[{"author":[{"last_name":"Ahmed","full_name":"Ahmed, Umair","first_name":"Umair"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Gulwani, Sumit","first_name":"Sumit","last_name":"Gulwani"}],"page":"13","related_material":{"record":[{"id":"1481","relation":"later_version","status":"public"}]},"ddc":["000","005"],"date_published":"2013-12-03T00:00:00Z","_id":"5410","publication_identifier":{"issn":["2664-1690"]},"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2013-146-v1-1","publication_status":"published","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. \r\nOur approach generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. ","lang":"eng"}],"date_created":"2018-12-12T11:39:10Z","date_updated":"2025-05-19T11:10:16Z","file_date_updated":"2020-07-14T12:46:46Z","publisher":"IST Austria","year":"2013","has_accepted_license":"1","type":"technical_report","citation":{"ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, <i>Automatic generation of alternative starting positions for traditional board games</i>. IST Austria, 2013.","short":"U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013.","apa":"Ahmed, U., Chatterjee, K., &#38; Gulwani, S. (2013). <i>Automatic generation of alternative starting positions for traditional board games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">https://doi.org/10.15479/AT:IST-2013-146-v1-1</a>","mla":"Ahmed, Umair, et al. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">10.15479/AT:IST-2013-146-v1-1</a>.","ama":"Ahmed U, Chatterjee K, Gulwani S. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">10.15479/AT:IST-2013-146-v1-1</a>","ista":"Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p.","chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">https://doi.org/10.15479/AT:IST-2013-146-v1-1</a>."},"oa":1,"day":"03","month":"12","pubrep_id":"146","status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Automatic generation of alternative starting positions for traditional board games","file":[{"date_created":"2018-12-12T11:54:06Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"IST-2013-146-v1+1_main.pdf","file_size":818189,"checksum":"409f3aaaf1184e4057b89cbb449dac80","date_updated":"2020-07-14T12:46:46Z","file_id":"5528","creator":"system"}]},{"publication_identifier":{"eisbn":["9783642397998"],"eissn":["1611-3349"],"isbn":["9783642397981"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"page":"174-190","date_published":"2013-08-01T00:00:00Z","title":"Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates","file":[{"relation":"main_file","file_name":"2013_CAV_Dragoi.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:10Z","file_size":236480,"checksum":"a901cc6b71db08b61c0d4c0cbacc6287","file_id":"5748","creator":"dernst","date_created":"2018-12-18T13:13:33Z","access_level":"open_access"}],"day":"01","series_title":"CAV","year":"2013","citation":{"short":"C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190.","ieee":"C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates,” in <i>Computer Aided Verification</i>, vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.","chicago":"Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” In <i>Computer Aided Verification</i>, 8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">https://doi.org/10.1007/978-3-642-39799-8_11</a>.","ama":"Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: <i>Computer Aided Verification</i>. Vol 8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">10.1007/978-3-642-39799-8_11</a>","ista":"Dragoi C, Gupta A, Henzinger TA. 2013.Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: Computer Aided Verification. vol. 8044, 174–190.","mla":"Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” <i>Computer Aided Verification</i>, vol. 8044, Springer Berlin Heidelberg, 2013, pp. 174–90, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">10.1007/978-3-642-39799-8_11</a>.","apa":"Dragoi, C., Gupta, A., &#38; Henzinger, T. A. (2013). Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In <i>Computer Aided Verification</i> (Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">https://doi.org/10.1007/978-3-642-39799-8_11</a>"},"intvolume":"      8044","place":"Berlin, Heidelberg","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:10Z","project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer Berlin Heidelberg","date_created":"2018-12-18T13:10:21Z","conference":{"start_date":"2013-07-13","location":"Saint Petersburg, Russia","end_date":"2013-07-19","name":"CAV: Computer Aided Verification"},"publication_status":"published","scopus_import":"1","department":[{"_id":"ToHe"}],"doi":"10.1007/978-3-642-39799-8_11","quality_controlled":"1","author":[{"full_name":"Dragoi, Cezara","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"ddc":["005"],"_id":"5747","pubrep_id":"195","oa_version":"None","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Computer Aided Verification","month":"08","type":"book_chapter","has_accepted_license":"1","ec_funded":1,"oa":1,"volume":8044,"date_updated":"2025-07-10T11:52:57Z"},{"day":"01","month":"01","status":"public","title":"Polarization dependent focusing","publist_id":"7217","date_updated":"2021-01-12T08:05:10Z","publisher":"OSA","year":"2013","citation":{"ama":"Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing. In: OSA; 2013. doi:<a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">10.1364/QIM.2013.W6.23</a>","ista":"Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference Papers, .","chicago":"Schmid, David, Ting Huang, Radhika Dirks, Onur Hosten, and Paul Kwiat. “Polarization Dependent Focusing.” OSA, 2013. <a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">https://doi.org/10.1364/QIM.2013.W6.23</a>.","apa":"Schmid, D., Huang, T., Dirks, R., Hosten, O., &#38; Kwiat, P. (2013). Polarization dependent focusing. Presented at the QIM: Quantum Information and Measurement, OSA. <a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">https://doi.org/10.1364/QIM.2013.W6.23</a>","mla":"Schmid, David, et al. <i>Polarization Dependent Focusing</i>. OSA, 2013, doi:<a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">10.1364/QIM.2013.W6.23</a>.","ieee":"D. Schmid, T. Huang, R. Dirks, O. Hosten, and P. Kwiat, “Polarization dependent focusing,” presented at the QIM: Quantum Information and Measurement, 2013.","short":"D. Schmid, T. Huang, R. Dirks, O. Hosten, P. Kwiat, in:, OSA, 2013."