My Bibliography

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Xu F, Ziebarth JD, Goeminne LJ, Gao J, Williams EG, Quarles LD, Makowski L, Cui Y, Williams RW, Auwerx J, Lu L. Gene network based analysis identifies a coexpression module involved in regulating plasma lipids with high-fat diet response. J Nutr Biochem. 2023 Sep;119:109398. doi: 10.1016/j.jnutbio.2023.109398. Epub 2023 Jun 10. PubMed PMID: 37302664.

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Gao Y, Sharma T, Cui Y. Addressing the Challenge of Biomedical Data Inequality: An Artificial Intelligence Perspective. Annu Rev Biomed Data Sci. 2023 Aug 10;6:153-171. doi: 10.1146/annurev-biodatasci-020722-020704. Epub 2023 Apr 27. Review. PubMed PMID: 37104653; NIHMSID:NIHMS1913459.

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Gao Y, Cui Y. Clinical time-to-event prediction enhanced by incorporating compatible related outcomes. PLOS Digit Health. 2022;1(5). doi: 10.1371/journal.pdig.0000038. Epub 2022 May 26. PubMed PMID: 35757279; PubMed Central PMCID: PMC9222982.

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Roy S, Sleiman MB, Jha P, Ingels JF, Chapman CJ, McCarty MS, Ziebarth JD, Hook M, Sun A, Zhao W, Huang J, Neuner SM, Wilmott LA, Shapaker TM, Centeno AG, Ashbrook DG, Mulligan MK, Kaczorowski CC, Makowski L, Cui Y, Read RW, Miller RA, Mozhui K, Williams EG, Sen S, Lu L, Auwerx J, Williams RW. Gene-by-environment modulation of lifespan and weight gain in the murine BXD family. Nat Metab. 2021 Sep;3(9):1217-1227. doi: 10.1038/s42255-021-00449-w. Epub 2021 Sep 22. PubMed PMID: 34552269; PubMed Central PMCID: PMC8478125.

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Xu F, Chen Y, Tillman KA, Cui Y, Williams RW, Bhattacharya SK, Lu L, Sun Y. Characterizing modifier genes of cardiac fibrosis phenotype in hypertrophic cardiomyopathy. Int J Cardiol. 2021 May 1;330:135-141. doi: 10.1016/j.ijcard.2021.01.047. Epub 2021 Jan 30. PubMed PMID: 33529666; PubMed Central PMCID: PMC8105878.

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Xu F, Gao J, Bergmann S, Sims AC, Ashbrook DG, Baric RS, Cui Y, Jonsson CB, Li K, Williams RW, Schughart K, Lu L. Genetic Dissection of the Regulatory Mechanisms of Ace2 in the Infected Mouse Lung. Front Immunol. 2020;11:607314. doi: 10.3389/fimmu.2020.607314. eCollection 2020. PubMed PMID: 33488611; PubMed Central PMCID: PMC7819859.

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Gao Y, Cui Y. Multi-ethnic Survival Analysis: Transfer Learning with Cox Neural Networks. AAAI Symposium on Survival Prediction - Algorithms, Challenges, and Applications, Proceedings of Machine Learning Research. 2021; 146:252-257.

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Xu F, Gao J, Munkhsaikhan U, Li N, Gu Q, Pierre JF, Starlard-Davenport A, Towbin JA, Cui Y, Purevjav E, Lu L. The Genetic Dissection of Ace2 Expression Variation in the Heart of Murine Genetic Reference Population. Front Cardiovasc Med. 2020;7:582949. doi: 10.3389/fcvm.2020.582949. eCollection 2020. PubMed PMID: 33330645; PubMed Central PMCID: PMC7714829.

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Gao Y, Cui Y. Deep transfer learning for reducing health care disparities arising from biomedical data inequality. Nat Commun. 2020 Oct 12;11(1):5131. doi: 10.1038/s41467-020-18918-3. PubMed PMID: 33046699; PubMed Central PMCID: PMC7552387.

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Sevakula RK, Singh V, Verma NK, Kumar C, Cui Y. Transfer Learning for Molecular Cancer Classification Using Deep Neural Networks. IEEE/ACM Trans Comput Biol Bioinform. 2019 Nov-Dec;16(6):2089-2100. doi: 10.1109/TCBB.2018.2822803. Epub 2018 Apr 4. PubMed PMID: 29993662.

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Mohammed A, Cui Y, Mas VR, Kamaleswaran R. Differential gene expression analysis reveals novel genes and pathways in pediatric septic shock patients. Sci Rep. 2019 Aug 2;9(1):11270. doi: 10.1038/s41598-019-47703-6. PubMed PMID: 31375728; PubMed Central PMCID: PMC6677896.

