[{"publisher":"Proceedings of the National Academy of Sciences","intvolume":" 114","title":"Detection and quantification of inbreeding depression for complex traits from SNP data","status":"public","publication_status":"published","_id":"7729","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","volume":114,"oa_version":"None","date_updated":"2021-01-12T08:15:09Z","date_created":"2020-04-30T10:47:19Z","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.1718598115","relation":"other"}]},"author":[{"first_name":"Loic","last_name":"Yengo","full_name":"Yengo, Loic"},{"full_name":"Zhu, Zhihong","first_name":"Zhihong","last_name":"Zhu"},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"full_name":"Weir, Bruce S.","last_name":"Weir","first_name":"Bruce S."},{"full_name":"Yang, Jian","first_name":"Jian","last_name":"Yang"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."}],"type":"journal_article","extern":"1","issue":"32","abstract":[{"text":"Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000 participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs for complete inbreeding; P<0.001). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data.","lang":"eng"}],"page":"8602-8607","article_type":"original","quality_controlled":"1","citation":{"ama":"Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 2017;114(32):8602-8607. doi:10.1073/pnas.1621096114","ista":"Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607.","ieee":"L. Yengo et al., “Detection and quantification of inbreeding depression for complex traits from SNP data,” Proceedings of the National Academy of Sciences, vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607, 2017.","apa":"Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., & Visscher, P. M. (2017). Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1621096114","mla":"Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences, vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07, doi:10.1073/pnas.1621096114.","short":"L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher, Proceedings of the National Academy of Sciences 114 (2017) 8602–8607.","chicago":"Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621096114."},"publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1621096114","date_published":"2017-08-08T00:00:00Z","publication_identifier":{"issn":["0027-8424","1091-6490"]},"article_processing_charge":"No","day":"08","month":"08"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is plausible. Existing studies on the adaptation of plasticity typically focus on single traits and a few populations, while theory about interactions among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale (for example, multiple populations) perspective is required. We present data from a landscape scale, replicated, multi-trait experiment using a classic predator–prey system centred on the water flea Daphnia pulex. We find predator regime-driven differences in genetic variation of multivariate plasticity. These differences are associated with strong divergent selection linked to a predation regime. Our findings are evidence for local adaptation of plasticity, suggesting that responses of populations to environmental variation depend on the conditions in which they evolved in the past."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7725","year":"2017","intvolume":" 2","publisher":"Springer Nature","title":"Predation drives local adaptation of phenotypic plasticity","publication_status":"published","status":"public","author":[{"first_name":"Julia","last_name":"Reger","full_name":"Reger, Julia"},{"first_name":"Martin I.","last_name":"Lind","full_name":"Lind, Martin I."},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"full_name":"Beckerman, Andrew P.","first_name":"Andrew P.","last_name":"Beckerman"}],"oa_version":"None","volume":2,"date_created":"2020-04-30T10:46:02Z","date_updated":"2021-01-12T08:15:07Z","article_processing_charge":"No","publication_identifier":{"issn":["2397-334X"]},"day":"27","month":"11","citation":{"apa":"Reger, J., Lind, M. I., Robinson, M. R., & Beckerman, A. P. (2017). Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0373-6","ieee":"J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives local adaptation of phenotypic plasticity,” Nature Ecology & Evolution, vol. 2. Springer Nature, pp. 100–107, 2017.","ista":"Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2, 100–107.","ama":"Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2017;2:100-107. doi:10.1038/s41559-017-0373-6","chicago":"Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution. Springer Nature, 2017. https://doi.org/10.1038/s41559-017-0373-6.","short":"J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology & Evolution 2 (2017) 100–107.","mla":"Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution, vol. 2, Springer Nature, 2017, pp. 100–07, doi:10.1038/s41559-017-0373-6."