[{"article_processing_charge":"No","citation":{"short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. 2020.","ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, 2020. https://doi.org/10.1101/2020.04.18.047886.","mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, 2020, doi:10.1101/2020.04.18.047886.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. https://doi.org/10.1101/2020.04.18.047886"},"main_file_link":[{"url":"https://doi.org/10.1101/2020.04.18.047886 ","open_access":"1"}],"_id":"7673","status":"public","date_created":"2020-04-22T08:27:56Z","oa":1,"doi":"10.1101/2020.04.18.047886","author":[{"orcid":"0000-0001-6041-254X","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","full_name":"Kavcic, Bor"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"full_name":"Bollenbach, Tobias","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"}],"date_updated":"2026-07-31T22:31:05Z","das_tickbox":"1","related_material":{"record":[{"id":"8997","relation":"later_version","status":"public"},{"id":"8657","status":"public","relation":"dissertation_contains"}]},"abstract":[{"text":"Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions.","lang":"eng"}],"title":"A minimal biophysical model of combined antibiotic action","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","language":[{"iso":"eng"}],"oa_version":"Preprint","month":"04","department":[{"_id":"GaTk"}],"year":"2020","project":[{"grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"date_published":"2020-04-18T00:00:00Z","publication":"bioRxiv","day":"18","publication_status":"published"},{"corr_author":"1","title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":21,"quality_controlled":"1","file_date_updated":"2020-09-21T14:08:58Z","publication_status":"published","isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","ddc":["570"],"oa":1,"author":[{"last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David"},{"last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","first_name":"Pradeep"},{"first_name":"Matthew J","full_name":"Case, Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"}],"has_accepted_license":"1","intvolume":" 21","issue":"18","type":"journal_article","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"month":"09","department":[{"_id":"RySh"}],"year":"2020","article_number":"6737","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus","_id":"25D32BC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"785907","call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 2"}],"date_published":"2020-09-14T00:00:00Z","publisher":"MDPI","file":[{"file_name":"2020_JournMolecSciences_Kleindienst.pdf","relation":"main_file","creator":"dernst","date_updated":"2020-09-21T14:08:58Z","file_size":5748456,"content_type":"application/pdf","date_created":"2020-09-21T14:08:58Z","file_id":"8551","access_level":"open_access","checksum":"2e4f62f3cfe945b7391fc3070e5a289f","success":1}],"license":"https://creativecommons.org/licenses/by/4.0/","publication":"International Journal of Molecular Sciences","day":"14","article_processing_charge":"No","citation":{"mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences, vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737.","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737.","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” International Journal of Molecular Sciences, vol. 21, no. 18. MDPI, 2020.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21186737"},"_id":"8532","ec_funded":1,"date_created":"2020-09-20T22:01:35Z","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","external_id":{"isi":["000579945300001"]},"article_type":"original","doi":"10.3390/ijms21186737","date_updated":"2026-07-31T22:31:08Z","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"abstract":[{"lang":"eng","text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography."}]},{"day":"24","date_published":"2020-04-24T00:00:00Z","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"file":[{"creator":"stgingl","relation":"main_file","date_updated":"2021-10-31T23:30:05Z","file_size":3268017,"file_name":"Thesis_without-signatures_PDFA.pdf","embargo":"2021-10-30","checksum":"fb9a4468eb27be92690728e35c823796","access_level":"open_access","content_type":"application/pdf","file_id":"7692","date_created":"2020-04-28T11:19:21Z"},{"embargo_to":"open_access","date_created":"2020-04-28T11:19:24Z","file_id":"7693","content_type":"application/octet-stream","access_level":"closed","checksum":"f6c80ca97104a631a328cb79a2c53493","file_name":"Thesis_without signatures.docx","file_size":5167703,"date_updated":"2021-10-31T23:30:05Z","creator":"stgingl","relation":"source_file"}],"month":"04","department":[{"_id":"CaGu"}],"year":"2020","type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"abstract":[{"text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo.","lang":"eng"}],"date_updated":"2026-07-08T05:54:07Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1028"}]},"date_created":"2020-04-24T16:00:51Z","doi":"10.15479/AT:ISTA:7680","article_processing_charge":"No","degree_awarded":"PhD","citation":{"apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020."