• 1175 Citations
  • 20 h-Index
20042019

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

2019

A New Approach to Batch Effect Removal Based on Distribution Matching in Latent Space

Li, H., Dogan, H. & Cui, J., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 423-430 8 p. 8983417. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Bioinformatics databases and tools on dietary MicroRNA

Cui, J., Jan 5 2019, Handbook of Nutrition, Diet, and Epigenetics. Springer International Publishing, Vol. 3. p. 2219-2232 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

9 Scopus citations

Elucidation of MicroRNA-Gene Regulation in Human Cancer with Integrative Network Models

Dogan, H., Hakguder, Z., Scott, S. & Cui, J., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2729-2734 6 p. 8983024. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Identification of age- and gender-associated long noncoding RNAs in the human brain with Alzheimer's disease

Cao, M., Li, H., Zhao, J., Cui, J. & Hu, G., Sep 2019, In : Neurobiology of Aging. 81, p. 116-126 11 p.

Research output: Contribution to journalArticle

2 Scopus citations
2018
13 Scopus citations

Analysis of genetic and nongenetic factors influencing triglycerides-lowering drug effects based on paired observations

Xu, Z., Duan, Q., Cui, J., Qiu, Y., Jia, Q., Wu, C. & Clarke, J., Sep 17 2018, In : BMC Proceedings. 12, 46.

Research output: Contribution to journalArticle

3 Scopus citations

Astrocyte EV-Induced lincRNA-Cox2 Regulates Microglial Phagocytosis: Implications for Morphine-Mediated Neurodegeneration

Hu, G., Liao, K., Niu, F., Yang, L., Dallon, B. W., Callen, S., Tian, C., Shu, J., Cui, J., Sun, Z., Lyubchenko, Y. L., Ka, M., Chen, X. M. & Buch, S., Dec 7 2018, In : Molecular Therapy - Nucleic Acids. 13, p. 450-463 14 p.

Research output: Contribution to journalArticle

15 Scopus citations

A systematic approach to RNA-associated motif discovery

Gao, T., Shu, J. & Cui, J., Feb 14 2018, In : BMC genomics. 19, 1, 146.

Research output: Contribution to journalArticle

4 Scopus citations

Concentrations of purine metabolites are elevated in fluids from adults and infants and in livers from mice fed diets depleted of bovine milk exosomes and their RNA cargos

Aguilar-Lozano, A., Baier, S., Grove, R., Shu, J., Giraud, D., Leiferman, A., Mercer, K. E., Cui, J., Badger, T. M., Adamec, J., Andres, A. & Zempleni, J., 2018, In : Journal of Nutrition. 148, 12, p. 1886-1894 9 p.

Research output: Contribution to journalArticle

2 Scopus citations
12 Scopus citations

Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model 06 Biological Sciences 0604 Genetics

Hakguder, Z., Shu, J., Liao, C., Pan, K. & Cui, J., Sep 24 2018, In : BMC genomics. 19, 658.

Research output: Contribution to journalArticle

miRDis: A Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis

Zhang, H., e Silva, B. V. R. & Cui, J., May 1 2018, In : Briefings in bioinformatics. 19, 3, p. 415-424 10 p.

Research output: Contribution to journalArticle

5 Scopus citations

Reply to B Fromm et al

Cui, J. & Zempleni, J., Sep 1 2018, In : The Journal of nutrition. 148, 9, 1 p.

Research output: Contribution to journalComment/debate

1 Scopus citations
2017

Aberrant expression of microRNA induced by high-fructose diet: implications in the pathogenesis of hyperlipidemia and hepatic insulin resistance

Sud, N., Zhang, H., Pan, K., Cheng, X., Cui, J. & Su, Q., May 1 2017, In : Journal of Nutritional Biochemistry. 43, p. 125-131 7 p.

Research output: Contribution to journalArticle

24 Scopus citations

A new statistical model for genome-scale MicroRNA target prediction

Hakguder, Z., Liao, C., Shu, J. & Cui, J., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 101-107 7 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

A new system for human microRNA functional evaluation and network

Han, J., Shu, J. & Cui, J., Jan 17 2017, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Burrage, K., Zhu, Q., Liu, Y., Tian, T., Wang, Y., Hu, X. T., Jiang, Q., Song, J., Morishita, S., Burrage, K. & Wang, G. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 278-283 6 p. 7822531. (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A simulation model of glucose-insulin metabolism and implementation on OSG

Rad, M. G., Immaneni, A., McCabe, M., Pierobon, M. & Cui, J., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1832-1839 8 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Dynamic and modularized MicroRNA regulation and its implication in human cancers

Shu, J., Resende E Silva, B. V., Gao, T., Xu, Z. & Cui, J., Dec 1 2017, In : Scientific reports. 7, 1, 13356.

