[{"oa_version":"Submitted Version","language":[{"iso":"eng"}],"publication_status":"published","date_updated":"2025-09-23T08:21:28Z","scopus_import":"1","external_id":{"pmid":["26061224"],"isi":["000360380400008"]},"abstract":[{"lang":"eng","text":"Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding &quot;core&quot; that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue."}],"title":"Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction","doi":"10.1002/pro.2721","publication":"Protein Science","page":"1412 - 1422","date_created":"2018-12-11T11:53:01Z","isi":1,"month":"09","intvolume":"        24","oa":1,"year":"2015","day":"01","date_published":"2015-09-01T00:00:00Z","department":[{"_id":"HaJa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1611","article_processing_charge":"No","author":[{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"first_name":"Michel","full_name":"Herde, Michel","last_name":"Herde"},{"last_name":"Clifton","full_name":"Clifton, Ben","first_name":"Ben"},{"first_name":"Johanna","full_name":"Radziejewski, Johanna","last_name":"Radziejewski"},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"publisher":"Wiley","volume":24,"status":"public","publist_id":"5555","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/"}],"issue":"9","citation":{"ista":"Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.","ama":"Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. <i>Protein Science</i>. 2015;24(9):1412-1422. doi:<a href=\"https://doi.org/10.1002/pro.2721\">10.1002/pro.2721</a>","apa":"Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. <i>Protein Science</i>. Wiley. <a href=\"https://doi.org/10.1002/pro.2721\">https://doi.org/10.1002/pro.2721</a>","ieee":"J. Whitfield <i>et al.</i>, “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” <i>Protein Science</i>, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015.","short":"J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.","chicago":"Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” <i>Protein Science</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/pro.2721\">https://doi.org/10.1002/pro.2721</a>.","mla":"Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” <i>Protein Science</i>, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:<a href=\"https://doi.org/10.1002/pro.2721\">10.1002/pro.2721</a>."},"pmid":1,"type":"journal_article","quality_controlled":"1","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012"}]},{"scopus_import":"1","publication_status":"published","date_updated":"2025-09-23T10:49:39Z","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1073/pnas.1412996112","abstract":[{"text":"GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. ","lang":"eng"}],"title":"Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells","external_id":{"isi":["000348417000066"],"pmid":["25583495"]},"month":"01","isi":1,"ddc":["570"],"date_created":"2018-12-11T11:53:02Z","publication":"PNAS","page":"1220 - 1225","oa":1,"intvolume":"       112","publisher":"National Academy of Sciences","_id":"1614","author":[{"first_name":"Michael","full_name":"Strüber, Michael","last_name":"Strüber"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Marlene","full_name":"Bartos, Marlene","last_name":"Bartos"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"PeJo"}],"date_published":"2015-01-27T00:00:00Z","year":"2015","day":"27","publist_id":"5552","status":"public","ec_funded":1,"file":[{"relation":"main_file","file_id":"5838","creator":"dernst","file_name":"2015_PNAS_Strueber.pdf","content_type":"application/pdf","checksum":"6703309a1f58493cf5a704211fb6ebed","date_created":"2019-01-17T07:52:40Z","file_size":1280860,"date_updated":"2020-07-14T12:45:07Z","access_level":"open_access"}],"file_date_updated":"2020-07-14T12:45:07Z","volume":112,"issue":"4","has_accepted_license":"1","quality_controlled":"1","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P24909-B24"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"}],"type":"journal_article","pmid":1,"citation":{"ama":"Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. <i>PNAS</i>. 2015;112(4):1220-1225. doi:<a href=\"https://doi.org/10.1073/pnas.1412996112\">10.1073/pnas.1412996112</a>","ista":"Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225.","chicago":"Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1412996112\">https://doi.org/10.1073/pnas.1412996112</a>.","short":"M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.","apa":"Strüber, M., Jonas, P. M., &#38; Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1412996112\">https://doi.org/10.1073/pnas.1412996112</a>","ieee":"M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” <i>PNAS</i>, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.","mla":"Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” <i>PNAS</i>, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:<a href=\"https://doi.org/10.1073/pnas.1412996112\">10.1073/pnas.1412996112</a>."}},{"intvolume":"        13","oa":1,"page":"516 - 523","publication":"Cell Reports","date_created":"2018-12-11T11:53:02Z","isi":1,"ddc":["570"],"month":"10","title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism","abstract":[{"lang":"eng","text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches."}],"external_id":{"isi":["000363780000008"]},"doi":"10.1016/j.celrep.2015.09.011","oa_version":"Published Version","language":[{"iso":"eng"}],"scopus_import":"1","date_updated":"2025-09-23T09:48:31Z","publication_status":"published","citation":{"ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. 2015;13(3):516-523. doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>","ieee":"M. Hammer <i>et al.</i>, “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” <i>Cell Reports</i>, vol. 13, no. 3. Cell Press, pp. 516–523, 2015.","apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523.","chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>.","mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","issue":"3","file":[{"file_size":2314406,"date_created":"2018-12-12T10:13:23Z","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","relation":"main_file","file_id":"5005","creator":"system","content_type":"application/pdf","checksum":"44d30fbb543774b076b4938bd36af9d7","file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf"}],"status":"public","file_date_updated":"2020-07-14T12:45:07Z","volume":13,"acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","publist_id":"5551","department":[{"_id":"PeJo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","day":"20","pubrep_id":"470","date_published":"2015-10-20T00:00:00Z","publisher":"Cell Press","_id":"1615","article_processing_charge":"No","author":[{"first_name":"Matthieu","full_name":"Hammer, Matthieu","last_name":"Hammer"},{"first_name":"Dilja","last_name":"Krueger Burg","full_name":"Krueger Burg, Dilja"},{"full_name":"Tuffy, Liam","last_name":"Tuffy","first_name":"Liam"},{"full_name":"Cooper, Benjamin","last_name":"Cooper","first_name":"Benjamin"},{"first_name":"Holger","last_name":"Taschenberger","full_name":"Taschenberger, Holger"},{"first_name":"Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","last_name":"Goswami","full_name":"Goswami, Sarit"},{"last_name":"Ehrenreich","full_name":"Ehrenreich, Hannelore","first_name":"Hannelore"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M"},{"first_name":"Frederique","last_name":"Varoqueaux","full_name":"Varoqueaux, Frederique"},{"first_name":"Jeong","full_name":"Rhee, Jeong","last_name":"Rhee"},{"first_name":"Nils","full_name":"Brose, Nils","last_name":"Brose"}]},{"issue":"27","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/"}],"pmid":1,"type":"journal_article","quality_controlled":"1","project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7"}],"citation":{"mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>.","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166.","ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. 