[{"doi":"10.1002/wrcr.20450","main_file_link":[{"url":"https://doi.org/10.1002/wrcr.20450","open_access":"1"}],"oa_version":"Published Version","oa":1,"keyword":["Water Science and Technology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"American Geophysical Union","abstract":[{"lang":"eng","text":"In the headwater catchments of the main Asian rivers, glaciohydrological models are a useful tool to anticipate impacts of climatic changes. However, the reliability of their projections strongly depends on the quality and quantity of data that are available for parameter estimation, model calibration and validation, as well as on the accuracy of climate change projections. In this study the physically oriented, glaciohydrological model TOPKAPI-ETH is used to simulate future changes in snow, glacier, and runoff from the Hunza River Basin in northern Pakistan. Three key sources of model uncertainty in future runoff projections are compared: model parameters, climate projections, and natural climate variability. A novel approach, applicable also to ungauged catchments, is used to determine which model parameters and model components significantly affect the overall model uncertainty. We show that the model is capable of reproducing streamflow and glacier mass balances, but that all analyzed sources of uncertainty significantly affect the reliability of future projections, and that their effect is variable in time and in space. The effect of parametric uncertainty often exceeds the impact of climate uncertainty and natural climate variability, especially in heavily glacierized subcatchments. The results of the uncertainty analysis allow detailed recommendations on network design and the timing and location of field measurements, which could efficiently help to reduce model uncertainty in the future."}],"_id":"12639","publication_identifier":{"issn":["0043-1397"]},"intvolume":"        49","title":"Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change","day":"01","article_processing_charge":"No","extern":"1","status":"public","type":"journal_article","date_published":"2013-03-01T00:00:00Z","month":"03","date_updated":"2023-02-24T08:16:19Z","author":[{"last_name":"Ragettli","first_name":"S.","full_name":"Ragettli, S."},{"last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca"},{"full_name":"Bordoy, R.","last_name":"Bordoy","first_name":"R."},{"first_name":"W. W.","last_name":"Immerzeel","full_name":"Immerzeel, W. W."}],"page":"6048-6066","article_type":"original","volume":49,"date_created":"2023-02-20T08:17:12Z","issue":"9","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","citation":{"short":"S. Ragettli, F. Pellicciotti, R. Bordoy, W.W. Immerzeel, Water Resources Research 49 (2013) 6048–6066.","chicago":"Ragettli, S., Francesca Pellicciotti, R. Bordoy, and W. W. Immerzeel. “Sources of Uncertainty in Modeling the Glaciohydrological Response of a Karakoram Watershed to Climate Change.” <i>Water Resources Research</i>. American Geophysical Union, 2013. <a href=\"https://doi.org/10.1002/wrcr.20450\">https://doi.org/10.1002/wrcr.20450</a>.","ama":"Ragettli S, Pellicciotti F, Bordoy R, Immerzeel WW. Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. <i>Water Resources Research</i>. 2013;49(9):6048-6066. doi:<a href=\"https://doi.org/10.1002/wrcr.20450\">10.1002/wrcr.20450</a>","ista":"Ragettli S, Pellicciotti F, Bordoy R, Immerzeel WW. 2013. Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. Water Resources Research. 49(9), 6048–6066.","ieee":"S. Ragettli, F. Pellicciotti, R. Bordoy, and W. W. Immerzeel, “Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change,” <i>Water Resources Research</i>, vol. 49, no. 9. American Geophysical Union, pp. 6048–6066, 2013.","mla":"Ragettli, S., et al. “Sources of Uncertainty in Modeling the Glaciohydrological Response of a Karakoram Watershed to Climate Change.” <i>Water Resources Research</i>, vol. 49, no. 9, American Geophysical Union, 2013, pp. 6048–66, doi:<a href=\"https://doi.org/10.1002/wrcr.20450\">10.1002/wrcr.20450</a>.","apa":"Ragettli, S., Pellicciotti, F., Bordoy, R., &#38; Immerzeel, W. W. (2013). Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/wrcr.20450\">https://doi.org/10.1002/wrcr.20450</a>"},"publication":"Water Resources Research","year":"2013"},{"publication":"Nature Geoscience","year":"2013","citation":{"apa":"Immerzeel, W. W., Pellicciotti, F., &#38; Bierkens, M. F. P. (2013). Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. <i>Nature Geoscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ngeo1896\">https://doi.org/10.1038/ngeo1896</a>","mla":"Immerzeel, W. W., et al. “Rising River Flows throughout the Twenty-First Century in Two Himalayan Glacierized Watersheds.” <i>Nature Geoscience</i>, vol. 6, no. 9, Springer Nature, 2013, pp. 742–45, doi:<a href=\"https://doi.org/10.1038/ngeo1896\">10.1038/ngeo1896</a>.","ieee":"W. W. Immerzeel, F. Pellicciotti, and M. F. P. Bierkens, “Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds,” <i>Nature Geoscience</i>, vol. 6, no. 9. Springer Nature, pp. 742–745, 2013.","ista":"Immerzeel WW, Pellicciotti F, Bierkens MFP. 2013. Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. Nature Geoscience. 6(9), 742–745.","ama":"Immerzeel WW, Pellicciotti F, Bierkens MFP. Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. <i>Nature Geoscience</i>. 2013;6(9):742-745. doi:<a href=\"https://doi.org/10.1038/ngeo1896\">10.1038/ngeo1896</a>","short":"W.W. Immerzeel, F. Pellicciotti, M.F.P. Bierkens, Nature Geoscience 6 (2013) 742–745.","chicago":"Immerzeel, W. W., Francesca Pellicciotti, and M. F. P. Bierkens. “Rising River Flows throughout the Twenty-First Century in Two Himalayan Glacierized Watersheds.” <i>Nature Geoscience</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1038/ngeo1896\">https://doi.org/10.1038/ngeo1896</a>."},"publication_status":"published","language":[{"iso":"eng"}],"volume":6,"issue":"9","scopus_import":"1","date_created":"2023-02-20T08:17:17Z","author":[{"full_name":"Immerzeel, W. W.","last_name":"Immerzeel","first_name":"W. W."},{"full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti"},{"full_name":"Bierkens, M. F. P.","last_name":"Bierkens","first_name":"M. F. P."}],"article_type":"letter_note","page":"742-745","date_updated":"2023-02-21T10:46:37Z","month":"09","date_published":"2013-09-13T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","extern":"1","intvolume":"         6","day":"13","title":"Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds","_id":"12640","publication_identifier":{"eissn":["1752-0908"],"issn":["1752-0894"]},"abstract":[{"lang":"eng","text":"Greater Himalayan glaciers are retreating and losing mass at rates comparable to glaciers in other regions of the world1,2,3,4,5. Assessments of future changes and their associated hydrological impacts are scarce, oversimplify glacier dynamics or include a limited number of climate models6,7,8,9. Here, we use results from the latest ensemble of climate models in combination with a high-resolution glacio-hydrological model to assess the hydrological impact of climate change on two climatically contrasting watersheds in the Greater Himalaya, the Baltoro and Langtang watersheds that drain into the Indus and Ganges rivers, respectively. We show that the largest uncertainty in future runoff is a result of variations in projected precipitation between climate models. In both watersheds, strong, but highly variable, increases in future runoff are projected and, despite the different characteristics of the watersheds, their responses are surprisingly similar. In both cases, glaciers will recede but net glacier melt runoff is on a rising limb at least until 2050. In combination with a positive change in precipitation, water availability during this century is not likely to decline. We conclude that river basins that depend on monsoon rains and glacier melt will continue to sustain the increasing water demands expected in these areas10."