[{"date_created":"2023-01-16T09:22:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2007","author":[{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"last_name":"Dickinson","first_name":"Hugh G.","full_name":"Dickinson, Hugh G."}],"pmid":1,"acknowledgement":"X.F. holds a Clarendon Scholarship from the University of Oxford. We thank Angela Hay and Jill Harrison for helpful advice and discussion.","citation":{"chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>. Elsevier BV, 2007. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>.","ama":"Feng X, Dickinson HG. Packaging the male germline in plants. <i>Trends in Genetics</i>. 2007;23(10):503-510. doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>","short":"X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.","apa":"Feng, X., &#38; Dickinson, H. G. (2007). Packaging the male germline in plants. <i>Trends in Genetics</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>.","ieee":"X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” <i>Trends in Genetics</i>, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007.","ista":"Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends in Genetics. 23(10), 503–510."},"abstract":[{"lang":"eng","text":"The development of plant lateral organs is interesting because, although many of the same genes seem to be involved in the early growth of primordia, completely different gene combinations are required for the complete development of organs such as leaves and stamens. Thus, the genes common to the development of most organs, which generally form and polarize the primordial ‘envelope’, must at some stage interact with those that ‘install’ the functional content of the organ – in the case of the stamen, the four microsporangia. Although distinct genetic pathways of organ initiation, polarity establishment and setting up the reproductive cell line can readily be recognized, they do not occur sequentially. Rather, they are activated early and run in parallel. There is evidence for continuing crosstalk between these pathways."}],"publisher":"Elsevier BV","date_published":"2007-10-01T00:00:00Z","_id":"12201","date_updated":"2023-05-08T10:58:47Z","scopus_import":"1","month":"10","extern":"1","keyword":["Genetics"],"article_type":"original","volume":23,"oa_version":"None","issue":"10","article_processing_charge":"No","type":"journal_article","department":[{"_id":"XiFe"}],"doi":"10.1016/j.tig.2007.08.005","language":[{"iso":"eng"}],"intvolume":"        23","quality_controlled":"1","title":"Packaging the male germline in plants","page":"503-510","external_id":{"pmid":["17825943"]},"publication":"Trends in Genetics","publication_identifier":{"issn":["0168-9525"]},"status":"public"},{"acknowledgement":"National Science Foundation\r\nThis work was supported with NSF Grant No. PHY-0653623. We thank Dr. W. Bickel and Dr. J. Jones for diagnostic equipment, K. Guerin for assistance with mechanical drawings, and M. Parker of Rincon Research Inc. for optics components.","abstract":[{"lang":"eng","text":"A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. "}],"citation":{"ista":"Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. 2007. Cover slip external cavity diode laser. Review of Scientific Instruments. 78(10), 106108.","ieee":"A. Carr, Y. Serchest, S. R. Waitukaitis, J. Perreault, V. Lonij, and A. Cronin, “Cover slip external cavity diode laser,” <i>Review of Scientific Instruments</i>, vol. 78, no. 10. American Institute of Physics, 2007.","mla":"Carr, Adra, et al. “Cover Slip External Cavity Diode Laser.” <i>Review of Scientific Instruments</i>, vol. 78, no. 10, 106108, American Institute of Physics, 2007, doi:<a href=\"https://doi.org/10.1063/1.2801006\">10.1063/1.2801006</a>.","apa":"Carr, A., Serchest, Y., Waitukaitis, S. R., Perreault, J., Lonij, V., &#38; Cronin, A. (2007). Cover slip external cavity diode laser. <i>Review of Scientific Instruments</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.2801006\">https://doi.org/10.1063/1.2801006</a>","short":"A. Carr, Y. Serchest, S.R. Waitukaitis, J. Perreault, V. Lonij, A. Cronin, Review of Scientific Instruments 78 (2007).","ama":"Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. Cover slip external cavity diode laser. <i>Review of Scientific Instruments</i>. 2007;78(10). doi:<a href=\"https://doi.org/10.1063/1.2801006\">10.1063/1.2801006</a>","chicago":"Carr, Adra, Yancey Serchest, Scott R Waitukaitis, John Perreault, Vincent Lonij, and Alexander Cronin. “Cover Slip External Cavity Diode Laser.” <i>Review of Scientific Instruments</i>. American Institute of Physics, 2007. <a href=\"https://doi.org/10.1063/1.2801006\">https://doi.org/10.1063/1.2801006</a>."},"publisher":"American Institute of Physics","publist_id":"7925","date_published":"2007-10-29T00:00:00Z","_id":"128","date_updated":"2021-01-12T06:49:35Z","month":"10","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:46Z","year":"2007","author":[{"full_name":"Carr, Adra","last_name":"Carr","first_name":"Adra"},{"last_name":"Serchest","first_name":"Yancey","full_name":"Serchest, Yancey"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"},{"full_name":"Perreault, John","last_name":"Perreault","first_name":"John"},{"last_name":"Lonij","first_name":"Vincent","full_name":"Lonij, Vincent"},{"first_name":"Alexander","last_name":"Cronin","full_name":"Cronin, Alexander"}],"doi":"10.1063/1.2801006","language":[{"iso":"eng"}],"intvolume":"        78","quality_controlled":"1","title":"Cover slip external cavity diode laser","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/0708.0014","open_access":"1"}],"publication":"Review of Scientific Instruments","external_id":{"arxiv":["0708.0014"]},"status":"public","extern":"1","volume":78,"article_number":"106108","oa_version":"Preprint","arxiv":1,"issue":"10","type":"journal_article","day":"29"},{"day":"01","type":"journal_article","author":[{"first_name":"Shamprasad","last_name":"Raghu","full_name":"Raghu, Shamprasad V"},{"orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Maximilian Jösch"},{"full_name":"Borst, Alexander","first_name":"Alexander","last_name":"Borst"},{"first_name":"Dierk","last_name":"Reiff","full_name":"Reiff, Dierk F"}],"year":"2007","issue":"4","publication_status":"published","date_created":"2018-12-11T11:51:13Z","volume":502,"extern":1,"status":"public","date_updated":"2021-01-12T06:49:42Z","month":"06","_id":"1297","date_published":"2007-06-01T00:00:00Z","publist_id":"5974","publication":"Journal of Comparative Neurology","publisher":"Wiley-Blackwell","page":"598 - 610","quality_controlled":0,"title":"Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites","intvolume":"       502","doi":"10.1002/cne.21319","citation":{"short":"S. Raghu, M.A. Jösch, A. Borst, D. Reiff, Journal of Comparative Neurology 502 (2007) 598–610.","ama":"Raghu S, Jösch MA, Borst A, Reiff D. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. <i>Journal of Comparative Neurology</i>. 2007;502(4):598-610. doi:<a href=\"https://doi.org/10.1002/cne.21319\">10.1002/cne.21319</a>","chicago":"Raghu, Shamprasad, Maximilian A Jösch, Alexander Borst, and Dierk Reiff. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” <i>Journal of Comparative Neurology</i>. Wiley-Blackwell, 2007. <a href=\"https://doi.org/10.1002/cne.21319\">https://doi.org/10.1002/cne.21319</a>.","mla":"Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” <i>Journal of Comparative Neurology</i>, vol. 502, no. 4, Wiley-Blackwell, 2007, pp. 598–610, doi:<a href=\"https://doi.org/10.1002/cne.21319\">10.1002/cne.21319</a>.","apa":"Raghu, S., Jösch, M. A., Borst, A., &#38; Reiff, D. (2007). Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. <i>Journal of Comparative Neurology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cne.21319\">https://doi.org/10.1002/cne.21319</a>","ieee":"S. Raghu, M. A. Jösch, A. Borst, and D. Reiff, “Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites,” <i>Journal of Comparative Neurology</i>, vol. 502, no. 4. Wiley-Blackwell, pp. 598–610, 2007.","ista":"Raghu S, Jösch MA, Borst A, Reiff D. 2007. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. 502(4), 598–610."},"abstract":[{"text":"In flies, the large tangential cells of the lobula plate represent an important processing center for visual navigation based on optic flow. Although the visual response properties of these cells have been well studied in blowflies, information on their synaptic organization is mostly lacking. Here we study the distribution of presynaptic release and postsynaptic inhibitory sites in the same set of cells in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry, our results suggest that HS and VS cells of Drosophila express γ-aminobutyric acid (GABA) receptors in their dendritic region within the lobula plate, thus being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum, both cell types express synaptobrevin, suggesting the presence of presynaptic specializations there. HS- and VS-cell terminals additionally show evidence for postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings are in line with the general circuit for visual motion detection and receptive field properties as postulated from electrophysiological and optical recordings in blowflies, suggesting a similar functional organization of lobula plate tangential cells in the two species.","lang":"eng"}]},{"publication_status":"published","date_created":"2018-12-11T12:03:11Z","volume":93,"extern":1,"day":"01","type":"journal_article","author":[{"first_name":"Johannes","last_name":"Preiner","full_name":"Preiner, Johannes"},{"full_name":"Harald Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","first_name":"Harald L"},{"full_name":"Rankl, Christian","last_name":"Rankl","first_name":"Christian"},{"full_name":"Knaus, Helene","first_name":"Helene","last_name":"Knaus"},{"full_name":"Cisneros, David A","last_name":"Cisneros","first_name":"David"},{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"last_name":"Kienberger","first_name":"Ferry","full_name":"Kienberger, Ferry"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"},{"full_name":"Hinterdorfer, Peter","last_name":"Hinterdorfer","first_name":"Peter"}],"year":"2007","issue":"3","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913163/","open_access":"1"}],"publisher":"Biophysical Society","oa":1,"page":"930 - 937","quality_controlled":0,"title":"Free energy of membrane protein unfolding derived from single-molecule force measurements","intvolume":"        93","doi":"10.1529/biophysj.106.096982","abstract":[{"lang":"eng","text":"Mechanical single-molecule techniques offer exciting possibilities to investigate protein folding and stability in native environments at submolecular resolution. By applying a free-energy reconstruction procedure developed by Hummer and Szabo, which is based on a statistical theorem introduced by Jarzynski, we determined the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin, and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium unfolding free energy was independent of pulling rate and temperature ranging between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties in individual transmembrane helices. In halorhodopsin, the stabilization of a short helical segment yielded a characteristic signature in the energy profile. In NhaA, a pronounced peak was observed at a functionally important site in the protein. Since a large variety of single- and multispan membrane proteins can be tackled in mechanical unfolding experiments, our approach provides a basis for systematically elucidating energetic properties of membrane proteins with the resolution of individual secondary-structure elements."}],"citation":{"ieee":"J. Preiner <i>et al.</i>, “Free energy of membrane protein unfolding derived from single-molecule force measurements,” <i>Biophysical Journal</i>, vol. 93, no. 3. Biophysical Society, pp. 930–937, 2007.","ista":"Preiner J, Janovjak HL, Rankl C, Knaus H, Cisneros D, Kedrov A, Kienberger F, Mueller D, Hinterdorfer P. 2007. Free energy of membrane protein unfolding derived from single-molecule force measurements. Biophysical Journal. 93(3), 930–937.","chicago":"Preiner, Johannes, Harald L Janovjak, Christian Rankl, Helene Knaus, David Cisneros, Alexej Kedrov, Ferry Kienberger, Daniel Mueller, and Peter Hinterdorfer. “Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force Measurements.” <i>Biophysical Journal</i>. Biophysical Society, 2007. <a href=\"https://doi.org/10.1529/biophysj.106.096982\">https://doi.org/10.1529/biophysj.106.096982</a>.","ama":"Preiner J, Janovjak HL, Rankl C, et al. Free energy of membrane protein unfolding derived from single-molecule force measurements. <i>Biophysical Journal</i>. 2007;93(3):930-937. doi:<a href=\"https://doi.org/10.1529/biophysj.106.096982\">10.1529/biophysj.106.096982</a>","short":"J. Preiner, H.L. Janovjak, C. Rankl, H. Knaus, D. Cisneros, A. Kedrov, F. Kienberger, D. Mueller, P. Hinterdorfer, Biophysical Journal 93 (2007) 930–937.","apa":"Preiner, J., Janovjak, H. L., Rankl, C., Knaus, H., Cisneros, D., Kedrov, A., … Hinterdorfer, P. (2007). Free energy of membrane protein unfolding derived from single-molecule force measurements. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1529/biophysj.106.096982\">https://doi.org/10.1529/biophysj.106.096982</a>","mla":"Preiner, Johannes, et al. “Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force Measurements.” <i>Biophysical Journal</i>, vol. 93, no. 3, Biophysical Society, 2007, pp. 930–37, doi:<a href=\"https://doi.org/10.1529/biophysj.106.096982\">10.1529/biophysj.106.096982</a>."},"status":"public","date_updated":"2021-01-12T07:43:18Z","month":"08","_id":"3411","publist_id":"2990","date_published":"2007-08-01T00:00:00Z","publication":"Biophysical Journal"},{"date_updated":"2019-04-26T07:22:27Z","month":"06","status":"public","publist_id":"2989","date_published":"2007-06-01T00:00:00Z","publication":"Annual Review of Biophysics","_id":"3412","quality_controlled":0,"title":"Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy","publisher":"Annual Reviews","page":"233 - 260","doi":"10.1146/annurev.biophys.36.040306.132640","citation":{"ama":"Kedrov A, Janovjak HL, Sapra T, Mueller D. Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy. <i>Annual Review of Biophysics</i>. 2007;36:233-260. doi:<a href=\"https://doi.org/10.1146/annurev.biophys.36.040306.132640\">10.1146/annurev.biophys.36.040306.132640</a>","short":"A. Kedrov, H.L. Janovjak, T. Sapra, D. Mueller, Annual Review of Biophysics 36 (2007) 233–260.","chicago":"Kedrov, Alexej, Harald L Janovjak, Tanuj Sapra, and Daniel Mueller. “Deciphering Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2007. <a href=\"https://doi.org/10.1146/annurev.biophys.36.040306.132640\">https://doi.org/10.1146/annurev.biophys.36.040306.132640</a>.","mla":"Kedrov, Alexej, et al. “Deciphering Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.” <i>Annual Review of Biophysics</i>, vol. 36, Annual Reviews, 2007, pp. 233–60, doi:<a href=\"https://doi.org/10.1146/annurev.biophys.36.040306.132640\">10.1146/annurev.biophys.36.040306.132640</a>.","apa":"Kedrov, A., Janovjak, H. L., Sapra, T., &#38; Mueller, D. (2007). Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.biophys.36.040306.132640\">https://doi.org/10.1146/annurev.biophys.36.040306.132640</a>","ieee":"A. Kedrov, H. L. Janovjak, T. Sapra, and D. Mueller, “Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy,” <i>Annual Review of Biophysics</i>, vol. 36. Annual Reviews, pp. 233–260, 2007.","ista":"Kedrov A, Janovjak HL, Sapra T, Mueller D. 2007. Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy. Annual Review of Biophysics. 36, 233–260."},"abstract":[{"text":"Molecular interactions are the basic language of biological processes.