[{"article_number":"82","issue":"1","article_processing_charge":"No","type":"journal_article","related_material":{"record":[{"id":"5449","relation":"earlier_version","status":"public"}]},"has_accepted_license":"1","intvolume":"         7","title":"Amplification on undirected population structures: Comets beat stars","publist_id":"7307","year":"2017","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. ","lang":"eng"}],"file":[{"content_type":"application/pdf","checksum":"7d05cbdd914e194a019c0f91fb64e9a8","date_created":"2018-12-12T10:18:35Z","file_size":1536783,"relation":"main_file","creator":"system","file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","date_updated":"2020-07-14T12:46:36Z","access_level":"open_access","file_id":"5357"}],"month":"03","date_updated":"2025-09-18T09:50:10Z","publication":"Scientific Reports","scopus_import":"1","pubrep_id":"938","oa_version":"Published Version","language":[{"iso":"eng"}],"corr_author":"1","_id":"512","ddc":["004"],"ec_funded":1,"date_created":"2018-12-11T11:46:53Z","day":"06","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":7,"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"}],"oa":1,"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1038/s41598-017-00107-w","doi":"10.1038/s41598-017-00107-w","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"KrCh"}],"date_published":"2017-03-06T00:00:00Z","external_id":{"isi":["000396867800013"]},"publication_identifier":{"issn":["2045-2322"]},"publisher":"Nature Publishing Group","status":"public","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"quality_controlled":"1","citation":{"ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” <i>Scientific Reports</i>, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41598-017-00107-w\">10.1038/s41598-017-00107-w</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. <i>Scientific Reports</i>. 2017;7(1). doi:<a href=\"https://doi.org/10.1038/s41598-017-00107-w\">10.1038/s41598-017-00107-w</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-017-00107-w\">https://doi.org/10.1038/s41598-017-00107-w</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” <i>Scientific Reports</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41598-017-00107-w\">https://doi.org/10.1038/s41598-017-00107-w</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” <i>Scientific Reports</i>, vol. 7, no. 1. Nature Publishing Group, 2017."},"isi":1},{"day":"01","date_created":"2018-12-11T11:46:54Z","_id":"513","scopus_import":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","fulldoi":"https://doi.org/10.1103/PhysRevFluids.2.043904","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","oa":1,"volume":2,"date_published":"2017-04-01T00:00:00Z","external_id":{"isi":["000400249900003"],"arxiv":["1704.02619"]},"doi":"10.1103/PhysRevFluids.2.043904","department":[{"_id":"BjHo"}],"quality_controlled":"1","isi":1,"citation":{"ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904.","mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” <i>Physical Review Fluids</i>, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.2.043904\">10.1103/PhysRevFluids.2.043904</a>.","ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. <i>Physical Review Fluids</i>. 2017;2(4). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.2.043904\">10.1103/PhysRevFluids.2.043904</a>","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., &#38; Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.2.043904\">https://doi.org/10.1103/PhysRevFluids.2.043904</a>","chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” <i>Physical Review Fluids</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevFluids.2.043904\">https://doi.org/10.1103/PhysRevFluids.2.043904</a>.","short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” <i>Physical Review Fluids</i>, vol. 2, no. 4. American Physical Society, 2017."},"author":[{"id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","last_name":"Klotz","orcid":"0000-0003-1740-7635","first_name":"Lukasz","full_name":"Klotz, Lukasz"},{"first_name":"Grégoire M","full_name":"Lemoult, Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","last_name":"Lemoult"},{"full_name":"Frontczak, Idalia","first_name":"Idalia","last_name":"Frontczak"},{"full_name":"Tuckerman, Laurette","first_name":"Laurette","last_name":"Tuckerman"},{"last_name":"Wesfreid","first_name":"José","full_name":"Wesfreid, José"}],"status":"public","publisher":"American Physical Society","issue":"4","article_number":"043904","type":"journal_article","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1704.02619","open_access":"1"}],"abstract":[{"lang":"eng","text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction."}],"year":"2017","publist_id":"7306","intvolume":"         2","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","publication":"Physical Review Fluids","month":"04","arxiv":1,"date_updated":"2025-09-18T09:49:18Z"},{"publication_identifier":{"issn":["2041-1723"]},"external_id":{"isi":["000405901100001"]},"date_published":"2017-07-01T00:00:00Z","department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:46:36Z","doi":"10.1038/ncomms16032","author":[{"last_name":"Simonnet","full_name":"Simonnet, Jean","first_name":"Jean"},{"full_name":"Nassar, Mérie","first_name":"Mérie","last_name":"Nassar"},{"first_name":"Federico","full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","last_name":"Stella","orcid":"0000-0001-9439-3148"},{"last_name":"Cohen","first_name":"Ivan","full_name":"Cohen, Ivan"},{"last_name":"Mathon","first_name":"Bertrand","full_name":"Mathon, Bertrand"},{"first_name":"Charlotte","full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","last_name":"Boccara"},{"last_name":"Miles","first_name":"Richard","full_name":"Miles, Richard"},{"full_name":"Fricker, Desdemona","first_name":"Desdemona","last_name":"Fricker"}],"isi":1,"citation":{"apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms16032\">https://doi.org/10.1038/ncomms16032</a>","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms16032\">https://doi.org/10.1038/ncomms16032</a>.","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","ieee":"J. Simonnet <i>et al.</i>, “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032.","mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” <i>Nature Communications</i>, vol. 8, 16032, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms16032\">10.1038/ncomms16032</a>.","ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms16032\">10.1038/ncomms16032</a>"},"quality_controlled":"1","publisher":"Nature Publishing Group","status":"public","ddc":["571"],"date_created":"2018-12-11T11:46:54Z","day":"01","oa_version":"Published Version","language":[{"iso":"eng"}],"pubrep_id":"937","scopus_import":"1","_id":"514","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1038/ncomms16032","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":8,"oa":1,"publication_status":"published","publist_id":"7305","year":"2017","abstract":[{"lang":"eng","text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum."}],"title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","intvolume":"         8","has_accepted_license":"1","date_updated":"2025-09-18T09:48:43Z","month":"07","file":[{"creator":"system","relation":"main_file","date_created":"2018-12-12T10:14:31Z","file_size":2948357,"checksum":"76d8a2b72a58e56adb410ec37dfa7eee","content_type":"application/pdf","access_level":"open_access","file_id":"5083","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","date_updated":"2020-07-14T12:46:36Z"}],"publication":"Nature Communications","article_number":"16032","type":"journal_article","article_processing_charge":"No"},{"has_accepted_license":"1","intvolume":"        24","title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","year":"2017","publist_id":"7304","abstract":[{"text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.","lang":"eng"}],"month":"10","file":[{"content_type":"application/pdf","checksum":"9bc7e8c41b43636dd7566289e511f096","file_size":4118385,"date_created":"2019-11-07T12:51:07Z","relation":"main_file","creator":"lsazanov","date_updated":"2020-07-14T12:46:36Z","file_name":"29893_2_merged_1501257589_red.pdf","file_id":"6993","access_level":"open_access"}],"date_updated":"2025-09-18T09:47:41Z","publication":"Nature Structural and Molecular Biology","issue":"10","article_processing_charge":"No","type":"journal_article","doi":"10.1038/nsmb.3460","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"LeSa"}],"date_published":"2017-10-05T00:00:00Z","publication_identifier":{"issn":["1545-9993"]},"external_id":{"isi":["000412278000006"]},"article_type":"original","publisher":"Nature Publishing Group","status":"public","author":[{"orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","last_name":"Letts","first_name":"James A","full_name":"Letts, James A"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"page":"800 - 808","quality_controlled":"1","isi":1,"citation":{"chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/nsmb.3460\">https://doi.org/10.1038/nsmb.3460</a>.","apa":"Letts, J. A., &#38; Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.3460\">https://doi.org/10.1038/nsmb.3460</a>","ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” <i>Nature Structural and Molecular Biology</i>, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808.","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” <i>Nature Structural and Molecular Biology</i>, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:<a href=\"https://doi.org/10.1038/nsmb.3460\">10.1038/nsmb.3460</a>.","ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. <i>Nature Structural and Molecular Biology</i>. 2017;24(10):800-808. doi:<a href=\"https://doi.org/10.1038/nsmb.3460\">10.1038/nsmb.3460</a>"},"scopus_import":"1","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Submitted Version","_id":"515","ec_funded":1,"ddc":["572"],"date_created":"2018-12-11T11:46:54Z","day":"05","volume":24,"project":[{"grant_number":"701309","call_identifier":"H2020","name":"Atomic Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1038/nsmb.3460"},{"article_processing_charge":"No","pmid":1,"type":"journal_article","issue":"3","date_updated":"2025-09-18T09:45:41Z","month":"03","publication":"ACS Synthetic Biology","title":"Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803","intvolume":"         6","year":"2017","publist_id":"7298","abstract":[{"text":"Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here.","lang":"eng"}],"volume":6,"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1021/acssynbio.6b00235","oa_version":"None","language":[{"iso":"eng"}],"scopus_import":"1","_id":"520","date_created":"2018-12-11T11:46:56Z","day":"17","publisher":"American Chemical Society","status":"public","author":[{"first_name":"Wei","full_name":"Du, Wei","last_name":"Du"},{"last_name":"Angermayr","id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","first_name":"Andreas"},{"first_name":"Joeri","full_name":"Jongbloets, Joeri","last_name":"Jongbloets"},{"last_name":"Molenaar","first_name":"Douwe","full_name":"Molenaar, Douwe"},{"last_name":"Bachmann","full_name":"Bachmann, Herwig","first_name":"Herwig"},{"full_name":"Hellingwerf, Klaas","first_name":"Klaas","last_name":"Hellingwerf"},{"full_name":"Branco Dos Santos, Filipe","first_name":"Filipe","last_name":"Branco Dos Santos"}],"page":"395 - 401","citation":{"ista":"Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401.","mla":"Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” <i>ACS Synthetic Biology</i>, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00235\">10.1021/acssynbio.6b00235</a>.","ama":"Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. <i>ACS Synthetic Biology</i>. 2017;6(3):395-401. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00235\">10.1021/acssynbio.6b00235</a>","apa":"Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., &#38; Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00235\">https://doi.org/10.1021/acssynbio.6b00235</a>","chicago":"Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acssynbio.6b00235\">https://doi.org/10.1021/acssynbio.6b00235</a>.","short":"W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.","ieee":"W. Du <i>et al.</i>, “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” <i>ACS Synthetic Biology</i>, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017."},"isi":1,"quality_controlled":"1","department":[{"_id":"ToBo"}],"doi":"10.1021/acssynbio.6b00235","publication_identifier":{"issn":["2161-5063"]},"external_id":{"pmid":["27936615"],"isi":["000397080300002"]},"date_published":"2017-03-17T00:00:00Z","article_type":"letter_note"},{"type":"journal_article","article_processing_charge":"No","publication":"Topology and its Applications","date_updated":"2025-09-18T09:47:04Z","arxiv":1,"month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.03954"}],"abstract":[{"text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension.","lang":"eng"}],"publist_id":"7299","year":"2017","intvolume":"       215","title":"Higson compactification and dimension raising","fulldoi":"https://doi.org/10.1016/j.topol.2016.10.005","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"publication_status":"published","volume":215,"day":"01","date_created":"2018-12-11T11:46:56Z","_id":"521","corr_author":"1","language":[{"iso":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","citation":{"mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” <i>Topology and Its Applications</i>, vol. 215, Elsevier, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1016/j.topol.2016.10.005\">10.1016/j.topol.2016.10.005</a>.","ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","ama":"Austin K, Virk Z. Higson compactification and dimension raising. <i>Topology and its Applications</i>. 