[{"pubrep_id":"1069","volume":"Part F147772","file_date_updated":"2020-07-14T12:47:29Z","oa":1,"publication_status":"published","date_published":"2019-04-01T00:00:00Z","_id":"6378","abstract":[{"lang":"eng","text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin."}],"file":[{"date_created":"2019-05-06T12:09:27Z","file_id":"6379","relation":"main_file","content_type":"application/pdf","checksum":"fbfbcd5a0c7a743862bfc3045539a614","access_level":"open_access","date_updated":"2020-07-14T12:47:29Z","file_size":1023934,"creator":"dernst","file_name":"2019_ACM_Chatterjee.pdf"}],"article_processing_charge":"No","publication_identifier":{"isbn":["9781450359337"]},"scopus_import":"1","external_id":{"isi":["000474685800049"]},"date_updated":"2025-06-02T08:53:46Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","year":"2019","has_accepted_license":"1","status":"public","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","quality_controlled":"1","department":[{"_id":"KrCh"}],"isi":1,"publisher":"ACM","date_created":"2019-05-06T12:11:36Z","month":"04","page":"374-381","doi":"10.1145/3297280.3297319","ddc":["004"],"language":[{"iso":"eng"}],"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Pourdamghani","full_name":"Pourdamghani, Arash","first_name":"Arash"}],"type":"conference","day":"01","title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving","conference":{"name":"ACM Symposium on Applied Computing","start_date":"2019-04-08","end_date":"2019-04-12","location":"Limassol, Cyprus"},"citation":{"mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, vol. Part F147772, ACM, 2019, pp. 374–81, doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Part F147772:374–81. ACM, 2019. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>. Vol Part F147772. ACM; 2019:374-381. doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i> (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381."},"ec_funded":1},{"publication_identifier":{"issn":["2475-1421"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-25T23:30:18Z","year":"2019","has_accepted_license":"1","oa_version":"Published Version","pubrep_id":"1056","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":3,"file_date_updated":"2020-07-14T12:47:29Z","oa":1,"publication_status":"published","_id":"6380","date_published":"2019-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. "}],"file":[{"creator":"dernst","file_size":1294962,"file_name":"2019_ACM_POPL_Chatterjee.pdf","checksum":"c157752f96877b36685ad7063ada4524","access_level":"open_access","date_updated":"2020-07-14T12:47:29Z","file_id":"6381","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-06T12:23:11Z"}],"article_number":"53","issue":"POPL","ddc":["004"],"doi":"10.1145/3290366","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"type":"journal_article","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar"},{"full_name":"Okati, Nastaran","first_name":"Nastaran","last_name":"Okati"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis"}],"day":"01","title":"Efficient parameterized algorithms for data packing","citation":{"mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL, 53, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>.","ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53.","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL. ACM, 2019.","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. 2019;3(POPL). doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., &#38; Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. ACM. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019)."},"ec_funded":1,"status":"public","intvolume":"         3","publication":"Proceedings of the ACM on Programming Languages","department":[{"_id":"KrCh"}],"quality_controlled":"1","publisher":"ACM","date_created":"2019-05-06T12:18:17Z","month":"01"},{"day":"09","type":"dissertation","author":[{"last_name":"Lukacisin","first_name":"Martin","full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177"}],"alternative_title":["IST Austria Thesis"],"citation":{"apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>."},"title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.15479/AT:ISTA:6392","related_material":{"record":[{"relation":"part_of_dissertation","id":"1029","status":"public"}]},"month":"05","extern":"1","supervisor":[{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"date_created":"2019-05-09T19:53:00Z","page":"103","department":[{"_id":"ToBo"}],"status":"public","publisher":"IST Austria","oa_version":"Published Version","has_accepted_license":"1","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-22T09:19:41Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"file":[{"date_updated":"2020-07-14T12:47:29Z","access_level":"closed","checksum":"829bda074444857c7935171237bb7c0c","file_name":"Thesis_Draft_v3.4Final.docx","file_size":43740796,"creator":"mlukacisin","date_created":"2019-05-10T13:51:49Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"hidden","file_id":"6409"},{"creator":"mlukacisin","file_size":35228388,"file_name":"Thesis_Draft_v3.4FinalA.pdf","embargo":"2020-04-17","checksum":"56cb5e97f5f8fc41692401b53832d8e0","access_level":"open_access","date_updated":"2021-02-11T11:17:16Z","file_id":"6410","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-10T14:13:42Z"}],"_id":"6392","abstract":[{"text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. ","lang":"eng"}],"date_published":"2019-05-09T00:00:00Z","file_date_updated":"2021-02-11T11:17:16Z","publication_status":"published","oa":1},{"date_created":"2019-05-13T07:58:35Z","month":"04","isi":1,"publisher":"Springer Nature","intvolume":"        10","status":"public","publication":"Nature Communications","quality_controlled":"1","department":[{"_id":"SaSi"}],"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","citation":{"short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>","ieee":"H. F. Moussa <i>et al.