[{"intvolume":" 9","month":"12","main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-07862-y","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Male pattern baldness (MPB) is a sex-limited, age-related, complex trait. We study MPB genetics in 205,327 European males from the UK Biobank. Here we show that MPB is strongly heritable and polygenic, with pedigree-heritability of 0.62 (SE = 0.03) estimated from close relatives, and SNP-heritability of 0.39 (SE = 0.01) from conventionally-unrelated males. We detect 624 near-independent genome-wide loci, contributing SNP-heritability of 0.25 (SE = 0.01), of which 26 X-chromosome loci explain 11.6%. Autosomal genetic variance is enriched for common variants and regions of lower linkage disequilibrium. We identify plausible genetic correlations between MPB and multiple sex-limited markers of earlier puberty, increased bone mineral density (rg = 0.15) and pancreatic β-cell function (rg = 0.12). Correlations with reproductive traits imply an effect on fitness, consistent with an estimated linear selection gradient of -0.018 per MPB standard deviation. Overall, we provide genetic insights into MPB: a phenotype of interest in its own right, with value as a model sex-limited, complex trait."}],"date_created":"2020-04-30T10:41:19Z","volume":9,"date_published":"2018-12-20T00:00:00Z","doi":"10.1038/s41467-018-07862-y","publication":"Nature Communications","language":[{"iso":"eng"}],"day":"20","year":"2018","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"status":"public","type":"journal_article","article_type":"original","article_number":"5407","_id":"7712","title":"Dissection of genetic variation and evidence for pleiotropy in male pattern baldness","article_processing_charge":"No","author":[{"full_name":"Yap, Chloe X.","last_name":"Yap","first_name":"Chloe X."},{"full_name":"Sidorenko, Julia","last_name":"Sidorenko","first_name":"Julia"},{"full_name":"Wu, Yang","last_name":"Wu","first_name":"Yang"},{"first_name":"Kathryn E.","full_name":"Kemper, Kathryn E.","last_name":"Kemper"},{"first_name":"Jian","full_name":"Yang, Jian","last_name":"Yang"},{"last_name":"Wray","full_name":"Wray, Naomi R.","first_name":"Naomi R."},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ista":"Yap CX, Sidorenko J, Wu Y, Kemper KE, Yang J, Wray NR, Robinson MR, Visscher PM. 2018. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 9, 5407.","chicago":"Yap, Chloe X., Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang, Naomi R. Wray, Matthew Richard Robinson, and Peter M. Visscher. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-07862-y.","short":"C.X. Yap, J. Sidorenko, Y. Wu, K.E. Kemper, J. Yang, N.R. Wray, M.R. Robinson, P.M. Visscher, Nature Communications 9 (2018).","ieee":"C. X. Yap et al., “Dissection of genetic variation and evidence for pleiotropy in male pattern baldness,” Nature Communications, vol. 9. Springer Nature, 2018.","ama":"Yap CX, Sidorenko J, Wu Y, et al. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 2018;9. doi:10.1038/s41467-018-07862-y","apa":"Yap, C. X., Sidorenko, J., Wu, Y., Kemper, K. E., Yang, J., Wray, N. R., … Visscher, P. M. (2018). Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-07862-y","mla":"Yap, Chloe X., et al. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications, vol. 9, 5407, Springer Nature, 2018, doi:10.1038/s41467-018-07862-y."},"date_updated":"2021-01-12T08:15:02Z"},{"article_processing_charge":"No","author":[{"first_name":"Robert M.","full_name":"Maier, Robert M.","last_name":"Maier"},{"last_name":"Zhu","full_name":"Zhu, Zhihong","first_name":"Zhihong"},{"full_name":"Lee, Sang Hong","last_name":"Lee","first_name":"Sang Hong"},{"last_name":"Trzaskowski","full_name":"Trzaskowski, Maciej","first_name":"Maciej"},{"full_name":"Ruderfer, Douglas M.","last_name":"Ruderfer","first_name":"Douglas M."},{"last_name":"Stahl","full_name":"Stahl, Eli A.","first_name":"Eli A."},{"first_name":"Stephan","last_name":"Ripke","full_name":"Ripke, Stephan"},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"}],"title":"Improving genetic prediction by leveraging genetic correlations among human diseases and traits","date_updated":"2021-01-12T08:15:03Z","citation":{"ista":"Maier RM, Zhu Z, Lee SH, Trzaskowski M, Ruderfer DM, Stahl EA, Ripke S, Wray NR, Yang J, Visscher PM, Robinson MR. 2018. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 9, 989.","chicago":"Maier, Robert M., Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Douglas M. Ruderfer, Eli A. Stahl, Stephan Ripke, et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02769-6.","ama":"Maier RM, Zhu Z, Lee SH, et al. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 2018;9. doi:10.1038/s41467-017-02769-6","apa":"Maier, R. M., Zhu, Z., Lee, S. H., Trzaskowski, M., Ruderfer, D. M., Stahl, E. A., … Robinson, M. R. (2018). Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02769-6","ieee":"R. M. Maier et al., “Improving genetic prediction by leveraging genetic correlations among human diseases and traits,” Nature Communications, vol. 9. Springer Nature, 2018.","short":"R.M. Maier, Z. Zhu, S.H. Lee, M. Trzaskowski, D.M. Ruderfer, E.A. Stahl, S. Ripke, N.R. Wray, J. Yang, P.M. Visscher, M.R. Robinson, Nature Communications 9 (2018).","mla":"Maier, Robert M., et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications, vol. 9, 989, Springer Nature, 2018, doi:10.1038/s41467-017-02769-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"7716","article_number":"989","date_created":"2020-04-30T10:42:29Z","volume":9,"date_published":"2018-03-07T00:00:00Z","doi":"10.1038/s41467-017-02769-6","year":"2018","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"publication":"Nature Communications","language":[{"iso":"eng"}],"day":"07","oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-017-02769-6","open_access":"1"}],"quality_controlled":"1","publisher":"Springer Nature","intvolume":" 9","month":"03","abstract":[{"text":"Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait.","lang":"eng"}],"oa_version":"Published Version"},{"page":"948-954","date_created":"2020-04-30T10:42:12Z","doi":"10.1038/s41562-018-0476-3","issue":"12","date_published":"2018-11-26T00:00:00Z","volume":2,"publication_status":"published","year":"2018","publication_identifier":{"issn":["2397-3374"]},"publication":"Nature Human Behaviour","language":[{"iso":"eng"}],"day":"26","publisher":"Springer Nature","quality_controlled":"1","intvolume":" 