},"publication":"Nature Ecology & Evolution","page":"100-107","article_type":"original","quality_controlled":"1","date_published":"2017-11-27T00:00:00Z","doi":"10.1038/s41559-017-0373-6","language":[{"iso":"eng"}]},{"date_created":"2020-04-30T10:48:25Z","date_updated":"2021-01-12T08:15:10Z","volume":5,"author":[{"first_name":"Fleur C.","last_name":"Garton","full_name":"Garton, Fleur C."},{"full_name":"Benyamin, Beben","last_name":"Benyamin","first_name":"Beben"},{"full_name":"Zhao, Qiongyi","first_name":"Qiongyi","last_name":"Zhao"},{"full_name":"Liu, Zhijun","last_name":"Liu","first_name":"Zhijun"},{"full_name":"Gratten, Jacob","first_name":"Jacob","last_name":"Gratten"},{"full_name":"Henders, Anjali K.","first_name":"Anjali K.","last_name":"Henders"},{"full_name":"Zhang, Zong-Hong","first_name":"Zong-Hong","last_name":"Zhang"},{"first_name":"Janette","last_name":"Edson","full_name":"Edson, Janette"},{"first_name":"Sarah","last_name":"Furlong","full_name":"Furlong, Sarah"},{"first_name":"Sarah","last_name":"Morgan","full_name":"Morgan, Sarah"},{"first_name":"Susan","last_name":"Heggie","full_name":"Heggie, Susan"},{"first_name":"Kathryn","last_name":"Thorpe","full_name":"Thorpe, Kathryn"},{"last_name":"Pfluger","first_name":"Casey","full_name":"Pfluger, Casey"},{"first_name":"Karen A.","last_name":"Mather","full_name":"Mather, Karen A."},{"full_name":"Sachdev, Perminder S.","first_name":"Perminder S.","last_name":"Sachdev"},{"first_name":"Allan F.","last_name":"McRae","full_name":"McRae, Allan F."},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Shah","first_name":"Sonia","full_name":"Shah, Sonia"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"full_name":"Mangelsdorf, Marie","last_name":"Mangelsdorf","first_name":"Marie"},{"last_name":"Henderson","first_name":"Robert D.","full_name":"Henderson, Robert D."},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"full_name":"McCombe, Pamela A.","last_name":"McCombe","first_name":"Pamela A."}],"publication_status":"published","publisher":"Wiley","year":"2017","extern":"1","language":[{"iso":"eng"}],"doi":"10.1002/mgg3.302","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/mgg3.302"}],"oa":1,"month":"07","publication_identifier":{"issn":["2324-9269"]},"oa_version":"Published Version","title":"Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort","status":"public","intvolume":" 5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7733","abstract":[{"lang":"eng","text":"Sections\r\nPDFPDF\r\nTools\r\nShare\r\nAbstract\r\nBackground: Gene discovery has provided remarkable biological insights into amyotrophic lateral sclerosis (ALS). One challenge for clinical application of genetic testing is critical evaluation of the significance of reported variants.\r\nMethods: We use whole exome sequencing (WES) to develop a clinically relevant approach to identify a subset of ALS patients harboring likely pathogenic mutations. In parallel, we assess if DNA methylation can be used to screen for pathogenicity of novel variants since a methylation signature has been shown to associate with the pathogenic C9orf72 expansion, but has not been explored for other ALS mutations. Australian patients identified with ALS‐relevant variants were cross‐checked with population databases and case reports to critically assess whether they were “likely causal,” “uncertain significance,” or “unlikely causal.”\r\nResults: Published ALS variants were identified in >10% of patients; however, in only 3% of patients (4/120) could these be confidently considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential DNA methylation signature in these mutation carriers.\r\nConclusions: The use of WES in a typical ALS clinic demonstrates a critical approach to variant assessment with the capability to combine cohorts to enhance the largely unknown genetic basis of ALS."}],"issue":"4","type":"journal_article","date_published":"2017-07-01T00:00:00Z","article_type":"original","page":"418-428","publication":"Molecular Genetics & Genomic Medicine","citation":{"ista":"Garton FC, Benyamin B, Zhao Q, Liu Z, Gratten J, Henders AK, Zhang Z-H, Edson J, Furlong S, Morgan S, Heggie S, Thorpe K, Pfluger C, Mather KA, Sachdev PS, McRae AF, Robinson MR, Shah S, Visscher PM, Mangelsdorf M, Henderson RD, Wray NR, McCombe PA. 2017. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 5(4), 418–428.","apa":"Garton, F. C., Benyamin, B., Zhao, Q., Liu, Z., Gratten, J., Henders, A. K., … McCombe, P. A. (2017). Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. Wiley. https://doi.org/10.1002/mgg3.302","ieee":"F. C. Garton et al., “Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort,” Molecular Genetics & Genomic Medicine, vol. 5, no. 4. Wiley, pp. 418–428, 2017.","ama":"Garton FC, Benyamin B, Zhao Q, et al. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 2017;5(4):418-428. doi:10.1002/mgg3.302","chicago":"Garton, Fleur C., Beben Benyamin, Qiongyi Zhao, Zhijun Liu, Jacob Gratten, Anjali K. Henders, Zong-Hong Zhang, et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine. Wiley, 2017. https://doi.org/10.1002/mgg3.302.","mla":"Garton, Fleur C., et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine, vol. 5, no. 4, Wiley, 2017, pp. 418–28, doi:10.1002/mgg3.302.","short":"F.C. Garton, B. Benyamin, Q. Zhao, Z. Liu, J. Gratten, A.K. Henders, Z.-H. Zhang, J. Edson, S. Furlong, S. Morgan, S. Heggie, K. Thorpe, C. Pfluger, K.A. Mather, P.S. Sachdev, A.F. McRae, M.R. Robinson, S. Shah, P.M. Visscher, M. Mangelsdorf, R.D. Henderson, N.R. Wray, P.A. McCombe, Molecular Genetics & Genomic Medicine 5 (2017) 418–428."},"day":"01","article_processing_charge":"No"},{"type":"journal_article","extern":"1","issue":"2","abstract":[{"text":"Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n = 625) and skin (n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).","lang":"eng"}],"intvolume":" 206","publisher":"Genetics Society of America","status":"public","title":"Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7731","year":"2017","volume":206,"oa_version":"None","date_created":"2020-04-30T10:47:50Z","date_updated":"2021-01-12T08:15:10Z","author":[{"full_name":"Lloyd-Jones, Luke R.","last_name":"Lloyd-Jones","first_name":"Luke R."},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Moser, Gerhard","last_name":"Moser","first_name":"Gerhard"},{"full_name":"Zeng, Jian","first_name":"Jian","last_name":"Zeng"},{"full_name":"Beleza, Sandra","first_name":"Sandra","last_name":"Beleza"},{"full_name":"Barsh, Gregory S.","first_name":"Gregory S.","last_name":"Barsh"},{"full_name":"Tang, Hua","last_name":"Tang","first_name":"Hua"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."}],"article_processing_charge":"No","publication_identifier":{"issn":["0016-6731","1943-2631"]},"day":"01","month":"06","page":"1113-1126","quality_controlled":"1","article_type":"original","citation":{"mla":"Lloyd-Jones, Luke R., et al. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics, vol. 206, no. 2, Genetics Society of America, 2017, pp. 1113–26, doi:10.1534/genetics.116.193383.","short":"L.R. Lloyd-Jones, M.R. Robinson, G. Moser, J. Zeng, S. Beleza, G.S. Barsh, H. Tang, P.M. Visscher, Genetics 206 (2017) 1113–1126.","chicago":"Lloyd-Jones, Luke R., Matthew Richard Robinson, Gerhard Moser, Jian Zeng, Sandra Beleza, Gregory S. Barsh, Hua Tang, and Peter M. Visscher. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193383.","ama":"Lloyd-Jones LR, Robinson MR, Moser G, et al. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 2017;206(2):1113-1126. doi:10.1534/genetics.116.193383","ista":"Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, Tang H, Visscher PM. 2017. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 206(2), 1113–1126.","ieee":"L. R. Lloyd-Jones et al., “Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models,” Genetics, vol. 206, no. 2. Genetics Society of America, pp. 1113–1126, 2017.","apa":"Lloyd-Jones, L. R., Robinson, M. R., Moser, G., Zeng, J., Beleza, S., Barsh, G. S., … Visscher, P. M. (2017). Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193383"},"publication":"Genetics","language":[{"iso":"eng"}],"date_published":"2017-06-01T00:00:00Z","doi":"10.1534/genetics.116.193383"},{"month":"07","day":"01","publication_identifier":{"issn":["1531-7331","1545-4118"]},"article_processing_charge":"No","publication":"Annual Review of Materials Research","citation":{"ama":"Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 2017;47:217-246. doi:10.1146/annurev-matsci-070115-032036","ieee":"J. P. Sethna et al., “Deformation of crystals: Connections with statistical physics,” Annual Review of Materials Research, vol. 47. Annual Reviews, pp. 217–246, 2017.","apa":"Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J. R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. Annual Reviews. https://doi.org/10.1146/annurev-matsci-070115-032036","ista":"Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi S. 2017. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 47, 217–246.","short":"J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X. Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z. Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017) 217–246.","mla":"Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research, vol. 47, Annual Reviews, 2017, pp. 217–46, doi:10.1146/annurev-matsci-070115-032036.","chicago":"Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich, Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research. Annual Reviews, 2017. https://doi.org/10.1146/annurev-matsci-070115-032036."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1146/annurev-matsci-070115-032036","open_access":"1"}],"quality_controlled":"1","article_type":"original","page":"217-246","doi":"10.1146/annurev-matsci-070115-032036","date_published":"2017-07-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We give a bird's-eye view of the plastic deformation of crystals aimed at the statistical physics community, as well as a broad introduction to the statistical theories of forced rigid systems aimed at the plasticity community. Memory effects in magnets, spin glasses, charge density waves, and dilute colloidal suspensions are discussed in relation to the onset of plastic yielding in crystals. Dislocation avalanches and complex dislocation tangles are discussed via a brief introduction to the renormalization group and scaling. Analogies to emergent scale invariance in fracture, jamming, coarsening, and a variety of depinning transitions are explored. Dislocation dynamics in crystals challenge nonequilibrium statistical physics. Statistical physics provides both cautionary tales of subtle memory effects in nonequilibrium systems and systematic tools designed to address complex scale-invariant behavior on multiple length scales and timescales."}],"extern":"1","_id":"7755","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","publication_status":"published","status":"public","title":"Deformation of crystals: Connections with statistical physics","intvolume":" 47","publisher":"Annual Reviews","author":[{"last_name":"Sethna","first_name":"James P.","full_name":"Sethna, James P."},{"first_name":"Matthew K.","last_name":"Bierbaum","full_name":"Bierbaum, Matthew K."},{"last_name":"Dahmen","first_name":"Karin A.","full_name":"Dahmen, Karin A."},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"},{"full_name":"Greer, Julia R.","last_name":"Greer","first_name":"Julia R."},{"full_name":"Hayden, Lorien X.","first_name":"Lorien X.","last_name":"Hayden"},{"full_name":"Kent-Dobias, Jaron P.","first_name":"Jaron P.","last_name":"Kent-Dobias"},{"full_name":"Lee, Edward D.","last_name":"Lee","first_name":"Edward D."},{"last_name":"Liarte","first_name":"Danilo B.","full_name":"Liarte, Danilo B."},{"last_name":"Ni","first_name":"Xiaoyue","full_name":"Ni, Xiaoyue"},{"last_name":"Quinn","first_name":"Katherine N.","full_name":"Quinn, Katherine N."},{"last_name":"Raju","first_name":"Archishman","full_name":"Raju, Archishman"},{"full_name":"Rocklin, D. Zeb","first_name":"D. Zeb","last_name":"Rocklin"},{"last_name":"Shekhawat","first_name":"Ashivni","full_name":"Shekhawat, Ashivni"},{"last_name":"Zapperi","first_name":"Stefano","full_name":"Zapperi, Stefano"}],"date_updated":"2021-01-12T08:15:18Z","date_created":"2020-04-30T11:38:24Z","oa_version":"Published Version","volume":47},{"article_processing_charge":"No","publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"03","day":"07","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1612139114","date_published":"2017-03-07T00:00:00Z","page":"2520-2525","article_type":"original","quality_controlled":"1","citation":{"chicago":"Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1612139114.","short":"J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel, Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.","mla":"Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences, vol. 114, no. 10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:10.1073/pnas.1612139114.","apa":"Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2017). Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612139114","ieee":"J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” Proceedings of the National Academy of Sciences, vol. 114, no. 10. Proceedings of the National Academy of Sciences, pp. 2520–2525, 2017.","ista":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 114(10), 2520–2525.","ama":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 2017;114(10):2520-2525. doi:10.1073/pnas.1612139114"},"publication":"Proceedings of the National Academy of Sciences","extern":"1","issue":"10","abstract":[{"lang":"eng","text":"Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks."}],"type":"journal_article","oa_version":"None","volume":114,"date_updated":"2021-01-12T08:15:19Z","date_created":"2020-04-30T11:38:53Z","author":[{"full_name":"Rocks, Jason W.","last_name":"Rocks","first_name":"Jason W."},{"full_name":"Pashine, Nidhi","first_name":"Nidhi","last_name":"Pashine"},{"full_name":"Bischofberger, Irmgard","first_name":"Irmgard","last_name":"Bischofberger"},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."}],"publisher":"Proceedings of the National Academy of Sciences","intvolume":" 114","publication_status":"published","title":"Designing allostery-inspired response in mechanical networks","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7757","year":"2017"},{"page":"257-262","article_type":"original","quality_controlled":"1","citation":{"chicago":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1608838114.","mla":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:10.1073/pnas.1608838114.","short":"C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262.","ista":"Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262.","apa":"Goodrich, C. P., & Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1608838114","ieee":"C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” Proceedings of the National Academy of Sciences, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017.","ama":"Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 2017;114(2):257-262. doi:10.1073/pnas.1608838114"},"publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1608838114","date_published":"2017-01-10T00:00:00Z","publication_identifier":{"issn":["0027-8424","1091-6490"]},"article_processing_charge":"No","month":"01","day":"10","intvolume":" 114","publisher":"Proceedings of the National Academy of Sciences","status":"public","title":"Using active colloids as machines to weave and braid on the micrometer scale","publication_status":"published","_id":"7758","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","oa_version":"None","volume":114,"date_created":"2020-04-30T11:39:09Z","date_updated":"2021-01-12T08:15:20Z","author":[{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."}],"type":"journal_article","extern":"1","issue":"2","abstract":[{"text":"Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles.","lang":"eng"}]},{"year":"2017","_id":"7756","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 167","publisher":"Springer Nature","status":"public","title":"Emergent SO(3) symmetry of the frictionless shear jamming transition","publication_status":"published","author":[{"first_name":"Marco","last_name":"Baity-Jesi","full_name":"Baity-Jesi, Marco"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"},{"first_name":"James P.","last_name":"Sethna","full_name":"Sethna, James P."}],"volume":167,"oa_version":"None","date_updated":"2021-01-12T08:15:19Z","date_created":"2020-04-30T11:38:38Z","type":"journal_article","issue":"3-4","abstract":[{"lang":"eng","text":"We study the shear jamming of athermal frictionless soft spheres, and find that in the thermodynamic limit, a shear-jammed state exists with different elastic properties from the isotropically-jammed state. For example, shear-jammed states can have a non-zero residual shear stress in the thermodynamic limit that arises from long-range stress-stress correlations. As a result, the ratio of the shear and bulk moduli, which in isotropically-jammed systems vanishes as the jamming transition is approached from above, instead approaches a constant. Despite these striking differences, we argue that in a deeper sense, the shear jamming and isotropic jamming transitions actually have the same symmetry, and that the differences can be fully understood by rotating the six-dimensional basis of the elastic modulus tensor."}],"extern":"1","citation":{"apa":"Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., & Sethna, J. P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-016-1703-9","ieee":"M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent SO(3) symmetry of the frictionless shear jamming transition,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017.","ista":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 167(3–4), 735–748.","ama":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 2017;167(3-4):735-748. doi:10.1007/s10955-016-1703-9","chicago":"Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel, and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics. Springer Nature, 2017. https://doi.org/10.1007/s10955-016-1703-9.","short":"M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal of Statistical Physics 167 (2017) 735–748.","mla":"Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer Nature, 2017, pp. 735–48, doi:10.1007/s10955-016-1703-9."