2015;54(27):4163-4166. doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>","chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>.","short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.","ieee":"C. Veldkamp <i>et al.</i>, “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” <i>Biochemistry</i>, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>"},"author":[{"full_name":"Veldkamp, Christopher","last_name":"Veldkamp","first_name":"Christopher"},{"last_name":"Kiermaier","full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","first_name":"Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gabel Eissens, Skylar","last_name":"Gabel Eissens","first_name":"Skylar"},{"first_name":"Miranda","full_name":"Gillitzer, Miranda","last_name":"Gillitzer"},{"first_name":"David","full_name":"Lippner, David","last_name":"Lippner"},{"full_name":"Disilvio, Frank","last_name":"Disilvio","first_name":"Frank"},{"full_name":"Mueller, Casey","last_name":"Mueller","first_name":"Casey"},{"last_name":"Wantuch","full_name":"Wantuch, Paeton","first_name":"Paeton"},{"full_name":"Chaffee, Gary","last_name":"Chaffee","first_name":"Gary"},{"first_name":"Michael","last_name":"Famiglietti","full_name":"Famiglietti, Michael"},{"first_name":"Danielle","full_name":"Zgoba, Danielle","last_name":"Zgoba"},{"full_name":"Bailey, Asha","last_name":"Bailey","first_name":"Asha"},{"last_name":"Bah","full_name":"Bah, Yaya","first_name":"Yaya"},{"first_name":"Samantha","last_name":"Engebretson","full_name":"Engebretson, Samantha"},{"first_name":"David","full_name":"Graupner, David","last_name":"Graupner"},{"first_name":"Emily","full_name":"Lackner, Emily","last_name":"Lackner"},{"first_name":"Vincent","full_name":"Larosa, Vincent","last_name":"Larosa"},{"first_name":"Tysha","full_name":"Medeiros, Tysha","last_name":"Medeiros"},{"last_name":"Olson","full_name":"Olson, Michael","first_name":"Michael"},{"full_name":"Phillips, Andrew","last_name":"Phillips","first_name":"Andrew"},{"last_name":"Pyles","full_name":"Pyles, Harley","first_name":"Harley"},{"first_name":"Amanda","last_name":"Richard","full_name":"Richard, Amanda"},{"first_name":"Scott","last_name":"Schoeller","full_name":"Schoeller, Scott"},{"full_name":"Touzeau, Boris","last_name":"Touzeau","first_name":"Boris"},{"last_name":"Williams","full_name":"Williams, Larry","first_name":"Larry"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"first_name":"Francis","full_name":"Peterson, Francis","last_name":"Peterson"}],"_id":"1618","article_processing_charge":"No","publisher":"American Chemical Society","year":"2015","day":"26","date_published":"2015-06-26T00:00:00Z","department":[{"_id":"MiSi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5548","volume":54,"ec_funded":1,"status":"public","isi":1,"month":"06","publication":"Biochemistry","page":"4163 - 4166","date_created":"2018-12-11T11:53:03Z","oa":1,"intvolume":"        54","publication_status":"published","date_updated":"2025-09-23T10:47:25Z","scopus_import":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"doi":"10.1021/acs.biochem.5b00560","external_id":{"isi":["000358105100001"],"pmid":["26115234"]},"title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","abstract":[{"text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed.","lang":"eng"}]},{"issue":"1","article_number":"193","has_accepted_license":"1","type":"journal_article","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ista":"Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.","ama":"Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. <i>Biotechnology for Biofuels</i>. 2015;8(1). doi:<a href=\"https://doi.org/10.1186/s13068-015-0380-2\">10.1186/s13068-015-0380-2</a>","short":"P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).","chicago":"Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” <i>Biotechnology for Biofuels</i>. BioMed Central, 2015. <a href=\"https://doi.org/10.1186/s13068-015-0380-2\">https://doi.org/10.1186/s13068-015-0380-2</a>.","apa":"Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., &#38; Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. <i>Biotechnology for Biofuels</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13068-015-0380-2\">https://doi.org/10.1186/s13068-015-0380-2</a>","ieee":"P. Hammar <i>et al.</i>, “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” <i>Biotechnology for Biofuels</i>, vol. 8, no. 1. BioMed Central, 2015.","mla":"Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” <i>Biotechnology for Biofuels</i>, vol. 8, no. 1, 193, BioMed Central, 2015, doi:<a href=\"https://doi.org/10.1186/s13068-015-0380-2\">10.1186/s13068-015-0380-2</a>."},"article_processing_charge":"No","_id":"1623","author":[{"full_name":"Hammar, Petter","last_name":"Hammar","first_name":"Petter"},{"full_name":"Angermayr, Andreas","last_name":"Angermayr","id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0001-8619-2223"},{"first_name":"Staffan","full_name":"Sjostrom, Staffan","last_name":"Sjostrom"},{"full_name":"Van Der Meer, Josefin","last_name":"Van Der Meer","first_name":"Josefin"},{"first_name":"Klaas","full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf"},{"first_name":"Elton","full_name":"Hudson, Elton","last_name":"Hudson"},{"first_name":"Hakaan","full_name":"Joensson, Hakaan","last_name":"Joensson"}],"publisher":"BioMed Central","year":"2015","day":"25","pubrep_id":"467","date_published":"2015-11-25T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ToBo"}],"publist_id":"5537","file_date_updated":"2020-07-14T12:45:07Z","volume":8,"file":[{"relation":"main_file","file_id":"4796","creator":"system","content_type":"application/pdf","checksum":"172b0b6f4eb2e5c22b7cec1d57dc0107","file_name":"IST-2016-467-v1+1_s13068-015-0380-2.pdf","date_created":"2018-12-12T10:10:11Z","file_size":2914089,"date_updated":"2020-07-14T12:45:07Z","access_level":"open_access"}],"status":"public","isi":1,"ddc":["570"],"month":"11","publication":"Biotechnology for Biofuels","date_created":"2018-12-11T11:53:05Z","oa":1,"intvolume":"         8","publication_status":"published","date_updated":"2025-09-23T10:45:43Z","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.1186/s13068-015-0380-2","external_id":{"isi":["000365784000009"]},"title":"Single-cell screening of photosynthetic growth and lactate production by cyanobacteria","abstract":[{"text":"Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n","lang":"eng"}]},{"oa":1,"intvolume":"         5","corr_author":"1","month":"11","isi":1,"ddc":["000"],"date_created":"2018-12-11T11:53:06Z","publication":"Scientific Reports","doi":"10.1038/srep17147","external_id":{"isi":["000365299500001"]},"abstract":[{"text":"Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions.","lang":"eng"}],"title":"Cellular cooperation with shift updating and repulsion","publication_status":"published","date_updated":"2025-09-23T08:13:52Z","scopus_import":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ista":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation with shift updating and repulsion. Scientific Reports. 5, 17147.","ama":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift updating and repulsion. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep17147\">10.1038/srep17147</a>","ieee":"A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation with shift updating and repulsion,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015.","apa":"Pavlogiannis, A., Chatterjee, K., Adlam, B., &#38; Nowak, M. (2015). Cellular cooperation with shift updating and repulsion. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep17147\">https://doi.org/10.1038/srep17147</a>","short":"A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5 (2015).","chicago":"Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak. “Cellular Cooperation with Shift Updating and Repulsion.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep17147\">https://doi.org/10.1038/srep17147</a>.","mla":"Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and Repulsion.” <i>Scientific Reports</i>, vol. 5, 17147, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep17147\">10.1038/srep17147</a>."