2017;215:45-57. doi:<a href=\"https://doi.org/10.1016/j.topol.2016.10.005\">10.1016/j.topol.2016.10.005</a>","chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” <i>Topology and Its Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.topol.2016.10.005\">https://doi.org/10.1016/j.topol.2016.10.005</a>.","apa":"Austin, K., &#38; Virk, Z. (2017). Higson compactification and dimension raising. <i>Topology and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.topol.2016.10.005\">https://doi.org/10.1016/j.topol.2016.10.005</a>","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” <i>Topology and its Applications</i>, vol. 215. Elsevier, pp. 45–57, 2017.","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57."},"isi":1,"quality_controlled":"1","author":[{"last_name":"Austin","full_name":"Austin, Kyle","first_name":"Kyle"},{"first_name":"Ziga","full_name":"Virk, Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","last_name":"Virk"}],"page":"45 - 57","status":"public","publisher":"Elsevier","external_id":{"isi":["000390501400005"],"arxiv":["1608.03954"]},"publication_identifier":{"issn":["0166-8641"]},"date_published":"2017-01-01T00:00:00Z","department":[{"_id":"HeEd"}],"doi":"10.1016/j.topol.2016.10.005"},{"issue":"5","acknowledgement":"Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1 and BB/H020314/1\t","extern":"1","type":"journal_article","article_processing_charge":"No","year":"2017","publist_id":"7294","abstract":[{"text":"The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity. ","lang":"eng"}],"title":"Plant biology: Building barriers… in roots","intvolume":"        27","month":"03","file":[{"relation":"main_file","creator":"system","content_type":"application/pdf","checksum":"81fd4475c5a2a2c6f4313beeab215ed9","date_created":"2018-12-12T10:18:11Z","file_size":2840413,"access_level":"open_access","file_id":"5330","file_name":"IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf","date_updated":"2020-07-14T12:46:38Z"}],"date_updated":"2025-08-05T14:02:37Z","publication":"Current Biology","ddc":["580"],"date_created":"2018-12-11T11:46:58Z","day":"06","pubrep_id":"983","scopus_import":"1","oa_version":"None","language":[{"iso":"eng"}],"_id":"525","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1016/j.cub.2017.01.060","volume":27,"oa":1,"publication_status":"published","date_published":"2017-03-06T00:00:00Z","article_type":"original","file_date_updated":"2020-07-14T12:46:38Z","doi":"10.1016/j.cub.2017.01.060","author":[{"orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel","first_name":"Daniel"},{"first_name":"Tatsuaki","full_name":"Goh, Tatsuaki","last_name":"Goh"},{"last_name":"Dietrich","full_name":"Dietrich, Daniela","first_name":"Daniela"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"}],"page":"R172 - R174","quality_controlled":"1","citation":{"ista":"von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building barriers… in roots. Current Biology. 27(5), R172–R174.","mla":"von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.” <i>Current Biology</i>, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.01.060\">10.1016/j.cub.2017.01.060</a>.","ama":"von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers… in roots. <i>Current Biology</i>. 2017;27(5):R172-R174. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.01.060\">10.1016/j.cub.2017.01.060</a>","apa":"von Wangenheim, D., Goh, T., Dietrich, D., &#38; Bennett, M. (2017). Plant biology: Building barriers… in roots. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.01.060\">https://doi.org/10.1016/j.cub.2017.01.060</a>","chicago":"Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett. “Plant Biology: Building Barriers… in Roots.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.01.060\">https://doi.org/10.1016/j.cub.2017.01.060</a>.","short":"D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017) R172–R174.","ieee":"D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building barriers… in roots,” <i>Current Biology</i>, vol. 27, no. 5. Cell Press, pp. R172–R174, 2017."},"publisher":"Cell Press","status":"public"},{"pmid":1,"extern":"1","type":"journal_article","article_processing_charge":"No","acknowledgement":"This study was supported by startup funds from the Jefferson College of Pharmacy, and by the National Institutes of Health DA023204 (to M.E.A) and P30 DA 013429 to Center for Substance Abuse Research, Temple University.","month":"02","date_updated":"2025-08-05T13:58:42Z","publication":"Brain Research","year":"2017","publist_id":"7290","abstract":[{"text":"The pituitary adenylyl cyclase-activating polypeptide (PACAP) and its G protein-coupled receptors, PAC1, VPAC1 and VPAC2 form a system involved in a variety of biological processes. Although some sympathetic stimulatory effects of this system have been reported, its central cardiovascular regulatory properties are poorly characterized. VPAC1 receptors are expressed in the nucleus ambiguus (nAmb), a key center controlling cardiac parasympathetic tone. In this study, we report that selective VPAC1 activation in rhodamine-labeled cardiac vagal preganglionic neurons of the rat nAmb produces inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization, membrane depolarization and activation of P/Q-type Ca2+ channels. In vivo, this pathway converges onto transient reduction in heart rate of conscious rats. Therefore we demonstrate a VPAC1-dependent mechanism in the central parasympathetic regulation of the heart rate, adding to the complexity of PACAP-mediated cardiovascular modulation.","lang":"eng"}],"title":"Effects of VPAC1 activation in nucleus ambiguus neurons","intvolume":"      1657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1016/j.brainres.2016.12.026","volume":1657,"publication_status":"published","date_created":"2018-12-11T11:46:59Z","day":"15","scopus_import":"1","oa_version":"None","language":[{"iso":"eng"}],"_id":"529","page":"297 - 303","author":[{"last_name":"Gherghina","first_name":"Florin","full_name":"Gherghina, Florin"},{"last_name":"Tica","first_name":"Andrei","full_name":"Tica, Andrei"},{"full_name":"Deliu, Elena","first_name":"Elena","orcid":"0000-0002-7370-5293","last_name":"Deliu","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abood, Mary","first_name":"Mary","last_name":"Abood"},{"last_name":"Brailoiu","first_name":"G.","full_name":"Brailoiu, G."},{"last_name":"Brǎiloiu","first_name":"Eugen","full_name":"Brǎiloiu, Eugen"}],"quality_controlled":"1","citation":{"chicago":"Gherghina, Florin, Andrei Tica, Elena Deliu, Mary Abood, G. Brailoiu, and Eugen Brǎiloiu. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” <i>Brain Research</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.brainres.2016.12.026\">https://doi.org/10.1016/j.brainres.2016.12.026</a>.","apa":"Gherghina, F., Tica, A., Deliu, E., Abood, M., Brailoiu, G., &#38; Brǎiloiu, E. (2017). Effects of VPAC1 activation in nucleus ambiguus neurons. <i>Brain Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.brainres.2016.12.026\">https://doi.org/10.1016/j.brainres.2016.12.026</a>","ieee":"F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, and E. Brǎiloiu, “Effects of VPAC1 activation in nucleus ambiguus neurons,” <i>Brain Research</i>, vol. 1657. Elsevier, pp. 297–303, 2017.","short":"F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, E. Brǎiloiu, Brain Research 1657 (2017) 297–303.","mla":"Gherghina, Florin, et al. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” <i>Brain Research</i>, vol. 1657, Elsevier, 2017, pp. 297–303, doi:<a href=\"https://doi.org/10.1016/j.brainres.2016.12.026\">10.1016/j.brainres.2016.12.026</a>.","ista":"Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. 2017. Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 1657, 297–303.","ama":"Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. Effects of VPAC1 activation in nucleus ambiguus neurons. <i>Brain Research</i>. 2017;1657:297-303. doi:<a href=\"https://doi.org/10.1016/j.brainres.2016.12.026\">10.1016/j.brainres.2016.12.026</a>"},"publisher":"Elsevier","status":"public","date_published":"2017-02-15T00:00:00Z","external_id":{"pmid":["28043808"]},"article_type":"original","doi":"10.1016/j.brainres.2016.12.026"},{"article_processing_charge":"No","type":"journal_article","issue":"4","publication":"Discrete & Computational Geometry","month":"06","arxiv":1,"date_updated":"2025-09-18T09:45:02Z","intvolume":"        58","title":"Finding non-orientable surfaces in 3-Manifolds","related_material":{"record":[{"id":"1379","relation":"earlier_version","status":"public"}]},"abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.07907"}],"publist_id":"7283","year":"2017","oa":1,"publication_status":"published","volume":58,"fulldoi":"https://doi.org/10.1007/s00454-017-9900-0","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"534","scopus_import":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","corr_author":"1","date_created":"2018-12-11T11:47:01Z","day":"09","status":"public","publisher":"Springer","quality_controlled":"1","citation":{"ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. <i>Discrete &#38; Computational Geometry</i>. 2017;58(4):871-888. doi:<a href=\"https://doi.org/10.1007/s00454-017-9900-0\">10.1007/s00454-017-9900-0</a>","ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete &#38; Computational Geometry. 58(4), 871–888.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” <i>Discrete &#38; Computational Geometry</i>, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:<a href=\"https://doi.org/10.1007/s00454-017-9900-0\">10.1007/s00454-017-9900-0</a>.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete &#38; Computational Geometry 58 (2017) 871–888.","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” <i>Discrete &#38; Computational Geometry</i>, vol. 58, no. 4. Springer, pp. 871–888, 2017.","apa":"Burton, B., de Mesmay, A. N., &#38; Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-017-9900-0\">https://doi.org/10.1007/s00454-017-9900-0</a>","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-017-9900-0\">https://doi.org/10.1007/s00454-017-9900-0</a>."},"isi":1,"page":"871 - 888","author":[{"last_name":"Burton","full_name":"Burton, Benjamin","first_name":"Benjamin"},{"first_name":"Arnaud N","full_name":"De Mesmay, Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli"}],"doi":"10.1007/s00454-017-9900-0","department":[{"_id":"UlWa"}],"article_type":"original","date_published":"2017-06-09T00:00:00Z","publication_identifier":{"issn":["01795376"]},"external_id":{"arxiv":["1602.07907"],"isi":["000413958900006"]}},{"date_published":"2017-05-20T00:00:00Z","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"doi":"10.1002/ange.201611998","file_date_updated":"2020-07-14T12:46:39Z","page":"4679 - 4682","author":[{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie"},{"last_name":"Stadler","first_name":"Manuela","full_name":"Stadler, Manuela"},{"orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva"},{"last_name":"Distel","first_name":"Martin","full_name":"Distel, Martin"},{"last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L"}],"citation":{"ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” <i>Angewandte Chemie</i>, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” <i>Angewandte Chemie</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/ange.201611998\">https://doi.org/10.1002/ange.201611998</a>.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., &#38; Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.201611998\">https://doi.org/10.1002/ange.201611998</a>","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. <i>Angewandte Chemie</i>. 2017;129(16):4679-4682. doi:<a href=\"https://doi.org/10.1002/ange.201611998\">10.1002/ange.201611998</a>","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” <i>Angewandte Chemie</i>, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:<a href=\"https://doi.org/10.1002/ange.201611998\">10.1002/ange.201611998</a>.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682."},"quality_controlled":"1","publisher":"Wiley","status":"public","ddc":["571"],"ec_funded":1,"day":"20","date_created":"2018-12-11T11:47:02Z","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Published Version","pubrep_id":"932","_id":"538","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1002/ange.201611998","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":129,"project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303564"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24"}],"publication_status":"published","oa":1,"publist_id":"7279","year":"2017","abstract":[{"lang":"ger","text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. "}],"title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","intvolume":"       129","has_accepted_license":"1","date_updated":"2024-10-09T20:58:07Z","file":[{"file_size":1668557,"date_created":"2018-12-12T10:13:24Z","content_type":"application/pdf","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:46:39Z","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","file_id":"5007","access_level":"open_access"}],"month":"05","publication":"Angewandte Chemie","issue":"16","type":"journal_article"},{"article_processing_charge":"No","type":"journal_article","article_number":"e1006758","issue":"12","date_updated":"2025-09-18T09:43:05Z","month":"12","file":[{"date_updated":"2020-07-14T12:46:44Z","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","file_id":"4944","access_level":"open_access","content_type":"application/pdf","checksum":"1aa20f19a1e90664fadce6e7d5284fdc","file_size":4106772,"date_created":"2018-12-12T10:12:26Z","relation":"main_file","creator":"system"}],"publication":"PLoS Pathogens","title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","intvolume":"        13","has_accepted_license":"1","publist_id":"7276","year":"2017","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13,"publication_status":"published","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1371/journal.ppat.1006758","oa_version":"Published Version","language":[{"iso":"eng"}],"scopus_import":"1","pubrep_id":"931","_id":"540","ddc":["576","616"],"date_created":"2018-12-11T11:47:03Z","day":"01","publisher":"Public Library of Science","status":"public","author":[{"last_name":"Khamina","full_name":"Khamina, Kseniya","first_name":"Kseniya"},{"last_name":"Lercher","first_name":"Alexander","full_name":"Lercher, Alexander"},{"full_name":"Caldera, Michael","first_name":"Michael","last_name":"Caldera"},{"full_name":"Schliehe, Christopher","first_name":"Christopher","last_name":"Schliehe"},{"last_name":"Vilagos","full_name":"Vilagos, Bojan","first_name":"Bojan"},{"last_name":"Sahin","full_name":"Sahin, Mehmet","first_name":"Mehmet"},{"last_name":"Kosack","first_name":"Lindsay","full_name":"Kosack, Lindsay"},{"first_name":"Anannya","full_name":"Bhattacharya, Anannya","last_name":"Bhattacharya"},{"last_name":"Májek","first_name":"Peter","full_name":"Májek, Peter"},{"last_name":"Stukalov","full_name":"Stukalov, Alexey","first_name":"Alexey"},{"first_name":"Roberto","full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","last_name":"Sacco"},{"full_name":"James, Leo","first_name":"Leo","last_name":"James"},{"full_name":"Pinschewer, Daniel","first_name":"Daniel","last_name":"Pinschewer"},{"first_name":"Keiryn","full_name":"Bennett, Keiryn","last_name":"Bennett"},{"last_name":"Menche","first_name":"Jörg","full_name":"Menche, Jörg"},{"last_name":"Bergthaler","full_name":"Bergthaler, Andreas","first_name":"Andreas"}],"isi":1,"citation":{"ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” <i>PLoS Pathogens</i>, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1006758\">10.1371/journal.ppat.1006758</a>.","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. <i>PLoS Pathogens</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1006758\">10.1371/journal.ppat.1006758</a>","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1006758\">https://doi.org/10.1371/journal.ppat.1006758</a>","chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” <i>PLoS Pathogens</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.ppat.1006758\">https://doi.org/10.1371/journal.ppat.1006758</a>.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","ieee":"K. Khamina <i>et al.</i>, “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” <i>PLoS Pathogens</i>, vol. 13, no. 12. Public Library of Science, 2017."},"quality_controlled":"1","department":[{"_id":"GaNo"}],"doi":"10.1371/journal.ppat.1006758","file_date_updated":"2020-07-14T12:46:44Z","external_id":{"isi":["000419019800019"]},"publication_identifier":{"issn":["1553-7366"]},"date_published":"2017-12-01T00:00:00Z"},{"abstract":[{"text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed.","lang":"eng"}],"year":"2017","publist_id":"7275","intvolume":"        13","title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","has_accepted_license":"1","related_material":{"record":[{"id":"9844","status":"public","relation":"research_data"},{"id":"9845","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9846"}]},"publication":"PLoS Genetics","date_updated":"2025-09-18T09:42:09Z","month":"12","file":[{"date_updated":"2020-07-14T12:46:46Z","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","file_id":"5088","access_level":"open_access","file_size":1308475,"date_created":"2018-12-12T10:14:35Z","content_type":"application/pdf","checksum":"22426d9382f21554bad5fa5967afcfd0","creator":"system","relation":"main_file"}],"issue":"12","article_number":"e1007122","type":"journal_article","article_processing_charge":"No","publication_identifier":{"issn":["1553-7390"]},"external_id":{"isi":["000419103000015"]},"date_published":"2017-12-18T00:00:00Z","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:46Z","doi":"10.1371/journal.pgen.1007122","citation":{"mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” <i>PLoS Genetics</i>, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122\">10.1371/journal.pgen.1007122</a>.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. <i>PLoS Genetics</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122\">10.1371/journal.pgen.1007122</a>","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122\">https://doi.org/10.1371/journal.pgen.1007122</a>.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122\">https://doi.org/10.1371/journal.pgen.1007122</a>","ieee":"N. Nikolic <i>et al.</i>, “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” <i>PLoS Genetics</i>, vol. 13, no. 12. Public Library of Science, 2017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017)."},"isi":1,"quality_controlled":"1","author":[{"full_name":"Nikolic, Nela","first_name":"Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schreiber","first_name":"Frank","full_name":"Schreiber, Frank"},{"last_name":"Dal Co","first_name":"Alma","full_name":"Dal Co, Alma"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias"},{"last_name":"Littmann","first_name":"Sten","full_name":"Littmann, Sten"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"last_name":"Ackermann","full_name":"Ackermann, Martin","first_name":"Martin"}],"status":"public","publisher":"Public Library of Science","date_created":"2018-12-11T11:47:04Z","day":"18","ddc":["576","579"],"ec_funded":1,"_id":"541","corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"scopus_import":"1","pubrep_id":"959","fulldoi":"https://doi.org/10.1371/journal.pgen.1007122","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"publication_status":"published","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13},{"type":"book_chapter","article_processing_charge":"No","publist_id":"7269","year":"2017","series_title":"Plant Engineering","abstract":[{"text":"Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis.","lang":"eng"}],"editor":[{"first_name":"Snježana","full_name":"Jurić, Snježana","last_name":"Jurić"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1274"}]},"has_accepted_license":"1","title":"Vascular tissue development and regeneration in the model plant