},"type":"conference","conference":{"name":"QIM: Quantum Information and Measurement"},"alternative_title":["Optics InfoBase Conference Papers"],"publication_status":"published","date_created":"2018-12-11T11:47:22Z","abstract":[{"text":"We present two methods of creating two orthogonally-polarized focal points at customizable relative locations. These schemes may be critical for enhancing entanglement sources and other applications.","lang":"eng"}],"author":[{"last_name":"Schmid","full_name":"Schmid, David","first_name":"David"},{"first_name":"Ting","full_name":"Huang, Ting-Yu","last_name":"Huang"},{"last_name":"Dirks","first_name":"Radhika","full_name":"Dirks, Radhika"},{"full_name":"Onur Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten"},{"full_name":"Kwiat, Paul G","first_name":"Paul","last_name":"Kwiat"}],"_id":"590","date_published":"2013-01-01T00:00:00Z","extern":1,"quality_controlled":0,"doi":"10.1364/QIM.2013.W6.23"},{"status":"public","publication":"Optics Express","title":"Adjustable and robust methods for polarization-dependent focusing","publist_id":"7218","day":"01","month":"07","year":"2013","issue":"13","citation":{"ama":"Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent focusing. <i>Optics Express</i>. 2013;21(13):15538-15552. doi:<a href=\"https://doi.org/10.1364/OE.21.015538\">10.1364/OE.21.015538</a>","ista":"Schmid D, Huang T, Hazrat S, Dirks R, Hosten O, Quint S, Thian D, Kwiat P. 2013. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 21(13), 15538–15552.","chicago":"Schmid, David, Ting Huang, Shiraz Hazrat, Radhika Dirks, Onur Hosten, Stephan Quint, Dickson Thian, and Paul Kwiat. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” <i>Optics Express</i>. Optical Society of America, 2013. <a href=\"https://doi.org/10.1364/OE.21.015538\">https://doi.org/10.1364/OE.21.015538</a>.","apa":"Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat, P. (2013). Adjustable and robust methods for polarization-dependent focusing. <i>Optics Express</i>. Optical Society of America. <a href=\"https://doi.org/10.1364/OE.21.015538\">https://doi.org/10.1364/OE.21.015538</a>","mla":"Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” <i>Optics Express</i>, vol. 21, no. 13, Optical Society of America, 2013, pp. 15538–52, doi:<a href=\"https://doi.org/10.1364/OE.21.015538\">10.1364/OE.21.015538</a>.","ieee":"D. Schmid <i>et al.</i>, “Adjustable and robust methods for polarization-dependent focusing,” <i>Optics Express</i>, vol. 21, no. 13. Optical Society of America, pp. 15538–15552, 2013.","short":"D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian, P. Kwiat, Optics Express 21 (2013) 15538–15552."},"type":"journal_article","date_updated":"2021-01-12T08:05:12Z","volume":21,"intvolume":"        21","publisher":"Optical Society of America","date_created":"2018-12-11T11:47:22Z","abstract":[{"text":"We present two methods for the precise independent focusing of orthogonal linear polarizations of light at arbitrary relative locations. Our first scheme uses a displaced lens in a polarization Sagnac interferometer to provide adjustable longitudinal and lateral focal displacements via simple geometry; the second uses uniaxial crystals to achieve the same effect in a compact collinear setup. We develop the theoretical applications and limitations of our schemes, and provide experimental confirmation of our calculations.","lang":"eng"}],"publication_status":"published","extern":1,"doi":"10.1364/OE.21.015538","quality_controlled":0,"page":"15538 - 15552","author":[{"full_name":"Schmid, David","first_name":"David","last_name":"Schmid"},{"full_name":"Huang, Ting-Yu","first_name":"Ting","last_name":"Huang"},{"first_name":"Shiraz","full_name":"Hazrat, Shiraz","last_name":"Hazrat"},{"first_name":"Radhika","full_name":"Dirks, Radhika","last_name":"Dirks"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten"},{"first_name":"Stephan","full_name":"Quint, Stephan","last_name":"Quint"},{"last_name":"Thian","full_name":"Thian, Dickson","first_name":"Dickson"},{"full_name":"Kwiat, Paul G","first_name":"Paul","last_name":"Kwiat"}],"_id":"591","date_published":"2013-07-01T00:00:00Z"},{"date_created":"2019-02-05T08:48:24Z","publication_status":"published","quality_controlled":"1","doi":"10.1016/j.jsc.2012.06.006","OA_place":"publisher","_id":"5920","article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1016/j.jsc.2015.09.002","relation":"erratum"}]},"author":[{"last_name":"Hillar","full_name":"Hillar, Christopher J.","first_name":"Christopher J."},{"first_name":"Abraham","full_name":"Martin del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin del Campo Sanchez"}],"publication":"Journal of Symbolic Computation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","status":"public","month":"03","oa":1,"type":"journal_article","date_updated":"2025-05-20T06:30:08Z","volume":50,"abstract":[{"lang":"eng","text":"We study chains of lattice ideals that are invariant under a symmetric group action. In our setting, the ambient rings for these ideals are polynomial rings which are increasing in (Krull) dimension. Thus, these chains will fail to stabilize in the traditional commutative algebra sense. However, we prove a theorem which says that “up to the action of the group”, these chains locally stabilize. We also give an algorithm, which we have implemented in software, for explicitly constructing these stabilization generators for a family of Laurent toric ideals involved in applications to algebraic statistics. We close with several open problems and conjectures arising from our theoretical and computational investigations."}],"extern":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0747-7171"]},"date_published":"2013-03-01T00:00:00Z","page":"314-334","OA_type":"free access","title":"Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals","day":"01","citation":{"mla":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” <i>Journal of Symbolic Computation</i>, vol. 50, Elsevier, 2013, pp. 314–34, doi:<a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">10.1016/j.jsc.2012.06.006</a>.","apa":"Hillar, C. J., &#38; Martin del Campo Sanchez, A. (2013). Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">https://doi.org/10.1016/j.jsc.2012.06.006</a>","chicago":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” <i>Journal of Symbolic Computation</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">https://doi.org/10.1016/j.jsc.2012.06.006</a>.","ama":"Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. <i>Journal of Symbolic Computation</i>. 2013;50:314-334. doi:<a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">10.1016/j.jsc.2012.06.006</a>","ista":"Hillar CJ, Martin del Campo Sanchez A. 2013. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 50, 314–334.","short":"C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation 50 (2013) 314–334.","ieee":"C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals,” <i>Journal of Symbolic Computation</i>, vol. 50. Elsevier, pp. 314–334, 2013."},"year":"2013","publisher":"Elsevier","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1016/j.jsc.2012.06.006","open_access":"1"}],"intvolume":"        50"},{"month":"03","day":"20","title":"Struggling to let go: A non-coding RNA directs its own extension and destruction","publication":"EMBO Journal","publist_id":"7207","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","status":"public","publisher":"Wiley-Blackwell","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/","open_access":"1"}],"article_processing_charge":"No","date_updated":"2021-01-12T08:05:20Z","volume":32,"intvolume":"        32","oa":1,"citation":{"ama":"Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own extension and destruction. <i>EMBO Journal</i>. 2013;32(6):771-772. doi:<a href=\"https://doi.org/10.1038/emboj.2013.36\">10.1038/emboj.2013.36</a>","ista":"Bernecky C, Cramer P. 2013. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 32(6), 771–772.","chicago":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2013.36\">https://doi.org/10.1038/emboj.2013.36</a>.","apa":"Bernecky, C., &#38; Cramer, P. (2013). Struggling to let go: A non-coding RNA directs its own extension and destruction. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2013.36\">https://doi.org/10.1038/emboj.2013.36</a>","mla":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” <i>EMBO Journal</i>, vol. 32, no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:<a href=\"https://doi.org/10.1038/emboj.2013.36\">10.1038/emboj.2013.36</a>.","short":"C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772.","ieee":"C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs its own extension and destruction,” <i>EMBO Journal</i>, vol. 32, no. 6. Wiley-Blackwell, pp. 771–772, 2013."},"type":"journal_article","year":"2013","issue":"6","publication_status":"published","date_created":"2018-12-11T11:47:23Z","_id":"595","date_published":"2013-03-20T00:00:00Z","author":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","last_name":"Bernecky"},{"first_name":"Patrick","full_name":"Cramer, Patrick","last_name":"Cramer"}],"page":"771 - 772","extern":"1","language":[{"iso":"eng"}],"doi":"10.1038/emboj.2013.36"},{"issue":"12","type":"journal_article","has_accepted_license":"1","oa":1,"volume":9,"date_updated":"2021-01-12T08:06:15Z","oa_version":"Published Version","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"PLoS Genetics","month":"12","doi":"10.1371/journal.pgen.1004011","quality_controlled":"1","author":[{"full_name":"Kodama-Namba, Eiji","first_name":"Eiji","last_name":"Kodama-Namba"},{"first_name":"Lorenz A.","full_name":"Fenk, Lorenz A.","last_name":"Fenk"},{"last_name":"Bretscher","full_name":"Bretscher, Andrew J.","first_name":"Andrew J."},{"full_name":"Gross, Einav","first_name":"Einav","last_name":"Gross"},{"full_name":"Busch, K. Emanuel","first_name":"K. Emanuel","last_name":"Busch"},{"last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"ddc":["570"],"_id":"6128","date_created":"2019-03-19T14:58:51Z","pmid":1,"publication_status":"published","year":"2013","citation":{"apa":"Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., &#38; de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. <i>PLoS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1004011\">https://doi.org/10.1371/journal.pgen.1004011</a>","mla":"Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” <i>PLoS Genetics</i>, vol. 9, no. 12, e1004011, Public Library of Science (PLoS), 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004011\">10.1371/journal.pgen.1004011</a>.","ista":"Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. 2013. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 9(12), e1004011.","ama":"Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. <i>PLoS Genetics</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004011\">10.1371/journal.pgen.1004011</a>","chicago":"Kodama-Namba, Eiji, Lorenz A. Fenk, Andrew J. Bretscher, Einav Gross, K. Emanuel Busch, and Mario de Bono. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” <i>PLoS Genetics</i>. Public Library of Science (PLoS), 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1004011\">https://doi.org/10.1371/journal.pgen.1004011</a>.","ieee":"E. Kodama-Namba, L. A. Fenk, A. J. Bretscher, E. Gross, K. E. Busch, and M. de Bono, “Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans,” <i>PLoS Genetics</i>, vol. 9, no. 12. Public Library of Science (PLoS), 2013.","short":"E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono, PLoS Genetics 9 (2013)."},"intvolume":"         9","publisher":"Public Library of Science (PLoS)","file_date_updated":"2020-07-14T12:47:20Z","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2013_PLOS_Kodama-Namba.PDF","checksum":"299b6321be79931c7c17c5db6e69c711","file_size":4499039,"date_updated":"2020-07-14T12:47:20Z","file_id":"6129","creator":"kschuh","date_created":"2019-03-19T15:14:51Z","access_level":"open_access"}],"title":"Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans","day":"19","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_number":"e1004011","external_id":{"pmid":["24385919"]},"publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"extern":"1","date_published":"2013-12-19T00:00:00Z","abstract":[{"text":"Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O2 and CO2. CO2 is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO2 responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing neuron URX inhibits CO2 avoidance. This inhibition can be graded according to O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to modulate CO2 responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/"},{"publication_status":"published","date_created":"2019-03-20T13:54:05Z","page":"61-78","author":[{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono"},{"last_name":"Schafer","first_name":"W.R.","full_name":"Schafer, W.R."