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For: Yang C, Wang L, Zhang S, Zhao H. Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. ACTA ACUST UNITED AC 2013;29:1026-34. [PMID: 23419377 DOI: 10.1093/bioinformatics/btt075] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
1
Liu W, Lin H, Liu L, Ma Y, Wei Y, Li Y. Supervised structural learning of semiparametric regression on high-dimensional correlated covariates with applications to eQTL studies. Stat Med 2023;42:3145-3163. [PMID: 37458069 DOI: 10.1002/sim.9769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 02/18/2023] [Accepted: 04/26/2023] [Indexed: 07/18/2023]
2
Treppner M, Binder H, Hess M. Interpretable generative deep learning: an illustration with single cell gene expression data. Hum Genet 2022;141:1481-1498. [PMID: 34988661 PMCID: PMC9360114 DOI: 10.1007/s00439-021-02417-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
3
Wang Y, Sun F, Lin W, Zhang S. AC-PCoA: Adjustment for confounding factors using principal coordinate analysis. PLoS Comput Biol 2022;18:e1010184. [PMID: 35830390 PMCID: PMC9278763 DOI: 10.1371/journal.pcbi.1010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/08/2022] [Indexed: 12/01/2022]  Open
4
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
5
Zhou X, Cai X. Joint eQTL mapping and inference of gene regulatory network improves power of detecting both cis- and trans-eQTLs. Bioinformatics 2021;38:149-156. [PMID: 34487140 PMCID: PMC8696109 DOI: 10.1093/bioinformatics/btab609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/19/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023]  Open
6
Gerard D, Stephens M. UNIFYING AND GENERALIZING METHODS FOR REMOVING UNWANTED VARIATION BASED ON NEGATIVE CONTROLS. Stat Sin 2021;31:1145-1166. [PMID: 38148787 PMCID: PMC10751021 DOI: 10.5705/ss.202018.0345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
7
Variable selection in high-dimensional sparse multiresponse linear regression models. Stat Pap (Berl) 2020. [DOI: 10.1007/s00362-018-0989-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
8
Gerard D. Data-based RNA-seq simulations by binomial thinning. BMC Bioinformatics 2020;21:206. [PMID: 32448189 PMCID: PMC7245910 DOI: 10.1186/s12859-020-3450-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/10/2020] [Indexed: 11/23/2022]  Open
9
Rhyne J, Jeng XJ, Chi EC, Tzeng J. FastLORS: Joint modelling for expression quantitative trait loci mapping in R. Stat (Int Stat Inst) 2020. [DOI: 10.1002/sta4.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
10
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]
11
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]
12
Liu J, Wan X, Wang C, Yang C, Zhou X, Yang C. LLR: a latent low-rank approach to colocalizing genetic risk variants in multiple GWAS. Bioinformatics 2018;33:3878-3886. [PMID: 28961754 DOI: 10.1093/bioinformatics/btx512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 08/09/2017] [Indexed: 12/30/2022]  Open
13
Sun J, Herazo-Maya JD, Huang X, Kaminski N, Zhao H. Distance-correlation based gene set analysis in longitudinal studies. Stat Appl Genet Mol Biol 2018;17:sagmb-2017-0053. [PMID: 29397393 DOI: 10.1515/sagmb-2017-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
14
Li C, Zhou H. svt: Singular Value Thresholding in MATLAB. J Stat Softw 2017;81. [PMID: 32523475 DOI: 10.18637/jss.v081.c02] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]  Open
15
Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes. Sci Rep 2017;7:13587. [PMID: 29051597 PMCID: PMC5648789 DOI: 10.1038/s41598-017-13665-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/29/2017] [Indexed: 11/24/2022]  Open
16
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]
17
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
18
Simultaneous dimension reduction and adjustment for confounding variation. Proc Natl Acad Sci U S A 2016;113:14662-14667. [PMID: 27930330 DOI: 10.1073/pnas.1617317113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
19
Cheng W, Shi Y, Zhang X, Wang W. Sparse regression models for unraveling group and individual associations in eQTL mapping. BMC Bioinformatics 2016;17:136. [PMID: 27000043 PMCID: PMC4802846 DOI: 10.1186/s12859-016-0986-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 03/10/2016] [Indexed: 11/18/2022]  Open
20
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]
21
Cheng W, Shi Y, Zhang X, Wang W. Fast and robust group-wise eQTL mapping using sparse graphical models. BMC Bioinformatics 2015;16:2. [PMID: 25593000 PMCID: PMC4387667 DOI: 10.1186/s12859-014-0421-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023]  Open
22
Cheng W, Zhang X, Guo Z, Shi Y, Wang W. Graph-regularized dual Lasso for robust eQTL mapping. ACTA ACUST UNITED AC 2014;30:i139-48. [PMID: 24931977 PMCID: PMC4058913 DOI: 10.1093/bioinformatics/btu293] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
Ho YY, Baechler EC, Ortmann W, Behrens TW, Graham RR, Bhangale TR, Pan W. Using gene expression to improve the power of genome-wide association analysis. Hum Hered 2014;78:94-103. [PMID: 25096029 PMCID: PMC4152945 DOI: 10.1159/000362837] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/14/2014] [Indexed: 12/20/2022]  Open
24
Wang Y, Wang L, Yang D, Deng M. Imputing missing values for genetic interaction data. Methods 2014;67:269-77. [PMID: 24718098 DOI: 10.1016/j.ymeth.2014.03.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 03/19/2014] [Accepted: 03/27/2014] [Indexed: 11/26/2022]  Open
25
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] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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