Book Chapter

• Cui, Y (2011) Bioinformatics Tools for Gene Function Prediction. In Gu, W.K. (ed), Gene Discovery for Disease Models. John Wiley & Sons, Inc. Page 93-110.

• 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 in Complex Diseases. World Scientific, Page 433-448.

• Cui, Y (2006) Elucidating gene regulatory networks underlying complex phenotypes: Genetical genomics and Bayesian network. In Shannon, F. (ed), Microarrays and Transcription Networks. Landes Bioscience, Page 114-126.

Journal Article

• Bhattacharya A and Cui Y (2015) miR2GO: Comparative functional analysis for microRNAs. Bioinformatics. btv140

• 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, 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.

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

• 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.

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

• 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 (2013) miRNA biogenesis enzyme Drosha is required for vascular smooth muscle cell survival. PLoS One. 8: e60888.

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

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

• Bhattacharya A, Ziebarth JD, Cui Y (2012) Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome. PLoS One. 7:e46176.

• Ziebarth JD, Bhattacharya A, Cui Y (2012) Integrative Analysis of Somatic Mutations Altering MicroRNA Targeting in Cancer Genomes. PLoS One. 7: e47137.

• 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: e33781.

• Ziebarth JD, Bhattacharya A, Chen A, 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.

• 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.

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

• 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, 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.

• 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.

• He H, Cai L, Skogerbo G, Deng W, Liu T, Zhu X, Wang Y, Jia D, Zhang Z, Tao Y, Zeng H, Aftab MN, Cui Y, Liu G and Chen R (2006) Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Research 34:2976-2983.

• Bao L, Wei L, Peirce JL, Homayouni R, Li H, Zhou M, Chen H, Lu L, Williams RW, Pfeffer LM, Goldowitz D and Cui Y (2006) Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relations. Mammalian Genome 17:575-583.

• Bao L and Cui Y (2006) Functional impacts of nonsynonymous single nucleotide polymorphisms: selective constraint and structural environments. FEBS Letters 580: 1231-1234.

• 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.

• Deng W, Zhu X, Skogerbo 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 and Chen R (2006) Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Research 16:20-29.

• 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.

• Bao L, Zhou M and Cui Y (2005) nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Research 33: W480-W482.

• Bao L and Cui Y (2005) Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information Bioinformatics 21:2185-2190.

• Li H, Zhou M and Cui Y (2005) Ranking Gene Regulatory Network Models with Microarray Data and Bayesian Network. in Lecture Notes in Computer Science Volume 3327:109 - 118 Springer, Heidelberg.

• Cui Y, Zhou M and Wong WH (2004) Integrated analysis of microarray data and gene function Information. OMICS: A Journal of Integrative Biology 8: 106-117.

• Zhou M and Cui Y (2004) GeneInfoViz: constructing and visualizing gene relation networks. In Silico Biology 4:323-332.

• Qi Z, Cui Y, Fang W, Ling L and Chen RS (2004) Autosomal Similarity Revealed by Eukaryotic Genomic Comparison. Journal of Biological Physics, 30:305-312.

• Ling L, Wang J, Cui Y, Li W and Chen RS (2002) Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms. Molecular Phylogenetics and Evolution 25: 101-111.

• 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.

• 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, 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.

• Sun ZR, Cui Y, Ling LJ, Guo Q and Chen RS (1998) Molecular dynamics simulation of protein folding with supersecondary structure constraints. Journal of Protein Chemistry 17:765-769.

• Wong WH, Cui Y and Chen RS (1998) Torsional Relaxation for Biopolymers. Journal of Computational Biology 5:655-665.

• Cui Y, Chen RS and Wong WH (1998) Molecular dynamic simulation of chaperonin-mediated protein folding. Journal of Protein Chemistry 17:377-380.

• 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.

Conference Paper

• Ziebarth JD, Cook MN, Li B, Williams RW, Lu L and Cui Y (2010) Systems Genetics Analysis of Molecular Pathways Underlying Ethanol-Induced Behavioral Phenotypes. The 2010 Biomedical Science and Engineering Conference - Biomedical Research and Analysis in Neuroscience (BRAiN). Oak Ridge, USA. [May 25-26, 2010]

• 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, Agrawal P and Cui Y (2009) Fuzzy Rule Based Unsupervised Approach for Gene Saliency. Applied Imagery Pattern Recognition (AIPR): Vision: Humans, Animals, and Machines. Washington DC, USA. [October 14-16, 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]

• Verma NK, Roy A, Gupta S and Cui Y (2009) Improved Mountain Clustering Technique for Microarray Data. Joint International Conference on Applied Systems Research (ASR) and XXXIII National Systems Conference (NSC 2009). Agra, India. [November 27-29, 2009]