},"article_number":"17147","has_accepted_license":"1","publist_id":"5536","acknowledgement":"The research was supported by the Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton foundation is gratefully acknowledged.","volume":5,"file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"status":"public","file":[{"date_created":"2018-12-12T10:12:29Z","file_size":1021931,"access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","file_id":"4947","relation":"main_file","file_name":"IST-2016-466-v1+1_srep17147.pdf","checksum":"38e06d8310d2087cae5f6d4d4bfe082b","content_type":"application/pdf","creator":"system"}],"article_processing_charge":"No","_id":"1624","author":[{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Adlam","full_name":"Adlam, Ben","first_name":"Ben"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publisher":"Nature Publishing Group","date_published":"2015-11-25T00:00:00Z","pubrep_id":"466","day":"25","year":"2015","department":[{"_id":"KrCh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"publist_id":"5535","conference":{"start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Los Angeles, CA, United States","end_date":"2015-08-13"},"volume":34,"status":"public","_id":"1625","author":[{"last_name":"Bermano","full_name":"Bermano, Amit","first_name":"Amit"},{"last_name":"Beeler","full_name":"Beeler, Thabo","first_name":"Thabo"},{"last_name":"Kozlov","full_name":"Kozlov, Yeara","first_name":"Yeara"},{"first_name":"Derek","full_name":"Bradley, Derek","last_name":"Bradley"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Markus","full_name":"Gross, Markus","last_name":"Gross"}],"article_processing_charge":"No","publisher":"ACM","date_published":"2015-07-27T00:00:00Z","day":"27","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"BeBi"}],"quality_controlled":"1","type":"conference","citation":{"mla":"Bermano, Amit, et al. <i>Detailed Spatio-Temporal Reconstruction of Eyelids</i>. Vol. 34, no. 4, 44, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766924\">10.1145/2766924</a>.","chicago":"Bermano, Amit, Thabo Beeler, Yeara Kozlov, Derek Bradley, Bernd Bickel, and Markus Gross. “Detailed Spatio-Temporal Reconstruction of Eyelids,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766924\">https://doi.org/10.1145/2766924</a>.","short":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, M. Gross, in:, ACM, 2015.","ieee":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, and M. Gross, “Detailed spatio-temporal reconstruction of eyelids,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","apa":"Bermano, A., Beeler, T., Kozlov, Y., Bradley, D., Bickel, B., &#38; Gross, M. (2015). Detailed spatio-temporal reconstruction of eyelids (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766924\">https://doi.org/10.1145/2766924</a>","ista":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. 2015. Detailed spatio-temporal reconstruction of eyelids. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 44.","ama":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. Detailed spatio-temporal reconstruction of eyelids. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766924\">10.1145/2766924</a>"},"article_number":"44","issue":"4","doi":"10.1145/2766924","external_id":{"isi":["000358786600010"]},"title":"Detailed spatio-temporal reconstruction of eyelids","abstract":[{"lang":"eng","text":"In recent years we have seen numerous improvements on 3D scanning and tracking of human faces, greatly advancing the creation of digital doubles for film and video games. However, despite the high-resolution quality of the reconstruction approaches available, current methods are unable to capture one of the most important regions of the face - the eye region. In this work we present the first method for detailed spatio-temporal reconstruction of eyelids. Tracking and reconstructing eyelids is extremely challenging, as this region exhibits very complex and unique skin deformation where skin is folded under while opening the eye. Furthermore, eyelids are often only partially visible and obstructed due to selfocclusion and eyelashes. Our approach is to combine a geometric deformation model with image data, leveraging multi-view stereo, optical flow, contour tracking and wrinkle detection from local skin appearance. Our deformation model serves as a prior that enables reconstruction of eyelids even under strong self-occlusions caused by rolling and folding skin as the eye opens and closes. The output is a person-specific, time-varying eyelid reconstruction with anatomically plausible deformations. Our high-resolution detailed eyelids couple naturally with current facial performance capture approaches. As a result, our method can largely increase the fidelity of facial capture and the creation of digital doubles."}],"publication_status":"published","date_updated":"2025-09-23T08:25:37Z","scopus_import":"1","language":[{"iso":"eng"}],"oa_version":"None","intvolume":"        34","month":"07","isi":1,"date_created":"2018-12-11T11:53:06Z"},{"language":[{"iso":"eng"}],"oa_version":"None","scopus_import":"1","date_updated":"2025-09-23T09:42:49Z","publication_status":"published","abstract":[{"lang":"eng","text":"This paper introduces &quot;OmniAD,&quot; a novel data-driven pipeline to model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally, aerodynamics are examined through elaborate wind tunnel experiments or expensive fluid dynamics computations, and are only measured for a small number of discrete wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag and lift, for any incoming wind direction using a novel representation based on spherical harmonics. Our datadriven technique acquires the aerodynamic properties of an object simply by capturing its falling motion using a single camera. Once model parameters are estimated, OmniAD enables realistic realtime simulation of rigid bodies, such as the tumbling and gliding of leaves, without simulating the surrounding air. In addition, we propose an intuitive user interface based on OmniAD to interactively design three-dimensional kites that actually fly. Various nontraditional kites were designed to demonstrate the physical validity of our model."}],"title":"OmniAD: Data-driven omni-directional aerodynamics","external_id":{"isi":["000358786600079"]},"doi":"10.1145/2766919","date_created":"2018-12-11T11:53:06Z","month":"07","isi":1,"intvolume":"        34","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"BeBi"}],"date_published":"2015-07-27T00:00:00Z","day":"27","year":"2015","alternative_title":["ACM Transactions on Graphics"],"publisher":"ACM","_id":"1626","article_processing_charge":"No","author":[{"first_name":"Tobias","last_name":"Martin","full_name":"Martin, Tobias"},{"last_name":"Umetani","full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"status":"public","volume":34,"conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","location":"Los Angeles, CA, United States","end_date":"2015-08-13"},"publist_id":"5532","article_number":"113","issue":"4","citation":{"ista":"Martin T, Umetani N, Bickel B. 2015. OmniAD: Data-driven omni-directional aerodynamics. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 113.","ama":"Martin T, Umetani N, Bickel B. OmniAD: Data-driven omni-directional aerodynamics. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766919\">10.1145/2766919</a>","chicago":"Martin, Tobias, Nobuyuki Umetani, and Bernd Bickel. “OmniAD: Data-Driven Omni-Directional Aerodynamics,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766919\">https://doi.org/10.1145/2766919</a>.","short":"T. Martin, N. Umetani, B. Bickel, in:, ACM, 2015.","apa":"Martin, T., Umetani, N., &#38; Bickel, B. (2015). OmniAD: Data-driven omni-directional aerodynamics (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766919\">https://doi.org/10.1145/2766919</a>","ieee":"T. Martin, N. Umetani, and B. Bickel, “OmniAD: Data-driven omni-directional aerodynamics,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","mla":"Martin, Tobias, et al. <i>OmniAD: Data-Driven Omni-Directional Aerodynamics</i>. Vol. 34, no. 4, 113, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766919\">10.1145/2766919</a>."