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  1. 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.
  2. Bao L, Zhou M, Cui Y. nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W480-2. doi: 10.1093/nar/gki372. PubMed PMID: 15980516; PubMed Central PMCID: PMC1160133.
  3. Bao L, Cui Y. Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics. 2005 May 15;21(10):2185-90. doi: 10.1093/bioinformatics/bti365. Epub 2005 Mar 3. PubMed PMID: 15746281.
  4. 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.
  5. Bao L, Cui Y. Functional impacts of non-synonymous single nucleotide polymorphisms: selective constraint and structural environments. FEBS Lett. 2006 Feb 20;580(5):1231-4. doi: 10.1016/j.febslet.2006.01.035. Epub 2006 Jan 20. PubMed PMID: 16442527.
  6. 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.
  7. Bao L, Wei L, Peirce JL, Homayouni R, Li H, Zhou M, Chen H, Lu L, Williams RW, Pfeffer LM, Goldowitz D, Cui Y. Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships. Mamm Genome. 2006 Jun;17(6):575-83. doi: 10.1007/s00335-005-0172-2. Epub 2006 Jun 12. PubMed PMID: 16783639.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. Bhattacharya A, Cui Y. Knowledge-based analysis of functional impacts of mutations in microRNA seed regions. J Biosci. 2015 Oct;40(4):791-8. PubMed PMID: 26564979.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. Cui Y, Chen RS, Wong WH. Molecular dynamic simulation of chaperonin-mediated protein folding. J Protein Chem. 1998 May;17(4):377-80. PubMed PMID: 9619590.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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. PubMed PMID: 12383754.
  37. 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.
  38. 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.
  39. 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. 2018 Apr 4;. doi: 10.1109/TCBB.2018.2822803. [Epub ahead of print] PubMed PMID: 29993662.
  40. 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.
  41. 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/. .
  42. 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. PubMed PMID: 9988523.
  43. 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/. .
  44. 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/. .
  45. 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.
  46. 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.
  47. Zhou M, Cui Y. GeneInfoViz: constructing and visualizing gene relation networks. In Silico Biol. 2004;4(3):323-33. PubMed PMID: 15724283.
  48. 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.
  49. 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.
  50. 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.