--- _id: '438' abstract: - lang: eng text: The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress. article_processing_charge: Yes (in subscription journal) author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Alexandra full_name: Vandervelde, Alexandra last_name: Vandervelde - first_name: Tanino full_name: Albanese, Tanino last_name: Albanese - first_name: Lendert full_name: Gelens, Lendert last_name: Gelens - first_name: Isabella full_name: Moll, Isabella last_name: Moll citation: ama: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079 apa: Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., & Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gky079 chicago: Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079. ieee: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018. ista: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931. mla: Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079. short: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931. date_created: 2018-12-11T11:46:29Z date_published: 2018-04-06T00:00:00Z date_updated: 2024-02-21T13:44:45Z day: '06' ddc: - '576' department: - _id: CaGu doi: 10.1093/nar/gky079 external_id: isi: - '000429009500021' file: - access_level: open_access checksum: 3ff4f545c27e11a4cd20ccb30778793e content_type: application/pdf creator: system date_created: 2018-12-12T10:15:30Z date_updated: 2020-07-14T12:46:27Z file_id: '5151' file_name: IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf file_size: 5027978 relation: main_file file_date_updated: 2020-07-14T12:46:27Z has_accepted_license: '1' intvolume: ' 46' isi: 1 issue: '6' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 2918-2931 project: - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Nucleic Acids Research publication_status: published publisher: Oxford University Press pubrep_id: '971' quality_controlled: '1' related_material: record: - id: '5569' relation: popular_science status: public scopus_import: '1' status: public title: Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 46 year: '2018' ... --- _id: '131' abstract: - lang: eng text: 'XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. ' acknowledgement: We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript. article_number: e35684 article_processing_charge: No article_type: original author: - first_name: Marion A full_name: Picard, Marion A id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Celine full_name: Cosseau, Celine last_name: Cosseau - first_name: Sabrina full_name: Ferré, Sabrina last_name: Ferré - first_name: Thomas full_name: Quack, Thomas last_name: Quack - first_name: Christoph full_name: Grevelding, Christoph last_name: Grevelding - first_name: Yohann full_name: Couté, Yohann last_name: Couté - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684 apa: Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684 chicago: Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684. ieee: M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018. ista: Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684. mla: Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684. short: M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018). date_created: 2018-12-11T11:44:47Z date_published: 2018-08-13T00:00:00Z date_updated: 2024-02-21T13:45:12Z day: '13' ddc: - '570' department: - _id: BeVi doi: 10.7554/eLife.35684 external_id: isi: - '000441388200001' file: - access_level: open_access checksum: d6331d4385b1fffd6b47b45d5949d841 content_type: application/pdf creator: dernst date_created: 2018-12-17T11:55:05Z date_updated: 2020-07-14T12:44:43Z file_id: '5695' file_name: 2018_eLife_Picard.pdf file_size: 3158125 relation: main_file file_date_updated: 2020-07-14T12:44:43Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '7792' quality_controlled: '1' related_material: record: - id: '5586' relation: popular_science status: public scopus_import: '1' status: public title: Evolution of gene dosage on the Z-chromosome of schistosome parasites tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2018' ... --- _id: '5584' abstract: - lang: eng text: "This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. " article_processing_charge: No author: - first_name: Stephane full_name: Deny, Stephane last_name: Deny - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Vicente full_name: Botella-Soler, Vicente last_name: Botella-Soler - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98 apa: Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98 chicago: Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98. ieee: S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018. ista: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98. mla: Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98. short: S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018). datarep_id: '98' date_created: 2018-12-12T12:31:39Z date_published: 2018-03-29T00:00:00Z date_updated: 2024-02-21T13:45:26Z day: '29' ddc: - '570' department: - _id: ChLa - _id: GaTk doi: 10.15479/AT:ISTA:98 file: - access_level: open_access checksum: 6808748837b9afbbbabc2a356ca2b88a content_type: application/octet-stream creator: system date_created: 2018-12-12T13:02:24Z date_updated: 2020-07-14T12:47:07Z file_id: '5590' file_name: IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat file_size: 1142543971 relation: main_file - access_level: open_access checksum: d6d6cd07743038fe3a12352983fcf9dd content_type: application/pdf creator: system date_created: 2018-12-12T13:02:25Z date_updated: 2020-07-14T12:47:07Z file_id: '5591' file_name: IST-2018-98-v1+2_ExperimentStructure.pdf file_size: 702336 relation: main_file - access_level: open_access checksum: 0c9cfb4dab35bb3dc25a04395600b1c8 content_type: application/octet-stream creator: system date_created: 2018-12-12T13:02:26Z date_updated: 2020-07-14T12:47:07Z file_id: '5592' file_name: IST-2018-98-v1+3_GoodLocations_area2_20x20.mat file_size: 432 relation: main_file - access_level: open_access checksum: 2a83b011012e21e934b4596285b1a183 content_type: text/plain creator: system date_created: 2018-12-12T13:02:26Z date_updated: 2020-07-14T12:47:07Z file_id: '5593' file_name: IST-2018-98-v1+4_README.txt file_size: 986 relation: main_file file_date_updated: 2020-07-14T12:47:07Z has_accepted_license: '1' keyword: - retina - decoding - regression - neural networks - complex stimulus license: https://creativecommons.org/publicdomain/zero/1.0/ month: '03' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publisher: Institute of Science and Technology Austria related_material: record: - id: '292' relation: used_in_publication status: public status: public title: Nonlinear decoding of a complex movie from the mammalian retina tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '286' abstract: - lang: eng text: 'Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ' acknowledgement: 'ERC, Grant/Award Number: 250152' article_processing_charge: No author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782 apa: Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782 chicago: Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782. ieee: T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018. ista: Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999. mla: Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782. short: T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999. date_created: 2018-12-11T11:45:37Z date_published: 2018-09-01T00:00:00Z date_updated: 2024-02-21T13:45:00Z day: '01' department: - _id: NiBa doi: 10.1111/1755-0998.12782 ec_funded: 1 external_id: isi: - '000441753000007' intvolume: ' 18' isi: 1 issue: '5' language: - iso: eng month: '09' oa_version: None page: 988 - 999 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Molecular Ecology Resources publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '5583' relation: popular_science status: public scopus_import: '1' status: public title: Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 18 year: '2018' ... --- _id: '5586' abstract: - lang: eng text: Input files and scripts from "Evolution of gene dosage on the Z-chromosome of schistosome parasites" by Picard M.A.L., et al (2018). article_processing_charge: No author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109 apa: Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109 chicago: Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109. ieee: B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018. ista: Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109. mla: Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109. short: B. Vicoso, (2018). contributor: - first_name: Marion A id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 datarep_id: '109' date_created: 2018-12-12T12:31:40Z date_published: 2018-07-24T00:00:00Z date_updated: 2024-02-21T13:45:12Z day: '24' ddc: - '570' department: - _id: BeVi doi: 10.15479/AT:ISTA:109 file: - access_level: open_access checksum: e60b484bd6f55c08eb66a189cb72c923 content_type: application/zip creator: system date_created: 2018-12-12T13:02:35Z date_updated: 2020-07-14T12:47:08Z file_id: '5601' file_name: IST-2018-109-v1+1_SupplementaryMethods.zip file_size: 11918144 relation: main_file file_date_updated: 2020-07-14T12:47:08Z has_accepted_license: '1' keyword: - schistosoma - Z-chromosome - gene expression month: '07' oa: 1 oa_version: Published Version project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publisher: Institute of Science and Technology Austria related_material: record: - id: '131' relation: research_paper status: public status: public title: Input files and scripts from "Evolution of gene dosage on the Z-chromosome of schistosome parasites" by Picard M.A.L., et al (2018) tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '5583' abstract: - lang: eng text: "Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone." article_processing_charge: No author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 citation: ama: Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95 apa: Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95 chicago: Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95. ieee: T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018. ista: Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95. mla: Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95. short: T. Ellis, (2018). contributor: - first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field - first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton datarep_id: '95' date_created: 2018-12-12T12:31:39Z date_published: 2018-02-12T00:00:00Z date_updated: 2024-02-21T13:45:01Z day: '12' department: - _id: NiBa doi: 10.15479/AT:ISTA:95 file: - access_level: open_access