</i>, “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>.","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>."},"type":"journal_article","author":[{"first_name":"Hagar F.","full_name":"Moussa, Hagar F.","last_name":"Moussa"},{"last_name":"Bsteh","first_name":"Daniel","full_name":"Bsteh, Daniel"},{"last_name":"Yelagandula","full_name":"Yelagandula, Ramesh","first_name":"Ramesh"},{"full_name":"Pribitzer, Carina","first_name":"Carina","last_name":"Pribitzer"},{"last_name":"Stecher","full_name":"Stecher, Karin","first_name":"Karin"},{"id":"4D883232-F248-11E8-B48F-1D18A9856A87","last_name":"Bartalska","full_name":"Bartalska, Katarina","first_name":"Katarina"},{"last_name":"Michetti","first_name":"Luca","full_name":"Michetti, Luca"},{"last_name":"Wang","first_name":"Jingkui","full_name":"Wang, Jingkui"},{"last_name":"Zepeda-Martinez","full_name":"Zepeda-Martinez, Jorge A.","first_name":"Jorge A."},{"last_name":"Elling","first_name":"Ulrich","full_name":"Elling, Ulrich"},{"full_name":"Stuckey, Jacob I.","first_name":"Jacob I.","last_name":"Stuckey"},{"last_name":"James","full_name":"James, Lindsey I.","first_name":"Lindsey I."},{"first_name":"Stephen V.","full_name":"Frye, Stephen V.","last_name":"Frye"},{"last_name":"Bell","full_name":"Bell, Oliver","first_name":"Oliver"}],"day":"29","ddc":["570"],"doi":"10.1038/s41467-019-09628-6","language":[{"iso":"eng"}],"article_processing_charge":"No","issue":"1","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"_id":"6412","date_published":"2019-04-29T00:00:00Z","file":[{"checksum":"6550a328335396c856db4cbdda7d2994","date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","file_name":"2019_NatureComm_Moussa.pdf","creator":"dernst","file_size":1223647,"date_created":"2019-05-14T08:45:51Z","content_type":"application/pdf","file_id":"6448","relation":"main_file"}],"article_number":"1931","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":10,"file_date_updated":"2020-07-14T12:47:29Z","oa_version":"Published Version","has_accepted_license":"1","year":"2019","publication_identifier":{"eissn":["20411723"]},"external_id":{"isi":["000466118700002"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:31:56Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:19:55Z","scopus_import":"1","external_id":{"arxiv":["1902.07351"],"isi":["000474496000002"]},"publication_identifier":{"issn":["03019322"]},"article_type":"original","oa_version":"Preprint","year":"2019","volume":117,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07351"}],"oa":1,"date_published":"2019-08-01T00:00:00Z","_id":"6413","abstract":[{"text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase.","lang":"eng"}],"arxiv":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1016/j.ijmultiphaseflow.2019.04.027","day":"01","author":[{"full_name":"Song, Baofang","first_name":"Baofang","last_name":"Song"},{"first_name":"Carlos","full_name":"Plana, Carlos","last_name":"Plana"},{"orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M","first_name":"Jose M","last_name":"Lopez Alonso"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"}],"type":"journal_article","citation":{"apa":"Song, B., Plana, C., Lopez Alonso, J. M., &#38; Avila, M. (2019). Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. 2019;117:14-24. doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>, vol. 117, Elsevier, 2019, pp. 14–24, doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>.","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” <i>International Journal of Multiphase Flow</i>, vol. 117. Elsevier, pp. 14–24, 2019.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>."},"title":"Phase-field simulation of core-annular pipe flow","quality_controlled":"1","department":[{"_id":"BjHo"}],"publication":"International Journal of Multiphase Flow","status":"public","intvolume":"       117","publisher":"Elsevier","isi":1,"month":"08","date_created":"2019-05-13T07:58:35Z","page":"14-24"},{"page":"63-68","article_processing_charge":"No","month":"06","date_published":"2019-06-01T00:00:00Z","_id":"6415","abstract":[{"text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success.","lang":"eng"}],"date_created":"2019-05-13T07:58:36Z","publication_status":"published","publisher":"Elsevier","isi":1,"department":[{"_id":"SyCr"}],"quality_controlled":"1","publication":"Current Opinion in Insect Science","volume":33,"status":"public","intvolume":"        33","citation":{"ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68.","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” <i>Current Opinion in Insect Science</i>, vol. 33. Elsevier, pp. 63–68, 2019.","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>.","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>, vol. 33, Elsevier, 2019, pp. 63–68, doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>.","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>","ama":"Cremer S. Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. 