My Bibliography

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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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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 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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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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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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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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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, 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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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. 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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Zhou M, Cui Y. GeneInfoViz: constructing and visualizing gene relation networks. In Silico Biol. 2004;4(3):323-33. PubMed PMID: 15724283.

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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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Wong WH, Cui Y, Chen RS. Torsional relaxation for biopolymers. J Comput Biol. 1998 Winter;5(4):655-65. doi: 10.1089/cmb.1998.5.655. PubMed PMID: 10072082.

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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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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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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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Sun ZR, Cui Y, Ling LJ, Guo Q, Chen RS. Molecular dynamics simulation of protein folding with supersecondary structure constraints. J Protein Chem. 1998 Nov;17(8):765-9. doi: 10.1023/a:1020722117182. PubMed PMID: 9988523.

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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: Computational Intelligence: Theories, Applications and Future Directions. Verma NK, Ghosh A, editors. Singapore: Springer; 2019. 53-66p.

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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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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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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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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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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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Qi Z, Cui Y, Fang W, Ling L, Chen R. Autosomal similarity revealed by eukaryotic genomic comparison. J Biol Phys. 2004 Jan;30(4):305-12. doi: 10.1007/s10867-004-0996-0. PubMed PMID: 23345874; PubMed Central PMCID: PMC3456315.

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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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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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Ling L, Wang J, Cui Y, Li W, Chen R. Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms. Mol Phylogenet Evol. 2002 Oct;25(1):101-11. doi: 10.1016/s1055-7903(02)00354-8. PubMed PMID: 12383754.

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Li H, Chen H, Bao L, Manly KF, Chesler EJ, Lu L, Wang J, Zhou M, Williams RW, Cui Y. Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits. Hum Mol Genet. 2006 Feb 1;15(3):481-92. doi: 10.1093/hmg/ddi462. Epub 2005 Dec 21. PubMed PMID: 16371421.

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Li H, Lu L, Manly KF, Chesler EJ, Bao L, Wang J, Zhou M, Williams RW, Cui Y. Inferring gene transcriptional modulatory relations: a genetical genomics approach. Hum Mol Genet. 2005 May 1;14(9):1119-25. doi: 10.1093/hmg/ddi124. Epub 2005 Mar 16. PubMed PMID: 15772094.

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He H, Cai L, Skogerbø G, Deng W, Liu T, Zhu X, Wang Y, Jia D, Zhang Z, Tao Y, Zeng H, Aftab MN, Cui Y, Liu G, Chen R. Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Res. 2006;34(10):2976-83. doi: 10.1093/nar/gkl371. Print 2006. PubMed PMID: 16738136; PubMed Central PMCID: PMC1474057.

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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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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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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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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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Deng W, Zhu X, Skogerbø G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R. Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Res. 2006 Jan;16(1):20-9. doi: 10.1101/gr.4139206. Epub 2005 Dec 12. PubMed PMID: 16344563; PubMed Central PMCID: PMC1356125.

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Cui Y. Microarrays and Transcription Networks . In: Elucidating gene regulatory networks underlying complex phenotypes: Genetical genomics and Bayesian network. Shannon F, editor. Austin, TX: Landes Bioscience; 2006. 114-126p.

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

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

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Cui Y, Zhou M, Wong WH. Integrated analysis of microarray data and gene function information. OMICS. 2004 Summer;8(2):106-17. doi: 10.1089/1536231041388320. PubMed PMID: 15268770.

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Cui Y, Chen RS, Wong WH. Protein folding simulation with genetic algorithm and supersecondary structure constraints. Proteins. 1998 May 15;31(3):247-57. PubMed PMID: 9593196.

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Cui Y, Wong WH. Multiple-sequence information provides protection against mis-specified potential energy functions in the lattice model of proteins. Phys Rev Lett. 2000 Dec 11;85(24):5242-5. doi: 10.1103/PhysRevLett.85.5242. PubMed PMID: 11102231.

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Cui Y, Chen RS, Wong WH. Molecular dynamic simulation of chaperonin-mediated protein folding. J Protein Chem. 1998 May;17(4):377-80. doi: 10.1023/a:1022511417343. PubMed PMID: 9619590.

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Cui Y, Chen RS, Wong WH. The coevolution of cell senescence and diploid sexual reproduction in unicellular organisms. Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3330-5. doi: 10.1073/pnas.97.7.3330. PubMed PMID: 10737794; PubMed Central PMCID: PMC16239.

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Cui Y, Wong WH, Bornberg-Bauer E, Chan HS. Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):809-14. doi: 10.1073/pnas.022240299. PubMed PMID: 11805332; PubMed Central PMCID: PMC117387.

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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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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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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, 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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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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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.