}],"quality_controlled":"1","keyword":["General Earth and Planetary Sciences"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","doi":"10.1038/ngeo1896","oa_version":"None"},{"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"International Glaciological Society","abstract":[{"text":"We investigate the sensitivity of a distributed enhanced temperature-index (ETI) melt model, in order to understand which parameters have the largest influence on model outputs and thus need to be accurately known. We use melt and meteorological data from two Alpine glaciers and one glacier in the Andes of Chile. Sensitivity analysis is conducted in a systematic way in terms of parameters and the different conditions (day, night, clear-sky, overcast), melt seasons and glaciers examined. The sensitivity of total melt to changes in individual parameters is calculated using a local method around the optimal value of the parameters. We verify that the parameters are optimal at the distributed scale and assess the model uncertainty induced by uncertainty in the parameters using a Monte Carlo technique. Model sensitivity to parameters is consistent across melt seasons, glaciers, different conditions and the daily statistics examined. The parameters to which the model is most sensitive are the shortwave-radiation factor, the temperature lapse rate for extrapolation of air temperature, the albedo parameters, the temperature threshold and the cloud transmittance factor parameters. A parameter uncertainty of 5% results in a model uncertainty of 5.6% of mean melt on Haut Glacier d’Arolla, Switzerland.","lang":"eng"}],"doi":"10.3189/2013aog63a537","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.3189/2013aog63a537","open_access":"1"}],"oa":1,"article_processing_charge":"No","status":"public","extern":"1","date_published":"2013-08-01T00:00:00Z","type":"journal_article","_id":"12641","publication_identifier":{"issn":["0260-3055"],"eissn":["1727-5644"]},"intvolume":"        54","day":"01","title":"Parameter sensitivity of a distributed enhanced temperature-index melt model","author":[{"first_name":"Martin","last_name":"Heynen","full_name":"Heynen, Martin"},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"first_name":"Marco","last_name":"Carenzo","full_name":"Carenzo, Marco"}],"page":"311-321","article_type":"original","volume":54,"issue":"63","scopus_import":"1","date_created":"2023-02-20T08:17:21Z","date_updated":"2023-02-21T10:43:42Z","month":"08","citation":{"chicago":"Heynen, Martin, Francesca Pellicciotti, and Marco Carenzo. “Parameter Sensitivity of a Distributed Enhanced Temperature-Index Melt Model.” <i>Annals of Glaciology</i>. International Glaciological Society, 2013. <a href=\"https://doi.org/10.3189/2013aog63a537\">https://doi.org/10.3189/2013aog63a537</a>.","short":"M. Heynen, F. Pellicciotti, M. Carenzo, Annals of Glaciology 54 (2013) 311–321.","ieee":"M. Heynen, F. Pellicciotti, and M. Carenzo, “Parameter sensitivity of a distributed enhanced temperature-index melt model,” <i>Annals of Glaciology</i>, vol. 54, no. 63. International Glaciological Society, pp. 311–321, 2013.","ista":"Heynen M, Pellicciotti F, Carenzo M. 2013. Parameter sensitivity of a distributed enhanced temperature-index melt model. Annals of Glaciology. 54(63), 311–321.","ama":"Heynen M, Pellicciotti F, Carenzo M. Parameter sensitivity of a distributed enhanced temperature-index melt model. <i>Annals of Glaciology</i>. 2013;54(63):311-321. doi:<a href=\"https://doi.org/10.3189/2013aog63a537\">10.3189/2013aog63a537</a>","mla":"Heynen, Martin, et al. “Parameter Sensitivity of a Distributed Enhanced Temperature-Index Melt Model.” <i>Annals of Glaciology</i>, vol. 54, no. 63, International Glaciological Society, 2013, pp. 311–21, doi:<a href=\"https://doi.org/10.3189/2013aog63a537\">10.3189/2013aog63a537</a>.","apa":"Heynen, M., Pellicciotti, F., &#38; Carenzo, M. (2013). Parameter sensitivity of a distributed enhanced temperature-index melt model. <i>Annals of Glaciology</i>. International Glaciological Society. <a href=\"https://doi.org/10.3189/2013aog63a537\">https://doi.org/10.3189/2013aog63a537</a>"},"publication":"Annals of Glaciology","year":"2013","language":[{"iso":"eng"}],"publication_status":"published"},{"date_published":"2013-08-01T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","extern":"1","intvolume":"        54","day":"01","title":"Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative","_id":"12642","publication_identifier":{"eissn":["1727-5644"],"issn":["0260-3055"]},"abstract":[{"lang":"eng","text":"Near-surface air temperature, typically measured at a height of 2 m, is the most important control on the energy exchange and the melt rate at a snow or ice surface. It is distributed in a simplistic manner in most glacier melt models by using constant linear lapse rates, which poorly represent the actual spatial and temporal variability of air temperature. In this paper, we test a simple thermodynamic model proposed by Greuell and Böhm in 1998 as an alternative, using a new dataset of air temperature measurements from along the flowline of Haut Glacier d’Arolla, Switzerland. The unmodified model performs little better than assuming a constant linear lapse rate. When modified to allow the ratio of the boundary layer height to the bulk heat transfer coefficient to vary along the flowline, the model matches measured air temperatures better, and a further reduction of the root-mean-square error is obtained, although there is still considerable scope for improvement. The modified model is shown to perform best under conditions favourable to the development of katabatic winds – few clouds, positive ambient air temperature, limited influence of synoptic or valley winds and a long fetch – but its performance is poor under cloudy conditions."}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Earth-Surface Processes"],"publisher":"International Glaciological Society","oa":1,"doi":"10.3189/2013aog63a477","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.3189/2013aog63a477","open_access":"1"}],"publication":"Annals of Glaciology","year":"2013","citation":{"apa":"Petersen, L., Pellicciotti, F., Juszak, I., Carenzo, M., &#38; Brock, B. (2013). Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. <i>Annals of Glaciology</i>. International Glaciological Society. <a href=\"https://doi.org/10.3189/2013aog63a477\">https://doi.org/10.3189/2013aog63a477</a>","ama":"Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. <i>Annals of Glaciology</i>. 