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For: Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res 2014;24:14-24. [PMID: 24092820 DOI: 10.1101/gr.155192.113] [Citation(s) in RCA: 396] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Number Cited by Other Article(s)
201
Bien SA, Su YR, Conti DV, Harrison TA, Qu C, Guo X, Lu Y, Albanes D, Auer PL, Banbury BL, Berndt SI, Bézieau S, Brenner H, Buchanan DD, Caan BJ, Campbell PT, Carlson CS, Chan AT, Chang-Claude J, Chen S, Connolly CM, Easton DF, Feskens EJM, Gallinger S, Giles GG, Gunter MJ, Hampe J, Huyghe JR, Hoffmeister M, Hudson TJ, Jacobs EJ, Jenkins MA, Kampman E, Kang HM, Kühn T, Küry S, Lejbkowicz F, Le Marchand L, Milne RL, Li L, Li CI, Lindblom A, Lindor NM, Martín V, McNeil CE, Melas M, Moreno V, Newcomb PA, Offit K, Pharaoh PDP, Potter JD, Qu C, Riboli E, Rennert G, Sala N, Schafmayer C, Scacheri PC, Schmit SL, Severi G, Slattery ML, Smith JD, Trichopoulou A, Tumino R, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Casey G, Nickerson DA, Gruber SB, Hsu L, Zheng W, Peters U. Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer. Hum Genet 2019;138:307-326. [PMID: 30820706 PMCID: PMC6483948 DOI: 10.1007/s00439-019-01989-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/20/2019] [Indexed: 02/02/2023]
202
Mancuso N, Freund MK, Johnson R, Shi H, Kichaev G, Gusev A, Pasaniuc B. Probabilistic fine-mapping of transcriptome-wide association studies. Nat Genet 2019;51:675-682. [PMID: 30926970 DOI: 10.1038/s41588-019-0367-1] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 02/01/2019] [Indexed: 11/09/2022]
203
Gaspar HA, Gerring Z, Hübel C, Middeldorp CM, Derks EM, Breen G. Using genetic drug-target networks to develop new drug hypotheses for major depressive disorder. Transl Psychiatry 2019;9:117. [PMID: 30877270 PMCID: PMC6420656 DOI: 10.1038/s41398-019-0451-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 01/28/2019] [Accepted: 02/12/2019] [Indexed: 12/25/2022]  Open
204
Unlu G, Gamazon ER, Qi X, Levic DS, Bastarache L, Denny JC, Roden DM, Mayzus I, Breyer M, Zhong X, Konkashbaev AI, Rzhetsky A, Knapik EW, Cox NJ. GRIK5 Genetically Regulated Expression Associated with Eye and Vascular Phenomes: Discovery through Iteration among Biobanks, Electronic Health Records, and Zebrafish. Am J Hum Genet 2019;104:503-519. [PMID: 30827500 PMCID: PMC6407495 DOI: 10.1016/j.ajhg.2019.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/29/2019] [Indexed: 12/15/2022]  Open
205
Vilgalys TP, Rogers J, Jolly CJ, Baboon Genome Analysis, Mukherjee S, Tung J. Evolution of DNA Methylation in Papio Baboons. Mol Biol Evol 2019;36:527-540. [PMID: 30521003 PMCID: PMC6389319 DOI: 10.1093/molbev/msy227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
206
A Multivariate Genome-Wide Association Study of Wing Shape in Drosophila melanogaster. Genetics 2019;211:1429-1447. [PMID: 30792267 DOI: 10.1534/genetics.118.301342] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/03/2019] [Indexed: 02/02/2023]  Open
207
Ali AT, Boehme L, Carbajosa G, Seitan VC, Small KS, Hodgkinson A. Nuclear genetic regulation of the human mitochondrial transcriptome. eLife 2019;8:e41927. [PMID: 30775970 PMCID: PMC6420317 DOI: 10.7554/elife.41927] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022]  Open
208
Yao Y, Liu Z, Wei Q, Ramsey SA. CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. BMC Bioinformatics 2019;20:63. [PMID: 30727967 PMCID: PMC6364436 DOI: 10.1186/s12859-019-2637-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023]  Open
209
Sun S, Zhu J, Mozaffari S, Ober C, Chen M, Zhou X. Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies. Bioinformatics 2019;35:487-496. [PMID: 30020412 PMCID: PMC6361238 DOI: 10.1093/bioinformatics/bty644] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/24/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022]  Open
210
Hu Y, Zhao T, Zang T, Zhang Y, Cheng L. Identification of Alzheimer's Disease-Related Genes Based on Data Integration Method. Front Genet 2019;9:703. [PMID: 30740125 PMCID: PMC6355707 DOI: 10.3389/fgene.2018.00703] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/14/2018] [Indexed: 01/18/2023]  Open
211
Alasoo K, Rodrigues J, Danesh J, Freitag DF, Paul DS, Gaffney DJ. Genetic effects on promoter usage are highly context-specific and contribute to complex traits. eLife 2019;8:e41673. [PMID: 30618377 PMCID: PMC6349408 DOI: 10.7554/elife.41673] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022]  Open