checksum: fc6aab51439f2622ba6df8632e66fd4f content_type: text/csv creator: system date_created: 2018-12-12T13:02:41Z date_updated: 2020-07-14T12:47:07Z file_id: '5606' file_name: IST-2018-95-v1+1_amajus_GPS_2012.csv file_size: 122048 relation: main_file - access_level: open_access checksum: 92347586ae4f8a6eb7c04354797bf314 content_type: text/csv creator: system date_created: 2018-12-12T13:02:42Z date_updated: 2020-07-14T12:47:07Z file_id: '5607' file_name: IST-2018-95-v1+2_offspring_SNPs_2012.csv file_size: 235980 relation: main_file - access_level: open_access checksum: 3300813645a54e6c5c39f41917228354 content_type: text/csv creator: system date_created: 2018-12-12T13:02:43Z date_updated: 2020-07-14T12:47:07Z file_id: '5608' file_name: IST-2018-95-v1+3_parents_SNPs_2012.csv file_size: 311712 relation: main_file - access_level: open_access checksum: e739fc473567fd8f39438b445fc46147 content_type: application/zip creator: system date_created: 2018-12-12T13:02:44Z date_updated: 2020-07-14T12:47:07Z file_id: '5609' file_name: IST-2018-95-v1+4_faps_scripts.zip file_size: 342090 relation: main_file file_date_updated: 2020-07-14T12:47:07Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '286' relation: research_paper status: public status: public title: Data and Python scripts supporting Python package FAPS tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '5569' abstract: - lang: eng text: "Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic." article_processing_charge: No author: - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 citation: ama: Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74 apa: Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74 chicago: Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74. ieee: T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018. ista: Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74. mla: Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74. short: T. Bergmiller, N. Nikolic, (2018). datarep_id: '74' date_created: 2018-12-12T12:31:35Z date_published: 2018-02-07T00:00:00Z date_updated: 2024-02-21T13:44:45Z day: '07' ddc: - '579' department: - _id: CaGu doi: 10.15479/AT:ISTA:74 file: - access_level: open_access checksum: 61ebb92213cfffeba3ddbaff984b81af content_type: application/zip creator: system date_created: 2018-12-12T13:04:39Z date_updated: 2020-07-14T12:47:04Z file_id: '5637' file_name: IST-2018-74-v1+2_15-11-05.zip file_size: 3558703796 relation: main_file - access_level: open_access checksum: bf26649af310ef6892d68576515cde6d content_type: application/zip creator: system date_created: 2018-12-12T13:04:55Z date_updated: 2020-07-14T12:47:04Z file_id: '5638' file_name: IST-2018-74-v1+3_15-07-31.zip file_size: 1830422606 relation: main_file - access_level: open_access checksum: 8e46eedce06f22acb2be1a9b9d3f56bd content_type: application/zip creator: system date_created: 2018-12-12T13:05:11Z date_updated: 2020-07-14T12:47:04Z file_id: '5639' file_name: IST-2018-74-v1+4_Images_for_analysis.zip file_size: 2140849248 relation: main_file file_date_updated: 2020-07-14T12:47:04Z has_accepted_license: '1' keyword: - microscopy - microfluidics month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria publist_id: '7385' related_material: record: - id: '438' relation: research_paper status: public status: public title: Time-lapse microscopy data tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '161' abstract: - lang: eng text: 'Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells.' article_number: '2988' article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Andersson Anna full_name: Mc, Andersson Anna last_name: Mc - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9 apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9 chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9. ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018. ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988. mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9. short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018). date_created: 2018-12-11T11:44:57Z date_published: 2018-07-30T00:00:00Z date_updated: 2024-02-21T13:45:39Z day: '30' ddc: - '570' department: - _id: GaTk - _id: CaGu doi: 10.1038/s41467-018-05417-9 ec_funded: 1 external_id: isi: - '000440149300021' file: - access_level: open_access checksum: 3ba7ab27b27723c7dcf633e8fc1f8f18 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:44:28Z date_updated: 2020-07-14T12:45:06Z file_id: '5728' file_name: 2018_NatureComm_DeMartino.pdf file_size: 1043205 relation: main_file file_date_updated: 2020-07-14T12:45:06Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Communications publication_status: published publisher: Springer Nature publist_id: '7760' quality_controlled: '1' related_material: record: - id: '5587' relation: popular_science status: public scopus_import: '1' status: public title: Statistical mechanics for metabolic networks during steady state growth tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2018' ... --- _id: '5587' abstract: - lang: eng text: "Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)." article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62 apa: De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62 chicago: De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62. ieee: D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. ista: De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62. mla: De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62. short: D. De Martino, G. Tkačik, (2018). datarep_id: '111' date_created: 2018-12-12T12:31:41Z date_published: 2018-09-21T00:00:00Z date_updated: 2024-02-21T13:45:39Z day: '21' ddc: - '530' department: - _id: GaTk doi: 10.15479/AT:ISTA:62 ec_funded: 1 file: - access_level: open_access checksum: 97992e3e8cf8544ec985a48971708726 content_type: application/zip creator: system date_created: 2018-12-12T13:05:13Z date_updated: 2020-07-14T12:47:08Z file_id: '5641' file_name: IST-2018-111-v1+1_CODES.zip file_size: 14376 relation: main_file file_date_updated: 2020-07-14T12:47:08Z has_accepted_license: '1' keyword: - metabolic networks - e.coli core - maximum entropy - monte carlo markov chain sampling - ellipsoidal rounding month: '09' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publisher: Institute of Science and Technology Austria related_material: record: - id: '161' relation: research_paper status: public status: public title: Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH" tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '542' abstract: - lang: eng text: The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter. article_processing_charge: No article_type: original author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513 apa: Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300513 chicago: Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300513. ieee: R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018. ista: Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375. mla: Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513. short: R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375. date_created: 2018-12-11T11:47:04Z date_published: 2018-01-01T00:00:00Z date_updated: 2024-02-21T13:48:27Z day: '01' ddc: - '576' department: - _id: BeVi doi: 10.1534/genetics.117.300513 ec_funded: 1 external_id: isi: - '000419356300024' file: - access_level: open_access checksum: 2123845e7031a0cf043905be160f9e69 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:14Z date_updated: 2020-07-14T12:46:50Z file_id: '5132' file_name: IST-2018-1058-v1+1_365.full__1_.pdf file_size: 1311661 relation: main_file file_date_updated: 2020-07-14T12:46:50Z has_accepted_license: '1' intvolume: ' 208' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 365 - 375 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '7274' pubrep_id: '1058' quality_controlled: '1' related_material: record: - id: '5571' relation: popular_science status: public - id: '5572' relation: popular_science status: public scopus_import: '1' status: public title: Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 208 year: '2018' ... --- _id: '5751' abstract: - lang: eng text: 'Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.' article_number: '71' article_processing_charge: No author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7 apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7 chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7. ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018. ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71. mla: Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7. short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018). date_created: 2018-12-18T13:22:58Z date_published: 2018-06-14T00:00:00Z date_updated: 2024-02-21T13:48:42Z day: '14' ddc: - '004' - '519' - '576' department: - _id: KrCh doi: 10.1038/s42003-018-0078-7 ec_funded: 1 external_id: isi: - '000461126500071' file: - access_level: open_access checksum: a9db825fa3b64a51ff3de035ec973b3e content_type: application/pdf creator: dernst date_created: 2018-12-18T13:37:04Z date_updated: 2020-07-14T12:47:10Z file_id: '5752' file_name: 2018_CommBiology_Pavlogiannis.pdf file_size: 1804194 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 1' isi: 1 issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Communications Biology publication_identifier: issn: - 2399-3642 publication_status: published publisher: Springer Nature pubrep_id: '1045' quality_controlled: '1' related_material: record: - id: '7196' relation: part_of_dissertation status: public - id: '5559' relation: popular_science status: public scopus_import: '1' status: public title: Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 1 year: '2018' ... --- _id: '5757' abstract: - lang: eng text: "File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants." article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 citation: ama: Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757 apa: Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757 chicago: Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757. ieee: C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018. ista: Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757. mla: Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757. short: C. Fraisse, (2018). contributor: - first_name: Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse - first_name: Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 date_created: 2018-12-19T14:22:35Z date_published: 2018-12-19T00:00:00Z date_updated: 2024-02-21T13:59:18Z day: '19' ddc: - '576' department: - _id: BeVi - _id: NiBa doi: 10.15479/at:ista:/5757 ec_funded: 1 file: - access_level: open_access checksum: aed7ee9ca3f4dc07d8a66945f68e13cd content_type: application/zip creator: cfraisse date_created: 2018-12-19T14:19:52Z date_updated: 2020-07-14T12:47:11Z file_id: '5758' file_name: FileS1.zip file_size: 369837892 relation: main_file - access_level: open_access checksum: 3592e467b4d8206650860b612d6e12f3 content_type: application/zip creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5759' file_name: FileS2.zip file_size: 84856909 relation: main_file - access_level: open_access checksum: c37ac5d5437c457338afc128c1240655 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5760' file_name: FileS3.txt file_size: 881133 relation: main_file - access_level: open_access checksum: 943dfd14da61817441e33e3e3cb8cdb9 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5761' file_name: FileS4.txt file_size: 883742 relation: main_file - access_level: open_access checksum: 1c669b6c4690ec1bbca3e2da9f566d17 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5762' file_name: FileS5.txt file_size: 2495437 relation: main_file - access_level: open_access checksum: f40f661b987ca6fb6b47f650cbbb04e6 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5763' file_name: FileS6.txt file_size: 15913457 relation: main_file - access_level: open_access checksum: 25f41e5b8a075669c6c88d4c6713bf6f content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5764' file_name: FileS7.txt file_size: 2584120 relation: main_file - access_level: open_access checksum: f6c0bd3e63e14ddf5445bd69b43a9152 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5765' file_name: FileS8.txt file_size: 2446059 relation: main_file - access_level: open_access checksum: 0fe7a58a030b11bf3b9c8ff7a7addcae content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5766' file_name: FileS9.txt file_size: 100737 relation: main_file file_date_updated: 2020-07-14T12:47:11Z has_accepted_license: '1' keyword: - (mal)adaptation - pleiotropy - selective constraint - evo-devo - gene expression - Drosophila melanogaster month: '12' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publisher: Institute of Science and Technology Austria related_material: record: - id: '6089' relation: research_paper status: public status: public title: Supplementary Files for "Pleiotropy modulates the efficacy of selection in Drosophila melanogaster" type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '149' abstract: - lang: eng text: The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt citation: ama: Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040 apa: Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040 chicago: Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040. ieee: J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018. ista: Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. mla: Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040. short: J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:53Z date_published: 2018-07-12T00:00:00Z date_updated: 2024-02-22T14:34:33Z day: '12' ddc: - '515' - '519' degree_awarded: PhD department: - _id: LaEr doi: 10.15479/AT:ISTA:TH_1040 ec_funded: 1 file: - access_level: open_access checksum: d4dad55a7513f345706aaaba90cb1bb8 content_type: application/pdf creator: dernst date_created: 2019-04-08T13:55:20Z date_updated: 2020-07-14T12:44:57Z file_id: '6241' file_name: 2018_thesis_Alt.pdf file_size: 5801709 relation: main_file - access_level: closed checksum: d73fcf46300dce74c403f2b491148ab4 content_type: application/zip creator: dernst date_created: 2019-04-08T13:55:20Z date_updated: 2020-07-14T12:44:57Z file_id: '6242' file_name: 2018_thesis_Alt_source.zip file_size: 3802059 relation: source_file file_date_updated: 2020-07-14T12:44:57Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '456' project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7772' pubrep_id: '1040' related_material: record: - id: '1677' relation: part_of_dissertation status: public - id: '550' relation: part_of_dissertation status: public - id: '6183' relation: part_of_dissertation status: public - id: '566' relation: part_of_dissertation status: public - id: '1010' relation: part_of_dissertation status: public - id: '6240' relation: part_of_dissertation status: public - id: '6184' relation: part_of_dissertation status: public status: public supervisor: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 title: Dyson equation and eigenvalue statistics of random matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '415' abstract: - lang: eng text: Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field. acknowledgement: "We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n" article_number: '104307' article_processing_charge: No article_type: original author: - first_name: Wojciech full_name: Rzadkowski, Wojciech id: 48C55298-F248-11E8-B48F-1D18A9856A87 last_name: Rzadkowski orcid: 0000-0002-1106-4419 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591 apa: Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591 chicago: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591. ieee: W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018. ista: Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307. mla: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591. short: W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018). date_created: 2018-12-11T11:46:21Z date_published: 