[{"ec_funded":1,"quality_controlled":"1","file_date_updated":"2018-12-12T10:15:15Z","publisher":"Nature Publishing Group","_id":"1080","scopus_import":"1","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter","first_name":"Johannes"},{"full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore","first_name":"Alvin"},{"full_name":"Gerold, Jeffrey","first_name":"Jeffrey","last_name":"Gerold"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Iacobuzio Donahue","first_name":"Christine","full_name":"Iacobuzio Donahue, Christine"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"publication_status":"published","department":[{"_id":"KrCh"}],"article_processing_charge":"No","date_created":"2018-12-11T11:50:02Z","pubrep_id":"786","title":"Reconstructing metastatic seeding patterns of human cancers","intvolume":"         8","volume":8,"ddc":["004","006"],"date_updated":"2023-09-20T11:55:31Z","citation":{"mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>.","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>."},"year":"2017","isi":1,"external_id":{"isi":["000393096600001"]},"doi":"10.1038/ncomms14114","day":"31","abstract":[{"text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods.","lang":"eng"}],"language":[{"iso":"eng"}],"publication":"Nature Communications","has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"month":"01","article_number":"14114","file":[{"date_updated":"2018-12-12T10:15:15Z","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:15:15Z","file_size":897050,"file_id":"5133","creator":"system","access_level":"open_access","relation":"main_file"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2017-01-31T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["20411723"]},"oa":1,"publist_id":"6301"},{"citation":{"ama":"Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>","apa":"Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>","chicago":"Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>.","ieee":"A. Wright <i>et al.</i>, “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","short":"A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).","mla":"Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>, vol. 8, 14251, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>.","ista":"Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251."},"year":"2017","date_updated":"2023-09-20T11:48:16Z","external_id":{"isi":["000392953700001"]},"isi":1,"day":"31","doi":"10.1038/ncomms14251","abstract":[{"lang":"eng","text":"Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution."}],"volume":8,"ddc":["570","576"],"scopus_import":"1","_id":"1085","author":[{"first_name":"Alison","last_name":"Wright","full_name":"Wright, Alison"},{"first_name":"Iulia","last_name":"Darolti","full_name":"Darolti, Iulia"},{"first_name":"Natasha","last_name":"Bloch","full_name":"Bloch, Natasha"},{"full_name":"Oostra, Vicencio","last_name":"Oostra","first_name":"Vicencio"},{"last_name":"Sandkam","first_name":"Benjamin","full_name":"Sandkam, Benjamin"},{"last_name":"Buechel","first_name":"Séverine","full_name":"Buechel, Séverine"},{"first_name":"Niclas","last_name":"Kolm","full_name":"Kolm, Niclas"},{"full_name":"Breden, Felix","last_name":"Breden","first_name":"Felix"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mank","first_name":"Judith","full_name":"Mank, Judith"}],"department":[{"_id":"BeVi"}],"article_processing_charge":"No","date_created":"2018-12-11T11:50:04Z","publication_status":"published","intvolume":"         8","pubrep_id":"791","title":"Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation","quality_controlled":"1","file_date_updated":"2018-12-12T10:15:22Z","publisher":"Nature Publishing Group","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2017-01-31T00:00:00Z","publication_identifier":{"issn":["20411723"]},"oa":1,"publist_id":"6292","file":[{"date_created":"2018-12-12T10:15:22Z","file_size":955256,"date_updated":"2018-12-12T10:15:22Z","file_name":"IST-2017-791-v1+1_ncomms14251.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5141","creator":"system"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","publication":"Nature Communications","oa_version":"Published Version","article_number":"14251","month":"01","language":[{"iso":"eng"}]},{"volume":8,"ddc":["571"],"day":"06","doi":"10.1038/s41467-017-02159-y","abstract":[{"text":"In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems.","lang":"eng"}],"citation":{"mla":"Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” <i>Nature Communications</i>, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-02159-y\">10.1038/s41467-017-02159-y</a>.","short":"S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).","ista":"Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.","apa":"Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-02159-y\">https://doi.org/10.1038/s41467-017-02159-y</a>","ama":"Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-02159-y\">10.1038/s41467-017-02159-y</a>","chicago":"Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-02159-y\">https://doi.org/10.1038/s41467-017-02159-y</a>.","ieee":"S. Deny <i>et al.