},"_id":"7680","file_date_updated":"2021-10-31T23:30:05Z","publication_status":"published","oa_version":"None","title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"98","language":[{"iso":"eng"}],"has_accepted_license":"1","author":[{"full_name":"Kainrath, Stephanie","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","orcid":"0000-0002-6709-2195"}],"oa":1,"supervisor":[{"full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"ddc":["570"],"status":"public"},{"year":"2020","department":[{"_id":"ToHe"}],"month":"05","publication_identifier":{"issn":["1751-570X"]},"OA_type":"green","type":"journal_article","day":"01","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"100856","date_published":"2020-05-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"Nonlinear Analysis: Hybrid Systems","file":[{"access_level":"open_access","checksum":"560abfddb53f9fe921b6744f59f2cfaa","embargo":"2022-05-15","content_type":"application/pdf","date_created":"2020-10-21T13:16:45Z","file_id":"8688","relation":"main_file","creator":"dernst","date_updated":"2022-05-16T22:30:04Z","file_size":818774,"file_name":"2020_NAHS_GarciaSoto.pdf"}],"publisher":"Elsevier","article_type":"original","date_created":"2020-02-02T23:00:59Z","external_id":{"isi":["000528828600003"]},"doi":"10.1016/j.nahs.2020.100856","article_processing_charge":"No","_id":"7426","citation":{"apa":"Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2020.100856","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5. Elsevier, 2020.","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5). doi:10.1016/j.nahs.2020.100856","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020)."},"abstract":[{"lang":"eng","text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method."}],"date_updated":"2026-07-28T12:57:27Z","scopus_import":"1","oa_version":"Submitted Version","volume":36,"title":"Abstraction based verification of stability of polyhedral switched systems","corr_author":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file_date_updated":"2022-05-16T22:30:04Z","quality_controlled":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"OA_place":"repository","isi":1,"ddc":["000"],"status":"public","has_accepted_license":"1","intvolume":" 36","issue":"5","author":[{"full_name":"Garcia Soto, Miriam","first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","last_name":"Garcia Soto"},{"full_name":"Prabhakar, Pavithra","first_name":"Pavithra","last_name":"Prabhakar"}]},{"publication_status":"published","quality_controlled":"1","volume":52,"oa_version":"Submitted Version","page":"1247-1255","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","intvolume":" 52","author":[{"last_name":" Galan","full_name":" Galan, Silvia","first_name":"Silvia"},{"full_name":"Machnik, Nick N","first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik","orcid":"0000-0001-6617-9742"},{"first_name":"Kai","full_name":"Kruse, Kai","last_name":"Kruse"},{"last_name":"Díaz","full_name":"Díaz, Noelia","first_name":"Noelia"},{"first_name":"Marc A","full_name":"Marti-Renom, Marc A","last_name":"Marti-Renom"},{"first_name":"Juan M","full_name":"Vaquerizas, Juan M","last_name":"Vaquerizas"}],"pmid":1,"oa":1,"status":"public","OA_place":"repository","isi":1,"day":"19","publication":"Nature Genetics","publisher":"Springer Nature","date_published":"2020-10-19T00:00:00Z","year":"2020","month":"10","department":[{"_id":"FyKo"}],"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"OA_type":"green","type":"journal_article","abstract":[{"text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.","lang":"eng"}],"scopus_import":"1","related_material":{"record":[{"id":"18642","status":"public","relation":"dissertation_contains"}]},"date_updated":"2026-07-31T22:31:14Z","doi":"10.1038/s41588-020-00712-y","article_type":"original","date_created":"2020-10-25T23:01:20Z","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","external_id":{"isi":["000579693500004"],"pmid":["33077914"]},"_id":"8707","citation":{"apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y.","ieee":"S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020.","short":"S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y"},"main_file_link":[{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7610641/","open_access":"1"}],"article_processing_charge":"No"},{"publication":"Research in Number Theory","publisher":"Springer Nature","article_number":"9","date_published":"2019-01-02T00:00:00Z","day":"02","publication_identifier":{"eissn":["2363-9555"],"issn":["2522-0160"]},"type":"journal_article","year":"2019","month":"01","department":[{"_id":"TiBr"}],"scopus_import":"1","date_updated":"2023-09-05T15:39:31Z","abstract":[{"lang":"eng","text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM."}],"_id":"10874","citation":{"ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6.","mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9.","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6"},"main_file_link":[{"url":"https://arxiv.org/abs/1807.08986","open_access":"1"}],"article_processing_charge":"No","doi":"10.1007/s40993-018-0146-6","article_type":"original","external_id":{"arxiv":["1807.08986"]},"acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","date_created":"2022-03-18T12:09:48Z","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","keyword":["Algebra and Number Theory"],"arxiv":1,"title":"Modular invariants for genus 3 hyperelliptic curves","volume":5,"oa_version":"Preprint","author":[{"last_name":"Ionica","first_name":"Sorina","full_name":"Ionica, Sorina"},{"first_name":"Pınar","full_name":"Kılıçer, Pınar","last_name":"Kılıçer"},{"first_name":"Kristin","full_name":"Lauter, Kristin","last_name":"Lauter"},{"full_name":"Lorenzo