2013;54(63):120-130. doi:<a href=\"https://doi.org/10.3189/2013aog63a477\">10.3189/2013aog63a477</a>","ista":"Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. 2013. Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. Annals of Glaciology. 54(63), 120–130.","ieee":"L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, and B. Brock, “Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative,” <i>Annals of Glaciology</i>, vol. 54, no. 63. International Glaciological Society, pp. 120–130, 2013.","mla":"Petersen, Lene, et al. “Suitability of a Constant Air Temperature Lapse Rate over an Alpine Glacier: Testing the Greuell and Böhm Model as an Alternative.” <i>Annals of Glaciology</i>, vol. 54, no. 63, International Glaciological Society, 2013, pp. 120–30, doi:<a href=\"https://doi.org/10.3189/2013aog63a477\">10.3189/2013aog63a477</a>.","short":"L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, B. Brock, Annals of Glaciology 54 (2013) 120–130.","chicago":"Petersen, Lene, Francesca Pellicciotti, Inge Juszak, Marco Carenzo, and Ben Brock. “Suitability of a Constant Air Temperature Lapse Rate over an Alpine Glacier: Testing the Greuell and Böhm Model as an Alternative.” <i>Annals of Glaciology</i>. International Glaciological Society, 2013. <a href=\"https://doi.org/10.3189/2013aog63a477\">https://doi.org/10.3189/2013aog63a477</a>."},"publication_status":"published","language":[{"iso":"eng"}],"volume":54,"scopus_import":"1","issue":"63","date_created":"2023-02-20T08:17:29Z","author":[{"full_name":"Petersen, Lene","first_name":"Lene","last_name":"Petersen"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti"},{"first_name":"Inge","last_name":"Juszak","full_name":"Juszak, Inge"},{"last_name":"Carenzo","first_name":"Marco","full_name":"Carenzo, Marco"},{"full_name":"Brock, Ben","first_name":"Ben","last_name":"Brock"}],"page":"120-130","article_type":"original","date_updated":"2023-02-21T10:18:24Z","month":"08"},{"publication_status":"published","language":[{"iso":"eng"}],"publication":"Journal of Geophysical Research: Atmospheres","year":"2013","citation":{"short":"I. Juszak, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 118 (2013) 3066–3084.","chicago":"Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal Variability.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2013. <a href=\"https://doi.org/10.1002/jgrd.50277\">https://doi.org/10.1002/jgrd.50277</a>.","mla":"Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal Variability.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 118, no. 8, American Geophysical Union, 2013, pp. 3066–84, doi:<a href=\"https://doi.org/10.1002/jgrd.50277\">10.1002/jgrd.50277</a>.","ama":"Juszak I, Pellicciotti F. A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. <i>Journal of Geophysical Research: Atmospheres</i>. 2013;118(8):3066-3084. doi:<a href=\"https://doi.org/10.1002/jgrd.50277\">10.1002/jgrd.50277</a>","ista":"Juszak I, Pellicciotti F. 2013. A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. Journal of Geophysical Research: Atmospheres. 118(8), 3066–3084.","ieee":"I. Juszak and F. Pellicciotti, “A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 118, no. 8. American Geophysical Union, pp. 3066–3084, 2013.","apa":"Juszak, I., &#38; Pellicciotti, F. (2013). A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/jgrd.50277\">https://doi.org/10.1002/jgrd.50277</a>"},"date_updated":"2023-02-21T10:10:46Z","month":"04","volume":118,"issue":"8","scopus_import":"1","date_created":"2023-02-20T08:17:34Z","author":[{"first_name":"I.","last_name":"Juszak","full_name":"Juszak, I."},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"page":"3066-3084","article_type":"original","intvolume":"       118","day":"27","title":"A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability","_id":"12643","publication_identifier":{"issn":["2169-897X"]},"date_published":"2013-04-27T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","extern":"1","oa":1,"doi":"10.1002/jgrd.50277","main_file_link":[{"url":"https://doi.org/10.1002/jgrd.50277","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Parameterizations of incoming longwave radiation are increasingly receiving attention for both low and high elevation glacierized sites. In this paper, we test 13 clear-sky parameterizations combined with seven cloud corrections for all-sky atmospheric emissivity at one location on Haut Glacier d'Arolla. We also analyze the four seasons separately and conduct a cross-validation to test the parameters’ robustness. The best parameterization is the one by Dilley and O'Brien, B for clear-sky conditions combined with Unsworth and Monteith cloud correction. This model is also the most robust when tested in cross-validation. When validated at different sites in the southern Alps of Switzerland and north-western Italian Alps, all parameterizations show a substantial decrease in performance, except for one site, thus suggesting that it is important to recalibrate parameterizations of incoming longwave radiation for different locations. We argue that this is due to differences in the structure of the atmosphere at the sites. We also quantify the effect that the incoming longwave radiation parameterizations have on energy-balance melt modeling, and show that recalibration of model parameters is needed. Using parameters from other sites leads to a significant underestimation of melt and to an error that is larger than that associated with using different parameterizations. Once recalibrated, however, the parameters of most models seem to be stable over seasons and years at the location on Haut Glacier d'Arolla.","lang":"eng"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"publisher":"American Geophysical Union"},{"doi":"10.1523/JNEUROSCI.0340-13.2013","date_updated":"2021-01-12T06:49:45Z","month":"01","page":"13927 - 13934","publisher":"Society for Neuroscience","quality_controlled":0,"author":[{"first_name":"Väinö","last_name":"Haikala","full_name":"Haikala, Väinö"},{"full_name":"Maximilian Jösch","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Borst","full_name":"Borst, Alexander"},{"full_name":"Mauss, Alex S","last_name":"Mauss","first_name":"Alex"}],"issue":"34","date_created":"2018-12-11T11:51:16Z","volume":33,"abstract":[{"text":"When confronted with a large-field stimulus rotating around the vertical body axis, flies display a following behavior called &quot;optomotor response.&quot; As neural control elements, the large tangential horizontal system (HS) cells of the lobula plate have been prime candidates for long. Here, we applied optogenetic stimulation of HS cells to evaluate their behavioral role in Drosophila. To minimize interference of the optical activation of channelrhodopsin-2 with the visual perception of the flies, we used a bistable variant called ChR2-C128S. By applying pulses of blue and yellow light, we first demonstrate electrophysiologically that lobula plate tangential cells can be activated and deactivated repeatedly with no evident change in depolarization strength over trials. We next show that selective optogenetic activation of HS cells elicits robust yaw head movements and yaw turning responses in fixed and tethered flying flies, respectively.","lang":"eng"}],"acknowledgement":"This work was supported by the Max Planck Society. ","_id":"1304","day":"01","title":"Optogenetic control of fly optomotor responses","publication_status":"published","intvolume":"        33","publist_id":"5967","status":"public","extern":1,"citation":{"apa":"Haikala, V., Jösch, M. A., Borst, A., &#38; Mauss, A. (2013). Optogenetic control of fly optomotor responses. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">https://doi.org/10.1523/JNEUROSCI.0340-13.2013</a>","ista":"Haikala V, Jösch MA, Borst A, Mauss A. 2013. Optogenetic control of fly optomotor responses. Journal of Neuroscience. 33(34), 13927–13934.","ama":"Haikala V, Jösch MA, Borst A, Mauss A. Optogenetic control of fly optomotor responses. <i>Journal of Neuroscience</i>. 2013;33(34):13927-13934. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">10.1523/JNEUROSCI.0340-13.2013</a>","ieee":"V. Haikala, M. A. Jösch, A. Borst, and A. Mauss, “Optogenetic control of fly optomotor responses,” <i>Journal of Neuroscience</i>, vol. 33, no. 34. Society for Neuroscience, pp. 13927–13934, 2013.","mla":"Haikala, Väinö, et al. “Optogenetic Control of Fly Optomotor Responses.” <i>Journal of Neuroscience</i>, vol. 33, no. 34, Society for Neuroscience, 2013, pp. 13927–34, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">10.1523/JNEUROSCI.0340-13.2013</a>.","short":"V. Haikala, M.A. Jösch, A. Borst, A. Mauss, Journal of Neuroscience 33 (2013) 13927–13934.","chicago":"Haikala, Väinö, Maximilian A Jösch, Alexander Borst, and Alex Mauss. “Optogenetic Control of Fly Optomotor Responses.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2013. <a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">https://doi.org/10.1523/JNEUROSCI.0340-13.2013</a>."},"year":"2013","date_published":"2013-01-01T00:00:00Z","publication":"Journal of Neuroscience","type":"journal_article"},{"date_created":"2018-12-11T11:51:16Z","issue":"3","abstract":[{"text":"In the fly Drosophila melanogaster, photoreceptor input to motion vision is split into two parallel pathways as represented by first-order interneurons L1 and L2 (Rister et al., 2007; Joesch et al., 2010). However, how these pathways are functionally specialized remains controversial. One study (Eichner et al., 2011) proposed that the L1-pathway evaluates only sequences of brightness increments (ON-ON), while the L2-pathway processes exclusively brightness decrements (OFF-OFF). Another study (Clark et al., 2011) proposed that each of the two pathways evaluates both ON-ON and OFF-OFF sequences. To decide between these alternatives, we recorded from motionsensitive neurons in flies in which the output from either L1 or L2 was genetically blocked. We found that blocking L1 abolishes ON-ON responses but leaves OFF-OFF responses intact. The opposite was true, when the output from L2 was blocked. We conclude that the L1 and L2 pathways are functionally specialized to detect ON-ON and OFF-OFF sequences, respectively.","lang":"eng"}],"volume":33,"page":"902 - 905","publisher":"Society for Neuroscience","author":[{"full_name":"Maximilian Jösch","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weber, Franz","last_name":"Weber","first_name":"Franz"},{"first_name":"Hubert","last_name":"Eichner","full_name":"Eichner, Hubert"},{"full_name":"Borst, Alexander","last_name":"Borst","first_name":"Alexander"}],"quality_controlled":0,"month":"01","date_updated":"2021-01-12T06:49:45Z","doi":"10.1523/JNEUROSCI.3374-12.2013","year":"2013","publication":"Journal of Neuroscience","type":"journal_article","date_published":"2013-01-16T00:00:00Z","extern":1,"status":"public","citation":{"chicago":"Jösch, Maximilian A, Franz Weber, Hubert Eichner, and Alexander Borst. “Functional Specialization of Parallel Motion Detection Circuits in the Fly.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2013. <a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">https://doi.org/10.1523/JNEUROSCI.3374-12.2013</a>.","short":"M.A. Jösch, F. Weber, H. Eichner, A. Borst, Journal of Neuroscience 33 (2013) 902–905.","mla":"Jösch, Maximilian A., et al. “Functional Specialization of Parallel Motion Detection Circuits in the Fly.” <i>Journal of Neuroscience</i>, vol. 33, no. 3, Society for Neuroscience, 2013, pp. 902–05, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">10.1523/JNEUROSCI.3374-12.2013</a>.","ista":"Jösch MA, Weber F, Eichner H, Borst A. 2013. Functional specialization of parallel motion detection circuits in the fly. Journal of Neuroscience. 33(3), 902–905.","ama":"Jösch MA, Weber F, Eichner H, Borst A. Functional specialization of parallel motion detection circuits in the fly. <i>Journal of Neuroscience</i>. 2013;33(3):902-905. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">10.1523/JNEUROSCI.3374-12.2013</a>","ieee":"M. A. Jösch, F. Weber, H. Eichner, and A. Borst, “Functional specialization of parallel motion detection circuits in the fly,” <i>Journal of Neuroscience</i>, vol. 33, no. 3. Society for Neuroscience, pp. 902–905, 2013.","apa":"Jösch, M. A., Weber, F., Eichner, H., &#38; Borst, A. (2013). Functional specialization of parallel motion detection circuits in the fly. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">https://doi.org/10.1523/JNEUROSCI.3374-12.2013</a>"},"publication_status":"published","title":"Functional specialization of parallel motion detection circuits in the fly","day":"16","publist_id":"5968","intvolume":"        33","acknowledgement":"This work was supported by the Max-Planck-Society and the SFB 870 of the Deutsche Forschungsgemeinschaft.","_id":"1305"},{"volume":38,"abstract":[{"lang":"eng","text":"We prove uniqueness of solutions of the DLSS equation in a class of sufficiently regular functions. The global weak solutions of the DLSS equation constructed by Jüngel and Matthes belong to this class of uniqueness. We also show uniqueness of solutions for the quantum drift-diffusion equation, which contains additional drift and second-order diffusion terms. The results hold in case of periodic or Dirichlet-Neumann boundary conditions. Our proof is based on a monotonicity property of the DLSS operator and sophisticated approximation arguments; we derive a PDE satisfied by the pointwise square root of the solution, which enables us to exploit the monotonicity property of the operator."}],"issue":"11","date_created":"2018-12-11T11:51:17Z","quality_controlled":0,"author":[{"full_name":"Julian Fischer","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"page":"2004 - 2047","publisher":"Taylor & Francis","date_updated":"2021-01-12T06:49:46Z","month":"11","doi":"10.1080/03605302.2013.823548","date_published":"2013-11-01T00:00:00Z","type":"journal_article","publication":"Communications in Partial Differential Equations","year":"2013","citation":{"mla":"Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift Diffusion Models.” <i>Communications in Partial Differential Equations</i>, vol. 38, no. 11, Taylor &#38; Francis, 2013, pp. 2004–47, doi:<a href=\"https://doi.org/10.1080/03605302.2013.823548\">10.1080/03605302.2013.823548</a>.","ista":"Fischer JL. 2013. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. Communications in Partial Differential Equations. 38(11), 2004–2047.","ieee":"J. L. Fischer, “Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models,” <i>Communications in Partial Differential Equations</i>, vol. 38, no. 11. Taylor &#38; Francis, pp. 2004–2047, 2013.","ama":"Fischer JL. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. <i>Communications in Partial Differential Equations</i>. 2013;38(11):2004-2047. doi:<a href=\"https://doi.org/10.1080/03605302.2013.823548\">10.1080/03605302.2013.823548</a>","short":"J.L. Fischer, Communications in Partial Differential Equations 38 (2013) 2004–2047.","chicago":"Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift Diffusion Models.” <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis, 2013. <a href=\"https://doi.org/10.1080/03605302.2013.823548\">https://doi.org/10.1080/03605302.2013.823548</a>.","apa":"Fischer, J. L. (2013). Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/03605302.2013.823548\">https://doi.org/10.1080/03605302.2013.823548</a>"},"status":"public","extern":1,"intvolume":"        38","publist_id":"5962","day":"01","publication_status":"published","title":"Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models","_id":"1307"},{"citation":{"apa":"Fischer, J. L. (2013). Advection-driven support shrinking in a chemotaxis model with degenerate mobility. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/120874291\">https://doi.org/10.1137/120874291</a>","mla":"Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis Model with Degenerate Mobility.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 45, no. 3, Society for Industrial and Applied Mathematics , 2013, pp. 1585–615, doi:<a href=\"https://doi.org/10.1137/120874291\">10.1137/120874291</a>.","ista":"Fischer JL. 2013. Advection-driven support shrinking in a chemotaxis model with degenerate mobility. SIAM Journal on Mathematical Analysis. 45(3), 1585–1615.","ama":"Fischer JL. Advection-driven support shrinking in a chemotaxis model with degenerate mobility. <i>SIAM Journal on Mathematical Analysis</i>. 2013;45(3):1585-1615. doi:<a href=\"https://doi.org/10.1137/120874291\">10.1137/120874291</a>","ieee":"J. L. Fischer, “Advection-driven support shrinking in a chemotaxis model with degenerate mobility,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 45, no. 3. Society for Industrial and Applied Mathematics , pp. 1585–1615, 2013.","short":"J.L. Fischer, SIAM Journal on Mathematical Analysis 45 (2013) 1585–1615.","chicago":"Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis Model with Degenerate Mobility.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics , 2013. <a href=\"https://doi.org/10.1137/120874291\">https://doi.org/10.1137/120874291</a>."},"extern":1,"status":"public","publication":"SIAM Journal on Mathematical Analysis","type":"journal_article","date_published":"2013-01-01T00:00:00Z","year":"2013","_id":"1308","publist_id":"5963","intvolume":"        45","publication_status":"published","title":"Advection-driven support shrinking in a chemotaxis model with degenerate mobility","day":"01","author":[{"full_name":"Julian Fischer","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer"}],"quality_controlled":0,"publisher":"Society for Industrial and Applied Mathematics ","page":"1585 - 1615","abstract":[{"text":"We derive sufficient conditions for advection-driven backward motion of the free boundary in a chemotaxis model with degenerate mobility. In this model, a porous-medium-type diffusive term and an advection term are in competition. The former induces forward motion, the latter may induce backward motion of the free boundary depending on the direction of advection. We deduce conditions on the growth of the initial data at the free boundary which ensure that at least initially the advection term is dominant. This implies local backward motion of the free boundary provided the advection is (locally) directed appropriately. Our result is based on a new class of moving test functions and Stampacchia's lemma. As a by-product of our estimates, we obtain quantitative bounds on the spreading of the support of solutions for the chemotaxis model and provide a proof for the finite speed of the support propagation property of solutions.","lang":"eng"}],"volume":45,"date_created":"2018-12-11T11:51:17Z","issue":"3","doi":"10.1137/120874291","month":"01","date_updated":"2021-01-12T06:49:46Z"},{"author":[{"full_name":"Julian Fischer","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":0,"publisher":"Academic Press","page":"3127 - 3149","abstract":[{"text":"We derive lower bounds on asymptotic support propagation rates for strong solutions of the Cauchy problem for the thin-film equation. The bounds coincide up to a constant factor with the previously known upper bounds and thus are sharp. Our results hold in case of at most three spatial dimensions and n∈. (1, 2.92). The result is established using weighted backward entropy inequalities with singular weight functions to yield a differential inequality; combined with some entropy production estimates, the optimal rate of propagation is obtained. To the best of our knowledge, these are the first lower bounds on asymptotic support propagation rates for higher-order nonnegativity-preserving parabolic equations.","lang":"eng"}],"volume":255,"date_created":"2018-12-11T11:51:18Z","issue":"10","doi":"10.1016/j.jde.2013.07.028","month":"11","date_updated":"2021-01-12T06:49:47Z","citation":{"chicago":"Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation Rates for the Thin-Film Equation.” <i>Journal of Differential Equations</i>. Academic Press, 2013. <a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">https://doi.org/10.1016/j.jde.2013.07.028</a>.","short":"J.L. Fischer, Journal of Differential Equations 255 (2013) 3127–3149.","mla":"Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation Rates for the Thin-Film Equation.” <i>Journal of Differential Equations</i>, vol. 255, no. 10, Academic Press, 2013, pp. 3127–49, doi:<a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">10.1016/j.jde.2013.07.028</a>.","ama":"Fischer JL. Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. <i>Journal of Differential Equations</i>. 2013;255(10):3127-3149. doi:<a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">10.1016/j.jde.2013.07.028</a>","ieee":"J. L. Fischer, “Optimal lower bounds on asymptotic support propagation rates for the thin-film equation,” <i>Journal of Differential Equations</i>, vol. 255, no. 10. Academic Press, pp. 3127–3149, 2013.","ista":"Fischer JL. 2013. Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. Journal of Differential Equations. 255(10), 3127–3149.","apa":"Fischer, J. L. (2013). Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. <i>Journal of Differential Equations</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">https://doi.org/10.1016/j.jde.2013.07.028</a>"},"extern":1,"status":"public","type":"journal_article","publication":"Journal of Differential Equations","date_published":"2013-11-15T00:00:00Z","year":"2013","_id":"1310","publist_id":"5961","intvolume":"       255","publication_status":"published","title":"Optimal lower bounds on asymptotic support propagation rates for the thin-film equation","day":"15"},{"doi":"10.1038/nature11871","month":"02","date_updated":"2021-01-12T06:54:28Z","publisher":"Nature Publishing Group","page":"443 - 448","author":[{"last_name":"Baradaran","first_name":"Rozbeh","full_name":"Baradaran, Rozbeh "},{"full_name":"Berrisford, John M","first_name":"John","last_name":"Berrisford"},{"full_name":"Minhas, Gurdeep S","last_name":"Minhas","first_name":"Gurdeep"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Leonid Sazanov"}],"quality_controlled":0,"date_created":"2018-12-11T11:55:01Z","issue":"7438","abstract":[{"text":"Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.","lang":"eng"}],"volume":494,"acknowledgement":"This work was funded by the Medical Research Council.","_id":"1978","title":"Crystal structure of the entire respiratory complex i","publication_status":"published","day":"28","publist_id":"5107","intvolume":"       494","extern":1,"status":"public","citation":{"apa":"Baradaran, R., Berrisford, J., Minhas, G., &#38; Sazanov, L. A. (2013). Crystal structure of the entire respiratory complex i. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>","ieee":"R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure of the entire respiratory complex i,” <i>Nature</i>, vol. 494, no. 7438. Nature Publishing Group, pp. 443–448, 2013.","ista":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of the entire respiratory complex i. Nature. 494(7438), 443–448.","ama":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire respiratory complex i. <i>Nature</i>. 2013;494(7438):443-448. doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>","mla":"Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48, doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>.","chicago":"Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>.","short":"R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448."},"year":"2013","type":"journal_article","publication":"Nature","date_published":"2013-02-28T00:00:00Z"},{"volume":9,"abstract":[{"lang":"eng","text":"The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally."}],"issue":"12","date_created":"2018-12-11T11:55:04Z","quality_controlled":0,"author":[{"full_name":"Bonny, Mike ","first_name":"Mike","last_name":"Bonny"},{"first_name":"Elisabeth","last_name":"Fischer Friedrich","full_name":"Fischer-Friedrich, Elisabeth"},{"full_name":"Martin Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "},{"full_name":"Kruse, Karsten","last_name":"Kruse","first_name":"Karsten"}],"publisher":"Public Library of Science","date_updated":"2021-01-12T06:54:32Z","month":"12","doi":"10.1371/journal.pcbi.1003347","date_published":"2013-12-01T00:00:00Z","type":"journal_article","publication":"PLoS Computational Biology","year":"2013","citation":{"apa":"Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., &#38; Kruse, K. (2013). Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>","short":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013).","chicago":"Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille, and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>.","mla":"Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>, vol. 9, no. 12, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>.","ista":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 9(12).","ieee":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation,” <i>PLoS Computational Biology</i>, vol. 9, no. 12. Public Library of Science, 2013.","ama":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>"},"status":"public","extern":1,"intvolume":"         9","publist_id":"5095","day":"01","title":"Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation","publication_status":"published","_id":"1988"},{"title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","publication_status":"published","day":"18","publist_id":"5092","intvolume":"       499","acknowledgement":"Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B.","_id":"1991","year":"2013","publication":"Nature","type":"journal_article","date_published":"2013-07-18T00:00:00Z","extern":1,"status":"public","citation":{"apa":"Vicoso, B., &#38; Bachtrog, D. (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>.","short":"B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.","ama":"Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. 2013;499(7458):332-335. doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>","ieee":"B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome in Drosophila,” <i>Nature</i>, vol. 499, no. 7458. Nature Publishing Group, pp. 332–335, 2013.","ista":"Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335.","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>, vol. 499, no. 7458, Nature Publishing Group, 2013, pp. 332–35, doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>."},"month":"07","date_updated":"2021-01-12T06:54:33Z","doi":"10.1038/nature12235","date_created":"2018-12-11T11:55:05Z","issue":"7458","abstract":[{"lang":"eng","text":"Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur."}],"volume":499,"publisher":"Nature Publishing Group","page":"332 - 335","author":[{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso"},{"last_name":"Bachtrog","first_name":"Doris","full_name":"Bachtrog, Doris"}],"quality_controlled":0},{"conference":{"location":"Znojmo, Czech Republic","start_date":"2012-10-25","end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"date_updated":"2025-09-23T09:24:13Z","month":"01","page":"106-117","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"}],"project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"scopus_import":"1","date_created":"2025-07-10T14:08:49Z","volume":7721,"language":[{"iso":"eng"}],"OA_type":"green","publication_status":"published","external_id":{"arxiv":["1209.3617"]},"citation":{"apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 106–117). Znojmo, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721, Springer Nature, 2013, pp. 106–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “Strategy complexity of finite-horizon Markov decision processes and simple stochastic games,” in <i>Mathematical and Engineering Methods in Computer Science</i>, Znojmo, Czech Republic, 2013, vol. 7721, pp. 106–117.","ama":"Chatterjee K, Ibsen-Jensen R. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In: <i>Mathematical and Engineering Methods in Computer Science</i>. Vol 7721. Springer Nature; 2013:106-117. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2013. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. Mathematical and Engineering Methods in Computer Science. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7721, 106–117.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” In <i>Mathematical and Engineering Methods in Computer Science</i>, 7721:106–17. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Mathematical and Engineering Methods in Computer Science, Springer Nature, 2013, pp. 106–117."