</i>, “Multiplexed computations in retinal ganglion cells of a single type,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017."},"year":"2017","date_updated":"2023-09-20T11:41:19Z","external_id":{"isi":["000417241200004"]},"isi":1,"publisher":"Nature Publishing Group","ec_funded":1,"quality_controlled":"1","file_date_updated":"2018-12-12T10:16:06Z","article_processing_charge":"No","date_created":"2018-12-11T11:50:10Z","department":[{"_id":"GaTk"}],"publication_status":"published","intvolume":"         8","pubrep_id":"921","title":"Multiplexed computations in retinal ganglion cells of a single type","scopus_import":"1","_id":"1104","issue":"1","author":[{"full_name":"Deny, Stephane","first_name":"Stephane","last_name":"Deny"},{"first_name":"Ulisse","last_name":"Ferrari","full_name":"Ferrari, Ulisse"},{"first_name":"Emilie","last_name":"Mace","full_name":"Mace, Emilie"},{"full_name":"Yger, Pierre","last_name":"Yger","first_name":"Pierre"},{"last_name":"Caplette","first_name":"Romain","full_name":"Caplette, Romain"},{"last_name":"Picaud","first_name":"Serge","full_name":"Picaud, Serge"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"}],"file":[{"file_name":"IST-2018-921-v1+1_s41467-017-02159-y.pdf","content_type":"application/pdf","date_updated":"2018-12-12T10:16:06Z","file_size":2872887,"date_created":"2018-12-12T10:16:06Z","creator":"system","file_id":"5191","access_level":"open_access","relation":"main_file"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["20411723"]},"oa":1,"publist_id":"6266","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2017-12-06T00:00:00Z","language":[{"iso":"eng"}],"project":[{"_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","grant_number":"604102"},{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes"}],"oa_version":"Published Version","article_number":"1964","month":"12","has_accepted_license":"1","publication":"Nature Communications"},{"article_number":"1304","month":"10","project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"publist_id":"6855","oa":1,"publication_identifier":{"issn":["20411723"]},"type":"journal_article","date_published":"2017-10-16T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"b68dafa71d1834c23b742cd9987a3d5f","file_size":1467696,"date_created":"2018-12-12T10:15:25Z","content_type":"application/pdf","file_name":"IST-2017-867-v1+1_s41467-017-01304-x.pdf","date_updated":"2020-07-14T12:48:06Z","access_level":"open_access","relation":"main_file","creator":"system","file_id":"5145"}],"intvolume":"         8","title":"Mechanical on chip microwave circulator","pubrep_id":"867","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"JoFi"}],"date_created":"2018-12-11T11:48:33Z","publication_status":"published","issue":"1","author":[{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"first_name":"Matthias","last_name":"Wulf","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kalaee, Mahmoud","last_name":"Kalaee","first_name":"Mahmoud"},{"first_name":"Paul","last_name":"Dieterle","full_name":"Dieterle, Paul"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"798","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:48:06Z","ec_funded":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout."}],"day":"16","doi":"10.1038/s41467-017-01304-x","external_id":{"isi":["000412999700021"]},"isi":1,"year":"2017","citation":{"ieee":"S. Barzanjeh <i>et al.</i>, “Mechanical on chip microwave circulator,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>.","ama":"Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>","apa":"Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., &#38; Fink, J. M. (2017). Mechanical on chip microwave circulator. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>","ista":"Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304.","mla":"Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>.","short":"S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017)."