\nThey establish the forces interacting between the building blocks of\nproteins and other macromolecules, thus determining their functional\nroles. Because molecular interactions trigger virtually every\nbiological process, approaches to decipher their language are needed.\nSingle-molecule force spectroscopy (SMFS) has been used to detect\nand characterize different types of molecular interactions that occur\nbetween and within native membrane proteins. The first experiments\ndetected and localized molecular interactions that stabilized\nmembrane proteins, including how these interactions were established\nduring folding of α-helical secondary structure elements into\nthe native protein and how they changed with oligomerization, temperature,\nand mutations. SMFS also enables investigators to detect\nand locate molecular interactions established during ligand and inhibitor\nbinding. These exciting applications provide opportunities\nfor studying the molecular forces of life. Further developments will\nelucidate the origins of molecular interactions encoded in their lifetimes,\ninteraction ranges, interplay, and dynamics characteristic of biological systems.","lang":"eng"}],"intvolume":"        36","year":"2007","day":"01","type":"review","author":[{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"full_name":"Harald Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"full_name":"Sapra, Tanuj K","last_name":"Sapra","first_name":"Tanuj"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"date_created":"2018-12-11T12:03:11Z","publication_status":"published","volume":36,"extern":1},{"oa":1,"publisher":"American Institute of Physics","main_file_link":[{"url":"http://arxiv.org/abs/q-bio/0609011v1","open_access":"1"}],"title":"Morphogen transport in epithelia","intvolume":"        75","doi":"10.1103/PhysRevE.75.011901","citation":{"ieee":"M. T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, and F. Julicher, “Morphogen transport in epithelia,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 75, no. 1. American Institute of Physics, 2007.","ista":"Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. 2007. Morphogen transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter Physics. 75(1).","chicago":"Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos Gonzalez Gaitan, and Frank Julicher. “Morphogen Transport in Epithelia.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2007. <a href=\"https://doi.org/10.1103/PhysRevE.75.011901\">https://doi.org/10.1103/PhysRevE.75.011901</a>.","ama":"Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. Morphogen transport in epithelia. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2007;75(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.75.011901\">10.1103/PhysRevE.75.011901</a>","short":"M.T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, F. Julicher, Physical Review E Statistical Nonlinear and Soft Matter Physics 75 (2007).","apa":"Bollenbach, M. T., Kruse, K., Pantazis, P., Gonzalez Gaitan, M., &#38; Julicher, F. (2007). Morphogen transport in epithelia. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.75.011901\">https://doi.org/10.1103/PhysRevE.75.011901</a>","mla":"Bollenbach, Mark Tobias, et al. “Morphogen Transport in Epithelia.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 75, no. 1, American Institute of Physics, 2007, doi:<a href=\"https://doi.org/10.1103/PhysRevE.75.011901\">10.1103/PhysRevE.75.011901</a>."},"abstract":[{"lang":"eng","text":"We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the wing disk of the fruit fly Drosophila.\r\n© 2007 The American Physical Society"}],"language":[{"iso":"eng"}],"status":"public","date_updated":"2021-01-12T07:43:24Z","month":"01","_id":"3427","publist_id":"2974","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","external_id":{"arxiv":["q-bio/0609011v1"]},"date_published":"2007-01-01T00:00:00Z","arxiv":1,"oa_version":"Preprint","date_created":"2018-12-11T12:03:16Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":75,"extern":"1","type":"journal_article","day":"01","author":[{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X"},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"},{"last_name":"Pantazis","first_name":"Periklis","full_name":"Pantazis, Periklis"},{"full_name":"Gonzalez Gaitan, Marcos","first_name":"Marcos","last_name":"Gonzalez Gaitan"},{"last_name":"Julicher","first_name":"Frank","full_name":"Julicher, Frank"}],"year":"2007","article_processing_charge":"No","issue":"1"},{"type":"book_chapter","day":"01","author":[{"full_name":"Jonathan Bollback","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gardner, Paul P","last_name":"Gardner","first_name":"Paul"},{"last_name":"Nielsen","first_name":"Rasmus","full_name":"Nielsen, Rasmus"}],"year":"2007","editor":[{"full_name":"Liberles, David A","last_name":"Liberles","first_name":"David"}],"extern":1,"publication_status":"published","date_created":"2018-12-11T12:03:18Z","_id":"3432","publist_id":"2968","date_published":"2007-01-01T00:00:00Z","publication":"Ancestral Sequence Reconstruction","status":"public","date_updated":"2021-01-12T07:43:26Z","month":"01","doi":"10.1093/acprof:oso/9780199299188.003.0006","abstract":[{"text":"Evolution has left its signature on the molecules and morphology of living organisms. Ancestral reconstruction offers an excellent tool for understanding the process of evolution using comparative information. Methods for ancestral reconstruction have generally focused on reconstructing the ancestral states at the internal nodes of a phylogeny. Often, we are not interested in particular nodes of the phylogeny but the whole history of a character. This chapter focuses on a Bayesian method for estimating these histories, or mutational paths, on phylogenies. Mutational path methods differ most notably from other approaches in their ability to estimate not only the ancestral states at the internal nodes of a phylogeny, but also the order and timing of mutational changes across the phylogeny. The chapter provides a concise introduction to the statistical tools needed for sampling mutational paths on a phylogeny.","lang":"eng"}],"citation":{"ista":"Bollback JP, Gardner P, Nielsen R. 2007.Estimating the history of mutations on a phylogeny. In: Ancestral Sequence Reconstruction. , 69–79.","ieee":"J. P. Bollback, P. Gardner, and R. Nielsen, “Estimating the history of mutations on a phylogeny,” in <i>Ancestral Sequence Reconstruction</i>, D. Liberles, Ed. Oxford University Press, 2007, pp. 69–79.","mla":"Bollback, Jonathan P., et al. “Estimating the History of Mutations on a Phylogeny.” <i>Ancestral Sequence Reconstruction</i>, edited by David Liberles, Oxford University Press, 2007, pp. 69–79, doi:<a href=\"https://doi.org/10.1093/acprof:oso/9780199299188.003.0006\">10.1093/acprof:oso/9780199299188.003.0006</a>.","apa":"Bollback, J. P., Gardner, P., &#38; Nielsen, R. (2007). Estimating the history of mutations on a phylogeny. In D. Liberles (Ed.), <i>Ancestral Sequence Reconstruction</i> (pp. 69–79). Oxford University Press. <a href=\"https://doi.org/10.1093/acprof:oso/9780199299188.003.0006\">https://doi.org/10.1093/acprof:oso/9780199299188.003.0006</a>","ama":"Bollback JP, Gardner P, Nielsen R. Estimating the history of mutations on a phylogeny. In: Liberles D, ed. <i>Ancestral Sequence Reconstruction</i>. Oxford University Press; 2007:69-79. doi:<a href=\"https://doi.org/10.1093/acprof:oso/9780199299188.003.0006\">10.1093/acprof:oso/9780199299188.003.0006</a>","short":"J.P. Bollback, P. Gardner, R. Nielsen, in:, D. Liberles (Ed.), Ancestral Sequence Reconstruction, Oxford University Press, 2007, pp. 69–79.","chicago":"Bollback, Jonathan P, Paul Gardner, and Rasmus Nielsen. “Estimating the History of Mutations on a Phylogeny.” In <i>Ancestral Sequence Reconstruction</i>, edited by David Liberles, 69–79. Oxford University Press, 2007. <a href=\"https://doi.org/10.1093/acprof:oso/9780199299188.003.0006\">https://doi.org/10.1093/acprof:oso/9780199299188.003.0006</a>."