Publications

Publications

Book

  • Shen H, Yan Q, Shen X (沈恒范, 严钦容, 沈侠) (2017): Probability and Mathematical Statistics (6th Edition Textbook) (概率论与数理统计教程 第六版, “十二五”普通高等教育本科国家级规划教材). Higher Education Press (高等教育出版社). ISBN 978-7-04-048049-8. [R Solutions for Examples (例题的R解答)]

Papers

2021

  • Ying K, Zhai R, Pyrkov TV, Shindyapina AV, Mariotti M, Fedichev PO, Shen X, Gladyshev VN (2021). Genetic and phenotypic analysis of the causal relationship between aging and COVID-19. Communications Medicine, in press.

  • He Y, Shu C, Li T, Wu Q, Wang Z, Chen X, Shen X (2021). Non-inferiority in cancer clinical trials was associated with more lenient margins and higher hypothesized outcome event rates. Journal of Clinical Epidemiology, online, in press. LINK

  • Li T, Ning Z, Shen X (2021). Improved estimation of phenotypic correlations using summary association statistics. Frontiers in Genetics, 12: 665252. LINK

  • Li T, Ning Z, Yang Z, Zhai R, Xu W, Ying K, Wang Y, Chen Y, Shen X (2020). Total genetic contribution assessment across the human genome. Nature Communications, 12, 1845; doi: 10.1038/s41467-021-23124-w. LINK

  • Ning Z, Tsepilov YA, Sharapov SZ, Wang Z, Grishenko AK, Feng X, Shirali M, Joshi PK, Wilson JF, Pawitan Y, Haley CS, Aulchenko YS, Shen X (2021). Nontrivial Replication of Loci Detected by Multi-Trait Methods. Frontiers in Genetics, 12: 627989. LINK

2020

  • Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, Furniss J, Richmond A, Gountouna E, Wrobel N, Harrison D, Wang B, Wu Y, Meynert A, Griffiths F, Oosthuyzen W, Kousathanas A, Moutsianas L, Yang Z, Zhai R, Zheng C, Grimes G, Beale R, Millar J, Shih B, Keating S, Zechner M, Haley C, Porteous DJ, Hayward C, Yang J, Knight J, Summers C, Shankar-Hari M, Klenerman P, Turtle L, Ho A, Moore SC, Hinds C, Horby P, Nichol A, Maslove D, Ling L, McAuley D, Montgomery H, Walsh T, Pereira A, Renieri A; GenOMICC Investigators; ISARICC Investigators; COVID-19 Human Genetics Initiative; 23andMe Investigators; BRACOVID Investigators; Gen-COVID Investigators, Shen X, Ponting CP, Fawkes A, Tenesa A, Caulfield M, Scott R, Rowan K, Murphy L, Openshaw PJM, Semple MG, Law A, Vitart V, Wilson JF, Baillie JK (2020). Genetic mechanisms of critical illness in Covid-19. Nature. LINK

  • Ning Z, Pawitan Y, Shen X (2020). High-definition likelihood inference of genetic correlations across human complex traits. Nature Genetics, 52: 859–864. LINK

  • Luo R, Zheng C, Yang H, Chen X, Jiang P, Wu X, Yang Z, Shen X, Li X (2020). Identification of potential candidate genes and pathways in atrioventricular nodal reentry tachycardia by whole-exome Sequencing. Clinical and Translational Medicine, 10: 238-257. LINK

2019

  • Wu D, Yan J, Shen X, Sun Y, Thulin M, Cai Y, Wik L, Shen Q, Oelrich J, Qian X, Dubois KL, Ronquist KG, Nilsson M, Landegren U, Kamali-Moghaddam M (2019). Profiling surface proteins on individual exosomes using a proximity barcoding assay. Nature Communications, 10, 3854; doi: 10.1038/s41467-017-00934-5. LINK

  • Fang F, Zhan Y, Hammar N, Shen X , Wirdefeldt K, Walldius G, Mariosa D (2019). Lipids, Apolipoproteins, and the Risk of Parkinson Disease: A Prospective Cohort Study and a Mendelian Randomization Analysis. Circulation Research, 125: 643–652. LINK

