My Bibliography

select

He B, Xie L, Varathan P, Nho K, Risacher SL, Saykin AJ, Yan J. Fused multi-modal similarity network as prior in guiding brain imaging genetic association. Front Big Data. 2023;6:1151893. doi: 10.3389/fdata.2023.1151893. eCollection 2023. PubMed PMID: 37215688; PubMed Central PMCID: PMC10196480.

select

Varathan P, Gorijala P, Jacobson T, Chasioti D, Nho K, Risacher SL, Saykin AJ, Yan J. Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains. BMC Med Genomics. 2022 Apr 23;15(Suppl 2):93. doi: 10.1186/s12920-022-01245-5. PubMed PMID: 35461270; PubMed Central PMCID: PMC9035239.

select

He B, Gorijala P, Xie L, Cao S, Yan J. Gene co-expression changes underlying the functional connectomic alterations in Alzheimer's disease. BMC Med Genomics. 2022 Apr 23;15(Suppl 2):92. doi: 10.1186/s12920-022-01244-6. PubMed PMID: 35461274; PubMed Central PMCID: PMC9035246.

select

Cong S, Yao X, Xie L, Yan J, Shen L. Genetic Influence Underlying Brain Connectivity Phenotype: A Study on Two Age-Specific Cohorts. Front Genet. 2021;12:782953. doi: 10.3389/fgene.2021.782953. eCollection 2021. PubMed PMID: 35237294; PubMed Central PMCID: PMC8884108.

select

Kim M, Min EJ, Liu K, Yan J, Saykin AJ, Moore JH, Long Q, Shen L. Multi-task learning based structured sparse canonical correlation analysis for brain imaging genetics. Med Image Anal. 2022 Feb;76:102297. doi: 10.1016/j.media.2021.102297. Epub 2021 Nov 13. PubMed PMID: 34871929; PubMed Central PMCID: PMC8792314.

select

Li J, Chen F, Liang H, Yan J. MoNET: an R package for multi-omic network analysis. Bioinformatics. 2022 Jan 27;38(4):1165-1167. doi: 10.1093/bioinformatics/btab722. PubMed PMID: 34694378; PubMed Central PMCID: PMC10060724.

select

Xie L, He B, Varathan P, Nho K, Risacher SL, Saykin AJ, Salama P, Yan J. Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease. Brief Bioinform. 2021 Nov 5;22(6). doi: 10.1093/bib/bbab121. PubMed PMID: 33971669; PubMed Central PMCID: PMC8574309.

select

Zhang L, Wang L, Gao J, Risacher SL, Yan J, Li G, Liu T, Zhu D. Deep Fusion of Brain Structure-Function in Mild Cognitive Impairment. Med Image Anal. 2021 Aug;72:102082. doi: 10.1016/j.media.2021.102082. Epub 2021 Apr 23. PubMed PMID: 34004495.

select

Baloni P, Funk CC, Yan J, Yurkovich JT, Kueider-Paisley A, Nho K, Heinken A, Jia W, Mahmoudiandehkordi S, Louie G, Saykin AJ, Arnold M, Kastenmüller G, Griffiths WJ, Thiele I, Kaddurah-Daouk R, Price ND. Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease. Cell Rep Med. 2020 Nov 17;1(8):100138. doi: 10.1016/j.xcrm.2020.100138. eCollection 2020 Nov 17. PubMed PMID: 33294859; PubMed Central PMCID: PMC7691449.

select

Xie L, Varathan P, Nho K, Saykin AJ, Salama P, Yan J. Identification of functionally connected multi-omic biomarkers for Alzheimer's disease using modularity-constrained Lasso. PLoS One. 2020;15(6):e0234748. doi: 10.1371/journal.pone.0234748. eCollection 2020. PubMed PMID: 32555747; PubMed Central PMCID: PMC7299377.

select

Yao X, Cong S, Yan J, Risacher SL, Saykin AJ, Moore JH, Shen L. Regional imaging genetic enrichment analysis. Bioinformatics. 2020 Apr 15;36(8):2554-2560. doi: 10.1093/bioinformatics/btz948. PubMed PMID: 31860065; PubMed Central PMCID: PMC7178438.

