[{"abstract":[{"text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions.","lang":"eng"}],"page":"155-187","article_processing_charge":"No","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture"}],"external_id":{"isi":["000557875100009"]},"scopus_import":"1","date_created":"2019-12-04T16:07:50Z","title":"Transient memory in gene regulation","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","oa_version":"None","isi":1,"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"_id":"7147","date_published":"2019-09-17T00:00:00Z","month":"09","alternative_title":["LNCS"],"year":"2019","date_updated":"2023-09-06T11:18:08Z","day":"17","publication":"17th International Conference on Computational Methods in Systems Biology","doi":"10.1007/978-3-030-31304-3_9","language":[{"iso":"eng"}],"intvolume":" 11773","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030313036","9783030313043"],"issn":["0302-9743"]},"author":[{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"},{"orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","full_name":"Sezgin, Ali"}],"citation":{"mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International Conference on Computational Methods in Systems Biology, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9.","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference on Computational Methods in Systems Biology, 11773:155–87. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31304-3_9.","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: 17th International Conference on Computational Methods in Systems Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9","ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.","short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019). Transient memory in gene regulation. In 17th International Conference on Computational Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. https://doi.org/10.1007/978-3-030-31304-3_9","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187."},"volume":11773,"type":"conference","status":"public","publication_status":"published","conference":{"location":"Trieste, Italy","start_date":"2019-09-18","name":"CMSB: Computational Methods in Systems Biology","end_date":"2019-09-20"}},{"doi":"10.1007/s00294-018-0879-8","publication":"Current Genetics","intvolume":" 65","language":[{"iso":"eng"}],"publist_id":"7785","author":[{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:44:47Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","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","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.","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.","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.","ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","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"},"status":"public","volume":65,"type":"journal_article","publication_status":"published","_id":"138","department":[{"_id":"CaGu"}],"isi":1,"month":"02","date_published":"2019-02-01T00:00:00Z","year":"2019","date_updated":"2023-09-08T13:23:42Z","day":"01","oa":1,"ddc":["570"],"ec_funded":1,"date_created":"2018-12-11T11:44:50Z","issue":"1","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","oa_version":"Published Version","quality_controlled":"1","page":"133-138","has_accepted_license":"1","file":[{"access_level":"open_access","relation":"main_file","file_size":776399,"creator":"dernst","checksum":"6779708b0b632a1a6ed28c56f5161142","date_updated":"2020-07-14T12:44:47Z","file_id":"5930","content_type":"application/pdf","date_created":"2019-02-06T07:50:58Z","file_name":"2019_CurrentGenetics_Nikolic.pdf"}],"abstract":[{"lang":"eng","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."}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000456958800017"]},"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/"},{"author":[{"full_name":"Lang, Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz"},{"full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Shkolnikov"}],"publication_identifier":{"eissn":["1091-6490"]},"intvolume":" 116","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1812015116","acknowledgement":"M.L. is grateful to the members of the C Guet and G Tkacik groups for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring communications.\r\n","publication":"Proceedings of the National Academy of Sciences","publication_status":"published","status":"public","type":"journal_article","volume":116,"citation":{"short":"M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.","apa":"Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1812015116","ieee":"M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences, vol. 116, no. 8. National Academy of Sciences, pp. 2821–2830, 2019.","mla":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences, vol. 116, no. 8, National Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.","chicago":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.","ista":"Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 116(8), 2821–2830.","ama":"Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116"},"month":"02","date_published":"2019-02-19T00:00:00Z","_id":"196","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}],"isi":1,"related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/"}]},"day":"19","date_updated":"2023-09-11T14:09:34Z","year":"2019","date_created":"2018-12-11T11:45:08Z","oa":1,"article_type":"original","quality_controlled":"1","oa_version":"Published Version","publisher":"National Academy of Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Harmonic dynamics of the Abelian sandpile","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1812015116"}],"issue":"8","article_processing_charge":"No","page":"2821-2830","abstract":[{"lang":"eng","text":"The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. "}],"scopus_import":"1","external_id":{"pmid":[" 