2","month":"11","abstract":[{"lang":"eng","text":"Preference for mates with similar phenotypes; that is, assortative mating, is widely observed in humans1,2,3,4,5 and has evolutionary consequences6,7,8. Under Fisher's classical theory6, assortative mating is predicted to induce a signature in the genome at trait-associated loci that can be detected and quantified. Here, we develop and apply a method to quantify assortative mating on a specific trait by estimating the correlation (θ) between genetic predictors of the trait from single nucleotide polymorphisms on odd- versus even-numbered chromosomes. We show by theory and simulation that the effect of assortative mating can be quantified in the presence of population stratification. We applied this approach to 32 complex traits and diseases using single nucleotide polymorphism data from ~400,000 unrelated individuals of European ancestry. We found significant evidence of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%), both of which were consistent with theoretical predictions. Overall, our results imply that assortative mating involves multiple traits and affects the genomic architecture of loci that are associated with these traits, and that the consequence of mate choice can be detected from a random sample of genomes."}],"oa_version":"None","article_processing_charge":"No","author":[{"first_name":"Loic","last_name":"Yengo","full_name":"Yengo, Loic"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Keller, Matthew C.","last_name":"Keller","first_name":"Matthew C."},{"full_name":"Kemper, Kathryn E.","last_name":"Kemper","first_name":"Kathryn E."},{"last_name":"Yang","full_name":"Yang, Yuanhao","first_name":"Yuanhao"},{"last_name":"Trzaskowski","full_name":"Trzaskowski, Maciej","first_name":"Maciej"},{"first_name":"Jacob","full_name":"Gratten, Jacob","last_name":"Gratten"},{"first_name":"Patrick","last_name":"Turley","full_name":"Turley, Patrick"},{"first_name":"David","full_name":"Cesarini, David","last_name":"Cesarini"},{"last_name":"Benjamin","full_name":"Benjamin, Daniel J.","first_name":"Daniel J."},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"full_name":"Goddard, Michael E.","last_name":"Goddard","first_name":"Michael E."},{"first_name":"Jian","last_name":"Yang","full_name":"Yang, Jian"},{"first_name":"Peter M.","full_name":"Visscher, Peter M.","last_name":"Visscher"}],"title":"Imprint of assortative mating on the human genome","date_updated":"2021-01-12T08:15:03Z","citation":{"chicago":"Yengo, Loic, Matthew Richard Robinson, Matthew C. Keller, Kathryn E. Kemper, Yuanhao Yang, Maciej Trzaskowski, Jacob Gratten, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour. Springer Nature, 2018. https://doi.org/10.1038/s41562-018-0476-3.","ista":"Yengo L, Robinson MR, Keller MC, Kemper KE, Yang Y, Trzaskowski M, Gratten J, Turley P, Cesarini D, Benjamin DJ, Wray NR, Goddard ME, Yang J, Visscher PM. 2018. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2(12), 948–954.","mla":"Yengo, Loic, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour, vol. 2, no. 12, Springer Nature, 2018, pp. 948–54, doi:10.1038/s41562-018-0476-3.","ama":"Yengo L, Robinson MR, Keller MC, et al. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2018;2(12):948-954. doi:10.1038/s41562-018-0476-3","apa":"Yengo, L., Robinson, M. R., Keller, M. C., Kemper, K. E., Yang, Y., Trzaskowski, M., … Visscher, P. M. (2018). Imprint of assortative mating on the human genome. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-018-0476-3","short":"L. Yengo, M.R. Robinson, M.C. Keller, K.E. Kemper, Y. Yang, M. Trzaskowski, J. Gratten, P. Turley, D. Cesarini, D.J. Benjamin, N.R. Wray, M.E. Goddard, J. Yang, P.M. Visscher, Nature Human Behaviour 2 (2018) 948–954.","ieee":"L. Yengo et al., “Imprint of assortative mating on the human genome,” Nature Human Behaviour, vol. 2, no. 12. Springer Nature, pp. 948–954, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"7715"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ista":"Zhu Z, Zheng Z, Zhang F, Wu Y, Trzaskowski M, Maier R, Robinson MR, McGrath JJ, Visscher PM, Wray NR, Yang J. 2018. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 9, 224.","chicago":"Zhu, Zhihong, Zhili Zheng, Futao Zhang, Yang Wu, Maciej Trzaskowski, Robert Maier, Matthew Richard Robinson, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02317-2.","short":"Z. Zhu, Z. Zheng, F. Zhang, Y. Wu, M. Trzaskowski, R. Maier, M.R. Robinson, J.J. McGrath, P.M. Visscher, N.R. Wray, J. Yang, Nature Communications 9 (2018).","ieee":"Z. Zhu et al., “Causal associations between risk factors and common diseases inferred from GWAS summary data,” Nature Communications, vol. 9. Springer Nature, 2018.","apa":"Zhu, Z., Zheng, Z., Zhang, F., Wu, Y., Trzaskowski, M., Maier, R., … Yang, J. (2018). Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02317-2","ama":"Zhu Z, Zheng Z, Zhang F, et al. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 2018;9. doi:10.1038/s41467-017-02317-2","mla":"Zhu, Zhihong, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications, vol. 9, 224, Springer Nature, 2018, doi:10.1038/s41467-017-02317-2."},"date_updated":"2021-01-12T08:15:03Z","title":"Causal associations between risk factors and common diseases inferred from GWAS summary data","article_processing_charge":"No","author":[{"first_name":"Zhihong","full_name":"Zhu, Zhihong","last_name":"Zhu"},{"last_name":"Zheng","full_name":"Zheng, Zhili","first_name":"Zhili"},{"full_name":"Zhang, Futao","last_name":"Zhang","first_name":"Futao"},{"last_name":"Wu","full_name":"Wu, Yang","first_name":"Yang"},{"last_name":"Trzaskowski","full_name":"Trzaskowski, Maciej","first_name":"Maciej"},{"last_name":"Maier","full_name":"Maier, Robert","first_name":"Robert"},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"first_name":"John J.","full_name":"McGrath, John J.","last_name":"McGrath"},{"last_name":"Visscher","full_name":"Visscher, Peter M.","first_name":"Peter M."