},{"first_name":"A.","full_name":"Gottschalk, A.","last_name":"Gottschalk"}],"_id":"6132","date_published":"2013-08-28T00:00:00Z","publication_identifier":{"isbn":["9783110270723; 9783110270716"]},"extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"month":"08","day":"28","oa_version":"None","status":"public","title":"Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans","publication":"Optogenetics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:16Z","editor":[{"last_name":"Hegemann","full_name":"Hegemann, Peter","first_name":"Peter"},{"full_name":"Sigrist, Stephan","first_name":"Stephan","last_name":"Sigrist"}],"publisher":"Walter de Gruyter","year":"2013","citation":{"ama":"de Bono M, Schafer WR, Gottschalk A. Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Hegemann P, Sigrist S, eds. <i>Optogenetics</i>. Walter de Gruyter; 2013:61-78.","ista":"de Bono M, Schafer WR, Gottschalk A. 2013.Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Optogenetics. , 61–78.","chicago":"Bono, Mario de, W.R. Schafer, and A. Gottschalk. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” In <i>Optogenetics</i>, edited by Peter Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013.","apa":"de Bono, M., Schafer, W. R., &#38; Gottschalk, A. (2013). Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In P. Hegemann &#38; S. Sigrist (Eds.), <i>Optogenetics</i> (pp. 61–78). Walter de Gruyter.","mla":"de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” <i>Optogenetics</i>, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter, 2013, pp. 61–78.","short":"M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.), Optogenetics, Walter de Gruyter, 2013, pp. 61–78.","ieee":"M. de Bono, W. R. Schafer, and A. Gottschalk, “Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans,” in <i>Optogenetics</i>, P. Hegemann and S. Sigrist, Eds. Walter de Gruyter, 2013, pp. 61–78."},"type":"book_chapter"},{"type":"journal_article","has_accepted_license":"1","oa":1,"issue":"35","date_updated":"2021-01-12T08:06:16Z","volume":110,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the National Academy of Sciences","oa_version":"Published Version","status":"public","month":"08","quality_controlled":"1","doi":"10.1073/pnas.1217428110","ddc":["570"],"_id":"6133","author":[{"first_name":"A.","full_name":"Couto, A.","last_name":"Couto"},{"last_name":"Oda","full_name":"Oda, S.","first_name":"S."},{"first_name":"V. O.","full_name":"Nikolaev, V. O.","last_name":"Nikolaev"},{"last_name":"Soltesz","first_name":"Z.","full_name":"Soltesz, Z."},{"last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","full_name":"de Bono, Mario"}],"date_created":"2019-03-20T14:05:06Z","publication_status":"published","pmid":1,"citation":{"ieee":"A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 35. Proceedings of the National Academy of Sciences, pp. E3301–E3310, 2013.","short":"A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the National Academy of Sciences 110 (2013) E3301–E3310.","ista":"Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 110(35), E3301–E3310.","ama":"Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(35):E3301-E3310. doi:<a href=\"https://doi.org/10.1073/pnas.1217428110\">10.1073/pnas.1217428110</a>","chicago":"Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217428110\">https://doi.org/10.1073/pnas.1217428110</a>.","apa":"Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., &#38; de Bono, M. (2013). In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217428110\">https://doi.org/10.1073/pnas.1217428110</a>","mla":"Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 35, Proceedings of the National Academy of Sciences, 2013, pp. E3301–10, doi:<a href=\"https://doi.org/10.1073/pnas.1217428110\">10.1073/pnas.1217428110</a>."},"year":"2013","publisher":"Proceedings of the National Academy of Sciences","file_date_updated":"2020-07-14T12:47:20Z","intvolume":"       110","file":[{"access_level":"open_access","date_created":"2019-03-20T14:07:53Z","creator":"kschuh","file_id":"6134","file_size":2198763,"checksum":"3ee28a694f74a49f0d098970ae391a91","date_updated":"2020-07-14T12:47:20Z","content_type":"application/pdf","file_name":"2013_PNAS_Couto.pdf","relation":"main_file"}],"title":"In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor","external_id":{"pmid":["23940325"]},"day":"27","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"date_published":"2013-08-27T00:00:00Z","page":"E3301-E3310","abstract":[{"lang":"eng","text":"cGMP signaling is widespread in the nervous system. However, it has proved difficult to visualize and genetically probe endogenously evoked cGMP dynamics in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical O2-binding soluble guanylate cyclase and that is sustained until oxygen levels fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2) and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation following a rise in O2, apparently by keeping in check gating of cGMP channels and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible when the same neuron in an individual animal is stimulated repeatedly, suggesting that cGMP transduction has high intrinsic reliability. However, responses vary substantially across individuals, despite animals being genetically identical and similarly reared. This variability may reflect stochastic differences in expression of cGMP signaling components. Our work provides in vivo insights into the architecture of neuronal cGMP signaling."}]},{"date_published":"2013-06-01T00:00:00Z","_id":"6135","author":[{"last_name":"Rodriguez","full_name":"Rodriguez, Miriam","first_name":"Miriam"},{"last_name":"Snoek","first_name":"L. Basten","full_name":"Snoek, L. Basten"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono"},{"last_name":"Kammenga","full_name":"Kammenga, Jan E.","first_name":"Jan E."}],"page":"367-374","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.tig.2013.01.010","extern":"1","publication_identifier":{"issn":["0168-9525"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery."}],"date_created":"2019-03-20T14:17:42Z","publisher":"Elsevier","intvolume":"        29","date_updated":"2021-01-12T08:06:17Z","volume":29,"type":"journal_article","citation":{"ieee":"M. Rodriguez, L. B. Snoek, M. de Bono, and J. E. Kammenga, “Worms under stress: C. elegans stress response and its relevance to complex human disease and aging,” <i>Trends in Genetics</i>, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.","short":"M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29 (2013) 367–374.","mla":"Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” <i>Trends in Genetics</i>, vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:<a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">10.1016/j.tig.2013.01.010</a>.","apa":"Rodriguez, M., Snoek, L. B., de Bono, M., &#38; Kammenga, J. E. (2013). Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">https://doi.org/10.1016/j.tig.2013.01.010</a>","chicago":"Rodriguez, Miriam, L. Basten Snoek, Mario de Bono, and Jan E. Kammenga. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” <i>Trends in Genetics</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">https://doi.org/10.1016/j.tig.2013.01.010</a>.","ista":"Rodriguez M, Snoek LB, de Bono M, Kammenga JE. 2013. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 29(6), 367–374.","ama":"Rodriguez M, Snoek LB, de Bono M, Kammenga JE. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. <i>Trends in Genetics</i>. 2013;29(6):367-374. doi:<a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">10.1016/j.tig.2013.01.010</a>"},"issue":"6","year":"2013","month":"06","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Trends in Genetics","title":"Worms under stress: C. elegans stress response and its relevance to complex human disease and aging","oa_version":"None","status":"public"},{"date_published":"2013-05-09T00:00:00Z","_id":"6370","author":[{"last_name":"Lin","full_name":"Lin, Tze-Chia","first_name":"Tze-Chia"},{"last_name":"Cole","first_name":"Jacqueline M.","full_name":"Cole, Jacqueline M."},{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"},{"full_name":"Edwards, Alison J.","first_name":"Alison J.","last_name":"Edwards"},{"first_name":"Ross O.","full_name":"Piltz, Ross O.","last_name":"Piltz"},{"full_name":"Pérez-Moreno, Javier","first_name":"Javier","last_name":"Pérez-Moreno"},{"full_name":"Seo, Ji-Youn","first_name":"Ji-Youn","last_name":"Seo"},{"full_name":"Lee, Seung-Chul","first_name":"Seung-Chul","last_name":"Lee"},{"last_name":"Clays","full_name":"Clays, Koen","first_name":"Koen"},{"full_name":"Kwon, O-Pil","first_name":"O-Pil","last_name":"Kwon"}],"page":"9416-9430","quality_controlled":"1","doi":"10.1021/jp400648q","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"issn":["1932-7447","1932-7455"]},"publication_status":"published","abstract":[{"lang":"eng","text":"The molecular and supramolecular origins of the superior nonlinear optical (NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile), are presented. The molecular charge-transfer distribution is topographically mapped, demonstrating that a uniformly delocalized passive electronic medium facilitates the charge-transfer between the phenolic electron donor and the cyano electron acceptors which lie at opposite ends of the molecule. Its ability to act as a “push–pull” π-conjugated molecule is quantified, relative to similar materials, by supporting empirical calculations; these include bond-length alternation and harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with frontier molecular orbital considerations, reveal that OH1 can exist readily in its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals a correlation between the quinoidal resonance contribution to the overall structure of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally locked polyene framework materials. Solid-state tensorial coefficients of the molecular dipole, polarizability, and the first hyperpolarizability for OH1 are derived from the first-, second-, and third-order electronic moments of the experimental charge-density distribution. The overall solid-state molecular dipole moment is compared with those from gas-phase calculations, revealing that crystal field effects are very significant in OH1. The solid-state hyperpolarizability derived from this charge-density study affords good agreement with gas-phase calculations as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced second harmonic (EFISH) generation. This lends support to the further use of charge-density studies to calculate solid-state hyperpolarizability coefficients in other organic NLO materials. Finally, this charge-density study is also employed to provide an advanced classification of hydrogen bonds in OH1, which requires more stringent criteria than those from conventional structure analysis. As a result, only the strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed, it is this electrostatic interaction that influences the molecular charge transfer: the other four, weaker, nonbonded contacts nonetheless affect the crystal packing. Overall, the establishment of these structure–property relationships lays a blueprint for designing further, more NLO efficient, materials in this industrially leading organic family of compounds."}],"date_created":"2019-05-03T09:40:31Z","publisher":"American Chemical Society (ACS)","intvolume":"       117","date_updated":"2021-01-12T08:07:17Z","volume":117,"type":"journal_article","citation":{"ieee":"T.-C. Lin <i>et al.</i>, “Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations,” <i>The Journal of Physical Chemistry C</i>, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.","short":"T.-C. Lin, J.M. Cole, A.P. Higginbotham, A.J. Edwards, R.O. Piltz, J. Pérez-Moreno, J.-Y. Seo, S.-C. Lee, K. Clays, O.-P. Kwon, The Journal of Physical Chemistry C 117 (2013) 9416–9430.","mla":"Lin, Tze-Chia, et al. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” <i>The Journal of Physical Chemistry C</i>, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:<a href=\"https://doi.org/10.1021/jp400648q\">10.1021/jp400648q</a>.","apa":"Lin, T.