},"publisher":"Oxford University Press","page":"69 - 79","quality_controlled":0,"title":"Estimating the history of mutations on a phylogeny"},{"extern":1,"date_created":"2018-12-11T12:03:19Z","publication_status":"published","volume":124,"issue":"3","year":"2007","type":"journal_article","day":"01","author":[{"first_name":"Sheila","last_name":"Reynolds","full_name":"Reynolds, Sheila M"},{"full_name":"Dryer, Katie","last_name":"Dryer","first_name":"Katie"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Jonathan Bollback"},{"full_name":"Uy, J Albert","last_name":"Uy","first_name":"J Albert"},{"last_name":"Patricelli","first_name":"Gail","full_name":"Patricelli, Gail L"},{"full_name":"Robson, Timothy","first_name":"Timothy","last_name":"Robson"},{"last_name":"Borgia","first_name":"Gerald","full_name":"Borgia, Gerald"},{"first_name":"Michael","last_name":"Braun","full_name":"Braun, Michael J"}],"doi":"10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2","abstract":[{"text":"he potential for di? erences between genetic paternity and paternity inferred from behavioral observation has long been recognized. These di? erences are associated with the challenge for females of seeking both genetic and material bene? ts; this challenge is less severe in species with polygynous, non-resource-based mating systems (such as leks) than in those with resource-based systems. We pres- ent the ? rst study of paternity patt erns in a non-resource-based species that does not form true leks. We compared paternity inferred from observed mating behavior to genetically assigned paternity in the Satin Bowerbird (Ptilonorhynchus violaceus) using eight microsatellite markers. Mating behavior was observed and recorded via automated video-cameras positioned at all bowers (29?34 bowers each year) in the study site throughout each mating season. We obtained blood samples and identi- ? ed mothers for 11 chicks in 9 nests. For all chicks, the most likely genetic father had been observed to mate with the mother in the year the chick was sampled. All most likely genetic fathers were assigned with high con? dence and all were bower- holding males. These results demonstrate that genetic paternity can be inferred from observed mating behavior with reasonable con? dence in Satin Bowerbirds. Observed male mating-success is therefore a reliable predictor of reproductive success, and this suggests that high skew in observed male mating-success translates directly to high skew in reproductive success. ","lang":"eng"}],"citation":{"apa":"Reynolds, S., Dryer, K., Bollback, J. P., Uy, J. A., Patricelli, G., Robson, T., … Braun, M. (2007). Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. <i>The Auk</i>. University of California Press. <a href=\"https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2\">https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2</a>","mla":"Reynolds, Sheila, et al. “Behavioral Paternity Predicts Genetic Paternity in Satin Bowerbirds, a Species with a Non-Resource-Based Mating System.” <i>The Auk</i>, vol. 124, no. 3, University of California Press, 2007, pp. 857–67, doi:<a href=\"https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2\">10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2</a>.","chicago":"Reynolds, Sheila, Katie Dryer, Jonathan P Bollback, J Albert Uy, Gail Patricelli, Timothy Robson, Gerald Borgia, and Michael Braun. “Behavioral Paternity Predicts Genetic Paternity in Satin Bowerbirds, a Species with a Non-Resource-Based Mating System.” <i>The Auk</i>. University of California Press, 2007. <a href=\"https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2\">https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2</a>.","ama":"Reynolds S, Dryer K, Bollback JP, et al. Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. <i>The Auk</i>. 2007;124(3):857-867. doi:<a href=\"https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2\">10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2</a>","short":"S. Reynolds, K. Dryer, J.P. Bollback, J.A. Uy, G. Patricelli, T. Robson, G. Borgia, M. Braun, The Auk 124 (2007) 857–867.","ista":"Reynolds S, Dryer K, Bollback JP, Uy JA, Patricelli G, Robson T, Borgia G, Braun M. 2007. Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. The Auk. 124(3), 857–867.","ieee":"S. Reynolds <i>et al.</i>, “Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system,” <i>The Auk</i>, vol. 124, no. 3. University of California Press, pp. 857–867, 2007."},"intvolume":"       124","quality_controlled":0,"title":"Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system","publisher":"University of California Press","page":"857 - 867","publication":"The Auk","date_published":"2007-01-01T00:00:00Z","publist_id":"2964","_id":"3436","date_updated":"2021-01-12T07:43:27Z","month":"01","status":"public"},{"author":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas"},{"last_name":"Buzsáki","first_name":"György","full_name":"Buzsáki, György"}],"day":"01","type":"journal_article","year":"2007","extern":1,"volume":2,"date_created":"2018-12-11T12:03:23Z","publication_status":"published","_id":"3450","date_published":"2007-01-01T00:00:00Z","publist_id":"2937","publication":"Scholarpedia","status":"public","month":"01","date_updated":"2021-01-12T07:43:32Z","intvolume":"         2","citation":{"ista":"Jonas PM, Buzsáki G. 2007. Neural inhibition. Scholarpedia. 2.","ieee":"P. M. Jonas and G. Buzsáki, “Neural inhibition,” <i>Scholarpedia</i>, vol. 2. Scholarpedia, 2007.","mla":"Jonas, Peter M., and György Buzsáki. “Neural Inhibition.” <i>Scholarpedia</i>, vol. 2, Scholarpedia, 2007, doi:<a href=\"https://doi.org/10.4249/scholarpedia.3286\">10.4249/scholarpedia.3286</a>.","apa":"Jonas, P. M., &#38; Buzsáki, G. (2007). Neural inhibition. <i>Scholarpedia</i>. Scholarpedia. <a href=\"https://doi.org/10.4249/scholarpedia.3286\">https://doi.org/10.4249/scholarpedia.3286</a>","short":"P.M. Jonas, G. Buzsáki, Scholarpedia 2 (2007).","ama":"Jonas PM, Buzsáki G. Neural inhibition. <i>Scholarpedia</i>. 2007;2. doi:<a href=\"https://doi.org/10.4249/scholarpedia.3286\">10.4249/scholarpedia.3286</a>","chicago":"Jonas, Peter M, and György Buzsáki. “Neural Inhibition.” <i>Scholarpedia</i>. Scholarpedia, 2007. <a href=\"https://doi.org/10.4249/scholarpedia.3286\">https://doi.org/10.4249/scholarpedia.3286</a>."},"doi":"10.4249/scholarpedia.3286","publisher":"Scholarpedia","title":"Neural inhibition","quality_controlled":0},{"issue":"3","year":"2007","day":"01","type":"journal_article","author":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Jozsef Csicsvari"},{"full_name":"Joseph O'Neill","first_name":"Joseph","last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kevin","last_name":"Allen","full_name":"Allen, Kevin"},{"last_name":"Senior","first_name":"Timothy","full_name":"Senior,Timothy"}],"publication_status":"published","date_created":"2018-12-11T12:03:46Z","volume":26,"extern":1,"date_updated":"2021-01-12T07:44:03Z","month":"08","status":"public","date_published":"2007-08-01T00:00:00Z","publist_id":"2862","publication":"European Journal of Neuroscience","_id":"3523","quality_controlled":0,"title":"Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration","publisher":"Wiley-Blackwell","page":"704 - 716","doi":"10.1111/j.1460-9568.2007.05684.x","citation":{"ieee":"J. L. Csicsvari, J. O’Neill, K. Allen, and T. Senior, “Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration,” <i>European Journal of Neuroscience</i>, vol. 26, no. 3. Wiley-Blackwell, pp. 704–716, 2007.","ista":"Csicsvari JL, O’Neill J, Allen K, Senior T. 2007. Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration. European Journal of Neuroscience. 26(3), 704–716.","chicago":"Csicsvari, Jozsef L, Joseph O’Neill, Kevin Allen, and Timothy Senior. “Place-Selective Firing Contributes to the Reverse-Order Reactivation of CA1 Pyramidal Cells during Sharp Waves in Open-Field Exploration.