},"quality_controlled":"1","type":"conference"},{"title":"Design and fabrication of flexible rod meshes","abstract":[{"lang":"eng","text":"We present a computational tool for fabrication-oriented design of flexible rod meshes. Given a deformable surface and a set of deformed poses as input, our method automatically computes a printable rod mesh that, once manufactured, closely matches the input poses under the same boundary conditions. The core of our method is formed by an optimization scheme that adjusts the cross-sectional profiles of the rods and their rest centerline in order to best approximate the target deformations. This approach allows us to locally control the bending and stretching resistance of the surface with a single material, yielding high design flexibility and low fabrication cost."}],"external_id":{"isi":["000358786600104"]},"doi":"10.1145/2766998","language":[{"iso":"eng"}],"oa_version":"None","scopus_import":"1","publication_status":"published","date_updated":"2025-09-23T08:24:55Z","intvolume":"        34","date_created":"2018-12-11T11:53:07Z","month":"07","isi":1,"status":"public","volume":34,"acknowledgement":"This work was supported in part by grants from the Spanish Ministry of Economy (TIN2012-35840), and the European Research Council (ERC Starting Grant no. 280135 Animetrics).","conference":{"location":"Los Angeles, CA, United States","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09"},"publist_id":"5530","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"BeBi"}],"date_published":"2015-07-27T00:00:00Z","year":"2015","day":"27","publisher":"ACM","_id":"1627","author":[{"full_name":"Pérez, Jesús","last_name":"Pérez","first_name":"Jesús"},{"full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski","first_name":"Bernhard"},{"last_name":"Coros","full_name":"Coros, Stelian","first_name":"Stelian"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"last_name":"Canabal","full_name":"Canabal, José","first_name":"José"},{"last_name":"Sumner","full_name":"Sumner, Robert","first_name":"Robert"},{"last_name":"Otaduy","full_name":"Otaduy, Miguel","first_name":"Miguel"}],"article_processing_charge":"No","citation":{"mla":"Pérez, Jesús, et al. <i>Design and Fabrication of Flexible Rod Meshes</i>. Vol. 34, no. 4, 138, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766998\">10.1145/2766998</a>.","chicago":"Pérez, Jesús, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, José Canabal, Robert Sumner, and Miguel Otaduy. “Design and Fabrication of Flexible Rod Meshes,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766998\">https://doi.org/10.1145/2766998</a>.","short":"J. Pérez, B. Thomaszewski, S. Coros, B. Bickel, J. Canabal, R. Sumner, M. Otaduy, in:, ACM, 2015.","apa":"Pérez, J., Thomaszewski, B., Coros, S., Bickel, B., Canabal, J., Sumner, R., &#38; Otaduy, M. (2015). Design and fabrication of flexible rod meshes (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766998\">https://doi.org/10.1145/2766998</a>","ieee":"J. Pérez <i>et al.</i>, “Design and fabrication of flexible rod meshes,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ista":"Pérez J, Thomaszewski B, Coros S, Bickel B, Canabal J, Sumner R, Otaduy M. 2015. Design and fabrication of flexible rod meshes. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 138.","ama":"Pérez J, Thomaszewski B, Coros S, et al. Design and fabrication of flexible rod meshes. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766998\">10.1145/2766998</a>"},"quality_controlled":"1","type":"conference","article_number":"138","issue":"4"},{"scopus_import":"1","date_updated":"2025-09-23T09:34:10Z","publication_status":"published","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.1145/2766926","title":"Microstructures to control elasticity in 3D printing","abstract":[{"text":"We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications.","lang":"eng"}],"external_id":{"isi":["000358786600102"]},"isi":1,"month":"08","date_created":"2018-12-11T11:53:07Z","oa":1,"intvolume":"        34","publisher":"ACM","author":[{"first_name":"Christian","full_name":"Schumacher, Christian","last_name":"Schumacher"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Rys, Jan","last_name":"Rys"},{"full_name":"Marschner, Steve","last_name":"Marschner","first_name":"Steve"},{"first_name":"Chiara","full_name":"Daraio, Chiara","last_name":"Daraio"},{"last_name":"Gross","full_name":"Gross, Markus","first_name":"Markus"}],"_id":"1628","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"BeBi"}],"year":"2015","day":"01","date_published":"2015-08-01T00:00:00Z","conference":{"start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Los Angeles, CA, USA","end_date":"2015-08-13"},"publist_id":"5529","status":"public","volume":34,"main_file_link":[{"url":"https://doi.org/10.1145/2766926","open_access":"1"}],"issue":"4","article_number":"136","type":"conference","quality_controlled":"1","citation":{"mla":"Schumacher, Christian, et al. <i>Microstructures to Control Elasticity in 3D Printing</i>. Vol. 34, no. 4, 136, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766926\">10.1145/2766926</a>.","ieee":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross, “Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","apa":"Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., &#38; Gross, M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2766926\">https://doi.org/10.1145/2766926</a>","short":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:, ACM, 2015.","chicago":"Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio, and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766926\">https://doi.org/10.1145/2766926</a>.","ama":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766926\">10.1145/2766926</a>","ista":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 136."}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ChWo"}],"day":"27","year":"2015","pubrep_id":"576","date_published":"2015-07-27T00:00:00Z","publisher":"ACM","_id":"1630","author":[{"first_name":"Paul","last_name":"Guerrero","full_name":"Guerrero, Paul"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Wimmer, Michael","last_name":"Wimmer"},{"first_name":"Peter","last_name":"Wonka","full_name":"Wonka, Peter"}],"article_processing_charge":"No","file":[{"file_size":11902290,"date_created":"2018-12-12T10:07:49Z","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","relation":"main_file","file_id":"4647","creator":"system","content_type":"application/pdf","file_name":"IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf","checksum":"8b05a51e372c9b0b5af9a00098a9538b"}],"status":"public","volume":34,"file_date_updated":"2020-07-14T12:45:07Z","conference":{"end_date":"2015-08-13","location":"Los Angeles, CA, United States","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09"},"acknowledgement":"This publication is based upon work supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no. P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23).","publist_id":"5525","has_accepted_license":"1","issue":"4","article_number":"108","citation":{"mla":"Guerrero, Paul, et al. <i>Learning Shape Placements by Example</i>. Vol. 34, no. 4, 108, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766933\">10.1145/2766933</a>.","apa":"Guerrero, P., Jeschke, S., Wimmer, M., &#38; Wonka, P. (2015). Learning shape placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766933\">https://doi.org/10.1145/2766933</a>","ieee":"P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","chicago":"Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning Shape Placements by Example,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766933\">https://doi.org/10.1145/2766933</a>.","short":"P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015.","ista":"Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 108.","ama":"Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766933\">10.1145/2766933</a>"},"type":"conference","project":[{"grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"scopus_import":"1","publication_status":"published","date_updated":"2025-09-23T09:26:17Z","title":"Learning shape placements by example","abstract":[{"text":"We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D    scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction.","lang":"eng"}],"external_id":{"isi":["000358786600074"]},"doi":"10.1145/2766933","date_created":"2018-12-11T11:53:08Z","ddc":["000"],"isi":1,"month":"07","intvolume":"        34","oa":1},{"scopus_import":"1","publication_status":"published","date_updated":"2025-09-23T07:27:29Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"doi":"10.1145/2766935","abstract":[{"lang":"eng","text":"This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling."}],"title":"A stream function solver for liquid simulations","external_id":{"isi":["000358786600019"]},"ddc":["000"],"isi":1,"month":"07","date_created":"2018-12-11T11:53:09Z","oa":1,"intvolume":"        34","publisher":"ACM","alternative_title":["ACM Transactions on Graphics"],"author":[{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"},{"last_name":"Thuerey","full_name":"Thuerey, Nils","first_name":"Nils"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"_id":"1632","article_processing_charge":"No","department":[{"_id":"ChWo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","day":"27","pubrep_id":"610","date_published":"2015-07-27T00:00:00Z","acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014 realFlow and ERC-2014- StG-638176 BigSplash.","conference":{"location":"Los Angeles, CA, USA","end_date":"2015-08-13","start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"publist_id":"5523","file":[{"file_size":21831121,"date_created":"2018-12-12T10:11:52Z","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","file_id":"4909","relation":"main_file","content_type":"application/pdf","file_name":"IST-2016-610-v1+1_vecpotential.pdf","checksum":"7a9afdfaba9209157ce19376e15bc90b","creator":"system"}],"status":"public","volume":34,"file_date_updated":"2020-07-14T12:45:07Z","issue":"4","article_number":"53","has_accepted_license":"1","type":"conference","quality_controlled":"1","citation":{"ista":"Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 53.","ama":"Ando R, Thuerey N, Wojtan C. A stream function solver for liquid simulations. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766935\">10.1145/2766935</a>","short":"R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015.","chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver for Liquid Simulations,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766935\">https://doi.org/10.1145/2766935</a>.","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","apa":"Ando, R., Thuerey, N., &#38; Wojtan, C. (2015). A stream function solver for liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2766935\">https://doi.org/10.1145/2766935</a>","mla":"Ando, Ryoichi, et al. <i>A Stream Function Solver for Liquid Simulations</i>. Vol. 34, no. 4, 53, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766935\">10.1145/2766935</a>."}},{"day":"27","year":"2015","date_published":"2015-07-27T00:00:00Z","pubrep_id":"608","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ChWo"}],"_id":"1634","author":[{"first_name":"Fang","full_name":"Da, Fang","last_name":"Da"},{"first_name":"Christopher","last_name":"Batty","full_name":"Batty, Christopher"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"},{"last_name":"Grinspun","full_name":"Grinspun, Eitan","first_name":"Eitan"}],"article_processing_charge":"No","publisher":"ACM","file_date_updated":"2020-07-14T12:45:07Z","volume":34,"file":[{"file_id":"4867","relation":"main_file","checksum":"57b07d78d2d612a8052744b37d4a71fa","content_type":"application/pdf","file_name":"IST-2016-608-v1+1_doublebubbles.pdf","creator":"system","date_created":"2018-12-12T10:11:14Z","file_size":8973215,"access_level":"open_access","date_updated":"2020-07-14T12:45:07Z"}],"ec_funded":1,"status":"public","publist_id":"5521","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","location":"Los Angeles, CA, United States","end_date":"2015-08-13"},"has_accepted_license":"1","issue":"4","article_number":"149","citation":{"mla":"Da, Fang, et al. <i>Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams</i>. Vol. 34, no. 4, 149, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2767003\">10.1145/2767003</a>.","ama":"Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2767003\">10.1145/2767003</a>","ista":"Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 149.","apa":"Da, F., Batty, C., Wojtan, C., &#38; Grinspun, E. (2015). Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2767003\">https://doi.org/10.1145/2767003</a>","ieee":"F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","short":"F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015.","chicago":"Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2767003\">https://doi.org/10.1145/2767003</a>."},"type":"conference","project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"publication_status":"published","date_updated":"2025-09-23T08:28:56Z","scopus_import":"1","external_id":{"isi":["000358786600115"]},"title":"Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams","abstract":[{"lang":"eng","text":"Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart."}],"doi":"10.1145/2767003","date_created":"2018-12-11T11:53:09Z","ddc":["000"],"isi":1,"month":"07","intvolume":"        34","oa":1},{"month":"01","corr_author":"1","date_created":"2018-12-11T11:53:10Z","page":"781 - 800","publication":"Annales de la faculté des sciences de Toulouse","oa":1,"intvolume":"        24","publication_status":"published","date_updated":"2024-10-09T20:56:07Z","language":[{"iso":"eng"}],"oa_version":"Preprint","doi":"10.5802/afst.1464","abstract":[{"text":"We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.","lang":"eng"}],"title":"Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models","external_id":{"arxiv":["1409.8605"]},"issue":"4","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.8605"}],"quality_controlled":"1","type":"journal_article","citation":{"ieee":"M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” <i>Annales de la faculté des sciences de Toulouse</i>, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.","apa":"Erbar, M., Maas, J., &#38; Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. <i>Annales de La Faculté Des Sciences de Toulouse</i>. Faculté des sciences de Toulouse. <a href=\"https://doi.org/10.5802/afst.1464\">https://doi.org/10.5802/afst.1464</a>","short":"M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800.","chicago":"Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” <i>Annales de La Faculté Des Sciences de Toulouse</i>. Faculté des sciences de Toulouse, 2015. <a href=\"https://doi.org/10.5802/afst.1464\">https://doi.org/10.5802/afst.1464</a>.","ama":"Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. <i>Annales de la faculté des sciences de Toulouse</i>. 2015;24(4):781-800. doi:<a href=\"https://doi.org/10.5802/afst.1464\">10.5802/afst.1464</a>","ista":"Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800.","mla":"Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” <i>Annales de La Faculté Des Sciences de Toulouse</i>, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:<a href=\"https://doi.org/10.5802/afst.1464\">10.5802/afst.1464</a>."