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For: Gao C, Tignor NL, Salit J, Strulovici-Barel Y, Hackett NR, Crystal RG, Mezey JG. HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. ACTA ACUST UNITED AC 2013;30:369-76. [PMID: 24307700 DOI: 10.1093/bioinformatics/btt690] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Number Cited by Other Article(s)
1
Gao X, Li J, Liu X, Peng Q, Jing H, Hadi S, Teschendorff AE, Wang S, Liu F. FastQTLmapping: an ultra-fast and memory efficient package for mQTL-like analysis. BMC Bioinformatics 2025;26:112. [PMID: 40289089 PMCID: PMC12036243 DOI: 10.1186/s12859-025-06130-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Accepted: 04/02/2025] [Indexed: 04/30/2025]  Open
2
Gao C, Wei H, Zhang K. LORSEN: Fast and Efficient eQTL Mapping With Low Rank Penalized Regression. Front Genet 2021;12:690926. [PMID: 34868194 PMCID: PMC8636089 DOI: 10.3389/fgene.2021.690926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 10/08/2021] [Indexed: 12/02/2022]  Open
3
Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform 2021;22:6330938. [PMID: 34329375 DOI: 10.1093/bib/bbab259] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]  Open
4
Fantauzzi MF, Aguiar JA, Tremblay BJM, Mansfield MJ, Yanagihara T, Chandiramohan A, Revill S, Ryu MH, Carlsten C, Ask K, Stämpfli M, Doxey AC, Hirota JA. Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status. ERJ Open Res 2020;6:00128-2020. [PMID: 33344628 PMCID: PMC7737429 DOI: 10.1183/23120541.00128-2020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022]  Open
5
Jeng XJ, Rhyne J, Zhang T, Tzeng JY. Effective SNP ranking improves the performance of eQTL mapping. Genet Epidemiol 2020;44:611-619. [PMID: 32216117 DOI: 10.1002/gepi.22293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/21/2020] [Accepted: 03/11/2020] [Indexed: 11/06/2022]
6
A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine. Trends Genet 2020;36:318-336. [PMID: 32294413 DOI: 10.1016/j.tig.2020.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 02/07/2023]
7
Lukowski SW, Lloyd-Jones LR, Holloway A, Kirsten H, Hemani G, Yang J, Small K, Zhao J, Metspalu A, Dermitzakis ET, Gibson G, Spector TD, Thiery J, Scholz M, Montgomery GW, Esko T, Visscher PM, Powell JE. Genetic correlations reveal the shared genetic architecture of transcription in human peripheral blood. Nat Commun 2017;8:483. [PMID: 28883458 PMCID: PMC5589780 DOI: 10.1038/s41467-017-00473-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/30/2017] [Indexed: 01/29/2023]  Open
8
Yuan L, Zhu L, Guo WL, Zhou X, Zhang Y, Huang Z, Huang DS. Nonconvex Penalty Based Low-Rank Representation and Sparse Regression for eQTL Mapping. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:1154-1164. [PMID: 28114074 DOI: 10.1109/tcbb.2016.2609420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
9
Salerno S, Mehrmohamadi M, Liberti MV, Wan M, Wells MT, Booth JG, Locasale JW. RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards. PLoS One 2017;12:e0179530. [PMID: 28662051 PMCID: PMC5491020 DOI: 10.1371/journal.pone.0179530] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 05/31/2017] [Indexed: 01/22/2023]  Open
10
