[{"oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 15","month":"04","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1744957X"],"issn":["17449561"]},"ec_funded":1,"volume":15,"related_material":{"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}],"record":[{"relation":"research_data","status":"public","id":"9798"},{"relation":"research_data","status":"public","id":"9799"}]},"issue":"4","_id":"6467","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-25T10:34:41Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa":1,"publisher":"Royal Society of London","quality_controlled":"1","publication":"Biology Letters","day":"03","year":"2019","isi":1,"date_created":"2019-05-19T21:59:15Z","date_published":"2019-04-03T00:00:00Z","doi":"10.1098/rsbl.2018.0881","article_number":"0881","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881."},"title":"The distribution of epistasis on simple fitness landscapes","article_processing_charge":"No","external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Welch","full_name":"Welch, John J.","first_name":"John J."}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00223751"],"eissn":["14697793"]},"issue":"11","volume":597,"pmid":1,"oa_version":"Published Version","abstract":[{"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%. ","lang":"eng"}],"intvolume":" 597","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1113/JP277681"}],"scopus_import":"1","date_updated":"2023-08-25T10:34:15Z","department":[{"_id":"GaNo"}],"_id":"6470","status":"public","article_type":"original","type":"journal_article","publication":"Journal of Physiology","day":"01","year":"2019","isi":1,"date_created":"2019-05-19T21:59:17Z","date_published":"2019-06-01T00:00:00Z","doi":"10.1113/JP277681","page":"2925–2947","oa":1,"publisher":"Wiley","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.","short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","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,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","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. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., & 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. Wiley. https://doi.org/10.1113/JP277681","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.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681."},"title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"article_processing_charge":"No","author":[{"full_name":"Éltes, Tímea","last_name":"Éltes","first_name":"Tímea"},{"last_name":"Szoboszlay","full_name":"Szoboszlay, Miklos","first_name":"Miklos"},{"id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","first_name":"Margit Katalin","last_name":"Szigeti","full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758"},{"full_name":"Nusser, Zoltan","last_name":"Nusser","first_name":"Zoltan"}]},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"citation":{"mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16.","ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000491468000016"]},"article_processing_charge":"No","author":[{"first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Soto, Miriam","orcid":"0000−0003−2936−5719","last_name":"Garcia Soto"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"},{"full_name":"Zeleznik, Luka","last_name":"Zeleznik","id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","first_name":"Luka"}],"title":"Membership-based synthesis of linear hybrid automata","oa":1,"quality_controlled":"1","publisher":"Springer","year":"2019","isi":1,"has_accepted_license":"1","publication":"31st International Conference on Computer-Aided Verification","day":"12","page":"297-314","date_created":"2019-05-27T07:09:53Z","doi":"10.1007/978-3-030-25540-4_16","date_published":"2019-07-12T00:00:00Z","_id":"6493","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer-Aided Verification","start_date":"2019-07-15","end_date":"2019-07-18","location":"New York City, NY, USA"},"type":"conference","keyword":["Synthesis","Linear hybrid automaton","Membership"],"status":"public","date_updated":"2023-08-25T10:40:41Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:32Z","abstract":[{"text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 11561","month":"07","publication_status":"published","publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6817","checksum":"1f1d61b83a151031745ef70a501da3d6","creator":"dernst","file_size":674795,"date_updated":"2020-07-14T12:47:32Z","file_name":"2019_CAV_GarciaSoto.pdf","date_created":"2019-08-14T11:05:30Z"}],"ec_funded":1,"volume":11561},{"quality_controlled":"1","publisher":"ACM Press","month":"02","abstract":[{"text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations.","lang":"eng"}],"oa_version":"None","page":"417-418","doi":"10.1145/3293883.3297000","date_published":"2019-02-01T00:00:00Z","date_created":"2019-05-24T10:09:12Z","publication_identifier":{"isbn":["9781450362252"]},"isi":1,"publication_status":"published","year":"2019","day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming","type":"conference_poster","conference":{"name":"PPoPP: Principles and Practice of Parallel Programming","start_date":"2019-02-16","location":"Washington, NY, United States","end_date":"2019-02-20"},"status":"public","_id":"6485","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","full_name":"Koval, Nikita","last_name":"Koval"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"external_id":{"isi":["000587604600044"]},"article_processing_charge":"No","department":[{"_id":"DaAl"}],"title":"Lock-free channels for programming via communicating sequential processes","citation":{"mla":"Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming via communicating sequential processes. ACM Press, 2019, pp. 417–418.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM Press, 2019.","ama":"Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels for programming via communicating sequential processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming (pp. 417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels for Programming via Communicating Sequential Processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming. ACM Press, 2019. https://doi.org/10.1145/3293883.3297000.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM Press,p."},"date_updated":"2023-08-25T10:41:20Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_updated":"2023-08-28T08:40:13Z","ddc":["580"],"file_date_updated":"2020-10-14T08:59:33Z","department":[{"_id":"JiFr"}],"_id":"6504","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-10-14T08:59:33Z","file_name":"2019_NewPhytologist_Zhang_accepted.pdf","date_updated":"2020-10-14T08:59:33Z","file_size":1099061,"creator":"dernst","checksum":"6488243334538f5c39099a701cbf76b9","file_id":"8661","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"volume":224,"issue":"2","abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 224","month":"10","citation":{"mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932","ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774.","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932.","ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["31111487"],"isi":["000487184200024"]},"article_processing_charge":"No","author":[{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956"},{"first_name":"P","last_name":"He","full_name":"He, P"},{"first_name":"X","last_name":"Ma","full_name":"Ma, X"},{"first_name":"Z","last_name":"Yang","full_name":"Yang, Z"},{"first_name":"C","full_name":"Pang, C","last_name":"Pang"},{"first_name":"J","last_name":"Yu","full_name":"Yu, J"},{"last_name":"Wang","full_name":"Wang, G","first_name":"G"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"G","full_name":"Xiao, G","last_name":"Xiao"}],"title":"Auxin-mediated statolith production for root gravitropism","year":"2019","has_accepted_license":"1","isi":1,"publication":"New Phytologist","day":"01","page":"761-774","date_created":"2019-05-28T14:33:26Z","doi":"10.1111/nph.15932","date_published":"2019-10-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Wiley"}]