},"article_type":"original","publisher":"Faculté des sciences de Toulouse","author":[{"first_name":"Matthias","last_name":"Erbar","full_name":"Erbar, Matthias"},{"full_name":"Maas, Jan","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"first_name":"Prasad","full_name":"Tetali, Prasad","last_name":"Tetali"}],"_id":"1635","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"date_published":"2015-01-01T00:00:00Z","year":"2015","day":"01","arxiv":1,"publist_id":"5520","status":"public","volume":24},{"intvolume":"      9472","oa":1,"publication":"26th International Symposium","page":"566 - 577","date_created":"2018-12-11T11:53:10Z","isi":1,"month":"12","abstract":[{"lang":"eng","text":"Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism R→ΓΓ between two relational structures, e.g. between two directed graphs. Analyzing its complexity has been a prominent research direction, especially for the fixed template CSPs where the right side ΓΓ is fixed and the left side R is unconstrained.\r\n\r\nFar fewer results are known for the hybrid setting that restricts both sides simultaneously. It assumes that R belongs to a certain class of relational structures (called a structural restriction in this paper). We study which structural restrictions are effective, i.e. there exists a fixed template ΓΓ (from a certain class of languages) for which the problem is tractable when R is restricted, and NP-hard otherwise. We provide a characterization for structural restrictions that are closed under inverse homomorphisms. The criterion is based on the chromatic number of a relational structure defined in this paper; it generalizes the standard chromatic number of a graph.\r\n\r\nAs our main tool, we use the algebraic machinery developed for fixed template CSPs. To apply it to our case, we introduce a new construction called a “lifted language”. We also give a characterization for structural restrictions corresponding to minor-closed families of graphs, extend results to certain Valued CSPs (namely conservative valued languages), and state implications for (valued) CSPs with ordered variables and for the maximum weight independent set problem on some restricted families of graphs."}],"title":"Effectiveness of structural restrictions for hybrid CSPs","external_id":{"isi":["000375151300048"],"arxiv":["1504.07067"]},"doi":"10.1007/978-3-662-48971-0_48","oa_version":"Preprint","language":[{"iso":"eng"}],"scopus_import":"1","date_updated":"2025-09-23T08:39:38Z","publication_status":"published","citation":{"mla":"Kolmogorov, Vladimir, et al. “Effectiveness of Structural Restrictions for Hybrid CSPs.” <i>26th International Symposium</i>, vol. 9472, Springer Nature, 2015, pp. 566–77, doi:<a href=\"https://doi.org/10.1007/978-3-662-48971-0_48\">10.1007/978-3-662-48971-0_48</a>.","ieee":"V. Kolmogorov, M. Rolinek, and R. Takhanov, “Effectiveness of structural restrictions for hybrid CSPs,” in <i>26th International Symposium</i>, Nagoya, Japan, 2015, vol. 9472, pp. 566–577.","apa":"Kolmogorov, V., Rolinek, M., &#38; Takhanov, R. (2015). Effectiveness of structural restrictions for hybrid CSPs. In <i>26th International Symposium</i> (Vol. 9472, pp. 566–577). Nagoya, Japan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-48971-0_48\">https://doi.org/10.1007/978-3-662-48971-0_48</a>","chicago":"Kolmogorov, Vladimir, Michal Rolinek, and Rustem Takhanov. “Effectiveness of Structural Restrictions for Hybrid CSPs.” In <i>26th International Symposium</i>, 9472:566–77. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/978-3-662-48971-0_48\">https://doi.org/10.1007/978-3-662-48971-0_48</a>.","short":"V. Kolmogorov, M. Rolinek, R. Takhanov, in:, 26th International Symposium, Springer Nature, 2015, pp. 566–577.","ama":"Kolmogorov V, Rolinek M, Takhanov R. Effectiveness of structural restrictions for hybrid CSPs. In: <i>26th International Symposium</i>. Vol 9472. Springer Nature; 2015:566-577. doi:<a href=\"https://doi.org/10.1007/978-3-662-48971-0_48\">10.1007/978-3-662-48971-0_48</a>","ista":"Kolmogorov V, Rolinek M, Takhanov R. 2015. Effectiveness of structural restrictions for hybrid CSPs. 26th International Symposium. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 9472, 566–577."},"type":"conference","quality_controlled":"1","project":[{"grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["978-3-662-48970-3"]},"main_file_link":[{"url":"http://arxiv.org/abs/1504.07067","open_access":"1"}],"status":"public","ec_funded":1,"volume":9472,"conference":{"start_date":"2015-12-09","name":"ISAAC: International Symposium on Algorithms and Computation","location":"Nagoya, Japan","end_date":"2015-12-11"},"arxiv":1,"publist_id":"5519","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"VlKo"}],"day":"01","year":"2015","date_published":"2015-12-01T00:00:00Z","publisher":"Springer Nature","alternative_title":["LNCS"],"_id":"1636","article_processing_charge":"No","author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek"},{"last_name":"Takhanov","full_name":"Takhanov, Rustem","first_name":"Rustem"}]},{"language":[{"iso":"eng"}],"oa_version":"Preprint","scopus_import":"1","date_updated":"2025-09-23T13:45:57Z","publication_status":"published","title":"The complexity of general-valued CSPs","abstract":[{"text":"An instance of the Valued Constraint Satisfaction Problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P ≠ NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one deals only with the feasibility issue and there is no optimization. This case is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which constraint languages CSPs are tractable (i.e. solvable in polynomial time) and for which NP-hard. The case when all allowed functions take only finite values corresponds to finite-valued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Zivny. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e. the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.","lang":"eng"}],"external_id":{"arxiv":["1502.07327"],"isi":["000379204700071"]},"doi":"10.1109/FOCS.2015.80","date_created":"2018-12-11T11:53:10Z","page":"1246 - 1258","month":"12","isi":1,"corr_author":"1","oa":1,"department":[{"_id":"VlKo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-12-01T00:00:00Z","year":"2015","day":"01","alternative_title":["56th Annual Symposium on Foundations of Computer Science"],"publisher":"IEEE","article_processing_charge":"No","_id":"1637","author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krokhin, Andrei","last_name":"Krokhin","first_name":"Andrei"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek"}],"status":"public","ec_funded":1,"arxiv":1,"conference":{"name":"FOCS: Foundations of Computer Science","start_date":"2015-10-18","end_date":"2015-10-20","location":"Berkeley, CA, United States"},"publist_id":"5518","main_file_link":[{"url":"http://arxiv.org/abs/1502.07327","open_access":"1"}],"related_material":{"record":[{"relation":"other","status":"public","id":"644"}]},"citation":{"ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. In: IEEE; 2015:1246-1258. doi:<a href=\"https://doi.org/10.1109/FOCS.2015.80\">10.1109/FOCS.2015.80</a>","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2015. The complexity of general-valued CSPs. FOCS: Foundations of Computer Science, 56th Annual Symposium on Foundations of Computer Science, , 1246–1258.","chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs,” 1246–58. IEEE, 2015. <a href=\"https://doi.org/10.1109/FOCS.2015.80\">https://doi.org/10.1109/FOCS.2015.80</a>.","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, in:, IEEE, 2015, pp. 1246–1258.","ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States, 2015, pp. 1246–1258.","apa":"Kolmogorov, V., Krokhin, A., &#38; Rolinek, M. (2015). The complexity of general-valued CSPs (pp. 1246–1258). Presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/FOCS.2015.80\">https://doi.org/10.1109/FOCS.2015.80</a>","mla":"Kolmogorov, Vladimir, et al. <i>The Complexity of General-Valued CSPs</i>. IEEE, 2015, pp. 1246–58, doi:<a href=\"https://doi.org/10.1109/FOCS.2015.80\">10.1109/FOCS.2015.80</a>."