, vol. 100, no. 8. American Physical Society, 2008.","ista":"Gustavsson M, Haller E, Mark M, Danzl JG, Rojas Kopeinig G, Nägerl H. 2008. Control of interaction-induced dephasing of bloch oscillations. Physical Review Letters. 100(8).","mla":"Gustavsson, Mattias, et al. “Control of Interaction-Induced Dephasing of Bloch Oscillations.” <i>Physical Review Letters</i>, vol. 100, no. 8, American Physical Society, 2008, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.100.080404\">10.1103/PhysRevLett.100.080404</a>."},"doi":"10.1103/PhysRevLett.100.080404","acknowledgement":"We thank A. Daley for theoretical support and for help with\r\nsetting  up the  numerical  calculations  and  A. Buchleitner\r\nand  his  group  for  useful  discussions.  We  are  grateful  to\r\nA. Liem and H. Zellmer for valuable assistance in setting\r\nup the 1064 nm fiber amplifier system. We acknowledge\r\ncontributions  by  P.  Unterwaditzer  and  T.  Flir  during  the\r\nearly   stages   of   the   experiment.   We   are   indebted   to\r\nR.  Grimm  for  generous  support  and  gratefully  acknowledge  funding  by  the  Austrian  Ministry  of  Science  and\r\nResearch (BMWF) and the Austrian Science Fund (FWF).","language":[{"iso":"eng"}],"year":"2008","intvolume":"       100","arxiv":1,"external_id":{"arxiv":["0710.5083"]},"oa":1,"abstract":[{"text":"We report on the control of interaction-induced dephasing of Bloch oscillations for an atomic Bose-Einstein condensate in an optical lattice. We quantify the dephasing in terms of the width of the quasimomentum distribution and measure its dependence on time for different interaction strengths which we control by means of a Feshbach resonance. For minimal interaction, the dephasing time is increased from a few to more than 20 thousand Bloch oscillation periods, allowing us to realize a BEC-based atom interferometer in the noninteracting limit.","lang":"eng"}],"issue":"8","article_processing_charge":"No","_id":"1036","type":"journal_article","publication":"Physical Review Letters","date_created":"2018-12-11T11:49:48Z","oa_version":"None","author":[{"full_name":"Gustavsson, Mattias","last_name":"Gustavsson","first_name":"Mattias"},{"last_name":"Haller","first_name":"Elmar","full_name":"Haller, Elmar"},{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"first_name":"Gabriel","last_name":"Rojas Kopeinig","full_name":"Rojas Kopeinig, Gabriel"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"day":"28","status":"public","volume":100,"title":"Control of interaction-induced dephasing of bloch oscillations","main_file_link":[{"url":"https://arxiv.org/abs/0710.5083","open_access":"1"}],"date_published":"2008-02-28T00:00:00Z","month":"02","publisher":"American Physical Society","date_updated":"2021-01-12T06:47:49Z","publist_id":"6353","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"main_file_link":[{"url":"https://arxiv.org/abs/0710.4052","open_access":"1"}],"date_updated":"2021-01-12T06:47:50Z","publist_id":"6352","publisher":"American Physical Society","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2008-02-29T00:00:00Z","month":"02","author":[{"first_name":"Steven","last_name":"Knoop","full_name":"Knoop, Steven"},{"last_name":"Mark","first_name":"Michael","full_name":"Mark, Michael"},{"first_name":"Francesca","last_name":"Ferlaino","full_name":"Ferlaino, Francesca"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kraemer","first_name":"Tobias","full_name":"Kraemer, Tobias"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"},{"full_name":"Grimm, Rudolf","first_name":"Rudolf","last_name":"Grimm"}],"publication":"Physical Review Letters","issue":"8","type":"journal_article","article_processing_charge":"No","_id":"1037","date_created":"2018-12-11T11:49:49Z","oa_version":"None","status":"public","title":"Metastable feshbach molecules in high rotational states","volume":100,"day":"29","external_id":{"arxiv":["0710.4052"]},"abstract":[{"text":"We experimentally demonstrate Cs2 Feshbach molecules well above the dissociation threshold, which are stable against spontaneous decay on the time scale of 1s. An optically trapped sample of ultracold dimers is prepared in a high rotational state and magnetically tuned into a region with a negative binding energy. The metastable character of these molecules arises from the large centrifugal barrier in combination with negligible coupling to states with low rotational angular momentum. A sharp onset of dissociation with increasing magnetic field is mediated by a crossing with a lower rotational dimer state and facilitates dissociation on demand with a well-defined energy.","lang":"eng"}],"oa":1,"acknowledgement":"We thank S. Du ̈rr and T. Volz for fruitful discussions. We acknowledge support by the Austrian Science Fund (FWF) within No. SFB 15 (project part 16). S.K. is supported within the Marie Curie Intra-European Program of the European Commission. F.F. is supported within the Lise Meitner program of the FWF.","extern":"1","doi":"10.1103/PhysRevLett.100.083002","citation":{"apa":"Knoop, S., Mark, M., Ferlaino, F., Danzl, J. G., Kraemer, T., Nägerl, H., &#38; Grimm, R. (2008). Metastable feshbach molecules in high rotational states. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.100.083002\">https://doi.org/10.1103/PhysRevLett.100.083002</a>","short":"S. Knoop, M. Mark, F. Ferlaino, J.G. Danzl, T. Kraemer, H. Nägerl, R. Grimm, Physical Review Letters 100 (2008).","chicago":"Knoop, Steven, Michael Mark, Francesca Ferlaino, Johann G Danzl, Tobias Kraemer, Hanns Nägerl, and Rudolf Grimm. “Metastable Feshbach Molecules in High Rotational States.” <i>Physical Review Letters</i>. American Physical Society, 2008. <a href=\"https://doi.org/10.1103/PhysRevLett.100.083002\">https://doi.org/10.1103/PhysRevLett.100.083002</a>.","ista":"Knoop S, Mark M, Ferlaino F, Danzl JG, Kraemer T, Nägerl H, Grimm R. 2008. Metastable feshbach molecules in high rotational states. Physical Review Letters. 100(8).","ieee":"S. Knoop <i>et al.</i>, “Metastable feshbach molecules in high rotational states,” <i>Physical Review Letters</i>, vol. 100, no. 8. American Physical Society, 2008.","mla":"Knoop, Steven, et al. “Metastable Feshbach Molecules in High Rotational States.” <i>Physical Review Letters</i>, vol. 100, no. 8, American Physical Society, 2008, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.100.083002\">10.1103/PhysRevLett.100.083002</a>.","ama":"Knoop S, Mark M, Ferlaino F, et al. Metastable feshbach molecules in high rotational states. <i>Physical Review Letters</i>. 2008;100(8). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.100.083002\">10.1103/PhysRevLett.100.083002</a>"},"arxiv":1,"intvolume":"       100","language":[{"iso":"eng"}],"year":"2008"},{"acknowledgement":" We thank the team of J. Hecker Denschlag, the LevT team in our group, and T. Bergeman for very helpful discussions and M. Prevedelli for technical assistance. We are indebted to R. Grimm for generous support and gratefully acknowledge funding by the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form of a START prize grant and by the European Science Foundation in the framework of the EuroQUAM collective research project QuDipMol.\r\n","extern":"1","citation":{"ieee":"J. G. Danzl <i>et al.</i>, “Quantum gas of deeply bound ground state molecules,” <i>Science</i>, vol. 321, no. 5892. American Association for the Advancement of Science, pp. 1062–1066, 2008.","ista":"Danzl JG, Haller E, Gustavsson M, Mark M, Hart R, Bouloufa N, Dulieu O, Ritsch H, Nägerl H. 2008. Quantum gas of deeply bound ground state molecules. Science. 321(5892), 1062–1066.","mla":"Danzl, Johann G., et al. “Quantum Gas of Deeply Bound Ground State Molecules.” <i>Science</i>, vol. 321, no. 5892, American Association for the Advancement of Science, 2008, pp. 1062–66, doi:<a href=\"https://doi.org/10.1126/science.1159909\">10.1126/science.1159909</a>.","apa":"Danzl, J. G., Haller, E., Gustavsson, M., Mark, M., Hart, R., Bouloufa, N., … Nägerl, H. (2008). Quantum gas of deeply bound ground state molecules. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1159909\">https://doi.org/10.1126/science.1159909</a>","short":"J.G. Danzl, E. Haller, M. Gustavsson, M. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, H. Nägerl, Science 321 (2008) 1062–1066.","chicago":"Danzl, Johann G, Elmar Haller, Mattias Gustavsson, Manfred Mark, Russell Hart, Nadia Bouloufa, Olivier Dulieu, Helmut Ritsch, and Hanns Nägerl. “Quantum Gas of Deeply Bound Ground State Molecules.” <i>Science</i>. American Association for the Advancement of Science, 2008. <a href=\"https://doi.org/10.1126/science.1159909\">https://doi.org/10.1126/science.1159909</a>.","ama":"Danzl JG, Haller E, Gustavsson M, et al. Quantum gas of deeply bound ground state molecules. <i>Science</i>. 