select

Upadhyaya Y, Xie L, Salama P, Cao S, Nho K, Saykin AJ, Yan J, Alzheimer's Disease Neuroimaging Initiative FT. Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer's disease. BMC Med Genomics. 2020 Apr 3;13(Suppl 5):53. doi: 10.1186/s12920-020-0689-y. PubMed PMID: 32241275; PubMed Central PMCID: PMC7118822.

select

Yan J, Raja V V, Huang Z, Amico E, Nho K, Fang S, Sporns O, Wu YC, Saykin A, Goni J, Shen L. Brain-wide structural connectivity alterations under the control of Alzheimer risk genes. Int J Comput Biol Drug Des. 2020;13(1):58-70. doi: 10.1504/ijcbdd.2020.10026789. Epub 2020 Feb 7. PubMed PMID: 32095160; PubMed Central PMCID: PMC7039398.

select

Yao X, Cong S, Yan J, Risacher SL, Saykin AJ, Moore JH, Shen L. Mining Regional Imaging Genetic Associations via Voxel-wise Enrichment Analysis. IEEE EMBS Int Conf Biomed Health Inform. 2019 May;2019. doi: 10.1109/BHI.2019.8834450. Epub 2019 Sep 12. PubMed PMID: 31742256; PubMed Central PMCID: PMC6860973.

select

Chasioti D, Yan J, Nho K, Saykin AJ. Progress in Polygenic Composite Scores in Alzheimer's and Other Complex Diseases. Trends Genet. 2019 May;35(5):371-382. doi: 10.1016/j.tig.2019.02.005. Epub 2019 Mar 25. Review. PubMed PMID: 30922659; PubMed Central PMCID: PMC6475476.

select

Wu Z, Yan J, Wang K, Liu X, Guo Y, Zhi D, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications. BMC Genomics. 2019 Feb 4;20(Suppl 1):80. doi: 10.1186/s12864-018-5369-3. PubMed PMID: 30712512; PubMed Central PMCID: PMC6360715.

select

Li J, Chen F, Zhang Q, Meng X, Yao X, Risacher SL, Yan J, Saykin AJ, Liang H, Shen L. Genome-wide Network-assisted Association and Enrichment Study of Amyloid Imaging Phenotype in Alzheimer's Disease. Curr Alzheimer Res. 2019;16(13):1163-1174. doi: 10.2174/1567205016666191121142558. PubMed PMID: 31755389; PubMed Central PMCID: PMC8407042.

select

Yan J, Risacher SL, Shen L, Saykin AJ. Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. Brief Bioinform. 2018 Nov 27;19(6):1370-1381. doi: 10.1093/bib/bbx066. Review. PubMed PMID: 28679163; PubMed Central PMCID: PMC6454489.

select

Zigon B, Li H, Yao X, Fang S, Hasan MA, Yan J, Moore JH, Saykin AJ, Shen L. GPU Accelerated Browser for Neuroimaging Genomics. Neuroinformatics. 2018 Oct;16(3-4):393-402. doi: 10.1007/s12021-018-9376-y. PubMed PMID: 29691798; PubMed Central PMCID: PMC6092242.

select

Xie L, Amico E, Salama P, Wu YC, Fang S, Sporns O, Saykin AJ, Goñi J, Yan J, Shen L. Heritability Estimation of Reliable Connectomic Features. Connect Neuroimaging (2018). 2018 Sep;11083:58-66. doi: 10.1007/978-3-030-00755-3_7. Epub 2018 Sep 15. PubMed PMID: 30906933; PubMed Central PMCID: PMC6425273.

select

Wang X, Chen H, Yan J, Nho K, Risacher SL, Saykin AJ, Shen L, Huang H. Quantitative trait loci identification for brain endophenotypes via new additive model with random networks. Bioinformatics. 2018 Sep 1;34(17):i866-i874. doi: 10.1093/bioinformatics/bty557. PubMed PMID: 30423101; PubMed Central PMCID: PMC6129276.