},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"}],"article_number":"224","_id":"7714","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication":"Nature Communications","day":"15","year":"2018","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"date_created":"2020-04-30T10:41:55Z","doi":"10.1038/s41467-017-02317-2","volume":9,"date_published":"2018-01-15T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"Health risk factors such as body mass index (BMI) and serum cholesterol are associated with many common diseases. It often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. We develop and apply a method (called GSMR) that performs a multi-SNP Mendelian randomization analysis using summary-level data from genome-wide association studies to test the causal associations of BMI, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (EduYears) with common diseases (sample sizes of up to 405,072). We identify a number of causal associations including a protective effect of LDL-cholesterol against type-2 diabetes (T2D) that might explain the side effects of statins on T2D, a protective effect of EduYears against Alzheimer’s disease, and bidirectional associations with opposite effects (e.g., higher BMI increases the risk of T2D but the effect of T2D on BMI is negative).","lang":"eng"}],"intvolume":" 9","month":"01","oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-017-02317-2","open_access":"1"}],"publisher":"Springer Nature","quality_controlled":"1"},{"oa_version":"Published Version","abstract":[{"text":"There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height (P=2.46×10−5), waist-to-hip ratio (P=2.77×10−4), and schizophrenia (P=3.96×10−5) are significantly more differentiated among populations than matched “control” SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height (P=2.01×10−6) and schizophrenia (P=5.16×10−18) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations.","lang":"eng"}],"intvolume":" 9","month":"05","main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-04191-y","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","language":[{"iso":"eng"}],"day":"14","publication_status":"published","year":"2018","publication_identifier":{"issn":["2041-1723"]},"date_created":"2020-04-30T10:41:36Z","volume":9,"doi":"10.1038/s41467-018-04191-y","date_published":"2018-05-14T00:00:00Z","article_number":"1865","_id":"7713","status":"public","article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:15:02Z","citation":{"apa":"Guo, J., Wu, Y., Zhu, Z., Zheng, Z., Trzaskowski, M., Zeng, J., … Yang, J. (2018). Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04191-y","ama":"Guo J, Wu Y, Zhu Z, et al. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 2018;9. doi:10.1038/s41467-018-04191-y","short":"J. Guo, Y. Wu, Z. Zhu, Z. Zheng, M. Trzaskowski, J. Zeng, M.R. Robinson, P.M. Visscher, J. Yang, Nature Communications 9 (2018).","ieee":"J. Guo et al., “Global genetic differentiation of complex traits shaped by natural selection in humans,” Nature Communications, vol. 9. Springer Nature, 2018.","mla":"Guo, Jing, et al. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications, vol. 9, 1865, Springer Nature, 2018, doi:10.1038/s41467-018-04191-y.","ista":"Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J. 2018. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 9, 1865.","chicago":"Guo, Jing, Yang Wu, Zhihong Zhu, Zhili Zheng, Maciej Trzaskowski, Jian Zeng, Matthew Richard Robinson, Peter M. Visscher, and Jian Yang. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04191-y."},"title":"Global genetic differentiation of complex traits shaped by natural selection in humans","article_processing_charge":"No","author":[{"first_name":"Jing","last_name":"Guo","full_name":"Guo, Jing"},{"first_name":"Yang","last_name":"Wu","full_name":"Wu, Yang"},{"first_name":"Zhihong","last_name":"Zhu","full_name":"Zhu, Zhihong"},{"full_name":"Zheng, Zhili","last_name":"Zheng","first_name":"Zhili"},{"full_name":"Trzaskowski, Maciej","last_name":"Trzaskowski","first_name":"Maciej"},{"full_name":"Zeng, Jian","last_name":"Zeng","first_name":"Jian"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"first_name":"Peter M.","full_name":"Visscher, Peter M.","last_name":"Visscher"},{"last_name":"Yang","full_name":"Yang, Jian","first_name":"Jian"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Maier RM, Visscher PM, Robinson MR, Wray NR. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 2018;48(7):1055-1067. doi:10.1017/s0033291717002318","apa":"Maier, R. M., Visscher, P. M., Robinson, M. R., & Wray, N. R. (2018). Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. Cambridge University Press. https://doi.org/10.1017/s0033291717002318","short":"R.M. Maier, P.M. Visscher, M.R. Robinson, N.R. Wray, Psychological Medicine 48 (2018) 1055–1067.","ieee":"R. M. Maier, P. M. Visscher, M. R. Robinson, and N. R. Wray, “Embracing polygenicity: A review of methods and tools for psychiatric genetics research,” Psychological Medicine, vol. 48, no. 7. Cambridge University Press, pp. 1055–1067, 2018.","mla":"Maier, R. M., et al. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine, vol. 48, no. 7, Cambridge University Press, 2018, pp. 1055–67, doi:10.1017/s0033291717002318.","ista":"Maier RM, Visscher PM, Robinson MR, Wray NR. 2018. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 48(7), 1055–1067.","chicago":"Maier, R. M., P. M. Visscher, Matthew Richard Robinson, and N. R. Wray. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine. Cambridge University Press, 2018. https://doi.org/10.1017/s0033291717002318."},"title":"Embracing polygenicity: A review of methods and tools for psychiatric genetics research","author":[{"first_name":"R. M.","full_name":"Maier, R. M.","last_name":"Maier"},{"last_name":"Visscher","full_name":"Visscher, P. M.","first_name":"P. M."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"first_name":"N. R.","full_name":"Wray, N. R.","last_name":"Wray"}],"article_processing_charge":"No","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"day":"01","publication":"Psychological Medicine","year":"2018","date_published":"2018-05-01T00:00:00Z","doi":"10.1017/s0033291717002318","date_created":"2020-04-30T10:44:35Z","page":"1055-1067","_id":"7721","status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-01-12T08:15:05Z","oa_version":"Published Version","abstract":[{"text":"The availability of genome-wide genetic data on hundreds of thousands of people has led to an equally rapid growth in methodologies available to analyse these data. While the motivation for undertaking genome-wide association studies (GWAS) is identification of genetic markers associated with complex traits, once generated these data can be used for many other analyses. GWAS have demonstrated that complex traits exhibit a highly polygenic genetic architecture, often with shared genetic