212
Zhu S, Qian T, Hoshida Y, Shen Y, Yu J, Hao K. GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data. Bioinformatics 2019;35:160-163. [PMID: 30010968 PMCID: PMC6298047 DOI: 10.1093/bioinformatics/bty529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/11/2018] [Accepted: 07/11/2018] [Indexed: 11/12/2022]  Open
213
Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model. PLoS Genet 2018;14:e1007875. [PMID: 30586357 PMCID: PMC6324826 DOI: 10.1371/journal.pgen.1007875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 01/06/2023]  Open
214
van der Wijst MGP, de Vries DH, Brugge H, Westra HJ, Franke L. An integrative approach for building personalized gene regulatory networks for precision medicine. Genome Med 2018;10:96. [PMID: 30567569 PMCID: PMC6299585 DOI: 10.1186/s13073-018-0608-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
215
Evidence for Weak Selective Constraint on Human Gene Expression. Genetics 2018;211:757-772. [PMID: 30554168 PMCID: PMC6366908 DOI: 10.1534/genetics.118.301833] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/01/2018] [Indexed: 01/01/2023]  Open
216
Saha A, Battle A. False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors. F1000Res 2018;7:1860. [PMID: 30613398 PMCID: PMC6305209 DOI: 10.12688/f1000research.17145.2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2019] [Indexed: 12/29/2022]  Open
217
Saha A, Battle A. False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors. F1000Res 2018;7:1860. [PMID: 30613398 PMCID: PMC6305209 DOI: 10.12688/f1000research.17145.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 12/19/2022]  Open
218
High-resolution genetic mapping of putative causal interactions between regions of open chromatin. Nat Genet 2018;51:128-137. [PMID: 30478436 PMCID: PMC6330062 DOI: 10.1038/s41588-018-0278-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 10/15/2018] [Indexed: 01/04/2023]
219
Salisbury-Ruf CT, Bertram CC, Vergeade A, Lark DS, Shi Q, Heberling ML, Fortune NL, Okoye GD, Jerome WG, Wells QS, Fessel J, Moslehi J, Chen H, Roberts LJ, Boutaud O, Gamazon ER, Zinkel SS. Bid maintains mitochondrial cristae structure and function and protects against cardiac disease in an integrative genomics study. eLife 2018;7:40907. [PMID: 30281024 PMCID: PMC6234033 DOI: 10.7554/elife.40907] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/27/2018] [Indexed: 01/07/2023]  Open
220
Ioannidis NM, Davis JR, DeGorter MK, Larson NB, McDonnell SK, French AJ, Battle AJ, Hastie TJ, Thibodeau SN, Montgomery SB, Bustamante CD, Sieh W, Whittemore AS. FIRE: functional inference of genetic variants that regulate gene expression. Bioinformatics 2018;33:3895-3901. [PMID: 28961785 DOI: 10.1093/bioinformatics/btx534] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022]  Open
221
Mogil LS, Andaleon A, Badalamenti A, Dickinson SP, Guo X, Rotter JI, Johnson WC, Im HK, Liu Y, Wheeler HE. Genetic architecture of gene expression traits across diverse populations. PLoS Genet 2018;14:e1007586. [PMID: 30096133 PMCID: PMC6105030 DOI: 10.1371/journal.pgen.1007586] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 08/22/2018] [Accepted: 07/24/2018] [Indexed: 01/14/2023]  Open
222
Albert FW, Bloom JS, Siegel J, Day L, Kruglyak L. Genetics of trans-regulatory variation in gene expression. eLife 2018;7:e35471. [PMID: 30014850 PMCID: PMC6072440 DOI: 10.7554/elife.35471] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 06/30/2018] [Indexed: 12/02/2022]  Open
223
Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nat Genet 2018;50:1140-1150. [PMID: 29988122 PMCID: PMC6097927 DOI: 10.1038/s41588-018-0156-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 05/22/2018] [Indexed: 12/15/2022]
224
Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J, Nicolae DL, Eskin E, Kellis M, Getz G, McCarthy MI, Dermitzakis ET, Cox NJ, Ardlie KG. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nat Genet 2018;50:956-967. [PMID: 29955180 PMCID: PMC6248311 DOI: 10.1038/s41588-018-0154-4] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 05/08/2018] [Indexed: 12/27/2022]
225
Weissbrod O, Rothschild D, Barkan E, Segal E. Host genetics and microbiome associations through the lens of genome wide association studies. Curr Opin Microbiol 2018;44:9-19. [PMID: 29909175 DOI: 10.1016/j.mib.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/15/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022]