select

Wang X, Yan J, Yao X, Kim S, Nho K, Risacher SL, Saykin AJ, Shen L, Huang H. Longitudinal Genotype-Phenotype Association Study through Temporal Structure Auto-Learning Predictive Model. J Comput Biol. 2018 Jul;25(7):809-824. doi: 10.1089/cmb.2018.0008. PubMed PMID: 30011249; PubMed Central PMCID: PMC6067099.

select

Yan J, Liu K, Li H, Amico E, Risacher SL, Wu YC, Fang S, Sporns O, Saykin AJ, Goñi J, Shen L. JOINT EXPLORATION AND MINING OF MEMORY-RELEVANT BRAIN ANATOMIC AND CONNECTOMIC PATTERNS VIA A THREE-WAY ASSOCIATION MODEL. Proc IEEE Int Symp Biomed Imaging. 2018 Apr;2018:6-9. doi: 10.1109/ISBI.2018.8363511. Epub 2018 May 24. PubMed PMID: 30271529; PubMed Central PMCID: PMC6155994.

select

Du L, Liu K, Zhang T, Yao X, Yan J, Risacher SL, Han J, Guo L, Saykin AJ, Shen L. A novel SCCA approach via truncated ℓ1-norm and truncated group lasso for brain imaging genetics. Bioinformatics. 2018 Jan 15;34(2):278-285. doi: 10.1093/bioinformatics/btx594. PubMed PMID: 28968815; PubMed Central PMCID: PMC5860211.

select

Yao X, Yan J, Ginda M, Börner K, Saykin AJ, Shen L. Mapping longitudinal scientific progress, collaboration and impact of the Alzheimer's disease neuroimaging initiative. PLoS One. 2017;12(11):e0186095. doi: 10.1371/journal.pone.0186095. eCollection 2017. PubMed PMID: 29095836; PubMed Central PMCID: PMC5667864.

select

Du L, Liu K, Yao X, Yan J, Risacher SL, Han J, Guo L, Saykin AJ, Shen L. Pattern Discovery in Brain Imaging Genetics via SCCA Modeling with a Generic Non-convex Penalty. Sci Rep. 2017 Oct 25;7(1):14052. doi: 10.1038/s41598-017-13930-y. PubMed PMID: 29070790; PubMed Central PMCID: PMC5656688.

select

Yao X, Yan J, Liu K, Kim S, Nho K, Risacher SL, Greene CS, Moore JH, Saykin AJ, Shen L. Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinformatics. 2017 Oct 15;33(20):3250-3257. doi: 10.1093/bioinformatics/btx344. PubMed PMID: 28575147; PubMed Central PMCID: PMC6410887.

select

Liu K, Yao X, Yan J, Chasioti D, Risacher S, Nho K, Saykin A, Shen L. Transcriptome-Guided Imaging Genetic Analysis via a Novel Sparse CCA Algorithm. Graphs Biomed Image Anal Comput Anat Imaging Genet (2017). 2017;10551:220-229. doi: 10.1007/978-3-319-67675-3_20. Epub 2017 Sep 8. PubMed PMID: 30294724; PubMed Central PMCID: PMC6171533.

select

Li J, Zhang Q, Chen F, Meng X, Liu W, Chen D, Yan J, Kim S, Wang L, Feng W, Saykin AJ, Liang H, Shen L. Genome-wide association and interaction studies of CSF T-tau/Aβ(42) ratio in ADNI cohort. Neurobiol Aging. 2017 Sep;57:247.e1-247.e8. doi: 10.1016/j.neurobiolaging.2017.05.007. Epub 2017 May 15. PubMed PMID: 28641921; PubMed Central PMCID: PMC5869719.

select

Hao X, Li C, Yan J, Yao X, Risacher SL, Saykin AJ, Shen L, Zhang D. Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis. Bioinformatics. 2017 Jul 15;33(14):i341-i349. doi: 10.1093/bioinformatics/btx245. PubMed PMID: 28881979; PubMed Central PMCID: PMC5870577.

select

Yao X, Yan J, Risacher S, Moore J, Saykin A, Shen L. NETWORK-BASED GENOME WIDE STUDY OF HIPPOCAMPAL IMAGING PHENOTYPE IN ALZHEIMER'S DISEASE TO IDENTIFY FUNCTIONAL INTERACTION MODULES. Proc IEEE Int Conf Acoust Speech Signal Process. 2017;2017:6170-6174. doi: 10.1109/ICASSP.2017.7953342. Epub 2017 Jun 19. PubMed PMID: 28989328; PubMed Central PMCID: PMC5627518.