risk factors across traits. New methods to analyse data from GWAS are increasingly being used to address a diverse set of questions about the aetiology of complex traits and diseases, including psychiatric disorders. Here, we give an overview of some of these methods and present examples of how they have contributed to our understanding of psychiatric disorders. We consider: (i) estimation of the extent of genetic influence on traits, (ii) uncovering of shared genetic control between traits, (iii) predictions of genetic risk for individuals, (iv) uncovering of causal relationships between traits, (v) identifying causal single-nucleotide polymorphisms and genes or (vi) the detection of genetic heterogeneity. This classification helps organise the large number of recently developed methods, although some could be placed in more than one category. While some methods require GWAS data on individual people, others simply use GWAS summary statistics data, allowing novel well-powered analyses to be conducted at a low computational burden.","lang":"eng"}],"month":"05","intvolume":" 48","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/s0033291717002318"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0033-2917","1469-8978"]},"publication_status":"published","volume":48,"issue":"7"},{"type":"journal_article","article_type":"original","status":"public","_id":"7723","article_processing_charge":"No","author":[{"first_name":"Luke R.","full_name":"Lloyd-Jones, Luke R.","last_name":"Lloyd-Jones"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"last_name":"Yang","full_name":"Yang, Jian","first_name":"Jian"},{"first_name":"Peter M.","full_name":"Visscher, Peter M.","last_name":"Visscher"}],"title":"Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio","date_updated":"2021-01-12T08:15:06Z","citation":{"chicago":"Lloyd-Jones, Luke R., Matthew Richard Robinson, Jian Yang, and Peter M. Visscher. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300360.","ista":"Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. 2018. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 208(4), 1397–1408.","mla":"Lloyd-Jones, Luke R., et al. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1397–408, doi:10.1534/genetics.117.300360.","apa":"Lloyd-Jones, L. R., Robinson, M. R., Yang, J., & Visscher, P. M. (2018). Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300360","ama":"Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 2018;208(4):1397-1408. doi:10.1534/genetics.117.300360","short":"L.R. Lloyd-Jones, M.R. Robinson, J. Yang, P.M. Visscher, Genetics 208 (2018) 1397–1408.","ieee":"L. R. Lloyd-Jones, M. R. Robinson, J. Yang, and P. M. Visscher, “Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1397–1408, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","quality_controlled":"1","publisher":"Genetics Society of America","intvolume":" 208","month":"04","abstract":[{"lang":"eng","text":"Genome-wide association studies (GWAS) have identified thousands of loci that are robustly associated with complex diseases. The use of linear mixed model (LMM) methodology for GWAS is becoming more prevalent due to its ability to control for population structure and cryptic relatedness and to increase power. The odds ratio (OR) is a common measure of the association of a disease with an exposure (e.g., a genetic variant) and is readably available from logistic regression. However, when the LMM is applied to all-or-none traits it provides estimates of genetic effects on the observed 0–1 scale, a different scale to that in logistic regression. This limits the comparability of results across studies, for example in a meta-analysis, and makes the interpretation of the magnitude of an effect from an LMM GWAS difficult. In this study, we derived transformations from the genetic effects estimated under the LMM to the OR that only rely on summary statistics. To test the proposed transformations, we used real genotypes from two large, publicly available data sets to simulate all-or-none phenotypes for a set of scenarios that differ in underlying model, disease prevalence, and heritability. Furthermore, we applied these transformations to GWAS summary statistics for type 2 diabetes generated from 108,042 individuals in the UK Biobank. In both simulation and real-data application, we observed very high concordance between the transformed OR from the LMM and either the simulated truth or estimates from logistic regression. The transformations derived and validated in this study improve the comparability of results from prospective and already performed LMM GWAS on complex diseases by providing a reliable transformation to a common comparative scale for the genetic effects."}],"oa_version":"None","page":"1397-1408","date_created":"2020-04-30T10:45:19Z","date_published":"2018-04-01T00:00:00Z","doi":"10.1534/genetics.117.300360","issue":"4","volume":208,"year":"2018","publication_status":"published","publication_identifier":{"issn":["0016-6731","1943-2631"]},"language":[{"iso":"eng"}],"publication":"Genetics","day":"01"},{"abstract":[{"text":"We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"Springer Nature","month":"04","intvolume":" 50","publication_identifier":{"issn":["1061-4036","1546-1718"]},"publication_status":"published","year":"2018","day":"16","language":[{"iso":"eng"}],"publication":"Nature Genetics","page":"746-753","issue":"5","volume":50,"doi":"10.1038/s41588-018-0101-4","date_published":"2018-04-16T00:00:00Z","date_created":"2020-04-30T10:44:57Z","_id":"7722","article_type":"original","type":"journal_article","status":"public","citation":{"mla":"Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics, vol. 50, no. 5, Springer Nature, 2018, pp. 746–53, doi:10.1038/s41588-018-0101-4.","ieee":"J. Zeng et al., “Signatures of negative selection in the genetic architecture of human complex traits,” Nature Genetics, vol. 50, no. 5. Springer Nature, pp. 746–753, 2018.","short":"J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo, C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu, T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018) 746–753.","ama":"Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 2018;50(5):746-753. doi:10.1038/s41588-018-0101-4","apa":"Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-018-0101-4","chicago":"Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics. Springer Nature, 2018. https://doi.org/10.1038/s41588-018-0101-4.","ista":"Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753."