Publications

Books:
cancerBioinformatics    
 
   Xu Y, Cui J and J. Dave Puett. Cancer Bioinformatics, Springer, New York, 2014


Invited Chapters:

Cancer and Noncoding RNAs - 1st Edition - ISBN: 9780128110225

  Cui J. Non-coding RNAs as a cause of cancer: evidence from GWAS and reverse genetics. In Cancer and Noncoding RNAs. Edited by Jayprokas Chakrabarti, Sanga Mitra, and Peter Linsley. Elsevier book series Translational Epigenetics, 2017 ( in press)

 Cui J. Bioinformatics Databases and Tools on Dietary microRNA. In The Handbook of Nutrition, Diet and Epigenetics. Edited by Vinood B. Patel and Victor R. Preedy. Springer, 2017 ( in press)

pressChapter
  Cui J
. Genomic Data Analysis for Personalized Healthcare. In Healthcare Data Analytics. Edited by Chandan K. Reddy, Charu C. Aggarwal. CRC Press (Data Mining and Knowledge Discovery Series), 2015.



ovarian cancer
  Cui J
, Xu Y, Puett D. Microarray-Based Transcriptome Profiling of Ovarian Cancer Cells. In Ovarian cancer - Methods and Protocols. Humana Press, doi:10.1007/978-1-62703-547-7, 2013



ovarian cancer basic science perspective
  Cui J
, Xu Y, Puett D. Transcriptomic Analysis of Human Ovarian Cancer Cells: Changes Mediated by Luteinizing Hormone Receptor Activation. In Ovarian Cancer -Basic Science Perspective. InTech, edited by Samir A. Farghaly, ISBN 978-953-307-812-0, 418 pages,  doi: 10.5772/1268, February 17, 2012



Papers:     

(# Corresponding authors; * co-first authors; _ UNL CSE students and post-docs )

2017     

  1. Shu J, Silva B, Cui J#. Dynamic and Modularized MicroRNA Regulation and Its Implication in Human Cancer. Accepted at Scientific Reports.
  2. Hakguder ZLiao CXShu J, Cui J#. A New Statistical Model for Genome-Scale MicroRNA Target Prediction. Accepted at IEEE BIBM 2017 (Accepted Rate: 19%)
  3. Silva B, Cui J# (2017). A Survey on Automated Food Monitoring and Dietary Management Systems. Journal of Health & Medical Informatics 8: 272. doi: 10.4172/2157-7420.1000272
  4. Xu Z, Duan Q, Cui J, Qiu YM, Jia QD, Wu C, Clarke J. Analysis of Genetic and Non-genetic Factors Influencing Triglycerides-Lowering Drug Effects Based on Paired Observations”. Accepted at GAW20 and BMC Proceedings

          ( under review )

  • Gao T*Shu J*, Cui J#. MDS2: A Graph-Based Method for Systematic Motif Discovery Based on Short Nucleotide Sequences (Bioinformatics). 
  • Silva BRad MiladMcCabe M, Pan KY, Cui J#. A Mobile-Based Diet Monitoring System For Obesity Management (IEEE Journal of Biomedical and Health Informatics) 
  • Zhao DY, Zhong W, Shi LM, Cui J#, Xu T#.Multi-Platform Normalization of Human RNA-Seq Data Using A Set of Endogenous Reference Genes.
  • Wang HQ, Gan B, Jing GJ, Zhang ZR, Yang WL, Cui J. CrosstalkPath: A Pathway Crosstalk-Based Analysis of Transcriptomics data for Differential Pathway Identification.

2016

  1. Zhang HY, Silva B, Cui J#. MiRDis: A Web Tool for Endogenous and Exogenous MicroRNA Discovery Based on Deep Sequencing Data Analysis. Briefings in Bioinformatics. Jan. 2017, page 1-10, doi: 10.1093/bib/bbw140 
  2. Sud N, Zhang HY, Cui J, and Su QZ. ­­­Aberrant Expression of microRNA induced by high fructose diet impairs hepatic energy metabolic signaling. Journal of Nutritional Biochemistry. 43 (2017), pp. 125–131. doi: 10.1016/j.jnutbio.2017.02.003
  3. Han JCShu J, Cui J#. A New System For Human MicroRNA Functional Evaluation and Network Construction. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shengzhen, China, 15 - 18 December 2016.
  4. Cui J, Zhou BY, Ross S, Zempleni J. Nutrition, microRNAs and human health. Advances in Nutrition January 2017, vol. 8: 105-112