2018-03-14T00:00:00Z date_updated: 2024-02-28T13:01:59Z day: '14' department: - _id: MiLe doi: 10.1063/1.5017591 ec_funded: 1 external_id: arxiv: - '1711.09904' isi: - '000427517200065' intvolume: ' 148' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.09904 month: '03' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: The Journal of Chemical Physics publication_status: published publisher: AIP Publishing publist_id: '7408' quality_controlled: '1' related_material: record: - id: '10759' relation: dissertation_contains status: public scopus_import: '1' status: public title: Effect of a magnetic field on molecule–solvent angular momentum transfer type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 148 year: '2018' ... --- _id: '134' abstract: - lang: eng text: "The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface." acknowledged_ssus: - _id: ScienComp alternative_title: - SIGGRAPH article_number: '94' article_processing_charge: No author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Tomas full_name: Skrivan, Tomas id: 486A5A46-F248-11E8-B48F-1D18A9856A87 last_name: Skrivan - first_name: Matthias full_name: Mueller Fischer, Matthias last_name: Mueller Fischer - first_name: Nuttapong full_name: Chentanez, Nuttapong last_name: Chentanez - first_name: Miles full_name: Macklin, Miles last_name: Macklin - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336 apa: Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336 chicago: Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336. ieee: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018. ista: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94. mla: Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336. short: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018). date_created: 2018-12-11T11:44:48Z date_published: 2018-07-30T00:00:00Z date_updated: 2024-02-28T13:58:51Z day: '30' ddc: - '000' department: - _id: ChWo doi: 10.1145/3197517.3201336 ec_funded: 1 external_id: isi: - '000448185000055' file: - access_level: open_access checksum: db75ebabe2ec432bf41389e614d6ef62 content_type: application/pdf creator: dernst date_created: 2018-12-18T09:59:23Z date_updated: 2020-07-14T12:44:45Z file_id: '5744' file_name: 2018_ACM_Jeschke.pdf file_size: 22185016 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '7789' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/ scopus_import: '1' status: public title: Water surface wavelets tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2018' ... --- _id: '6339' abstract: - lang: eng text: We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment. article_number: '165301' article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Timur full_name: Tscherbul, Timur last_name: Tscherbul - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301 apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301 chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301. ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018. ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301. mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301. short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018). date_created: 2019-04-17T10:53:38Z date_published: 2018-10-16T00:00:00Z date_updated: 2024-02-28T13:15:09Z day: '16' department: - _id: MiLe doi: 10.1103/physrevlett.121.165301 external_id: arxiv: - '1803.07990' isi: - '000447468400008' intvolume: ' 121' isi: 1 issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.07990 month: '10' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/ scopus_import: '1' status: public title: Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2018' ... --- _id: '417' abstract: - lang: eng text: 'We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ' article_number: '165301' article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Timur full_name: Tscherbul, Timur last_name: Tscherbul - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301 apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301 chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301. ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018. ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301. mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301. short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018). date_created: 2018-12-11T11:46:22Z date_published: 2018-10-16T00:00:00Z date_updated: 2024-02-28T13:14:53Z day: '16' department: - _id: MiLe doi: 10.1103/PhysRevLett.121.165301 external_id: arxiv: - '1803.07990' intvolume: ' 121' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.07990 month: '10' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '8025' quality_controlled: '1' scopus_import: '1' status: public title: Diagrammatic Monte Carlo approach to rotating molecular impurities type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2018' ... --- _id: '412' abstract: - lang: eng text: Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana. acknowledgement: We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417. article_processing_charge: No article_type: original author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Urszula full_name: Kania, Urszula id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785 apa: Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785 chicago: Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785. ieee: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018. ista: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716. mla: Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785. short: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716. date_created: 2018-12-11T11:46:20Z date_published: 2018-04-09T00:00:00Z date_updated: 2024-03-28T23:30:06Z day: '09' ddc: - '580' department: - _id: JiFr doi: 10.1105/tpc.17.00785 ec_funded: 1 external_id: isi: - '000429441400018' pmid: - '29511054' file: - access_level: open_access checksum: 4e165e653b67d3f0684697f21aace5a1 content_type: application/pdf creator: dernst date_created: 2022-05-23T09:12:38Z date_updated: 2022-05-23T09:12:38Z file_id: '11406' file_name: 2018_PlantCell_Adamowski.pdf file_size: 4407538 relation: main_file success: 1 file_date_updated: 2022-05-23T09:12:38Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 700 - 716 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: The Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: published publisher: American Society of Plant Biologists publist_id: '7417' quality_controlled: '1' related_material: record: - id: '6269' relation: dissertation_contains status: public scopus_import: '1' status: public title: A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2018' ... --- _id: '5914' abstract: - lang: eng text: With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task. article_number: e0087 article_processing_charge: No author: - first_name: Dámaris K full_name: Rangel Guerrero, Dámaris K id: 4871BCE6-F248-11E8-B48F-1D18A9856A87 last_name: Rangel Guerrero orcid: 0000-0002-8602-4374 - first_name: James G. full_name: Donnett, James G. last_name: Donnett - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Krisztián full_name: Kovács, Krisztián id: 2AB5821E-F248-11E8-B48F-1D18A9856A87 last_name: Kovács orcid: 0000-0001-6251-1007 citation: ama: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018' apa: 'Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018' chicago: 'Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.' ieee: 'D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.' ista: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087.' mla: 'Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.' short: D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018). date_created: 2019-02-03T22:59:16Z date_published: 2018-07-27T00:00:00Z date_updated: 2024-03-28T23:30:10Z day: '27' ddc: - '570' department: - _id: JoCs doi: 10.1523/ENEURO.0087-18.2018 ec_funded: 1 external_id: isi: - '000443994700007' file: - access_level: open_access checksum: f4915d45fc7ad4648b7b7a13fdecca01 content_type: application/pdf creator: dernst date_created: 2019-02-05T12:48:36Z date_updated: 2020-07-14T12:47:13Z file_id: '5921' file_name: 2018_ENeuro_Guerrero.pdf file_size: 3746884 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 257D4372-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I2072-B27 name: Interneuron plasticity during spatial learning publication: eNeuro publication_status: published publisher: Society of Neuroscience quality_controlled: '1' related_material: record: - id: '6849' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 5 year: '2018' ... --- _id: '402' abstract: - lang: eng text: During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined. acknowledged_ssus: - _id: Bio acknowledgement: "M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line." article_processing_charge: No article_type: original author: - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Frank P full_name: Assen, Frank P id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87 last_name: Assen orcid: 0000-0003-3470-6119 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: Helga full_name: Schachner, Helga last_name: Schachner - first_name: Gabriele full_name: Asfour, Gabriele last_name: Asfour - first_name: Zsuzsanna full_name: Bagó Horváth, Zsuzsanna last_name: Bagó Horváth - first_name: Jens full_name: Stein, Jens last_name: Stein - first_name: Pavel full_name: Uhrin, Pavel last_name: Uhrin - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Dontscho full_name: Kerjaschki, Dontscho last_name: Kerjaschki citation: ama: Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662 apa: Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662 chicago: Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662. ieee: M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018. ista: Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411. mla: Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662. short: M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411. date_created: 2018-12-11T11:46:16Z date_published: 2018-03-23T00:00:00Z date_updated: 2024-03-28T23:30:09Z day: '23' department: - _id: MiSi doi: 10.1126/science.aal3662 ec_funded: 1 external_id: isi: - '000428043600047' pmid: - '29567714' intvolume: ' 359' isi: 1 issue: '6382' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/science.aal3662 month: '03' oa: 1 oa_version: Published Version page: 1408 - 1411 pmid: 1 project: - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '7428' quality_controlled: '1' related_material: record: - id: '6947' relation: dissertation_contains status: public scopus_import: '1' status: public title: Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 359 year: '2018' ...