-C., Cole, J. M., Higginbotham, A. P., Edwards, A. J., Piltz, R. O., Pérez-Moreno, J., … Kwon, O.-P. (2013). Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. <i>The Journal of Physical Chemistry C</i>. American Chemical Society (ACS). <a href=\"https://doi.org/10.1021/jp400648q\">https://doi.org/10.1021/jp400648q</a>","chicago":"Lin, Tze-Chia, Jacqueline M. Cole, Andrew P Higginbotham, Alison J. Edwards, Ross O. Piltz, Javier Pérez-Moreno, Ji-Youn Seo, Seung-Chul Lee, Koen Clays, and O-Pil Kwon. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” <i>The Journal of Physical Chemistry C</i>. American Chemical Society (ACS), 2013. <a href=\"https://doi.org/10.1021/jp400648q\">https://doi.org/10.1021/jp400648q</a>.","ista":"Lin T-C, Cole JM, Higginbotham AP, Edwards AJ, Piltz RO, Pérez-Moreno J, Seo J-Y, Lee S-C, Clays K, Kwon O-P. 2013. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 117(18), 9416–9430.","ama":"Lin T-C, Cole JM, Higginbotham AP, et al. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. <i>The Journal of Physical Chemistry C</i>. 2013;117(18):9416-9430. doi:<a href=\"https://doi.org/10.1021/jp400648q\">10.1021/jp400648q</a>"},"issue":"18","year":"2013","day":"09","month":"05","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations","publication":"The Journal of Physical Chemistry C","oa_version":"None","status":"public"},{"quality_controlled":0,"doi":"10.1038/nature11871","extern":1,"date_published":"2013-02-28T00:00:00Z","_id":"1978","page":"443 - 448","author":[{"last_name":"Baradaran","full_name":"Baradaran, Rozbeh ","first_name":"Rozbeh"},{"full_name":"Berrisford, John M","first_name":"John","last_name":"Berrisford"},{"last_name":"Minhas","full_name":"Minhas, Gurdeep S","first_name":"Gurdeep"},{"last_name":"Sazanov","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle."}],"date_created":"2018-12-11T11:55:01Z","acknowledgement":"This work was funded by the Medical Research Council.","publication_status":"published","type":"journal_article","citation":{"ieee":"R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure of the entire respiratory complex i,” <i>Nature</i>, vol. 494, no. 7438. Nature Publishing Group, pp. 443–448, 2013.","short":"R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.","chicago":"Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>.","ista":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of the entire respiratory complex i. Nature. 494(7438), 443–448.","ama":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire respiratory complex i. <i>Nature</i>. 2013;494(7438):443-448. doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>","mla":"Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48, doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>.","apa":"Baradaran, R., Berrisford, J., Minhas, G., &#38; Sazanov, L. A. (2013). Crystal structure of the entire respiratory complex i. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>"},"issue":"7438","year":"2013","publisher":"Nature Publishing Group","intvolume":"       494","volume":494,"date_updated":"2021-01-12T06:54:28Z","publist_id":"5107","publication":"Nature","title":"Crystal structure of the entire respiratory complex i","status":"public","day":"28","month":"02"},{"author":[{"last_name":"Bonny","full_name":"Bonny, Mike ","first_name":"Mike"},{"first_name":"Elisabeth","full_name":"Fischer-Friedrich, Elisabeth","last_name":"Fischer Friedrich"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","full_name":"Martin Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"}],"_id":"1988","date_published":"2013-12-01T00:00:00Z","extern":1,"quality_controlled":0,"doi":"10.1371/journal.pcbi.1003347","publication_status":"published","date_created":"2018-12-11T11:55:04Z","abstract":[{"text":"The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally.","lang":"eng"}],"volume":9,"date_updated":"2021-01-12T06:54:32Z","intvolume":"         9","publisher":"Public Library of Science","year":"2013","issue":"12","citation":{"short":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013).","ieee":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation,” <i>PLoS Computational Biology</i>, vol. 9, no. 12. Public Library of Science, 2013.","mla":"Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>, vol. 9, no. 12, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>.","apa":"Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., &#38; Kruse, K. (2013). Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>","chicago":"Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille, and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>.","ama":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>","ista":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 9(12)."},"type":"journal_article","day":"01","month":"12","status":"public","title":"Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation","publication":"PLoS Computational Biology","publist_id":"5095"},{"quality_controlled":0,"doi":"10.1038/nature12235","extern":1,"date_published":"2013-07-18T00:00:00Z","_id":"1991","author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bachtrog","full_name":"Bachtrog, Doris","first_name":"Doris"}],"page":"332 - 335","abstract":[{"lang":"eng","text":"Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur."}],"date_created":"2018-12-11T11:55:05Z","publication_status":"published","acknowledgement":"Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B.","type":"journal_article","citation":{"ista":"Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335.","ama":"Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. 2013;499(7458):332-335. doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>.","apa":"Vicoso, B., &#38; Bachtrog, D. (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>, vol. 499, no. 7458, Nature Publishing Group, 2013, pp. 332–35, doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>.","ieee":"B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome in Drosophila,” <i>Nature</i>, vol. 499, no. 7458. Nature Publishing Group, pp. 332–335, 2013.","short":"B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335."