select

Du L, Zhang T, Liu K, Yan J, Yao X, Risacher SL, Saykin AJ, Han J, Guo L, Shen L. Identifying Associations Between Brain Imaging Phenotypes and Genetic Factors via A Novel Structured SCCA Approach. Inf Process Med Imaging. 2017 Jun;10265:543-555. doi: 10.1007/978-3-319-59050-9_43. Epub 2017 May 23. PubMed PMID: 28867917; PubMed Central PMCID: PMC5576511.

select

Wang X, Liu K, Yan J, Risacher SL, Saykin AJ, Shen L, Huang H. Predicting Interrelated Alzheimer's Disease Outcomes via New Self-Learned Structured Low-Rank Model. Inf Process Med Imaging. 2017 Jun;10265:198-209. doi: 10.1007/978-3-319-59050-9_16. Epub 2017 May 23. PubMed PMID: 28848302; PubMed Central PMCID: PMC5571742.

select

Cong W, Meng X, Li J, Zhang Q, Chen F, Liu W, Wang Y, Cheng S, Yao X, Yan J, Kim S, Saykin AJ, Liang H, Shen L. Genome-wide network-based pathway analysis of CSF t-tau/Aβ1-42 ratio in the ADNI cohort. BMC Genomics. 2017 May 30;18(1):421. doi: 10.1186/s12864-017-3798-z. PubMed PMID: 28558704; PubMed Central PMCID: PMC5450240.

select

Wang X, Yan J, Yao X, Kim S, Nho K, Risacher SL, Saykin AJ, Shen L, Huang H. Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-Learning Predictive Model. Res Comput Mol Biol. 2017 May;10229:287-302. doi: 10.1007/978-3-319-56970-3_18. Epub 2017 Apr 12. PubMed PMID: 29696245; PubMed Central PMCID: PMC5912922.

select

Hao X, Li C, Du L, Yao X, Yan J, Risacher SL, Saykin AJ, Shen L, Zhang D. Mining Outcome-relevant Brain Imaging Genetic Associations via Three-way Sparse Canonical Correlation Analysis in Alzheimer's Disease. Sci Rep. 2017 Mar 14;7:44272. doi: 10.1038/srep44272. PubMed PMID: 28291242; PubMed Central PMCID: PMC5349597.

select

Yao X, Yan J, Kim S, Nho K, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L. Two-dimensional enrichment analysis for mining high-level imaging genetic associations. Brain Inform. 2017 Mar;4(1):27-37. doi: 10.1007/s40708-016-0052-4. Epub 2016 May 13. PubMed PMID: 27747820; PubMed Central PMCID: PMC5118198.

select

Du L, Zhang T, Liu K, Yao X, Yan J, Risacher SL, Guo L, Saykin AJ, Shen L. Sparse Canonical Correlation Analysis via Truncated ℓ(1)-norm with Application to Brain Imaging Genetics. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2016;2016:707-711. doi: 10.1109/BIBM.2016.7822605. Epub 2017 Jan 19. PubMed PMID: 28989812; PubMed Central PMCID: PMC5627624.

select

Yan J, Risacher SL, Nho K, Saykin AJ, Shen LI. IDENTIFICATION OF DISCRIMINATIVE IMAGING PROTEOMICS ASSOCIATIONS IN ALZHEIMER'S DISEASE VIA A NOVEL SPARSE CORRELATION MODEL. Pac Symp Biocomput. 2017;22:94-104. doi: 10.1142/9789813207813_0010. PubMed PMID: 27896965; PubMed Central PMCID: PMC5147740.

select

Hao X, Yao X, Yan J, Risacher SL, Saykin AJ, Zhang D, Shen L. Identifying Multimodal Intermediate Phenotypes Between Genetic Risk Factors and Disease Status in Alzheimer's Disease. Neuroinformatics. 2016 Oct;14(4):439-52. doi: 10.1007/s12021-016-9307-8. PubMed PMID: 27277494; PubMed Central PMCID: PMC5010986.