},"date_updated":"2023-09-27T12:11:28Z","ddc":["539"],"volume":8},{"intvolume":"         8","pubrep_id":"914","title":"Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus","article_processing_charge":"No","department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:48:34Z","publication_status":"published","issue":"1","author":[{"last_name":"Strüber","first_name":"Michael","full_name":"Strüber, Michael"},{"full_name":"Sauer, Jonas","last_name":"Sauer","first_name":"Jonas"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"},{"full_name":"Bartos, Marlene","last_name":"Bartos","first_name":"Marlene"}],"scopus_import":"1","_id":"800","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:48:07Z","quality_controlled":"1","ec_funded":1,"abstract":[{"text":"Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers.","lang":"eng"}],"day":"02","doi":"10.1038/s41467-017-00936-3","external_id":{"isi":["000412053100004"]},"isi":1,"year":"2017","citation":{"chicago":"Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>.","ieee":"M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ama":"Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>","apa":"Strüber, M., Sauer, J., Jonas, P. M., &#38; Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>","ista":"Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758.","short":"M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).","mla":"Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>."},"date_updated":"2023-09-27T10:59:41Z","ddc":["571"],"volume":8,"article_number":"758","month":"10","project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"publist_id":"6853","oa":1,"publication_identifier":{"issn":["20411723"]},"type":"journal_article","date_published":"2017-10-02T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","file":[{"access_level":"open_access","relation":"main_file","creator":"system","file_id":"5135","file_size":4261832,"checksum":"7e2c7621afd5f802338e92e8619f024d","date_created":"2018-12-12T10:15:17Z","content_type":"application/pdf","file_name":"IST-2017-914-v1+1_s41467-017-00936-3.pdf","date_updated":"2020-07-14T12:48:07Z"}]},{"date_updated":"2023-09-26T15:51:28Z","year":"2017","citation":{"ama":"Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15990\">10.1038/ncomms15990</a>","apa":"Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K., … Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15990\">https://doi.org/10.1038/ncomms15990</a>","chicago":"Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15990\">https://doi.org/10.1038/ncomms15990</a>.","ieee":"K. Makhijani <i>et al.</i>, “Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","mla":"Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” <i>Nature Communications</i>, vol. 8, 15990, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15990\">10.1038/ncomms15990</a>.","short":"K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I. Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications 8 (2017).","ista":"Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I, Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 8, 15990."},"isi":1,"external_id":{"isi":["000406360100001"]},"doi":"10.1038/ncomms15990","day":"27","abstract":[{"text":"An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined.","lang":"eng"}],"volume":8,"extern":"1","ddc":["570","576","616"],"_id":"835","author":[{"full_name":"Makhijani, Kalpana","first_name":"Kalpana","last_name":"Makhijani"},{"full_name":"Alexander, Brandy","last_name":"Alexander","first_name":"Brandy"},{"first_name":"Deepti","last_name":"Rao","full_name":"Rao, Deepti"},{"full_name":"Petraki, Sophia","first_name":"Sophia","last_name":"Petraki"},{"full_name":"Herboso, Leire","last_name":"Herboso","first_name":"Leire"},{"last_name":"Kukar","first_name":"Katelyn","full_name":"Kukar, Katelyn"},{"full_name":"Batool, Itrat","last_name":"Batool","first_name":"Itrat"},{"full_name":"Wachner, Stephanie","last_name":"Wachner","first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gold","first_name":"Katrina","full_name":"Gold, Katrina"},{"last_name":"Wong","first_name":"Corinna","full_name":"Wong, Corinna"},{"full_name":"O'Connor, Michael","last_name":"O'Connor","first_name":"Michael"},{"full_name":"Brückner, Katja","first_name":"Katja","last_name":"Brückner"}],"publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T11:48:45Z","title":"Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons","pubrep_id":"859","intvolume":"         8","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:12Z","publisher":"Nature Publishing Group","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2017-07-27T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["20411723"]},"publist_id":"6813","oa":1,"file":[{"file_size":3027104,"checksum":"99a3d63308d4250eda0a35341171f80e","date_created":"2018-12-12T10:15:32Z","content_type":"application/pdf","file_name":"IST-2017-859-v1+1_ncomms15990.pdf","date_updated":"2020-07-14T12:48:12Z","access_level":"open_access","relation":"main_file","creator":"system","file_id":"5153"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication":"Nature Communications","has_accepted_license":"1","oa_version":"Published Version","month":"07","article_number":"15990","language":[{"iso":"eng"}]},{"file_date_updated":"2020-07-14T12:47:58Z","quality_controlled":"1","publisher":"Nature Publishing Group","author":[{"full_name":"Aloisi, Elisabetta","last_name":"Aloisi","first_name":"Elisabetta"},{"full_name":"Le Corf, Katy","last_name":"Le