2019;33:63-68. doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>"},"title":"Pathogens and disease defense of invasive ants","day":"01","year":"2019","oa_version":"None","type":"journal_article","author":[{"last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"date_updated":"2023-08-25T10:31:31Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000477666000012"]},"doi":"10.1016/j.cois.2019.03.011","publication_identifier":{"eissn":["22145753"],"issn":["22145745"]}},{"oa_version":"Published Version","has_accepted_license":"1","year":"2019","external_id":{"isi":["000476569800003"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-02-21T12:45:41Z","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"eissn":["1759-6653"]},"file":[{"date_created":"2019-05-14T08:29:38Z","content_type":"application/pdf","file_id":"6446","relation":"main_file","date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_name":"2019_GBE_Huylmans.pdf","creator":"dernst","file_size":1256303}],"abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"_id":"6418","date_published":"2019-04-01T00:00:00Z","article_processing_charge":"No","issue":"4","file_date_updated":"2020-07-14T12:47:29Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":11,"publication_status":"published","oa":1,"day":"01","type":"journal_article","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana"},{"id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","last_name":"Gammerdinger","first_name":"William J","full_name":"Gammerdinger, William J"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"citation":{"mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044."},"ec_funded":1,"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","language":[{"iso":"eng"}],"doi":"10.1093/gbe/evz053","ddc":["570"],"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"related_material":{"record":[{"status":"public","id":"6060","relation":"popular_science"}]},"month":"04","date_created":"2019-05-13T07:58:38Z","page":"1033-1044","publication":"Genome biology and evolution","quality_controlled":"1","department":[{"_id":"BeVi"}],"status":"public","intvolume":"        11","publisher":"Oxford University Press","isi":1},{"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1371/journal.pgen.1008079","related_material":{"record":[{"id":"9789","relation":"research_data","status":"public"},{"status":"public","id":"9790","relation":"research_data"},{"relation":"research_data","id":"9797","status":"public"}]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"day":"10","author":[{"first_name":"Victoria","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Usmanova","full_name":"Usmanova, Dinara R.","first_name":"Dinara R."},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V.","first_name":"Ekaterina V."},{"first_name":"Lorena","full_name":"Espinar, Lorena","last_name":"Espinar"},{"orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen","first_name":"Karen"},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S.","last_name":"Bogatyreva"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry"},{"last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Avvakumov","first_name":"Sergey","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"last_name":"Filion","full_name":"Filion, Guillaume J.","first_name":"Guillaume J."},{"last_name":"Carey","first_name":"Lucas B.","full_name":"Carey, Lucas B."},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","citation":{"apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>.","ieee":"V. Pokusaeva <i>et al.</i>, “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” <i>PLoS Genetics</i>, vol. 15, no. 4. Public Library of Science, 2019.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>."},"ec_funded":1,"title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","publication":"PLoS Genetics","department":[{"_id":"FyKo"}],"quality_controlled":"1","intvolume":"        15","status":"public","publisher":"Public Library of Science","isi":1,"month":"04","date_created":"2019-05-13T07:58:38Z","scopus_import":"1","external_id":{"isi":["000466866000029"]},"date_updated":"2023-08-25T10:30:37Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["15537404"]},"year":"2019","oa_version":"Published Version","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:30Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":15,"publication_status":"published","oa":1,"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"6445","date_created":"2019-05-14T08:26:08Z","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","creator":"dernst","file_size":3726017,"checksum":"cf3889c8a8a16053dacf9c3776cbe217","date_updated":"2020-07-14T12:47:30Z","access_level":"open_access"}],"article_number":"e1008079","_id":"6419","abstract":[{"lang":"eng","text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible."}],"date_published":"2019-04-10T00:00:00Z","article_processing_charge":"No","issue":"4"},{"article_processing_charge":"No","date_published":"2019-04-16T00:00:00Z","_id":"6428","abstract":[{"lang":"eng","text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system."