[{"day":"15","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2011-03-15T00:00:00Z","title":"Cells on the move in Philadelphia","publication":"Molecular Biology and Evolution","has_accepted_license":"1","type":"journal_article","scopus_import":1,"quality_controlled":"1","publication_status":"published","publisher":"Oxford University Press","article_type":"original","month":"03","citation":{"chicago":"Sixt, Michael K, and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>.","mla":"Sixt, Michael K., and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6, Oxford University Press, 2011, p. 724, doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>.","short":"M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724.","ieee":"M. K. Sixt and C. Parent, “Cells on the move in Philadelphia,” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6. Oxford University Press, p. 724, 2011.","ama":"Sixt MK, Parent C. Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. 2011;22(6):724. doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>","apa":"Sixt, M. K., &#38; Parent, C. (2011). Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>","ista":"Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology and Evolution. 22(6), 724."},"department":[{"_id":"MiSi"}],"publist_id":"3238","date_created":"2018-12-11T12:02:57Z","date_updated":"2021-01-12T07:43:01Z","intvolume":"        22","file":[{"content_type":"application/pdf","checksum":"3467986ab7a64e7694ffd1013b5d9da9","file_id":"5283","date_created":"2018-12-12T10:17:29Z","date_updated":"2020-07-14T12:46:11Z","access_level":"open_access","relation":"main_file","file_name":"IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf","file_size":105421,"creator":"system"}],"volume":22,"doi":"10.1091/mbc.E10-12-0958","issue":"6","_id":"3371","ddc":["570"],"oa":1,"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The Minisymposium “Cell Migration and Motility” was attended by approximately 500 visitors and covered a broad range of questions in the field using diverse model systems. Topics comprised actin dynamics, cell polarity, force transduction, signal transduction, bar- rier transmigration, and chemotactic guidance."}],"author":[{"full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carole","last_name":"Parent","full_name":"Parent, Carole"}],"page":"724","oa_version":"Published Version","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"pubrep_id":"373","year":"2011"},{"pmid":1,"language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["21430721"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Nowak et al.1 argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues."}],"oa_version":"Submitted Version","status":"public","author":[{"first_name":"Patrick","last_name":"Abbot","full_name":"Abbot, Patrick"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"last_name":"Alcock","full_name":"Alcock, John","first_name":"John"},{"last_name":"Alizon","full_name":"Alizon, Samuel","first_name":"Samuel"},{"first_name":"Joao","full_name":"Alpedrinha, Joao","last_name":"Alpedrinha"},{"full_name":"Andersson, Malte","last_name":"Andersson","first_name":"Malte"},{"first_name":"Jean","last_name":"Andre","full_name":"Andre, Jean"},{"full_name":"Van Baalen, Minus","last_name":"Van Baalen","first_name":"Minus"},{"full_name":"Balloux, Francois","last_name":"Balloux","first_name":"Francois"},{"first_name":"Sigal","last_name":"Balshine","full_name":"Balshine, Sigal"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Beukeboom","full_name":"Beukeboom, Leo","first_name":"Leo"},{"last_name":"Biernaskie","full_name":"Biernaskie, Jay","first_name":"Jay"},{"first_name":"Trine","last_name":"Bilde","full_name":"Bilde, Trine"},{"last_name":"Borgia","full_name":"Borgia, Gerald","first_name":"Gerald"},{"last_name":"Breed","full_name":"Breed, Michael","first_name":"Michael"},{"first_name":"Sam","full_name":"Brown, Sam","last_name":"Brown"},{"first_name":"Redouan","full_name":"Bshary, Redouan","last_name":"Bshary"},{"full_name":"Buckling, Angus","last_name":"Buckling","first_name":"Angus"},{"full_name":"Burley, Nancy","last_name":"Burley","first_name":"Nancy"},{"last_name":"Burton Chellew","full_name":"Burton Chellew, Max","first_name":"Max"},{"full_name":"Cant, Michael","last_name":"Cant","first_name":"Michael"},{"full_name":"Chapuisat, Michel","last_name":"Chapuisat","first_name":"Michel"},{"first_name":"Eric","last_name":"Charnov","full_name":"Charnov, Eric"},{"first_name":"Tim","full_name":"Clutton Brock, Tim","last_name":"Clutton Brock"},{"full_name":"Cockburn, Andrew","last_name":"Cockburn","first_name":"Andrew"},{"last_name":"Cole","full_name":"Cole, Blaine","first_name":"Blaine"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"},{"last_name":"Cosmides","full_name":"Cosmides, Leda","first_name":"Leda"},{"first_name":"Iain","full_name":"Couzin, Iain","last_name":"Couzin"},{"first_name":"Jerry","full_name":"Coyne, Jerry","last_name":"Coyne"},{"first_name":"Scott","full_name":"Creel, Scott","last_name":"Creel"},{"last_name":"Crespi","full_name":"Crespi, Bernard","first_name":"Bernard"},{"full_name":"Curry, Robert","last_name":"Curry","first_name":"Robert"},{"first_name":"Sasha","last_name":"Dall","full_name":"Dall, Sasha"},{"last_name":"Day","full_name":"Day, Troy","first_name":"Troy"},{"last_name":"Dickinson","full_name":"Dickinson, Janis","first_name":"Janis"},{"first_name":"Lee","full_name":"Dugatkin, 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Michael","last_name":"Gardner","first_name":"Michael"},{"first_name":"Thomas","full_name":"Getty, Thomas","last_name":"Getty"},{"last_name":"Goodisman","full_name":"Goodisman, Michael","first_name":"Michael"},{"full_name":"Grafen, Alan","last_name":"Grafen","first_name":"Alan"},{"full_name":"Grosberg, Rick","last_name":"Grosberg","first_name":"Rick"},{"last_name":"Grozinger","full_name":"Grozinger, Christina","first_name":"Christina"},{"full_name":"Gouyon, Pierre","last_name":"Gouyon","first_name":"Pierre"},{"full_name":"Gwynne, Darryl","last_name":"Gwynne","first_name":"Darryl"},{"first_name":"Paul","last_name":"Harvey","full_name":"Harvey, Paul"},{"last_name":"Hatchwell","full_name":"Hatchwell, Ben","first_name":"Ben"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"full_name":"Helantera, Heikki","last_name":"Helantera","first_name":"Heikki"},{"first_name":"Ken","full_name":"Helms, Ken","last_name":"Helms"},{"last_name":"Hill","full_name":"Hill, 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Olav","last_name":"Rueppell"},{"last_name":"Sachs","full_name":"Sachs, Joel","first_name":"Joel"},{"first_name":"Lorenzo","full_name":"Santorelli, Lorenzo","last_name":"Santorelli"},{"first_name":"Paul","last_name":"Schmid Hempel","full_name":"Schmid Hempel, Paul"},{"first_name":"Michael","last_name":"Schwarz","full_name":"Schwarz, Michael"},{"last_name":"Scott Phillips","full_name":"Scott Phillips, Tom","first_name":"Tom"},{"full_name":"Shellmann Sherman, Janet","last_name":"Shellmann Sherman","first_name":"Janet"},{"full_name":"Sherman, Paul","last_name":"Sherman","first_name":"Paul"},{"first_name":"David","last_name":"Shuker","full_name":"Shuker, David"},{"full_name":"Smith, Jeff","last_name":"Smith","first_name":"Jeff"},{"first_name":"Joseph","last_name":"Spagna","full_name":"Spagna, Joseph"},{"first_name":"Beverly","last_name":"Strassmann","full_name":"Strassmann, Beverly"},{"first_name":"Andrew","last_name":"Suarez","full_name":"Suarez, Andrew"},{"first_name":"Liselotte","full_name":"Sundström, Liselotte","last_name":"Sundström"},{"full_name":"Taborsky, Michael","last_name":"Taborsky","first_name":"Michael"},{"full_name":"Taylor, Peter","last_name":"Taylor","first_name":"Peter"},{"first_name":"Graham","full_name":"Thompson, Graham","last_name":"Thompson"},{"first_name":"John","full_name":"Tooby, John","last_name":"Tooby"},{"first_name":"Neil","last_name":"Tsutsui","full_name":"Tsutsui, Neil"},{"last_name":"Tsuji","full_name":"Tsuji, Kazuki","first_name":"Kazuki"},{"first_name":"Stefano","full_name":"Turillazzi, Stefano","last_name":"Turillazzi"},{"full_name":"Úbeda, Francisco","last_name":"Úbeda","first_name":"Francisco"},{"first_name":"Edward","full_name":"Vargo, Edward","last_name":"Vargo"},{"first_name":"Bernard","last_name":"Voelkl","full_name":"Voelkl, Bernard"},{"full_name":"Wenseleers, Tom","last_name":"Wenseleers","first_name":"Tom"},{"first_name":"Stuart","full_name":"West, Stuart","last_name":"West"},{"last_name":"West Eberhard","full_name":"West Eberhard, Mary","first_name":"Mary"},{"first_name":"David","full_name":"Westneat, David","last_name":"Westneat"},{"full_name":"Wiernasz, Diane","last_name":"Wiernasz","first_name":"Diane"},{"last_name":"Wild","full_name":"Wild, Geoff","first_name":"Geoff"},{"last_name":"Wrangham","full_name":"Wrangham, Richard","first_name":"Richard"},{"first_name":"Andrew","last_name":"Young","full_name":"Young, Andrew"},{"full_name":"Zeh, David","last_name":"Zeh","first_name":"David"},{"first_name":"Jeanne","last_name":"Zeh","full_name":"Zeh, Jeanne"},{"last_name":"Zink","full_name":"Zink, Andrew","first_name":"Andrew"}],"page":"E1 - E4","year":"2011","day":"23","date_published":"2011-03-23T00:00:00Z","title":"Inclusive fitness theory and eusociality","publication":"Nature","publication_status":"published","quality_controlled":"1","scopus_import":1,"type":"journal_article","publisher":"Nature Publishing Group","publist_id":"3237","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:43:02Z","date_created":"2018-12-11T12:02:57Z","intvolume":"       471","month":"03","citation":{"mla":"Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>.","short":"P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4.","ieee":"P. Abbot <i>et al.</i>, “Inclusive fitness theory and eusociality,” <i>Nature</i>, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.","chicago":"Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>.","ista":"Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4.","ama":"Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. <i>Nature</i>. 2011;471(7339):E1-E4. doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>","apa":"Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>"},"issue":"7339","_id":"3372","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/"}],"volume":471,"doi":"10.1038/nature09831"},{"main_file_link":[{"open_access":"1","url":"https://www.osapublishing.org/ol/abstract.cfm?uri=ol-36-7-1260"}],"volume":36,"doi":"10.1364/OL.36.001260","issue":"7","_id":"3373","month":"03","citation":{"apa":"Jahnel, M., Behrndt, M., Jannasch, A., Schaeffer, E., &#38; Grill, S. (2011). Measuring the complete force field of an optical trap. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.36.001260\">https://doi.org/10.1364/OL.36.001260</a>","ama":"Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. Measuring the complete force field of an optical trap. <i>Optics Letters</i>. 2011;36(7):1260-1262. doi:<a href=\"https://doi.org/10.1364/OL.36.001260\">10.1364/OL.36.001260</a>","ista":"Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. 2011. Measuring the complete force field of an optical trap. Optics Letters. 36(7), 1260–1262.","chicago":"Jahnel, Marcus, Martin Behrndt, Anita Jannasch, Erik Schaeffer, and Stephan Grill. “Measuring the Complete Force Field of an Optical Trap.” <i>Optics Letters</i>. Optica Publishing Group, 2011. <a href=\"https://doi.org/10.1364/OL.36.001260\">https://doi.org/10.1364/OL.36.001260</a>.","ieee":"M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, and S. Grill, “Measuring the complete force field of an optical trap,” <i>Optics Letters</i>, vol. 36, no. 7. Optica Publishing Group, pp. 1260–1262, 2011.","mla":"Jahnel, Marcus, et al. “Measuring the Complete Force Field of an Optical Trap.” <i>Optics Letters</i>, vol. 36, no. 7, Optica Publishing Group, 2011, pp. 1260–62, doi:<a href=\"https://doi.org/10.1364/OL.36.001260\">10.1364/OL.36.001260</a>.","short":"M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, S. Grill, Optics Letters 36 (2011) 1260–1262."},"department":[{"_id":"CaHe"}],"publist_id":"3234","date_created":"2018-12-11T12:02:58Z","date_updated":"2023-10-17T12:16:58Z","intvolume":"        36","publication_status":"published","scopus_import":"1","type":"journal_article","quality_controlled":"1","publisher":"Optica Publishing Group","day":"30","title":"Measuring the complete force field of an optical trap","date_published":"2011-03-30T00:00:00Z","publication":"Optics Letters","year":"2011","author":[{"full_name":"Jahnel, Marcus","last_name":"Jahnel","first_name":"Marcus"},{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Jannasch, Anita","last_name":"Jannasch","first_name":"Anita"},{"first_name":"Erik","last_name":"Schaeffer","full_name":"Schaeffer, Erik"},{"full_name":"Grill, Stephan","last_name":"Grill","first_name":"Stephan"}],"page":"1260 - 1262","related_material":{"record":[{"id":"1403","status":"public","relation":"dissertation_contains"}]},"oa_version":"Published Version","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The use of optical traps to measure or apply forces on the molecular level requires a precise knowledge of the trapping force field. Close to the trap center, this field is typically approximated as linear in the displacement of the trapped microsphere. However, applications demanding high forces at low laser intensities can probe the light-microsphere interaction beyond the linear regime. Here, we measured the full nonlinear force and displacement response of an optical trap in two dimensions using a dual-beam optical trap setup with back-focal-plane photodetection. We observed a substantial stiffening of the trap beyond the linear regime that depends on microsphere size, in agreement with Mie theory calculations. Surprisingly, we found that the linear detection range for forces exceeds the one for displacement by far. Our approach allows for a complete calibration of an optical trap.","lang":"eng"}],"article_processing_charge":"No","oa":1,"language":[{"iso":"eng"}]},{"intvolume":"        23","status":"public","department":[{"_id":"GaTk"}],"publist_id":"3233","oa_version":"Submitted Version","date_created":"2018-12-11T12:02:58Z","date_updated":"2021-01-12T07:43:03Z","citation":{"ista":"Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.","ama":"Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. 2011;23(15). doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>","apa":"Tkačik, G., &#38; Walczak, A. (2011). Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>","mla":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>.","short":"G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).","ieee":"G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15. IOP Publishing Ltd., 2011.","chicago":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing Ltd., 2011. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>."},"author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Aleksandra","last_name":"Walczak","full_name":"Walczak, Aleksandra"}],"month":"04","_id":"3374","year":"2011","issue":"15","doi":"10.1088/0953-8984/23/15/153102","main_file_link":[{"url":"http://arxiv.org/abs/1101.4240","open_access":"1"}],"volume":23,"publication":"Journal of Physics: Condensed Matter","language":[{"iso":"eng"}],"day":"01","title":"Information transmission in genetic regulatory networks a review","date_published":"2011-04-01T00:00:00Z","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"IOP Publishing Ltd.","abstract":[{"lang":"eng","text":"Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'."}],"publication_status":"published","type":"journal_article","scopus_import":1,"quality_controlled":"1","article_number":"153102"},{"language":[{"iso":"eng"}],"pmid":1,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states.","lang":"eng"}],"article_processing_charge":"No","external_id":{"pmid":["21084341"]},"status":"public","oa_version":"Submitted Version","author":[{"full_name":"de Vladar, Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653","first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"page":"720 - 739","year":"2011","ec_funded":1,"publication":"Journal of the Royal Society Interface","day":"01","title":"The statistical mechanics of a polygenic character under stabilizing selection mutation and drift","date_published":"2011-05-01T00:00:00Z","publisher":"The Royal Society","type":"journal_article","publication_status":"published","quality_controlled":"1","scopus_import":"1","intvolume":"         8","department":[{"_id":"NiBa"}],"publist_id":"3232","date_updated":"2025-05-28T11:42:45Z","date_created":"2018-12-11T12:02:58Z","citation":{"ista":"de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 8(58), 720–739.","apa":"de Vladar, H., &#38; Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2010.0438\">https://doi.org/10.1098/rsif.2010.0438</a>","ama":"de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. <i>Journal of the Royal Society Interface</i>. 2011;8(58):720-739. doi:<a href=\"https://doi.org/10.1098/rsif.2010.0438\">10.1098/rsif.2010.0438</a>","ieee":"H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” <i>Journal of the Royal Society Interface</i>, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011.","short":"H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739.","mla":"de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” <i>Journal of the Royal Society Interface</i>, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:<a href=\"https://doi.org/10.1098/rsif.2010.0438\">10.1098/rsif.2010.0438</a>.","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2011. <a href=\"https://doi.org/10.1098/rsif.2010.0438\">https://doi.org/10.1098/rsif.2010.0438</a>."},"article_type":"original","month":"05","_id":"3375","issue":"58","doi":"10.1098/rsif.2010.0438","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/","open_access":"1"}],"volume":8},{"publisher":"Cell Press","publication_status":"published","scopus_import":1,"quality_controlled":"1","type":"journal_article","publication":"Molecular Cell","day":"20","date_published":"2011-05-20T00:00:00Z","title":"Resolution of gene regulatory conflicts caused by combinations of antibiotics","_id":"3376","issue":"4","doi":"10.1016/j.molcel.2011.04.016","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/"}],"volume":42,"intvolume":"        42","publist_id":"3231","department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T07:43:03Z","date_created":"2018-12-11T12:02:59Z","citation":{"chicago":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>.","short":"M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.","mla":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>.","ieee":"M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” <i>Molecular Cell</i>, vol. 42, no. 4. Cell Press, pp. 413–425, 2011.","ama":"Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. 2011;42(4):413-425. doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>","apa":"Bollenbach, M. T., &#38; Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>","ista":"Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425."},"acknowledgement":"This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.).","month":"05","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"year":"2011","status":"public","oa_version":"Submitted Version","author":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"},{"last_name":"Kishony","full_name":"Kishony, Roy","first_name":"Roy"}],"page":"413 - 425"},{"day":"01","date_published":"2011-06-01T00:00:00Z","title":"Quantifying transversality by measuring the robustness of intersections","publication":"Foundations of Computational Mathematics","scopus_import":1,"type":"journal_article","publication_status":"published","quality_controlled":"1","publisher":"Springer","month":"06","citation":{"apa":"Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2011). Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>","ama":"Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. 2011;11(3):345-361. doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>","ista":"Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361.","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>.","ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by measuring the robustness of intersections,” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3. Springer, pp. 345–361, 2011.","short":"H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361.","mla":"Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>."},"acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","department":[{"_id":"HeEd"}],"publist_id":"3230","date_created":"2018-12-11T12:02:59Z","date_updated":"2021-01-12T07:43:04Z","intvolume":"        11","volume":11,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0911.2142"}],"doi":"10.1007/s10208-011-9090-8","issue":"3","_id":"3377","oa":1,"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"By definition, transverse intersections are stable under in- finitesimal perturbations. Using persistent homology, we ex- tend this notion to sizeable perturbations. Specifically, we assign to each homology class of the intersection its robust- ness, the magnitude of a perturbation necessary to kill it, and prove that robustness is stable. Among the applications of this result is a stable notion of robustness for fixed points of continuous mappings and a statement of stability for con- tours of smooth mappings."}],"author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Dmitriy","full_name":"Morozov, Dmitriy","last_name":"Morozov"},{"id":"34A254A0-F248-11E8-B48F-1D18A9856A87","first_name":"Amit","full_name":"Patel, Amit","last_name":"Patel"}],"page":"345 - 361","oa_version":"Submitted Version","status":"public","year":"2011"},{"article_processing_charge":"No","abstract":[{"text":"Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa":1,"year":"2011","status":"public","oa_version":"Published Version","page":"221 - 232","author":[{"full_name":"Logeswaran, Sayanthan","last_name":"Logeswaran","first_name":"Sayanthan"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publisher":"Cambridge University Press","publication_status":"published","type":"journal_article","quality_controlled":"1","scopus_import":1,"publication":"Genetical Research","date_published":"2011-05-18T00:00:00Z","title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency","day":"18","_id":"3380","issue":"3","doi":"10.1017/S0016672311000115","volume":93,"main_file_link":[{"open_access":"1","url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf"}],"intvolume":"        93","date_created":"2018-12-11T12:03:00Z","date_updated":"2021-01-12T07:43:05Z","department":[{"_id":"NiBa"}],"publist_id":"3227","citation":{"ama":"Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. 2011;93(3):221-232. doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>","apa":"Logeswaran, S., &#38; Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>","ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232.","chicago":"Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>. Cambridge University Press, 2011. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>.","short":"S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.","mla":"Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>.","ieee":"S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” <i>Genetical Research</i>, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011."},"article_type":"original","month":"05"},{"abstract":[{"lang":"eng","text":"In this survey, we compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. All these languages — matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models — describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, and ease of use. Moreover, they provide different support for checking the well-formedness of a model and for analyzing a model."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:11Z","language":[{"iso":"eng"}],"oa":1,"ddc":["000"],"year":"2011","pubrep_id":"628","status":"public","oa_version":"Submitted Version","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3841"}]},"page":"823 - 841","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"},{"first_name":"Verena","last_name":"Wolf","full_name":"Wolf, Verena"}],"publisher":"World Scientific Publishing","type":"journal_article","scopus_import":1,"quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publication":"IJFCS: International Journal of Foundations of Computer Science","date_published":"2011-06-01T00:00:00Z","title":"Formalisms for specifying Markovian population models","day":"01","_id":"3381","issue":"4","doi":"10.1142/S0129054111008441","volume":22,"file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:11Z","relation":"main_file","date_created":"2018-12-12T10:08:45Z","file_id":"4707","checksum":"df88431872586c773fbcfea37d7b36a2","file_size":222840,"file_name":"IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf","creator":"system"}],"intvolume":"        22","date_updated":"2023-02-23T11:45:03Z","date_created":"2018-12-11T12:03:00Z","department":[{"_id":"ToHe"}],"publist_id":"3226","citation":{"mla":"Henzinger, Thomas A., et al. “Formalisms for Specifying Markovian Population Models.” <i>IJFCS: International Journal of Foundations of Computer Science</i>, vol. 22, no. 4, World Scientific Publishing, 2011, pp. 823–41, doi:<a href=\"https://doi.org/10.1142/S0129054111008441\">10.1142/S0129054111008441</a>.","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations of Computer Science 22 (2011) 823–841.","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” <i>IJFCS: International Journal of Foundations of Computer Science</i>, vol. 22, no. 4. World Scientific Publishing, pp. 823–841, 2011.","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models.” <i>IJFCS: International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2011. <a href=\"https://doi.org/10.1142/S0129054111008441\">https://doi.org/10.1142/S0129054111008441</a>.","ista":"Henzinger TA, Jobstmann B, Wolf V. 2011. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 22(4), 823–841.","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. <i>IJFCS: International Journal of Foundations of Computer Science</i>. 2011;22(4):823-841. doi:<a href=\"https://doi.org/10.1142/S0129054111008441\">10.1142/S0129054111008441</a>","apa":"Henzinger, T. A., Jobstmann, B., &#38; Wolf, V. (2011). Formalisms for specifying Markovian population models. <i>IJFCS: International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054111008441\">https://doi.org/10.1142/S0129054111008441</a>"},"month":"06"},{"intvolume":"         6","publist_id":"3223","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T07:43:07Z","date_created":"2018-12-11T12:03:01Z","citation":{"ista":"Tkačik G, Garrigan P, Ratliff C, Milcinski G, Klein J, Seyfarth L, Sterling P, Brainard D, Balasubramanian V. 2011. Natural images from the birthplace of the human eye. PLoS One. 6(6), e20409.","ama":"Tkačik G, Garrigan P, Ratliff C, et al. Natural images from the birthplace of the human eye. <i>PLoS One</i>. 2011;6(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0020409\">10.1371/journal.pone.0020409</a>","apa":"Tkačik, G., Garrigan, P., Ratliff, C., Milcinski, G., Klein, J., Seyfarth, L., … Balasubramanian, V. (2011). Natural images from the birthplace of the human eye. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0020409\">https://doi.org/10.1371/journal.pone.0020409</a>","mla":"Tkačik, Gašper, et al. “Natural Images from the Birthplace of the Human Eye.” <i>PLoS One</i>, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0020409\">10.1371/journal.pone.0020409</a>.","short":"G. Tkačik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).","ieee":"G. Tkačik <i>et al.</i>, “Natural images from the birthplace of the human eye,” <i>PLoS One</i>, vol. 6, no. 6. Public Library of Science, 2011.","chicago":"Tkačik, Gašper, Patrick Garrigan, Charles Ratliff, Grega Milcinski, Jennifer Klein, Lucia Seyfarth, Peter Sterling, David Brainard, and Vijay Balasubramanian. “Natural Images from the Birthplace of the Human Eye.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0020409\">https://doi.org/10.1371/journal.pone.0020409</a>."},"month":"06","_id":"3384","issue":"6","doi":"10.1371/journal.pone.0020409","file":[{"creator":"system","file_name":"IST-2015-379-v1+1_journal.pone.0020409.pdf","file_size":1424768,"access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:09:25Z","date_updated":"2020-07-14T12:46:11Z","checksum":"307d4356916471306e3705ac65b82fa1","file_id":"4749","content_type":"application/pdf"}],"volume":6,"publication":"PLoS One","license":"https://creativecommons.org/licenses/by/4.0/","day":"16","date_published":"2011-06-16T00:00:00Z","title":"Natural images from the birthplace of the human eye","publisher":"Public Library of Science","type":"journal_article","publication_status":"published","scopus_import":1,"quality_controlled":"1","has_accepted_license":"1","status":"public","oa_version":"Published Version","author":[{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Garrigan","full_name":"Garrigan, Patrick","first_name":"Patrick"},{"last_name":"Ratliff","full_name":"Ratliff, Charles","first_name":"Charles"},{"first_name":"Grega","full_name":"Milcinski, Grega","last_name":"Milcinski"},{"full_name":"Klein, Jennifer","last_name":"Klein","first_name":"Jennifer"},{"first_name":"Lucia","full_name":"Seyfarth, Lucia","last_name":"Seyfarth"},{"first_name":"Peter","last_name":"Sterling","full_name":"Sterling, Peter"},{"first_name":"David","last_name":"Brainard","full_name":"Brainard, David"},{"full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian","first_name":"Vijay"}],"year":"2011","pubrep_id":"379","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"ddc":["570"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Here we introduce a database of calibrated natural images publicly available through an easy-to-use web interface. Using a Nikon D70 digital SLR camera, we acquired about  six-megapixel images of Okavango Delta of Botswana, a tropical savanna habitat similar to where the human eye is thought to have evolved. Some sequences of images were captured unsystematically while following a baboon troop, while others were designed to vary a single parameter such as aperture, object distance, time of day or position on the horizon. Images are available in the raw RGB format and in grayscale. Images are also available in units relevant to the physiology of human cone photoreceptors, where pixel values represent the expected number of photoisomerizations per second for cones sensitive to long (L), medium (M) and short (S) wavelengths. This database is distributed under a Creative Commons Attribution-Noncommercial Unported license to facilitate research in computer vision, psychophysics of perception, and visual neuroscience."}],"file_date_updated":"2020-07-14T12:46:11Z","article_number":"e20409"},{"has_accepted_license":"1","publisher":"BioMed Central","type":"journal_article","publication_status":"published","scopus_import":1,"quality_controlled":"1","publication":"BMC Evolutionary Biology","day":"13","date_published":"2011-07-13T00:00:00Z","title":"Split based computation of majority rule supertrees","doi":"10.1186/1471-2148-11-205","file":[{"creator":"system","file_size":465042,"file_name":"IST-2015-372-v1+1_1471-2148-11-205.pdf","date_created":"2018-12-12T10:14:09Z","date_updated":"2020-07-14T12:46:11Z","access_level":"open_access","relation":"main_file","file_id":"5058","checksum":"68da8d04af1b97b4cbe8606e2f92ddd8","content_type":"application/pdf"}],"volume":11,"_id":"3387","issue":"205","citation":{"ista":"Kupczok A. 2011. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 11(205), 205.","ama":"Kupczok A. Split based computation of majority rule supertrees. <i>BMC Evolutionary Biology</i>. 2011;11(205). doi:<a href=\"https://doi.org/10.1186/1471-2148-11-205\">10.1186/1471-2148-11-205</a>","apa":"Kupczok, A. (2011). Split based computation of majority rule supertrees. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-11-205\">https://doi.org/10.1186/1471-2148-11-205</a>","short":"A. Kupczok, BMC Evolutionary Biology 11 (2011).","mla":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” <i>BMC Evolutionary Biology</i>, vol. 11, no. 205, 205, BioMed Central, 2011, doi:<a href=\"https://doi.org/10.1186/1471-2148-11-205\">10.1186/1471-2148-11-205</a>.","ieee":"A. Kupczok, “Split based computation of majority rule supertrees,” <i>BMC Evolutionary Biology</i>, vol. 11, no. 205. BioMed Central, 2011.","chicago":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2011. <a href=\"https://doi.org/10.1186/1471-2148-11-205\">https://doi.org/10.1186/1471-2148-11-205</a>."},"month":"07","intvolume":"        11","publist_id":"3219","department":[{"_id":"JoBo"}],"date_updated":"2021-01-12T07:43:08Z","date_created":"2018-12-11T12:03:03Z","file_date_updated":"2020-07-14T12:46:11Z","article_number":"205","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Background: Supertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods. Results: Here, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/ plumist. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well. Conclusions: The presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework.","lang":"eng"}],"oa":1,"ddc":["576"],"language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2011","pubrep_id":"372","author":[{"first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne","last_name":"Kupczok"}],"status":"public","oa_version":"Published Version"},{"oa_version":"Published Version","status":"public","author":[{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883"},{"last_name":"Nielsen","full_name":"Nielsen, Per","first_name":"Per"},{"first_name":"Jacobus","last_name":"Boomsma","full_name":"Boomsma, Jacobus"},{"first_name":"David","last_name":"Nash","full_name":"Nash, David"}],"pubrep_id":"371","year":"2011","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"ddc":["576"],"oa":1,"abstract":[{"text":"Background: Fragmentation of terrestrial ecosystems has had detrimental effects on metapopulations of habitat specialists. Maculinea butterflies have been particularly affected because of their specialized lifecycles, requiring both specific food-plants and host-ants. However, the interaction between dispersal, effective population size, and long-term genetic erosion of these endangered butterflies remains unknown. Using non-destructive sampling, we investigated the genetic diversity of the last extant population of M. arion in Denmark, which experienced critically low numbers in the 1980s. Results: Using nine microsatellite markers, we show that the population is genetically impoverished compared to nearby populations in Sweden, but less so than monitoring programs suggested. Ten additional short repeat microsatellites were used to reconstruct changes in genetic diversity and population structure over the last 77 years from museum specimens. We also tested amplification efficiency in such historical samples as a function of repeat length and sample age. Low population numbers in the 1980s did not affect genetic diversity, but considerable turnover of alleles has characterized this population throughout the time-span of our analysis. Conclusions: Our results suggest that M. arion is less sensitive to genetic erosion via population bottlenecks than previously thought, and that managing clusters of high quality habitat may be key for long-term conservation.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"201","file_date_updated":"2020-07-14T12:46:11Z","date_updated":"2021-01-12T07:43:08Z","date_created":"2018-12-11T12:03:03Z","publist_id":"3220","department":[{"_id":"SyCr"}],"intvolume":"        11","month":"07","citation":{"chicago":"Ugelvig, Line V, Per Nielsen, Jacobus Boomsma, and David Nash. “Reconstructing Eight Decades of Genetic Variation in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2011. <a href=\"https://doi.org/10.1186/1471-2148-11-201\">https://doi.org/10.1186/1471-2148-11-201</a>.","ieee":"L. V. Ugelvig, P. Nielsen, J. Boomsma, and D. Nash, “Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion,” <i>BMC Evolutionary Biology</i>, vol. 11, no. 201. BioMed Central, 2011.","mla":"Ugelvig, Line V., et al. “Reconstructing Eight Decades of Genetic Variation in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.” <i>BMC Evolutionary Biology</i>, vol. 11, no. 201, 201, BioMed Central, 2011, doi:<a href=\"https://doi.org/10.1186/1471-2148-11-201\">10.1186/1471-2148-11-201</a>.","short":"L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11 (2011).","apa":"Ugelvig, L. V., Nielsen, P., Boomsma, J., &#38; Nash, D. (2011). Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-11-201\">https://doi.org/10.1186/1471-2148-11-201</a>","ama":"Ugelvig LV, Nielsen P, Boomsma J, Nash D. Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. <i>BMC Evolutionary Biology</i>. 2011;11(201). doi:<a href=\"https://doi.org/10.1186/1471-2148-11-201\">10.1186/1471-2148-11-201</a>","ista":"Ugelvig LV, Nielsen P, Boomsma J, Nash D. 2011. Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. BMC Evolutionary Biology. 11(201), 201."},"issue":"201","_id":"3388","volume":11,"file":[{"creator":"system","file_name":"IST-2015-371-v1+1_1471-2148-11-201.pdf","file_size":2166556,"file_id":"5069","checksum":"9ebfed0740f1fa071d02ec32c2b8c17f","date_updated":"2020-07-14T12:46:11Z","date_created":"2018-12-12T10:14:18Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"doi":"10.1186/1471-2148-11-201","date_published":"2011-07-11T00:00:00Z","title":"Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion","day":"11","publication":"BMC Evolutionary Biology","publication_status":"published","scopus_import":1,"type":"journal_article","quality_controlled":"1","publisher":"BioMed Central","has_accepted_license":"1"},{"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1534/genetics.111.127555","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/"}],"volume":188,"_id":"3390","issue":"4","citation":{"ista":"Barton NH, Etheridge A. 2011. The relation between reproductive value and genetic contribution. Genetics. 188(4), 953–973.","apa":"Barton, N. H., &#38; Etheridge, A. (2011). The relation between reproductive value and genetic contribution. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.111.127555\">https://doi.org/10.1534/genetics.111.127555</a>","ama":"Barton NH, Etheridge A. The relation between reproductive value and genetic contribution. <i>Genetics</i>. 2011;188(4):953-973. doi:<a href=\"https://doi.org/10.1534/genetics.111.127555\">10.1534/genetics.111.127555</a>","ieee":"N. H. Barton and A. Etheridge, “The relation between reproductive value and genetic contribution,” <i>Genetics</i>, vol. 188, no. 4. Genetics Society of America, pp. 953–973, 2011.","mla":"Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” <i>Genetics</i>, vol. 188, no. 4, Genetics Society of America, 2011, pp. 953–73, doi:<a href=\"https://doi.org/10.1534/genetics.111.127555\">10.1534/genetics.111.127555</a>.","short":"N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.","chicago":"Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” <i>Genetics</i>. Genetics Society of America, 2011. <a href=\"https://doi.org/10.1534/genetics.111.127555\">https://doi.org/10.1534/genetics.111.127555</a>."},"month":"08","intvolume":"       188","date_updated":"2021-01-12T07:43:09Z","date_created":"2018-12-11T12:03:04Z","publist_id":"3217","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","type":"journal_article","quality_controlled":"1","scopus_import":1,"publication_status":"published","publication":"Genetics","title":"The relation between reproductive value and genetic contribution","date_published":"2011-08-01T00:00:00Z","day":"01","ec_funded":1,"year":"2011","page":"953 - 973","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"status":"public","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a 'pedigree' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual's reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time"}],"status":"public","oa_version":"Submitted Version","author":[{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","orcid":"0000-0002-5985-7653","last_name":"de Vladar","full_name":"de Vladar, Harold"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"page":"424 - 432","year":"2011","ec_funded":1,"publication":"Trends in Ecology and Evolution","day":"01","date_published":"2011-08-01T00:00:00Z","title":"The contribution of statistical physics to evolutionary biology","publisher":"Cell Press","scopus_import":1,"publication_status":"published","type":"journal_article","quality_controlled":"1","intvolume":"        26","department":[{"_id":"NiBa"}],"publist_id":"3216","date_created":"2018-12-11T12:03:04Z","date_updated":"2021-01-12T07:43:10Z","citation":{"ieee":"H. de Vladar and N. H. Barton, “The contribution of statistical physics to evolutionary biology,” <i>Trends in Ecology and Evolution</i>, vol. 26, no. 8. Cell Press, pp. 424–432, 2011.","mla":"de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” <i>Trends in Ecology and Evolution</i>, vol. 26, no. 8, Cell Press, 2011, pp. 424–32, doi:<a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">10.1016/j.tree.2011.04.002</a>.","short":"H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” <i>Trends in Ecology and Evolution</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">https://doi.org/10.1016/j.tree.2011.04.002</a>.","ista":"de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 26(8), 424–432.","apa":"de Vladar, H., &#38; Barton, N. H. (2011). The contribution of statistical physics to evolutionary biology. <i>Trends in Ecology and Evolution</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">https://doi.org/10.1016/j.tree.2011.04.002</a>","ama":"de Vladar H, Barton NH. The contribution of statistical physics to evolutionary biology. <i>Trends in Ecology and Evolution</i>. 2011;26(8):424-432. doi:<a href=\"https://doi.org/10.1016/j.tree.2011.04.002\">10.1016/j.tree.2011.04.002</a>"},"month":"08","_id":"3391","issue":"8","doi":"10.1016/j.tree.2011.04.002","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.2854"}],"volume":26},{"department":[{"_id":"NiBa"}],"publist_id":"3214","date_updated":"2023-10-18T08:01:43Z","date_created":"2018-12-11T12:03:05Z","intvolume":"       178","month":"09","article_type":"original","citation":{"mla":"Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” <i>American Naturalist</i>, vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:<a href=\"https://doi.org/10.1086/661246\">10.1086/661246</a>.","short":"N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.","ieee":"N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects,” <i>American Naturalist</i>, vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.","chicago":"Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” <i>American Naturalist</i>. The University of Chicago Press, 2011. <a href=\"https://doi.org/10.1086/661246\">https://doi.org/10.1086/661246</a>.","ista":"Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3), E48–E75.","ama":"Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. <i>American Naturalist</i>. 2011;178(3):E48-E75. doi:<a href=\"https://doi.org/10.1086/661246\">10.1086/661246</a>","apa":"Barton, N. H., &#38; Turelli, M. (2011). Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. <i>American Naturalist</i>. The University of Chicago Press. <a href=\"https://doi.org/10.1086/661246\">https://doi.org/10.1086/661246</a>"},"issue":"3","_id":"3393","file":[{"content_type":"application/pdf","file_id":"4692","checksum":"7fd22a2ef3321a6fca6a439b3be5d8f4","date_created":"2018-12-12T10:08:31Z","date_updated":"2020-07-14T12:46:11Z","access_level":"open_access","relation":"main_file","file_size":629130,"file_name":"IST-2016-554-v1+1_BartonTurelli2011_copy.pdf","creator":"system"}],"volume":178,"doi":"10.1086/661246","day":"01","title":"Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects","date_published":"2011-09-01T00:00:00Z","publication":"American Naturalist","publication_status":"published","type":"journal_article","scopus_import":"1","quality_controlled":"1","publisher":"The University of Chicago Press","has_accepted_license":"1","oa_version":"Submitted Version","status":"public","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"}],"page":"E48 - E75","pubrep_id":"554","year":"2011","publication_identifier":{"issn":["0003-0147"],"eissn":["1537-5323"]},"language":[{"iso":"eng"}],"ddc":["570"],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications."}],"file_date_updated":"2020-07-14T12:46:11Z"},{"day":"01","title":"Genetic drift widens the expected cline but narrows the expected cline width","date_published":"2011-09-01T00:00:00Z","publication":"Genetics","scopus_import":1,"publication_status":"published","quality_controlled":"1","type":"journal_article","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publist_id":"3213","date_updated":"2021-01-12T07:43:11Z","date_created":"2018-12-11T12:03:05Z","intvolume":"       189","month":"09","citation":{"chicago":"Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” <i>Genetics</i>. Genetics Society of America, 2011. <a href=\"https://doi.org/10.1534/genetics.111.129817\">https://doi.org/10.1534/genetics.111.129817</a>.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” <i>Genetics</i>, vol. 189, no. 1, Genetics Society of America, 2011, pp. 227–35, doi:<a href=\"https://doi.org/10.1534/genetics.111.129817\">10.1534/genetics.111.129817</a>.","short":"J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.","ieee":"J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but narrows the expected cline width,” <i>Genetics</i>, vol. 189, no. 1. Genetics Society of America, pp. 227–235, 2011.","ama":"Polechova J, Barton NH. Genetic drift widens the expected cline but narrows the expected cline width. <i>Genetics</i>. 2011;189(1):227-235. doi:<a href=\"https://doi.org/10.1534/genetics.111.129817\">10.1534/genetics.111.129817</a>","apa":"Polechova, J., &#38; Barton, N. H. (2011). Genetic drift widens the expected cline but narrows the expected cline width. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.111.129817\">https://doi.org/10.1534/genetics.111.129817</a>","ista":"Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 189(1), 227–235."},"issue":"1","_id":"3394","volume":189,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/"}],"doi":"10.1534/genetics.111.129817","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Random genetic drift shifts clines in space, alters their width, and distorts their shape. Such random fluctuations complicate inferences from cline width and position. Notably, the effect of genetic drift on the expected shape of the cline is opposite to the naive (but quite common) misinterpretation of classic results on the expected cline. While random drift on average broadens the overall cline in expected allele frequency, it narrows the width of any particular cline. The opposing effects arise because locally, drift drives alleles to fixation—but fluctuations in position widen the expected cline. The effect of genetic drift can be predicted from standardized variance in allele frequencies, averaged across the habitat: 〈F〉. A cline maintained by spatially varying selection (step change) is expected to be narrower by a factor of  relative to the cline in the absence of drift. The expected cline is broader by the inverse of this factor. In a tension zone maintained by underdominance, the expected cline width is narrower by about 1 – 〈F〉relative to the width in the absence of drift. Individual clines can differ substantially from the expectation, and we give quantitative predictions for the variance in cline position and width. The predictions apply to clines in almost one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or along a coast line and give a guide to what patterns to expect in two dimensions."}],"oa_version":"Submitted Version","status":"public","author":[{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","last_name":"Polechova","full_name":"Polechova, Jitka"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"page":"227 - 235","year":"2011","ec_funded":1},{"publisher":"Elsevier","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Recent advances in microscopy techniques and biophysical measurements have provided novel insight into the molecular, cellular and biophysical basis of cell adhesion. However, comparably little is known about a core element of cell–cell adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss approaches to understand the nature and regulation of adhesion energy, and propose strategies to determine adhesion energy between cells in vitro and in vivo."}],"publication_status":"published","quality_controlled":"1","type":"journal_article","scopus_import":1,"oa":1,"language":[{"iso":"eng"}],"publication":"Current Opinion in Cell Biology","day":"01","title":"The role of adhesion energy in controlling cell-cell contacts","date_published":"2011-10-01T00:00:00Z","doi":"10.1016/j.ceb.2011.07.004","volume":23,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188705/","open_access":"1"}],"_id":"3397","year":"2011","issue":"5","citation":{"ista":"Maître J-L, Heisenberg C-PJ. 2011. The role of adhesion energy in controlling cell-cell contacts. Current Opinion in Cell Biology. 23(5), 508–514.","apa":"Maître, J.-L., &#38; Heisenberg, C.-P. J. (2011). The role of adhesion energy in controlling cell-cell contacts. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2011.07.004\">https://doi.org/10.1016/j.ceb.2011.07.004</a>","ama":"Maître J-L, Heisenberg C-PJ. The role of adhesion energy in controlling cell-cell contacts. <i>Current Opinion in Cell Biology</i>. 2011;23(5):508-514. doi:<a href=\"https://doi.org/10.1016/j.ceb.2011.07.004\">10.1016/j.ceb.2011.07.004</a>","ieee":"J.-L. Maître and C.-P. J. Heisenberg, “The role of adhesion energy in controlling cell-cell contacts,” <i>Current Opinion in Cell Biology</i>, vol. 23, no. 5. Elsevier, pp. 508–514, 2011.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Opinion in Cell Biology 23 (2011) 508–514.","mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “The Role of Adhesion Energy in Controlling Cell-Cell Contacts.” <i>Current Opinion in Cell Biology</i>, vol. 23, no. 5, Elsevier, 2011, pp. 508–14, doi:<a href=\"https://doi.org/10.1016/j.ceb.2011.07.004\">10.1016/j.ceb.2011.07.004</a>.","chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “The Role of Adhesion Energy in Controlling Cell-Cell Contacts.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ceb.2011.07.004\">https://doi.org/10.1016/j.ceb.2011.07.004</a>."},"author":[{"first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"page":"508 - 514","month":"10","intvolume":"        23","status":"public","oa_version":"Submitted Version","publist_id":"3211","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T07:43:12Z","date_created":"2018-12-11T12:03:06Z"},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"377","year":"2011","author":[{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"last_name":"Schrempf","full_name":"Schrempf, Alexandra","first_name":"Alexandra"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"}],"oa_version":"Published Version","status":"public","article_number":"e17323","file_date_updated":"2020-07-14T12:46:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Context-dependent adjustment of mating tactics can drastically increase the mating success of behaviourally flexible animals. We used the ant Cardiocondyla obscurior as a model system to study adaptive adjustment of male mating tactics. This species shows a male diphenism of wingless fighter males and peaceful winged males. Whereas the wingless males stay and exclusively mate in the maternal colony, the mating behaviour of winged males is plastic. They copulate with female sexuals in their natal nests early in life but later disperse in search for sexuals outside. In this study, we observed the nest-leaving behaviour of winged males under different conditions and found that they adaptively adjust the timing of their dispersal to the availability of mating partners, as well as the presence, and even the type of competitors in their natal nests. In colonies with virgin female queens winged males stayed longest when they were the only male in the nest. They left earlier when mating partners were not available or when other males were present. In the presence of wingless, locally mating fighter males, winged males dispersed earlier than in the presence of docile, winged competitors. This suggests that C. obscurior males are capable of estimating their local breeding chances and adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive way, thus showing hitherto unknown behavioural plasticity in social insect males.","lang":"eng"}],"ddc":["576"],"oa":1,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:15:40Z","date_updated":"2020-07-14T12:46:12Z","file_id":"5162","checksum":"46f8cbde61f06fcacf8fa297cacfa0e5","file_size":147367,"file_name":"IST-2015-377-v1+1_journal.pone.0017323.pdf","creator":"system"}],"volume":6,"doi":"10.1371/journal.pone.0017323","issue":"3","_id":"3399","month":"03","citation":{"mla":"Cremer, Sylvia, et al. “Competition and Opportunity Shape the Reproductive Tactics of Males in the Ant Cardiocondyla Obscurior.” <i>PLoS One</i>, vol. 6, no. 3, e17323, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0017323\">10.1371/journal.pone.0017323</a>.","short":"S. Cremer, A. Schrempf, J. Heinze, PLoS One 6 (2011).","ieee":"S. Cremer, A. Schrempf, and J. Heinze, “Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior,” <i>PLoS One</i>, vol. 6, no. 3. Public Library of Science, 2011.","chicago":"Cremer, Sylvia, Alexandra Schrempf, and Jürgen Heinze. “Competition and Opportunity Shape the Reproductive Tactics of Males in the Ant Cardiocondyla Obscurior.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0017323\">https://doi.org/10.1371/journal.pone.0017323</a>.","ista":"Cremer S, Schrempf A, Heinze J. 2011. Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS One. 6(3), e17323.","ama":"Cremer S, Schrempf A, Heinze J. Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior. <i>PLoS One</i>. 2011;6(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0017323\">10.1371/journal.pone.0017323</a>","apa":"Cremer, S., Schrempf, A., &#38; Heinze, J. (2011). Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0017323\">https://doi.org/10.1371/journal.pone.0017323</a>"},"acknowledgement":"This work was supported by the German Science Foundation (www.dfg.de, He 1623/23).","publist_id":"3059","department":[{"_id":"SyCr"}],"date_updated":"2021-01-12T07:43:12Z","date_created":"2018-12-11T12:03:07Z","intvolume":"         6","has_accepted_license":"1","publication_status":"published","quality_controlled":"1","type":"journal_article","scopus_import":1,"publisher":"Public Library of Science","day":"29","date_published":"2011-03-29T00:00:00Z","title":"Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior","publication":"PLoS One"},{"pubrep_id":"832","year":"2011","author":[{"full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"last_name":"Sandoz","full_name":"Sandoz, Guillaume","first_name":"Guillaume"},{"first_name":"Ehud","full_name":"Isacoff, Ehud","last_name":"Isacoff"}],"page":"1 - 6","oa_version":"Submitted Version","status":"public","file_date_updated":"2020-07-14T12:46:12Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system and gates non-selective cation channels. The origins of glutamate receptors are not well understood as they differ structurally and functionally from simple bacterial ligand-gated ion channels. Here we report the discovery of an ionotropic glutamate receptor that combines the typical eukaryotic domain architecture with the 'TXVGYG' signature sequence of the selectivity filter found in K+ channels. This receptor exhibits functional properties intermediate between bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors.","lang":"eng"}],"ddc":["570","571"],"oa":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:11:36Z","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:12Z","checksum":"6b68d65aadd97c18d663eb117a0a9d35","file_id":"4891","content_type":"application/pdf","creator":"system","file_name":"IST-2017-832-v1+1_janovjak.pdf","file_size":387654}],"volume":2,"doi":"10.1038/ncomms1231","issue":"232","_id":"3405","month":"03","citation":{"apa":"Janovjak, H. L., Sandoz, G., &#38; Isacoff, E. (2011). Modern ionotropic glutamate receptor with a K+ selectivity signature sequence. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms1231\">https://doi.org/10.1038/ncomms1231</a>","ama":"Janovjak HL, Sandoz G, Isacoff E. Modern ionotropic glutamate receptor with a K+ selectivity signature sequence. <i>Nature Communications</i>. 2011;2(232):1-6. doi:<a href=\"https://doi.org/10.1038/ncomms1231\">10.1038/ncomms1231</a>","ista":"Janovjak HL, Sandoz G, Isacoff E. 2011. Modern ionotropic glutamate receptor with a K+ selectivity signature sequence. Nature Communications. 2(232), 1–6.","chicago":"Janovjak, Harald L, Guillaume Sandoz, and Ehud Isacoff. “Modern Ionotropic Glutamate Receptor with a K+ Selectivity Signature Sequence.” <i>Nature Communications</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/ncomms1231\">https://doi.org/10.1038/ncomms1231</a>.","ieee":"H. L. Janovjak, G. Sandoz, and E. Isacoff, “Modern ionotropic glutamate receptor with a K+ selectivity signature sequence,” <i>Nature Communications</i>, vol. 2, no. 232. Nature Publishing Group, pp. 1–6, 2011.","mla":"Janovjak, Harald L., et al. “Modern Ionotropic Glutamate Receptor with a K+ Selectivity Signature Sequence.” <i>Nature Communications</i>, vol. 2, no. 232, Nature Publishing Group, 2011, pp. 1–6, doi:<a href=\"https://doi.org/10.1038/ncomms1231\">10.1038/ncomms1231</a>.","short":"H.L. Janovjak, G. Sandoz, E. Isacoff, Nature Communications 2 (2011) 1–6."},"publist_id":"2997","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T07:43:15Z","date_created":"2018-12-11T12:03:09Z","intvolume":"         2","has_accepted_license":"1","type":"journal_article","scopus_import":1,"quality_controlled":"1","publication_status":"published","publisher":"Nature Publishing Group","day":"08","title":"Modern ionotropic glutamate receptor with a K+ selectivity signature sequence","date_published":"2011-03-08T00:00:00Z","publication":"Nature Communications"},{"year":"2011","page":"149 - 165","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Lämmermann, Tim","last_name":"Lämmermann","first_name":"Tim"}],"status":"public","oa_version":"Published Version","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Cell migration on two-dimensional (2D) substrates follows entirely different rules than cell migration in three-dimensional (3D) environments. This is especially relevant for leukocytes that are able to migrate in the absence of adhesion receptors within the confined geometry of artificial 3D extracellular matrix scaffolds and within the interstitial space in vivo. Here, we describe in detail a simple and economical protocol to visualize dendritic cell migration in 3D collagen scaffolds along chemotactic gradients. This method can be adapted to other cell types and may serve as a physiologically relevant paradigm for the directed locomotion of most amoeboid cells."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-1-61779-207-6_11","main_file_link":[{"url":"https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf","open_access":"1"}],"volume":769,"_id":"3505","citation":{"ama":"Sixt MK, Lämmermann T. In vitro analysis of chemotactic leukocyte migration in 3D environments. <i>Cell Migration</i>. 2011;769:149-165. doi:<a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">10.1007/978-1-61779-207-6_11</a>","apa":"Sixt, M. K., &#38; Lämmermann, T. (2011). In vitro analysis of chemotactic leukocyte migration in 3D environments. <i>Cell Migration</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">https://doi.org/10.1007/978-1-61779-207-6_11</a>","ista":"Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 769, 149–165.","chicago":"Sixt, Michael K, and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” <i>Cell Migration</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">https://doi.org/10.1007/978-1-61779-207-6_11</a>.","mla":"Sixt, Michael K., and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” <i>Cell Migration</i>, vol. 769, Springer, 2011, pp. 149–65, doi:<a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">10.1007/978-1-61779-207-6_11</a>.","short":"M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165.","ieee":"M. K. Sixt and T. Lämmermann, “In vitro analysis of chemotactic leukocyte migration in 3D environments,” <i>Cell Migration</i>, vol. 769. Springer, pp. 149–165, 2011."},"article_type":"original","month":"05","intvolume":"       769","date_created":"2018-12-11T12:03:41Z","date_updated":"2021-01-12T07:43:55Z","publist_id":"2882","department":[{"_id":"MiSi"}],"alternative_title":["Methods in Molecular Biology"],"publisher":"Springer","quality_controlled":"1","publication_status":"published","type":"journal_article","publication":"Cell Migration","date_published":"2011-05-17T00:00:00Z","title":"In vitro analysis of chemotactic leukocyte migration in 3D environments","day":"17"}]