  • Li T, Shen X (2019). Pleiotropy complicates human gene editing: CCR5Δ32 and beyond. Frontiers in Genetics, 10: 669. LINK

  • Ooi BNS, Loh H, Ho PJ, Milne R, Giles G, Gao C, Kraft P, John EM, Swerdlow A, Brenner H, Wu AH, Haiman C, Evans DG, Zheng W, Fasching P, Castelao JE, Kwong A, Shen X, Czene K, Hall P, Dunning A, Easton D, Hartman M, Li J (2019). The genetic interplay between body mass index, breast size and breast cancer risk: a Mendelian randomization analysis. International Journal of Epidemiology, 48(3): 781–794. LINK

  • Noordam R, Young WJ, Salman R, Kanters JK, van den Berg ME, van Heemst D, Lin HJ, Barreto SM, Biggs ML, Biino G, Catamo E, Concas MP, Ding J, Evans DS, Foco L, Grarup N, Lyytikäinen LP, Mangino M, Mei H, van der Most PJ, Müller-Nurasyid M, Nelson CP, Qian Y, Repetto L, Said MA, Shah N, Schramm K, Vidigal PG, Weiss S, Yao J, Zilhao NR, Brody JA, Braund PS, Brumat M, Campana E, Christofidou P, Caulfield MJ, De Grandi A, Dominiczak AF, Doney ASF, Eiriksdottir G, Ellervik C, Giatti L, Gögele M, Graff C, Guo X, van der Harst P, Joshi PK, Kähönen M, Kestenbaum B, Lima-Costa MF, Linneberg A, Maan AC, Meitinger T, Padmanabhan S, Pattaro C, Peters A, Petersmann A, Sever P, Sinner MF, Shen X, Stanton A, Strauch K, Soliman EZ, Tarasov KV, Taylor KD, Thio CHL, Uitterlinden AG, Vaccargiu S, Waldenberger M, Robino A, Correa A, Cucca F, Cummings SR, Dörr M, Girotto G, Gudnason V, Hansen T, Heckbert SR, Juhl CR, Kääb S, Lehtimäki T, Liu Y, Lotufo PA, Palmer CNA, Pirastu M, Pramstaller PP, Ribeiro ALP, Rotter JI, Samani NJ, Snieder H, Spector TD, Stricker BH, Verweij N, Wilson JF, Wilson JG, Jukema JW, Tinker A, Newton-Cheh CH, Sotoodehnia N, Mook-Kanamori DO, Munroe PB, Warren HR (2019). Effects of Calcium, Magnesium, and Potassium Concentrations on Ventricular Repolarization in Unselected Individuals. Journal of the American College of Cardiology, 73(24): 3118-3131. LINK

  • Timmers PRHJ, Mounier N, Läll K, Fischer K, Ning Z, Feng X, Bretherick A, Clark DW, eQTLGen Consortium, Shen X, Esko T, Kutalik Z, Wilson JF, Joshi PK (2019): Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances. eLife, 8:e39856. LINK

2018

  • Nowak C, Hetty S, Salihovic S, Castillejo-Lopez C, Ganna A, Cook N, Broeckling CD, Prenni J, Shen X, Giedraitis V, Ärnlöv J, Lind L, Berne C, Sundström J, Fall T, Ingelsson E (2018): Glucose challenge metabolomics implicates medium-chain acylcarnitines in insulin resistance. Scientific Reports, 8, 8691. LINK

  • Li X, Meng X, Spiliopoulou A, Timofeeva M, Wei W-Q, Gifford A, Shen X, He Y, Varley T, Tzoulaki I, Wright AF, Denny JC, Campbell H, Theodoratou E (2018): MR-PheWAS: exploring the causal effect of SUA level on multiple disease outcomes by using genetic instruments in UK Biobank. Annals of the Rheumatic Diseases, 77(7): 1039-1047. LINK

2017

  • Ning Z, Lee Y, Joshi PK, Wilson JF, Pawitan Y, Shen X (2017): A selection operator for summary association statistics reveals allelic heterogeneity of complex traits. American Journal of Human Genetics, 101(6): 903-912; doi: 10.1016/j.ajhg.2017.09.027. LINK