Corf","first_name":"Katy"},{"last_name":"Dupuis","first_name":"Julien","full_name":"Dupuis, Julien"},{"last_name":"Zhang","first_name":"Pei","full_name":"Zhang, Pei"},{"full_name":"Ginger, Melanie","first_name":"Melanie","last_name":"Ginger"},{"last_name":"Labrousse","first_name":"Virginie","full_name":"Labrousse, Virginie"},{"last_name":"Spatuzza","first_name":"Michela","full_name":"Spatuzza, Michela"},{"full_name":"Georg Haberl, Matthias","last_name":"Georg Haberl","first_name":"Matthias"},{"full_name":"Costa, Lara","first_name":"Lara","last_name":"Costa"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Tappe Theodor, Anke","last_name":"Tappe Theodor","first_name":"Anke"},{"full_name":"Drago, Fillippo","first_name":"Fillippo","last_name":"Drago"},{"first_name":"Pier","last_name":"Vincenzo Piazza","full_name":"Vincenzo Piazza, Pier"},{"full_name":"Mulle, Christophe","last_name":"Mulle","first_name":"Christophe"},{"full_name":"Groc, Laurent","first_name":"Laurent","last_name":"Groc"},{"full_name":"Ciranna, Lucia","last_name":"Ciranna","first_name":"Lucia"},{"full_name":"Catania, Maria","first_name":"Maria","last_name":"Catania"},{"first_name":"Andreas","last_name":"Frick","full_name":"Frick, Andreas"}],"issue":"1","_id":"746","scopus_import":"1","pubrep_id":"915","title":"Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice","intvolume":"         8","publication_status":"published","article_processing_charge":"No","department":[{"_id":"RySh"}],"date_created":"2018-12-11T11:48:17Z","ddc":["571"],"volume":8,"isi":1,"external_id":{"isi":["000413571300004"]},"date_updated":"2023-09-27T12:27:30Z","citation":{"apa":"Aloisi, E., Le Corf, K., Dupuis, J., Zhang, P., Ginger, M., Labrousse, V., … Frick, A. (2017). Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01191-2\">https://doi.org/10.1038/s41467-017-01191-2</a>","ama":"Aloisi E, Le Corf K, Dupuis J, et al. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01191-2\">10.1038/s41467-017-01191-2</a>","chicago":"Aloisi, Elisabetta, Katy Le Corf, Julien Dupuis, Pei Zhang, Melanie Ginger, Virginie Labrousse, Michela Spatuzza, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01191-2\">https://doi.org/10.1038/s41467-017-01191-2</a>.","ieee":"E. Aloisi <i>et al.</i>, “Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Aloisi, Elisabetta, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” <i>Nature Communications</i>, vol. 8, no. 1, 1103, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01191-2\">10.1038/s41467-017-01191-2</a>.","short":"E. Aloisi, K. Le Corf, J. Dupuis, P. Zhang, M. Ginger, V. Labrousse, M. Spatuzza, M. Georg Haberl, L. Costa, R. Shigemoto, A. Tappe Theodor, F. Drago, P. Vincenzo Piazza, C. Mulle, L. Groc, L. Ciranna, M. Catania, A. Frick, Nature Communications 8 (2017).","ista":"Aloisi E, Le Corf K, Dupuis J, Zhang P, Ginger M, Labrousse V, Spatuzza M, Georg Haberl M, Costa L, Shigemoto R, Tappe Theodor A, Drago F, Vincenzo Piazza P, Mulle C, Groc L, Ciranna L, Catania M, Frick A. 2017. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 8(1), 1103."},"year":"2017","abstract":[{"lang":"eng","text":"Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics."}],"doi":"10.1038/s41467-017-01191-2","day":"01","language":[{"iso":"eng"}],"publication":"Nature Communications","has_accepted_license":"1","month":"12","article_number":"1103","oa_version":"Published Version","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"5287","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:58Z","content_type":"application/pdf","file_name":"IST-2017-915-v1+1_s41467-017-01191-2.pdf","date_created":"2018-12-12T10:17:32Z","checksum":"99ceee57549dc0461e3adfc037ec70a9","file_size":1841650}],"date_published":"2017-12-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publist_id":"6921","publication_identifier":{"issn":["20411723"]}},{"language":[{"iso":"eng"}],"month":"07","article_number":"16032","oa_version":"Published Version","publication":"Nature Communications","has_accepted_license":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:14:31Z","checksum":"76d8a2b72a58e56adb410ec37dfa7eee","file_size":2948357,"date_updated":"2020-07-14T12:46:36Z","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5083","creator":"system"}],"publist_id":"7305","oa":1,"publication_identifier":{"issn":["20411723"]},"date_published":"2017-07-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:46:36Z","quality_controlled":"1","title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","pubrep_id":"937","intvolume":"         8","publication_status":"published","date_created":"2018-12-11T11:46:54Z","department":[{"_id":"JoCs"}],"author":[{"full_name":"Simonnet, Jean","first_name":"Jean","last_name":"Simonnet"},{"full_name":"Nassar, Mérie","first_name":"Mérie","last_name":"Nassar"},{"last_name":"Stella","first_name":"Federico","full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cohen, Ivan","last_name":"Cohen","first_name":"Ivan"},{"full_name":"Mathon, Bertrand","first_name":"Bertrand","last_name":"Mathon"},{"id":"3FC06552-F248-11E8-B48F-1D18A9856A87","first_name":"Charlotte","last_name":"Boccara","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte"},{"last_name":"Miles","first_name":"Richard","full_name":"Miles, Richard"},{"full_name":"Fricker, Desdemona","last_name":"Fricker","first_name":"Desdemona"}],"_id":"514","scopus_import":1,"ddc":["571"],"volume":8,"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."