2008;321(5892):1062-1066. doi:<a href=\"https://doi.org/10.1126/science.1159909\">10.1126/science.1159909</a>"},"doi":"10.1126/science.1159909","arxiv":1,"intvolume":"       321","language":[{"iso":"eng"}],"year":"2008","external_id":{"arxiv":["0806.2284"]},"page":"1062 - 1066","abstract":[{"lang":"eng","text":"Molecular cooling techniques face the hurdle of dissipating translational as well as internal energy in the presence of a rich electronic, vibrational, and rotational energy spectrum. In our experiment, we create a translationally ultracold, dense quantum gas of molecules bound by more than 1000 wave numbers in the electronic ground state. Specifically, we stimulate with 80% efficiency, a two-photon transfer of molecules associated on a Feshbach resonance from a Bose-Einstein condensate of cesium atoms. In the process, the initial loose, long-range electrostatic bond of the Feshbach molecule is coherently transformed into a tight chemical bond. We demonstrate coherence of the transfer in a Ramsey-type experiment and show that the molecular sample is not heated during the transfer. Our results show that the preparation of a quantum gas of molecules in specific rovibrational states is possible and that the creation of a Bose-Einstein condensate of molecules in their rovibronic ground state is within reach."}],"oa":1,"author":[{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"last_name":"Haller","first_name":"Elmar","full_name":"Haller, Elmar"},{"full_name":"Gustavsson, Mattias","first_name":"Mattias","last_name":"Gustavsson"},{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"full_name":"Hart, Russell","first_name":"Russell","last_name":"Hart"},{"full_name":"Bouloufa, Nadia","first_name":"Nadia","last_name":"Bouloufa"},{"full_name":"Dulieu, Olivier","last_name":"Dulieu","first_name":"Olivier"},{"full_name":"Ritsch, Helmut","first_name":"Helmut","last_name":"Ritsch"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"publication":"Science","_id":"1039","issue":"5892","type":"journal_article","article_processing_charge":"No","date_created":"2018-12-11T11:49:49Z","oa_version":"None","status":"public","volume":321,"title":"Quantum gas of deeply bound ground state molecules","day":"22","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0806.2284"}],"publist_id":"6351","date_updated":"2021-01-12T06:47:50Z","publisher":"American Association for the Advancement of Science","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2008-08-22T00:00:00Z","month":"08"},{"publisher":"Springer Nature","date_updated":"2021-12-14T08:54:36Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","date_published":"2008-11-06T00:00:00Z","month":"11","article_type":"letter_note","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/"}],"status":"public","volume":456,"title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","day":"06","department":[{"_id":"DaZi"}],"author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"first_name":"Tracy","last_name":"Ballinger","full_name":"Ballinger, Tracy"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"type":"journal_article","_id":"9457","issue":"7218","article_processing_charge":"No","publication":"Nature","oa_version":"Submitted Version","date_created":"2021-06-04T11:49:32Z","oa":1,"abstract":[{"text":"Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.","lang":"eng"}],"keyword":["Multidisciplinary"],"external_id":{"pmid":["18815594"]},"page":"125-129","pmid":1,"intvolume":"       456","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"year":"2008","extern":"1","doi":"10.1038/nature07324","citation":{"apa":"Zilberman, D., Coleman-Derr, D., Ballinger, T., &#38; Henikoff, S. (2008). Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>","chicago":"Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>. Springer Nature, 2008. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>.","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.","ieee":"D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” <i>Nature</i>, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.","ista":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129.","mla":"Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>, vol. 456, no. 7218, Springer Nature, 2008, pp. 125–29, doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>.","ama":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. 