  • Joshi PK, Pirastu N, Kentistou KA, Fischer K, Hofer E, Schraut KE, Clark DW, Nutile T, Barnes CLK, Timmers PRHJ, Shen X, Gandin I, McDaid AF, Hansen TF, Gordon SD, Giulianini F, Boutin TS, Abdellaoui A, Zhao W, Medina-Gomez C, Bartz TM, Trompet S, Lange LA, Raffield L, van der Spek A, Galesloot TE, Proitsi P, Yanek LR, Bielak LF, Payton A, Murgia F, Concas MP, Biino G, Tajuddin SM, Seppälä I, Amin N, Boerwinkle E, Børglum AD, Campbell A, Demerath EW, Demuth I, Faul JD, Ford I, Gialluisi A, Gögele M, Graff M, Hingorani A, Hottenga JJ, Hougaard DM, Hurme MA, Ikram MA, Jylhä M, Kuh D, Ligthart L, Lill CM, Lindenberger U, Lumley T, Mägi R, Marques-Vidal P, Medland SE, Milani L, Nagy R, Ollier WER, Peyser PA, Pramstaller PP, Ridker PM, Rivadeneira F, Ruggiero D, Saba Y, Schmidt R, Schmidt H, Slagboom PE, Smith BH, Smith JA, Sotoodehnia N, Steinhagen-Thiessen E, van Rooij FJA, Verbeek AL, Vermeulen SH, Vollenweider P, Wang Y, Werge T, Whitfield JB, Zonderman AB, Lehtimäki T, Evans MK, Pirastu M, Fuchsberger C, Bertram L, Pendleton N, Kardia SLR, Ciullo M, Becker DM, Wong A, Psaty BM, van Duijn CM, Wilson JG, Jukema JW, Kiemeney L, Uitterlinden AG, Franceschini N, North KE, Weir DR, Metspalu A, Boomsma DI, Hayward C, Chasman D, Martin NG, Sattar N, Campbell H, Esko T, Kutalik Z, Wilson JF (2017): Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity. Nature Communications, 8, 910; doi: 10.1038/s41467-017-00934-5. LINK

  • Shen X, Klarić L, Sharapov S, Mangino M, Ning Z, Wu D, Trbojević-Akmačić I, Pučić-Baković M, Rudan I, Polašek O, Hayward C, Spector TD, Wilson JF, Lauc G, Aulchenko YS (2017): Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation. Nature Communications, 8, 447; doi: 10.1038/s41467-017-00453-3. LINK

  • Wang B, Li Z, Xu W, Feng X, Wan Q, Zan Y, Sheng S, Shen X (2017): Bivariate genomic analysis identifies a hidden locus associated with bacteria hypersensitive response in Arabidopsis thaliana. Scientific Reports, 7, 45281; doi: 10.1038/srep45281. LINK

2016

  • Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A; BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC; LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC (2016): Genome-wide analysis identifies 12 loci influencing human reproductive behavior. Nature Genetics, 48, 1462-1472. LINK

  • Weng Z, Wolc A, Shen X, Fernando RL, Dekkers JCM, Arango J, Settar P, Fulton JE, O’Sullivan NP and Garrick DJ (2016): Effects of number of training generations on genomic prediction for various traits in a layer chicken population. Genetics Selection Evolution, 48:22. LINK

  • Zan Y, Shen X, Forsberg S, and Carlborg O (2016): Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions. G3, 6(8):2319-2328. LINK

  • (Authors in alphabetical order) Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S; Alzheimer’s Disease Neuroimaging Initiative (2016): Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s disease. Alzheimer’s & Dementia, 12(6): 645-53. LINK

2015

  • Lachowiec J, Shen X, Queitsch C and Carlborg O (2015): A genome-wide association analysis reveals epistatic cancellation of additive genetic variance for root length in Arabidopsis thaliana. PLoS Genetics, 11(9), e1005541. LINK

  • Shen X and Zhan Y (2015): RE: The effect on melanoma risk of genes previously associated with telomere length. Journal of the National Cancer Institute, 107(10): djv237. LINK