}],"doi":"10.1038/ncomms16032","day":"01","date_updated":"2021-01-12T08:01:16Z","year":"2017","citation":{"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>.","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.","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>.","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>","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>"}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2017-06-06T00:00:00Z","publication_identifier":{"issn":["20411723"]},"oa":1,"publist_id":"7203","file":[{"date_created":"2019-01-21T14:48:10Z","checksum":"940742282a9a285dc4aeae0c2b5ebe96","file_size":3018075,"date_updated":"2020-07-14T12:47:16Z","content_type":"application/pdf","file_name":"2017_NatureComm_Xu.pdf","relation":"main_file","access_level":"open_access","file_id":"5865","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","has_accepted_license":"1","publication":"Nature Communications","oa_version":"Published Version","article_number":"15741","month":"06","language":[{"iso":"eng"}],"year":"2017","citation":{"short":"Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko, H. Urlaub, P. Cramer, Nature Communications 8 (2017).","mla":"Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>, vol. 8, 15741, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>.","ista":"Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741.","apa":"Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer, P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>","ama":"Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>","ieee":"Y. Xu <i>et al.</i>, “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","chicago":"Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>."},"date_updated":"2021-01-12T08:05:40Z","day":"06","doi":"10.1038/ncomms15741","abstract":[{"text":"The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. ","lang":"eng"}],"volume":8,"ddc":["570"],"extern":"1","_id":"601","author":[{"last_name":"Xu","first_name":"Youwei","full_name":"Xu, Youwei"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"},{"first_name":"Chung","last_name":"Lee","full_name":"Lee, Chung"},{"last_name":"Maier","first_name":"Kerstin","full_name":"Maier, Kerstin"},{"full_name":"Schwalb, Björn","first_name":"Björn","last_name":"Schwalb"},{"last_name":"Tegunov","first_name":"Dimitri","full_name":"Tegunov, Dimitri"},{"first_name":"Jürgen","last_name":"Plitzko","full_name":"Plitzko, Jürgen"},{"full_name":"Urlaub, Henning","last_name":"Urlaub","first_name":"Henning"},{"first_name":"Patrick","last_name":"Cramer","full_name":"Cramer, Patrick"}],"date_created":"2018-12-11T11:47:25Z","article_processing_charge":"No","publication_status":"published","intvolume":"         8","title":"Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:16Z","publisher":"Nature Publishing Group"},{"intvolume":"         8","pubrep_id":"911","title":"Shaping bacterial population behavior through computer interfaced control of individual cells","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_created":"2018-12-11T11:47:30Z","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","issue":"1","author":[{"full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"scopus_import":1,"_id":"613","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:47:20Z","quality_controlled":"1","ec_funded":1,"abstract":[{"text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.","lang":"eng"}],"day":"01","doi":"10.1038/s41467-017-01683-1","year":"2017","citation":{"apa":"Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., &#38; Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>","ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>","ieee":"R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>.","mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>.","short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535."