García, Elisa","first_name":"Elisa","last_name":"Lorenzo García"},{"last_name":"Manzateanu","id":"be8d652e-a908-11ec-82a4-e2867729459c","first_name":"Maria-Adelina","full_name":"Manzateanu, Maria-Adelina"},{"full_name":"Massierer, Maike","first_name":"Maike","last_name":"Massierer"},{"first_name":"Christelle","full_name":"Vincent, Christelle","last_name":"Vincent"}],"intvolume":" 5","status":"public","oa":1},{"quality_controlled":"1","publication_status":"published","page":"3037-3067","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","keyword":["Applied Mathematics","Discrete Mathematics and Combinatorics","Analysis"],"arxiv":1,"title":"A mean-field model with discontinuous coefficients for neurons with spatial interaction","corr_author":"1","volume":39,"oa_version":"Preprint","author":[{"full_name":"Flandoli, Franco","first_name":"Franco","last_name":"Flandoli"},{"full_name":"Priola, Enrico","first_name":"Enrico","last_name":"Priola"},{"id":"47491882-F248-11E8-B48F-1D18A9856A87","last_name":"Zanco","full_name":"Zanco, Giovanni A","first_name":"Giovanni A"}],"issue":"6","intvolume":" 39","status":"public","isi":1,"oa":1,"publication":"Discrete and Continuous Dynamical Systems","publisher":"American Institute of Mathematical Sciences","project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"date_published":"2019-06-01T00:00:00Z","day":"01","publication_identifier":{"issn":["1553-5231"]},"type":"journal_article","year":"2019","month":"06","department":[{"_id":"JaMa"}],"scopus_import":"1","date_updated":"2025-04-15T08:31:32Z","abstract":[{"lang":"eng","text":"Starting from a microscopic model for a system of neurons evolving in time which individually follow a stochastic integrate-and-fire type model, we study a mean-field limit of the system. Our model is described by a system of SDEs with discontinuous coefficients for the action potential of each neuron and takes into account the (random) spatial configuration of neurons allowing the interaction to depend on it. In the limit as the number of particles tends to infinity, we obtain a nonlinear Fokker-Planck type PDE in two variables, with derivatives only with respect to one variable and discontinuous coefficients. We also study strong well-posedness of the system of SDEs and prove the existence and uniqueness of a weak measure-valued solution to the PDE, obtained as the limit of the laws of the empirical measures for the system of particles."}],"_id":"10878","citation":{"apa":"Flandoli, F., Priola, E., & Zanco, G. A. (2019). A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences. https://doi.org/10.3934/dcds.2019126","ista":"Flandoli F, Priola E, Zanco GA. 2019. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 39(6), 3037–3067.","mla":"Flandoli, Franco, et al. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems, vol. 39, no. 6, American Institute of Mathematical Sciences, 2019, pp. 3037–67, doi:10.3934/dcds.2019126.","chicago":"Flandoli, Franco, Enrico Priola, and Giovanni A Zanco. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences, 2019. https://doi.org/10.3934/dcds.2019126.","ieee":"F. Flandoli, E. Priola, and G. A. Zanco, “A mean-field model with discontinuous coefficients for neurons with spatial interaction,” Discrete and Continuous Dynamical Systems, vol. 39, no. 6. American Institute of Mathematical Sciences, pp. 3037–3067, 2019.","short":"F. Flandoli, E. Priola, G.A. Zanco, Discrete and Continuous Dynamical Systems 39 (2019) 3037–3067.","ama":"Flandoli F, Priola E, Zanco GA. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 2019;39(6):3037-3067. doi:10.3934/dcds.2019126"},"main_file_link":[{"url":"https://arxiv.org/abs/1708.04156","open_access":"1"}],"article_processing_charge":"No","doi":"10.3934/dcds.2019126","article_type":"original","date_created":"2022-03-18T12:33:34Z","external_id":{"isi":["000459954800003"],"arxiv":["1708.04156"]},"acknowledgement":"The second author has been partially supported by INdAM through the GNAMPA Research\r\nProject (2017) “Sistemi stocastici singolari: buona posizione e problemi di controllo”. The third\r\nauthor was partly funded by the Austrian Science Fund (FWF) project F 65."},{"type":"journal_article","publication_identifier":{"issn":["1550-4131"]},"department":[{"_id":"MaHe"}],"month":"08","year":"2019","publisher":"Elsevier","publication":"Cell Metabolism","date_published":"2019-08-06T00:00:00Z","extern":"1","day":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cmet.2019.05.010"}],"citation":{"ama":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 2019;30(2):343-351.e3. doi:10.1016/j.cmet.2019.05.010","chicago":"Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra, Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism. Elsevier, 2019. https://doi.org/10.1016/j.cmet.2019.05.010.","short":"R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E. Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism 30 (2019) 343–351.e3.","ieee":"R. Arrojo e Drigo et al., “Age mosaicism across multiple scales in adult tissues,” Cell Metabolism, vol. 30, no. 2. Elsevier, p. 343–351.e3, 2019.","mla":"Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3, doi:10.1016/j.cmet.2019.05.010.","ista":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3.","apa":"Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T., Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult tissues. Cell Metabolism. Elsevier. https://doi.org/10.1016/j.cmet.2019.05.010"},"_id":"11062","article_processing_charge":"No","doi":"10.1016/j.cmet.2019.05.010","external_id":{"pmid":["31178361"]},"date_created":"2022-04-07T07:45:21Z","article_type":"original","scopus_import":"1","date_updated":"2025-12-15T10:02:11Z","abstract":[{"text":"Most neurons are not replaced during an animal’s lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Cell Biology","Molecular Biology","Physiology"],"page":"343-351.e3","language":[{"iso":"eng"}],"title":"Age mosaicism across multiple scales in adult tissues","volume":30,"oa_version":"Published Version","quality_controlled":"1","publication_status":"published","status":"public","oa":1,"pmid":1,"author":[{"first_name":"Rafael","full_name":"Arrojo e Drigo, Rafael","last_name":"Arrojo e Drigo"},{"first_name":"Varda","full_name":"Lev-Ram, Varda","last_name":"Lev-Ram"},{"last_name":"Tyagi","first_name":"Swati","full_name":"Tyagi, Swati"},{"last_name":"Ramachandra","full_name":"Ramachandra, Ranjan","first_name":"Ranjan"},{"first_name":"Thomas","full_name":"Deerinck, Thomas","last_name":"Deerinck"},{"first_name":"Eric","full_name":"Bushong, Eric","last_name":"Bushong"},{"last_name":"Phan","full_name":"Phan, Sebastien","first_name":"Sebastien"},{"last_name":"Orphan","full_name":"Orphan, Victoria","first_name":"Victoria"},{"last_name":"Lechene","first_name":"Claude","full_name":"Lechene, Claude"},{"first_name":"Mark H.","full_name":"Ellisman, Mark H.","last_name":"Ellisman"},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X"}],"issue":"2","intvolume":" 30"},{"file_date_updated":"2020-07-14T12:45:45Z","publication_status":"published","quality_controlled":"1","volume":149,"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"12-26","language":[{"iso":"eng"}],"title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","corr_author":"1","issue":"1","intvolume":" 149","has_accepted_license":"1","author":[{"last_name":"Amberg","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","full_name":"Amberg, Nicole"},{"first_name":"Susanne","full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"oa":1,"ddc":["570"],"status":"public","isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","publisher":"Wiley","file":[{"content_type":"application/pdf","file_id":"7239","date_created":"2020-01-07T13:35:52Z","checksum":"db027721a95d36f5de36aadcd0bdf7e6","access_level":"open_access","file_name":"2019_Wiley_Amberg.pdf","relation":"main_file","creator":"kschuh","file_size":889709,"date_updated":"2020-07-14T12:45:45Z"}],"publication":"Journal of Neurochemistry","project":[{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"date_published":"2019-04-01T00:00:00Z","month":"04","department":[{"_id":"SiHi"}],"year":"2019","type":"journal_article","abstract":[{"lang":"eng","text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved."}],"scopus_import":"1","date_updated":"2025-04-14T07:43:05Z","doi":"10.1111/jnc.14601","acknowledgement":" This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung \r\nn[f+b] (C13-002) to SH; a program grant from the Human Frontiers Science Program (RGP0053/2014) to SH; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n","date_created":"2018-12-11T11:44:14Z","ec_funded":1,"external_id":{"isi":["000462680200002"]},"article_type":"review","citation":{"apa":"Amberg, N., Laukoter, S., & Hippenmeyer, S. (2019). Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14601","ista":"Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 149(1), 12–26.","mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601.","ama":"Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 2019;149(1):12-26. doi:10.1111/jnc.14601","ieee":"N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex,” Journal of Neurochemistry, vol. 149, no. 1. Wiley, pp. 12–26, 2019."},"_id":"27","article_processing_charge":"Yes (via OA deal)"},{"type":"journal_article","department":[{"_id":"JaMa"}],"month":"03","year":"2019","publisher":"Elsevier","publication":"Stochastic Processes and their Applications","date_published":"2019-03-01T00:00:00Z","day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1611.04177","open_access":"1"}],"citation":{"apa":"Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003","ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012.","mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.","chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003.","short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012.","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019."},"_id":"301","article_processing_charge":"No","doi":"10.1016/j.spa.2018.04.003","external_id":{"arxiv":["1611.04177"],"isi":["000458945300012"]},"date_created":"2018-12-11T11:45:42Z","article_type":"original","scopus_import":"1","date_updated":"2023-08-24T14:20:49Z","abstract":[{"lang":"eng","text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"995-1012","language":[{"iso":"eng"}],"title":"A Feynman–Kac formula for stochastic Dirichlet problems","arxiv":1,"volume":129,"oa_version":"Preprint","quality_controlled":"1","publication_status":"published","status":"public","isi":1,"oa":1,"author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate"},{"last_name":"Gyöngy","first_name":"István","full_name":"Gyöngy, István"}],"issue":"3","intvolume":" 129"},{"publication_status":"published","quality_controlled":"1","oa_version":"None","volume":29,"title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"page":"2676-2686.e3","language":[{"iso":"eng"}],"intvolume":" 29","issue":"16","author":[{"full_name":"Lawrence, Emma J.","first_name":"Emma J.","last_name":"Lawrence"},{"first_name":"Hongbo","full_name":"Gao, Hongbo","last_name":"Gao"},{"first_name":"Andrew J.","full_name":"Tock, Andrew J.","last_name":"Tock"},{"full_name":"Lambing, Christophe","first_name":"Christophe","last_name":"Lambing"},{"last_name":"Blackwell","first_name":"Alexander R.","full_name":"Blackwell, Alexander R."