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Singh V, Verma NK, Cui Y. Type-2 Fuzzy PCA Approach in Extracting Salient Features for Molecular Cancer Diagnostics and Prognostics. IEEE Trans Nanobioscience. 2019 Jul;18(3):482-489. doi: 10.1109/TNB.2019.2917814. Epub 2019 May 20. PubMed PMID: 31107656.

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Singh V, Verma NK, Islam ZU, Cui Y. Feature Learning using Stacked Autoencoder for Shared and Multimodal Fusion of Medical Images. In: Verma NK, Ghosh A, editors. Computational Intelligence: Theories, Applications and Future Directions [Internet] Singapore: Springer; 2019. 53-66p. Available from: https://link.springer.com/chapter/10.1007/978-981-13-1132-1_5.

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Singh V, Sharma T, Verma K, Cui Y. Feature Ranking using Robust Fuzzy Score Function for Gene Expression Data. IEEE International Conference on Fuzzy Systems (FUZZ-IEEE). 2019. doi: 10.1109/FUZZ-IEEE.2019.8858907.

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Ziebarth JD, Cui Y. Multiscalar genetic pathway modeling with hybrid Bayesian networks. Wiley Interdisciplinary Reviews: Computational Statistics. 2019; :e1479. doi: 10.1002/wics.1479.

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Ziebarth JD, Bhattacharya A, Cui Y. Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources. Methods Mol Biol. 2019;1970:101-120. doi: 10.1007/978-1-4939-9207-2_8. PubMed PMID: 30963491.

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Zou Y, Chen Z, Jennings BL, Zhao G, Gu Q, Bhattacharya A, Cui Y, Yu B, Malik KU, Yue J. Deletion of DGCR8 in VSMCs of adult mice results in loss of vascular reactivity, reduced blood pressure and neointima formation. Sci Rep. 2018 Jan 23;8(1):1468. doi: 10.1038/s41598-018-19660-z. PubMed PMID: 29362439; PubMed Central PMCID: PMC5780492.

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Singh V, Vardhan H, Verma NK, Cui Y. Optimal Feature Selection using Fuzzy Combination of Feature Subset for Transcriptome Data. IEEE International Conference on Fuzzy Systems (FUZZ-IEEE). 2018. doi: 10.1109/FUZZ-IEEE.2018.8491683.

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Bhattacharya A, Cui Y. A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules. Sci Rep. 2017 Jun 23;7(1):4162. doi: 10.1038/s41598-017-04070-4. PubMed PMID: 28646174; PubMed Central PMCID: PMC5482832.

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Bhattacharya A, Cui Y. Systematic Prediction of the Impacts of Mutations in MicroRNA Seed Sequences. J Integr Bioinform. 2017 May 18;14(1). doi: 10.1515/jib-2017-0001. PubMed PMID: 28637929; PubMed Central PMCID: PMC6042800.

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Ziebarth JD, Cui Y. Precise Network Modeling of Systems Genetics Data Using the Bayesian Network Webserver. Methods Mol Biol. 2017;1488:319-335. doi: 10.1007/978-1-4939-6427-7_15. PubMed PMID: 27933532.

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Rouchka EC, Chariker JH, Harrison BJ, Park JW, Cao X, Pounds S, Raimondi S, Downing J, Ribeiro R, Rubnitz J, Lamba J, Daigle BJ Jr, Burgess D, Gehrlich S, Carmen JC, Johnson N, Emani C, Gehrlich S, Burgess D, Carmen JC, De Silva K, Heaton MP, Kalbfleisch TS, Viangteeravat T, Mudunuri R, Ajayi O, Şen F, Huang EY, Mohebbi M, Florian L, Jackson DJ, Naber JF, Sabbir AKM, Ellingson SR, Lu Y, Phillips CA, Langston MA, Sevakula RK, Thirukovalluru R, Verma NK, Cui Y, Sayed M, Park JW, Wang J, Liu Q, Shyr Y, Zhang X, Ellingson SR, Prodduturi N, Oliver GR, Grill D, Na J, Eckel-Passow J, Klee EW, Goodin MM, Farman M, Inocencio H, Jang C, Jaromczyk JW, Moore N, Sovacool K, Dent L, Izban M, Mandape S, Sakhare S, Pratap S, Marshall D, DePriest MS, MacLeod JN, Kalbfleisch TS, Emani C, Adam H, Blandford E, Campbell J, Castlen J, Dixon B, Gilbert G, Hall A, Kreisle P, Lasher J, Oakes B, Speer A, Valentine M, Nagisetty NSVR, Jose R, Viangteeravat T, Rooney R, Hains D. Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016 : Cadiz, KY, USA. 8-10 April 2016. BMC Bioinformatics. 2016 Aug 19;17(Suppl 10):297. doi: 10.1186/s12859-016-1154-y. PubMed PMID: 28166713; PubMed Central PMCID: PMC5001208.