},"date_updated":"2021-01-12T08:06:15Z","ddc":["576","579"],"acknowledgement":"We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).","volume":8,"article_number":"1535","month":"12","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"oa":1,"publist_id":"7191","publication_identifier":{"issn":["20411723"]},"type":"journal_article","date_published":"2017-12-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"date_updated":"2020-07-14T12:47:20Z","content_type":"application/pdf","file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf","date_created":"2018-12-12T10:16:05Z","checksum":"44bb5d0229926c23a9955d9fe0f9723f","file_size":1951699,"file_id":"5190","creator":"system","access_level":"open_access","relation":"main_file"}]},{"language":[{"iso":"eng"}],"article_number":"1486","month":"12","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Communications","related_material":{"record":[{"relation":"popular_science","id":"7163","status":"public"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"4da2651303c8afc2f7fc419be42a2433","file_size":1201520,"date_created":"2020-03-03T15:55:50Z","file_name":"2017_NatureComm_Fraisse.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:20Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"7562"}],"oa":1,"publist_id":"7190","publication_identifier":{"issn":["20411723"]},"type":"journal_article","date_published":"2017-12-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:47:20Z","quality_controlled":"1","intvolume":"         8","pubrep_id":"910","title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_created":"2018-12-11T11:47:30Z","publication_status":"published","issue":"1","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle"},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","last_name":"Picard","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A"},{"last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"pmid":1,"_id":"614","ddc":["570","576"],"volume":8,"abstract":[{"lang":"eng","text":"Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes."}],"day":"01","doi":"10.1038/s41467-017-01663-5","external_id":{"pmid":["29133797"]},"year":"2017","citation":{"ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486.","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>.","chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>.","ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>","apa":"Fraisse, C., Picard, M. A. L., &#38; Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>"},"date_updated":"2024-02-21T13:47:47Z"},{"year":"2017","citation":{"ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14832\">10.1038/ncomms14832</a>","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14832\">https://doi.org/10.1038/ncomms14832</a>","chicago":"Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14832\">https://doi.org/10.1038/ncomms14832</a>.","ieee":"F. Kage <i>et al.</i>, “FMNL formins boost lamellipodial force generation,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017).","mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” <i>Nature Communications</i>, vol. 8, 14832, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14832\">10.1038/ncomms14832</a>.","ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832."},"date_updated":"2021-01-12T08:08:06Z","day":"22","doi":"10.1038/ncomms14832","abstract":[{"lang":"eng","text":"Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching."}],"volume":8,"ddc":["570"],"scopus_import":1,"_id":"659","author":[{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"last_name":"Winterhoff","first_name":"Moritz","full_name":"Winterhoff, Moritz"},{"first_name":"Vanessa","last_name":"Dimchev","full_name":"Dimchev, Vanessa"},{"last_name":"Müller","first_name":"Jan","full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D"},{"last_name":"Thalheim","first_name":"Tobias","full_name":"Thalheim, Tobias"},{"full_name":"Freise, Anika","last_name":"Freise","first_name":"Anika"},{"first_name":"Stefan","last_name":"Brühmann","full_name":"Brühmann, Stefan"},{"first_name":"Jana","last_name":"Kollasser","full_name":"Kollasser, Jana"},{"last_name":"Block","first_name":"Jennifer","full_name":"Block, Jennifer"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A"},{"first_name":"Matthias","last_name":"Geyer","full_name":"Geyer, Matthias"},{"last_name":"Schnittler","first_name":"Hams","full_name":"Schnittler, Hams"},{"first_name":"Cord","last_name":"Brakebusch","full_name":"Brakebusch, Cord"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia"},{"last_name":"Carlier","first_name":"Marie","full_name":"Carlier, Marie"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Käs, Josef","last_name":"Käs","first_name":"Josef"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"}],"date_created":"2018-12-11T11:47:46Z","department":[{"_id":"MiSi"}],"article_processing_charge":"No","publication_status":"published","intvolume":"         8","pubrep_id":"902","title":"FMNL formins boost lamellipodial force generation","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:34Z","publisher":"Nature Publishing Group","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2017-03-22T00:00:00Z","publication_identifier":{"issn":["20411723"]},"oa":1,"publist_id":"7075","file":[{"date_updated":"2020-07-14T12:47:34Z","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:14:21Z","checksum":"dae30190291c3630e8102d8714a8d23e","file_size":9523746,"file_id":"5072","creator":"system","access_level":"open_access","relation":"main_file"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","has_accepted_license":"1","publication":"Nature Communications","oa_version":"Published Version","article_number":"14832","month":"03","language":[{"iso":"eng"}]},{"volume":8,"ddc":["539","576"],"year":"2017","citation":{"mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00238-8\">10.1038/s41467-017-00238-8</a>.