},"publication":"Journal of Statistical Physics","page":"735-748","article_type":"original","quality_controlled":"1","date_published":"2017-01-03T00:00:00Z","doi":"10.1007/s10955-016-1703-9","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-4715","1572-9613"]},"article_processing_charge":"No","month":"01","day":"03"},{"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09937"}],"external_id":{"arxiv":["1706.09937"]},"language":[{"iso":"eng"}],"conference":{"name":"DNA Computing and Molecular Programming"},"doi":"10.1007/978-3-319-66799-7_11","month":"01","publication_status":"published","publisher":"Springer","year":"2017","acknowledgement":"D. Alistarh - Supported by an SNF Ambizione Fellowship. A. Kosowski — Supported by Inria project GANG, ANR project DESCARTES, and\r\nNCN grant 2015/17/B/ST6/01897. D. Soloveichik — Supported by NSF grants CCF-1618895 and CCF-1652824.\r\n\r\n","date_created":"2018-12-11T11:48:30Z","date_updated":"2022-03-18T12:48:02Z","volume":"10467 LNCS","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Dudek, Bartłomiej","last_name":"Dudek","first_name":"Bartłomiej"},{"last_name":"Kosowski","first_name":"Adrian","full_name":"Kosowski, Adrian"},{"last_name":"Soloveichik","first_name":"David","full_name":"Soloveichik, David"},{"last_name":"Uznański","first_name":"Przemysław","full_name":"Uznański, Przemysław"}],"extern":"1","publist_id":"6868","page":"155 - 171","citation":{"mla":"Alistarh, Dan-Adrian, et al. Robust Detection in Leak-Prone Population Protocols. Vol. 10467 LNCS, Springer, 2017, pp. 155–71, doi:10.1007/978-3-319-66799-7_11.","short":"D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, P. Uznański, in:, Springer, 2017, pp. 155–171.","chicago":"Alistarh, Dan-Adrian, Bartłomiej Dudek, Adrian Kosowski, David Soloveichik, and Przemysław Uznański. “Robust Detection in Leak-Prone Population Protocols,” 10467 LNCS:155–71. Springer, 2017. https://doi.org/10.1007/978-3-319-66799-7_11.","ama":"Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. Robust detection in leak-prone population protocols. In: Vol 10467 LNCS. Springer; 2017:155-171. doi:10.1007/978-3-319-66799-7_11","ista":"Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. 2017. Robust detection in leak-prone population protocols. DNA Computing and Molecular Programming, LNCS, vol. 10467 LNCS, 155–171.","apa":"Alistarh, D.-A., Dudek, B., Kosowski, A., Soloveichik, D., & Uznański, P. (2017). Robust detection in leak-prone population protocols (Vol. 10467 LNCS, pp. 155–171). Presented at the DNA Computing and Molecular Programming, Springer. https://doi.org/10.1007/978-3-319-66799-7_11","ieee":"D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, and P. Uznański, “Robust detection in leak-prone population protocols,” presented at the DNA Computing and Molecular Programming, 2017, vol. 10467 LNCS, pp. 155–171."},"date_published":"2017-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Robust detection in leak-prone population protocols","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"788","oa_version":"None","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed with an appropriate error model in mind. Here we consider the model of chemical reaction networks that preserve molecular count (population protocols), and ask whether computation can be made robust to a natural model of unintended “leak” reactions. Our definition of leak is motivated by both the particular spurious behavior seen when implementing chemical reaction networks with DNA strand displacement cascades, as well as the unavoidable side reactions in any implementation due to the basic laws of chemistry. We develop a new “Robust Detection” algorithm for the problem of fast (logarithmic time) single molecule detection, and prove that it is robust to this general model of leaks. Besides potential applications in single molecule detection, the error-correction ideas developed here might enable a new class of robust-by-design chemical algorithms. Our analysis is based on a non-standard hybrid argument, combining ideas from discrete analysis of population protocols with classic Markov chain techniques.","lang":"eng"}]},{"_id":"787","acknowledgement":"Dan Alistarh was supported by a Swiss National Science\r\nFoundation Ambizione Fellowship. James Aspnes was supported by the National Science Foundation under grants\r\nCCF-1637385 and CCF-1650596. Rati Gelashvili was supported by the National Science Foundation under grants\r\nCCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and\r\nOracle and Intel corporations.