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Bhattacharya A, Cui Y. SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. Nucleic Acids Res. 2016 Jan 4;44(D1):D1005-10. doi: 10.1093/nar/gkv1220. Epub 2015 Nov 17. PubMed PMID: 26578591; PubMed Central PMCID: PMC4702864.

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Singh V, Baranwal N, Sevakula RK, Verma NK, Cui Y. Layerwise feature selection in Stacked Sparse Auto-Encoder for tumor type prediction. IEEE International Conference on Bioinformatics and Biomedicine (BIBM).; 2016. Available from: http://ieeexplore.ieee.org/document/7822750/.

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Bhattacharya A, Cui Y. Knowledge-based analysis of functional impacts of mutations in microRNA seed regions. J Biosci. 2015 Oct;40(4):791-8. doi: 10.1007/s12038-015-9560-2. PubMed PMID: 26564979.

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Bhattacharya A, Cui Y. miR2GO: comparative functional analysis for microRNAs. Bioinformatics. 2015 Jul 15;31(14):2403-5. doi: 10.1093/bioinformatics/btv140. Epub 2015 Mar 10. PubMed PMID: 25762653.

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Verma NK, Dutta E, Cui Y. Hausdorff Distance and Global Silhouette Index as Novel Measures for Estimating Quality of Biclusters. IEEE International Conference on Bioinformatics and Biomedicine (BIBM).; 2015. Available from: ieeexplore.ieee.org/document/7359691/.

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Ha T, Swanson D, Larouche M, Glenn R, Weeden D, Zhang P, Hamre K, Langston M, Phillips C, Song M, Ouyang Z, Chesler E, Duvvurru S, Yordanova R, Cui Y, Campbell K, Ricker G, Phillips C, Homayouni R, Goldowitz D. CbGRiTS: cerebellar gene regulation in time and space. Dev Biol. 2015 Jan 1;397(1):18-30. doi: 10.1016/j.ydbio.2014.09.032. Epub 2014 Oct 23. PubMed PMID: 25446528; NIHMSID:NIHMS639544.

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Cashion AK, Hathaway DK, Stanfill A, Thomas F, Ziebarth JD, Cui Y, Cowan PA, Eason J. Pre-transplant predictors of one yr weight gain after kidney transplantation. Clin Transplant. 2014 Nov;28(11):1271-8. doi: 10.1111/ctr.12456. PubMed PMID: 25159302; PubMed Central PMCID: PMC4576829.

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Cui Y. In silico mapping of polymorphic miRNA-mRNA interactions in autoimmune thyroid diseases. Autoimmunity. 2014 Aug;47(5):327-33. doi: 10.3109/08916934.2014.893575. Epub 2014 Mar 10. PubMed PMID: 24611733.

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Emery FD, Parvathareddy J, Pandey AK, Cui Y, Williams RW, Miller MA. Genetic control of weight loss during pneumonic Burkholderia pseudomallei infection. Pathog Dis. 2014 Jul;71(2):249-64. doi: 10.1111/2049-632X.12172. Epub 2014 Apr 22. PubMed PMID: 24687986; PubMed Central PMCID: PMC4107055.

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Bhattacharya A, Ziebarth JD, Cui Y. PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Res. 2014 Jan;42(Database issue):D86-91. doi: 10.1093/nar/gkt1028. Epub 2013 Oct 24. PubMed PMID: 24163105; PubMed Central PMCID: PMC3965097.

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Ziebarth JD, Bhattacharya A, Cui Y. Bayesian Network Webserver: a comprehensive tool for biological network modeling. Bioinformatics. 2013 Nov 1;29(21):2801-3. doi: 10.1093/bioinformatics/btt472. Epub 2013 Aug 21. PubMed PMID: 23969134.

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Fan P, Chen Z, Tian P, Liu W, Jiao Y, Xue Y, Bhattacharya A, Wu J, Lu M, Guo Y, Cui Y, Gu W, Gu W, Yue J. miRNA biogenesis enzyme Drosha is required for vascular smooth muscle cell survival. PLoS One. 2013;8(4):e60888. doi: 10.1371/journal.pone.0060888. Print 2013. PubMed PMID: 23637774; PubMed Central PMCID: PMC3630177.

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Bhattacharya A, Ziebarth JD, Cui Y. SomamiR: a database for somatic mutations impacting microRNA function in cancer. Nucleic Acids Res. 2013 Jan;41(Database issue):D977-82. doi: 10.1093/nar/gks1138. Epub 2012 Nov 24. PubMed PMID: 23180788; PubMed Central PMCID: PMC3531132.