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","apa":"Friedlander, T., Prizak, R., Barton, N. H., &#38; Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-00238-8\">https://doi.org/10.1038/s41467-017-00238-8</a>","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00238-8\">10.1038/s41467-017-00238-8</a>","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00238-8\">https://doi.org/10.1038/s41467-017-00238-8</a>.","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017."},"date_updated":"2025-05-28T11:42:50Z","external_id":{"isi":["000407198800005"]},"isi":1,"day":"09","doi":"10.1038/s41467-017-00238-8","abstract":[{"lang":"eng","text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components."}],"ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:48:16Z","publisher":"Nature Publishing Group","scopus_import":"1","_id":"955","issue":"1","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"date_created":"2018-12-11T11:49:23Z","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","intvolume":"         8","pubrep_id":"864","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","file":[{"date_created":"2018-12-12T10:14:14Z","file_size":998157,"checksum":"29a1b5db458048d3bd5c67e0e2a56818","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","relation":"main_file","access_level":"open_access","file_id":"5064","creator":"system"},{"file_size":9715993,"checksum":"7b78401e52a576cf3e6bbf8d0abadc17","date_created":"2018-12-12T10:14:15Z","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5065"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"6071","relation":"dissertation_contains"}]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2017-08-09T00:00:00Z","publication_identifier":{"issn":["20411723"]},"publist_id":"6459","oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Communications","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","article_number":"216","month":"08"},{"_id":"993","scopus_import":"1","author":[{"full_name":"Levina (Martius), Anna","first_name":"Anna","last_name":"Levina (Martius)","id":"35AF8020-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Priesemann, Viola","last_name":"Priesemann","first_name":"Viola"}],"publication_status":"published","date_created":"2018-12-11T11:49:35Z","department":[{"_id":"GaTk"},{"_id":"JoCs"}],"article_processing_charge":"Yes (in subscription journal)","pubrep_id":"819","title":"Subsampling scaling","intvolume":"         8","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:48:19Z","publisher":"Nature Publishing Group","date_updated":"2023-09-22T09:54:07Z","citation":{"ista":"Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140.","mla":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” <i>Nature Communications</i>, vol. 8, 15140, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15140\">10.1038/ncomms15140</a>.","short":"A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).","ieee":"A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","chicago":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15140\">https://doi.org/10.1038/ncomms15140</a>.","apa":"Levina (Martius), A., &#38; Priesemann, V. (2017). Subsampling scaling. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15140\">https://doi.org/10.1038/ncomms15140</a>","ama":"Levina (Martius) A, Priesemann V. Subsampling scaling. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15140\">10.1038/ncomms15140</a>"},"year":"2017","isi":1,"external_id":{"isi":["000400560700001"]},"doi":"10.1038/ncomms15140","day":"04","abstract":[{"text":"In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development.","lang":"eng"}],"volume":8,"ddc":["005","571"],"publication":"Nature Communications","has_accepted_license":"1","oa_version":"Published Version","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"month":"05","article_number":"15140","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2017-05-04T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["20411723"]},"oa":1,"publist_id":"6406","file":[{"creator":"system","file_id":"5122","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf","date_updated":"2020-07-14T12:48:19Z","checksum":"9880212f8c4c53404c7c6fbf9023c53a","file_size":746224,"date_created":"2018-12-12T10:15:05Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public"}]