},"year":"2013","publication":"Mathematical and Engineering Methods in Computer Science","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1209.3617"}],"oa_version":"Preprint","doi":"10.1007/978-3-642-36046-6_11","OA_place":"repository","oa":1,"corr_author":"1","publisher":"Springer Nature","quality_controlled":"1","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Markov decision processes (MDPs) and simple stochastic games (SSGs) provide a rich mathematical framework to study many important problems related to probabilistic systems. MDPs and SSGs with finite-horizon objectives, where the goal is to maximize the probability to reach a target state in a given finite time, is a classical and well-studied problem. In this work we consider the strategy complexity of finite-horizon MDPs and SSGs. We show that for all ε > 0, the natural class of counter-based strategies require at most log log/(1/ε) + n + 1 memory states, and memory of size Omega(log log(1/ε) + n) is required, for ε-optimality, where n is the number of states of the MDP (resp. SSG). Thus our bounds are asymptotically optimal. We then study the periodic property of optimal strategies, and show a sub-exponential lower bound on the period for optimal strategies.","lang":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642360442"],"eisbn":["9783642360466"],"issn":["0302-9743"]},"acknowledgement":"Work of the second author supported by the Sino-Danish Center for the Theory of Interactive Computation, funded by the Danish National Research Foundation and the National Science Foundation of China (under the grant 61061130540). The second author acknowledge support from the Center for research in the Foundations of Electronic Markets (CFEM), supported by the Danish Strategic Research Council. The first author was supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","_id":"19995","department":[{"_id":"KrCh"}],"day":"17","title":"Strategy complexity of finite-horizon Markov decision processes and simple stochastic games","ec_funded":1,"intvolume":"      7721","status":"public","article_processing_charge":"No","alternative_title":["LNCS"],"date_published":"2013-01-17T00:00:00Z","type":"conference"},{"article_processing_charge":"No","citation":{"short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166.","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>"},"status":"public","publication":"Journal of Privacy and Confidentiality ","type":"journal_article","date_published":"2013-08-01T00:00:00Z","year":"2013","department":[{"_id":"CaUh"}],"_id":"2009","language":[{"iso":"eng"}],"intvolume":"         5","publist_id":"5067","publication_status":"published","title":"Privacy-preserving data sharing for genome-wide association studies","day":"01","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline"},{"full_name":"Slavkovic, Aleksandra","first_name":"Aleksandra","last_name":"Slavkovic"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","page":"137 - 166","publisher":"Carnegie Mellon University","abstract":[{"lang":"eng","text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression."}],"volume":5,"date_created":"2018-12-11T11:55:11Z","issue":"1","doi":"10.29012/jpc.v5i1.629","oa_version":"Published Version","main_file_link":[{"url":"http://repository.cmu.edu/jpc/vol5/iss1/6","open_access":"1"}],"month":"08","oa":1,"date_updated":"2021-01-12T06:54:41Z"},{"publication_status":"published","external_id":{"isi":["000320488200002"],"arxiv":["1207.0547"]},"publist_id":"5066","language":[{"iso":"eng"}],"year":"2013","publication":"The Annals of Statistics","citation":{"mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463.","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>","ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013.","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>.","apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>"},"isi":1,"month":"04","date_updated":"2025-09-29T14:31:39Z","date_created":"2018-12-11T11:55:11Z","issue":"2","scopus_import":"1","volume":41,"page":"436 - 463","author":[{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline"},{"full_name":"Raskutti, Garvesh","first_name":"Garvesh","last_name":"Raskutti"},{"full_name":"Bühlmann, Peter","last_name":"Bühlmann","first_name":"Peter"},{"full_name":"Yu, Bin","first_name":"Bin","last_name":"Yu"}],"title":"Geometry of the faithfulness assumption in causal inference","day":"01","intvolume":"        41","department":[{"_id":"CaUh"}],"_id":"2010","type":"journal_article","date_published":"2013-04-01T00:00:00Z","status":"public","article_processing_charge":"No","oa":1,"oa_version":"Published Version","main_file_link":[{"url":"www.doi.org/10.1214/12-AOS1080","open_access":"1"}],"doi":"10.1214/12-AOS1080","abstract":[{"lang":"eng","text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case."}],"publisher":"Institute of Mathematical Statistics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"quality_controlled":"1"},{"month":"04","date_updated":"2021-01-12T06:55:08Z","doi":"10.1073/pnas.1217027110","abstract":[{"lang":"eng","text":"Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. "}],"volume":110,"date_created":"2018-12-11T11:55:33Z","issue":"16","author":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Beatriz Vicoso"},{"first_name":"Vera","last_name":"Kaiser","full_name":"Kaiser, Vera B"},{"last_name":"Bachtrog","first_name":"Doris","full_name":"Bachtrog, Doris"}],"quality_controlled":0,"publisher":"National Academy of Sciences","page":"6453 - 6458","intvolume":"       110","publist_id":"4964","title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution","publication_status":"published","day":"16","_id":"2074","type":"journal_article","publication":"PNAS","date_published":"2013-04-16T00:00:00Z","year":"2013","citation":{"chicago":"Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>.","short":"B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.","mla":"Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>.","ista":"Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458.","ama":"Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. 2013;110(16):6453-6458. doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>","ieee":"B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” <i>PNAS</i>, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.","apa":"Vicoso, B., Kaiser, V., &#38; Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>"},"extern":1,"status":"public"},{"status":"public","extern":1,"citation":{"apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., &#38; Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>","ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. 