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2007. <a href=\"https://doi.org/10.1111/j.1460-9568.2007.05684.x\">https://doi.org/10.1111/j.1460-9568.2007.05684.x</a>.","short":"J.L. Csicsvari, J. O’Neill, K. Allen, T. Senior, European Journal of Neuroscience 26 (2007) 704–716.","ama":"Csicsvari JL, O’Neill J, Allen K, Senior T. Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration. <i>European Journal of Neuroscience</i>. 2007;26(3):704-716. doi:<a href=\"https://doi.org/10.1111/j.1460-9568.2007.05684.x\">10.1111/j.1460-9568.2007.05684.x</a>","apa":"Csicsvari, J. L., O’Neill, J., Allen, K., &#38; Senior, T. (2007). Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1460-9568.2007.05684.x\">https://doi.org/10.1111/j.1460-9568.2007.05684.x</a>","mla":"Csicsvari, Jozsef L., et al. “Place-Selective Firing Contributes to the Reverse-Order Reactivation of CA1 Pyramidal Cells during Sharp Waves in Open-Field Exploration.” <i>European Journal of Neuroscience</i>, vol. 26, no. 3, Wiley-Blackwell, 2007, pp. 704–16, doi:<a href=\"https://doi.org/10.1111/j.1460-9568.2007.05684.x\">10.1111/j.1460-9568.2007.05684.x</a>."},"abstract":[{"lang":"eng","text":"On the linear track, the recent firing sequences of CA1 place cells recur during sharp wave/ripple patterns (SWRs) in a reverse temporal order [Foster &amp; Wilson (2006) Nature, 440, 680-683]. We have found similar reverse-order reactivation during SWRs in open-field exploration where the firing sequence of cells varied before each SWR. Both the onset times and the firing patterns of cells showed a tendency for reversed sequences during SWRs. These effects were observed for SWRs that occurred during exploration, but not for those during longer immobility periods. Additionally, reverse reactivation was stronger when it was preceded by higher speed (&gt; 5 cm/s) run periods. The trend for reverse-order SWR reactivation was not significantly different in familiar and novel environments, even though SWR-associated firing rates of both pyramidal cells and interneurons were reduced in novel environments as compared with familiar. During exploration-associated SWRs (eSWR) place cells retain place-selective firing [O'Neill et al. (2006) Neuron, 49, 143-155]. Here, we have shown that each cell's firing onset was more delayed and firing probability more reduced during eSWRs the further the rat was from the middle of the cell's place field; that is, cells receiving less momentary place-related excitatory drive fired later during SWR events. However, even controlling for place field distance, the recent firing of cells was still significantly correlated with SWR reactivation sequences. We therefore propose that both place-related drive and the firing history of cells contribute to reverse reactivation during eSWRs."}],"intvolume":"        26"},{"publication_status":"published","date_created":"2018-12-11T12:03:58Z","extern":1,"year":"2007","conference":{"name":"SPM: Symposium on Solid and Physical Modeling"},"day":"01","type":"conference","author":[{"full_name":"Attali, Dominique","last_name":"Attali","first_name":"Dominique"},{"full_name":"Herbert Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mileyko","first_name":"Yuriy","full_name":"Mileyko, Yuriy"}],"quality_controlled":0,"title":"Weak witnesses for Delaunay triangulations of submanifolds","oa":1,"publisher":"ACM","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-00201055"}],"page":"143 - 150","doi":"10.1145/1236246.1236267","citation":{"apa":"Attali, D., Edelsbrunner, H., &#38; Mileyko, Y. (2007). Weak witnesses for Delaunay triangulations of submanifolds (pp. 143–150). Presented at the SPM: Symposium on Solid and Physical Modeling, ACM. <a href=\"https://doi.org/10.1145/1236246.1236267\">https://doi.org/10.1145/1236246.1236267</a>","mla":"Attali, Dominique, et al. <i>Weak Witnesses for Delaunay Triangulations of Submanifolds</i>. ACM, 2007, pp. 143–50, doi:<a href=\"https://doi.org/10.1145/1236246.1236267\">10.1145/1236246.1236267</a>.","chicago":"Attali, Dominique, Herbert Edelsbrunner, and Yuriy Mileyko. “Weak Witnesses for Delaunay Triangulations of Submanifolds,” 143–50. ACM, 2007. <a href=\"https://doi.org/10.1145/1236246.1236267\">https://doi.org/10.1145/1236246.1236267</a>.","ama":"Attali D, Edelsbrunner H, Mileyko Y. Weak witnesses for Delaunay triangulations of submanifolds. In: ACM; 2007:143-150. doi:<a href=\"https://doi.org/10.1145/1236246.1236267\">10.1145/1236246.1236267</a>","short":"D. Attali, H. Edelsbrunner, Y. Mileyko, in:, ACM, 2007, pp. 143–150.","ista":"Attali D, Edelsbrunner H, Mileyko Y. 2007. Weak witnesses for Delaunay triangulations of submanifolds. SPM: Symposium on Solid and Physical Modeling, 143–150.","ieee":"D. Attali, H. Edelsbrunner, and Y. Mileyko, “Weak witnesses for Delaunay triangulations of submanifolds,” presented at the SPM: Symposium on Solid and Physical Modeling, 2007, pp. 143–150."},"abstract":[{"lang":"eng","text":"The main result of this paper is an extension of de Silva's Weak Delaunay Theorem to smoothly embedded curves and surfaces in Euclidean space. Assuming a sufficiently fine sampling, we prove that i + 1 points in the sample span an i-simplex in the restricted Delaunay triangulation iff every subset of the i + 1 points has a weak witness."}],"date_updated":"2021-01-12T07:44:19Z","month":"06","status":"public","date_published":"2007-06-01T00:00:00Z","publist_id":"2824","_id":"3561"},{"conference":{"name":"AHS: NASA/ESA Conference on Adaptive Hardware and Systems"},"day":"20","type":"conference","author":[{"full_name":"Yang, Erfu","last_name":"Yang","first_name":"Erfu"},{"last_name":"Haridas","first_name":"Nakul","full_name":"Haridas, Nakul"},{"last_name":"El Rayis","first_name":"Ahmed","full_name":"El-Rayis, Ahmed O"},{"last_name":"Erdogan","first_name":"Ahmet","full_name":"Erdogan, Ahmet T"},{"full_name":"Arslan, Tughrul","last_name":"Arslan","first_name":"Tughrul"},{"full_name":"Nicholas Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"year":"2007","publication_status":"published","date_created":"2018-12-11T12:04:11Z","extern":1,"status":"public","date_updated":"2021-01-12T07:44:35Z","month":"08","_id":"3601","date_published":"2007-08-20T00:00:00Z","publist_id":"2782","publisher":"IEEE","page":"27 - 34","quality_controlled":0,"title":"Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications","doi":"10.1109/AHS.2007.76","citation":{"chicago":"Yang, Erfu, Nakul Haridas, Ahmed El Rayis, Ahmet Erdogan, Tughrul Arslan, and Nicholas H Barton. “Multiobjective Optimal Design of MEMS-Based Reconfigurable and Evolvable Sensor Networks for Space Applications,” 27–34. IEEE, 2007. <a href=\"https://doi.org/10.1109/AHS.2007.76\">https://doi.org/10.1109/AHS.2007.76</a>.","short":"E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, N.H. Barton, in:, IEEE, 2007, pp. 27–34.","ama":"Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications. In: IEEE; 2007:27-34. doi:<a href=\"https://doi.org/10.1109/AHS.2007.76\">10.1109/AHS.2007.76</a>","apa":"Yang, E., Haridas, N., El Rayis, A., Erdogan, A., Arslan, T., &#38; Barton, N. H. (2007). Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications (pp. 27–34). Presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, IEEE. <a href=\"https://doi.org/10.1109/AHS.2007.76\">https://doi.org/10.1109/AHS.2007.76</a>","mla":"Yang, Erfu, et al. <i>Multiobjective Optimal Design of MEMS-Based Reconfigurable and Evolvable Sensor Networks for Space Applications</i>. IEEE, 2007, pp. 27–34, doi:<a href=\"https://doi.org/10.1109/AHS.2007.76\">10.1109/AHS.2007.76</a>.","ieee":"E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, and N. H. Barton, “Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications,” presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 2007, pp. 27–34.","ista":"Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. 2007. Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications. AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 27–34."