Research output: Contribution to journalArticle

12 Scopus citations

MiRDR-OSG: MicroRNA dynamic regulation analysis utilizing open science grid

Shu, J. & Cui, J., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1846-1851 6 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Nutrition, microRNAs, and human health

Cui, J., Zhou, B., Ross, S. A. & Zempleni, J., 2017, In : Advances in Nutrition. 8, 1, p. 105-112 8 p.

Research output: Contribution to journalReview article

56 Scopus citations
2016

A markov clustering based link clustering method to identify overlapping modules in protein-protein interaction networks

Wang, Y., Wang, G., Meng, D., Huang, L., Blanzieri, E. & Cui, J., Apr 1 2016, In : Current Bioinformatics. 11, 2, p. 221-233 13 p.

Research output: Contribution to journalArticle

2015

Comprehensive characterization of the genomic alterations in human gastric cancer

Cui, J., Yin, Y., Ma, Q., Wang, G., Olman, V., Zhang, Y., Chou, W. C., Hong, C. S., Zhang, C., Cao, S., Mao, X., Li, Y., Qin, S., Zhao, S., Jiang, J., Hastings, P., Li, F. & Xu, Y., Jul 1 2015, In : International Journal of Cancer. 137, 1, p. 86-95 10 p.

Research output: Contribution to journalArticle

27 Scopus citations

Computational characterization of exogenous microRNAs that can be transferred into human circulation

Shu, J., Chiang, K., Zempleni, J. & Cui, J., Nov 3 2015, In : PloS one. 10, 11, e0140587.

Research output: Contribution to journalArticle

32 Scopus citations

Dietary microRNA database (DMD): An archive database and analytic tool for food-borne microRNAs

Chiang, K., Shu, J., Zempleni, J. & Cui, J., Jun 1 2015, In : PloS one. 10, 6, e0128089.

Research output: Contribution to journalArticle

21 Scopus citations

Gene regulation by dietary microRNAs

Zempleni, J., Baier, S. R., Howard, K. M. & Cui, J., Sep 25 2015, In : Canadian journal of physiology and pharmacology. 93, 12, p. 1097-1102 6 p.

Research output: Contribution to journalReview article

26 Scopus citations

Genomic data analysis for personalized medicine

Cui, J., Jan 1 2015, Healthcare Data Analytics. CRC Press, p. 187-218 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Human absorbable microRNA prediction based on an ensemble manifold ranking model

Shu, J., Chiang, K., Zhao, D. & Cui, J., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 295-300 6 p. 7359697. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations
2014

A phylogenetic model for understanding the effect of gene duplication on cancer progression

Ma, Q., Reeves, J. H., Liberles, D. A., Yu, L., Chang, Z., Zhao, J., Cui, J., Xu, Y. & Liu, L., 2014, In : Nucleic acids research. 42, 5, p. 2870-2878 9 p.

Research output: Contribution to journalArticle

6 Scopus citations

Cancer bioinformatics

Xu, Y., Cui, J. & Puett, D., Jan 1 2014, Springer New York. 368 p.

Research output: Book/ReportBook

14 Scopus citations

IPEAP: Integrating multiple omics and genetic data for pathway enrichment analysis

Sun, H., Wang, H., Zhu, R., Tang, K., Gong, Q., Cui, J., Cao, Z. & Liu, Q., Mar 2014, In : Bioinformatics. 30, 5, p. 737-739 3 p.

Research output: Contribution to journalArticle

25 Scopus citations

Is serotonin transporter genotype associated with epigenetic susceptibility or vulnerability? Examination of the impact of socioeconomic status risk on African American youth

Beach, S. R. H., Brody, G. H., Lei, M. K., Kim, S., Cui, J. & Philibert, R. A., May 2014, In : Development and psychopathology. 26, 2, p. 289-304 16 p.

Research output: Contribution to journalArticle

28 Scopus citations
2013

Computational prediction of human salivary proteins from blood circulation and application to diagnostic biomarker identification

Wang, J., Liang, Y., Wang, Y., Cui, J., Liu, M., Du, W. & Xu, Y., Nov 12 2013, In : PloS one. 8, 11, e80211.

Research output: Contribution to journalArticle

13 Scopus citations

Elucidation of How Cancer Cells Avoid Acidosis through Comparative Transcriptomic Data Analysis

Xu, K., Mao, X., Mehta, M., Cui, J., Zhang, C., Mao, F. & Xu, Y., Aug 14 2013, In : PloS one. 8, 8, e71177.

