[{"year":"2017","oa":1,"date_updated":"2021-01-12T08:11:57Z","article_number":"e25125","date_published":"2017-08-14T00:00:00Z","month":"08","intvolume":"         6","oa_version":"Published Version","publication":"eLife","doi":"10.7554/eLife.25125","day":"14","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"date_created":"2018-12-11T11:48:05Z","volume":6,"pubrep_id":"885","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"},{"_id":"SiHi"}],"publist_id":"6971","title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","author":[{"full_name":"Andergassen, Daniel","first_name":"Daniel","last_name":"Andergassen"},{"last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph"},{"first_name":"Dyniel","last_name":"Wenzel","full_name":"Wenzel, Dyniel"},{"first_name":"Verena","last_name":"Sigl","full_name":"Sigl, Verena"},{"last_name":"Bammer","first_name":"Philipp","full_name":"Bammer, Philipp"},{"first_name":"Markus","last_name":"Muckenhuber","full_name":"Muckenhuber, Markus"},{"full_name":"Mayer, Daniela","last_name":"Mayer","first_name":"Daniela"},{"first_name":"Tomasz","last_name":"Kulinski","full_name":"Kulinski, Tomasz"},{"first_name":"Hans","last_name":"Theussl","full_name":"Theussl, Hans"},{"first_name":"Josef","last_name":"Penninger","full_name":"Penninger, Josef"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"last_name":"Barlow","first_name":"Denise","full_name":"Barlow, Denise"},{"full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"full_name":"Hudson, Quanah","last_name":"Hudson","first_name":"Quanah"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:13:36Z","date_updated":"2020-07-14T12:47:50Z","file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","access_level":"open_access","relation":"main_file","checksum":"1ace3462e64a971b9ead896091829549","file_id":"5020","content_type":"application/pdf","file_size":6399510,"creator":"system"},{"file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","date_created":"2018-12-12T10:13:36Z","date_updated":"2020-07-14T12:47:50Z","creator":"system","file_size":4264398,"file_id":"5021","content_type":"application/pdf","access_level":"open_access","checksum":"6241dc31eeb87b03facadec3a53a6827","relation":"main_file"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","publication_status":"published","project":[{"name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF"}],"quality_controlled":"1","_id":"713","abstract":[{"text":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.","lang":"eng"}],"scopus_import":1,"type":"journal_article","file_date_updated":"2020-07-14T12:47:50Z","citation":{"ama":"Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25125\">10.7554/eLife.25125</a>","short":"D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017).","ista":"Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125.","ieee":"D. Andergassen <i>et al.</i>, “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","chicago":"Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25125\">https://doi.org/10.7554/eLife.25125</a>.","apa":"Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25125\">https://doi.org/10.7554/eLife.25125</a>","mla":"Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” <i>ELife</i>, vol. 6, e25125, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25125\">10.7554/eLife.25125</a>."},"publication_identifier":{"issn":["2050084X"]}},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705","open_access":"1"}],"doi":"10.1016/j.drugalcdep.2017.04.015","publication":"Drug and Alcohol Dependence","oa_version":"Submitted Version","pmid":1,"volume":178,"date_created":"2018-12-11T11:48:05Z","day":"01","status":"public","page":"7 - 14","external_id":{"pmid":["28623807"]},"year":"2017","month":"09","intvolume":"       178","date_published":"2017-09-01T00:00:00Z","acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","date_updated":"2021-01-12T08:12:00Z","oa":1,"publication_status":"published","publication_identifier":{"issn":["03768716"]},"citation":{"chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” <i>Drug and Alcohol Dependence</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">https://doi.org/10.1016/j.drugalcdep.2017.04.015</a>.","ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. <i>Drug and Alcohol Dependence</i>. 2017;178:7-14. doi:<a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">10.1016/j.drugalcdep.2017.04.015</a>","ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14.","short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","ieee":"G. Brailoiu <i>et al.</i>, “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” <i>Drug and Alcohol Dependence</i>, vol. 178. Elsevier, pp. 7–14, 2017.","mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” <i>Drug and Alcohol Dependence</i>, vol. 178, Elsevier, 2017, pp. 7–14, doi:<a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">10.1016/j.drugalcdep.2017.04.015</a>.","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. <i>Drug and Alcohol Dependence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">https://doi.org/10.1016/j.drugalcdep.2017.04.015</a>"},"type":"journal_article","abstract":[{"lang":"eng","text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients."}],"scopus_import":1,"_id":"714","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"GaNo"}],"publist_id":"6967","language":[{"iso":"eng"}],"article_type":"original","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Gabriela","last_name":"Brailoiu","full_name":"Brailoiu, Gabriela"},{"full_name":"Deliu, Elena","first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5293","last_name":"Deliu"},{"last_name":"Barr","first_name":"Jeffrey","full_name":"Barr, Jeffrey"},{"full_name":"Console Bram, Linda","last_name":"Console Bram","first_name":"Linda"},{"last_name":"Ciuciu","first_name":"Alexandra","full_name":"Ciuciu, Alexandra"},{"last_name":"Abood","first_name":"Mary","full_name":"Abood, Mary"},{"last_name":"Unterwald","first_name":"Ellen","full_name":"Unterwald, Ellen"},{"full_name":"Brǎiloiu, Eugen","first_name":"Eugen","last_name":"Brǎiloiu"}],"title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens"},{"status":"public","day":"30","quality_controlled":"1","date_created":"2018-12-11T11:48:06Z","_id":"715","type":"journal_article","scopus_import":1,"abstract":[{"text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome.","lang":"eng"}],"publication_identifier":{"issn":["19466234"]},"citation":{"mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” <i>Science Translational Medicine</i>, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">10.1126/scitranslmed.aao4218</a>.","apa":"Novarino, G. (2017). More excitation for Rett syndrome. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">https://doi.org/10.1126/scitranslmed.aao4218</a>","chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">https://doi.org/10.1126/scitranslmed.aao4218</a>.","ama":"Novarino G. More excitation for Rett syndrome. <i>Science Translational Medicine</i>. 2017;9(405). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">10.1126/scitranslmed.aao4218</a>","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “More excitation for Rett syndrome,” <i>Science Translational Medicine</i>, vol. 9, no. 405. American Association for the Advancement of Science, 2017."},"volume":9,"oa_version":"None","publication_status":"published","doi":"10.1126/scitranslmed.aao4218","publication":"Science Translational Medicine","issue":"405","title":"More excitation for Rett syndrome","author":[{"orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:12:04Z","publisher":"American Association for the Advancement of Science","article_number":"aao4218","month":"08","intvolume":"         9","date_published":"2017-08-30T00:00:00Z","year":"2017","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"publist_id":"6968"},{"type":"journal_article","scopus_import":1,"arxiv":1,"abstract":[{"text":"Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.","lang":"eng"}],"publication_identifier":{"issn":["00045411"]},"citation":{"apa":"Chatterjee, K., &#38; Velner, Y. (2017). The complexity of mean-payoff pushdown games. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3121408\">https://doi.org/10.1145/3121408</a>","mla":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” <i>Journal of the ACM</i>, vol. 64, no. 5, ACM, 2017, p. 34, doi:<a href=\"https://doi.org/10.1145/3121408\">10.1145/3121408</a>.","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. <i>Journal of the ACM</i>. 2017;64(5):34. doi:<a href=\"https://doi.org/10.1145/3121408\">10.1145/3121408</a>","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.","ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","ieee":"K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” <i>Journal of the ACM</i>, vol. 64, no. 5. ACM, p. 34, 2017.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” <i>Journal of the ACM</i>. ACM, 2017. <a href=\"https://doi.org/10.1145/3121408\">https://doi.org/10.1145/3121408</a>."},"quality_controlled":"1","_id":"716","publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"}],"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The complexity of mean-payoff pushdown games","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"department":[{"_id":"KrCh"}],"publist_id":"6964","article_type":"original","language":[{"iso":"eng"}],"volume":64,"day":"01","status":"public","date_created":"2018-12-11T11:48:06Z","doi":"10.1145/3121408","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.2829"}],"publication":"Journal of the ACM","ec_funded":1,"oa_version":"Preprint","intvolume":"        64","month":"09","date_published":"2017-09-01T00:00:00Z","issue":"5","oa":1,"date_updated":"2021-01-12T08:12:08Z","page":"34","external_id":{"arxiv":["1201.2829"]},"year":"2017"},{"article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2017","month":"12","has_accepted_license":"1","date_published":"2017-12-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:47:47Z","file":[{"content_type":"application/zip","file_id":"7164","creator":"cfraisse","file_size":841375478,"relation":"main_file","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","access_level":"open_access","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-10T08:46:46Z"}],"title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"}],"project":[{"call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"doi":"10.15479/AT:ISTA:7163","related_material":{"record":[{"id":"614","relation":"research_paper","status":"public"}]},"contributor":[{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","orcid":"0000-0002-8101-2518","last_name":"Picard"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","citation":{"ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>","ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","ista":"Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","short":"C. Fraisse, (2017).","chicago":"Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>.","apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>","mla":"Fraisse, Christelle. <i>Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>."},"type":"research_data","file_date_updated":"2020-07-14T12:47:50Z","abstract":[{"text":"The de novo genome assemblies generated for this study, and the associated metadata.","lang":"eng"}],"_id":"7163","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-12-09T23:03:03Z","ddc":["576"],"status":"public","day":"01"},{"status":"public","day":"01","date_created":"2018-12-11T11:48:07Z","volume":88,"ec_funded":1,"oa_version":"Preprint","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2329"}]},"doi":"10.1016/j.jcss.2017.04.005","main_file_link":[{"url":"https://arxiv.org/abs/1210.3141","open_access":"1"}],"publication":"Journal of Computer and System Sciences","oa":1,"date_updated":"2023-02-23T10:38:15Z","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","intvolume":"        88","month":"09","date_published":"2017-09-01T00:00:00Z","year":"2017","page":"236 - 259","quality_controlled":"1","_id":"717","type":"journal_article","scopus_import":1,"abstract":[{"text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard.","lang":"eng"}],"citation":{"ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” <i>Journal of Computer and System Sciences</i>, vol. 88. Academic Press, pp. 236–259, 2017.","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. <i>Journal of Computer and System Sciences</i>. 2017;88:236-259. doi:<a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">10.1016/j.jcss.2017.04.005</a>","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” <i>Journal of Computer and System Sciences</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">https://doi.org/10.1016/j.jcss.2017.04.005</a>.","apa":"Chatterjee, K., &#38; Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. <i>Journal of Computer and System Sciences</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">https://doi.org/10.1016/j.jcss.2017.04.005</a>","mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” <i>Journal of Computer and System Sciences</i>, vol. 88, Academic Press, 2017, pp. 236–59, doi:<a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">10.1016/j.jcss.2017.04.005</a>."},"publication_status":"published","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Hyperplane separation technique for multidimensional mean-payoff games","publisher":"Academic Press","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publist_id":"6963"},{"page":"745 - 767","external_id":{"arxiv":["1607.05915"]},"year":"2017","intvolume":"        49","month":"09","date_published":"2017-09-01T00:00:00Z","date_updated":"2023-09-07T12:07:12Z","issue":"3","oa":1,"doi":"10.1017/apr.2017.20","main_file_link":[{"url":"https://arxiv.org/abs/1607.05915","open_access":"1"}],"publication":"Advances in Applied Probability","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6287"}]},"oa_version":"Preprint","ec_funded":1,"volume":49,"date_created":"2018-12-11T11:48:07Z","day":"01","status":"public","department":[{"_id":"HeEd"}],"publist_id":"6962","language":[{"iso":"eng"}],"publisher":"Cambridge University Press","title":"Expected sizes of poisson Delaunay mosaics and their discrete Morse functions","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"last_name":"Nikitenko","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton","full_name":"Nikitenko, Anton"},{"full_name":"Reitzner, Matthias","first_name":"Matthias","last_name":"Reitzner"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"},{"grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"publication_status":"published","citation":{"apa":"Edelsbrunner, H., Nikitenko, A., &#38; Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. <i>Advances in Applied Probability</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/apr.2017.20\">https://doi.org/10.1017/apr.2017.20</a>","mla":"Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” <i>Advances in Applied Probability</i>, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:<a href=\"https://doi.org/10.1017/apr.2017.20\">10.1017/apr.2017.20</a>.","ama":"Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. <i>Advances in Applied Probability</i>. 2017;49(3):745-767. doi:<a href=\"https://doi.org/10.1017/apr.2017.20\">10.1017/apr.2017.20</a>","short":"H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767.","ista":"Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767.","ieee":"H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” <i>Advances in Applied Probability</i>, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” <i>Advances in Applied Probability</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/apr.2017.20\">https://doi.org/10.1017/apr.2017.20</a>."},"publication_identifier":{"issn":["00018678"]},"type":"journal_article","arxiv":1,"abstract":[{"lang":"eng","text":"Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4."}],"scopus_import":1,"_id":"718","quality_controlled":"1"},{"oa_version":"None","doi":"10.1007/s00236-017-0299-0","publication_status":"published","publication":"Acta Informatica","quality_controlled":"1","day":"01","status":"public","date_created":"2018-12-11T11:48:07Z","_id":"719","type":"journal_article","abstract":[{"lang":"eng","text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains."}],"scopus_import":1,"citation":{"mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” <i>Acta Informatica</i>, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:<a href=\"https://doi.org/10.1007/s00236-017-0299-0\">10.1007/s00236-017-0299-0</a>.","apa":"Chatterjee, K., &#38; Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-017-0299-0\">https://doi.org/10.1007/s00236-017-0299-0</a>","chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-017-0299-0\">https://doi.org/10.1007/s00236-017-0299-0</a>.","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” <i>Acta Informatica</i>, vol. 54, no. 6. Springer, pp. 543–544, 2017.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. <i>Acta Informatica</i>. 2017;54(6):543-544. doi:<a href=\"https://doi.org/10.1007/s00236-017-0299-0\">10.1007/s00236-017-0299-0</a>"},"publication_identifier":{"issn":["00015903"]},"volume":54,"year":"2017","language":[{"iso":"eng"}],"publist_id":"6961","department":[{"_id":"KrCh"}],"page":"543 - 544","issue":"6","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Ehlers, Rüdiger","first_name":"Rüdiger","last_name":"Ehlers"}],"title":"Special issue: Synthesis and SYNT 2014","date_updated":"2021-01-12T08:12:18Z","publisher":"Springer","month":"09","intvolume":"        54","date_published":"2017-09-01T00:00:00Z"},{"project":[{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"},{"call_identifier":"FWF","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes"}],"publication_status":"published","_id":"720","quality_controlled":"1","publication_identifier":{"issn":["1553734X"]},"citation":{"mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>.","apa":"Humplik, J., &#38; Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” <i>PLoS Computational Biology</i>, vol. 13, no. 9. Public Library of Science, 2017.","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. 2017;13(9). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>"},"scopus_import":1,"abstract":[{"lang":"eng","text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality."}],"type":"journal_article","file_date_updated":"2020-07-14T12:47:53Z","language":[{"iso":"eng"}],"pubrep_id":"884","article_processing_charge":"Yes","department":[{"_id":"GaTk"}],"publist_id":"6960","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Humplik, Jan","last_name":"Humplik","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","file":[{"file_size":14167050,"creator":"system","file_id":"5352","content_type":"application/pdf","checksum":"81107096c19771c36ddbe6f0282a3acb","access_level":"open_access","relation":"main_file","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","date_created":"2018-12-12T10:18:30Z","date_updated":"2020-07-14T12:47:53Z"}],"has_accepted_license":"1","publisher":"Public Library of Science","oa_version":"Published Version","publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1005763","date_created":"2018-12-11T11:48:08Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530","571"],"status":"public","day":"19","volume":13,"year":"2017","date_updated":"2021-01-12T08:12:21Z","oa":1,"issue":"9","date_published":"2017-09-19T00:00:00Z","intvolume":"        13","month":"09","article_number":"e1005763"},{"publication_identifier":{"issn":["00103640"]},"citation":{"apa":"Ajanki, O. H., Krüger, T. H., &#38; Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cpa.21639\">https://doi.org/10.1002/cpa.21639</a>","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” <i>Communications on Pure and Applied Mathematics</i>, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:<a href=\"https://doi.org/10.1002/cpa.21639\">10.1002/cpa.21639</a>.","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” <i>Communications on Pure and Applied Mathematics</i>, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. <i>Communications on Pure and Applied Mathematics</i>. 2017;70(9):1672-1705. doi:<a href=\"https://doi.org/10.1002/cpa.21639\">10.1002/cpa.21639</a>","chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1002/cpa.21639\">https://doi.org/10.1002/cpa.21639</a>."},"abstract":[{"lang":"eng","text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur."}],"scopus_import":1,"type":"journal_article","_id":"721","quality_controlled":"1","project":[{"grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"publication_status":"published","publisher":"Wiley-Blackwell","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"full_name":"Krüger, Torben H","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","last_name":"Krüger"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"}],"title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","department":[{"_id":"LaEr"}],"publist_id":"6959","language":[{"iso":"eng"}],"volume":70,"date_created":"2018-12-11T11:48:08Z","status":"public","day":"01","publication":"Communications on Pure and Applied Mathematics","doi":"10.1002/cpa.21639","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1512.03703"}],"ec_funded":1,"oa_version":"Submitted Version","date_published":"2017-09-01T00:00:00Z","month":"09","intvolume":"        70","date_updated":"2021-01-12T08:12:24Z","oa":1,"issue":"9","page":"1672 - 1705","year":"2017"},{"publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:47:54Z","type":"journal_article","abstract":[{"lang":"eng","text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises."}],"scopus_import":1,"publication_identifier":{"issn":["09609822"]},"citation":{"short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","ieee":"E. Morris <i>et al.</i>, “Shaping 3D root system architecture,” <i>Current Biology</i>, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. <i>Current Biology</i>. 2017;27(17):R919-R930. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">10.1016/j.cub.2017.06.043</a>","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">https://doi.org/10.1016/j.cub.2017.06.043</a>.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">https://doi.org/10.1016/j.cub.2017.06.043</a>","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” <i>Current Biology</i>, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">10.1016/j.cub.2017.06.043</a>."},"quality_controlled":"1","_id":"722","publist_id":"6956","department":[{"_id":"JiFr"}],"pubrep_id":"982","language":[{"iso":"eng"}],"publisher":"Cell Press","has_accepted_license":"1","file":[{"file_name":"2017_CurrentBiology_Morris.pdf","date_created":"2019-04-17T07:46:40Z","date_updated":"2020-07-14T12:47:54Z","file_id":"6332","content_type":"application/pdf","creator":"dernst","file_size":1576593,"relation":"main_file","checksum":"e45588b21097b408da6276a3e5eedb2e","access_level":"open_access"}],"title":"Shaping 3D root system architecture","author":[{"full_name":"Morris, Emily","first_name":"Emily","last_name":"Morris"},{"full_name":"Griffiths, Marcus","first_name":"Marcus","last_name":"Griffiths"},{"first_name":"Agata","last_name":"Golebiowska","full_name":"Golebiowska, Agata"},{"first_name":"Stefan","last_name":"Mairhofer","full_name":"Mairhofer, Stefan"},{"last_name":"Burr Hersey","first_name":"Jasmine","full_name":"Burr Hersey, Jasmine"},{"full_name":"Goh, Tatsuaki","last_name":"Goh","first_name":"Tatsuaki"},{"first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel"},{"full_name":"Atkinson, Brian","last_name":"Atkinson","first_name":"Brian"},{"first_name":"Craig","last_name":"Sturrock","full_name":"Sturrock, Craig"},{"last_name":"Lynch","first_name":"Jonathan","full_name":"Lynch, Jonathan"},{"full_name":"Vissenberg, Kris","first_name":"Kris","last_name":"Vissenberg"},{"full_name":"Ritz, Karl","first_name":"Karl","last_name":"Ritz"},{"first_name":"Darren","last_name":"Wells","full_name":"Wells, Darren"},{"last_name":"Mooney","first_name":"Sacha","full_name":"Mooney, Sacha"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.cub.2017.06.043","publication":"Current Biology","ec_funded":1,"oa_version":"Submitted Version","pmid":1,"volume":27,"day":"11","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["581"],"date_created":"2018-12-11T11:48:08Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"R919 - R930","external_id":{"pmid":["28898665"]},"year":"2017","intvolume":"        27","month":"09","date_published":"2017-09-11T00:00:00Z","issue":"17","oa":1,"date_updated":"2021-01-12T08:12:29Z"},{"_id":"724","quality_controlled":"1","citation":{"mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” <i>Physical Review B</i>, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">10.1103/PhysRevB.96.104203</a>.","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., &#38; Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">https://doi.org/10.1103/PhysRevB.96.104203</a>","chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">https://doi.org/10.1103/PhysRevB.96.104203</a>.","short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017).","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” <i>Physical Review B</i>, vol. 96, no. 10. American Physical Society, 2017.","ista":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203.","ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. <i>Physical Review B</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">10.1103/PhysRevB.96.104203</a>"},"publication_identifier":{"issn":["24699950"]},"type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic."}],"scopus_import":1,"publication_status":"published","title":"Noninteracting central site model localization and logarithmic entanglement growth","author":[{"full_name":"Hetterich, Daniel","last_name":"Hetterich","first_name":"Daniel"},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"full_name":"Domínguez, Fernando","first_name":"Fernando","last_name":"Domínguez"},{"last_name":"Pollmann","first_name":"Frank","full_name":"Pollmann, Frank"},{"last_name":"Trauzettel","first_name":"Björn","full_name":"Trauzettel, Björn"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"publist_id":"6955","date_created":"2018-12-11T11:48:09Z","day":"13","status":"public","volume":96,"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"doi":"10.1103/PhysRevB.96.104203","publication":"Physical Review B","date_updated":"2021-01-12T08:12:35Z","issue":"10","oa":1,"month":"09","intvolume":"        96","date_published":"2017-09-13T00:00:00Z","article_number":"104203","acknowledgement":"We  would  like  to  thank  Dmitry  Abanin,  Christophe  De\r\nBeule,  Joel  Moore,  Romain  Vasseur,  and  Norman  Yao  for\r\nmany  stimulating  discussions.  Financial  support  has  been\r\nprovided  by  the  Deutsche  Forschungsgemeinschaft  (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB  Graduate  School  on  Topological  Insulators.  M.S.  was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1.","year":"2017"},{"quality_controlled":"1","_id":"725","abstract":[{"text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.","lang":"eng"}],"scopus_import":1,"type":"journal_article","publication_identifier":{"issn":["00278424"]},"citation":{"mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>.","apa":"Harpaz, R., Tkačik, G., &#38; Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. 2017;114(38):10149-10154. doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” <i>PNAS</i>, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154."},"publication_status":"published","author":[{"last_name":"Harpaz","first_name":"Roy","full_name":"Harpaz, Roy"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"}],"title":"Discrete modes of social information processing predict individual behavior of fish in a group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"publist_id":"6953","department":[{"_id":"GaTk"}],"status":"public","day":"19","date_created":"2018-12-11T11:48:10Z","volume":114,"pmid":1,"oa_version":"Submitted Version","publication":"PNAS","doi":"10.1073/pnas.1703817114","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"oa":1,"issue":"38","date_updated":"2021-01-12T08:12:36Z","date_published":"2017-09-19T00:00:00Z","month":"09","intvolume":"       114","year":"2017","external_id":{"pmid":["28874581"]},"page":"10149 - 10154"},{"author":[{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Scheele, Colinda","last_name":"Scheele","first_name":"Colinda"},{"last_name":"Moad","first_name":"Mohammad","full_name":"Moad, Mohammad"},{"last_name":"Drogo","first_name":"Nicholas","full_name":"Drogo, Nicholas"},{"full_name":"Heer, Rakesh","first_name":"Rakesh","last_name":"Heer"},{"full_name":"Sampogna, Rosemary","first_name":"Rosemary","last_name":"Sampogna"},{"full_name":"Van Rheenen, Jacco","first_name":"Jacco","last_name":"Van Rheenen"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"title":"A unifying theory of branching morphogenesis","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":12670204,"creator":"system","content_type":"application/pdf","file_id":"4870","checksum":"7a036d93a9e2e597af9bb504d6133aca","access_level":"open_access","relation":"main_file","file_name":"IST-2017-883-v1+1_PIIS0092867417309510.pdf","date_created":"2018-12-12T10:11:17Z","date_updated":"2020-07-14T12:47:55Z"}],"publisher":"Cell Press","has_accepted_license":"1","pubrep_id":"883","language":[{"iso":"eng"}],"publist_id":"6952","department":[{"_id":"EdHa"}],"article_processing_charge":"No","quality_controlled":"1","_id":"726","scopus_import":"1","abstract":[{"lang":"eng","text":"The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events."}],"file_date_updated":"2020-07-14T12:47:55Z","type":"journal_article","publication_identifier":{"issn":["00928674"]},"citation":{"ama":"Hannezo EB, Scheele C, Moad M, et al. A unifying theory of branching morphogenesis. <i>Cell</i>. 2017;171(1):242-255. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">10.1016/j.cell.2017.08.026</a>","short":"E.B. Hannezo, C. Scheele, M. Moad, N. Drogo, R. Heer, R. Sampogna, J. Van Rheenen, B. Simons, Cell 171 (2017) 242–255.","ista":"Hannezo EB, Scheele C, Moad M, Drogo N, Heer R, Sampogna R, Van Rheenen J, Simons B. 2017. A unifying theory of branching morphogenesis. Cell. 171(1), 242–255.","ieee":"E. B. Hannezo <i>et al.</i>, “A unifying theory of branching morphogenesis,” <i>Cell</i>, vol. 171, no. 1. Cell Press, pp. 242–255, 2017.","chicago":"Hannezo, Edouard B, Colinda Scheele, Mohammad Moad, Nicholas Drogo, Rakesh Heer, Rosemary Sampogna, Jacco Van Rheenen, and Benjamin Simons. “A Unifying Theory of Branching Morphogenesis.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">https://doi.org/10.1016/j.cell.2017.08.026</a>.","apa":"Hannezo, E. B., Scheele, C., Moad, M., Drogo, N., Heer, R., Sampogna, R., … Simons, B. (2017). A unifying theory of branching morphogenesis. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">https://doi.org/10.1016/j.cell.2017.08.026</a>","mla":"Hannezo, Edouard B., et al. “A Unifying Theory of Branching Morphogenesis.” <i>Cell</i>, vol. 171, no. 1, Cell Press, 2017, pp. 242–55, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">10.1016/j.cell.2017.08.026</a>."