},"abstract":[{"lang":"eng","text":"In this paper, the multiobjective optimal design of space-based reconfigurable sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II) is employed to obtain multi-criteria Pareto-optimal solutions, which allows system designers to easily make a reasonable trade-off choice from the set of non-dominated solutions according to their preferences and system requirements. As a case study, a cluster-based satellite sensing network is simulated under multiple objectives. Most importantly, this paper also presents the application of our newly designed adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal design of space-based reconfigurable sensor networks."}]},{"publication_identifier":{"isbn":["978-087969684-9"]},"status":"public","month":"06","date_updated":"2021-12-21T15:55:28Z","_id":"3674","publist_id":"2709","date_published":"2007-06-30T00:00:00Z","page":"XIV, 833","publisher":"Cold Spring Harbor Laboratory Press","title":"Evolution","quality_controlled":"1","abstract":[{"text":"Evolution permeates all of biology. But researchers in molecular and cellular biology, genetics, developmental biology, microbiology, and neuroscience have only recently begun to think seriously in terms of evolution. The chief reasons for this shift are the growing list of organisms with sequenced genomes; the increasingly sophisticated ways of interpreting those sequences; and the ever more powerful experimental techniques (and wider range of model organisms) with which to ask questions about evolution as well as mechanism.\r\n\r\nEvolution serves as a primary text for undergraduate and graduate courses in evolution. It is also a text working scientists can use to educate themselves on how evolution affects their fields. It differs from currently available alternatives in containing more molecular biology than is traditionally the case. But this is not at the expense of traditional evolutionary theory. Indeed, a glance at the Table of Contents and the authors' interests reveals the range of material covered in this book. The authors are world-renowned in population genetics, bacterial genomics, paleontology, human genetics, and developmental biology. The integration of molecular biology and evolutionary biology reflects the current direction of much research among evolutionary scientists.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"ieee":"N. H. Barton, D. Briggs, J. Eisen, D. Goldstein, and N. Patel, <i>Evolution</i>. Cold Spring Harbor Laboratory Press, 2007.","ista":"Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. 2007. Evolution, Cold Spring Harbor Laboratory Press, XIV, 833p.","ama":"Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. <i>Evolution</i>. Cold Spring Harbor Laboratory Press; 2007.","short":"N.H. Barton, D. Briggs, J. Eisen, D. Goldstein, N. Patel, Evolution, Cold Spring Harbor Laboratory Press, 2007.","chicago":"Barton, Nicholas H, Derek Briggs, Jonathan Eisen, David Goldstein, and Nipam Patel. <i>Evolution</i>. Cold Spring Harbor Laboratory Press, 2007.","mla":"Barton, Nicholas H., et al. <i>Evolution</i>. Cold Spring Harbor Laboratory Press, 2007.","apa":"Barton, N. H., Briggs, D., Eisen, J., Goldstein, D., &#38; Patel, N. (2007). <i>Evolution</i>. Cold Spring Harbor Laboratory Press."},"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Briggs, Derek","first_name":"Derek","last_name":"Briggs"},{"full_name":"Eisen, Jonathan","last_name":"Eisen","first_name":"Jonathan"},{"full_name":"Goldstein, David","first_name":"David","last_name":"Goldstein"},{"full_name":"Patel, Nipam","last_name":"Patel","first_name":"Nipam"}],"type":"book","day":"30","article_processing_charge":"No","year":"2007","related_material":{"link":[{"url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=3251&query_desc=au%2Cwrdl%3A%20nicholas%20barton","description":"available via catalog IST BookList","relation":"other"},{"relation":"supplementary_material","url":"http://www.evolution-textbook.org/"}]},"oa_version":"None","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","date_created":"2018-12-11T12:04:33Z","extern":"1"},{"publication_status":"published","date_created":"2018-12-11T12:04:35Z","volume":4713,"extern":1,"conference":{"name":"DAGM: German Association For Pattern Recognition"},"day":"09","type":"conference","author":[{"first_name":"Adrian","last_name":"Ulges","full_name":"Ulges, Adrian"},{"full_name":"Christoph Lampert","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Keysers,Daniel","first_name":"Daniel","last_name":"Keysers"},{"last_name":"Breuel","first_name":"Thomas","full_name":"Breuel,Thomas M"}],"year":"2007","publisher":"Springer","page":"204 - 213","quality_controlled":0,"title":"Optimal dominant motion estimation using adaptive search of transformation space","intvolume":"      4713","doi":"10.1007/978-3-540-74936-3_21","citation":{"apa":"Ulges, A., Lampert, C., Keysers, D., &#38; Breuel, T. (2007). Optimal dominant motion estimation using adaptive search of transformation space (Vol. 4713, pp. 204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer. <a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">https://doi.org/10.1007/978-3-540-74936-3_21</a>","mla":"Ulges, Adrian, et al. <i>Optimal Dominant Motion Estimation Using Adaptive Search of Transformation Space</i>. Vol. 4713, Springer, 2007, pp. 204–13, doi:<a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">10.1007/978-3-540-74936-3_21</a>.","chicago":"Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">https://doi.org/10.1007/978-3-540-74936-3_21</a>.","ama":"Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213. doi:<a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">10.1007/978-3-540-74936-3_21</a>","short":"A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213.","ista":"Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation using adaptive search of transformation space. DAGM: German Association For Pattern Recognition, LCNS, vol. 4713, 204–213.","ieee":"A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion estimation using adaptive search of transformation space,” presented at the DAGM: German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213."},"alternative_title":["LCNS"],"abstract":[{"lang":"eng","text":"The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.\n\nOur main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior."}],"status":"public","date_updated":"2021-01-12T07:45:06Z","month":"11","_id":"3681","date_published":"2007-11-09T00:00:00Z","publist_id":"2695"},{"status":"public","month":"08","date_updated":"2019-04-26T07:22:33Z","_id":"3687","date_published":"2007-08-01T00:00:00Z","publication":"Unknown","publist_id":"2681","main_file_link":[{"url":"http://www.kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/TR-164_[0].pdf","open_access":"0"}],"publisher":"Max-Planck-Institute for Biological Cybernetics","title":"Efficient subwindow search for object localization","quality_controlled":0,"citation":{"ista":"Blaschko M, Hofmann T, Lampert C. 2007. Efficient subwindow search for object localization, Max-Planck-Institute for Biological Cybernetics,p.","ieee":"M. Blaschko, T. Hofmann, and C. Lampert, <i>Efficient subwindow search for object localization</i>, no. 164. Max-Planck-Institute for Biological Cybernetics, 2007.","apa":"Blaschko, M., Hofmann, T., &#38; Lampert, C. (2007). <i>Efficient subwindow search for object localization</i>. <i>Unknown</i>. Max-Planck-Institute for Biological Cybernetics.","mla":"Blaschko, Matthew, et al. “Efficient Subwindow Search for Object Localization.” <i>Unknown</i>, no. 164, Max-Planck-Institute for Biological Cybernetics, 2007.","chicago":"Blaschko, Matthew, Thomas Hofmann, and Christoph Lampert. <i>Efficient Subwindow Search for Object Localization</i>. <i>Unknown</i>. Max-Planck-Institute for Biological Cybernetics, 2007.","ama":"Blaschko M, Hofmann T, Lampert C. <i>Efficient Subwindow Search for Object Localization</i>. Max-Planck-Institute for Biological Cybernetics; 2007.","short":"M. Blaschko, T. Hofmann, C. Lampert, Efficient Subwindow Search for Object Localization, Max-Planck-Institute for Biological Cybernetics, 2007."