},"date_updated":"2021-01-12T08:15:06Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jian","full_name":"Zeng, Jian","last_name":"Zeng"},{"first_name":"Ronald","last_name":"de Vlaming","full_name":"de Vlaming, Ronald"},{"first_name":"Yang","last_name":"Wu","full_name":"Wu, Yang"},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Luke R.","full_name":"Lloyd-Jones, Luke R.","last_name":"Lloyd-Jones"},{"first_name":"Loic","full_name":"Yengo, Loic","last_name":"Yengo"},{"first_name":"Chloe X.","full_name":"Yap, Chloe X.","last_name":"Yap"},{"full_name":"Xue, Angli","last_name":"Xue","first_name":"Angli"},{"full_name":"Sidorenko, Julia","last_name":"Sidorenko","first_name":"Julia"},{"full_name":"McRae, Allan F.","last_name":"McRae","first_name":"Allan F."},{"full_name":"Powell, Joseph E.","last_name":"Powell","first_name":"Joseph E."},{"first_name":"Grant W.","last_name":"Montgomery","full_name":"Montgomery, Grant W."},{"full_name":"Metspalu, Andres","last_name":"Metspalu","first_name":"Andres"},{"first_name":"Tonu","full_name":"Esko, Tonu","last_name":"Esko"},{"first_name":"Greg","full_name":"Gibson, Greg","last_name":"Gibson"},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"last_name":"Visscher","full_name":"Visscher, Peter M.","first_name":"Peter M."},{"first_name":"Jian","last_name":"Yang","full_name":"Yang, Jian"}],"article_processing_charge":"No","title":"Signatures of negative selection in the genetic architecture of human complex traits"},{"oa_version":"None","abstract":[{"lang":"eng","text":"Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species."}],"month":"01","intvolume":" 115","quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","day":"02","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","publication_identifier":{"issn":["0027-8424","1091-6490"]},"year":"2018","publication_status":"published","volume":115,"issue":"1","date_published":"2018-01-02T00:00:00Z","doi":"10.1073/pnas.1707227114","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.1806837115"}]},"date_created":"2020-04-30T10:45:43Z","page":"151-156","_id":"7724","status":"public","type":"journal_article","article_type":"original","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 115(1), 151–156.","chicago":"Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R. Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114.","short":"J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings of the National Academy of Sciences 115 (2018) 151–156.","ieee":"J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher, “Evidence of directional and stabilizing selection in contemporary humans,” Proceedings of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National Academy of Sciences, pp. 151–156, 2018.","ama":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114","apa":"Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher, P. M. (2018). Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114","mla":"Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences, vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56, doi:10.1073/pnas.1707227114."},"date_updated":"2021-01-12T08:15:07Z","title":"Evidence of directional and stabilizing selection in contemporary humans","author":[{"first_name":"Jaleal S.","full_name":"Sanjak, Jaleal S.","last_name":"Sanjak"},{"last_name":"Sidorenko","full_name":"Sidorenko, Julia","first_name":"Julia"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson"},{"full_name":"Thornton, Kevin R.","last_name":"Thornton","first_name":"Kevin R."},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."}],"article_processing_charge":"No"},{"title":"Enhanced diffusion by binding to the crosslinks of a polymer gel","article_processing_charge":"No","author":[{"first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich"},{"last_name":"Brenner","full_name":"Brenner, Michael P.","first_name":"Michael P."},{"first_name":"Katharina","last_name":"Ribbeck","full_name":"Ribbeck, Katharina"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"apa":"Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06851-5","ama":"Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5","ieee":"C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer Nature, 2018.","short":"C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018).","mla":"Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature, 2018, doi:10.1038/s41467-018-06851-5.","ista":"Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348.","chicago":"Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5."},"date_updated":"2021-01-12T08:15:18Z","status":"public","article_type":"original","type":"journal_article","article_number":"4348","_id":"7754","date_created":"2020-04-30T11:38:01Z","doi":"10.1038/s41467-018-06851-5","date_published":"2018-10-19T00:00:00Z","volume":9,"language":[{"iso":"eng"}],"publication":"Nature Communications","day":"19","publication_status":"published","year":"2018","publication_identifier":{"issn":["2041-1723"]},"intvolume":" 9","month":"10","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-018-06851-5"}],"publisher":"Springer Nature","quality_controlled":"1","oa_version":"Published Version","abstract":[{"text":"Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex.","lang":"eng"}]},{"month":"11","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/466771 "}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies."}],"date_published":"2018-11-09T00:00:00Z","date_created":"2020-04-30T13:09:37Z","page":"49","day":"09","language":[{"iso":"eng"}],"publication":"bioRxiv","year":"2018","publication_status":"published","status":"public","type":"preprint","_id":"7783","title":"Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel","author":[{"first_name":"Roel P.J.","full_name":"Bevers, Roel P.J.","last_name":"Bevers"},{"last_name":"Litovchenko","full_name":"Litovchenko, Maria","first_name":"Maria"},{"last_name":"Kapopoulou","full_name":"Kapopoulou, Adamandia","first_name":"Adamandia"},{"first_name":"Virginie S.","last_name":"Braman","full_name":"Braman, Virginie S."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"full_name":"Auwerx, Johan","last_name":"Auwerx","first_name":"Johan"},{"full_name":"Hollis, Brian","last_name":"Hollis","first_name":"Brian"},{"last_name":"Deplancke","full_name":"Deplancke, Bart","first_name":"Bart"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:30Z","citation":{"apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. Cold Spring Harbor Laboratory.","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. 