},"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"quality_controlled":"1","type":"conference"},{"month":"05","isi":1,"corr_author":"1","date_created":"2018-12-11T11:53:11Z","page":"375 - 388","publication":"Nature Reviews Molecular Cell Biology","intvolume":"        16","scopus_import":"1","publication_status":"published","date_updated":"2025-09-22T14:30:27Z","language":[{"iso":"eng"}],"oa_version":"None","doi":"10.1038/nrm3997","abstract":[{"text":"The mitochondrial respiratory chain, also known as the electron transport chain (ETC), is crucial to life, and energy production in the form of ATP is the main mitochondrial function. Three proton-translocating enzymes of the ETC, namely complexes I, III and IV, generate proton motive force, which in turn drives ATP synthase (complex V). The atomic structures and basic mechanisms of most respiratory complexes have previously been established, with the exception of complex I, the largest complex in the ETC. Recently, the crystal structure of the entire complex I was solved using a bacterial enzyme. The structure provided novel insights into the core architecture of the complex, the electron transfer and proton translocation pathways, as well as the mechanism that couples these two processes.","lang":"eng"}],"title":"A giant molecular proton pump: structure and mechanism of respiratory complex I","external_id":{"isi":["000354960900009"]},"issue":"6","quality_controlled":"1","type":"journal_article","citation":{"short":"L.A. Sazanov, Nature Reviews Molecular Cell Biology 16 (2015) 375–388.","chicago":"Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism of Respiratory Complex I.” <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nrm3997\">https://doi.org/10.1038/nrm3997</a>.","ieee":"L. A. Sazanov, “A giant molecular proton pump: structure and mechanism of respiratory complex I,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 16, no. 6. Nature Publishing Group, pp. 375–388, 2015.","apa":"Sazanov, L. A. (2015). A giant molecular proton pump: structure and mechanism of respiratory complex I. <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrm3997\">https://doi.org/10.1038/nrm3997</a>","ista":"Sazanov LA. 2015. A giant molecular proton pump: structure and mechanism of respiratory complex I. Nature Reviews Molecular Cell Biology. 16(6), 375–388.","ama":"Sazanov LA. A giant molecular proton pump: structure and mechanism of respiratory complex I. <i>Nature Reviews Molecular Cell Biology</i>. 2015;16(6):375-388. doi:<a href=\"https://doi.org/10.1038/nrm3997\">10.1038/nrm3997</a>","mla":"Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism of Respiratory Complex I.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 16, no. 6, Nature Publishing Group, 2015, pp. 375–88, doi:<a href=\"https://doi.org/10.1038/nrm3997\">10.1038/nrm3997</a>."},"publisher":"Nature Publishing Group","author":[{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"_id":"1638","article_processing_charge":"No","department":[{"_id":"LeSa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-05-22T00:00:00Z","year":"2015","day":"22","publist_id":"5517","status":"public","volume":16},{"citation":{"ama":"Maas J, Rumpf M, Schönlieb C, Simon S. A generalized model for optimal transport of images including dissipation and density modulation. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. 2015;49(6):1745-1769. doi:<a href=\"https://doi.org/10.1051/m2an/2015043\">10.1051/m2an/2015043</a>","ista":"Maas J, Rumpf M, Schönlieb C, Simon S. 2015. A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. 49(6), 1745–1769.","chicago":"Maas, Jan, Martin Rumpf, Carola Schönlieb, and Stefan Simon. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences, 2015. <a href=\"https://doi.org/10.1051/m2an/2015043\">https://doi.org/10.1051/m2an/2015043</a>.","short":"J. Maas, M. Rumpf, C. Schönlieb, S. Simon, ESAIM: Mathematical Modelling and Numerical Analysis 49 (2015) 1745–1769.","apa":"Maas, J., Rumpf, M., Schönlieb, C., &#38; Simon, S. (2015). A generalized model for optimal transport of images including dissipation and density modulation. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/m2an/2015043\">https://doi.org/10.1051/m2an/2015043</a>","ieee":"J. Maas, M. Rumpf, C. Schönlieb, and S. Simon, “A generalized model for optimal transport of images including dissipation and density modulation,” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 49, no. 6. EDP Sciences, pp. 1745–1769, 2015.","mla":"Maas, Jan, et al. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 49, no. 6, EDP Sciences, 2015, pp. 1745–69, doi:<a href=\"https://doi.org/10.1051/m2an/2015043\">10.1051/m2an/2015043</a>."},"type":"journal_article","quality_controlled":"1","issue":"6","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.01988"}],"status":"public","volume":49,"arxiv":1,"acknowledgement":"The authors acknowledge support of the Collaborative Research Centre 1060 funded by the German Science foundation. This work is further supported by the King Abdullah University for Science and Technology (KAUST) Award No. KUK-I1-007-43 and the EPSRC grant Nr. EP/M00483X/1.","publist_id":"5514","department":[{"_id":"JaMa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","day":"01","date_published":"2015-11-01T00:00:00Z","publisher":"EDP Sciences","article_processing_charge":"No","_id":"1639","author":[{"last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Martin","last_name":"Rumpf","full_name":"Rumpf, Martin"},{"first_name":"Carola","last_name":"Schönlieb","full_name":"Schönlieb, Carola"},{"first_name":"Stefan","full_name":"Simon, Stefan","last_name":"Simon"}],"intvolume":"        49","oa":1,"page":"1745 - 1769","publication":"ESAIM: Mathematical Modelling and Numerical Analysis","date_created":"2018-12-11T11:53:11Z","isi":1,"month":"11","title":"A generalized model for optimal transport of images including dissipation and density modulation","abstract":[{"lang":"eng","text":"In this paper the optimal transport and the metamorphosis perspectives are combined. For a pair of given input images geodesic paths in the space of images are defined as minimizers of a resulting path energy. To this end, the underlying Riemannian metric measures the rate of transport cost and the rate of viscous dissipation. Furthermore, the model is capable to deal with strongly varying image contrast and explicitly allows for sources and sinks in the transport equations which are incorporated in the metric related to the metamorphosis approach by Trouvé and Younes. In the non-viscous case with source term existence of geodesic paths is proven in the space of measures. The proposed model is explored on the range from merely optimal transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals. These functionals are defined on corresponding pairs of intensity functions and on associated pairwise matching deformations. Existence of time discrete geodesics is demonstrated. Furthermore, a finite element implementation is proposed and applied to instructive test cases and to real images. In the non-viscous case this is compared to the algorithm proposed by Benamou and Brenier including a discretization of the source term. Finally, the model is generalized to define discrete weighted barycentres with applications to textures and objects."