Research output: Contribution to journalArticle

17 Scopus citations

Microarray-based transcriptome profiling of ovarian cancer cells

Cui, J., Xu, Y. & Puett, D., 2013, Ovarian Cancer: Methods and Protocols. Malek, A. & Tchernitsa, O. (eds.). p. 119-137 19 p. (Methods in Molecular Biology; vol. 1049).

Research output: Chapter in Book/Report/Conference proceedingChapter

The endothelial lipase protein is promising urinary biomarker for diagnosis of gastric cancer

Dong, X., Wang, G., Zhang, G., Ni, Z., Suo, J., Cui, J., Cui, A., Yang, Q., Xu, Y. & Li, F., Mar 19 2013, In : Diagnostic Pathology. 8, 1, 731.

Research output: Contribution to journalArticle

9 Scopus citations
2012

Aberrant expression of microRNAs in gastric cancer and biological significance of miR-574-3p

Su, Y., Ni, Z., Wang, G., Cui, J., Wei, C., Wang, J., Yang, Q., Xu, Y. & Li, F., Aug 2012, In : International Immunopharmacology. 13, 4, p. 468-475 8 p.

Research output: Contribution to journalArticle

55 Scopus citations

A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers

Xu, K., Mao, X., Mehta, M., Cui, J., Zhang, C. & Xu, Y., Jan 25 2012, In : PloS one. 7, 1, e30750.

Research output: Contribution to journalArticle

14 Scopus citations

Hypoxia and miscoupling between reduced energy efficiency and signaling to cell proliferation drive cancer to grow increasingly faster

Cui, J., Mao, X., Olman, V., Hastings, P. J. & Xu, Y., Jun 2012, In : Journal of Molecular Cell Biology. 4, 3, p. 174-176 3 p.

Research output: Contribution to journalLetter

17 Scopus citations

Reconsideration of in-silico siRNA design based on feature selection: A cross-platform data integration perspective

Liu, Q., Zhou, H., Cui, J., Cao, Z. & Xu, Y., May 24 2012, In : PloS one. 7, 5, e37879.

Research output: Contribution to journalArticle

8 Scopus citations

Systems biology in the frontier of cancer research: A report of the second International workshop of cancer systems biology

Cui, J., Liang, Y. C. & Xu, Y., 2012, In : Chinese Journal of Cancer. 31, 9, p. 409-412 4 p.

Research output: Contribution to journalArticle

2011

A computational method for prediction of excretory proteins and application to identification of gastric cancer markers in urine

Hong, C. S., Cui, J., Ni, Z., Su, Y., Puett, D., Li, F. & Xu, Y., 2011, In : PloS one. 6, 2, e16875.

Research output: Contribution to journalArticle

20 Scopus citations

An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

Cui, J., Chen, Y., Chou, W. C., Sun, L., Chen, L., Suo, J., Ni, Z., Zhang, M., Kong, X., Hoffman, L. L., Kang, J., Su, Y., Olman, V., Johnson, D., Tench, D. W., Amster, I. J., Orlando, R., Puett, D., Li, F. & Xu, Y., Mar 2011, In : Nucleic acids research. 39, 4, p. 1197-1207 11 p.

Research output: Contribution to journalArticle

122 Scopus citations

Gene-expression signatures can distinguish gastric cancer grades and stages

Cui, J., Li, F., Wang, G., Fang, X., Puett, J. D. & Xu, Y., 2011, In : PloS one. 6, 3, e17819.

Research output: Contribution to journalArticle

51 Scopus citations

Identification of potential predictors for subtype IgA nephropathy through analyses of blood biochemical indicators

Gao, J., Cui, J., Wang, Y., Dong, Z., Tian, Y. & Xu, Y., Feb 20 2011, In : Clinica Chimica Acta. 412, 5-6, p. 441-445 5 p.

Research output: Contribution to journalArticle

5 Scopus citations

Microrna expression and regulation in human ovarian carcinoma cells by luteinizing hormone

Cui, J., Eldredge, J. B., Xu, Y. & Puett, D., 2011, In : PloS one. 6, 7, e21730.

Research output: Contribution to journalArticle

20 Scopus citations

Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation

Cui, J., Miner, B. M., Eldredge, J. B., Warrenfeltz, S. W., Dam, P., Xu, Y. & Puett, D., Jun 28 2011, In : BMC cancer. 11, 280.

Research output: Contribution to journalArticle

22 Scopus citations
2010

A comparative analysis of gene-expression data of multiple cancer types

Xu, K., Cui, J., Olman, V., Yang, Q., Puett, D. & Xu, Y., 2010, In : PloS one. 5, 10, e13696.

Research output: Contribution to journalArticle

28 Scopus citations

A study of health effects of long-distance ocean voyages on seamen using a data classification approach

Lu, Y., Gao, Y., Cao, Z., Cui, J., Dong, Z., