--- _id: '3370' abstract: - lang: eng text: Supertree methods are widely applied and give rise to new conclusions about phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have been studied in greater detail, examples include shape bias (Wilkinson et al. 2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at two matrix representation methods, matrix representation with compatibility (MRC) and matrix representation with parsimony (MRP). Different null models of random data are studied and the resulting tree shapes are investigated. Thereby I consider unrooted trees and a bias in tree shape is determined by a tree balance measure. The measure for unrooted trees is a modification of a tree balance measure for rooted trees. I observe that depending on the underlying null model of random data, the methods may resolve conflict in favor of more balanced tree shapes. The analyses refer only to trees with the same taxon set, also known as the consensus setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions on how to deal with missing data. author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok citation: ama: Kupczok A. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 2011;60(2):218-225. doi:10.1093/sysbio/syq086 apa: Kupczok, A. (2011). Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. Oxford University Press. https://doi.org/10.1093/sysbio/syq086 chicago: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” Systematic Biology. Oxford University Press, 2011. https://doi.org/10.1093/sysbio/syq086. ieee: A. Kupczok, “Consequences of different null models on the tree shape bias of supertree methods,” Systematic Biology, vol. 60, no. 2. Oxford University Press, pp. 218–225, 2011. ista: Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225. mla: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” Systematic Biology, vol. 60, no. 2, Oxford University Press, 2011, pp. 218–25, doi:10.1093/sysbio/syq086. short: A. Kupczok, Systematic Biology 60 (2011) 218–225. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-01T00:00:00Z date_updated: 2021-01-12T07:43:01Z day: '01' department: - _id: JoBo doi: 10.1093/sysbio/syq086 intvolume: ' 60' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://eprints.cs.univie.ac.at/3226/ month: '03' oa: 1 oa_version: Submitted Version page: 218 - 225 publication: Systematic Biology publication_status: published publisher: Oxford University Press publist_id: '3241' quality_controlled: '1' status: public title: Consequences of different null models on the tree shape bias of supertree methods type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2011' ... --- _id: '3371' 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. article_type: original author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Carole full_name: Parent, Carole last_name: Parent citation: ama: Sixt MK, Parent C. Cells on the move in Philadelphia. Molecular Biology and Evolution. 2011;22(6):724. doi:10.1091/mbc.E10-12-0958 apa: Sixt, M. K., & Parent, C. (2011). Cells on the move in Philadelphia. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1091/mbc.E10-12-0958 chicago: Sixt, Michael K, and Carole Parent. “Cells on the Move in Philadelphia.” Molecular Biology and Evolution. Oxford University Press, 2011. https://doi.org/10.1091/mbc.E10-12-0958. ieee: M. K. Sixt and C. Parent, “Cells on the move in Philadelphia,” Molecular Biology and Evolution, vol. 22, no. 6. Oxford University Press, p. 724, 2011. ista: Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology and Evolution. 22(6), 724. mla: Sixt, Michael K., and Carole Parent. “Cells on the Move in Philadelphia.” Molecular Biology and Evolution, vol. 22, no. 6, Oxford University Press, 2011, p. 724, doi:10.1091/mbc.E10-12-0958. short: M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-15T00:00:00Z date_updated: 2021-01-12T07:43:01Z day: '15' ddc: - '570' department: - _id: MiSi doi: 10.1091/mbc.E10-12-0958 file: - access_level: open_access checksum: 3467986ab7a64e7694ffd1013b5d9da9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:29Z date_updated: 2020-07-14T12:46:11Z file_id: '5283' file_name: IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf file_size: 105421 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 22' issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '03' oa: 1 oa_version: Published Version page: '724' publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '3238' pubrep_id: '373' quality_controlled: '1' scopus_import: 1 status: public title: Cells on the move in Philadelphia tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2011' ... --- _id: '3372' 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. author: - first_name: Patrick full_name: Abbot, Patrick last_name: Abbot - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: John full_name: Alcock, John last_name: Alcock - first_name: Samuel full_name: Alizon, Samuel last_name: Alizon - first_name: Joao full_name: Alpedrinha, Joao last_name: Alpedrinha - first_name: Malte full_name: Andersson, Malte last_name: Andersson - first_name: Jean full_name: Andre, Jean last_name: Andre - first_name: Minus full_name: Van Baalen, Minus last_name: Van Baalen - first_name: Francois full_name: Balloux, Francois last_name: Balloux - first_name: Sigal full_name: Balshine, Sigal last_name: Balshine - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Leo full_name: Beukeboom, Leo last_name: Beukeboom - first_name: Jay full_name: Biernaskie, Jay last_name: Biernaskie - first_name: Trine full_name: Bilde, Trine last_name: Bilde - first_name: Gerald full_name: Borgia, Gerald last_name: Borgia - first_name: Michael full_name: Breed, Michael last_name: Breed - first_name: Sam full_name: Brown, Sam last_name: Brown - first_name: Redouan full_name: Bshary, Redouan last_name: Bshary - first_name: Angus full_name: Buckling, Angus last_name: Buckling - first_name: Nancy full_name: Burley, Nancy last_name: Burley - first_name: Max full_name: Burton Chellew, Max last_name: Burton Chellew - first_name: Michael full_name: Cant, Michael last_name: Cant - first_name: Michel full_name: Chapuisat, Michel last_name: Chapuisat - first_name: Eric full_name: Charnov, Eric last_name: Charnov - first_name: Tim full_name: Clutton Brock, Tim last_name: Clutton Brock - first_name: Andrew full_name: Cockburn, Andrew last_name: Cockburn - first_name: Blaine full_name: Cole, Blaine last_name: Cole - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave - first_name: Leda full_name: Cosmides, Leda last_name: Cosmides - 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 - first_name: Bernard full_name: Crespi, Bernard last_name: Crespi - first_name: Robert full_name: Curry, Robert last_name: Curry - first_name: Sasha full_name: Dall, Sasha last_name: Dall - first_name: Troy full_name: Day, Troy last_name: Day - first_name: Janis full_name: Dickinson, Janis last_name: Dickinson - first_name: Lee full_name: Dugatkin, Lee last_name: Dugatkin - first_name: Claire full_name: El Mouden, Claire last_name: El Mouden - first_name: Stephen full_name: Emlen, Stephen last_name: Emlen - first_name: Jay full_name: Evans, Jay last_name: Evans - first_name: Regis full_name: Ferriere, Regis last_name: Ferriere - first_name: Jeremy full_name: Field, Jeremy last_name: Field - first_name: Susanne full_name: Foitzik, Susanne last_name: Foitzik - first_name: Kevin full_name: Foster, Kevin last_name: Foster - first_name: William full_name: Foster, William last_name: Foster - first_name: Charles full_name: Fox, Charles last_name: Fox - first_name: Juergen full_name: Gadau, Juergen last_name: Gadau - first_name: Sylvain full_name: Gandon, Sylvain last_name: Gandon - first_name: Andy full_name: Gardner, Andy last_name: Gardner - first_name: Michael full_name: Gardner, Michael last_name: Gardner - first_name: Thomas full_name: Getty, Thomas last_name: Getty - first_name: Michael full_name: Goodisman, Michael last_name: Goodisman - first_name: Alan full_name: Grafen, Alan last_name: Grafen - first_name: Rick full_name: Grosberg, Rick last_name: Grosberg - first_name: Christina full_name: Grozinger, Christina last_name: Grozinger - first_name: Pierre full_name: Gouyon, Pierre last_name: Gouyon - first_name: Darryl full_name: Gwynne, Darryl last_name: Gwynne - first_name: Paul full_name: Harvey, Paul last_name: Harvey - first_name: Ben full_name: Hatchwell, Ben last_name: Hatchwell - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Heikki full_name: Helantera, Heikki last_name: Helantera - first_name: Ken full_name: Helms, Ken last_name: Helms - first_name: Kim full_name: Hill, Kim last_name: Hill - first_name: Natalie full_name: Jiricny, Natalie last_name: Jiricny - first_name: Rufus full_name: Johnstone, Rufus last_name: Johnstone - first_name: Alex full_name: Kacelnik, Alex last_name: Kacelnik - first_name: E Toby full_name: Kiers, E Toby last_name: Kiers - first_name: Hanna full_name: Kokko, Hanna last_name: Kokko - first_name: Jan full_name: Komdeur, Jan last_name: Komdeur - first_name: Judith full_name: Korb, Judith last_name: Korb - first_name: Daniel full_name: Kronauer, Daniel last_name: Kronauer - first_name: Rolf full_name: Kümmerli, Rolf last_name: Kümmerli - first_name: Laurent full_name: Lehmann, Laurent last_name: Lehmann - first_name: Timothy full_name: Linksvayer, Timothy last_name: Linksvayer - first_name: Sébastien full_name: Lion, Sébastien last_name: Lion - first_name: Bruce full_name: Lyon, Bruce last_name: Lyon - first_name: James full_name: Marshall, James last_name: Marshall - first_name: Richard full_name: Mcelreath, Richard last_name: Mcelreath - first_name: Yannis full_name: Michalakis, Yannis last_name: Michalakis - first_name: Richard full_name: Michod, Richard last_name: Michod - first_name: Douglas full_name: Mock, Douglas last_name: Mock - first_name: Thibaud full_name: Monnin, Thibaud last_name: Monnin - first_name: Robert full_name: Montgomerie, Robert last_name: Montgomerie - first_name: Allen full_name: Moore, Allen last_name: Moore - first_name: Ulrich full_name: Mueller, Ulrich last_name: Mueller - first_name: Ronald full_name: Noë, Ronald last_name: Noë - first_name: Samir full_name: Okasha, Samir last_name: Okasha - first_name: Pekka full_name: Pamilo, Pekka last_name: Pamilo - first_name: Geoff full_name: Parker, Geoff last_name: Parker - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen - first_name: Ido full_name: Pen, Ido last_name: Pen - first_name: David full_name: Pfennig, David last_name: Pfennig - first_name: David full_name: Queller, David last_name: Queller - first_name: Daniel full_name: Rankin, Daniel last_name: Rankin - first_name: Sarah full_name: Reece, Sarah last_name: Reece - first_name: Hudson full_name: Reeve, Hudson last_name: Reeve - first_name: Max full_name: Reuter, Max last_name: Reuter - first_name: Gilbert full_name: Roberts, Gilbert last_name: Roberts - first_name: Simon full_name: Robson, Simon last_name: Robson - first_name: Denis full_name: Roze, Denis last_name: Roze - first_name: Francois full_name: Rousset, Francois last_name: Rousset - first_name: Olav full_name: Rueppell, Olav last_name: Rueppell - first_name: Joel full_name: Sachs, Joel last_name: Sachs - first_name: Lorenzo full_name: Santorelli, Lorenzo last_name: Santorelli - first_name: Paul full_name: Schmid Hempel, Paul last_name: Schmid Hempel - first_name: Michael full_name: Schwarz, Michael last_name: Schwarz - first_name: Tom full_name: Scott Phillips, Tom last_name: Scott Phillips - first_name: Janet full_name: Shellmann Sherman, Janet last_name: Shellmann Sherman - first_name: Paul full_name: Sherman, Paul last_name: Sherman - first_name: David full_name: Shuker, David last_name: Shuker - first_name: Jeff full_name: Smith, Jeff last_name: Smith - first_name: Joseph full_name: Spagna, Joseph last_name: Spagna - first_name: Beverly full_name: Strassmann, Beverly last_name: Strassmann - first_name: Andrew full_name: Suarez, Andrew last_name: Suarez - first_name: Liselotte full_name: Sundström, Liselotte last_name: Sundström - first_name: Michael full_name: Taborsky, Michael last_name: Taborsky - first_name: Peter full_name: Taylor, Peter last_name: Taylor - first_name: Graham full_name: Thompson, Graham last_name: Thompson - first_name: John full_name: Tooby, John last_name: Tooby - first_name: Neil full_name: Tsutsui, Neil last_name: Tsutsui - first_name: Kazuki full_name: Tsuji, Kazuki last_name: Tsuji - first_name: Stefano full_name: Turillazzi, Stefano last_name: Turillazzi - first_name: Francisco full_name: Úbeda, Francisco last_name: Úbeda - first_name: Edward full_name: Vargo, Edward last_name: Vargo - first_name: Bernard full_name: Voelkl, Bernard last_name: Voelkl - first_name: Tom full_name: Wenseleers, Tom last_name: Wenseleers - first_name: Stuart full_name: West, Stuart last_name: West - first_name: Mary full_name: West Eberhard, Mary last_name: West Eberhard - first_name: David full_name: Westneat, David last_name: Westneat - first_name: Diane full_name: Wiernasz, Diane last_name: Wiernasz - first_name: Geoff full_name: Wild, Geoff last_name: Wild - first_name: Richard full_name: Wrangham, Richard last_name: Wrangham - first_name: Andrew full_name: Young, Andrew last_name: Young - first_name: David full_name: Zeh, David last_name: Zeh - first_name: Jeanne full_name: Zeh, Jeanne last_name: Zeh - first_name: Andrew full_name: Zink, Andrew last_name: Zink citation: ama: Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831 apa: Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09831 chicago: Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831. ieee: P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011. ista: Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4. mla: Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831. 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. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-23T00:00:00Z date_updated: 2021-01-12T07:43:02Z day: '23' department: - _id: NiBa doi: 10.1038/nature09831 external_id: pmid: - '21430721' intvolume: ' 471' issue: '7339' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/ month: '03' oa: 1 oa_version: Submitted Version page: E1 - E4 pmid: 1 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3237' quality_controlled: '1' scopus_import: 1 status: public title: Inclusive fitness theory and eusociality type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2011' ... --- _id: '3373' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Marcus full_name: Jahnel, Marcus last_name: Jahnel - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Anita full_name: Jannasch, Anita last_name: Jannasch - first_name: Erik full_name: Schaeffer, Erik last_name: Schaeffer - first_name: Stephan full_name: Grill, Stephan last_name: Grill citation: ama: Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. Measuring the complete force field of an optical trap. Optics Letters. 2011;36(7):1260-1262. doi:10.1364/OL.36.001260 apa: Jahnel, M., Behrndt, M., Jannasch, A., Schaeffer, E., & Grill, S. (2011). Measuring the complete force field of an optical trap. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.36.001260 chicago: Jahnel, Marcus, Martin Behrndt, Anita Jannasch, Erik Schaeffer, and Stephan Grill. “Measuring the Complete Force Field of an Optical Trap.” Optics Letters. Optica Publishing Group, 2011. https://doi.org/10.1364/OL.36.001260. ieee: M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, and S. Grill, “Measuring the complete force field of an optical trap,” Optics Letters, vol. 36, no. 7. Optica Publishing Group, pp. 1260–1262, 2011. 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. mla: Jahnel, Marcus, et al. “Measuring the Complete Force Field of an Optical Trap.” Optics Letters, vol. 36, no. 7, Optica Publishing Group, 2011, pp. 1260–62, doi:10.1364/OL.36.001260. short: M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, S. Grill, Optics Letters 36 (2011) 1260–1262. date_created: 2018-12-11T12:02:58Z date_published: 2011-03-30T00:00:00Z date_updated: 2023-10-17T12:16:58Z day: '30' department: - _id: CaHe doi: 10.1364/OL.36.001260 intvolume: ' 36' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.osapublishing.org/ol/abstract.cfm?uri=ol-36-7-1260 month: '03' oa: 1 oa_version: Published Version page: 1260 - 1262 publication: Optics Letters publication_status: published publisher: Optica Publishing Group publist_id: '3234' quality_controlled: '1' related_material: record: - id: '1403' relation: dissertation_contains status: public scopus_import: '1' status: public title: Measuring the complete force field of an optical trap type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2011' ... --- _id: '3374' 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'. article_number: '153102' author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Aleksandra full_name: Walczak, Aleksandra last_name: Walczak citation: ama: 'Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 2011;23(15). doi:10.1088/0953-8984/23/15/153102' apa: 'Tkačik, G., & Walczak, A. (2011). Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/0953-8984/23/15/153102' chicago: 'Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2011. https://doi.org/10.1088/0953-8984/23/15/153102.' ieee: 'G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” Journal of Physics: Condensed Matter, vol. 23, no. 15. IOP Publishing Ltd., 2011.' ista: 'Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.' mla: 'Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.' short: 'G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).' date_created: 2018-12-11T12:02:58Z date_published: 2011-04-01T00:00:00Z date_updated: 2021-01-12T07:43:03Z day: '01' department: - _id: GaTk doi: 10.1088/0953-8984/23/15/153102 intvolume: ' 23' issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1101.4240 month: '04' oa: 1 oa_version: Submitted Version publication: 'Journal of Physics: Condensed Matter' publication_status: published publisher: IOP Publishing Ltd. publist_id: '3233' quality_controlled: '1' scopus_import: 1 status: public title: Information transmission in genetic regulatory networks a review type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2011' ... --- _id: '3375' abstract: - lang: eng 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.' article_processing_charge: No article_type: original author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438 apa: de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2010.0438 chicago: Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface. The Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438. ieee: H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” Journal of the Royal Society Interface, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011. 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. mla: de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:10.1098/rsif.2010.0438. short: H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739. date_created: 2018-12-11T12:02:58Z date_published: 2011-05-01T00:00:00Z date_updated: 2025-05-28T11:42:45Z day: '01' department: - _id: NiBa doi: 10.1098/rsif.2010.0438 ec_funded: 1 external_id: pmid: - '21084341' intvolume: ' 8' issue: '58' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/ month: '05' oa: 1 oa_version: Submitted Version page: 720 - 739 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Journal of the Royal Society Interface publication_status: published publisher: The Royal Society publist_id: '3232' quality_controlled: '1' scopus_import: '1' status: public title: The statistical mechanics of a polygenic character under stabilizing selection mutation and drift type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2011' ... --- _id: '3376' abstract: - lang: eng 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. acknowledgement: This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.). author: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 2011;42(4):413-425. doi:10.1016/j.molcel.2011.04.016 apa: Bollenbach, M. T., & Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2011.04.016 chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” Molecular Cell. Cell Press, 2011. https://doi.org/10.1016/j.molcel.2011.04.016. ieee: M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” Molecular Cell, vol. 42, no. 4. Cell Press, pp. 413–425, 2011. ista: Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425. mla: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” Molecular Cell, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:10.1016/j.molcel.2011.04.016. short: M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425. date_created: 2018-12-11T12:02:59Z date_published: 2011-05-20T00:00:00Z date_updated: 2021-01-12T07:43:03Z day: '20' department: - _id: ToBo doi: 10.1016/j.molcel.2011.04.016 intvolume: ' 42' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/ month: '05' oa: 1 oa_version: Submitted Version page: 413 - 425 publication: Molecular Cell publication_status: published publisher: Cell Press publist_id: '3231' quality_controlled: '1' scopus_import: 1 status: public title: Resolution of gene regulatory conflicts caused by combinations of antibiotics type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2011' ... --- _id: '3377' 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. 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. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Amit full_name: Patel, Amit id: 34A254A0-F248-11E8-B48F-1D18A9856A87 last_name: Patel citation: ama: Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 2011;11(3):345-361. doi:10.1007/s10208-011-9090-8 apa: Edelsbrunner, H., Morozov, D., & Patel, A. (2011). Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-011-9090-8 chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality by Measuring the Robustness of Intersections.” Foundations of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-011-9090-8. ieee: H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by measuring the robustness of intersections,” Foundations of Computational Mathematics, vol. 11, no. 3. Springer, pp. 345–361, 2011. ista: Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361. mla: Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the Robustness of Intersections.” Foundations of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:10.1007/s10208-011-9090-8. short: H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361. date_created: 2018-12-11T12:02:59Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T07:43:04Z day: '01' department: - _id: HeEd doi: 10.1007/s10208-011-9090-8 intvolume: ' 11' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/0911.2142 month: '06' oa: 1 oa_version: Submitted Version page: 345 - 361 publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '3230' quality_controlled: '1' scopus_import: 1 status: public title: Quantifying transversality by measuring the robustness of intersections type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2011' ... --- _id: '3378' abstract: - lang: eng text: The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology. acknowledgement: This research was partially supported by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0007. author: - first_name: Paul full_name: Bendich, Paul id: 43F6EC54-F248-11E8-B48F-1D18A9856A87 last_name: Bendich - first_name: John full_name: Harer, John last_name: Harer citation: ama: Bendich P, Harer J. Persistent intersection homology. Foundations of Computational Mathematics. 2011;11(3):305-336. doi:10.1007/s10208-010-9081-1 apa: Bendich, P., & Harer, J. (2011). Persistent intersection homology. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-010-9081-1 chicago: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-010-9081-1. ieee: P. Bendich and J. Harer, “Persistent intersection homology,” Foundations of Computational Mathematics, vol. 11, no. 3. Springer, pp. 305–336, 2011. ista: Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of Computational Mathematics. 11(3), 305–336. mla: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 305–36, doi:10.1007/s10208-010-9081-1. short: P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011) 305–336. date_created: 2018-12-11T12:02:59Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T07:43:04Z day: '01' department: - _id: HeEd doi: 10.1007/s10208-010-9081-1 intvolume: ' 11' issue: '3' language: - iso: eng month: '06' oa_version: None page: 305 - 336 publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '3229' quality_controlled: '1' scopus_import: 1 status: public title: Persistent intersection homology type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2011' ... --- _id: '3379' abstract: - lang: eng text: The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion. article_type: original author: - first_name: Richard full_name: Row, Richard last_name: Row - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 - first_name: Benjamin full_name: Martin, Benjamin last_name: Martin - first_name: Petra full_name: Stockinger, Petra id: 261CB030-E90D-11E9-B182-F697D44B663C last_name: Stockinger - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: David full_name: Kimelman, David last_name: Kimelman citation: ama: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 2011;354(1):102-110. doi:10.1016/j.ydbio.2011.03.025 apa: Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., & Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2011.03.025 chicago: Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology. Elsevier, 2011. https://doi.org/10.1016/j.ydbio.2011.03.025. ieee: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D. Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail,” Developmental Biology, vol. 354, no. 1. Elsevier, pp. 102–110, 2011. ista: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 354(1), 102–110. mla: Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology, vol. 354, no. 1, Elsevier, 2011, pp. 102–10, doi:10.1016/j.ydbio.2011.03.025. short: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman, Developmental Biology 354 (2011) 102–110. date_created: 2018-12-11T12:03:00Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T07:43:04Z day: '01' department: - _id: CaHe doi: 10.1016/j.ydbio.2011.03.025 external_id: pmid: - '1463614' intvolume: ' 354' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/ month: '06' oa: 1 oa_version: Submitted Version page: 102 - 110 pmid: 1 publication: Developmental Biology publication_status: published publisher: Elsevier publist_id: '3228' quality_controlled: '1' scopus_import: 1 status: public title: Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 354 year: '2011' ... --- _id: '3380' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Sayanthan full_name: Logeswaran, Sayanthan last_name: Logeswaran - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 2011;93(3):221-232. doi:10.1017/S0016672311000115 apa: Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672311000115 chicago: Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research. Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115. ieee: S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” Genetical Research, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011. ista: Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232. mla: Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115. short: S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232. date_created: 2018-12-11T12:03:00Z date_published: 2011-05-18T00:00:00Z date_updated: 2021-01-12T07:43:05Z day: '18' department: - _id: NiBa doi: 10.1017/S0016672311000115 intvolume: ' 93' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf month: '05' oa: 1 oa_version: Published Version page: 221 - 232 publication: Genetical Research publication_status: published publisher: Cambridge University Press publist_id: '3227' quality_controlled: '1' scopus_import: 1 status: public title: Mapping Mendelian traits in asexual progeny using changes in marker allele frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2011' ... --- _id: '3381' 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. author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Verena full_name: Wolf, Verena last_name: Wolf citation: ama: 'Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 2011;22(4):823-841. doi:10.1142/S0129054111008441' apa: 'Henzinger, T. A., Jobstmann, B., & Wolf, V. (2011). Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054111008441' chicago: 'Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models.” IJFCS: International Journal of Foundations of Computer Science. World Scientific Publishing, 2011. https://doi.org/10.1142/S0129054111008441.' ieee: 'T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” IJFCS: International Journal of Foundations of Computer Science, vol. 22, no. 4. World Scientific Publishing, pp. 823–841, 2011.' 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.' mla: 'Henzinger, Thomas A., et al. “Formalisms for Specifying Markovian Population Models.” IJFCS: International Journal of Foundations of Computer Science, vol. 22, no. 4, World Scientific Publishing, 2011, pp. 823–41, doi:10.1142/S0129054111008441.' short: 'T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations of Computer Science 22 (2011) 823–841.' date_created: 2018-12-11T12:03:00Z date_published: 2011-06-01T00:00:00Z date_updated: 2023-02-23T11:45:03Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1142/S0129054111008441 file: - access_level: open_access checksum: df88431872586c773fbcfea37d7b36a2 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:45Z date_updated: 2020-07-14T12:46:11Z file_id: '4707' file_name: IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf file_size: 222840 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 22' issue: '4' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 823 - 841 publication: 'IJFCS: International Journal of Foundations of Computer Science' publication_status: published publisher: World Scientific Publishing publist_id: '3226' pubrep_id: '628' quality_controlled: '1' related_material: record: - id: '3841' relation: earlier_version status: public scopus_import: 1 status: public title: Formalisms for specifying Markovian population models type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2011' ... --- _id: '3382' abstract: - lang: eng text: Dynamic tactile sensing is a fundamental ability to recognize materials and objects. However, while humans are born with partially developed dynamic tactile sensing and quickly master this skill, today's robots remain in their infancy. The development of such a sense requires not only better sensors but the right algorithms to deal with these sensors' data as well. For example, when classifying a material based on touch, the data are noisy, high-dimensional, and contain irrelevant signals as well as essential ones. Few classification methods from machine learning can deal with such problems. In this paper, we propose an efficient approach to infer suitable lower dimensional representations of the tactile data. In order to classify materials based on only the sense of touch, these representations are autonomously discovered using visual information of the surfaces during training. However, accurately pairing vision and tactile samples in real-robot applications is a difficult problem. The proposed approach, therefore, works with weak pairings between the modalities. Experiments show that the resulting approach is very robust and yields significantly higher classification performance based on only dynamic tactile sensing. author: - first_name: Oliver full_name: Kroemer, Oliver last_name: Kroemer - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Jan full_name: Peters, Jan last_name: Peters citation: ama: Kroemer O, Lampert C, Peters J. Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. 2011;27(3):545-557. doi:10.1109/TRO.2011.2121130 apa: Kroemer, O., Lampert, C., & Peters, J. (2011). Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. IEEE. https://doi.org/10.1109/TRO.2011.2121130 chicago: Kroemer, Oliver, Christoph Lampert, and Jan Peters. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” IEEE Transactions on Robotics. IEEE, 2011. https://doi.org/10.1109/TRO.2011.2121130. ieee: O. Kroemer, C. Lampert, and J. Peters, “Learning dynamic tactile sensing with robust vision based training,” IEEE Transactions on Robotics, vol. 27, no. 3. IEEE, pp. 545–557, 2011. ista: Kroemer O, Lampert C, Peters J. 2011. Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. 27(3), 545–557. mla: Kroemer, Oliver, et al. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” IEEE Transactions on Robotics, vol. 27, no. 3, IEEE, 2011, pp. 545–57, doi:10.1109/TRO.2011.2121130. short: O. Kroemer, C. Lampert, J. Peters, IEEE Transactions on Robotics 27 (2011) 545–557. date_created: 2018-12-11T12:03:01Z date_published: 2011-05-21T00:00:00Z date_updated: 2021-01-12T07:43:06Z day: '21' department: - _id: ChLa doi: 10.1109/TRO.2011.2121130 intvolume: ' 27' issue: '3' language: - iso: eng month: '05' oa_version: None page: 545 - 557 publication: IEEE Transactions on Robotics publication_status: published publisher: IEEE publist_id: '3225' quality_controlled: '1' scopus_import: 1 status: public title: Learning dynamic tactile sensing with robust vision based training type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2011' ... --- _id: '3383' author: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Heisenberg C-PJ. Invited Lectures ‐ Symposia Area. FEBS Journal. 2011;278(S1):24-24. doi:10.1111/j.1742-4658.2011.08136.x apa: Heisenberg, C.-P. J. (2011). Invited Lectures ‐ Symposia Area. FEBS Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1742-4658.2011.08136.x chicago: Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” FEBS Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1742-4658.2011.08136.x. ieee: C.-P. J. Heisenberg, “Invited Lectures ‐ Symposia Area,” FEBS Journal, vol. 278, no. S1. Wiley-Blackwell, pp. 24–24, 2011. ista: Heisenberg C-PJ. 2011. Invited Lectures ‐ Symposia Area. FEBS Journal. 278(S1), 24–24. mla: Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” FEBS Journal, vol. 278, no. S1, Wiley-Blackwell, 2011, pp. 24–24, doi:10.1111/j.1742-4658.2011.08136.x. short: C.-P.J. Heisenberg, FEBS Journal 278 (2011) 24–24. date_created: 2018-12-11T12:03:01Z date_published: 2011-07-01T00:00:00Z date_updated: 2021-01-12T07:43:06Z day: '01' department: - _id: CaHe doi: 10.1111/j.1742-4658.2011.08136.x intvolume: ' 278' issue: S1 language: - iso: eng month: '07' oa_version: None page: 24 - 24 publication: FEBS Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3224' status: public title: Invited Lectures ‐ Symposia Area type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 278 year: '2011' ... --- _id: '3384' 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. article_number: e20409 author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Patrick full_name: Garrigan, Patrick last_name: Garrigan - first_name: Charles full_name: Ratliff, Charles last_name: Ratliff - first_name: Grega full_name: Milcinski, Grega last_name: Milcinski - first_name: Jennifer full_name: Klein, Jennifer last_name: Klein - first_name: Lucia full_name: Seyfarth, Lucia last_name: Seyfarth - first_name: Peter full_name: Sterling, Peter last_name: Sterling - first_name: David full_name: Brainard, David last_name: Brainard - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian citation: ama: Tkačik G, Garrigan P, Ratliff C, et al. Natural images from the birthplace of the human eye. PLoS One. 2011;6(6). doi:10.1371/journal.pone.0020409 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. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0020409 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.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0020409. ieee: G. Tkačik et al., “Natural images from the birthplace of the human eye,” PLoS One, vol. 6, no. 6. Public Library of Science, 2011. 