2008;456(7218):125-129. doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>"},"quality_controlled":"1"},{"status":"public","intvolume":"       154","volume":154,"title":"Nonlinear algebra and Bogoliubov's recursion","day":"01","year":"2008","acknowledgement":"This work is supported in part by the Dynasty Foundation (M. N. S.),  the\nRussian Foundation for Basic Research (Grant No\ns. 07-02-00878 and 07-02-00645), a joint grant (Grant\nNo. 06-01-92059-CE), the NWO (Project No. 047.011.2004.026), INTAS (Grant No. 05-1000008-7865), the\nProgram for Supporting Leading Scientific School\ns (Grant No. NSh-8004.2006.2), and also by a project\n(Project No. ANR-05-BLAN-0029-01, A. Yu. M.).","author":[{"full_name":"Morozov, Alexei Y","last_name":"Morozov","first_name":"Alexei"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn"}],"issue":"2","_id":"965","type":"journal_article","extern":1,"publication":"Theoretical and Mathematical Physics","citation":{"mla":"Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” <i>Theoretical and Mathematical Physics</i>, vol. 154, no. 2, Elsevier, 2008, pp. 270–93, doi:<a href=\"https://doi.org/10.1007/s11232-008-0026-7\">10.1007/s11232-008-0026-7</a>.","ista":"Morozov A, Serbyn M. 2008. Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. 154(2), 270–293.","ieee":"A. Morozov and M. Serbyn, “Nonlinear algebra and Bogoliubov’s recursion,” <i>Theoretical and Mathematical Physics</i>, vol. 154, no. 2. Elsevier, pp. 270–293, 2008.","chicago":"Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” <i>Theoretical and Mathematical Physics</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1007/s11232-008-0026-7\">https://doi.org/10.1007/s11232-008-0026-7</a>.","short":"A. Morozov, M. Serbyn, Theoretical and Mathematical Physics 154 (2008) 270–293.","apa":"Morozov, A., &#38; Serbyn, M. (2008). Nonlinear algebra and Bogoliubov’s recursion. <i>Theoretical and Mathematical Physics</i>. Elsevier. <a href=\"https://doi.org/10.1007/s11232-008-0026-7\">https://doi.org/10.1007/s11232-008-0026-7</a>","ama":"Morozov A, Serbyn M. Nonlinear algebra and Bogoliubov’s recursion. <i>Theoretical and Mathematical Physics</i>. 2008;154(2):270-293. doi:<a href=\"https://doi.org/10.1007/s11232-008-0026-7\">10.1007/s11232-008-0026-7</a>"},"doi":"10.1007/s11232-008-0026-7","quality_controlled":0,"date_created":"2018-12-11T11:49:26Z","publisher":"Elsevier","date_updated":"2021-01-12T08:22:17Z","publist_id":"6437","publication_status":"published","date_published":"2008-01-01T00:00:00Z","month":"01","oa":1,"abstract":[{"text":"We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.","lang":"eng"}],"page":"270 - 293","main_file_link":[{"url":"https://arxiv.org/abs/hep-th/0703258","open_access":"1"}]},{"publisher":"Genetics Society of America","publist_id":"2965","date_updated":"2021-01-12T07:43:27Z","publication_status":"published","date_published":"2008-05-01T00:00:00Z","month":"05","oa":1,"abstract":[{"text":"We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ~0.43.","lang":"eng"}],"page":"497 - 502","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390626"}],"status":"public","intvolume":"       179","volume":179,"title":"Estimation of 2Nes From Temporal Allele Frequency Data","day":"01","year":"2008","author":[{"orcid":"0000-0002-4624-4612","full_name":"Jonathan Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback"},{"full_name":"York, Thomas L","first_name":"Thomas","last_name":"York"},{"full_name":"Nielsen, Rasmus","last_name":"Nielsen","first_name":"Rasmus"}],"_id":"3435","issue":"1","type":"journal_article","publication":"Genetics","extern":1,"citation":{"ama":"Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency Data. <i>Genetics</i>. 2008;179(1):497-502. doi:<a href=\"https://doi.org/10.1534/genetics.107.085019\">10.1534/genetics.107.085019</a>","apa":"Bollback, J. P., York, T., &#38; Nielsen, R. (2008). Estimation of 2Nes From Temporal Allele Frequency Data. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.107.085019\">https://doi.org/10.1534/genetics.107.085019</a>","short":"J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.","chicago":"Bollback, Jonathan P, Thomas York, and Rasmus Nielsen. “Estimation of 2Nes From Temporal Allele Frequency Data.” <i>Genetics</i>. Genetics Society of America, 2008. <a href=\"https://doi.org/10.1534/genetics.107.085019\">https://doi.org/10.1534/genetics.107.085019</a>.","ieee":"J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal Allele Frequency Data,” <i>Genetics</i>, vol. 179, no. 1. Genetics Society of America, pp. 497–502, 2008.","ista":"Bollback JP, York T, Nielsen R. 2008. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. 179(1), 497–502.","mla":"Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency Data.” <i>Genetics</i>, vol. 179, no. 1, Genetics Society of America, 2008, pp. 497–502, doi:<a href=\"https://doi.org/10.1534/genetics.107.085019\">10.1534/genetics.107.085019</a>."},"doi":"10.1534/genetics.107.085019","date_created":"2018-12-11T12:03:19Z","quality_controlled":0},{"language":[{"iso":"eng"}],"year":"2008","intvolume":"         2","has_accepted_license":"1","extern":"1","quality_controlled":"1","citation":{"ama":"Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics. In: Vol 2. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:107-118. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745\">10.4230/LIPIcs.FSTTCS.2008.1745</a>","ieee":"K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game metrics,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, 2008, vol. 2, pp. 107–118.","ista":"Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2008. Algorithms for game metrics. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 2, 107–118.","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Game Metrics</i>. Vol. 2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 107–18, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745\">10.4230/LIPIcs.FSTTCS.2008.1745</a>.","apa":"Chatterjee, K., De Alfaro, L., Majumdar, R., &#38; Raman, V. (2008). Algorithms for game metrics (Vol. 2, pp. 107–118). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745\">https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745</a>","short":"K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 107–118.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath Raman. “Algorithms for Game Metrics,” 2:107–18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745\">https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745</a>."},"doi":"10.4230/LIPIcs.FSTTCS.2008.1745","acknowledgement":"This research was supported in part by the NSF grants CCR-0132780 and CNS-0720884.","conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"related_material":{"record":[{"relation":"later_version","status":"public","id":"3868"}]},"file":[{"date_updated":"2020-07-14T12:46:12Z","creator":"dernst","file_size":442139,"checksum":"0a447454a24e273f7ddf51dbfe47f877","file_name":"2008_LIPIcs_Chatterjee.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_created":"2019-05-10T10:01:21Z","file_id":"6398"}],"abstract":[{"text":"Simulation and bisimulation metrics for stochastic systems provide a quantitative gen- eralization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative μ-calculus and related probabilistic logics.\r\nWe present algorithms for computing the metrics on Markov decision processes (MDPs), turn- based stochastic games, and concurrent games. For turn-based games and MDPs, we provide a polynomial-time algorithm based on linear programming for the computation of the one-step metric distance between states. The algorithm improves on the previously known exponential-time algo- rithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known bound for Markov chains. For the bisimulation kernel of the metric, which corresponds to probabilistic bisimulation, our algorithm works in time O(n4) for both turn-based games and MDPs; improving the previously best known O(n9 · log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be accomplished via a reduction to the theory of real closed fields, involving a\r\nformula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity, improving the previously known reduction with O(|G|O(|G|7)) time complexity. These algorithms can be iterated\r\nto approximate the metrics using binary search.","lang":"eng"}],"oa":1,"ddc":["000"],"alternative_title":["LIPIcs"],"page":"107 - 118","day":"05","status":"public","volume":2,"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Algorithms for game metrics","file_date_updated":"2020-07-14T12:46:12Z","_id":"3504","type":"conference","date_created":"2018-12-11T12:03:40Z","oa_version":"Published Version","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"De Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"},{"full_name":"Raman, Vishwanath","last_name":"Raman","first_name":"Vishwanath"}],"date_published":"2008-12-05T00:00:00Z","month":"12","publist_id":"2883","date_updated":"2023-02-23T11:46:14Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475664","open_access":"1"}],"oa":1,"abstract":[{"text":"Gene expression levels fluctuate even under constant external conditions. Much emphasis has usually been placed on the components of this noise that are due to randomness in transcription and translation. Here we focus on the role of noise associated with the inputs to transcriptional regulation; in particular, we analyze the effects of random arrival times and binding of transcription factors to their target sites along the genome. This contribution to the total noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, universal models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally.","lang":"eng"}],"date_published":"2008-07-23T00:00:00Z","month":"07","publication_status":"published","publisher":"Public Library of Science","date_updated":"2021-01-12T07:51:49Z","publist_id":"2498","citation":{"ama":"Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation. <i>PLoS One</i>. 