arabidopsis","month":"11","file":[{"relation":"main_file","creator":"system","content_type":"application/pdf","checksum":"e1f05e5850dfd9f9434d2d373ca61941","date_created":"2018-12-12T10:12:49Z","file_size":7443683,"access_level":"open_access","file_id":"4969","file_name":"IST-2018-929-v1+1_56106.pdf","date_updated":"2020-07-14T12:46:58Z"}],"date_updated":"2025-09-22T08:43:49Z","alternative_title":["Agricultural and Biological Sciences"],"publication":"Plant Engineering","ec_funded":1,"ddc":["581"],"date_created":"2018-12-11T11:47:05Z","day":"17","pubrep_id":"929","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"545","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.5772/intechopen.69712","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"publication_status":"published","date_published":"2017-11-17T00:00:00Z","doi":"10.5772/intechopen.69712","file_date_updated":"2020-07-14T12:46:58Z","department":[{"_id":"JiFr"}],"author":[{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"page":"113 - 140","quality_controlled":"1","citation":{"mla":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” <i>Plant Engineering</i>, edited by Snježana Jurić, IntechOpen, 2017, pp. 113–40, doi:<a href=\"https://doi.org/10.5772/intechopen.69712\">10.5772/intechopen.69712</a>.","ista":"Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences, , 113–140.","ama":"Mazur E, Friml J. Vascular tissue development and regeneration in the model plant arabidopsis. In: Jurić S, ed. <i>Plant Engineering</i>. Plant Engineering. IntechOpen; 2017:113-140. doi:<a href=\"https://doi.org/10.5772/intechopen.69712\">10.5772/intechopen.69712</a>","chicago":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” In <i>Plant Engineering</i>, edited by Snježana Jurić, 113–40. Plant Engineering. IntechOpen, 2017. <a href=\"https://doi.org/10.5772/intechopen.69712\">https://doi.org/10.5772/intechopen.69712</a>.","apa":"Mazur, E., &#38; Friml, J. (2017). Vascular tissue development and regeneration in the model plant arabidopsis. In S. Jurić (Ed.), <i>Plant Engineering</i> (pp. 113–140). IntechOpen. <a href=\"https://doi.org/10.5772/intechopen.69712\">https://doi.org/10.5772/intechopen.69712</a>","ieee":"E. Mazur and J. Friml, “Vascular tissue development and regeneration in the model plant arabidopsis,” in <i>Plant Engineering</i>, S. Jurić, Ed. IntechOpen, 2017, pp. 113–140.","short":"E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, IntechOpen, 2017, pp. 113–140."},"publisher":"IntechOpen","status":"public"},{"publication_status":"published","oa":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"gold","type":"report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5450","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Published Version","pubrep_id":"724","date_created":"2018-12-12T11:39:24Z","day":"26","ddc":["020"],"status":"public","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Petritsch B. <i>Implementing the Institutional Data Repository IST DataRep</i>. Institute of Science and Technology Austria; 2017.","mla":"Petritsch, Barbara. <i>Implementing the Institutional Data Repository IST DataRep</i>. Institute of Science and Technology Austria, 2017.","ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, Institute of Science and Technology Austria,p.","ieee":"B. Petritsch, <i>Implementing the institutional data repository IST DataRep</i>. Institute of Science and Technology Austria, 2017.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, Institute of Science and Technology Austria, 2017.","chicago":"Petritsch, Barbara. <i>Implementing the Institutional Data Repository IST DataRep</i>. Institute of Science and Technology Austria, 2017.","apa":"Petritsch, B. (2017). <i>Implementing the institutional data repository IST DataRep</i>. Institute of Science and Technology Austria."},"date_updated":"2025-07-10T11:52:50Z","OA_place":"publisher","author":[{"first_name":"Barbara","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch"}],"month":"06","file":[{"date_updated":"2020-07-14T12:46:59Z","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","file_id":"5483","access_level":"open_access","file_size":3460985,"date_created":"2018-12-12T11:53:22Z","checksum":"6321792dcfa82bf490f17615a9b22355","content_type":"application/pdf","creator":"system","relation":"main_file"}],"title":"Implementing the institutional data repository IST DataRep","has_accepted_license":"1","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:46:59Z","abstract":[{"text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.","lang":"eng"}],"year":"2017","date_published":"2017-06-26T00:00:00Z"},{"file_date_updated":"2020-07-14T12:46:59Z","doi":"10.15479/AT:IST-2017-870-v1-1","department":[{"_id":"KrCh"}],"date_published":"2017-10-23T00:00:00Z","publication_identifier":{"issn":["2664-1690"]},"status":"public","publisher":"IST Austria","citation":{"short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017.","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, <i>Optimal Dyck reachability for data-dependence and alias analysis</i>. IST Austria, 2017.","apa":"Chatterjee, K., Choudhary, B., &#38; Pavlogiannis, A. (2017). <i>Optimal Dyck reachability for data-dependence and alias analysis</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-870-v1-1\">https://doi.org/10.15479/AT:IST-2017-870-v1-1</a>","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. <i>Optimal Dyck Reachability for Data-Dependence and Alias Analysis</i>. IST Austria, 2017. <a href=\"https://doi.org/10.15479/AT:IST-2017-870-v1-1\">https://doi.org/10.15479/AT:IST-2017-870-v1-1</a>.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. <i>Optimal Dyck Reachability for Data-Dependence and Alias Analysis</i>. IST Austria; 2017. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-870-v1-1\">10.15479/AT:IST-2017-870-v1-1</a>","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p.","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Dyck Reachability for Data-Dependence and Alias Analysis</i>. IST Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-870-v1-1\">10.15479/AT:IST-2017-870-v1-1</a>."},"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Choudhary","full_name":"Choudhary, Bhavya","first_name":"Bhavya"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas"}],"page":"37","_id":"5455","pubrep_id":"870","oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2018-12-12T11:39:26Z","day":"23","ddc":["000"],"publication_status":"published","oa":1,"fulldoi":"https://doi.org/10.15479/AT:IST-2017-870-v1-1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","title":"Optimal Dyck reachability for data-dependence and alias analysis","related_material":{"record":[{"status":"public","relation":"later_version","id":"10416"}]},"abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks."}],"year":"2017","month":"10","file":[{"file_size":960491,"date_created":"2018-12-12T11:54:02Z","content_type":"application/pdf","checksum":"177a84a46e3ac17e87b31534ad16a4c9","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:46:59Z","file_name":"IST-2017-870-v1+1_main.pdf","file_id":"5524","access_level":"open_access"}],"alternative_title":["IST Austria Technical Report"],"date_updated":"2025-04-15T08:12:18Z","article_processing_charge":"No","type":"technical_report"},{"alternative_title":["IST Austria Technical Report"],"date_updated":"2025-05-20T09:45:08Z","month":"10","file":[{"date_updated":"2020-07-14T12:46:59Z","file_name":"IST-2017-872-v1+1_main.pdf","file_id":"5487","access_level":"open_access","checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","content_type":"application/pdf","file_size":910347,"date_created":"2018-12-12T11:53:26Z","relation":"main_file","creator":"system"}],"abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.","lang":"eng"}],"year":"2017","title":"Data-centric dynamic partial order reduction","has_accepted_license":"1","related_material":{"record":[{"id":"5448","status":"public","relation":"earlier_version"},{"status":"public","relation":"later_version","id":"10417"}]},"type":"technical_report","citation":{"ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p.","mla":"Chalupa, Marek, et al. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">10.15479/AT:IST-2017-872-v1-1</a>.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria; 2017. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">10.15479/AT:IST-2017-872-v1-1</a>","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., &#38; Vaidya, K. (2017). <i>Data-centric dynamic partial order reduction</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">https://doi.org/10.15479/AT:IST-2017-872-v1-1</a>","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2017. <a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">https://doi.org/10.15479/AT:IST-2017-872-v1-1</a>.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, <i>Data-centric dynamic partial order reduction</i>. IST Austria, 2017."},"page":"36","author":[{"full_name":"Chalupa, Marek","first_name":"Marek","last_name":"Chalupa"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"full_name":"Sinha, Nishant","first_name":"Nishant","last_name":"Sinha"},{"first_name":"Kapil","full_name":"Vaidya, Kapil","last_name":"Vaidya"}],"status":"public","publisher":"IST Austria","publication_identifier":{"issn":["2664-1690"]},"date_published":"2017-10-23T00:00:00Z","department":[{"_id":"KrCh"}],"doi":"10.15479/AT:IST-2017-872-v1-1","file_date_updated":"2020-07-14T12:46:59Z","fulldoi":"https://doi.org/10.15479/AT:IST-2017-872-v1-1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"date_created":"2018-12-12T11:39:26Z","day":"23","ddc":["000"],"_id":"5456","language":[{"iso":"eng"}],"oa_version":"Published Version","pubrep_id":"872"},{"status":"public","publisher":"American Physical Society","isi":1,"citation":{"ama":"De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. 2017;96(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>","ista":"De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.","mla":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>.","short":"D. De Martino, Physical Review E 96 (2017).","ieee":"D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” <i>Physical Review E</i>, vol. 96, no. 6. American Physical Society, 2017.","apa":"De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>","chicago":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>."},"quality_controlled":"1","author":[{"last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele"}],"department":[{"_id":"GaTk"}],"doi":"10.1103/PhysRevE.96.060401","external_id":{"isi":["000418574400001"],"arxiv":["1707.00320"]},"publication_identifier":{"issn":["2470-0045"]},"date_published":"2017-12-21T00:00:00Z","publication_status":"published","oa":1,"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"volume":96,"fulldoi":"https://doi.org/10.1103/PhysRevE.96.060401","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"548","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Submitted Version","scopus_import":"1","date_created":"2018-12-11T11:47:06Z","day":"21","ec_funded":1,"publication":"Physical Review E","alternative_title":["Rapid Communications"],"date_updated":"2025-09-18T09:41:11Z","arxiv":1,"month":"12","title":"Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes","intvolume":"        96","main_file_link":[{"url":"https://arxiv.org/abs/1707.00320","open_access":"1"}],"abstract":[{"lang":"eng","text":"In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region."}],"publist_id":"7266","year":"2017","article_processing_charge":"No","type":"journal_article","article_number":"060401","issue":"6"},{"_id":"549","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Submitted Version","scopus_import":"1","pubrep_id":"925","day":"10","date_created":"2018-12-11T11:47:07Z","ddc":["004"],"oa":1,"publication_status":"published","conference":{"end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-29","name":"CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies"},"project":[{"grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"volume":259,"fulldoi":"https://doi.org/10.4204/EPTCS.259.3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:00Z","doi":"10.4204/EPTCS.259.3","external_id":{"isi":["000439358700004"],"arxiv":["1710.03391"]},"publication_identifier":{"issn":["2075-2180"]},"date_published":"2017-10-10T00:00:00Z","status":"public","publisher":"Open Publishing Association","citation":{"ama":"Finkbeiner B, Kupriyanov A. Causality-based model checking. In: <i>Electronic Proceedings in Theoretical Computer Science</i>. Vol 259. Open Publishing Association; 2017:31-38. doi:<a href=\"https://doi.org/10.4204/EPTCS.259.3\">10.4204/EPTCS.259.3</a>","mla":"Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” <i>Electronic Proceedings in Theoretical Computer Science</i>, vol. 259, Open Publishing Association, 2017, pp. 31–38, doi:<a href=\"https://doi.org/10.4204/EPTCS.259.3\">10.4204/EPTCS.259.3</a>.","ista":"Finkbeiner B, Kupriyanov A. 2017. Causality-based model checking. Electronic Proceedings in Theoretical Computer Science. CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies, EPTCS, vol. 259, 31–38.","ieee":"B. Finkbeiner and A. Kupriyanov, “Causality-based model checking,” in <i>Electronic Proceedings in Theoretical Computer Science</i>, Uppsala, Sweden, 2017, vol. 259, pp. 31–38.","short":"B. Finkbeiner, A. Kupriyanov, in:, Electronic Proceedings in Theoretical Computer Science, Open Publishing Association, 2017, pp. 31–38.","chicago":"Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” In <i>Electronic Proceedings in Theoretical Computer Science</i>, 259:31–38. Open Publishing Association, 2017. <a