226
Hanson C, Cairns J, Wang L, Sinha S. Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation. Genome Res 2018;28:1207-1216. [PMID: 29898900 PMCID: PMC6071639 DOI: 10.1101/gr.227066.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/31/2018] [Indexed: 12/12/2022]
227
Ferguson LB, Harris RA, Mayfield RD. From gene networks to drugs: systems pharmacology approaches for AUD. Psychopharmacology (Berl) 2018;235:1635-1662. [PMID: 29497781 PMCID: PMC6298603 DOI: 10.1007/s00213-018-4855-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/06/2018] [Indexed: 12/29/2022]
228
Koshiba S, Motoike I, Saigusa D, Inoue J, Shirota M, Katoh Y, Katsuoka F, Danjoh I, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Ogishima S, Fuse N, Kure S, Tamiya G, Tanabe O, Yasuda J, Kinoshita K, Yamamoto M. Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. Genes Cells 2018;23:406-417. [PMID: 29701317 DOI: 10.1111/gtc.12588] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/22/2018] [Indexed: 01/05/2023]
229
The dorsoventral patterning of Musca domestica embryos: insights into BMP/Dpp evolution from the base of the lower cyclorraphan flies. EvoDevo 2018;9:13. [PMID: 29796243 PMCID: PMC5956798 DOI: 10.1186/s13227-018-0102-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/06/2018] [Indexed: 01/09/2023]  Open
230
Mostafavi S, Gaiteri C, Sullivan SE, White CC, Tasaki S, Xu J, Taga M, Klein HU, Patrick E, Komashko V, McCabe C, Smith R, Bradshaw EM, Root DE, Regev A, Yu L, Chibnik LB, Schneider JA, Young-Pearse TL, Bennett DA, De Jager PL. A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease. Nat Neurosci 2018;21:811-819. [PMID: 29802388 PMCID: PMC6599633 DOI: 10.1038/s41593-018-0154-9] [Citation(s) in RCA: 359] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/20/2018] [Indexed: 02/07/2023]
231
Wang M, Hancock TP, Chamberlain AJ, Vander Jagt CJ, Pryce JE, Cocks BG, Goddard ME, Hayes BJ. Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits. BMC Genomics 2018;19:395. [PMID: 29793448 PMCID: PMC5968476 DOI: 10.1186/s12864-018-4800-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/17/2018] [Indexed: 12/18/2022]  Open
232
Barbeira AN, Dickinson SP, Bonazzola R, Zheng J, Wheeler HE, Torres JM, Torstenson ES, Shah KP, Garcia T, Edwards TL, Stahl EA, Huckins LM, Nicolae DL, Cox NJ, Im HK. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nat Commun 2018;9:1825. [PMID: 29739930 PMCID: PMC5940825 DOI: 10.1038/s41467-018-03621-1] [Citation(s) in RCA: 698] [Impact Index Per Article: 99.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/27/2017] [Indexed: 12/25/2022]  Open
233
Chen XF, Zhu DL, Yang M, Hu WX, Duan YY, Lu BJ, Rong Y, Dong SS, Hao RH, Chen JB, Chen YX, Yao S, Thynn HN, Guo Y, Yang TL. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation. Am J Hum Genet 2018;102:776-793. [PMID: 29706346 PMCID: PMC5986728 DOI: 10.1016/j.ajhg.2018.03.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/28/2018] [Indexed: 01/10/2023]  Open
234
Using Droplet Digital PCR to Analyze Allele-Specific RNA Expression. Methods Mol Biol 2018. [PMID: 29717456 DOI: 10.1007/978-1-4939-7778-9_23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
235
Su YR, Di C, Bien S, Huang L, Dong X, Abecasis G, Berndt S, Bezieau S, Brenner H, Caan B, Casey G, Chang-Claude J, Chanock S, Chen S, Connolly C, Curtis K, Figueiredo J, Gala M, Gallinger S, Harrison T, Hoffmeister M, Hopper J, Huyghe JR, Jenkins M, Joshi A, Le Marchand L, Newcomb P, Nickerson D, Potter J, Schoen R, Slattery M, White E, Zanke B, Peters U, Hsu L. A Mixed-Effects Model for Powerful Association Tests in Integrative Functional Genomics. Am J Hum Genet 2018;102:904-919. [PMID: 29727690 PMCID: PMC5986723 DOI: 10.1016/j.ajhg.2018.03.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/15/2018] [Indexed: 01/05/2023]  Open
236
Aguiar D, Cheng LF, Dumitrascu B, Mordelet F, Pai AA, Engelhardt BE. Bayesian nonparametric discovery of isoforms and individual specific quantification. Nat Commun 2018;9:1681. [PMID: 29703885 PMCID: PMC5923247 DOI: 10.1038/s41467-018-03402-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 02/11/2018] [Indexed: 12/18/2022]  Open
237