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. mla: Tkačik, Gašper, et al. “Natural Images from the Birthplace of the Human Eye.” PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409. short: G. Tkačik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011). date_created: 2018-12-11T12:03:01Z date_published: 2011-06-16T00:00:00Z date_updated: 2021-01-12T07:43:07Z day: '16' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pone.0020409 file: - access_level: open_access checksum: 307d4356916471306e3705ac65b82fa1 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:25Z date_updated: 2020-07-14T12:46:11Z file_id: '4749' file_name: IST-2015-379-v1+1_journal.pone.0020409.pdf file_size: 1424768 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 6' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3223' pubrep_id: '379' quality_controlled: '1' scopus_import: 1 status: public title: Natural images from the birthplace of the human eye tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2011' ... --- _id: '3385' article_type: review author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Sixt MK. Interstitial locomotion of leukocytes. Immunology Letters. 2011;138(1):32-34. doi:10.1016/j.imlet.2011.02.013 apa: Sixt, M. K. (2011). Interstitial locomotion of leukocytes. Immunology Letters. Elsevier. https://doi.org/10.1016/j.imlet.2011.02.013 chicago: Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” Immunology Letters. Elsevier, 2011. https://doi.org/10.1016/j.imlet.2011.02.013. ieee: M. K. Sixt, “Interstitial locomotion of leukocytes,” Immunology Letters, vol. 138, no. 1. Elsevier, pp. 32–34, 2011. ista: Sixt MK. 2011. Interstitial locomotion of leukocytes. Immunology Letters. 138(1), 32–34. mla: Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” Immunology Letters, vol. 138, no. 1, Elsevier, 2011, pp. 32–34, doi:10.1016/j.imlet.2011.02.013. short: M.K. Sixt, Immunology Letters 138 (2011) 32–34. date_created: 2018-12-11T12:03:02Z date_published: 2011-07-01T00:00:00Z date_updated: 2021-01-12T07:43:07Z day: '01' department: - _id: MiSi doi: 10.1016/j.imlet.2011.02.013 intvolume: ' 138' issue: '1' language: - iso: eng month: '07' oa_version: None page: 32 - 34 publication: Immunology Letters publication_status: published publisher: Elsevier publist_id: '3222' quality_controlled: '1' scopus_import: 1 status: public title: Interstitial locomotion of leukocytes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 138 year: '2011' ... --- _id: '3386' abstract: - lang: eng text: 'Evolutionary theories of ageing predict that life span increases with decreasing extrinsic mortality, and life span variation among queens in ant species seems to corroborate this prediction: queens, which are the only reproductive in a colony, live much longer than queens in multi-queen colonies. The latter often inhabit ephemeral nest sites and accordingly are assumed to experience a higher mortality risk. Yet, all prior studies compared queens from different single- and multi-queen species. Here, we demonstrate an effect of queen number on longevity and fecundity within a single, socially plastic species, where queens experience the similar level of extrinsic mortality. Queens from single- and two-queen colonies had significantly longer lifespan and higher fecundity than queens living in associations of eight queens. As queens also differ neither in morphology nor the mode of colony foundation, our study shows that the social environment itself strongly affects ageing rate.' author: - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: Schrempf A, Cremer S, Heinze J. Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary Biology. 2011;24(7):1455-1461. doi:10.1111/j.1420-9101.2011.02278.x apa: Schrempf, A., Cremer, S., & Heinze, J. (2011). Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/j.1420-9101.2011.02278.x chicago: Schrempf, Alexandra, Sylvia Cremer, and Jürgen Heinze. “Social Influence on Age and Reproduction Reduced Lifespan and Fecundity in Multi Queen Ant Colonies.” Journal of Evolutionary Biology. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1420-9101.2011.02278.x. ieee: A. Schrempf, S. Cremer, and J. Heinze, “Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies,” Journal of Evolutionary Biology, vol. 24, no. 7. Wiley-Blackwell, pp. 1455–1461, 2011. ista: Schrempf A, Cremer S, Heinze J. 2011. Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary Biology. 24(7), 1455–1461. mla: Schrempf, Alexandra, et al. “Social Influence on Age and Reproduction Reduced Lifespan and Fecundity in Multi Queen Ant Colonies.” Journal of Evolutionary Biology, vol. 24, no. 7, Wiley-Blackwell, 2011, pp. 1455–61, doi:10.1111/j.1420-9101.2011.02278.x. short: A. Schrempf, S. Cremer, J. Heinze, Journal of Evolutionary Biology 24 (2011) 1455–1461. date_created: 2018-12-11T12:03:02Z date_published: 2011-04-21T00:00:00Z date_updated: 2021-01-12T07:43:08Z day: '21' department: - _id: SyCr doi: 10.1111/j.1420-9101.2011.02278.x intvolume: ' 24' issue: '7' language: - iso: eng month: '04' oa_version: None page: 1455 - 1461 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley-Blackwell publist_id: '3221' quality_controlled: '1' scopus_import: 1 status: public title: Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2011' ... --- _id: '3387' abstract: - lang: eng 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.' article_number: '205' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok citation: ama: Kupczok A. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 2011;11(205). doi:10.1186/1471-2148-11-205 apa: Kupczok, A. (2011). Split based computation of majority rule supertrees. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-11-205 chicago: Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC Evolutionary Biology. BioMed Central, 2011. https://doi.org/10.1186/1471-2148-11-205. ieee: A. Kupczok, “Split based computation of majority rule supertrees,” BMC Evolutionary Biology, vol. 11, no. 205. BioMed Central, 2011. ista: Kupczok A. 2011. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 11(205), 205. mla: Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC Evolutionary Biology, vol. 11, no. 205, 205, BioMed Central, 2011, doi:10.1186/1471-2148-11-205. short: A. Kupczok, BMC Evolutionary Biology 11 (2011). date_created: 2018-12-11T12:03:03Z date_published: 2011-07-13T00:00:00Z date_updated: 2021-01-12T07:43:08Z day: '13' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-11-205 file: - access_level: open_access checksum: 68da8d04af1b97b4cbe8606e2f92ddd8 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:09Z date_updated: 2020-07-14T12:46:11Z file_id: '5058' file_name: IST-2015-372-v1+1_1471-2148-11-205.pdf file_size: 465042 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 11' issue: '205' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '3219' pubrep_id: '372' quality_controlled: '1' scopus_import: 1 status: public title: Split based computation of majority rule supertrees tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2011' ... --- _id: '3388' abstract: - lang: eng 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.' article_number: '201' author: - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Per full_name: Nielsen, Per last_name: Nielsen - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma - first_name: David full_name: Nash, David last_name: Nash citation: 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. BMC Evolutionary Biology. 2011;11(201). doi:10.1186/1471-2148-11-201 apa: Ugelvig, L. V., 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. BioMed Central. https://doi.org/10.1186/1471-2148-11-201 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.” BMC Evolutionary Biology. BioMed Central, 2011. https://doi.org/10.1186/1471-2148-11-201. 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,” BMC Evolutionary Biology, vol. 11, no. 201. BioMed Central, 2011. 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. mla: Ugelvig, Line V., et al. “Reconstructing Eight Decades of Genetic Variation in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.” BMC Evolutionary Biology, vol. 11, no. 201, 201, BioMed Central, 2011, doi:10.1186/1471-2148-11-201. short: L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11 (2011). date_created: 2018-12-11T12:03:03Z date_published: 2011-07-11T00:00:00Z date_updated: 2021-01-12T07:43:08Z day: '11' ddc: - '576' department: - _id: SyCr doi: 10.1186/1471-2148-11-201 file: - access_level: open_access checksum: 9ebfed0740f1fa071d02ec32c2b8c17f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:18Z date_updated: 2020-07-14T12:46:11Z file_id: '5069' file_name: IST-2015-371-v1+1_1471-2148-11-201.pdf file_size: 2166556 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 11' issue: '201' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '3220' pubrep_id: '371' quality_controlled: '1' scopus_import: 1 status: public title: Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2011' ... --- _id: '3389' abstract: - lang: eng text: Kernel canonical correlation analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying process that generates the data and can ignore high-variance noise directions. However, for data where acquisition in one or more modalities is expensive or otherwise limited, KCCA may suffer from small sample effects. We propose to use semi-supervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of KCCA on human fMRI data, with regression to single and multi-variate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of KCCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing. acknowledgement: The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 228180. This work was funded in part by the EC project CLASS, IST 027978, and the PASCAL2 network of excellence, IST 2002-506778. author: - first_name: Matthew full_name: Blaschko, Matthew last_name: Blaschko - first_name: Jacquelyn full_name: Shelton, Jacquelyn last_name: Shelton - first_name: Andreas full_name: Bartels, Andreas last_name: Bartels - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Arthur full_name: Gretton, Arthur last_name: Gretton citation: ama: Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. Semi supervised kernel canonical correlation analysis with application to human fMRI. Pattern Recognition Letters. 2011;32(11):1572-1583. doi:10.1016/j.patrec.2011.02.011 apa: Blaschko, M., Shelton, J., Bartels, A., Lampert, C., & Gretton, A. (2011). Semi supervised kernel canonical correlation analysis with application to human fMRI. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2011.02.011 chicago: Blaschko, Matthew, Jacquelyn Shelton, Andreas Bartels, Christoph Lampert, and Arthur Gretton. “Semi Supervised Kernel Canonical Correlation Analysis with Application to Human FMRI.” Pattern Recognition Letters. Elsevier, 2011. https://doi.org/10.1016/j.patrec.2011.02.011. ieee: M. Blaschko, J. Shelton, A. Bartels, C. Lampert, and A. Gretton, “Semi supervised kernel canonical correlation analysis with application to human fMRI,” Pattern Recognition Letters, vol. 32, no. 11. Elsevier, pp. 1572–1583, 2011. ista: Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. 2011. Semi supervised kernel canonical correlation analysis with application to human fMRI. Pattern Recognition Letters. 32(11), 1572–1583. mla: Blaschko, Matthew, et al. “Semi Supervised Kernel Canonical Correlation Analysis with Application to Human FMRI.” Pattern Recognition Letters, vol. 32, no. 11, Elsevier, 2011, pp. 1572–83, doi:10.1016/j.patrec.2011.02.011. short: M. Blaschko, J. Shelton, A. Bartels, C. Lampert, A. Gretton, Pattern Recognition Letters 32 (2011) 1572–1583. date_created: 2018-12-11T12:03:03Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:43:09Z day: '01' department: - _id: ChLa doi: 10.1016/j.patrec.2011.02.011 intvolume: ' 32' issue: '11' language: - iso: eng month: '08' oa_version: None page: 1572 - 1583 publication: Pattern Recognition Letters publication_status: published publisher: Elsevier publist_id: '3218' quality_controlled: '1' scopus_import: 1 status: public title: Semi supervised kernel canonical correlation analysis with application to human fMRI type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2011' ...