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For: Silver M, Montana G. Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Stat Appl Genet Mol Biol 2012;11:Article 7. [PMID: 22499682 PMCID: PMC3491888 DOI: 10.2202/1544-6115.1755] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Number Cited by Other Article(s)
1
Qian J, Tanigawa Y, Li R, Tibshirani R, Rivas MA, Hastie T. LARGE-SCALE MULTIVARIATE SPARSE REGRESSION WITH APPLICATIONS TO UK BIOBANK. Ann Appl Stat 2022;16:1891-1918. [PMID: 36091495 PMCID: PMC9454085 DOI: 10.1214/21-aoas1575] [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: 11/19/2022]
2
Wang W, Kong W, Wang S, Wei K. Detecting Biomarkers of Alzheimer's Disease Based on Multi-constrained Uncertainty-Aware Adaptive Sparse Multi-view Canonical Correlation Analysis. J Mol Neurosci 2022;72:841-865. [PMID: 35080765 DOI: 10.1007/s12031-021-01963-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/29/2021] [Indexed: 12/01/2022]
3
Li Y, Nan B, Zhu J. A Structured Brain-wide and Genome-wide Association Study Using ADNI PET Images. CAN J STAT 2021;49:182-202. [PMID: 34566241 DOI: 10.1002/cjs.11605] [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] [Indexed: 11/07/2022]
4
Lu P, Colliot O. Multilevel Survival Modeling with Structured Penalties for Disease Prediction from Imaging Genetics data. IEEE J Biomed Health Inform 2021;26:798-808. [PMID: 34329174 DOI: 10.1109/jbhi.2021.3100918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
5
Deng L, Ma L, Cheng KK, Xu X, Raftery D, Dong J. Sparse PLS-Based Method for Overlapping Metabolite Set Enrichment Analysis. J Proteome Res 2021;20:3204-3213. [PMID: 34002606 DOI: 10.1021/acs.jproteome.1c00064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
6
Huang M, Chen X, Yu Y, Lai H, Feng Q. Imaging Genetics Study Based on a Temporal Group Sparse Regression and Additive Model for Biomarker Detection of Alzheimer's Disease. IEEE TRANSACTIONS ON MEDICAL IMAGING 2021;40:1461-1473. [PMID: 33556003 DOI: 10.1109/tmi.2021.3057660] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
7
Zwep LB, Duisters KLW, Jansen M, Guo T, Meulman JJ, Upadhyay PJ, van Hasselt JGC. Identification of high-dimensional omics-derived predictors for tumor growth dynamics using machine learning and pharmacometric modeling. CPT Pharmacometrics Syst Pharmacol 2021;10:350-361. [PMID: 33792207 PMCID: PMC8099445 DOI: 10.1002/psp4.12603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/07/2021] [Accepted: 02/01/2021] [Indexed: 12/26/2022]  Open
8
Wen C, Yang Y, Xiao Q, Huang M, Pan W. Genome-wide association studies of brain imaging data via weighted distance correlation. Bioinformatics 2021;36:4942-4950. [PMID: 32619001 DOI: 10.1093/bioinformatics/btaa612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/17/2020] [Accepted: 06/26/2020] [Indexed: 11/13/2022]  Open
9
Zhou J, Qiu Y, Chen S, Liu L, Liao H, Chen H, Lv S, Li X. A Novel Three-Stage Framework for Association Analysis Between SNPs and Brain Regions. Front Genet 2020;11:572350. [PMID: 33193677 PMCID: PMC7542238 DOI: 10.3389/fgene.2020.572350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/17/2020] [Indexed: 12/17/2022]  Open
10
Zhang L, Papachristou C, Choudhary PK, Biswas S. A Bayesian Hierarchical Framework for Pathway Analysis in Genome-Wide Association Studies. Hum Hered 2020;84:240-255. [PMID: 32966977 DOI: 10.1159/000508664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 05/14/2020] [Indexed: 11/19/2022]  Open
11
Detecting genetic associations with brain imaging phenotypes in Alzheimer's disease via a novel structured SCCA approach. Med Image Anal 2020;61:101656. [PMID: 32062154 DOI: 10.1016/j.media.2020.101656] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 11/27/2019] [Accepted: 01/22/2020] [Indexed: 01/15/2023]