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi"},{"last_name":"Henderson","full_name":"Henderson, Ian R.","first_name":"Ian R."}],"pmid":1,"status":"public","day":"19","extern":"1","date_published":"2019-08-19T00:00:00Z","publisher":"Elsevier","publication":"Current Biology","month":"08","department":[{"_id":"XiFe"}],"year":"2019","type":"journal_article","publication_identifier":{"issn":["0960-9822"]},"abstract":[{"text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.","lang":"eng"}],"date_updated":"2025-01-14T14:31:02Z","scopus_import":"1","external_id":{"pmid":["31378616"]},"date_created":"2023-01-16T09:16:33Z","acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","article_type":"original","doi":"10.1016/j.cub.2019.06.084","article_processing_charge":"No","citation":{"apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.06.084","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084","ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier, p. 2676–2686.e3, 2019.","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.06.084.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084."},"_id":"12190"},{"abstract":[{"text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.","lang":"eng"}],"date_updated":"2025-01-14T14:31:41Z","scopus_import":"1","acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","external_id":{"unknown":["31135340"]},"date_created":"2023-01-16T09:17:21Z","article_type":"original","doi":"10.7554/elife.42530","article_processing_charge":"No","citation":{"apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.42530","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, 2019, doi:10.7554/elife.42530.","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.42530.","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, 2019.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019)."},"_id":"12192","day":"28","extern":"1","article_number":"42530","date_published":"2019-05-28T00:00:00Z","file":[{"file_size":2493837,"date_updated":"2023-02-07T09:42:46Z","relation":"main_file","creator":"alisjak","file_name":"2019_elife_He.pdf","success":1,"access_level":"open_access","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","date_created":"2023-02-07T09:42:46Z","file_id":"12525","content_type":"application/pdf"}],"publisher":"eLife Sciences Publications","publication":"eLife","department":[{"_id":"XiFe"}],"month":"05","year":"2019","type":"journal_article","publication_identifier":{"issn":["2050-084X"]},"has_accepted_license":"1","intvolume":" 8","author":[{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"first_name":"Jingyi","full_name":"Zhang, Jingyi","last_name":"Zhang"},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","ddc":["580"],"file_date_updated":"2023-02-07T09:42:46Z","publication_status":"published","quality_controlled":"1","oa_version":"Published Version","volume":8,"title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"oa_version":"Published Version","month":"02","department":[{"_id":"ScienComp"}],"year":"2019","title":"Is Debian suitable for running an HPC Cluster?","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference_abstract","language":[{"iso":"eng"}],"page":"25","day":"27","file_date_updated":"2023-05-16T07:27:09Z","publication_status":"published","date_published":"2019-02-27T00:00:00Z","publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","file":[{"success":1,"checksum":"acc8272027faaf30709c51ac5c58ffa4","access_level":"open_access","file_id":"12970","date_created":"2023-05-16T07:27:09Z","content_type":"application/pdf","file_size":1097603,"date_updated":"2023-05-16T07:27:09Z","relation":"main_file","creator":"dernst","file_name":"2019_AHPC_Schloegl.pdf"}],"publication":"AHPC19 - Austrian HPC Meeting 2019 ","date_created":"2023-05-05T12:48:48Z","oa":1,"article_processing_charge":"No","citation":{"ista":"Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz."},"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf"}],"_id":"12901","ddc":["000"],"status":"public","has_accepted_license":"1","conference":{"location":"Grundlsee, Austria","start_date":"2019-02-25","name":"AHPC: Austrian HPC Meeting","end_date":"2019-02-27"},"author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","last_name":"Schlögl","full_name":"Schlögl, Alois","first_name":"Alois"},{"full_name":"Kiss, Janos","first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","full_name":"Elefante, Stefano","first_name":"Stefano"}],"date_updated":"2024-10-09T21:05:24Z"},{"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","oa_version":"Published Version","month":"12","department":[{"_id":"NiBa"}],"year":"2019","date_published":"2019-12-02T00:00:00Z","publisher":"Dryad","license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"02","article_processing_charge":"No","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}],"citation":{"apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019."