}],"file":[{"date_created":"2020-10-08T17:25:45Z","success":1,"relation":"main_file","file_id":"8633","content_type":"application/pdf","checksum":"b8e967081e051d1c55ca5d18fb187890","access_level":"open_access","date_updated":"2020-10-08T17:25:45Z","file_size":1055421,"creator":"dernst","file_name":"2019_ACM_Ferrere.pdf"}],"oa":1,"publication_status":"published","file_date_updated":"2020-10-08T17:25:45Z","has_accepted_license":"1","year":"2019","oa_version":"Submitted Version","publication_identifier":{"isbn":["9781450362825"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:19:23Z","scopus_import":"1","external_id":{"isi":["000516713900007"]},"page":"57-66","date_created":"2019-05-13T08:13:46Z","month":"04","isi":1,"publisher":"ACM","status":"public","department":[{"_id":"ToHe"}],"quality_controlled":"1","publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","conference":{"location":"Montreal, Canada","start_date":"2019-04-16","end_date":"2019-04-18","name":"HSCC: Hybrid Systems Computation and Control"},"title":"Interface-aware signal temporal logic","citation":{"mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2019, pp. 57–66, doi:<a href=\"https://doi.org/10.1145/3302504.3311800\">10.1145/3302504.3311800</a>.","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, Montreal, Canada, 2019, pp. 57–66.","ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, 57–66. ACM, 2019. <a href=\"https://doi.org/10.1145/3302504.3311800\">https://doi.org/10.1145/3302504.3311800</a>.","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., &#38; Kapinski, J. (2019). Interface-aware signal temporal logic. In <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i> (pp. 57–66). Montreal, Canada: ACM. <a href=\"https://doi.org/10.1145/3302504.3311800\">https://doi.org/10.1145/3302504.3311800</a>","ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2019:57-66. doi:<a href=\"https://doi.org/10.1145/3302504.3311800\">10.1145/3302504.3311800</a>","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66."},"author":[{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Donzé","first_name":"Alexandre","full_name":"Donzé, Alexandre"},{"last_name":"Ito","first_name":"Hisahiro","full_name":"Ito, Hisahiro"},{"first_name":"James","full_name":"Kapinski, James","last_name":"Kapinski"}],"type":"conference","day":"16","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"ddc":["000"],"doi":"10.1145/3302504.3311800","language":[{"iso":"eng"}]},{"publication_identifier":{"eissn":["16113349"],"isbn":["9783030172589"],"issn":["03029743"]},"scopus_import":"1","date_updated":"2023-09-08T11:33:20Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","oa_version":"Preprint","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2018/426","open_access":"1"}],"publication_status":"published","volume":11443,"article_processing_charge":"No","_id":"6430","date_published":"2019-04-06T00:00:00Z","abstract":[{"lang":"eng","text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in  Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14)."}],"related_material":{"record":[{"status":"public","id":"10035","relation":"dissertation_contains"}]},"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-3-030-17259-6_11","language":[{"iso":"eng"}],"title":"Adaptively secure proxy re-encryption","conference":{"location":"Beijing, China","start_date":"2019-04-14","end_date":"2019-04-17","name":"PKC: Public-Key Cryptograhy"},"citation":{"short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346.","ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>","chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>.","ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.","mla":"Fuchsbauer, Georg, et al. <i>Adaptively Secure Proxy Re-Encryption</i>. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>."},"ec_funded":1,"type":"conference","author":[{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer"},{"last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Klein","first_name":"Karen","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["LNCS"],"day":"06","publisher":"Springer Nature","intvolume":"     11443","status":"public","department":[{"_id":"KrPi"}],"quality_controlled":"1","page":"317-346","date_created":"2019-05-13T08:13:46Z","month":"04"},{"title":"Collective defenses of garden ants against a fungal pathogen","citation":{"ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria."},"ec_funded":1,"author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"day":"07","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1999","status":"public"}]},"ddc":["570","006","578","592"],"doi":"10.15479/AT:ISTA:6435","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"language":[{"iso":"eng"}],"page":"183","supervisor":[{"first_name":"Sylvia M","full_name":"Cremer, Sylvia M","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-05-13T08:58:35Z","month":"05","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"SyCr"}],"has_accepted_license":"1","year":"2019","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T12:57:04Z","article_processing_charge":"No","_id":"6435","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"date_published":"2019-05-07T00:00:00Z","file":[{"checksum":"6daf2d2086111aa8fd3fbc919a3e2833","access_level":"open_access","date_updated":"2021-02-11T11:17:15Z","creator":"casillas","file_size":3895187,"file_name":"tesisDoctoradoBC.pdf","embargo":"2020-05-08","date_created":"2019-05-13T09:16:20Z","file_id":"6438","relation":"main_file","content_type":"application/pdf"},{"content_type":"application/zip","relation":"source_file","file_id":"6439","date_created":"2019-05-13T09:16:20Z","embargo_to":"open_access","file_name":"tesisDoctoradoBC.zip","creator":"casillas","file_size":7365118,"date_updated":"2020-07-14T12:47:30Z","access_level":"closed","checksum":"3d221aaff7559a7060230a1ff610594f"}],"oa":1,"publication_status":"published","file_date_updated":"2021-02-11T11:17:15Z"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:18:46Z","scopus_import":"1","external_id":{"isi":["000475740600104"]},"oa_version":"Submitted Version","has_accepted_license":"1","year":"2019","oa":1,"publication_status":"published","volume":38,"file_date_updated":"2020-07-14T12:47:30Z","issue":"4","article_processing_charge":"No","_id":"6442","date_published":"2019-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples."}],"article_number":"130","file":[{"date_created":"2019-05-14T07:03:55Z","file_id":"6443","relation":"main_file","content_type":"application/pdf","checksum":"1b737dfe3e051aba8f3f4ab1dceda673","access_level":"open_access","date_updated":"2020-07-14T12:47:30Z","file_size":44328918,"creator":"dernst","file_name":"2019_ACM_Schreck.pdf"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/","description":"News on IST Homepage"}]},"project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"doi":"10.1145/3306346.3323002","ddc":["000","005"],"language":[{"iso":"eng"}],"title":"Fundamental solutions for water wave animation","ec_funded":1,"citation":{"short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>","apa":"Schreck, C., Hafner, C., &#38; Wojtan, C. (2019). Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>.","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 130, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>."},"type":"journal_article","author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille","first_name":"Camille","last_name":"Schreck"},{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"day":"01","isi":1,"publisher":"ACM","status":"public","intvolume":"        38","quality_controlled":"1","department":[{"_id":"ChWo"}],"publication":"ACM Transactions on Graphics","date_created":"2019-05-14T07:04:06Z","month":"07"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":15,"file_date_updated":"2020-07-14T12:47:30Z","oa":1,"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"text":"Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis.","lang":"eng"}],"_id":"6451","date_published":"2019-05-31T00:00:00Z","file":[{"file_size":8365970,"creator":"dernst","file_name":"2019_iScience_Amberg.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:30Z","checksum":"a9ad2296726c9474ad5860c9c2f53622","relation":"main_file","file_id":"6452","content_type":"application/pdf","date_created":"2019-05-14T11:51:51Z"}],"article_processing_charge":"No","publication_identifier":{"issn":["2589-0042"]},"external_id":{"isi":["000470104600022"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-08T11:38:04Z","oa_version":"Published Version","year":"2019","has_accepted_license":"1","status":"public","intvolume":"        15","publication":"iScience","quality_controlled":"1","department":[{"_id":"SiHi"}],"isi":1,"publisher":"Elsevier","date_created":"2019-05-14T11:47:40Z","month":"05","page":"243-256","doi":"10.1016/j.isci.2019.04.018","ddc":["570"],"language":[{"iso":"eng"}],"type":"journal_article","author":[{"last_name":"Amberg","full_name":"Amberg, Nicole","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"last_name":"Sotiropoulou","full_name":"Sotiropoulou, Panagiota A.","first_name":"Panagiota A."},{"last_name":"Heller","full_name":"Heller, Gerwin","first_name":"Gerwin"},{"full_name":"Lichtenberger, Beate M.","first_name":"Beate M.","last_name":"Lichtenberger"},{"last_name":"Holcmann","first_name":"Martin","full_name":"Holcmann, Martin"},{"first_name":"Bahar","full_name":"Camurdanoglu, Bahar","last_name":"Camurdanoglu"},{"last_name":"Baykuscheva-Gentscheva","full_name":"Baykuscheva-Gentscheva, Temenuschka","first_name":"Temenuschka"},{"first_name":"Cedric","full_name":"Blanpain, Cedric","last_name":"Blanpain"},{"last_name":"Sibilia","first_name":"Maria","full_name":"Sibilia, Maria"}],"day":"31","title":"EGFR controls hair shaft differentiation in a p53-independent manner","citation":{"mla":"Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” <i>IScience</i>, vol. 15, Elsevier, 2019, pp. 243–56, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">10.1016/j.isci.2019.04.018</a>.","ista":"Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256.","ieee":"N. Amberg <i>et al.</i>, “EGFR controls hair shaft differentiation in a p53-independent manner,” <i>iScience</i>, vol. 15. Elsevier, pp. 243–256, 2019.","chicago":"Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">https://doi.org/10.1016/j.isci.2019.04.018</a>.","apa":"Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">https://doi.org/10.1016/j.isci.2019.04.018</a>","ama":"Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. <i>iScience</i>. 2019;15:243-256. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">10.1016/j.isci.2019.04.018</a>","short":"N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256."}},{"pmid":1,"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1016/j.neuron.2019.01.051","citation":{"mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">10.1016/j.neuron.2019.01.051</a>.","chicago":"Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">https://doi.org/10.1016/j.neuron.2019.01.051</a>.","ieee":"G. Ortiz-Álvarez <i>et al.</i>, “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” <i>Neuron</i>, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.","ista":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7.","ama":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. <i>Neuron</i>. 2019;102(1):159-172.e7. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">10.1016/j.neuron.2019.01.051</a>","apa":"Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">https://doi.org/10.1016/j.neuron.2019.01.051</a>","short":"G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7."