\r\nThe authors would like to thank David Doty, David\r\nSoloveichik, and Milan Vojnovic for insightful discussions\r\nand feedback during the development of this work.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","title":"Time-space trade-offs in population protocols","status":"public","publication_status":"published","publisher":"SIAM","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"Eisenstat, David","first_name":"David","last_name":"Eisenstat"},{"full_name":"Rivest, Ronald","first_name":"Ronald","last_name":"Rivest"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"}],"date_updated":"2023-02-23T13:19:13Z","date_created":"2018-12-11T11:48:30Z","oa_version":"None","type":"conference","abstract":[{"text":"Population protocols are a popular model of distributed computing, in which randomly-interacting agents with little computational power cooperate to jointly perform computational tasks. Inspired by developments in molecular computation, and in particular DNA computing, recent algorithmic work has focused on the complexity of solving simple yet fundamental tasks in the population model, such as leader election (which requires convergence to a single agent in a special "leader" state), and majority (in which agents must converge to a decision as to which of two possible initial states had higher initial count). Known results point towards an inherent trade-off between the time complexity of such algorithms, and the space complexity, i.e. size of the memory available to each agent. In this paper, we explore this trade-off and provide new upper and lower bounds for majority and leader election. First, we prove a unified lower bound, which relates the space available per node with the time complexity achievable by a protocol: for instance, our result implies that any protocol solving either of these tasks for n agents using O(log log n) states must take (n=polylogn) expected time. This is the first result to characterize time complexity for protocols which employ super-constant number of states per node, and proves that fast, poly-logarithmic running times require protocols to have relatively large space costs. On the positive side, we give algorithms showing that fast, poly-logarithmic convergence time can be achieved using O(log2 n) space per node, in the case of both tasks. Overall, our results highlight a time complexity separation between O(log log n) and (log2 n) state space size for both majority and leader election in population protocols, and introduce new techniques, which should be applicable more broadly.","lang":"eng"}],"publist_id":"6869","extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1602.08032","open_access":"1"}],"oa":1,"citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, David Eisenstat, Ronald Rivest, and Rati Gelashvili. “Time-Space Trade-Offs in Population Protocols,” 2560–79. SIAM, 2017. https://doi.org/doi.org/10.1137/1.9781611974782.169.","mla":"Alistarh, Dan-Adrian, et al. Time-Space Trade-Offs in Population Protocols. SIAM, 2017, pp. 2560–79, doi:doi.org/10.1137/1.9781611974782.169.","short":"D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, R. Gelashvili, in:, SIAM, 2017, pp. 2560–2579.","ista":"Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. 2017. Time-space trade-offs in population protocols. SODA: Symposium on Discrete Algorithms, 2560–2579.","ieee":"D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, and R. Gelashvili, “Time-space trade-offs in population protocols,” presented at the SODA: Symposium on Discrete Algorithms, 2017, pp. 2560–2579.","apa":"Alistarh, D.-A., Aspnes, J., Eisenstat, D., Rivest, R., & Gelashvili, R. (2017). Time-space trade-offs in population protocols (pp. 2560–2579). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/doi.org/10.1137/1.9781611974782.169","ama":"Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. Time-space trade-offs in population protocols. In: SIAM; 2017:2560-2579. doi:doi.org/10.1137/1.9781611974782.169"},"page":"2560 - 2579","conference":{"name":"SODA: Symposium on Discrete Algorithms"},"doi":"doi.org/10.1137/1.9781611974782.169","date_published":"2017-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"01"}]