},"_id":"13067","status":"public","ddc":["570"],"date_created":"2023-05-23T16:36:27Z","oa":1,"doi":"10.5061/DRYAD.TB2RBNZWK","author":[{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Zagrodzka","first_name":"Zuzanna","full_name":"Zagrodzka, Zuzanna"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"date_updated":"2025-07-10T11:54:22Z","related_material":{"record":[{"id":"7205","relation":"used_in_publication","status":"public"}]},"abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}]},{"type":"journal_article","year":"2019","month":"02","department":[{"_id":"CaGu"}],"date_published":"2019-02-01T00:00:00Z","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication":"Current Genetics","publisher":"Springer","file":[{"file_name":"2019_CurrentGenetics_Nikolic.pdf","date_updated":"2020-07-14T12:44:47Z","file_size":776399,"creator":"dernst","relation":"main_file","date_created":"2019-02-06T07:50:58Z","file_id":"5930","content_type":"application/pdf","access_level":"open_access","checksum":"6779708b0b632a1a6ed28c56f5161142"}],"day":"01","article_processing_charge":"Yes (via OA deal)","_id":"138","citation":{"apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8","ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:10.1007/s00294-018-0879-8.","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer, pp. 133–138, 2019.","chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8"},"external_id":{"isi":["000456958800017"]},"ec_funded":1,"date_created":"2018-12-11T11:44:50Z","doi":"10.1007/s00294-018-0879-8","date_updated":"2025-04-15T06:50:19Z","scopus_import":"1","abstract":[{"text":"Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.","lang":"eng"}],"publist_id":"7785","title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","language":[{"iso":"eng"}],"page":"133-138","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","volume":65,"quality_controlled":"1","publication_status":"published","file_date_updated":"2020-07-14T12:44:47Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"ddc":["570"],"status":"public","oa":1,"author":[{"full_name":"Nikolic, Nela","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","last_name":"Nikolic"}],"has_accepted_license":"1","issue":"1","intvolume":" 65"},{"main_file_link":[{"url":"https://arxiv.org/abs/1905.01258","open_access":"1"}],"citation":{"apa":"Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem, O. (2019). Disentangling factors of variation using few labels. In 8th International Conference on Learning Representations. Virtual.","ieee":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in 8th International Conference on Learning Representations, Virtual, 2019.","ama":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling factors of variation using few labels. In: 8th International Conference on Learning Representations. ; 2019.","short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019.","chicago":"Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.” In 8th International Conference on Learning Representations, 2019.","mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 2019.","ista":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019. Disentangling factors of variation using few labels. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"status":"public","_id":"14184","article_processing_charge":"No","oa":1,"date_created":"2023-08-22T14:06:37Z","external_id":{"arxiv":["1905.01258"]},"scopus_import":"1","conference":{"start_date":"2020-04-26","location":"Virtual","end_date":"2020-05-01","name":"ICLR: International Conference on Learning Representations"},"author":[{"first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Tschannen","first_name":"Michael","full_name":"Tschannen, Michael"},{"last_name":"Bauer","first_name":"Stefan","full_name":"Bauer, Stefan"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"}],"date_updated":"2023-09-12T07:01:34Z","abstract":[{"text":"Learning disentangled representations is considered a cornerstone problem in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible and that existing inductive biases and unsupervised methods do not\r\nallow to consistently learn disentangled representations. However, in many\r\npractical settings, one might have access to a limited amount of supervision,\r\nfor example through manual labeling of (some) factors of variation in a few\r\ntraining examples. In this paper, we investigate the impact of such supervision\r\non state-of-the-art disentanglement methods and perform a large scale study,\r\ntraining over 52000 models under well-defined and reproducible experimental\r\nconditions. We observe that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with potentially imprecise and incomplete labels, is sufficient\r\nto perform model selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate the benefit of incorporating supervision into the training process.\r\nOverall, we empirically validate that with little and imprecise supervision it\r\nis possible to reliably learn disentangled representations.