2018.","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018).","ieee":"R. P. J. Bevers et al., “Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018.","mla":"Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv, Cold Spring Harbor Laboratory, 2018.","ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv, .","chicago":"Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring Harbor Laboratory, 2018."}},{"_id":"6001","article_number":"18","type":"journal_article","status":"public","citation":{"apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897","ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018).","mla":"Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.","ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.","chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897."},"date_updated":"2023-02-23T13:17:54Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William","last_name":"Leiserson","full_name":"Leiserson, William"},{"last_name":"Matveev","full_name":"Matveev, Alexander","first_name":"Alexander"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"title":"ThreadScan: Automatic and scalable memory reclamation","department":[{"_id":"DaAl"}],"abstract":[{"lang":"eng","text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free."}],"oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"Association for Computing Machinery","month":"09","intvolume":" 4","publication_identifier":{"issn":["2329-4949"]},"publication_status":"published","year":"2018","day":"01","language":[{"iso":"eng"}],"publication":"ACM Transactions on Parallel Computing","issue":"4","doi":"10.1145/3201897","volume":4,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"779"}]},"date_published":"2018-09-01T00:00:00Z","date_created":"2019-02-14T13:24:11Z"},{"date_created":"2020-05-10T22:00:51Z","date_published":"2018-05-01T00:00:00Z","publication_status":"published","year":"2018","has_accepted_license":"1","publication":"6th International Conference on Learning Representations","language":[{"iso":"eng"}],"day":"01","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"a4336c167978e81891970e4e4517a8c3","file_id":"7894","creator":"dernst","file_size":308339,"date_updated":"2020-07-14T12:48:03Z","file_name":"2018_ICLR_Polino.pdf","date_created":"2020-05-26T13:02:00Z"}],"oa":1,"quality_controlled":"1","scopus_import":1,"month":"05","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"arxiv":["1802.05668"]},"author":[{"full_name":"Polino, Antonio","last_name":"Polino","first_name":"Antonio"},{"first_name":"Razvan","full_name":"Pascanu, Razvan","last_name":"Pascanu"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"title":"Model compression via distillation and quantization","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"DaAl"}],"citation":{"ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018."},"date_updated":"2023-02-23T13:18:41Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2018-04-30","end_date":"2018-05-03","location":"Vancouver, Canada","name":"ICLR: International Conference on Learning Representations"},"type":"conference","status":"public","_id":"7812"},{"quality_controlled":"1","publisher":"Wiley","oa":1,"doi":"10.1002/ange.201802277","date_published":"2018-05-04T00:00:00Z","date_created":"2020-06-19T08:33:24Z","page":"5627-5631","day":"04","publication":"Angewandte Chemie","has_accepted_license":"1","year":"2018","title":"Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff","author":[{"last_name":"Mahne","full_name":"Mahne, Nika","first_name":"Nika"},{"first_name":"Sara E.","last_name":"Renfrew","full_name":"Renfrew, Sara E."},{"first_name":"Bryan D.","last_name":"McCloskey","full_name":"McCloskey, Bryan D."},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277.","ista":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 130(19), 5627–5631.","mla":"Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018, pp. 5627–31, doi:10.1002/ange.201802277.","apa":"Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277","ama":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 2018;130(19):5627-5631. doi:10.1002/ange.201802277","short":"N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie 130 (2018) 5627–5631.","ieee":"N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie, vol. 130, no. 19. Wiley, pp. 5627–5631, 2018."},"month":"05","intvolume":" 130","oa_version":"Published Version","abstract":[{"text":"Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien, und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen >3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2 + O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir, dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird. Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.","lang":"ger"}],"volume":130,"issue":"19","file":[{"file_name":"2018_AngChemieDT_Mahne.pdf","date_created":"2020-06-19T11:58:06Z","file_size":674789,"date_updated":"2020-07-14T12:48:06Z","creator":"dernst","file_id":"7988","checksum":"81506e0f7079e1e3591f3cd9f626bf67","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0044-8249"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"7983","file_date_updated":"2020-07-14T12:48:06Z","extern":"1","ddc":["540"],"date_updated":"2021-01-12T08:16:21Z"},{"article_type":"original","type":"journal_article","status":"public","_id":"8015","date_updated":"2021-01-12T08:16:31Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2018.03.028"}],"month":"04","intvolume":" 98","abstract":[{"text":"The neural code of cortical processing remains uncracked; however, it must necessarily rely on faithful signal propagation between cortical areas. In this issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation balanced by local inhibition can enable reliable signal propagation in data-constrained network models of macaque cortex. ","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":98,"issue":"1","publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Jake P.","last_name":"Stroud","full_name":"Stroud, Jake P."