},"abstract":[{"text":"Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image.\n\nWe report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem.\n\nWe show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.","lang":"eng"}],"author":[{"last_name":"Blaschko","first_name":"Matthew","full_name":"Blaschko,Matthew B"},{"full_name":"Hofmann,Thomas","first_name":"Thomas","last_name":"Hofmann"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Christoph Lampert"}],"type":"report","day":"01","year":"2007","issue":"164","publication_status":"published","date_created":"2018-12-11T12:04:37Z","extern":1},{"author":[{"last_name":"Ulges","first_name":"Adrian","full_name":"Ulges, Adrian"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Christoph Lampert"},{"last_name":"Keysers","first_name":"Daniel","full_name":"Keysers,Daniel"},{"last_name":"Breuel","first_name":"Thomas","full_name":"Breuel,Thomas M"}],"type":"conference","day":"09","conference":{"name":"DAGM: German Association For Pattern Recognition"},"year":"2007","extern":1,"volume":4713,"publication_status":"published","date_created":"2018-12-11T12:04:42Z","_id":"3701","publist_id":"2656","date_published":"2007-11-09T00:00:00Z","status":"public","month":"11","date_updated":"2021-01-12T07:51:35Z","intvolume":"      4713","alternative_title":["LNCS"],"abstract":[{"text":"The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.\n\nOur main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.","lang":"eng"}],"citation":{"apa":"Ulges, A., Lampert, C., Keysers, D., &#38; Breuel, T. (2007). Optimal dominant motion estimation using adaptive search of transformation space (Vol. 4713, pp. 204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer. <a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">https://doi.org/10.1007/978-3-540-74936-3_21</a>","mla":"Ulges, Adrian, et al. <i>Optimal Dominant Motion Estimation Using Adaptive Search of Transformation Space</i>. Vol. 4713, Springer, 2007, pp. 204–13, doi:<a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">10.1007/978-3-540-74936-3_21</a>.","chicago":"Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">https://doi.org/10.1007/978-3-540-74936-3_21</a>.","ama":"Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213. doi:<a href=\"https://doi.org/10.1007/978-3-540-74936-3_21\">10.1007/978-3-540-74936-3_21</a>","short":"A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213.","ista":"Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation using adaptive search of transformation space. DAGM: German Association For Pattern Recognition, LNCS, vol. 4713, 204–213.","ieee":"A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion estimation using adaptive search of transformation space,” presented at the DAGM: German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213."},"doi":"10.1007/978-3-540-74936-3_21","page":"204 - 213","publisher":"Springer","title":"Optimal dominant motion estimation using adaptive search of transformation space","quality_controlled":0},{"year":"2007","issue":"2","author":[{"full_name":"Harald Janovjak","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Knaus, Helene","last_name":"Knaus","first_name":"Helene"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel J"}],"day":"17","type":"journal_article","extern":1,"volume":129,"date_created":"2018-12-11T12:04:49Z","publication_status":"published","date_published":"2007-01-17T00:00:00Z","publist_id":"2507","publication":"Journal of the American Chemical Society","_id":"3723","month":"01","date_updated":"2021-01-12T07:51:44Z","status":"public","citation":{"mla":"Janovjak, Harald L., et al. “Transmembrane Helices Have Rough Energy Surfaces.” <i>Journal of the American Chemical Society</i>, vol. 129, no. 2, ACS, 2007, pp. 246–47, doi:<a href=\"https://doi.org/10.1021/ja065684a\">10.1021/ja065684a</a>.","apa":"Janovjak, H. L., Knaus, H., &#38; Mueller, D. (2007). Transmembrane helices have rough energy surfaces. <i>Journal of the American Chemical Society</i>. ACS. <a href=\"https://doi.org/10.1021/ja065684a\">https://doi.org/10.1021/ja065684a</a>","short":"H.L. Janovjak, H. Knaus, D. Mueller, Journal of the American Chemical Society 129 (2007) 246–247.","ama":"Janovjak HL, Knaus H, Mueller D. Transmembrane helices have rough energy surfaces. <i>Journal of the American Chemical Society</i>. 2007;129(2):246-247. doi:<a href=\"https://doi.org/10.1021/ja065684a\">10.1021/ja065684a</a>","chicago":"Janovjak, Harald L, Helene Knaus, and Daniel Mueller. “Transmembrane Helices Have Rough Energy Surfaces.” <i>Journal of the American Chemical Society</i>. ACS, 2007. <a href=\"https://doi.org/10.1021/ja065684a\">https://doi.org/10.1021/ja065684a</a>.","ista":"Janovjak HL, Knaus H, Mueller D. 2007. Transmembrane helices have rough energy surfaces. Journal of the American Chemical Society. 129(2), 246–247.","ieee":"H. L. Janovjak, H. Knaus, and D. Mueller, “Transmembrane helices have rough energy surfaces,” <i>Journal of the American Chemical Society</i>, vol. 129, no. 2. ACS, pp. 246–247, 2007."},"abstract":[{"text":"The folding and function of proteins is guided by their multidimensional energy landscapes. Local corrugations on rugged energy surfaces determine the dynamics of functionally related conformational changes and molecular flexibilities. By varying the temperature during the force-induced unfolding of the membrane protein bacteriorhodopsin, we directly determined the energy roughness of individual transmembrane α-helices. All helices have rugged energy surfaces with an overall roughness scale of 4−6 kBT, in line with the vital roles of transmembrane helices as functional and structural building blocks. Interestingly, the mechanical unfolding of misfolded membrane proteins in vivo is likely to occur on similarly energy rugged surfaces, which may also provide an energetic framework for small vertical motions of functionally relevant helices. Finally, our results also indicate that transmembrane protein structures can have rough energy surfaces despite their highly restricted conformational spaces in confining lipid bilayer environments. ","lang":"eng"}],"doi":"10.1021/ja065684a","intvolume":"       129","title":"Transmembrane helices have rough energy surfaces","quality_controlled":0,"page":"246 - 247","publisher":"ACS"},{"author":[{"full_name":"Bippes, Christian A","last_name":"Bippes","first_name":"Christian"},{"orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Harald Janovjak"},{"full_name":"Kedrov, Alexej","first_name":"Alexej","last_name":"Kedrov"},{"last_name":"Mueller","first_name":"Daniel","full_name":"Mueller, Daniel J"}],"type":"journal_article","day":"31","year":"2007","issue":"4","volume":18,"date_created":"2018-12-11T12:04:50Z","publication_status":"published","extern":1,"status":"public","month":"01","date_updated":"2021-01-12T07:51:46Z","_id":"3727","date_published":"2007-01-31T00:00:00Z","publication":"Nanotechnology","publist_id":"2501","publisher":"IOP Publishing Ltd.","title":"Digital force-feedback for protein unfolding experiments using atomic force microscopy","quality_controlled":0,"intvolume":"        18","abstract":[{"text":"Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand–receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.","lang":"eng"}],"citation":{"ista":"Bippes C, Janovjak HL, Kedrov A, Mueller D. 2007. Digital force-feedback for protein unfolding experiments using atomic force microscopy. Nanotechnology. 