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Items: 26

1.

Building a schizophrenia genetic network: Transcription Factor 4 regulates genes involved in neuronal development and schizophrenia risk.

Xia H, Jahr FM, Kim NK, Xie L, Shabalin AA, Bryois J, Sweet DH, Kronfol MM, Palasuberniam P, McRae M, Riley BP, Sullivan PF, van den Oord EJ, McClay JL.

Hum Mol Genet. 2018 Jun 14. doi: 10.1093/hmg/ddy222. [Epub ahead of print]

PMID:
29905862
2.

Enhancing Psychosis-Spectrum Nosology Through an International Data Sharing Initiative.

Docherty AR, Fonseca-Pedrero E, Debbané M, Chan RCK, Linscott RJ, Jonas KG, Cicero DC, Green MJ, Simms LJ, Mason O, Watson D, Ettinger U, Waszczuk M, Rapp A, Grant P, Kotov R, DeYoung CG, Ruggero CJ, Eaton NR, Krueger RF, Patrick C, Hopwood C, O'Neill FA, Zald DH, Conway CC, Adkins DE, Waldman ID, van Os J, Sullivan PF, Anderson JS, Shabalin AA, Sponheim SR, Taylor SF, Grazioplene RG, Bacanu SA, Bigdeli TB, Haenschel C, Malaspina D, Gooding DC, Nicodemus K, Schultze-Lutter F, Barrantes-Vidal N, Mohr C, Carpenter WT, Cohen AS.

Schizophr Bull. 2018 May 16. doi: 10.1093/schbul/sby059. [Epub ahead of print]

PMID:
29788473
3.

Epigenetic Aging in Major Depressive Disorder.

Han LKM, Aghajani M, Clark SL, Chan RF, Hattab MW, Shabalin AA, Zhao M, Kumar G, Xie LY, Jansen R, Milaneschi Y, Dean B, Aberg KA, van den Oord EJCG, Penninx BWJH.

Am J Psychiatry. 2018 Aug 1;175(8):774-782. doi: 10.1176/appi.ajp.2018.17060595. Epub 2018 Apr 16.

PMID:
29656664
4.

RaMWAS: fast methylome-wide association study pipeline for enrichment platforms.

Shabalin AA, Hattab MW, Clark SL, Chan RF, Kumar G, Aberg KA, van den Oord EJCG.

Bioinformatics. 2018 Jul 1;34(13):2283-2285. doi: 10.1093/bioinformatics/bty069.

PMID:
29447401
5.

Methyl-CpG-Binding Domain Sequencing: MBD-seq.

Aberg KA, Chan RF, Xie L, Shabalin AA, van den Oord EJCG.

Methods Mol Biol. 2018;1708:171-189. doi: 10.1007/978-1-4939-7481-8_10.

PMID:
29224145
6.

An empirical Bayes approach for multiple tissue eQTL analysis.

Li G, Shabalin AA, Rusyn I, Wright FA, Nobel AB.

Biostatistics. 2018 Jul 1;19(3):391-406. doi: 10.1093/biostatistics/kxx048.

PMID:
29029013
7.

A MBD-seq protocol for large-scale methylome-wide studies with (very) low amounts of DNA.

Aberg KA, Chan RF, Shabalin AA, Zhao M, Turecki G, Staunstrup NH, Starnawska A, Mors O, Xie LY, van den Oord EJ.

Epigenetics. 2017 Sep;12(9):743-750. doi: 10.1080/15592294.2017.1335849. Epub 2017 Nov 6.

PMID:
28703682
8.

Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome.

Chan RF, Shabalin AA, Xie LY, Adkins DE, Zhao M, Turecki G, Clark SL, Aberg KA, van den Oord EJCG.

Nucleic Acids Res. 2017 Jun 20;45(11):e97. doi: 10.1093/nar/gkx143.

9.

Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence.

Clark SL, McClay JL, Adkins DE, Kumar G, Aberg KA, Nerella S, Xie L, Collins AL, Crowley JJ, Quackenbush CR, Hilliard CE, Shabalin AA, Vrieze SI, Peterson RE, Copeland WE, Silberg JL, McGue M, Maes H, Iacono WG, Sullivan PF, Costello EJ, van den Oord EJ.

Alcohol Clin Exp Res. 2017 Apr;41(4):711-718. doi: 10.1111/acer.13352. Epub 2017 Mar 24.

10.

Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies.

Hattab MW, Shabalin AA, Clark SL, Zhao M, Kumar G, Chan RF, Xie LY, Jansen R, Han LK, Magnusson PK, van Grootheest G, Hultman CM, Penninx BW, Aberg KA, van den Oord EJ.