  • Alam M and Ronnegard L and Shen X (2015): Fitting conditional and simultaneous autoregressive spatial models in hglm. The R Journal, 7(2): 5-18. LINK

  • Besnier F, Glover K, Lien S, Kent M, Hansen M, Shen X and Skaala O (2015). Identification of quantitative genetic components of fitness variation in farmed, hybrid and native salmon in the wild. Heredity, 115, 47-55. LINK

2014

  • Shen X, Forsberg S, Pettersson M, Sheng Z and Carlborg O (2014): Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genetics, 10(12), e1004842. LINK

  • Shen X and Hill WG (2014): Opportunities for improvement of phenotypic variability: influence of direct vs epistatic effects. Proceedings of the 10th WCGALP. LINK

  • Ronnegard L, Felleki M, Alam M and Shen X (2014): Simultaneous estimation of spatial and genetic effects using hierarchical generalized linear models. Proceedings of the 10th WCGALP. LINK

  • Shen X, Alam M and Ronnegard L (2014): Mixed models through the lens of hglm: applications and grand challenges. JSM Proceedings. LINK

  • Shen X, Li Y, Ronnegard L, Uden P and Carlborg O (2014): Application of a genomic model in chemometrics analysis. Journal of Chemometrics, 28: 548-557. LINK

2013

  • Shen X (2013): The curse of the missing heritability. Frontiers in Genetics, 4:225. LINK

  • Nelson RM, Nettelblad C, Pettersson ME, Shen X, Crooks L, Besnier F, Alvarez-Castro Jose, Ronnegard L, Ek W, Sheng Z, Kierczak M, Holmgren S, Carlborg O (2013): MAPfastR: QTL mapping in outbred line crosses. G3, 3(12): 2147-2149. LINK

  • Shen X and Ronnegard L (2013): Issues with data transformation in genome-wide association studies for phenotypic variability. F1000Research, 2:200. LINK

  • Shen X and Carlborg O (2013): Beware of risk for increased false positive rates in genome-wide association studies for phenotypic variability. Frontiers in Genetics, 4:93. LINK

  • Shen X, Alam M, Fikse F and Ronnegard L (2013): A novel generalized ridge regression method for quantitative genetics. Genetics,193, 1255-1268. LINK

  • Sheng Z, Pettersson ME, Hu X, Luo C, Qu H, Shu D, Shen X, Carlborg O and Li N (2013): Genetic dissection of growth traits in a Chinese indigenous x commercial broiler chicken cross. BMC Genomics, 14:151. LINK

  • Li X, Kierczak M, Shen X, Ahsan M, Carlborg O and Marklund S (2013): PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties. Frontiers in Genetics, 4:21. LINK

2012

  • Shen X, Pettersson M, Ronnegard L and Carlborg O (2012): Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana. PLoS Genetics, 8(8), e1002839. LINK

2011

  • Shen X, Ronnegard L and Carlborg O (2011): How to Deal with Genotype Uncertainty in Variance Component Quantitative Trait Loci Analyses. Genetics Research, Cambridge, 93(5), 333-342. LINK

  • Nelson R, Shen X and Carlborg O (2011): qtl.outbred: interfacing outbred line cross data with the R/qtl mapping software. BMC Research Notes, 4:154. LINK

  • Shen X, Ronnegard L and Carlborg O (2011): Hierarchical likelihood opens a new way of estimating genetic values using dense marker maps. BMC Proceedings, 5(Suppl 3):S14. LINK

2010

  • Ronnegard L, Shen X and Alam M (2010): hglm: A Package for Fitting Hierarchical Generalized Linear Models. The R Journal, 2(2):20-28. LINK

\(\leqslant\) 2009

  • Hou D, Shen X, Li X, Liu Y, Wang Y (2006): Digital Restoration of Historical Heritage by Reconstruction from Uncalibrated Images. Lecture Notes in Computer Science (LNCS), Volume 3942/2006, Page 1377-1382, Springer Berlin / Heidelberg, (SCI). LINK




All judgements are, in their rationale, statistics.

-- C. R. Rao





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