select

Du L, Huang H, Yan J, Kim S, Risacher S, Inlow M, Moore J, Saykin A, Shen L. Structured sparse CCA for brain imaging genetics via graph OSCAR. BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):68. doi: 10.1186/s12918-016-0312-1. PubMed PMID: 27585988; PubMed Central PMCID: PMC5009827.

select

Du L, Huang H, Yan J, Kim S, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L. Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method. Bioinformatics. 2016 May 15;32(10):1544-51. doi: 10.1093/bioinformatics/btw033. Epub 2016 Jan 21. PubMed PMID: 26801960; PubMed Central PMCID: PMC4907375.

select

Song A, Yan J, Kim S, Risacher SL, Wong AK, Saykin AJ, Shen L, Greene CS. Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. BioData Min. 2016;9:3. doi: 10.1186/s13040-016-0082-8. eCollection 2016. PubMed PMID: 26788126; PubMed Central PMCID: PMC4717572.

select

Hao X, Yan J, Yao X, Risacher SL, Saykin AJ, Zhang D, Shen L. DIAGNOSIS-GUIDED METHOD FOR IDENTIFYING MULTI-MODALITY NEUROIMAGING BIOMARKERS ASSOCIATED WITH GENETIC RISK FACTORS IN ALZHEIMER'S DISEASE. Pac Symp Biocomput. 2016;21:108-19. PubMed PMID: 26776178; PubMed Central PMCID: PMC4719777.

select

Li J, Zhang Q, Chen F, Yan J, Kim S, Wang L, Feng W, Saykin AJ, Liang H, Shen L. Genetic Interactions Explain Variance in Cingulate Amyloid Burden: An AV-45 PET Genome-Wide Association and Interaction Study in the ADNI Cohort. Biomed Res Int. 2015;2015:647389. doi: 10.1155/2015/647389. Epub 2015 Sep 3. PubMed PMID: 26421299; PubMed Central PMCID: PMC4573220.

select

Yao X, Yan J, Kim S, Nho K, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L. Two-dimensional Enrichment Analysis for Mining High-level Imaging Genetic Associations. Brain Inform Health (2015). 2015 Aug-Sep;9250:115-124. doi: 10.1007/978-3-319-23344-4_12. Epub 2015 Aug 21. PubMed PMID: 26568986; PubMed Central PMCID: PMC4640356.

select

Yan J, Kim S, Nho K, Chen R, Risacher SL, Moore JH, Saykin AJ, Shen L. Hippocampal transcriptome-guided genetic analysis of correlated episodic memory phenotypes in Alzheimer's disease. Front Genet. 2015;6:117. doi: 10.3389/fgene.2015.00117. eCollection 2015. PubMed PMID: 25859259; PubMed Central PMCID: PMC4374536.

select

Du L, Yan J, Kim S, Risacher SL, Huang H, Inlow M, Moore JH, Saykin AJ, Shen L. GN-SCCA: GraphNet based Sparse Canonical Correlation Analysis for Brain Imaging Genetics. Brain Inform Health (2015). 2015;9250:275-284. doi: 10.1007/978-3-319-23344-4_27. PubMed PMID: 26636135; PubMed Central PMCID: PMC4663463.

select

Yan J, Li T, Wang H, Huang H, Wan J, Nho K, Kim S, Risacher SL, Saykin AJ, Shen L. Cortical surface biomarkers for predicting cognitive outcomes using group l2,1 norm. Neurobiol Aging. 2015 Jan;36 Suppl 1:S185-93. doi: 10.1016/j.neurobiolaging.2014.07.045. Epub 2014 Aug 29. PubMed PMID: 25444599; PubMed Central PMCID: PMC4268071.

select

Gao H, Cai C, Yan J, Yan L, Cortes JG, Wang Y, Nie F, West J, Saykin A, Shen L, Huang H. Identifying Connectome Module Patterns via New Balanced Multi-Graph Normalized Cut. Med Image Comput Comput Assist Interv. 2015;9350:169-76. doi: 10.1007/978-3-319-24571-3_21. PubMed PMID: 26525952; PubMed Central PMCID: PMC4624338.