},{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"}],"article_processing_charge":"No","external_id":{"pmid":["29621492"]},"title":"Cortical signal propagation: Balance, amplify, transmit","citation":{"ieee":"J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify, transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.","short":"J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9.","apa":"Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance, amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028","ama":"Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit. Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028","mla":"Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.","ista":"Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify, transmit. Neuron. 98(1), 8–9.","chicago":"Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"8-9","doi":"10.1016/j.neuron.2018.03.028","date_published":"2018-04-04T00:00:00Z","date_created":"2020-06-25T12:53:39Z","year":"2018","day":"04","publication":"Neuron"},{"extern":"1","date_updated":"2021-01-12T08:16:46Z","_id":"8073","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1097-6256","1546-1726"]},"issue":"12","volume":21,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41593-018-0307-x","relation":"erratum"}]},"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support the generation of complex movements. Although recent neuronal-network models capture many qualitative aspects of M1 dynamics, they can generate only a few distinct movements. Additionally, it is unclear how M1 efficiently controls movements over a wide range of shapes and speeds. We demonstrate that modulation of neuronal input–output gains in recurrent neuronal-network models with a fixed architecture can dramatically reorganize neuronal activity and thus downstream muscle outputs. Consistent with the observation of diffuse neuromodulatory projections to M1, a relatively small number of modulatory control units provide sufficient flexibility to adjust high-dimensional network activity using a simple reward-based learning rule. Furthermore, it is possible to assemble novel movements from previously learned primitives, and one can separately change movement speed while preserving movement shape. Our results provide a new perspective on the role of modulatory systems in controlling recurrent cortical activity."}],"intvolume":" 21","month":"12","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/","open_access":"1"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12, Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0.","ieee":"J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives in space and time via targeted gain modulation in cortical networks,” Nature Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018.","short":"J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience 21 (2018) 1774–1783.","ama":"Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0","apa":"Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0","chicago":"Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0.","ista":"Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 21(12), 1774–1783."},"title":"Motor primitives in space and time via targeted gain modulation in cortical networks","article_processing_charge":"No","external_id":{"pmid":["30482949"]},"author":[{"full_name":"Stroud, Jake P.","last_name":"Stroud","first_name":"Jake P."},{"first_name":"Mason A.","full_name":"Porter, Mason A.","last_name":"Porter"},{"first_name":"Guillaume","full_name":"Hennequin, Guillaume","last_name":"Hennequin"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels"}],"publication":"Nature Neuroscience","day":"01","year":"2018","date_created":"2020-06-30T13:18:02Z","doi":"10.1038/s41593-018-0276-0","date_published":"2018-12-01T00:00:00Z","page":"1774-1783","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"article_processing_charge":"No","author":[{"orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit"},{"first_name":"Josef","last_name":"Singer","full_name":"Singer, Josef"},{"first_name":"Kristina M.","last_name":"Ilieva","full_name":"Ilieva, Kristina M."},{"first_name":"Miroslawa","last_name":"Matz","full_name":"Matz, Miroslawa"},{"last_name":"Herrmann","full_name":"Herrmann, Ina","first_name":"Ina"},{"first_name":"Edzard","full_name":"Spillner, Edzard","last_name":"Spillner"},{"full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis","first_name":"Sophia N."},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"}],"title":"AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor","date_updated":"2021-01-12T08:17:37Z","citation":{"mla":"Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:10.1016/j.jaci.2018.04.021.","ieee":"J. Singer et al., “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” Journal of Allergy and Clinical Immunology, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.","short":"J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N. Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142 (2018) 973–976.e11.","apa":"Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E., … Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2018.04.021","ama":"Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 2018;142(3):973-976.e11. doi:10.1016/j.jaci.2018.04.021","chicago":"Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann, Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology. Elsevier, 2018. https://doi.org/10.1016/j.jaci.2018.04.021.","ista":"Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 142(3), 973–976.e11."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_type":"letter_note","type":"journal_article","status":"public","_id":"8231","page":"973-976.e11","date_created":"2020-08-10T11:51:36Z","issue":"3","doi":"10.1016/j.jaci.2018.04.021","date_published":"2018-09-01T00:00:00Z","volume":142,"publication_status":"published","year":"2018","publication_identifier":{"issn":["0091-6749"]},"publication":"Journal of Allergy and Clinical Immunology","language":[{"iso":"eng"}],"day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jaci.2018.04.021"}],"oa":1,"publisher":"Elsevier","quality_controlled":"1","intvolume":" 142","month":"09","oa_version":"Published Version"},{"day":"13","publication":"Contrast Media & Molecular Imaging","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1555-4309","1555-4317"]},"year":"2018","publication_status":"published","volume":2018,"date_published":"2018-02-13T00:00:00Z","doi":"10.1155/2018/1269830","date_created":"2020-08-10T11:53:07Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY."}],"month":"02","intvolume":" 2018","quality_controlled":"1","publisher":"Hindawi","main_file_link":[{"url":"https://doi.org/10.1155/2018/1269830","open_access":"1"}],"oa":1,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:17:38Z","citation":{"chicago":"Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018. https://doi.org/10.1155/2018/1269830.","ista":"Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M, Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830.","mla":"Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018, doi:10.1155/2018/1269830.","ieee":"T. Balber et al., “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.","short":"T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker, E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular Imaging 2018 (2018).","apa":"Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer, J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830","ama":"Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018. doi:10.1155/2018/1269830"},"title":"Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer","author":[{"first_name":"T.","full_name":"Balber, T.","last_name":"Balber"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Singer"},{"first_name":"N.","last_name":"Berroterán-Infante","full_name":"Berroterán-Infante, N."},{"last_name":"Dumanic","full_name":"Dumanic, M.","first_name":"M."},{"first_name":"L.","full_name":"Fetty, L.","last_name":"Fetty"},{"first_name":"J.","last_name":"Fazekas-Singer","full_name":"Fazekas-Singer, J.","orcid":"0000-0002-8777-3502"},{"first_name":"C.","last_name":"Vraka","full_name":"Vraka, C."},{"first_name":"L.","last_name":"Nics","full_name":"Nics, L."},{"first_name":"M.","last_name":"Bergmann","full_name":"Bergmann, M."},{"last_name":"Pallitsch","full_name":"Pallitsch, K.","first_name":"K."},{"full_name":"Spreitzer, H.","last_name":"Spreitzer","first_name":"H."},{"full_name":"Wadsak, W.","orcid":"0000-0003-4479-8053","last_name":"Wadsak","first_name":"W."},{"first_name":"M.","last_name":"Hacker","full_name":"Hacker, M."},{"first_name":"E.","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, E."},{"last_name":"Viernstein","full_name":"Viernstein, H.","first_name":"H."},{"first_name":"M.","orcid":"0000-0003-3173-5272","full_name":"Mitterhauser, M.","last_name":"Mitterhauser"}],"article_processing_charge":"No","article_number":"1269830","_id":"8234","status":"public","article_type":"original","type":"journal_article"},{"day":"10","publication":"Oncotarget","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1949-2553"]},"year":"2018","publication_status":"published","doi":"10.18632/oncotarget.24876","volume":9,"date_published":"2018-04-10T00:00:00Z","date_created":"2020-08-10T11:52:54Z","page":"19026-19038","oa_version":"Published Version","abstract":[{"text":"Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans.","lang":"eng"}],"month":"04","intvolume":" 9","quality_controlled":"1","publisher":"Impact Journals","main_file_link":[{"url":"https://doi.org/10.18632/oncotarget.24876","open_access":"1"}],"oa":1,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis, S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.24876","ama":"Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876","ieee":"T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget, vol. 9. Impact Journals, pp. 19026–19038, 2018.","short":"T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis, J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget 9 (2018) 19026–19038.","mla":"Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876.","ista":"Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 9, 19026–19038.","chicago":"Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876."},"date_updated":"2021-01-12T08:17:37Z","title":"Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody","author":[{"first_name":"Tadanobu","full_name":"Nagaya, Tadanobu","last_name":"Nagaya"},{"full_name":"Okuyama, Shuhei","last_name":"Okuyama","first_name":"Shuhei"},{"full_name":"Ogata, Fusa","last_name":"Ogata","first_name":"Fusa"},{"full_name":"Maruoka, Yasuhiro","last_name":"Maruoka","first_name":"Yasuhiro"},{"first_name":"Deborah W.","last_name":"Knapp","full_name":"Knapp, Deborah W."},{"first_name":"Sophia N.","last_name":"Karagiannis","full_name":"Karagiannis, Sophia N."},{"last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter L.","last_name":"Choyke","full_name":"Choyke, Peter L."},{"full_name":"LeBlanc, Amy K.","last_name":"LeBlanc","first_name":"Amy K."},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"},{"full_name":"Kobayashi, Hisataka","last_name":"Kobayashi","first_name":"Hisataka"}],"article_processing_charge":"No","_id":"8232","status":"public","article_type":"original","type":"journal_article"},{"citation":{"ieee":"I. Herrmann et al., “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” Developmental & Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.","short":"I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127.","apa":"Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005","ama":"Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005","mla":"Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005.","ista":"Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim E. 2018. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 82(5), 118–127.","chicago":"Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ina","full_name":"Herrmann, Ina","last_name":"Herrmann"},{"full_name":"Gotovina, Jelena","last_name":"Gotovina","first_name":"Jelena"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer"},{"full_name":"Fischer, Michael B.","last_name":"Fischer","first_name":"Michael B."},{"full_name":"Hufnagl, Karin","last_name":"Hufnagl","first_name":"Karin"},{"full_name":"Bianchini, Rodolfo","last_name":"Bianchini","first_name":"Rodolfo"},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"}],"article_processing_charge":"No","title":"Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy","year":"2018","day":"01","publication":"Developmental & Comparative Immunology","page":"118-127","date_published":"2018-05-01T00:00:00Z","doi":"10.1016/j.dci.2018.01.005","date_created":"2020-08-10T11:53:01Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T08:17:38Z","extern":"1","_id":"8233","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"issn":["0145-305X"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"5","volume":82,"abstract":[{"text":"The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1016/j.dci.2018.01.005","open_access":"1"}],"month":"05","intvolume":" 82"}]