18(4).","ieee":"C. Bippes, H. L. Janovjak, A. Kedrov, and D. Mueller, “Digital force-feedback for protein unfolding experiments using atomic force microscopy,” <i>Nanotechnology</i>, vol. 18, no. 4. IOP Publishing Ltd., 2007.","apa":"Bippes, C., Janovjak, H. L., Kedrov, A., &#38; Mueller, D. (2007). Digital force-feedback for protein unfolding experiments using atomic force microscopy. <i>Nanotechnology</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0957-4484/18/4/044022\">https://doi.org/10.1088/0957-4484/18/4/044022</a>","mla":"Bippes, Christian, et al. “Digital Force-Feedback for Protein Unfolding Experiments Using Atomic Force Microscopy.” <i>Nanotechnology</i>, vol. 18, no. 4, IOP Publishing Ltd., 2007, doi:<a href=\"https://doi.org/10.1088/0957-4484/18/4/044022\">10.1088/0957-4484/18/4/044022</a>.","chicago":"Bippes, Christian, Harald L Janovjak, Alexej Kedrov, and Daniel Mueller. “Digital Force-Feedback for Protein Unfolding Experiments Using Atomic Force Microscopy.” <i>Nanotechnology</i>. IOP Publishing Ltd., 2007. <a href=\"https://doi.org/10.1088/0957-4484/18/4/044022\">https://doi.org/10.1088/0957-4484/18/4/044022</a>.","short":"C. Bippes, H.L. Janovjak, A. Kedrov, D. Mueller, Nanotechnology 18 (2007).","ama":"Bippes C, Janovjak HL, Kedrov A, Mueller D. Digital force-feedback for protein unfolding experiments using atomic force microscopy. <i>Nanotechnology</i>. 2007;18(4). doi:<a href=\"https://doi.org/10.1088/0957-4484/18/4/044022\">10.1088/0957-4484/18/4/044022</a>"},"doi":"10.1088/0957-4484/18/4/044022"},{"date_updated":"2021-01-12T07:51:48Z","month":"01","status":"public","date_published":"2007-01-09T00:00:00Z","publist_id":"2495","publication":"PNAS","_id":"3731","quality_controlled":0,"title":"Precise physical models of protein-DNA interaction from high-throughput data","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"0","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766414"}],"page":"501 - 506","doi":"10.1073/pnas.0609908104","citation":{"mla":"Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” <i>PNAS</i>, vol. 104, no. 2, National Academy of Sciences, 2007, pp. 501–06, doi:<a href=\"https://doi.org/10.1073/pnas.0609908104\">10.1073/pnas.0609908104</a>.","apa":"Kinney, J., Tkačik, G., &#38; Callan, C. (2007). Precise physical models of protein-DNA interaction from high-throughput data. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0609908104\">https://doi.org/10.1073/pnas.0609908104</a>","ama":"Kinney J, Tkačik G, Callan C. Precise physical models of protein-DNA interaction from high-throughput data. <i>PNAS</i>. 2007;104(2):501-506. doi:<a href=\"https://doi.org/10.1073/pnas.0609908104\">10.1073/pnas.0609908104</a>","short":"J. Kinney, G. Tkačik, C. Callan, PNAS 104 (2007) 501–506.","chicago":"Kinney, Justin, Gašper Tkačik, and Curtis Callan. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” <i>PNAS</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0609908104\">https://doi.org/10.1073/pnas.0609908104</a>.","ista":"Kinney J, Tkačik G, Callan C. 2007. Precise physical models of protein-DNA interaction from high-throughput data. PNAS. 104(2), 501–506.","ieee":"J. Kinney, G. Tkačik, and C. Callan, “Precise physical models of protein-DNA interaction from high-throughput data,” <i>PNAS</i>, vol. 104, no. 2. National Academy of Sciences, pp. 501–506, 2007."},"abstract":[{"lang":"eng","text":"A cell's ability to regulate gene transcription depends in large part on the energy with which transcription factors (TFs) bind their DNA regulatory sites. Obtaining accurate models of this binding energy is therefore an important goal for quantitative biology. In this article, we present a principled likelihood-based approach for inferring physical models of TF-DNA binding energy from the data produced by modern high-throughput binding assays. Central to our analysis is the ability to assess the relative likelihood of different model parameters given experimental observations. We take a unique approach to this problem and show how to compute likelihood without any explicit assumptions about the noise that inevitably corrupts such measurements. Sampling possible choices for model parameters according to this likelihood function, we can then make probabilistic predictions for the identities of binding sites and their physical binding energies. Applying this procedure to previously published data on the Saccharomyces cerevisiae TF Abf1p, we find models of TF binding whose parameters are determined with remarkable precision. Evidence for the accuracy of these models is provided by an astonishing level of phylogenetic conservation in the predicted energies of putative binding sites. Results from in vivo and in vitro experiments also provide highly consistent characterizations of Abf1p, a result that contrasts with a previous analysis of the same data."}],"intvolume":"       104","issue":"2","year":"2007","day":"09","type":"journal_article","author":[{"full_name":"Kinney,Justin B","last_name":"Kinney","first_name":"Justin"},{"first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Gasper Tkacik"},{"full_name":"Callan,Curtis G","first_name":"Curtis","last_name":"Callan"}],"publication_status":"published","date_created":"2018-12-11T12:04:51Z","volume":104,"extern":1},{"extern":1,"volume":"q-bio.QM","publication_status":"published","date_created":"2018-12-11T12:04:55Z","author":[{"last_name":"Broderick","first_name":"Tamara","full_name":"Broderick,Tamara"},{"last_name":"Dudik","first_name":"Miroslav","full_name":"Dudik,Miroslav"},{"full_name":"Gasper Tkacik","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schapire,Robert E","first_name":"Robert","last_name":"Schapire"},{"full_name":"Bialek, William S","first_name":"William","last_name":"Bialek"}],"day":"01","type":"preprint","year":"2007","citation":{"ista":"Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. 2007. Faster solutions of the inverse pairwise Ising problem. ArXiv, q-QM, .","ieee":"T. Broderick, M. Dudik, G. Tkačik, R. Schapire, and W. Bialek, “Faster solutions of the inverse pairwise Ising problem,” <i>ArXiv</i>, vol. q-QM. ArXiv, 2007.","apa":"Broderick, T., Dudik, M., Tkačik, G., Schapire, R., &#38; Bialek, W. (2007). Faster solutions of the inverse pairwise Ising problem. <i>ArXiv</i>. ArXiv.","mla":"Broderick, Tamara, et al. “Faster Solutions of the Inverse Pairwise Ising Problem.” <i>ArXiv</i>, vol. q-QM, ArXiv, 2007.","chicago":"Broderick, Tamara, Miroslav Dudik, Gašper Tkačik, Robert Schapire, and William Bialek. “Faster Solutions of the Inverse Pairwise Ising Problem.” <i>ArXiv</i>. ArXiv, 2007.","short":"T. Broderick, M. Dudik, G. Tkačik, R. Schapire, W. Bialek, ArXiv q-QM (2007).","ama":"Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. Faster solutions of the inverse pairwise Ising problem. <i>ArXiv</i>. 2007;q-QM."},"abstract":[{"text":"Recent work has shown that probabilistic models based on pairwise interactions-in the simplest case, the Ising model-provide surprisingly accurate descriptions of experiments on real biological networks ranging from neurons to genes. Finding these models requires us to solve an inverse problem: given experimentally measured expectation values, what are the parameters of the underlying Hamiltonian? This problem sits at the intersection of statistical physics and machine learning, and we suggest that more efficient solutions are possible by merging ideas from the two fields. We use a combination of recent coordinate descent algorithms with an adaptation of the histogram Monte Carlo method, and implement these techniques to take advantage of the sparseness found in data on real neurons. The resulting algorithm learns the parameters of an Ising model describing a network of forty neurons within a few minutes. This opens the possibility of analyzing much larger data sets now emerging, and thus testing hypotheses about the collective behaviors of these networks.","lang":"eng"}],"oa":1,"publisher":"ArXiv","main_file_link":[{"url":"http://arxiv.org/abs/0712.2437v2","open_access":"1"}],"title":"Faster solutions of the inverse pairwise Ising problem","quality_controlled":0,"_id":"3742","publication":"ArXiv","date_published":"2007-01-01T00:00:00Z","publist_id":"2486","status":"public","month":"01","date_updated":"2021-01-12T07:51:52Z"}]