30728300"],"isi":["000459074400013"],"arxiv":["1806.10823"]},"pmid":1},{"month":"11","date_published":"2019-11-13T00:00:00Z","file":[{"title":"Locus1_amplified","access_level":"open_access","relation":"main_file","file_size":2456192500,"checksum":"72441055043eda4cbf1398a422e2c118","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_name":"D8_S35_R2_001.fastq","date_created":"2019-11-13T08:52:21Z","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_id":"7017"},{"title":"Locus1_ancestral","creator":"itomanek","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","date_updated":"2020-07-14T12:47:47Z","relation":"main_file","access_level":"open_access","file_size":2833452234,"date_created":"2019-11-13T08:52:59Z","file_name":"IT028_S11_R2_001.fastq","file_id":"7018","description":"Illumina whole genome sequence data for Locus 1 - ancestral.","content_type":"application/octet-stream"},{"file_name":"D8-DOG1_S47_R2_001.fastq","date_created":"2019-11-13T08:54:10Z","content_type":"application/octet-stream","file_id":"7019","description":"Illumina whole genome sequence data for Locus 1 - amplified, after DOG-selection.","title":"Locus1_amplified_DOG","checksum":"5b227708ff478ca06e3f0448a4efdc2f","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","relation":"main_file","access_level":"open_access","file_size":2878017264},{"relation":"main_file","access_level":"open_access","file_size":2180826995,"checksum":"d9550a4c044116075fa83f8f2ea31d6f","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","title":"Locus2_amplified","description":"Illumina whole genome sequence data for Locus 2 - amplified.","file_id":"7020","content_type":"application/octet-stream","file_name":"D4_S71_R2_001.fastq","date_created":"2019-11-13T08:54:27Z"},{"title":"Locus2_ancestral","date_updated":"2020-07-14T12:47:47Z","checksum":"466ceb302c020ac013007a879fcde69d","creator":"itomanek","file_size":2108826444,"access_level":"open_access","relation":"main_file","date_created":"2019-11-13T08:55:58Z","file_name":"IT030_S23_R2_001.fastq","file_id":"7021","description":"Illumina whole genome sequence data for Locus 2 - 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see read_me_FACS","file_name":"FACS_data.xlsx.zip","date_created":"2020-01-22T15:44:16Z"},{"content_type":"text/rtf","file_id":"7352","date_created":"2020-01-22T15:44:16Z","file_name":"read_me_FACS.rtf","checksum":"a85caf092ae4b17668f70af2d93fad00","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","relation":"main_file","file_size":4996},{"access_level":"open_access","relation":"main_file","file_size":868,"checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_name":"read_me_microfluidics.rtf","date_created":"2020-01-22T15:44:16Z","content_type":"text/rtf","file_id":"7353"},{"file_size":8141727,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:47Z","checksum":"69c5dc5ca5c069a138183c934acc1778","creator":"itomanek","title":"microfluidics data","description":"microfluidics time trace data - see read_me_microfluidics","file_id":"7354","content_type":"application/zip","file_name":"microfuidics_data.zip","date_created":"2020-01-22T15:44:17Z"}],"abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"has_accepted_license":"1","_id":"7016","article_processing_charge":"No","department":[{"_id":"CaGu"}],"day":"13","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7652"}]},"year":"2019","date_updated":"2024-02-21T12:45:25Z","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"date_created":"2019-11-13T09:07:31Z","author":[{"orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella","last_name":"Tomanek","first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:47Z","doi":"10.15479/AT:ISTA:7016","oa":1,"ddc":["576"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","type":"research_data","oa_version":"Published Version","citation":{"ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","short":"I. Tomanek, (2019).","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016."},"contributor":[{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader","first_name":"Calin C","orcid":"0000-0001-6220-2052"}]},{"project":[{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"article_processing_charge":"No","page":"152","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n"}],"file":[{"date_updated":"2021-02-11T11:17:13Z","creator":"cigler","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_size":12597663,"access_level":"open_access","relation":"main_file","embargo":"2020-05-02","content_type":"application/pdf","file_id":"6373","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","date_created":"2019-05-03T11:54:52Z"},{"relation":"source_file","access_level":"closed","file_size":34644426,"checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","creator":"cigler","date_updated":"2020-07-14T12:47:28Z","file_id":"6374","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","date_created":"2019-05-03T11:54:54Z"}],"has_accepted_license":"1","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","oa":1,"ddc":["576","579"],"date_created":"2019-05-03T11:55:51Z","date_updated":"2024-02-21T13:45:52Z","year":"2019","degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"67"},{"status":"public","id":"5585","relation":"popular_science"}]},"day":"03","_id":"6371","department":[{"_id":"CaGu"}],"alternative_title":["ISTA Thesis"],"month":"05","date_published":"2019-05-03T00:00:00Z","citation":{"mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019."},"publication_status":"published","status":"public","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6371","author":[{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"}],"file_date_updated":"2021-02-11T11:17:13Z","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"]},{"year":"2018","date_updated":"2021-01-12T07:40:42Z","day":"01","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"305","date_published":"2018-01-01T00:00:00Z","month":"01","alternative_title":["MIMB"],"citation":{"ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15.","chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.","ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018.","apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15","short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202."