Computational systems biology  
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Research Interests and Selected Publications

  1. Artificial Intelligence for Genomic Medicine and Health Equity 

    • Bao L and Cui Y (2005) Prediction of the phenotypic effects of nonsynonymous single nucleotide polymorphisms. Bioinformatics 21:2185-2190.
    • Singh V, Baranwal N, Sevakula RK, Verma NK, and Cui Y (2016) Layerwise feature selection in Stacked Sparse Auto-Encoder for tumor type prediction. IEEE International Conference on Bioinformatics and Biomedicine. Shenzhen, China [December 15-18, 2016].

    • Sevakula RK, Singh V, Kumar C, Verma NK and Cui Y. (2018) Transfer Learning for Molecular Cancer Classification using Deep Neural Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics16: 2089-2100.

    • Singh V, Vardhan H, Verma NK, and Cui Y (2018) Optimal Feature Selection using Fuzzy Combination of Feature Subset for Transcriptome Data. IEEE International Conference on Fuzzy Systems. Rio de Janeiro, Brazil. [July 8-13, 2018].

    • Singh V, Verma NK and Cui Y (2019) Type-2 Fuzzy PCA Approach in Extracting Salient Features for Molecular Cancer Diagnostics and Prognostics. IEEE Transactions on NanoBioscience 18: 482-489.

    • Singh V, Verma NK and Cui Y (2019) Feature Ranking using Robust Fuzzy Score Function for Gene Expression Data. IEEE International Conference on Fuzzy Systems. New Orleans, USA [June 23-26, 2019].
    • Gao Y and Cui Y (2020) Deep transfer learning for reducing health care disparities arising from biomedical data inequality. Nature Communications 11:5131. 

  2. Systems Genomics and Network Biology
    • Li H, Lu L, Manly KF, Chesler EJ, Bao L, Wang J, Zhou M, Williams RW and Cui Y (2005) Inferring Gene Transcriptional Modulatory Relations: A Genetical Genomics Approach. Human Molecular Genetics 14:1119-1125.

    • Li H, Chen H, Bao L, Manly KF, Chesler EJ, Lu L, Wang J, Zhou M, Williams RW and Cui Y (2006) Integrative Genetic Analysis of Transcription Modules: Towards Filling the Gap between Genetic Loci and Inherited Traits. Human Molecular Genetics 15:481-492.

    • Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L and Cui Y (2007) An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Human Molecular Genetics 16:1381-1390.

    • Cui Y (2007) Bridging Genotype and Phenotype: Causal Pathways from DNA to Complex Traits. In Deng, H.W. (ed), Current Topics in Human Genetics: Studies of Complex Diseases. World Scientific, Page 433-448.

    • Bao L, Zhou M and Cui Y (2008) CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Research 36:D83-D87.

    • Bao L, Xia X and Cui Y (2010) Expression QTL modules as functional components underlying higher-order phenotypes. PLoS One 5(12): e14313.

    • Ziebarth JD, Cook MN, Wang X, Williams RW, Lu L and Cui Y (2012) Treatment- and population-dependent activity patterns of behavioral and expression QTLs. PLoS One 7: e31805.

    • Ziebarth JD, Bhattacharya A and Cui Y (2013) CTCFBSDB 2.0: A database for CTCF binding sites and genome organization. Nucleic Acids Research 41:D188-D194.

    • Emery FD, Parvathareddy J, Pandey AK, Cui Y, Williams RW and Miller MA (2014) Genetic control of weight loss during pneumonic Burkholderia pseudomallei infection. Pathogens and Disease, 71, 249-264.

    • 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 and Goldowitz D (2015) CbGRiTS: Cerebellar gene regulation in time and space. Developmental Biology 397, 18-30.

    • Bhattacharya A and Cui Y. (2017) A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules. Scientific Reports 7: 4162.

    • Mohammed A, Cui Y, Mas VR and Kamaleswaran R (2019) Differential gene expression analysis reveals novel genes and pathways in pediatric septic shock patients. Scientific Reports. 9:11270.

  3. Disease Phenotype Prediction with Bayesian Network Modeling

    • Miyairi I, Ziebarth J, Laxton JD, Wang X, van Rooijen N, Williams RW, Lu L, Byrne G and Cui Y (2012) Host Genetics and Chlamydia Disease: Prediction and Validation of Disease Severity Mechanisms. PLoS One. 7(3): e33781.

    • Ziebarth JD, Bhattacharya A and Cui Y (2013) Bayesian Network Webserver: a comprehensive tool for biological network modeling. Bioinformatics 29: 2801-2803.