},"publication_status":"published","oa":1,"issue":"1","date_updated":"2023-09-28T11:34:17Z","date_published":"2017-09-21T00:00:00Z","intvolume":"       171","month":"09","year":"2017","external_id":{"isi":["000411331800024"]},"page":"242 - 255","day":"21","status":"public","date_created":"2018-12-11T11:48:10Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["539"],"volume":171,"oa_version":"Published Version","isi":1,"publication":"Cell","doi":"10.1016/j.cell.2017.08.026"},{"date_updated":"2023-09-28T11:33:49Z","acknowledged_ssus":[{"_id":"ScienComp"}],"issue":"1","date_published":"2017-09-21T00:00:00Z","intvolume":"       171","month":"09","year":"2017","external_id":{"isi":["000411331800020"]},"page":"188 - 200","date_created":"2018-12-11T11:48:10Z","status":"public","day":"21","volume":171,"oa_version":"None","ec_funded":1,"isi":1,"publication":"Cell","doi":"10.1016/j.cell.2017.07.051","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Mueller, Jan","last_name":"Mueller","first_name":"Jan"},{"full_name":"Szep, Gregory","last_name":"Szep","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","first_name":"Gregory"},{"first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","full_name":"Nemethova, Maria"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries"},{"last_name":"Lieber","first_name":"Arnon","full_name":"Lieber, Arnon"},{"last_name":"Winkler","first_name":"Christoph","full_name":"Winkler, Christoph"},{"last_name":"Kruse","first_name":"Karsten","full_name":"Kruse, Karsten"},{"full_name":"Small, John","last_name":"Small","first_name":"John"},{"first_name":"Christian","last_name":"Schmeiser","full_name":"Schmeiser, Christian"},{"full_name":"Keren, Kinneret","last_name":"Keren","first_name":"Kinneret"},{"full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"title":"Load adaptation of lamellipodial actin networks","publisher":"Cell Press","language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"6951","department":[{"_id":"MiSi"},{"_id":"Bio"}],"_id":"727","quality_controlled":"1","citation":{"apa":"Mueller, J., Szep, G., Nemethova, M., de Vries, I., Lieber, A., Winkler, C., … Sixt, M. K. (2017). Load adaptation of lamellipodial actin networks. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">https://doi.org/10.1016/j.cell.2017.07.051</a>","mla":"Mueller, Jan, et al. “Load Adaptation of Lamellipodial Actin Networks.” <i>Cell</i>, vol. 171, no. 1, Cell Press, 2017, pp. 188–200, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">10.1016/j.cell.2017.07.051</a>.","ama":"Mueller J, Szep G, Nemethova M, et al. Load adaptation of lamellipodial actin networks. <i>Cell</i>. 2017;171(1):188-200. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">10.1016/j.cell.2017.07.051</a>","ieee":"J. Mueller <i>et al.</i>, “Load adaptation of lamellipodial actin networks,” <i>Cell</i>, vol. 171, no. 1. Cell Press, pp. 188–200, 2017.","short":"J. Mueller, G. Szep, M. Nemethova, I. de Vries, A. Lieber, C. Winkler, K. Kruse, J. Small, C. Schmeiser, K. Keren, R. Hauschild, M.K. Sixt, Cell 171 (2017) 188–200.","ista":"Mueller J, Szep G, Nemethova M, de Vries I, Lieber A, Winkler C, Kruse K, Small J, Schmeiser C, Keren K, Hauschild R, Sixt MK. 2017. Load adaptation of lamellipodial actin networks. Cell. 171(1), 188–200.","chicago":"Mueller, Jan, Gregory Szep, Maria Nemethova, Ingrid de Vries, Arnon Lieber, Christoph Winkler, Karsten Kruse, et al. “Load Adaptation of Lamellipodial Actin Networks.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">https://doi.org/10.1016/j.cell.2017.07.051</a>."},"publication_identifier":{"issn":["00928674"]},"abstract":[{"text":"Actin filaments polymerizing against membranes power endocytosis, vesicular traffic, and cell motility. In vitro reconstitution studies suggest that the structure and the dynamics of actin networks respond to mechanical forces. We demonstrate that lamellipodial actin of migrating cells responds to mechanical load when membrane tension is modulated. In a steady state, migrating cell filaments assume the canonical dendritic geometry, defined by Arp2/3-generated 70° branch points. Increased tension triggers a dense network with a broadened range of angles, whereas decreased tension causes a shift to a sparse configuration dominated by filaments growing perpendicularly to the plasma membrane. We show that these responses emerge from the geometry of branched actin: when load per filament decreases, elongation speed increases and perpendicular filaments gradually outcompete others because they polymerize the shortest distance to the membrane, where they are protected from capping. This network-intrinsic geometrical adaptation mechanism tunes protrusive force in response to mechanical load.","lang":"eng"}],"scopus_import":"1","type":"journal_article","project":[{"name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments","_id":"25AD6156-B435-11E9-9278-68D0E5697425","grant_number":"LS13-029"},{"grant_number":"281556","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"publist_id":"6949","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Chan, Chii","first_name":"Chii","last_name":"Chan"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hiiragi, Takashi","last_name":"Hiiragi","first_name":"Takashi"}],"title":"Coordination of morphogenesis and cell fate specification in development","publisher":"Cell Press","publication_status":"published","quality_controlled":"1","_id":"728","type":"journal_article","abstract":[{"lang":"eng","text":"During animal development, cell-fate-specific changes in gene expression can modify the material properties of a tissue and drive tissue morphogenesis. While mechanistic insights into the genetic control of tissue-shaping events are beginning to emerge, how tissue morphogenesis and mechanics can reciprocally impact cell-fate specification remains relatively unexplored. Here we review recent findings reporting how multicellular morphogenetic events and their underlying mechanical forces can feed back into gene regulatory pathways to specify cell fate. We further discuss emerging techniques that allow for the direct measurement and manipulation of mechanical signals in vivo, offering unprecedented access to study mechanotransduction during development. Examination of the mechanical control of cell fate during tissue morphogenesis will pave the way to an integrated understanding of the design principles that underlie robust tissue patterning in embryonic development."}],"scopus_import":"1","publication_identifier":{"issn":["09609822"]},"citation":{"chicago":"Chan, Chii, Carl-Philipp J Heisenberg, and Takashi Hiiragi. “Coordination of Morphogenesis and Cell Fate Specification in Development.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">https://doi.org/10.1016/j.cub.2017.07.010</a>.","ista":"Chan C, Heisenberg C-PJ, Hiiragi T. 2017. Coordination of morphogenesis and cell fate specification in development. Current Biology. 27(18), R1024–R1035.","ieee":"C. Chan, C.-P. J. Heisenberg, and T. Hiiragi, “Coordination of morphogenesis and cell fate specification in development,” <i>Current Biology</i>, vol. 27, no. 18. Cell Press, pp. R1024–R1035, 2017.","short":"C. Chan, C.-P.J. Heisenberg, T. Hiiragi, Current Biology 27 (2017) R1024–R1035.","ama":"Chan C, Heisenberg C-PJ, Hiiragi T. Coordination of morphogenesis and cell fate specification in development. <i>Current Biology</i>. 2017;27(18):R1024-R1035. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">10.1016/j.cub.2017.07.010</a>","mla":"Chan, Chii, et al. “Coordination of Morphogenesis and Cell Fate Specification in Development.” <i>Current Biology</i>, vol. 27, no. 18, Cell Press, 2017, pp. R1024–35, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">10.1016/j.cub.2017.07.010</a>.","apa":"Chan, C., Heisenberg, C.-P. J., &#38; Hiiragi, T. (2017). Coordination of morphogenesis and cell fate specification in development. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">https://doi.org/10.1016/j.cub.2017.07.010</a>"},"year":"2017","page":"R1024 - R1035","external_id":{"isi":["000411581800019"]},"issue":"18","date_updated":"2023-09-28T11:33:21Z","intvolume":"        27","month":"09","date_published":"2017-09-18T00:00:00Z","isi":1,"oa_version":"None","doi":"10.1016/j.cub.2017.07.010","publication":"Current Biology","status":"public","day":"18","date_created":"2018-12-11T11:48:11Z","volume":27},{"type":"journal_article","abstract":[{"lang":"eng","text":"The cellular mechanisms allowing tissues to efficiently regenerate are not fully understood. In this issue of Developmental Cell, Cao et al. (2017)) discover that during zebrafish heart regeneration, epicardial cells at the leading edge of regenerating tissue undergo endoreplication, possibly due to increased tissue tension, thereby boosting their regenerative capacity."}],"scopus_import":"1","citation":{"chicago":"Spiro, Zoltan P, and Carl-Philipp J Heisenberg. “Regeneration Tensed up Polyploidy Takes the Lead.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">https://doi.org/10.1016/j.devcel.2017.09.008</a>.","ieee":"Z. P. Spiro and C.-P. J. Heisenberg, “Regeneration tensed up polyploidy takes the lead,” <i>Developmental Cell</i>, vol. 42, no. 6. Cell Press, pp. 559–560, 2017.","ista":"Spiro ZP, Heisenberg C-PJ. 2017. Regeneration tensed up polyploidy takes the lead. Developmental Cell. 42(6), 559–560.","short":"Z.P. Spiro, C.-P.J. Heisenberg, Developmental Cell 42 (2017) 559–560.","ama":"Spiro ZP, Heisenberg C-PJ. Regeneration tensed up polyploidy takes the lead. <i>Developmental Cell</i>. 2017;42(6):559-560. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">10.1016/j.devcel.2017.09.008</a>","mla":"Spiro, Zoltan P., and Carl-Philipp J. Heisenberg. “Regeneration Tensed up Polyploidy Takes the Lead.” <i>Developmental Cell</i>, vol. 42, no. 6, Cell Press, 2017, pp. 559–60, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">10.1016/j.devcel.2017.09.008</a>.","apa":"Spiro, Z. P., &#38; Heisenberg, C.-P. J. (2017). Regeneration tensed up polyploidy takes the lead. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">https://doi.org/10.1016/j.devcel.2017.09.008</a>"},"publication_identifier":{"issn":["15345807"]},"quality_controlled":"1","_id":"729","publication_status":"published","publisher":"Cell Press","title":"Regeneration tensed up polyploidy takes the lead","author":[{"full_name":"Spiro, Zoltan P","last_name":"Spiro","id":"426AD026-F248-11E8-B48F-1D18A9856A87","first_name":"Zoltan P"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6948","department":[{"_id":"CaHe"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"volume":42,"status":"public","day":"01","date_created":"2018-12-11T11:48:11Z","doi":"10.1016/j.devcel.2017.09.008","publication":"Developmental Cell","isi":1,"oa_version":"None","month":"01","intvolume":"        42","date_published":"2017-01-01T00:00:00Z","issue":"6","date_updated":"2023-09-28T11:32:49Z","external_id":{"isi":["000411582800003"]},"page":"559 - 560","year":"2017"},{"article_processing_charge":"No","publist_id":"6943","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"publisher":"Elsevier","title":"Maximum entropy models as a tool for building precise neural controls","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Savin, Cristina","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"publication_status":"published","publication_identifier":{"issn":["09594388"]},"citation":{"short":"C. Savin, G. Tkačik, Current Opinion in Neurobiology 46 (2017) 120–126.","ista":"Savin C, Tkačik G. 2017. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 46, 120–126.","ieee":"C. Savin and G. Tkačik, “Maximum entropy models as a tool for building precise neural controls,” <i>Current Opinion in Neurobiology</i>, vol. 46. Elsevier, pp. 120–126, 2017.","ama":"Savin C, Tkačik G. Maximum entropy models as a tool for building precise neural controls. <i>Current Opinion in Neurobiology</i>. 2017;46:120-126. doi:<a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">10.1016/j.conb.2017.08.001</a>","chicago":"Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">https://doi.org/10.1016/j.conb.2017.08.001</a>.","apa":"Savin, C., &#38; Tkačik, G. (2017). Maximum entropy models as a tool for building precise neural controls. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">https://doi.org/10.1016/j.conb.2017.08.001</a>","mla":"Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” <i>Current Opinion in Neurobiology</i>, vol. 46, Elsevier, 2017, pp. 120–26, doi:<a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">10.1016/j.conb.2017.08.001</a>."