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","language":[{"iso":"eng"}],"title":"Disentangling factors of variation using few labels","arxiv":1,"month":"12","department":[{"_id":"FrLo"}],"year":"2019","oa_version":"Preprint","publication":"8th International Conference on Learning Representations","quality_controlled":"1","date_published":"2019-12-20T00:00:00Z","extern":"1","publication_status":"published","day":"20"},{"scopus_import":"1","conference":{"location":"Tel Aviv, Israel","start_date":"2019-07-22","name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2019-07-25"},"date_updated":"2023-09-12T08:07:38Z","abstract":[{"lang":"eng","text":"We consider the problem of recovering a common latent source with independent\r\ncomponents from multiple views. This applies to settings in which a variable is\r\nmeasured with multiple experimental modalities, and where the goal is to\r\nsynthesize the disparate measurements into a single unified representation. We\r\nconsider the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions of the sources. When the views are considered\r\nseparately, this reduces to nonlinear Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to undo the mixing. We present novel\r\nidentifiability proofs that this is possible when the multiple views are\r\nconsidered jointly, showing that the mixing can theoretically be undone using\r\nfunction approximators such as deep neural networks. In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that independent latent\r\nsources with arbitrary mixing can be recovered as long as multiple,\r\nsufficiently different noisy views are available."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.06642"}],"citation":{"apa":"Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf, B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.","ieee":"L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf, “The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA,” in Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.","chicago":"Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello, and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, 115:217–27. ML Research Press, 2019.","ama":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. Vol 115. ML Research Press; 2019:217-227.","short":"L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:, Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, ML Research Press, 2019, pp. 217–227.","ista":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227.","mla":"Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, vol. 115, ML Research Press, 2019, pp. 217–27."},"_id":"14189","article_processing_charge":"No","external_id":{"arxiv":["1905.06642"]},"date_created":"2023-08-22T14:08:35Z","alternative_title":["PMLR"],"publisher":"ML Research Press","publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence","date_published":"2019-05-16T00:00:00Z","extern":"1","day":"16","type":"conference","month":"05","department":[{"_id":"FrLo"}],"year":"2019","author":[{"last_name":"Gresele","full_name":"Gresele, Luigi","first_name":"Luigi"},{"full_name":"Rubenstein, Paul K.","first_name":"Paul K.","last_name":"Rubenstein"},{"last_name":"Mehrjou","first_name":"Arash","full_name":"Mehrjou, Arash"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"}],"intvolume":" 115","status":"public","oa":1,"quality_controlled":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"217-227","language":[{"iso":"eng"}],"title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","arxiv":1,"volume":115,"oa_version":"Preprint"},{"publication":"Advances in Neural Information Processing Systems","quality_controlled":"1","date_published":"2019-06-07T00:00:00Z","extern":"1","publication_status":"published","day":"07","type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"isbn":["9781713807933"]},"language":[{"iso":"eng"}],"title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","arxiv":1,"month":"06","department":[{"_id":"FrLo"}],"year":"2019","volume":32,"oa_version":"Preprint","author":[{"full_name":"Gondal, Muhammad Waleed","first_name":"Muhammad Waleed","last_name":"Gondal"},{"last_name":"Wüthrich","full_name":"Wüthrich, Manuel","first_name":"Manuel"},{"full_name":"Miladinović, Đorđe","first_name":"Đorđe","last_name":"Miladinović"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco"},{"full_name":"Breidt, Martin","first_name":"Martin","last_name":"Breidt"},{"last_name":"Volchkov","first_name":"Valentin","full_name":"Volchkov, Valentin"},{"last_name":"Akpo","full_name":"Akpo, Joel","first_name":"Joel"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"}],"conference":{"end_date":"2019-12-14","name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","location":"Vancouver, Canada"},"date_updated":"2023-09-13T09:46:38Z","intvolume":" 32","abstract":[{"text":"Learning meaningful and compact representations with disentangled semantic\r\naspects is considered to be of key importance in representation learning. Since\r\nreal-world data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose a novel data-set which consists of over one million images of\r\nphysical 3D objects with seven factors of variation, such as object color,\r\nshape, size and position. In order to be able to control all the factors of\r\nvariation precisely, we built an experimental platform where the objects are\r\nbeing moved by a robotic arm. In addition, we provide two more datasets which\r\nconsist of simulations of the experimental setup. These datasets provide for\r\nthe first time the possibility to systematically investigate how well different\r\ndisentanglement methods perform on real data in comparison to simulation, and\r\nhow simulated data can be leveraged to build better representations of the real\r\nworld. We provide a first experimental study of these questions and our results\r\nindicate that learned models transfer poorly, but that model and hyperparameter\r\nselection is an effective means of transferring information to the real world.