},"issue":"7458","year":"2013","publisher":"Nature Publishing Group","intvolume":"       499","volume":499,"date_updated":"2021-01-12T06:54:33Z","publist_id":"5092","title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","publication":"Nature","status":"public","month":"07","day":"18"},{"volume":7721,"date_updated":"2025-09-23T09:24:13Z","oa":1,"type":"conference","ec_funded":1,"month":"01","publication":"Mathematical and Engineering Methods in Computer Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","status":"public","corr_author":"1","_id":"19995","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"}],"quality_controlled":"1","doi":"10.1007/978-3-642-36046-6_11","OA_place":"repository","department":[{"_id":"KrCh"}],"arxiv":1,"scopus_import":"1","alternative_title":["LNCS"],"publication_status":"published","acknowledgement":"Work of the second author supported by the Sino-Danish Center for the Theory of Interactive Computation, funded by the Danish National Research Foundation and the National Science Foundation of China (under the grant 61061130540). The second author acknowledge support from the Center for research in the Foundations of Electronic Markets (CFEM), supported by the Danish Strategic Research Council. The first author was supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","conference":{"end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science","location":"Znojmo, Czech Republic","start_date":"2012-10-25"},"date_created":"2025-07-10T14:08:49Z","publisher":"Springer Nature","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1209.3617","open_access":"1"}],"article_processing_charge":"No","intvolume":"      7721","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, in:, Mathematical and Engineering Methods in Computer Science, Springer Nature, 2013, pp. 106–117.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “Strategy complexity of finite-horizon Markov decision processes and simple stochastic games,” in <i>Mathematical and Engineering Methods in Computer Science</i>, Znojmo, Czech Republic, 2013, vol. 7721, pp. 106–117.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721, Springer Nature, 2013, pp. 106–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 106–117). Znojmo, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” In <i>Mathematical and Engineering Methods in Computer Science</i>, 7721:106–17. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>.","ama":"Chatterjee K, Ibsen-Jensen R. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In: <i>Mathematical and Engineering Methods in Computer Science</i>. Vol 7721. Springer Nature; 2013:106-117. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2013. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. Mathematical and Engineering Methods in Computer Science. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7721, 106–117."},"year":"2013","external_id":{"arxiv":["1209.3617"]},"day":"17","OA_type":"green","title":"Strategy complexity of finite-horizon Markov decision processes and simple stochastic games","date_published":"2013-01-17T00:00:00Z","page":"106-117","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783642360466"],"isbn":["9783642360442"],"eissn":["1611-3349"],"issn":["0302-9743"]},"abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) and simple stochastic games (SSGs) provide a rich mathematical framework to study many important problems related to probabilistic systems. MDPs and SSGs with finite-horizon objectives, where the goal is to maximize the probability to reach a target state in a given finite time, is a classical and well-studied problem. In this work we consider the strategy complexity of finite-horizon MDPs and SSGs. We show that for all ε > 0, the natural class of counter-based strategies require at most log log/(1/ε) + n + 1 memory states, and memory of size Omega(log log(1/ε) + n) is required, for ε-optimality, where n is the number of states of the MDP (resp. SSG). Thus our bounds are asymptotically optimal. We then study the periodic property of optimal strategies, and show a sub-exponential lower bound on the period for optimal strategies."}]},{"language":[{"iso":"eng"}],"date_published":"2013-08-01T00:00:00Z","page":"137 - 166","abstract":[{"text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression.","lang":"eng"}],"citation":{"apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166.","chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013."},"year":"2013","main_file_link":[{"url":"http://repository.cmu.edu/jpc/vol5/iss1/6","open_access":"1"}],"article_processing_charge":"No","publisher":"Carnegie Mellon University","intvolume":"         5","title":"Privacy-preserving data sharing for genome-wide association studies","day":"01","quality_controlled":"1","doi":"10.29012/jpc.v5i1.629","department":[{"_id":"CaUh"}],"ddc":["000"],"_id":"2009","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","first_name":"Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler"},{"last_name":"Slavkovic","full_name":"Slavkovic, Aleksandra","first_name":"Aleksandra"},{"full_name":"Fienberg, Stephen","first_name":"Stephen","last_name":"Fienberg"}],"date_created":"2018-12-11T11:55:11Z","publication_status":"published","type":"journal_article","oa":1,"issue":"1","volume":5,"date_updated":"2026-06-18T18:20:21Z","publist_id":"5067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Privacy and Confidentiality ","oa_version":"Published Version","status":"public","month":"08"},{"ddc":["500"],"_id":"2010","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler"},{"last_name":"Raskutti","first_name":"Garvesh","full_name":"Raskutti, Garvesh"},{"first_name":"Peter","full_name":"Bühlmann, Peter","last_name":"Bühlmann"},{"first_name":"Bin","full_name":"Yu, Bin","last_name":"Yu"}],"doi":"10.1214/12-AOS1080","quality_controlled":"1","scopus_import":"1","arxiv":1,"department":[{"_id":"CaUh"}],"publication_status":"published","date_created":"2018-12-11T11:55:11Z","date_updated":"2026-06-18T18:20:45Z","volume":41,"type":"journal_article","oa":1,"issue":"2","month":"04","publist_id":"5066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"The Annals of Statistics","oa_version":"Published Version","status":"public","date_published":"2013-04-01T00:00:00Z","page":"436 - 463","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case."