},"ec_funded":1,"title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","day":"03","author":[{"last_name":"Ortiz-Álvarez","full_name":"Ortiz-Álvarez, G","first_name":"G"},{"last_name":"Daclin","full_name":"Daclin, M","first_name":"M"},{"first_name":"A","full_name":"Shihavuddin, A","last_name":"Shihavuddin"},{"first_name":"P","full_name":"Lansade, P","last_name":"Lansade"},{"last_name":"Fortoul","first_name":"A","full_name":"Fortoul, A"},{"last_name":"Faucourt","full_name":"Faucourt, M","first_name":"M"},{"last_name":"Clavreul","first_name":"S","full_name":"Clavreul, S"},{"last_name":"Lalioti","full_name":"Lalioti, ME","first_name":"ME"},{"last_name":"Taraviras","first_name":"S","full_name":"Taraviras, S"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"first_name":"J","full_name":"Livet, J","last_name":"Livet"},{"last_name":"Meunier","full_name":"Meunier, A","first_name":"A"},{"first_name":"A","full_name":"Genovesio, A","last_name":"Genovesio"},{"last_name":"Spassky","first_name":"N","full_name":"Spassky, N"}],"type":"journal_article","publisher":"Elsevier","isi":1,"publication":"Neuron","quality_controlled":"1","department":[{"_id":"SiHi"}],"status":"public","intvolume":"       102","page":"159-172.e7","month":"04","date_created":"2019-05-14T13:06:30Z","scopus_import":"1","external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T13:02:21Z","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"oa_version":"Published Version","year":"2019","has_accepted_license":"1","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:30Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":102,"article_processing_charge":"No","issue":"1","file":[{"content_type":"application/pdf","file_id":"6457","relation":"main_file","date_created":"2019-05-15T09:28:41Z","file_name":"2019_Neuron_Ortiz.pdf","creator":"dernst","file_size":7288572,"date_updated":"2020-07-14T12:47:30Z","access_level":"open_access","checksum":"1fb6e195c583eb0c5cabf26f69ff6675"}],"_id":"6454","date_published":"2019-04-03T00:00:00Z","abstract":[{"text":"Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.","lang":"eng"}]},{"title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","citation":{"short":"L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini, I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science 364 (2019).","apa":"Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., … Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aav2522\">https://doi.org/10.1126/science.aav2522</a>","ama":"Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. <i>Science</i>. 2019;364(6440). doi:<a href=\"https://doi.org/10.1126/science.aav2522\">10.1126/science.aav2522</a>","ieee":"L. Telley <i>et al.</i>, “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” <i>Science</i>, vol. 364, no. 6440. AAAS, 2019.","ista":"Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 364(6440), eaav2522.","chicago":"Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini, et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” <i>Science</i>. AAAS, 2019. <a href=\"https://doi.org/10.1126/science.aav2522\">https://doi.org/10.1126/science.aav2522</a>.","mla":"Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” <i>Science</i>, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:<a href=\"https://doi.org/10.1126/science.aav2522\">10.1126/science.aav2522</a>."},"ec_funded":1,"author":[{"last_name":"Telley","full_name":"Telley, L","first_name":"L"},{"last_name":"Agirman","first_name":"G","full_name":"Agirman, G"},{"first_name":"J","full_name":"Prados, J","last_name":"Prados"},{"last_name":"Amberg","full_name":"Amberg, Nicole","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"full_name":"Fièvre, S","first_name":"S","last_name":"Fièvre"},{"last_name":"Oberst","first_name":"P","full_name":"Oberst, P"},{"full_name":"Bartolini, G","first_name":"G","last_name":"Bartolini"},{"first_name":"I","full_name":"Vitali, I","last_name":"Vitali"},{"full_name":"Cadilhac, C","first_name":"C","last_name":"Cadilhac"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Nguyen, L","first_name":"L","last_name":"Nguyen"},{"full_name":"Dayer, A","first_name":"A","last_name":"Dayer"},{"full_name":"Jabaudon, D","first_name":"D","last_name":"Jabaudon"}],"type":"journal_article","day":"10","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/","description":"News on IST Homepage","relation":"press_release"}]},"pmid":1,"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.1126/science.aav2522","language":[{"iso":"eng"}],"date_created":"2019-05-14T13:07:47Z","month":"05","isi":1,"publisher":"AAAS","intvolume":"       364","status":"public","publication":"Science","quality_controlled":"1","department":[{"_id":"SiHi"}],"oa_version":"Published Version","year":"2019","article_type":"original","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"external_id":{"pmid":["31073041"],"isi":["000467631800034"]},"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T11:51:09Z","article_processing_charge":"No","issue":"6440","date_published":"2019-05-10T00:00:00Z","_id":"6455","abstract":[{"text":"During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity.","lang":"eng"}],"article_number":"eaav2522","oa":1,"main_file_link":[{"url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf","open_access":"1"}],"publication_status":"published","volume":364},{"page":"630-649","month":"07","date_created":"2019-05-16T11:22:30Z","publisher":"Springer","isi":1,"publication":"31st International Conference on Computer-Aided Verification","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"quality_controlled":"1","intvolume":"     11561","status":"public","citation":{"mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” <i>31st International Conference on Computer-Aided Verification</i>, vol. 11561, Springer, 2019, pp. 630–49, doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">10.1007/978-3-030-25540-4_36</a>.","chicago":"Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In <i>31st International Conference on Computer-Aided Verification</i>, 11561:630–49. Springer, 2019. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">https://doi.org/10.1007/978-3-030-25540-4_36</a>.","ista":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.","ieee":"G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in <i>31st International Conference on Computer-Aided Verification</i>, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: <i>31st International Conference on Computer-Aided Verification</i>. Vol 11561. Springer; 2019:630-649. doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">10.1007/978-3-030-25540-4_36</a>","apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., &#38; Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In <i>31st International Conference on Computer-Aided Verification</i> (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">https://doi.org/10.1007/978-3-030-25540-4_36</a>","short":"G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649."},"title":"Run-time optimization for learned controllers through quantitative games","conference":{"end_date":"2019-07-18","start_date":"2019-07-13","name":"CAV: Computer Aided Verification","location":"New York, NY, United States"},"day":"12","type":"conference","author":[{"last_name":"Avni","full_name":"Avni, Guy","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bettina","full_name":"Konighofer, Bettina","last_name":"Konighofer"},{"full_name":"Pranger, Stefan","first_name":"Stefan","last_name":"Pranger"}],"alternative_title":["LNCS"],"project":[{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-25540-4_36","ddc":["000"],"article_processing_charge":"No","file":[{"checksum":"c231579f2485c6fd4df17c9443a4d80b","access_level":"open_access","date_updated":"2020-07-14T12:47:31Z","creator":"dernst","file_size":659766,"file_name":"2019_CAV_Avni.pdf","date_created":"2019-08-14T09:35:24Z","file_id":"6816","relation":"main_file","content_type":"application/pdf"}],"_id":"6462","date_published":"2019-07-12T00:00:00Z","abstract":[{"text":"A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive  synthesis.  First,  we  abstract  the  plant  by  building  a  stochastic  model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles.","lang":"eng"}],"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:31Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":11561,"year":"2019","oa_version":"Published Version","has_accepted_license":"1","scopus_import":"1","external_id":{"isi":["000491468000036"]},"date_updated":"2023-08-25T10:33:27Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]}},{"citation":{"short":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019).","apa":"Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., &#38; Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-09974-5\">https://doi.org/10.1038/s41467-019-09974-5</a>","ama":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-09974-5\">10.1038/s41467-019-09974-5</a>","ista":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013.","ieee":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","chicago":"Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-09974-5\">https://doi.org/10.1038/s41467-019-09974-5</a>.","mla":"Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” <i>Nature Communications</i>, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-09974-5\">10.1038/s41467-019-09974-5</a>."},"title":"A modular degron library for synthetic circuits in mammalian cells","day":"01","type":"journal_article","author":[{"last_name":"Chassin","full_name":"Chassin, Hélène","first_name":"Hélène"},{"first_name":"Marius","full_name":"Müller, Marius","last_name":"Müller"},{"full_name":"Tigges, Marcel","first_name":"Marcel","last_name":"Tigges"},{"last_name":"Scheller","first_name":"Leo","full_name":"Scheller, Leo"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz","full_name":"Lang, Moritz"},{"last_name":"Fussenegger","first_name":"Martin","full_name":"Fussenegger, Martin"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-023-36111-0","relation":"erratum"}]},"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1038/s41467-019-09974-5","month":"05","date_created":"2019-05-19T21:59:14Z","publisher":"Springer Nature","isi":1,"publication":"Nature Communications","quality_controlled":"1","department":[{"_id":"CaGu"}],"intvolume":"        10","status":"public","year":"2019","oa_version":"Published Version","has_accepted_license":"1","external_id":{"isi":["000466338600006"]},"scopus_import":"1","date_updated":"2023-08-25T10:33:51Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["20411723"]},"article_processing_charge":"No","issue":"1","article_number":"2013","file":[{"date_created":"2019-05-20T07:33:54Z","content_type":"application/pdf","file_id":"6471","relation":"main_file","date_updated":"2020-07-14T12:47:31Z","access_level":"open_access","checksum":"e214d3e4f8c81e35981583c4569b51b8","file_name":"2019_NatureComm_Chassin.pdf","file_size":1191827,"creator":"dernst"}],"_id":"6465","date_published":"2019-05-01T00:00:00Z","abstract":[{"lang":"eng","text":"Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells."}],"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:31Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":10},{"title":"Breaking down barriers in morning glories","citation":{"apa":"Field, D., &#38; Fraisse, C. (2019). Breaking down barriers in morning glories. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. <i>Molecular ecology</i>. 