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Shabalin AA, Tjelmeland H, Fan C, Perou CM, Nobel AB. Merging two gene-expression studies via cross-platform normalization. Bioinformatics. 2008 May 1;24(9):1154-60. doi: 10.1093/bioinformatics/btn083. Epub 2008 Mar 5. PubMed PMID: 18325927.
Gatti DM, Shabalin AA, Lam TC, Wright FA, Rusyn I, Nobel AB. FastMap: fast eQTL mapping in homozygous populations. Bioinformatics. 2009 Feb 15;25(4):482-9. doi: 10.1093/bioinformatics/btn648. Epub 2008 Dec 17. PubMed PMID: 19091771; PubMed Central PMCID: PMC2642639.
Lickwar CR, Rao B, Shabalin AA, Nobel AB, Strahl BD, Lieb JD. The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency. PLoS One. 2009;4(3):e4886. doi: 10.1371/journal.pone.0004886. Epub 2009 Mar 19. PubMed PMID: 19295910; PubMed Central PMCID: PMC2654109.
Wright FA, Shabalin AA, Rusyn I. Computational tools for discovery and interpretation of expression quantitative trait loci. Pharmacogenomics. 2012 Feb;13(3):343-52. doi: 10.2217/pgs.11.185. Review. PubMed PMID: 22304583; PubMed Central PMCID: PMC3295835.
Xia K, Shabalin AA, Huang S, Madar V, Zhou YH, Wang W, Zou F, Sun W, Sullivan PF, Wright FA. seeQTL: a searchable database for human eQTLs. Bioinformatics. 2012 Feb 1;28(3):451-2. doi: 10.1093/bioinformatics/btr678. Epub 2011 Dec 13. PubMed PMID: 22171328; PubMed Central PMCID: PMC3268245.
Shabalin AA. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics. 2012 May 15;28(10):1353-8. doi: 10.1093/bioinformatics/bts163. Epub 2012 Apr 6. PubMed PMID: 22492648; PubMed Central PMCID: PMC3348564.
Weigman VJ, Chao HH, Shabalin AA, He X, Parker JS, Nordgard SH, Grushko T, Huo D, Nwachukwu C, Nobel A, Kristensen VN, Børresen-Dale AL, Olopade OI, Perou CM. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res Treat. 2012 Jun;133(3):865-80. doi: 10.1007/s10549-011-1846-y. Epub 2011 Nov 3. PubMed PMID: 22048815; PubMed Central PMCID: PMC3387500.
Ramasamy A, Trabzuni D, Gibbs JR, Dillman A, Hernandez DG, Arepalli S, Walker R, Smith C, Ilori GP, Shabalin AA, Li Y, Singleton AB, Cookson MR, Hardy J, Ryten M, Weale ME. Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies. Nucleic Acids Res. 2013 Apr;41(7):e88. doi: 10.1093/nar/gkt069. Epub 2013 Feb 21. PubMed PMID: 23435227; PubMed Central PMCID: PMC3627570.
The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. doi: 10.1038/ng.2653. PubMed PMID: 23715323; PubMed Central PMCID: PMC4010069.
Wright FA, Sullivan PF, Brooks AI, Zou F, Sun W, Xia K, Madar V, Jansen R, Chung W, Zhou YH, Abdellaoui A, Batista S, Butler C, Chen G, Chen TH, D'Ambrosio D, Gallins P, Ha MJ, Hottenga JJ, Huang S, Kattenberg M, Kochar J, Middeldorp CM, Qu A, Shabalin A, Tischfield J, Todd L, Tzeng JY, van Grootheest G, Vink JM, Wang Q, Wang W, Wang W, Willemsen G, Smit JH, de Geus EJ, Yin Z, Penninx BW, Boomsma DI. Heritability and genomics of gene expression in peripheral blood. Nat Genet. 2014 May;46(5):430-7. doi: 10.1038/ng.2951. Epub 2014 Apr 13. PubMed PMID: 24728292; PubMed Central PMCID: PMC4012342.
Gatti DM, Svenson KL, Shabalin A, Wu LY, Valdar W, Simecek P, Goodwin N, Cheng R, Pomp D, Palmer A, Chesler EJ, Broman KW, Churchill GA. Quantitative trait locus mapping methods for diversity outbred mice. G3 (Bethesda). 2014 Sep 18;4(9):1623-33. doi: 10.1534/g3.114.013748. PubMed PMID: 25237114; PubMed Central PMCID: PMC4169154.
Kumar G, Clark SL, McClay JL, Shabalin AA, Adkins DE, Xie L, Chan R, Nerella S, Kim Y, Sullivan PF, Hultman CM, Magnusson PK, Aberg KA, van den Oord EJ. Refinement of schizophrenia GWAS loci using methylome-wide association data. Hum Genet. 2015 Jan;134(1):77-87. doi: 10.1007/s00439-014-1494-5. Epub 2014 Oct 7. PubMed PMID: 25284466; PubMed Central PMCID: PMC4282961.
Shabalin AA, Aberg KA, van den Oord EJ. Candidate gene methylation studies are at high risk of erroneous conclusions. Epigenomics. 2015;7(1):13-5. doi: 10.2217/epi.14.70. PubMed PMID: 25687462; PubMed Central PMCID: PMC5503464.
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015 May 8;348(6235):648-60. doi: 10.1126/science.1262110. Epub 2015 May 7. PubMed PMID: 25954001; PubMed Central PMCID: PMC4547484.
Clark SL, Aberg KA, Nerella S, Kumar G, McClay JL, Chen W, Xie LY, Harada A, Shabalin AA, Gao G, Bergen SE, Hultman CM, Magnusson PK, Sullivan PF, van den Oord EJ. Combined Whole Methylome and Genomewide Association Study Implicates CNTN4 in Alcohol Use. Alcohol Clin Exp Res. 2015 Aug;39(8):1396-405. doi: 10.1111/acer.12790. Epub 2015 Jul 4. PubMed PMID: 26146898; PubMed Central PMCID: PMC4515164.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. PubMed PMID: 26432246; PubMed Central PMCID: PMC4617611.
McClay JL, Shabalin AA, Dozmorov MG, Adkins DE, Kumar G, Nerella S, Clark SL, Bergen SE, Hultman CM, Magnusson PK, Sullivan PF, Aberg KA, van den Oord EJ. High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction. Genome Biol. 2015 Dec 23;16:291. doi: 10.1186/s13059-015-0842-7. PubMed PMID: 26699738; PubMed Central PMCID: PMC4699364.
Clark SL, McClay JL, Adkins DE, Aberg KA, Kumar G, Nerella S, Xie L, Collins AL, Crowley JJ, Quakenbush CR, Hillard CE, Gao G, Shabalin AA, Peterson RE, Copeland WE, Silberg JL, Maes H, Sullivan PF, Costello EJ, van den Oord EJ. Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses. Nicotine Tob Res. 2016 May;18(5):626-31. doi: 10.1093/ntr/ntv166. Epub 2015 Aug 17. PubMed PMID: 26283763; PubMed Central PMCID: PMC5942610.
van den Oord EJ, Clark SL, Xie LY, Shabalin AA, Dozmorov MG, Kumar G, Vladimirov VI, Magnusson PK, Aberg KA. A Whole Methylome CpG-SNP Association Study of Psychosis in Blood and Brain Tissue. Schizophr Bull. 2016 Jul;42(4):1018-26. doi: 10.1093/schbul/sbv182. Epub 2015 Dec 9. PubMed PMID: 26656881; PubMed Central PMCID: PMC4903046.
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