2008;3(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0002774\">10.1371/journal.pone.0002774</a>","apa":"Tkačik, G., Gregor, T., &#38; Bialek, W. (2008). The role of input noise in transcriptional regulation. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0002774\">https://doi.org/10.1371/journal.pone.0002774</a>","short":"G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008).","chicago":"Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise in Transcriptional Regulation.” <i>PLoS One</i>. Public Library of Science, 2008. <a href=\"https://doi.org/10.1371/journal.pone.0002774\">https://doi.org/10.1371/journal.pone.0002774</a>.","ieee":"G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” <i>PLoS One</i>, vol. 3, no. 7. Public Library of Science, 2008.","ista":"Tkačik G, Gregor T, Bialek W. 2008. The role of input noise in transcriptional regulation. PLoS One. 3(7).","mla":"Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.” <i>PLoS One</i>, vol. 3, no. 7, Public Library of Science, 2008, doi:<a href=\"https://doi.org/10.1371/journal.pone.0002774\">10.1371/journal.pone.0002774</a>."},"doi":"10.1371/journal.pone.0002774","date_created":"2018-12-11T12:04:52Z","quality_controlled":0,"_id":"3734","issue":"7","type":"journal_article","extern":1,"publication":"PLoS One","author":[{"orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"full_name":"Bialek, William S","last_name":"Bialek","first_name":"William"}],"acknowledgement":"NSF Grant PHY-0650617; NIH grants P50 GM071508, R01 GM077599; Burroughs Wellcome Program in Biological Dynamics","year":"2008","day":"23","volume":3,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"The role of input noise in transcriptional regulation","intvolume":"         3","status":"public"},{"publication_status":"published","date_updated":"2021-01-12T07:51:52Z","publist_id":"2489","publisher":"National Academy of Sciences","abstract":[{"text":"In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early Drosophila embryo and that this system achieves approximately 90% of its theoretical maximum information transmission.","lang":"eng"}],"oa":1,"date_published":"2008-01-01T00:00:00Z","month":"01","page":"12265 - 12270","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900"}],"title":"Information flow and optimization in transcriptional regulation","volume":105,"status":"public","intvolume":"       105","year":"2008","day":"01","author":[{"full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"full_name":"Callan,Curtis G","last_name":"Callan","first_name":"Curtis"},{"full_name":"Bialek, William S","last_name":"Bialek","first_name":"William"}],"acknowledgement":"P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS NIH HHS/United States","quality_controlled":0,"date_created":"2018-12-11T12:04:54Z","doi":"10.1073/pnas.0806077105","citation":{"ama":"Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. <i>PNAS</i>. 2008;105(34):12265-12270. doi:<a href=\"https://doi.org/10.1073/pnas.0806077105\">10.1073/pnas.0806077105</a>","ista":"Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional regulation. PNAS. 105(34), 12265–12270.","ieee":"G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” <i>PNAS</i>, vol. 105, no. 34. National Academy of Sciences, pp. 12265–12270, 2008.","mla":"Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional Regulation.” <i>PNAS</i>, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:<a href=\"https://doi.org/10.1073/pnas.0806077105\">10.1073/pnas.0806077105</a>.","apa":"Tkačik, G., Callan, C., &#38; Bialek, W. (2008). Information flow and optimization in transcriptional regulation. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0806077105\">https://doi.org/10.1073/pnas.0806077105</a>","chicago":"Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and Optimization in Transcriptional Regulation.” <i>PNAS</i>. National Academy of Sciences, 2008. <a href=\"https://doi.org/10.1073/pnas.0806077105\">https://doi.org/10.1073/pnas.0806077105</a>.","short":"G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270."},"extern":1,"publication":"PNAS","issue":"34","_id":"3740","type":"journal_article"}]