2015

  1. Shu J, Chiang K, Zempleni J, Cui J#. Computational Characterization of Exogenous MicroRNAs That Can Be Transferred into Human Circulation. PLoS ONE, 11/2015; 10(11):e0140587.
  2. Chiang K, Shu J, Zempleni J, Cui J#. Dietary MicroRNA Database (DMD): An archive database and analytic tool for microRNAs in human foods. PLoS ONE, 2015 June 1; 10(6): e0128089. doi:10.1371/journal.pone.0128089.
  3. Shu JChiang KZhao DY, Cui J#. Human Absorbable MicroRNA Prediction based on an Ensemble Manifold Ranking Model. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington, D.C., 9 - 12 November 2015, 295-300, doi:10.1109/BIBM.2015.7359697
  4. Zempleni J, Baier SR, Howard KM, Cui J. Gene regulation by dietary microRNAs. Can J Physiol Pharmacol, 2015 Dec;93(12):1097-1102. doi: 10.1139/cjpp-2014-0392.
  5. Wang Y, Wang G, Meng D, Huang L, Blanzieri E, Cui J. A Markov Clustering based Link Clustering Method to Identify Overlapping Modules in Protein-protein Interaction Networks. Current Bioinformatics, 2015, 11(2) 221-233.

2014

  1. Cui J, Yin YB, et al. Comprehensive Characterization of Genomic Alterations in Human Gastric Cancer. International Journal of Cancer 2014 Nov 24. doi: 10.1002/ijc.29352.
  2. Beach S, Brody G, Lei GH, Kim S, Cui J, Philibert R. Is serotonin transporter genotype associated with epigenetic susceptibility or vulnerability? Examination of the impact of socioeconomic status risk on African American youth. Development and Psychopathology 26 (2014), 289–304 
  3. Ma Q, Reeves JH, Liberles DA, Yu LL, Chang Z, Zhao J, Cui J, Xu Y, Liu L. A phylogenetic model for understanding the effect of gene duplication on cancer progression. Nucleic Acids Research 2014 Mar; 42(5): 2870-8 
  4. Sun H, Wang HP, Tang KL, Qin G, Cui J, Cao ZW, Liu Qi. iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis. Bioinformatics  2014 Mar 1;30(5):737-9. 

2013

  1. Wang JX, Liang YC, Wang Y, Cui J, Liu M, Du W, Xu Y, Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification, submitted to PLoS ONE, 2013 Nov 12;8(11): e80211
  2. Dong XY, Wang GQ, Zhang GQ, Ni ZH, Suo J, Cui J, Cui A, Xu Y, Li F (2013) The endothelial lipase protein is promising urinary biomarker for diagnosis of gastric cancer. Diagnostic Pathology 8 (1), 45, 2013.
  3. Xu K, Mao XZ, Mehta M, Cui J, Zhang C, Mao FL, Xu Y (2013) Elucidation of How Cancer Cells Avoid Acidosis through Comparative Transcriptomic Data Analysis, PLoS ONE, e71177

2012

  1. Cui J, Mao X, Olman V, Hastings PJ, Xu Y (2012) Hypoxia and miscoupling between reduced energy efficiency and signaling to cell proliferation drive cancer to grow increasingly faster. Journal of Molecular Cell Biology 4: 174-176. 
  2. Cui J, Liang YC, Xu Y (2012) Systems biology in the frontier of cancer research: a report on the Second International Workshop of Cancer Systems Biology. Chin J Cancer. Aug 28. doi: 10.5732/cjc.012.10205.
  3. Su Y, Ni Z, Wang G, Cui J, Wei C, et al. (2012) Aberrant expression of microRNAs in gastric cancer and biological significance of miR-574-3p. International Immunopharmacology 13: 468-475.
  4. Liu Q, Zhou H, Cui J, Cao Z, Xu Y (2012) Reconsideration of in-silico siRNA design based on feature selection: a cross-platform data integration perspective. PLoS ONE 7: e37879.
  5. Xu K, Mao X, Mehta M, Cui J, Zhang C, et al. (2012) A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers. PLoS ONE 7: e30750.