12
Shen L, Thompson PM. Brain Imaging Genomics: Integrated Analysis and Machine Learning. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2020;108:125-162. [PMID: 31902950 PMCID: PMC6941751 DOI: 10.1109/jproc.2019.2947272] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
13
Stelzer AS, Maccioni L, Gerhold-Ay A, Smedby KE, Schumacher M, Nieters A, Binder H. A multivariable approach for risk markers from pooled molecular data with only partial overlap. BMC MEDICAL GENETICS 2019;20:128. [PMID: 31324155 PMCID: PMC6642584 DOI: 10.1186/s12881-019-0849-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/19/2019] [Indexed: 11/29/2022]
14
Jackknife Model Averaging Prediction Methods for Complex Phenotypes with Gene Expression Levels by Integrating External Pathway Information. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2019;2019:2807470. [PMID: 31089389 PMCID: PMC6476151 DOI: 10.1155/2019/2807470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/20/2019] [Indexed: 01/03/2023]
15
Tang Z, Lei S, Zhang X, Yi Z, Guo B, Chen JY, Shen Y, Yi N. Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information. BMC Bioinformatics 2019;20:94. [PMID: 30813883 PMCID: PMC6391807 DOI: 10.1186/s12859-019-2656-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 01/28/2019] [Indexed: 12/13/2022]  Open
16
Yang A, Miller D, Pan Q. Constrained maximum entropy models to select genotype interactions associated with censored failure times. J Bioinform Comput Biol 2018;16:1840024. [PMID: 30567478 DOI: 10.1142/s0219720018400243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
17
Tang Z, Shen Y, Li Y, Zhang X, Wen J, Qian C, Zhuang W, Shi X, Yi N. Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information. Bioinformatics 2018;34:901-910. [PMID: 29077795 PMCID: PMC5860634 DOI: 10.1093/bioinformatics/btx684] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/05/2017] [Accepted: 10/24/2017] [Indexed: 01/10/2023]  Open
18
Machine learning shows association between genetic variability in PPARG and cerebral connectivity in preterm infants. Proc Natl Acad Sci U S A 2017;114:13744-13749. [PMID: 29229843 PMCID: PMC5748164 DOI: 10.1073/pnas.1704907114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
19
Characterizing Gene and Protein Crosstalks in Subjects at Risk of Developing Alzheimer’s Disease: A New Computational Approach. Processes (Basel) 2017. [DOI: 10.3390/pr5030047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
20
Krishnan ML, Wang Z, Silver M, Boardman JP, Ball G, Counsell SJ, Walley AJ, Montana G, Edwards AD. Possible relationship between common genetic variation and white matter development in a pilot study of preterm infants. Brain Behav 2016;6:e00434. [PMID: 27110435 PMCID: PMC4821839 DOI: 10.1002/brb3.434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/16/2015] [Accepted: 12/19/2015] [Indexed: 12/19/2022]  Open
21
Edwards SM, Thomsen B, Madsen P, Sørensen P. Partitioning of genomic variance reveals biological pathways associated with udder health and milk production traits in dairy cattle. Genet Sel Evol 2015;47:60. [PMID: 26169777 PMCID: PMC4499908 DOI: 10.1186/s12711-015-0132-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 06/12/2015] [Indexed: 12/20/2022]  Open
22
Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Cedarbaum J, Green RC, Harvey D, Jack CR, Jagust W, Luthman J, Morris JC, Petersen RC, Saykin AJ, Shaw L, Shen L, Schwarz A, Toga AW, Trojanowski JQ. 2014 Update of the Alzheimer's Disease Neuroimaging Initiative: A review of papers published since its inception. Alzheimers Dement 2015;11:e1-120. [PMID: 26073027 PMCID: PMC5469297 DOI: 10.1016/j.jalz.2014.11.001] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/18/2013] [Indexed: 01/18/2023]
23
Lin D, Cao H, Calhoun VD, Wang YP. Sparse models for correlative and integrative analysis of imaging and genetic data. J Neurosci Methods 2014;237:69-78. [PMID: 25218561 DOI: 10.1016/j.jneumeth.2014.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/27/2014] [Accepted: 09/01/2014] [Indexed: 11/29/2022]
24
Shen L, Thompson PM, Potkin SG, Bertram L, Farrer LA, Foroud TM, Green RC, Hu X, Huentelman MJ, Kim S, Kauwe JSK, Li Q, Liu E, Macciardi F, Moore JH, Munsie L, Nho K, Ramanan VK, Risacher SL, Stone DJ, Swaminathan S, Toga AW, Weiner MW, Saykin AJ. Genetic analysis of quantitative phenotypes in AD and MCI: imaging, cognition and biomarkers. Brain Imaging Behav 2014;8:183-207. [PMID: 24092460 PMCID: PMC3976843 DOI: 10.1007/s11682-013-9262-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
25
Silver M, Chen P, Li R, Cheng CY, Wong TY, Tai ES, Teo YY, Montana G. Pathways-driven sparse regression identifies pathways and genes associated with high-density lipoprotein cholesterol in two Asian cohorts. PLoS Genet 2013;9:e1003939. [PMID: 24278029 PMCID: PMC3836716 DOI: 10.1371/journal.pgen.1003939] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 09/11/2013] [Indexed: 01/11/2023]  Open
26
Yang R, Li H, Fu L, Liu Y. An efficient approach to large-scale genotype-phenotype association analyses. Brief Bioinform 2013;15:814-22. [PMID: 23990269 DOI: 10.1093/bib/bbt061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
27
Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Green RC, Harvey D, Jack CR, Jagust W, Liu E, Morris JC, Petersen RC, Saykin AJ, Schmidt ME, Shaw L, Shen L, Siuciak JA, Soares H, Toga AW, Trojanowski JQ. The Alzheimer's Disease Neuroimaging Initiative: a review of papers published since its inception. Alzheimers Dement 2013;9:e111-94. [PMID: 23932184 DOI: 10.1016/j.jalz.2013.05.1769] [Citation(s) in RCA: 308] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/18/2013] [Indexed: 01/19/2023]
28
Ayers KL, Cordell HJ. Identification of grouped rare and common variants via penalized logistic regression. Genet Epidemiol 2013;37:592-602. [PMID: 23836590 PMCID: PMC3842118 DOI: 10.1002/gepi.21746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 05/24/2013] [Accepted: 05/24/2013] [Indexed: 11/09/2022]
29
Lehne B, Schlitt T. Breaking free from the chains of pathway annotation: de novo pathway discovery for the analysis of disease processes. Pharmacogenomics 2013;13:1967-78. [PMID: 23215889 DOI: 10.2217/pgs.12.170] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
30
Silver M, Janousova E, Hua X, Thompson PM, Montana G. Identification of gene pathways implicated in Alzheimer's disease using longitudinal imaging phenotypes with sparse regression. Neuroimage 2012;63:1681-94. [PMID: 22982105 PMCID: PMC3549495 DOI: 10.1016/j.neuroimage.2012.08.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 08/01/2012] [Accepted: 08/03/2012] [Indexed: 02/04/2023]  Open
31
Vounou M, Janousova E, Wolz R, Stein JL, Thompson PM, Rueckert D, Montana G. Sparse reduced-rank regression detects genetic associations with voxel-wise longitudinal phenotypes in Alzheimer's disease. Neuroimage 2011;60:700-16. [PMID: 22209813 DOI: 10.1016/j.neuroimage.2011.12.029] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 11/18/2011] [Accepted: 12/14/2011] [Indexed: 11/17/2022]  Open
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