    • Cashion AK, Hathaway DK, Stanfill A, Thomas F, Ziebarth JD, Cui Y, Cowan PA, and Eason J (2014) Pre-transplant predictors of one year weight gain after kidney transplantation. Clinical Transplantation. 28, 1271-1278.

    • Ziebarth JD and Cui Y (2017) Precise Network Modeling of Systems Genetics Data using the Bayesian Network Webserver. In Schughart K and Williams RW (eds.), Systems Genetics: Methods and Protocols. Methods in Molecular Biology 1488:319-335.

    • Ziebarth JD and Cui Y (2020) Multiscalar Genetic Pathway Modeling with Hybrid Bayesian Networks. WIREs Computational Statistics. 12: e1479.

  4. Functional Analysis of Genetic and Somatic DNA Variants Impacting microRNA Target Recognition

    • Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW and Cui Y (2007) PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Research 35: D51-D54.

    • Ziebarth JD, Bhattacharya A, Chen A and Cui Y (2012) PolymiRTS Database 2.0: Linking polymorphisms in microRNA target sites with human diseases and complex traits. Nucleic Acids Research 40: D216-D221.

    • Bhattacharya A, Ziebarth JD and Cui Y (2012) Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome. PLoS One 7(9): e46176.

    • Ziebarth JD, Bhattacharya A and Cui Y (2012) Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes. PLoS One 7(10): e47137.

    • Bhattacharya A, Ziebarth JD and Cui Y (2013) SomamiR: A database for somatic mutations impacting microRNA function in cancer. Nucleic Acids Research 41:D977-D982.

    • Cui Y (2014) In silico mapping of polymorphic miRNA-mRNA interactions in autoimmune thyroid diseases. Autoimmunity 47, 327-333.

    • Bhattacharya A, Ziebarth JD and Cui Y (2014) PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Research. 42: D86-D91.
    • Bhattacharya A and Cui Y (2015) miR2GO: Comparative functional analysis for microRNAs. Bioinformatics 31, 2403-2405.  

    • Bhattacharya A and Cui (2015) Knowledge-based analysis of functional impacts of mutations in microRNA seed regions . Journal of Biosciences 40, 791-798.

    • Bhattacharya A and Cui Y (2016) SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. Nucleic Acids Research 44, D1005-D1010.

    • Ziebarth JD, Bhattacharya A and Cui Y (2019) Functional analysis of Genetic Variants and Somatic Mutations Impacting microRNA-Target Recognition: Bioinformatics Resources. In Laganà A (ed.), microRNA Target Identification. Methods in Molecular Biology 1970:101-120.
  5. Medical Image Analysis with Deep Learning and Clustering Algorithms

    • Verma NK, Gupta P, Agrawal P, Hanmandlu M, Vasikarla S and Cui Y (2009) Medical Image Segmentation Using Improved Mountain Clustering Approach. The 6th IEEE International Conference on Information Technology (ITNG) - New Generation, Las Vegas, Nevada, USA. [April 27-29, 2009]

    • Verma NK, Gupta P, Agrawal P and Cui Y (2009) MRI Brain Image Segmentation for Spotting Tumors Using Improved Mountain Clustering Approach, Applied Imagery Pattern Recognition (AIPR): Vision: Humans, Animals, and Machines. Washington DC, USA [October 14-16, 2009]

    • Singh V, Verma NK, Islam Z and Cui Y (2019) Feature Learning using Stacked Autoencoder for Shared and Multimodal Fusion of Medical Images.In Verma, N.K. and Ghosh, A.K. (eds). Computational Intelligence: Theories, Applications and Future Directions. Springer, Singapore, pp. 53-66.

  6. Mathematical Modeling and Computational Simulation of Biological Systems

    • Cui Y, Chen RS and Wong WH (1998) Protein folding simulation using genetic algorithm and supersecondary structure constraints. Proteins: Structure, Function and Genetics 31:247-257.

    • Cui Y, Chen RS and Wong WH (2000) The coevolution of cell senescence and diploid sexual reproduction in unicellular organisms, Proceedings of the National Academy of Sciences USA 97:3330-3335.

    • Cui Y and Wong WH (2000) Multiple sequence information provides protection against mis-specified potential energy function, Physical Review Letters 85:5242-5245.

    • Cui Y, Wong WH, Bornberg-Bauer E and Chan HS (2002) Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes, Proceedings of the National Academy of Sciences USA 99:809-814.











Yan Cui
University of Tennessee Health Science Center
Department of Genetics Genomics and Informatics
71 South Manassas Street
Memphis, TN 38103

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