},"type":"journal_article","scopus_import":"1","abstract":[{"text":"Neural responses are highly structured, with population activity restricted to a small subset of the astronomical range of possible activity patterns. Characterizing these statistical regularities is important for understanding circuit computation, but challenging in practice. Here we review recent approaches based on the maximum entropy principle used for quantifying collective behavior in neural activity. We highlight recent models that capture population-level statistics of neural data, yielding insights into the organization of the neural code and its biological substrate. Furthermore, the MaxEnt framework provides a general recipe for constructing surrogate ensembles that preserve aspects of the data, but are otherwise maximally unstructured. This idea can be used to generate a hierarchy of controls against which rigorous statistical tests are possible.","lang":"eng"}],"_id":"730","quality_controlled":"1","page":"120 - 126","external_id":{"isi":["000416196400016"]},"year":"2017","month":"10","intvolume":"        46","date_published":"2017-10-01T00:00:00Z","date_updated":"2023-09-28T11:32:22Z","doi":"10.1016/j.conb.2017.08.001","publication":"Current Opinion in Neurobiology","isi":1,"oa_version":"None","ec_funded":1,"volume":46,"date_created":"2018-12-11T11:48:11Z","day":"01","status":"public"},{"publication_status":"published","doi":"10.1126/scitranslmed.aap8168","publication":"Science Translational Medicine","oa_version":"None","citation":{"mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” <i>Science Translational Medicine</i>, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">10.1126/scitranslmed.aap8168</a>.","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">https://doi.org/10.1126/scitranslmed.aap8168</a>","chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">https://doi.org/10.1126/scitranslmed.aap8168</a>.","ama":"Novarino G. The science of love in ASD and ADHD. <i>Science Translational Medicine</i>. 2017;9(411). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">10.1126/scitranslmed.aap8168</a>","ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168.","ieee":"G. Novarino, “The science of love in ASD and ADHD,” <i>Science Translational Medicine</i>, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","short":"G. Novarino, Science Translational Medicine 9 (2017)."},"publication_identifier":{"issn":["19466234"]},"volume":9,"type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently."}],"date_created":"2018-12-11T11:48:12Z","_id":"731","quality_controlled":"1","day":"11","status":"public","department":[{"_id":"GaNo"}],"publist_id":"6938","language":[{"iso":"eng"}],"year":"2017","intvolume":"         9","month":"10","date_published":"2017-10-11T00:00:00Z","publisher":"American Association for the Advancement of Science","article_number":"eaap8168","date_updated":"2021-01-12T08:12:57Z","issue":"411","author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"The science of love in ASD and ADHD"},{"department":[{"_id":"SyCr"}],"publist_id":"6937","article_processing_charge":"Yes","article_type":"original","pubrep_id":"882","language":[{"iso":"eng"}],"publisher":"BioMed Central","has_accepted_license":"1","author":[{"last_name":"Pull","orcid":"0000-0003-1122-3982","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour","file":[{"relation":"main_file","checksum":"3e24a2cfd48f49f7b3643d08d30fb480","access_level":"open_access","file_size":949857,"creator":"system","content_type":"application/pdf","file_id":"5271","date_created":"2018-12-12T10:17:18Z","date_updated":"2020-07-14T12:47:55Z","file_name":"IST-2017-882-v1+1_12862_2017_Article_1062.pdf"}],"publication_status":"published","project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","call_identifier":"FP7"}],"abstract":[{"lang":"eng","text":"Background: Social insects form densely crowded societies in environments with high pathogen loads, but have evolved collective defences that mitigate the impact of disease. However, colony-founding queens lack this protection and suffer high rates of mortality. The impact of pathogens may be exacerbated in species where queens found colonies together, as healthy individuals may contract pathogens from infectious co-founders. Therefore, we tested whether ant queens avoid founding colonies with pathogen-exposed conspecifics and how they might limit disease transmission from infectious individuals. Results: Using Lasius Niger queens and a naturally infecting fungal pathogen Metarhizium brunneum, we observed that queens were equally likely to found colonies with another pathogen-exposed or sham-treated queen. However, when one queen died, the surviving individual performed biting, burial and removal of the corpse. These undertaking behaviours were performed prophylactically, i.e. targeted equally towards non-infected and infected corpses, as well as carried out before infected corpses became infectious. Biting and burial reduced the risk of the queens contracting and dying from disease from an infectious corpse of a dead co-foundress. Conclusions: We show that co-founding ant queens express undertaking behaviours that, in mature colonies, are performed exclusively by workers. Such infection avoidance behaviours act before the queens can contract the disease and will therefore improve the overall chance of colony founding success in ant queens."}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:55Z","type":"journal_article","publication_identifier":{"issn":["14712148"]},"citation":{"chicago":"Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2017. <a href=\"https://doi.org/10.1186/s12862-017-1062-4\">https://doi.org/10.1186/s12862-017-1062-4</a>.","ista":"Pull C, Cremer S. 2017. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. 17(1), 219.","ieee":"C. Pull and S. Cremer, “Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour,” <i>BMC Evolutionary Biology</i>, vol. 17, no. 1. BioMed Central, 2017.","short":"C. Pull, S. Cremer, BMC Evolutionary Biology 17 (2017).","ama":"Pull C, Cremer S. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. <i>BMC Evolutionary Biology</i>. 2017;17(1). doi:<a href=\"https://doi.org/10.1186/s12862-017-1062-4\">10.1186/s12862-017-1062-4</a>","mla":"Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” <i>BMC Evolutionary Biology</i>, vol. 17, no. 1, 219, BioMed Central, 2017, doi:<a href=\"https://doi.org/10.1186/s12862-017-1062-4\">10.1186/s12862-017-1062-4</a>.","apa":"Pull, C., &#38; Cremer, S. (2017). Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12862-017-1062-4\">https://doi.org/10.1186/s12862-017-1062-4</a>"},"quality_controlled":"1","_id":"732","external_id":{"isi":["000412816800001"]},"year":"2017","article_number":"219","date_published":"2017-10-13T00:00:00Z","month":"10","intvolume":"        17","oa":1,"issue":"1","date_updated":"2023-09-28T11:31:32Z","publication":"BMC Evolutionary Biology","doi":"10.1186/s12862-017-1062-4","ec_funded":1,"oa_version":"Published Version","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"819"}]},"volume":17,"status":"public","day":"13","ddc":["576","592"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:48:12Z"}]