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Ziebarth JD, Bhattacharya A, Cui Y. CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. Nucleic Acids Res. 2013 Jan;41(Database issue):D188-94. doi: 10.1093/nar/gks1165. Epub 2012 Nov 27. PubMed PMID: 23193294; PubMed Central PMCID: PMC3531215.

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Ziebarth JD, Bhattacharya A, Cui Y. Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes. PLoS One. 2012;7(10):e47137. doi: 10.1371/journal.pone.0047137. Epub 2012 Oct 16. PubMed PMID: 23091610; PubMed Central PMCID: PMC3473044.

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Bhattacharya A, Ziebarth JD, Cui Y. Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome. PLoS One. 2012;7(9):e46176. doi: 10.1371/journal.pone.0046176. Epub 2012 Sep 25. PubMed PMID: 23049969; PubMed Central PMCID: PMC3457991.

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Miyairi I, Ziebarth J, Laxton JD, Wang X, van Rooijen N, Williams RW, Lu L, Byrne GI, Cui Y. Host genetics and Chlamydia disease: prediction and validation of disease severity mechanisms. PLoS One. 2012;7(3):e33781. doi: 10.1371/journal.pone.0033781. Epub 2012 Mar 16. PubMed PMID: 22438999; PubMed Central PMCID: PMC3306297.

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Ziebarth JD, Cook MN, Wang X, Williams RW, Lu L, Cui Y. Treatment- and population-dependent activity patterns of behavioral and expression QTLs. PLoS One. 2012;7(2):e31805. doi: 10.1371/journal.pone.0031805. Epub 2012 Feb 16. PubMed PMID: 22359631; PubMed Central PMCID: PMC3281015.

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Ziebarth JD, Bhattacharya A, Chen A, Cui Y. PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. Nucleic Acids Res. 2012 Jan;40(Database issue):D216-21. doi: 10.1093/nar/gkr1026. Epub 2011 Nov 10. PubMed PMID: 22080514; PubMed Central PMCID: PMC3245163.

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Cui Y. Gene Discovery for Disease Models Bioinformatics. In: Gu W, editor. Tools for Gene Function Prediction Hoboken, New Jersey: John Wiley & Sons, Inc.; 2012. 93-110p.

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Bao L, Xia X, Cui Y. Expression QTL modules as functional components underlying higher-order phenotypes. PLoS One. 2010 Dec 13;5(12):e14313. doi: 10.1371/journal.pone.0014313. PubMed PMID: 21179437; PubMed Central PMCID: PMC3001472.

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Ziebarth J, Cook M, Li B, Williams R, Lu L, Cui Y. Systems Genetics Analysis of Molecular Pathways Underlying Ethanol-Induced Behavioral Phenotypes. Biomedical Science and Engineering Conference - Biomedical Research and Analysis in Neuroscience (BRAiN); 2010. Available from: http://ieeexplore.ieee.org/document/5510821/. DOI: 10.1109/BSEC.2010.5510821.

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Verma NK, Meena S, Singh A, Bajpai S, Nagrare A, Cui Y. Comparison of biclustering algorithms. International Conference on Systems in Medicine and Biology.; 2010. Available from: http://ieeexplore.ieee.org/document/5735351/.

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Verma N, Gupta P, Agrawal P, Hanmandlu M, Vasikarla S, Cui Y. MRI Brain Image Segmentation for Spotting Tumors Using Improved Mountain Clustering Approach. Washington DC, USA: Applied Imagery Pattern Recognition (AIPR): Vision: Humans, Animals, and Machines; 2009. Available from: http://ieeexplore.ieee.org/document/5466301/. DOI: 10.1109/AIPR.2009.5466301.

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Bao L, Zhou M, Cui Y. CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Res. 2008 Jan;36(Database issue):D83-7. doi: 10.1093/nar/gkm875. Epub 2007 Nov 2. PubMed PMID: 17981843; PubMed Central PMCID: PMC2238977.

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Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L, Cui Y. An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Hum Mol Genet. 2007 Jun 1;16(11):1381-90. doi: 10.1093/hmg/ddm089. Epub 2007 Apr 11. PubMed PMID: 17428815.

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Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res. 2007 Jan;35(Database issue):D51-4. doi: 10.1093/nar/gkl797. Epub 2006 Nov 11. PubMed PMID: 17099235; PubMed Central PMCID: PMC1669716.

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Cui Y. Current Topics in Human Genetics: Studies of Complex Diseases. In: Deng H, editor. Bridging Genotype and Phenotype: Causal Pathways from DNA to Complex Traits New Jersey: World Scientific; 2007. 433-448p.