},"volume":1771,"type":"journal_article","status":"public","publication_status":"published","publication":"Methods in Molecular Biology","doi":"10.1007/978-1-4939-7792-5_15","acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","intvolume":" 1771","language":[{"iso":"eng"}],"publist_id":"7574","author":[{"last_name":"Misun","first_name":"Patrick","full_name":"Misun, Patrick"},{"first_name":"Axel","last_name":"Birchler","full_name":"Birchler, Axel"},{"full_name":"Lang, Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz"},{"full_name":"Hierlemann, Andreas","last_name":"Hierlemann","first_name":"Andreas"},{"first_name":"Olivier","last_name":"Frey","full_name":"Frey, Olivier"}],"scopus_import":1,"page":"183 - 202","abstract":[{"text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks.","lang":"eng"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"title":"Fabrication and operation of microfluidic hanging drop networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","oa_version":"None","quality_controlled":"1","date_created":"2018-12-11T11:45:43Z","ec_funded":1},{"title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer","quality_controlled":"1","oa_version":"Published Version","issue":"5","date_created":"2018-12-11T11:48:09Z","ec_funded":1,"ddc":["576"],"oa":1,"scopus_import":"1","external_id":{"isi":["000428239300010"]},"page":"1604 - 1633","abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"has_accepted_license":"1","file":[{"file_size":691245,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:54Z","creator":"system","checksum":"7d92f5d7be81e387edeec4f06442791c","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","date_created":"2018-12-12T10:08:14Z","file_id":"4674","content_type":"application/pdf"}],"article_processing_charge":"No","project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"type":"journal_article","volume":80,"status":"public","publication_status":"published","pubrep_id":"1014","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2"},"publist_id":"6957","file_date_updated":"2020-07-14T12:47:54Z","author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pérez Heredia","first_name":"Jorge","full_name":"Pérez Heredia, Jorge"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"publication":"Algorithmica","doi":"10.1007/s00453-017-0369-2","intvolume":" 80","language":[{"iso":"eng"}],"day":"01","year":"2018","date_updated":"2023-09-11T14:11:35Z","date_published":"2018-05-01T00:00:00Z","month":"05","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"isi":1,"_id":"723"},{"external_id":{"isi":["000425715100006"]},"scopus_import":"1","article_processing_charge":"No","page":"40 - 52","abstract":[{"text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"None","quality_controlled":"1","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:50Z","date_updated":"2023-09-13T08:24:51Z","year":"2018","day":"20","isi":1,"department":[{"_id":"CaGu"}],"_id":"503","date_published":"2018-02-20T00:00:00Z","month":"02","citation":{"ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018.","apa":"Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008."},"publication_status":"published","type":"journal_article","volume":268,"status":"public","intvolume":" 268","language":[{"iso":"eng"}],"publication":"Journal of Biotechnology","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","doi":"10.1016/j.jbiotec.2018.01.008","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"publist_id":"7317"},{"date_created":"2018-12-11T11:44:32Z","ddc":["570"],"oa":1,"quality_controlled":"1","oa_version":"Published Version","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Public Library of Science","issue":"8","article_processing_charge":"Yes","has_accepted_license":"1","file":[{"date_created":"2018-12-17T12:55:31Z","file_name":"2018_Plos_Chaudhry.pdf","content_type":"application/pdf","file_id":"5706","relation":"main_file","access_level":"open_access","file_size":4007095,"creator":"dernst","checksum":"527076f78265cd4ea192cd1569851587","date_updated":"2020-07-14T12:48:10Z"}],"abstract":[{"lang":"eng","text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”."}],"scopus_import":"1","external_id":{"isi":["000443383300024"]},"file_date_updated":"2020-07-14T12:48:10Z","author":[{"last_name":"Chaudhry","first_name":"Waqas","full_name":"Chaudhry, Waqas"},{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"first_name":"Nilang","last_name":"Shah","full_name":"Shah, Nilang"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"first_name":"Ingrid","last_name":"Mccall","full_name":"Mccall, Ingrid"},{"full_name":"Meyer, Justin","last_name":"Meyer","first_name":"Justin"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"full_name":"Levin, Bruce","first_name":"Bruce","last_name":"Levin"}],"publist_id":"7972","language":[{"iso":"eng"}],"intvolume":" 16","publication":"PLoS Biology","doi":"10.1371/journal.pbio.2005971","publication_status":"published","volume":16,"type":"journal_article","status":"public","citation":{"ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"2005971","date_published":"2018-08-16T00:00:00Z","month":"08","department":[{"_id":"CaGu"}],"isi":1,"_id":"82","related_material":{"record":[{"status":"public","relation":"research_data","id":"9810"}]},"day":"16","date_updated":"2023-09-13T08:45:41Z","year":"2018"},{"date_created":"2021-08-06T12:43:44Z","author":[{"first_name":"Waqas","last_name":"Chaudhry","full_name":"Chaudhry, Waqas"},{"orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","last_name":"Pleska","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shah, Nilang","first_name":"Nilang","last_name":"Shah"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"last_name":"Mccall","first_name":"Ingrid","full_name":"Mccall, Ingrid"},{"first_name":"Justin","last_name":"Meyer","full_name":"Meyer, Justin"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"}],"doi":"10.1371/journal.pbio.2005971.s008","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","title":"Numerical data used in figures","type":"research_data_reference","oa_version":"Published Version","citation":{"apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","ieee":"W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008.","mla":"Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008."},"month":"08","date_published":"2018-08-16T00:00:00Z","_id":"9810","article_processing_charge":"No","department":[{"_id":"CaGu"}],"day":"16","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"82"}]},"year":"2018","date_updated":"2023-09-13T08:45:41Z"}]