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"citation":{"short":"M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019.","ieee":"M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","ama":"Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","chicago":"Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","ista":"Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","mla":"Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, vol. 32, 2019.","apa":"Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada."},"status":"public","_id":"14190","article_processing_charge":"No","oa":1,"date_created":"2023-08-22T14:09:13Z","external_id":{"arxiv":["1906.03292"]}},{"oa":1,"status":"public","intvolume":" 32","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco"},{"full_name":"Yurtsever, Alp","first_name":"Alp","last_name":"Yurtsever"},{"last_name":"Fercoq","full_name":"Fercoq, Olivier","first_name":"Olivier"},{"full_name":"Cevher, Volkan","first_name":"Volkan","last_name":"Cevher"}],"volume":32,"oa_version":"Preprint","language":[{"iso":"eng"}],"page":"14291–14301","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"title":"Stochastic Frank-Wolfe for composite convex minimization","publication_status":"published","quality_controlled":"1","external_id":{"arxiv":["1901.10348"]},"date_created":"2023-08-22T14:09:35Z","_id":"14191","citation":{"mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.","ista":"Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in Neural Information Processing Systems, 32:14291–14301, 2019.","ieee":"F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.","ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14291–14301.","apa":"Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"A broad class of convex optimization problems can be formulated as a semidefinite program (SDP), minimization of a convex function over the positive-semidefinite cone subject to some affine constraints. The majority of classical SDP solvers are designed for the deterministic setting where problem data is readily available. In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type methods) provide scalable solutions by leveraging the so-called linear minimization oracle instead of the projection onto the semidefinite cone. Most problems in machine learning and modern engineering applications, however, contain some degree of stochasticity. In this work, we propose the first conditional-gradient-type method for solving stochastic optimization problems under affine constraints. Our method guarantees O(k−1/3) convergence rate in expectation on the objective residual and O(k−5/12) on the feasibility gap."}],"scopus_import":"1","date_updated":"2023-09-12T08:48:45Z","conference":{"location":"Vancouver, Canada","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14"},"year":"2019","month":"12","department":[{"_id":"FrLo"}],"publication_identifier":{"isbn":["9781713807933"]},"type":"conference","extern":"1","day":"29","publication":"Advances in Neural Information Processing Systems","date_published":"2019-12-29T00:00:00Z"},{"year":"2019","volume":32,"month":"05","department":[{"_id":"FrLo"}],"oa_version":"Preprint","publication_identifier":{"isbn":["9781713807933"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","arxiv":1,"title":"Are disentangled representations helpful for abstract visual reasoning?","publication_status":"published","extern":"1","day":"29","publication":"Advances in Neural Information Processing Systems","quality_controlled":"1","date_published":"2019-05-29T00:00:00Z","oa":1,"date_created":"2023-08-22T14:09:53Z","external_id":{"arxiv":["1905.12506"]},"_id":"14193","status":"public","citation":{"mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” Advances in Neural Information Processing Systems, vol. 32, 2019.","ista":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled representations helpful for abstract visual reasoning? Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","chicago":"Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","ieee":"S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled representations helpful for abstract visual reasoning?,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019.","ama":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","apa":"Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}],"article_processing_charge":"No","intvolume":" 32","abstract":[{"lang":"eng","text":"A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples."}],"date_updated":"2024-10-14T12:28:15Z","author":[{"last_name":"Steenkiste","first_name":"Sjoerd van","full_name":"Steenkiste, Sjoerd van"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco"},{"full_name":"Schmidhuber, Jürgen","first_name":"Jürgen","last_name":"Schmidhuber"},{"last_name":"Bachem","first_name":"Olivier","full_name":"Bachem, Olivier"}],"conference":{"location":"Vancouver, Canada","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14"}}]