Genome Biol. 2017 Jan 30;18(1):24. doi: 10.1186/s13059-017-1148-8.

11.

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction.

McClay JL, Shabalin AA, Dozmorov MG, Adkins DE, Kumar G, Nerella S, Clark SL, Bergen SE; Swedish Schizophrenia Consortium, Hultman CM, Magnusson PK, Sullivan PF, Aberg KA, van den Oord EJ.

Genome Biol. 2015 Dec 23;16:291. doi: 10.1186/s13059-015-0842-7.

12.

A Whole Methylome CpG-SNP Association Study of Psychosis in Blood and Brain Tissue.

van den Oord EJ, Clark SL, Xie LY, Shabalin AA, Dozmorov MG, Kumar G; Swedish Schizophrenia Consortium, Vladimirov VI, Magnusson PK, Aberg KA.

Schizophr Bull. 2016 Jul;42(4):1018-26. doi: 10.1093/schbul/sbv182. Epub 2015 Dec 9.

13.

An integrated map of structural variation in 2,504 human genomes.

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; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

14.

Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses.

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.

Nicotine Tob Res. 2016 May;18(5):626-31. doi: 10.1093/ntr/ntv166. Epub 2015 Aug 17.

15.

Combined Whole Methylome and Genomewide Association Study Implicates CNTN4 in Alcohol Use.

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.

Alcohol Clin Exp Res. 2015 Aug;39(8):1396-405. doi: 10.1111/acer.12790. Epub 2015 Jul 4.

16.

Candidate gene methylation studies are at high risk of erroneous conclusions.

Shabalin AA, Aberg KA, van den Oord EJ.

Epigenomics. 2015;7(1):13-5. doi: 10.2217/epi.14.70. No abstract available.

17.

Refinement of schizophrenia GWAS loci using methylome-wide association data.

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.

Hum Genet. 2015 Jan;134(1):77-87. doi: 10.1007/s00439-014-1494-5. Epub 2014 Oct 7.

18.

Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies.

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; NABEC, Hardy J; UKBEC, Ryten M, Weale ME.

Nucleic Acids Res. 2013 Apr;41(7):e88. doi: 10.1093/nar/gkt069. Epub 2013 Feb 21.

19.

Matrix eQTL: ultra fast eQTL analysis via large matrix operations.

Shabalin AA.

Bioinformatics. 2012 May 15;28(10):1353-8. doi: 10.1093/bioinformatics/bts163. Epub 2012 Apr 6.

20.

Computational tools for discovery and interpretation of expression quantitative trait loci.

Wright FA, Shabalin AA, Rusyn I.

Pharmacogenomics. 2012 Feb;13(3):343-52. doi: 10.2217/pgs.11.185. Review.

21.

seeQTL: a searchable database for human eQTLs.

Xia K, Shabalin AA, Huang S, Madar V, Zhou YH, Wang W, Zou F, Sun W, Sullivan PF, Wright FA.

Bioinformatics. 2012 Feb 1;28(3):451-2. doi: 10.1093/bioinformatics/btr678. Epub 2011 Dec 13.

22.

Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival.

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.

Breast Cancer Res Treat. 2012 Jun;133(3):865-80. doi: 10.1007/s10549-011-1846-y. Epub 2011 Nov 3.

23.

Sex-specific gene expression in the BXD mouse liver.

Gatti DM, Zhao N, Chesler EJ, Bradford BU, Shabalin AA, Yordanova R, Lu L, Rusyn I.

Physiol Genomics. 2010 Aug;42(3):456-68. doi: 10.1152/physiolgenomics.00110.2009. Epub 2010 Jun 15.

24.

The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency.

Lickwar CR, Rao B, Shabalin AA, Nobel AB, Strahl BD, Lieb JD.

PLoS One. 2009;4(3):e4886. doi: 10.1371/journal.pone.0004886. Epub 2009 Mar 19.

25.

FastMap: fast eQTL mapping in homozygous populations.

Gatti DM, Shabalin AA, Lam TC, Wright FA, Rusyn I, Nobel AB.

Bioinformatics. 2009 Feb 15;25(4):482-9. doi: 10.1093/bioinformatics/btn648. Epub 2008 Dec 17.

26.

Merging two gene-expression studies via cross-platform normalization.

Shabalin AA, Tjelmeland H, Fan C, Perou CM, Nobel AB.

Bioinformatics. 2008 May 1;24(9):1154-60. doi: 10.1093/bioinformatics/btn083. Epub 2008 Mar 5.

PMID:
18325927

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