}],"isi":1,"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1214/12-AOS1080"}],"article_processing_charge":"No","publisher":"Institute of Mathematical Statistics","intvolume":"        41","citation":{"ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463.","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>","chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>.","apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>","mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013."},"year":"2013","external_id":{"isi":["000320488200002"],"arxiv":["1207.0547"]},"day":"01","title":"Geometry of the faithfulness assumption in causal inference"},{"date_published":"2013-04-16T00:00:00Z","_id":"2074","author":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Beatriz Vicoso"},{"full_name":"Kaiser, Vera B","first_name":"Vera","last_name":"Kaiser"},{"last_name":"Bachtrog","first_name":"Doris","full_name":"Bachtrog, Doris"}],"page":"6453 - 6458","doi":"10.1073/pnas.1217027110","quality_controlled":0,"extern":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. "}],"date_created":"2018-12-11T11:55:33Z","publisher":"National Academy of Sciences","intvolume":"       110","volume":110,"date_updated":"2021-01-12T06:55:08Z","type":"journal_article","citation":{"ama":"Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. 2013;110(16):6453-6458. doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>","ista":"Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458.","chicago":"Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>.","apa":"Vicoso, B., Kaiser, V., &#38; Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>","mla":"Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>.","ieee":"B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” <i>PNAS</i>, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.","short":"B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458."},"issue":"16","year":"2013","month":"04","day":"16","publist_id":"4964","publication":"PNAS","title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution","status":"public"},{"doi":"10.1371/journal.pbio.1001643","quality_controlled":0,"extern":1,"date_published":"2013-08-27T00:00:00Z","_id":"2076","author":[{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"},{"last_name":"Emerson","first_name":"Jr","full_name":"Emerson, Jr J."},{"last_name":"Zektser","first_name":"Yulia","full_name":"Zektser, Yulia"},{"full_name":"Mahajan, Shivani","first_name":"Shivani","last_name":"Mahajan"},{"last_name":"Bachtrog","full_name":"Bachtrog, Doris","first_name":"Doris"}],"abstract":[{"text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n","lang":"eng"}],"date_created":"2018-12-11T11:55:34Z","acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB.","publication_status":"published","type":"journal_article","citation":{"ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” <i>PLoS Biology</i>, vol. 11, no. 8. Public Library of Science, 2013.","short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013).","apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., &#38; Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>, vol. 11, no. 8, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>.","ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. 2013;11(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).","chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>."},"issue":"8","year":"2013","publisher":"Public Library of Science","intvolume":"        11","date_updated":"2021-01-12T06:55:09Z","volume":11,"publist_id":"4962","publication":"PLoS Biology","title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","status":"public","month":"08","day":"27","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"month":"12","publication":"Physical Review Letters","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","oa_version":"Preprint","volume":111,"date_updated":"2021-11-29T14:05:19Z","oa":1,"type":"journal_article","issue":"24","acknowledgement":"This work was supported by the ERC Advanced Grant 227758, the National Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3 of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941 ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support from the Alexander von Humboldt Foundation.","publication_status":"published","pmid":1,"date_created":"2021-11-29T13:29:31Z","_id":"10384","article_type":"original","author":[{"full_name":"Mognetti, B. M.","first_name":"B. M.","last_name":"Mognetti"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"first_name":"S.","full_name":"Angioletti-Uberti, S.","last_name":"Angioletti-Uberti"},{"full_name":"Cacciuto, A.","first_name":"A.","last_name":"Cacciuto"},{"full_name":"Valeriani, C.","first_name":"C.","last_name":"Valeriani"},{"full_name":"Frenkel, D.","first_name":"D.","last_name":"Frenkel"}],"doi":"10.1103/physrevlett.111.245702","quality_controlled":"1","arxiv":1,"scopus_import":"1","external_id":{"pmid":["24483677"],"arxiv":["1311.4681"]},"article_number":"245702","day":"11","title":"Living clusters and crystals from low-density suspensions of active colloids","publisher":"American Physical Society","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.4681"}],"intvolume":"       111","citation":{"ieee":"B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel, “Living clusters and crystals from low-density suspensions of active colloids,” <i>Physical Review Letters</i>, vol. 111, no. 24. American Physical Society, 2013.","short":"B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013).","apa":"Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani, C., &#38; Frenkel, D. (2013). Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>","mla":"Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>, vol. 111, no. 24, 245702, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>.","ama":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. 2013;111(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>","ista":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. 2013. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 111(24), 245702.","chicago":"Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>."},"year":"2013","keyword":["general physics and astronomy"],"abstract":[{"text":"Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.","lang":"eng"}],"date_published":"2013-12-11T00:00:00Z","extern":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}}]