2013;11(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).","ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” <i>PLoS Biology</i>, vol. 11, no. 8. Public Library of Science, 2013.","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>, vol. 11, no. 8, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>.","short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013).","chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2013","date_published":"2013-08-27T00:00:00Z","type":"journal_article","publication":"PLoS Biology","acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB.","_id":"2076","day":"27","publication_status":"published","title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","publist_id":"4962","intvolume":"        11","publisher":"Public Library of Science","quality_controlled":0,"author":[{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso"},{"full_name":"Emerson, Jr J.","first_name":"Jr","last_name":"Emerson"},{"first_name":"Yulia","last_name":"Zektser","full_name":"Zektser, Yulia"},{"first_name":"Shivani","last_name":"Mahajan","full_name":"Mahajan, Shivani"},{"full_name":"Bachtrog, Doris","last_name":"Bachtrog","first_name":"Doris"}],"issue":"8","date_created":"2018-12-11T11:55:34Z","volume":11,"abstract":[{"text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n","lang":"eng"}],"doi":"10.1371/journal.pbio.1001643","date_updated":"2021-01-12T06:55:09Z","month":"08"},{"author":[{"full_name":"Leonid Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"},{"full_name":"Baradaran, Rozbeh ","first_name":"Rozbeh","last_name":"Baradaran"},{"first_name":"Rouslan","last_name":"Efremov","full_name":"Efremov, Rouslan G"},{"first_name":"John","last_name":"Berrisford","full_name":"Berrisford, John M"},{"full_name":"Minhas, Gurdeep S","last_name":"Minhas","first_name":"Gurdeep"}],"quality_controlled":0,"publisher":"Portland Press","page":"1265 - 1271","abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review."}],"volume":41,"date_created":"2018-12-11T11:55:00Z","issue":"5","doi":"10.1042/BST20130193","month":"10","date_updated":"2021-01-12T06:54:28Z","citation":{"mla":"Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>, vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>.","ama":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. 2013;41(5):1265-1271. doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>","ista":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 41(5), 1265–1271.","ieee":"L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A long road towards the structure of respiratory complex I, a giant molecular proton pump,” <i>Biochemical Society Transactions</i>, vol. 41, no. 5. Portland Press, pp. 1265–1271, 2013.","chicago":"Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford, and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>. Portland Press, 2013. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>.","short":"L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271.","apa":"Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., &#38; Minhas, G. (2013). A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>"},"extern":1,"status":"public","publication":"Biochemical Society Transactions","type":"journal_article","date_published":"2013-10-01T00:00:00Z","year":"2013","_id":"1977","acknowledgement":"This work was funded by the Medical Research Council.","intvolume":"        41","publist_id":"5106","publication_status":"published","title":"A long road towards the structure of respiratory complex I, a giant molecular proton pump","day":"01"},{"volume":9,"scopus_import":"1","issue":"11","date_created":"2024-03-21T07:58:57Z","author":[{"first_name":"Marcos H.","last_name":"Woehrmann","full_name":"Woehrmann, Marcos H."},{"first_name":"Walter M.","last_name":"Bray","full_name":"Bray, Walter M."},{"last_name":"Durbin","first_name":"James K.","full_name":"Durbin, James K."},{"full_name":"Nisam, Sean C.","last_name":"Nisam","first_name":"Sean C."},{"full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"full_name":"Glassey, Emerson","first_name":"Emerson","last_name":"Glassey"},{"first_name":"Joshua M.","last_name":"Stuart","full_name":"Stuart, Joshua M."},{"full_name":"Lokey, R. Scott","last_name":"Lokey","first_name":"R. Scott"}],"article_type":"original","date_updated":"2024-03-25T11:45:46Z","month":"08","publication":"Molecular BioSystems","year":"2013","citation":{"chicago":"Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” <i>Molecular BioSystems</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3mb70245f\">https://doi.org/10.1039/c3mb70245f</a>.","short":"M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey, J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013).","mla":"Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” <i>Molecular BioSystems</i>, vol. 9, no. 11, 2604, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3mb70245f\">10.1039/c3mb70245f</a>.","ama":"Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling for functional analysis of bioactive compounds. <i>Molecular BioSystems</i>. 2013;9(11). doi:<a href=\"https://doi.org/10.1039/c3mb70245f\">10.1039/c3mb70245f</a>","ieee":"M. H. Woehrmann <i>et al.</i>, “Large-scale cytological profiling for functional analysis of bioactive compounds,” <i>Molecular BioSystems</i>, vol. 9, no. 11. Royal Society of Chemistry, 2013.","ista":"Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 9(11), 2604.","apa":"Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K., Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional analysis of bioactive compounds. <i>Molecular BioSystems</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3mb70245f\">https://doi.org/10.1039/c3mb70245f</a>"},"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cytological profiling (CP) is an unbiased image-based screening technique that uses automated microscopy and image analysis to profile compounds based on numerous quantifiable phenotypic features. We used CP to evaluate a library of nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide range of biological pathways. We developed informatics techniques for generating dosage-independent phenotypic “fingerprints” for each compound, and for quantifying the likelihood that a compound's CP fingerprint corresponds to its annotated MOA. We identified groups of features that distinguish classes with closely related phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis vs. proteasome inhibitors. We tested several cases in which cytological profiles indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma ligand that acts as a proteasome inhibitor, using independent biochemical assays to confirm the MOAs predicted by the CP signatures. We also applied maximal-information statistics to identify correlations between cytological features and kinase inhibitory activities by combining the CP fingerprints of 24 kinase inhibitors with published data on their specificities against a diverse panel of kinases. The resulting analysis suggests a strategy for probing the biological functions of specific kinases by compiling cytological data from inhibitors of varying specificities."}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Molecular Biology","Biotechnology"],"publisher":"Royal Society of Chemistry","article_number":"2604","doi":"10.1039/c3mb70245f","oa_version":"None","date_published":"2013-08-20T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","extern":"1","intvolume":"         9","day":"20","title":"Large-scale cytological profiling for functional analysis of bioactive compounds","_id":"15162","publication_identifier":{"issn":["1742-206X"],"eissn":["1742-2051"]}}]