Ju JH, Shenoy SA, Crystal RG, Mezey JG. An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci. PLoS Comput Biol 2017;13:e1005537. [PMID: 28505156 PMCID: PMC5448815 DOI: 10.1371/journal.pcbi.1005537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/30/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022]  Open
11
Imprialou M, Petretto E, Bottolo L. Expression QTLs Mapping and Analysis: A Bayesian Perspective. Methods Mol Biol 2017;1488:189-215. [PMID: 27933525 DOI: 10.1007/978-1-4939-6427-7_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
12
Joshi AD, Andersson C, Buch S, Stender S, Noordam R, Weng LC, Weeke PE, Auer PL, Boehm B, Chen C, Choi H, Curhan G, Denny JC, De Vivo I, Eicher JD, Ellinghaus D, Folsom AR, Fuchs C, Gala M, Haessler J, Hofman A, Hu F, Hunter DJ, Janssen HL, Kang JH, Kooperberg C, Kraft P, Kratzer W, Lieb W, Lutsey PL, Murad SD, Nordestgaard BG, Pasquale LR, Reiner AP, Ridker PM, Rimm E, Rose LM, Shaffer CM, Schafmayer C, Tamimi RM, Uitterlinden AG, Völker U, Völzke H, Wakabayashi Y, Wiggs JL, Zhu J, Roden DM, Stricker BH, Tang W, Teumer A, Hampe J, Tybjærg-Hansen A, Chasman DI, Chan AT, Johnson AD. Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-Wide Association Studies. Gastroenterology 2016;151:351-363.e28. [PMID: 27094239 PMCID: PMC4959966 DOI: 10.1053/j.gastro.2016.04.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/01/2023]
13
Luo W, Obeidat M, Di Narzo AF, Chen R, Sin DD, Paré PD, Hao K. Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases. Am J Respir Cell Mol Biol 2016;54:177-87. [PMID: 26102239 DOI: 10.1165/rcmb.2014-0381oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
14
Grünewald TGP, Bernard V, Gilardi-Hebenstreit P, Raynal V, Surdez D, Aynaud MM, Mirabeau O, Cidre-Aranaz F, Tirode F, Zaidi S, Perot G, Jonker AH, Lucchesi C, Le Deley MC, Oberlin O, Marec-Bérard P, Véron AS, Reynaud S, Lapouble E, Boeva V, Rio Frio T, Alonso J, Bhatia S, Pierron G, Cancel-Tassin G, Cussenot O, Cox DG, Morton LM, Machiela MJ, Chanock SJ, Charnay P, Delattre O. Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite. Nat Genet 2015. [PMID: 26214589 DOI: 10.1038/ng.3363] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
15
Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015;16:197-212. [DOI: 10.1038/nrg3891] [Citation(s) in RCA: 675] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
16
Ganesh S, Chasman D, Larson M, Guo X, Verwoert G, Bis J, Gu X, Smith A, Yang ML, Zhang Y, Ehret G, Rose L, Hwang SJ, Papanicolau G, Sijbrands E, Rice K, Eiriksdottir G, Pihur V, Ridker P, Vasan R, Newton-Cheh C, Raffel LJ, Amin N, Rotter JI, Liu K, Launer LJ, Xu M, Caulfield M, Morrison AC, Johnson AD, Vaidya D, Dehghan A, Li G, Bouchard C, Harris TB, Zhang H, Boerwinkle E, Siscovick DS, Gao W, Uitterlinden AG, Rivadeneira F, Hofman A, Willer CJ, Franco OH, Huo Y, Witteman JC, Munroe PB, Gudnason V, Palmas W, van Duijn C, Fornage M, Levy D, Psaty BM, Chakravarti A, Newton-Cheh C, Johnson T, Gateva V, Tobin M, Bochud M, Coin L, Najjar S, Zhao J, Heath S, Eyheramendy S, Papadakis K, Voight B, Scott L, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers J, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee D, Onland-Moret N, Bots M, Wain L, Elliott K, Teumer A, Luan J, Lucas G, Kuusisto J, Burton P, Hadley D, McArdle W, Brown M, Dominiczak A, Newhouse S, Samani N, Webster J, Zeggini E, Beckmann J, Bergmann S, Lim N, Song K, Vollenweider P, Waeber G, et alGanesh S, Chasman D, Larson M, Guo