2011

  1. Cui J, Eldredge JB, Xu Y, Puett D (2011) MicroRNA expression and regulation in human ovarian carcinoma cells by luteinizing hormone. PLoS ONE 6.: e21730 
  2. Cui J, Miner BM, Eldredge JB, Warrenfeltz SW, Dam P, et al. (2011) Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation. BMC Cancer 11: 280
  3. Cui J, Chen Y, Chou WC, Sun L, Chen L, et al. (2011) An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. Nucleic Acids Research 39: 1197-1207.
  4. Cui J, Li F, Wang G, Fang X, Puett JD, et al. (2011) Gene-expression signatures can distinguish gastric cancer grades and stages. PLoS ONE 6: e17819 
  5. Gao J*, Cui J*, Wang Y, Dong ZN, Tian YP, et al. (2011) Identification of potential predictors for subtype IgA nephropathy through analyses of blood biochemical indicators. Clinica Chimica Acta 412: 441-445 
  6. Hong CS, Cui J, Ni Z, Su Y, Puett D, et al. (2011) A computational method for prediction of excretory proteins and application to identification of gastric cancer markers in urine. PLoS ONE 6: e16875.

2010

  1. Xu K*, Cui J*, Olman V, Yang Q, Puett D, et al. (2010) A comparative analysis of gene-expression data of multiple cancer types. PLoS ONE 5: e13696.
  2. Zhang X, Cui J, Nilsson D, Gunasekera K, Chanfon A, et al. (2010) The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development. Nucleic Acids Research 38: 7378-7387.
  3. Liu Q, Cui J, Yang Q, Xu Y (2010) In-silico prediction of blood-secretory human proteins using a ranking algorithm. BMC Bioinformatics 11: 250
  4. Lu Y, Gao Y, Cao Z, Cui J, Dong Z, et al. (2010) A study of health effects of long-distance ocean voyages on seamen using a data classification approach. BMC Med Inform Decis Mak 10: 13 
  5. Diao H, Xiao S, Cui J, Chun J, Xu Y, et al. (2010) Progesterone receptor-mediated up-regulation of transthyretin in preimplantation mouse uterus. Fertility and Sterility 93: 2750-2753.

2005-2009

  1. Jia J, Cui J, Liu X, Han J, Yang S, et al. (2009) Genome-scale search of tumor-specific antigens by collective analysis of mutations, expressions and T-cell recognition. Mol Immunol 46: 1824-1829.
  2. Cui J, Liu Q, Puett D, Xu Y (2008) Computational prediction of human proteins that can be secreted into the bloodstream. Bioinformatics 24: 2370-2375.
  3. Cui J, Han LY, Lin H, Tang ZQ, Ji Z, et al. (2007) Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology. Current Bioinformatics 2: 95-112.
  4. Tang ZQ, Han LY, Lin HH, Cui J, Jia J, et al. (2007) Derivation of stable microarray cancer-differentiating signatures using consensus scoring of multiple random sampling and gene-ranking consistency evaluation. Cancer Res 67: 9996-10003.
  5. Cui J, Han LY, Lin HH, Zhang HL, Tang ZQ, et al. (2007) Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties. Mol Immunol 44: 866-877.
  6. Cui J, Han LY, Li H, Ung CY, Tang ZQ, et al. (2007) Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Mol Immunol 44: 514-520.
  7. Xie B, Zheng CJ, Han LY, Ong S, Cui J, et al. (2007) PharmGED: pharmacogenetic effect database. Clin Pharmacol Ther 81: 29.
  8. Zheng CJ, Han LY, Xie B, Liew CY, Ong S, et al. (2007) PharmGED: Pharmacogenetic Effect Database. Nucleic Acids Research 35: D794-799.
  9. Cui J, Han LY, Lin HH, Tang ZQ, Jiang L, et al. (2006) MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties. Immunogenetics 58: 607-613.
  10. Han L, Cui J, Lin H, Ji Z, Cao Z, et al. (2006) Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity. Proteomics 6: 4023-4037.
  11. Zheng CJ, Han LY, Chen X, Cao ZW, Cui J, et al. (2006) Information of ADME-associated proteins and potential application for pharmacogenetic prediction of drug responses. Current Pharmacogenomics 4: 87-103.
  12. Cui J, Han LY, Cai CZ, Zheng CJ, Ji ZL, et al. (2005) Prediction of functional class of novel bacterial proteins without the use of sequence similarity by a statistical learning method. J Mol Microbiol Biotechnol 9: 86-100
  13. Han LY, Zheng CJ, Lin HH, Cui J, Li H, et al. (2005) Prediction of functional class of novel plant proteins by a statistical learning method. New Phytol 168: 109-121.
  14. Han LY, Cai CZ, Ji ZL, Cao ZW, Cui J, et al. (2004) Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. Nucleic Acids Research 32: 6437-6444.