2019;28(7):1579-1581. doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>.","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” <i>Molecular ecology</i>, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>."},"author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David","last_name":"Field"},{"last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"}],"type":"journal_article","day":"01","ddc":["580","576"],"doi":"10.1111/mec.15048","language":[{"iso":"eng"}],"page":"1579-1581","date_created":"2019-05-19T21:59:15Z","month":"04","isi":1,"publisher":"Wiley","status":"public","intvolume":"        28","publication":"Molecular ecology","quality_controlled":"1","department":[{"_id":"NiBa"}],"year":"2019","has_accepted_license":"1","oa_version":"Published Version","publication_identifier":{"eissn":["1365294X"]},"external_id":{"isi":["000474808300001"]},"scopus_import":"1","date_updated":"2023-08-25T10:37:30Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","issue":"7","_id":"6466","abstract":[{"lang":"eng","text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates."}],"date_published":"2019-04-01T00:00:00Z","file":[{"content_type":"application/pdf","file_id":"6472","relation":"main_file","date_created":"2019-05-20T11:49:06Z","file_name":"2019_MolecularEcology_Field.pdf","creator":"dernst","file_size":367711,"checksum":"521e3aff3e9263ddf2ffbfe0b6157715","date_updated":"2020-07-14T12:47:31Z","access_level":"open_access"}],"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":28,"file_date_updated":"2020-07-14T12:47:31Z"},{"oa_version":"Published Version","year":"2019","article_type":"original","publication_identifier":{"issn":["17449561"],"eissn":["1744957X"]},"date_updated":"2023-08-25T10:34:41Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"issue":"4","article_processing_charge":"No","_id":"6467","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"date_published":"2019-04-03T00:00:00Z","article_number":"0881","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"oa":1,"publication_status":"published","volume":15,"title":"The distribution of epistasis on simple fitness landscapes","ec_funded":1,"citation":{"ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” <i>Biology Letters</i>, vol. 15, no. 4. Royal Society of London, 2019.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>. Royal Society of London, 2019. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","apa":"Fraisse, C., &#38; Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>"},"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","first_name":"John J.","last_name":"Welch"}],"type":"journal_article","day":"03","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"pmid":1,"related_material":{"record":[{"id":"9798","relation":"research_data","status":"public"},{"status":"public","id":"9799","relation":"research_data"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}]},"doi":"10.1098/rsbl.2018.0881","language":[{"iso":"eng"}],"date_created":"2019-05-19T21:59:15Z","month":"04","isi":1,"publisher":"Royal Society of London","status":"public","intvolume":"        15","quality_controlled":"1","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication":"Biology Letters"},{"title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","citation":{"mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” <i>Journal of Physiology</i>, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:<a href=\"https://doi.org/10.1113/JP277681\">10.1113/JP277681</a>.","chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” <i>Journal of Physiology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1113/JP277681\">https://doi.org/10.1113/JP277681</a>.","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” <i>Journal of Physiology</i>, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947.","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. <i>Journal of Physiology</i>. 2019;597(11):2925–2947. doi:<a href=\"https://doi.org/10.1113/JP277681\">10.1113/JP277681</a>","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., &#38; Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. <i>Journal of Physiology</i>. Wiley. <a href=\"https://doi.org/10.1113/JP277681\">https://doi.org/10.1113/JP277681</a>","short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947."},"author":[{"last_name":"Éltes","full_name":"Éltes, Tímea","first_name":"Tímea"},{"last_name":"Szoboszlay","first_name":"Miklos","full_name":"Szoboszlay, Miklos"},{"id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9500-8758","first_name":"Margit Katalin","full_name":"Szigeti, Margit Katalin","last_name":"Szigeti"},{"last_name":"Nusser","full_name":"Nusser, Zoltan","first_name":"Zoltan"}],"type":"journal_article","day":"01","pmid":1,"doi":"10.1113/JP277681","language":[{"iso":"eng"}],"page":"2925–2947","date_created":"2019-05-19T21:59:17Z","month":"06","isi":1,"publisher":"Wiley","intvolume":"       597","status":"public","publication":"Journal of Physiology","quality_controlled":"1","department":[{"_id":"GaNo"}],"year":"2019","oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["14697793"],"issn":["00223751"]},"external_id":{"isi":["000470780400013"],"pmid":["31006863"]},"scopus_import":"1","date_updated":"2023-08-25T10:34:15Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","issue":"11","abstract":[{"lang":"eng","text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. "}],"_id":"6470","date_published":"2019-06-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1113/JP277681","open_access":"1"}],"oa":1,"publication_status":"published","volume":597}]