href=\"https://doi.org/10.4204/EPTCS.259.3\">https://doi.org/10.4204/EPTCS.259.3</a>.","apa":"Finkbeiner, B., &#38; Kupriyanov, A. (2017). Causality-based model checking. In <i>Electronic Proceedings in Theoretical Computer Science</i> (Vol. 259, pp. 31–38). Uppsala, Sweden: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.259.3\">https://doi.org/10.4204/EPTCS.259.3</a>"},"isi":1,"quality_controlled":"1","author":[{"full_name":"Finkbeiner, Bernd","first_name":"Bernd","last_name":"Finkbeiner"},{"first_name":"Andrey","full_name":"Kupriyanov, Andrey","id":"2C311BF8-F248-11E8-B48F-1D18A9856A87","last_name":"Kupriyanov"}],"page":"31 - 38","article_processing_charge":"No","type":"conference","intvolume":"       259","title":"Causality-based model checking","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a new class of model checking algorithms that capture the causal relationships in a special data structure called concurrent traces. Concurrent traces identify key events in an execution history and link them through their cause-effect relationships. The model checker builds a tableau of concurrent traces, where the case splits represent different causal explanations of a hypothetical error. Causality-based model checking has been implemented in the ARCTOR tool, and applied to previously intractable multi-threaded benchmarks."}],"main_file_link":[{"url":"https://arxiv.org/abs/1710.03391","open_access":"1"}],"year":"2017","publist_id":"7264","publication":"Electronic Proceedings in Theoretical Computer Science","date_updated":"2025-09-18T09:38:35Z","alternative_title":["EPTCS"],"arxiv":1,"month":"10","file":[{"file_id":"4939","access_level":"open_access","date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2018-925-v1+1_1710.03391v1.pdf","relation":"main_file","creator":"system","content_type":"application/pdf","checksum":"6274f6c0da3376a7b079180d81568518","file_size":209294,"date_created":"2018-12-12T10:12:21Z"}]},{"date_updated":"2026-04-08T14:11:36Z","month":"11","file":[{"file_id":"4663","access_level":"open_access","date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2018-926-v1+1_euclid.ecp.1511233247.pdf","relation":"main_file","creator":"system","checksum":"0ec05303a0de190de145654237984c79","content_type":"application/pdf","file_size":470876,"date_created":"2018-12-12T10:08:04Z"}],"publication":"Electronic Communications in Probability","publist_id":"7265","year":"2017","abstract":[{"text":"For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"intvolume":"        22","title":"Singularities of the density of states of random Gram matrices","has_accepted_license":"1","type":"journal_article","article_processing_charge":"No","article_number":"63","author":[{"full_name":"Alt, Johannes","first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Alt J. Singularities of the density of states of random Gram matrices. <i>Electronic Communications in Probability</i>. 2017;22. doi:<a href=\"https://doi.org/10.1214/17-ECP97\">10.1214/17-ECP97</a>","ista":"Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63.","mla":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” <i>Electronic Communications in Probability</i>, vol. 22, 63, Institute of Mathematical Statistics, 2017, doi:<a href=\"https://doi.org/10.1214/17-ECP97\">10.1214/17-ECP97</a>.","short":"J. Alt, Electronic Communications in Probability 22 (2017).","ieee":"J. Alt, “Singularities of the density of states of random Gram matrices,” <i>Electronic Communications in Probability</i>, vol. 22. Institute of Mathematical Statistics, 2017.","apa":"Alt, J. (2017). Singularities of the density of states of random Gram matrices. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/17-ECP97\">https://doi.org/10.1214/17-ECP97</a>","chicago":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2017. <a href=\"https://doi.org/10.1214/17-ECP97\">https://doi.org/10.1214/17-ECP97</a>."},"isi":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","status":"public","external_id":{"isi":["000416389200001"]},"publication_identifier":{"issn":["1083-589X"]},"date_published":"2017-11-21T00:00:00Z","department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:47:00Z","doi":"10.1214/17-ECP97","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1214/17-ECP97","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":22,"publication_status":"published","oa":1,"ec_funded":1,"ddc":["539"],"date_created":"2018-12-11T11:47:07Z","day":"21","language":[{"iso":"eng"}],"oa_version":"Published Version","corr_author":"1","pubrep_id":"926","scopus_import":"1","_id":"550"},{"status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in <i>Leibniz International Proceedings in Informatics</i>, Aalborg, Denmark, 2017, vol. 83.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">https://doi.org/10.4230/LIPIcs.MFCS.2017.61</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">https://doi.org/10.4230/LIPIcs.MFCS.2017.61</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">10.4230/LIPIcs.MFCS.2017.61</a>","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 61.","mla":"Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” <i>Leibniz International Proceedings in Informatics</i>, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">10.4230/LIPIcs.MFCS.2017.61</a>."},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"file_date_updated":"2020-07-14T12:47:00Z","doi":"10.4230/LIPIcs.MFCS.2017.61","department":[{"_id":"KrCh"}],"date_published":"2017-11-01T00:00:00Z","publication_identifier":{"isbn":["978-395977046-0"]},"oa":1,"publication_status":"published","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"conference":{"end_date":"2017-08-25","location":"Aalborg, Denmark","start_date":"2017-08-21","name":"MFCS: Mathematical Foundations of Computer Science"},"volume":83,"fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2017.61","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"551","pubrep_id":"924","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"corr_author":"1","day":"01","date_created":"2018-12-11T11:47:08Z","ddc":["004"],"publication":"Leibniz International Proceedings in Informatics","month":"11","file":[{"creator":"system","relation":"main_file","file_size":535077,"date_created":"2018-12-12T10:18:04Z","content_type":"application/pdf","checksum":"2eed5224c0e4e259484a1d71acb8ba6a","file_id":"5322","access_level":"open_access","date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf"}],"alternative_title":["LIPIcs"],"date_updated":"2025-07-10T11:52:51Z","has_accepted_license":"1","title":"Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs","intvolume":"        83","abstract":[{"lang":"eng","text":"Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. "}],"publist_id":"7263","year":"2017","article_processing_charge":"No","type":"conference","article_number":"61"}]