Kycia I, Wolford BN, Huyghe JR, Fuchsberger C, Vadlamudi S, Kursawe R, Welch RP, Albanus RD, Uyar A, Khetan S, Lawlor N, Bolisetty M, Mathur A, Kuusisto J, Laakso M, Ucar D, Mohlke KL, Boehnke M, Collins FS, Parker SCJ, Stitzel ML. A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression. Am J Hum Genet 2018;102:620-635. [PMID: 29625024 DOI: 10.1016/j.ajhg.2018.02.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/22/2018] [Indexed: 01/17/2023]  Open
238
Wanke KA, Devanna P, Vernes SC. Understanding Neurodevelopmental Disorders: The Promise of Regulatory Variation in the 3'UTRome. Biol Psychiatry 2018;83:548-557. [PMID: 29289333 DOI: 10.1016/j.biopsych.2017.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 01/28/2023]
239
Gene-by-environment interactions in urban populations modulate risk phenotypes. Nat Commun 2018;9:827. [PMID: 29511166 PMCID: PMC5840419 DOI: 10.1038/s41467-018-03202-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 01/26/2018] [Indexed: 01/21/2023]  Open
240
Zhang M, Lykke-Andersen S, Zhu B, Xiao W, Hoskins JW, Zhang X, Rost LM, Collins I, van de Bunt M, Jia J, Parikh H, Zhang T, Song L, Jermusyk A, Chung CC, Zhu B, Zhou W, Matters GL, Kurtz RC, Yeager M, Jensen TH, Brown KM, Ongen H, Bamlet WR, Murray BA, McCarthy MI, Chanock SJ, Chatterjee N, Wolpin BM, Smith JP, Olson SH, Petersen GM, Shi J, Amundadottir LT. Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues. Gut 2018;67:521-533. [PMID: 28634199 PMCID: PMC5762429 DOI: 10.1136/gutjnl-2016-313146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 02/06/2023]
241
Ge Y, Concannon P. Molecular-genetic characterization of common, noncoding UBASH3A variants associated with type 1 diabetes. Eur J Hum Genet 2018;26:1060-1064. [PMID: 29491471 DOI: 10.1038/s41431-018-0123-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 01/27/2018] [Accepted: 02/06/2018] [Indexed: 11/09/2022]  Open
242
Tian L, Khan A, Ning Z, Yuan K, Zhang C, Lou H, Yuan Y, Xu S. Genome-wide comparison of allele-specific gene expression between African and European populations. Hum Mol Genet 2018;27:1067-1077. [DOI: 10.1093/hmg/ddy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/05/2018] [Indexed: 11/12/2022]  Open
243
Park E, Pan Z, Zhang Z, Lin L, Xing Y. The Expanding Landscape of Alternative Splicing Variation in Human Populations. Am J Hum Genet 2018;102:11-26. [PMID: 29304370 PMCID: PMC5777382 DOI: 10.1016/j.ajhg.2017.11.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022]  Open
244
Li B, Verma SS, Veturi YC, Verma A, Bradford Y, Haas DW, Ritchie MD. Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018;23:448-459. [PMID: 29218904 PMCID: PMC5749400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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Veturi Y, Ritchie MD. How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures? PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018;23:228-239. [PMID: 29218884 PMCID: PMC5785784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lee PH, Lee C, Li X, Wee B, Dwivedi T, Daly M. Principles and methods of in-silico prioritization of non-coding regulatory variants. Hum Genet 2018;137:15-30. [PMID: 29288389 PMCID: PMC5892192 DOI: 10.1007/s00439-017-1861-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
247
Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018;70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
248
CRAWFORD DANAC, MORGAN ALEXANDERA, DENNY JOSHUAC, ARONOW BRUCEJ, BRENNER STEVENE. PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018;23:389-399. [PMID: 29218899 PMCID: PMC6182117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
249
Dendrou CA, Cortes A, Shipman L, Evans HG, Attfield KE, Jostins L, Barber T, Kaur G, Kuttikkatte SB, Leach OA, Desel C, Faergeman SL, Cheeseman J, Neville MJ, Sawcer S, Compston A, Johnson AR, Everett C, Bell JI, Karpe F, Ultsch M, Eigenbrot C, McVean G, Fugger L. Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity. Sci Transl Med 2017;8:363ra149. [PMID: 27807284 DOI: 10.1126/scitranslmed.aag1974] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/14/2016] [Indexed: 01/08/2023]
250
Ecker S, Pancaldi V, Valencia A, Beck S, Paul DS. Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity. Bioessays 2017;40. [PMID: 29251357 DOI: 10.1002/bies.201700148] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/31/2017] [Indexed: 12/15/2022]
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