}],"external_id":{"arxiv":["1504.01988"],"isi":["000365047600013"]},"doi":"10.1051/m2an/2015043","oa_version":"Preprint","language":[{"iso":"eng"}],"scopus_import":"1","publication_status":"published","date_updated":"2025-09-22T14:29:56Z"},{"scopus_import":"1","date_updated":"2025-09-23T08:24:11Z","publication_status":"published","oa_version":"Submitted Version","language":[{"iso":"eng"}],"doi":"10.1038/ncomms9717","title":"Cytokinin response factors regulate PIN-FORMED auxin transporters","abstract":[{"lang":"eng","text":"Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"external_id":{"isi":["000366289800001"]},"isi":1,"ddc":["580"],"month":"01","corr_author":"1","publication":"Nature Communications","date_created":"2018-12-11T11:53:12Z","oa":1,"intvolume":"         6","publisher":"Nature Publishing Group","_id":"1640","author":[{"first_name":"Mária","last_name":"Šimášková","full_name":"Šimášková, Mária"},{"full_name":"O'Brien, José","last_name":"O'Brien","first_name":"José"},{"first_name":"Mamoona","id":"391B5BBC-F248-11E8-B48F-1D18A9856A87","last_name":"Khan-Djamei","full_name":"Khan-Djamei, Mamoona"},{"first_name":"Giel","last_name":"Van Noorden","full_name":"Van Noorden, Giel"},{"orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös","full_name":"Ötvös, Krisztina"},{"full_name":"Vieten, Anne","last_name":"Vieten","first_name":"Anne"},{"first_name":"Inge","last_name":"De Clercq","full_name":"De Clercq, Inge"},{"first_name":"Johanna","full_name":"Van Haperen, Johanna","last_name":"Van Haperen"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta"},{"last_name":"Hoyerová","full_name":"Hoyerová, Klára","first_name":"Klára"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter","last_name":"Marhavy"},{"orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T"},{"full_name":"Van Breusegem, Frank","last_name":"Van Breusegem","first_name":"Frank"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"},{"last_name":"Murphy","full_name":"Murphy, Angus","first_name":"Angus"},{"last_name":"Friml","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"year":"2015","day":"01","pubrep_id":"1020","date_published":"2015-01-01T00:00:00Z","acknowledgement":"This work was supported by the European Research Council Starting Independent Research grant (ERC-2007-Stg-207362-HCPO to E.B., M.S., C.C.), by the Ghent University Multidisciplinary Research Partnership ‘Biotechnology for a Sustainable Economy’ no.01MRB510W, by the Research Foundation—Flanders (grant 3G033711 to J.-A.O.), by the Austrian Science Fund (FWF01_I1774S) to K.Ö.,E.B., and by the Interuniversity Attraction Poles Programme (IUAP P7/29 ‘MARS’) initiated by the Belgian Science Policy Office. I.D.C. and S.V. are post-doctoral fellows of the Research Foundation—Flanders (FWO). This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF).","publist_id":"5513","file":[{"date_updated":"2020-07-14T12:45:08Z","access_level":"open_access","date_created":"2018-12-12T10:18:36Z","file_size":1471217,"creator":"system","file_name":"IST-2018-1020-v1+1_Simaskova_et_al_NatCom_2015.pdf","checksum":"c2c84bca37401435fedf76bad0ba0579","content_type":"application/pdf","relation":"main_file","file_id":"5358"}],"ec_funded":1,"status":"public","volume":6,"file_date_updated":"2020-07-14T12:45:08Z","article_number":"8717","has_accepted_license":"1","type":"journal_article","project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"},{"grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","citation":{"apa":"Šimášková, M., O’Brien, J., Khan-Djamei, M., Van Noorden, G., Ötvös, K., Vieten, A., … Benková, E. (2015). Cytokinin response factors regulate PIN-FORMED auxin transporters. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms9717\">https://doi.org/10.1038/ncomms9717</a>","ieee":"M. Šimášková <i>et al.</i>, “Cytokinin response factors regulate PIN-FORMED auxin transporters,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","chicago":"Šimášková, Mária, José O’Brien, Mamoona Khan-Djamei, Giel Van Noorden, Krisztina Ötvös, Anne Vieten, Inge De Clercq, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms9717\">https://doi.org/10.1038/ncomms9717</a>.","short":"M. Šimášková, J. O’Brien, M. Khan-Djamei, G. Van Noorden, K. Ötvös, A. Vieten, I. De Clercq, J. Van Haperen, C. Cuesta, K. Hoyerová, S. Vanneste, P. Marhavý, K.T. Wabnik, F. Van Breusegem, M. Nowack, A. Murphy, J. Friml, D. Weijers, T. Beeckman, E. Benková, Nature Communications 6 (2015).","ama":"Šimášková M, O’Brien J, Khan-Djamei M, et al. Cytokinin response factors regulate PIN-FORMED auxin transporters. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9717\">10.1038/ncomms9717</a>","ista":"Šimášková M, O’Brien J, Khan-Djamei M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen J, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik KT, Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E. 2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 6, 8717.","mla":"Šimášková, Mária, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” <i>Nature Communications</i>, vol. 6, 8717, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9717\">10.1038/ncomms9717</a>."}},{"corr_author":"1","ddc":["514","516"],"month":"11","publication":"Electronic Journal of Combinatorics","date_created":"2018-12-11T11:53:12Z","oa":1,"intvolume":"        22","publication_status":"published","date_updated":"2025-06-26T07:57:45Z","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.37236/5002","external_id":{"arxiv":["1305.4519"]},"title":"Clustered planarity testing revisited","abstract":[{"text":"The Hanani-Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this result to clustered graphs with two disjoint clusters, and show that a straightforward extension to flat clustered graphs with three or more disjoint clusters is not possible. For general clustered graphs we show a variant of the Hanani-Tutte theorem in the case when each cluster induces a connected subgraph. Di Battista and Frati proved that clustered planarity of embedded clustered graphs whose every face is incident to at most five vertices can be tested in polynomial time. We give a new and short proof of this result, using the matroid intersection algorithm.","lang":"eng"}],"related_material":{"record":[{"id":"10793","relation":"earlier_version","status":"public"}]},"issue":"4","article_number":"P4.24 ","publication_identifier":{"eissn":["1077-8926"]},"has_accepted_license":"1","type":"journal_article","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"quality_controlled":"1","article_type":"original","citation":{"mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” <i>Electronic Journal of Combinatorics</i>, vol. 22, no. 4, P4.24, Electronic Journal of Combinatorics, 2015, doi:<a href=\"https://doi.org/10.37236/5002\">10.37236/5002</a>.","ama":"Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. Clustered planarity testing revisited. <i>Electronic Journal of Combinatorics</i>. 2015;22(4). doi:<a href=\"https://doi.org/10.37236/5002\">10.37236/5002</a>","ista":"Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. 2015. Clustered planarity testing revisited. Electronic Journal of Combinatorics. 22(4), P4.24.","chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinovič, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2015. <a href=\"https://doi.org/10.37236/5002\">https://doi.org/10.37236/5002</a>.","short":"R. Fulek, J. Kynčl, I. Malinovič, D. Pálvölgyi, Electronic Journal of Combinatorics 22 (2015).","apa":"Fulek, R., Kynčl, J., Malinovič, I., &#38; Pálvölgyi, D. (2015). Clustered planarity testing revisited. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/5002\">https://doi.org/10.37236/5002</a>","ieee":"R. Fulek, J. Kynčl, I. Malinovič, and D. Pálvölgyi, “Clustered planarity testing revisited,” <i>Electronic Journal of Combinatorics</i>, vol. 22, no. 4. Electronic Journal of Combinatorics, 2015."},"_id":"1642","article_processing_charge":"No","author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"},{"last_name":"Malinovič","full_name":"Malinovič, Igor","first_name":"Igor"},{"last_name":"Pálvölgyi","full_name":"Pálvölgyi, Dömötör","first_name":"Dömötör"}],"publisher":"Electronic Journal of Combinatorics","year":"2015","day":"13","pubrep_id":"714","date_published":"2015-11-13T00:00:00Z","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5511","arxiv":1,"acknowledgement":"e research leading to these results has received funding fromthe People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no [291734], and ESF Eurogiga project GraDR as GAˇCRGIG/11/E023.","volume":22,"file_date_updated":"2020-07-14T12:45:08Z","file":[{"file_size":443655,"date_created":"2018-12-12T10:15:03Z","date_updated":"2020-07-14T12:45:08Z","access_level":"open_access","relation":"main_file","file_id":"5120","creator":"system","content_type":"application/pdf","file_name":"IST-2016-714-v1+1_5002-15499-3-PB.pdf","checksum":"40b5920b49ee736694f59f39588ee206"}],"status":"public","ec_funded":1}]