X, Verwoert G, Bis J, Gu X, Smith A, Yang ML, Zhang Y, Ehret G, Rose L, Hwang SJ, Papanicolau G, Sijbrands E, Rice K, Eiriksdottir G, Pihur V, Ridker P, Vasan R, Newton-Cheh C, Raffel LJ, Amin N, Rotter JI, Liu K, Launer LJ, Xu M, Caulfield M, Morrison AC, Johnson AD, Vaidya D, Dehghan A, Li G, Bouchard C, Harris TB, Zhang H, Boerwinkle E, Siscovick DS, Gao W, Uitterlinden AG, Rivadeneira F, Hofman A, Willer CJ, Franco OH, Huo Y, Witteman JC, Munroe PB, Gudnason V, Palmas W, van Duijn C, Fornage M, Levy D, Psaty BM, Chakravarti A, Newton-Cheh C, Johnson T, Gateva V, Tobin M, Bochud M, Coin L, Najjar S, Zhao J, Heath S, Eyheramendy S, Papadakis K, Voight B, Scott L, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers J, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee D, Onland-Moret N, Bots M, Wain L, Elliott K, Teumer A, Luan J, Lucas G, Kuusisto J, Burton P, Hadley D, McArdle W, Brown M, Dominiczak A, Newhouse S, Samani N, Webster J, Zeggini E, Beckmann J, Bergmann S, Lim N, Song K, Vollenweider P, Waeber G, Waterworth D, Yuan X, Groop L, Orho-Melander M, Allione A, Di Gregorio A, Guarrera S, Panico S, Ricceri F, Romanazzi V, Sacerdote C, Vineis P, Barroso I, Sandhu M, Luben R, Crawford G, Jousilahti P, Perola M, Boehnke M, Bonnycastle L, Collins F, Jackson A, Mohlke K, Stringham H, Valle T, Willer C, Bergman R, Morken M, Döring A, Gieger C, Illig T, Meitinger T, Org E, Pfeufer A, Wichmann H, Kathiresan S, Marrugat J, O’Donnell C, Schwartz S, Siscovick D, Subirana I, Freimer N, Hartikainen AL, McCarthy M, O’Reilly P, Peltonen L, Pouta A, de Jong P, Snieder H, van Gilst W, Clarke R, Goel A, Hamsten A, Peden J, Seedorf U, Syvänen AC, Tognoni G, Lakatta E, Sanna S, Scheet P, Schlessinger D, Scuteri A, Dörr M, Ernst F, Felix S, Homuth G, Lorbeer R, Reffelmann T, Rettig R, Völker U, Galan P, Gut I, Hercberg S, Lathrop G, Zeleneka D, Deloukas P, Soranzo N, Williams F, Zhai G, Salomaa V, Laakso M, Elosua R, Forouhi N, Völzke H, Uiterwaal C, van der Schouw Y, Numans M, Matullo G, Navis G, Berglund G, Bingham S, Kooner J, Paterson A, Connell J, Bandinelli S, Ferrucci L, Watkins H, Spector T, Tuomilehto J, Altshuler D, Strachan D, Laan M, Meneton P, Wareham N, Uda M, Jarvelin MR, Mooser V, Melander O, Loos R, Elliott P, Abecasis G, Caulfield M, Munroe P. Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations. Am J Hum Genet 2014;95:49-65. [PMID: 24975945 DOI: 10.1016/j.ajhg.2014.06.002] [Show More Authors] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/03/2014] [Indexed: 01/11/2023]  Open
17
Agler AH, Crystal RG, Mezey JG, Fuller J, Gao C, Hansen JG, Cassano PA. Differential expression of vitamin E and selenium-responsive genes by disease severity in chronic obstructive pulmonary disease. COPD 2014;10:450-8. [PMID: 23875740 DOI: 10.3109/15412555.2012.761958] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
18
Reardon BJ, Hansen JG, Crystal RG, Houston DK, Kritchevsky SB, Harris T, Lohman K, Liu Y, O'Connor GT, Wilk JB, Mezey J, Gao C, Cassano PA. Vitamin D-responsive SGPP2 variants associated with lung cell expression and lung function. BMC MEDICAL GENETICS 2013;14:122. [PMID: 24274704 PMCID: PMC3907038 DOI: 10.1186/1471-2350-14-122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 11/08/2013] [Indexed: 12/05/2022]
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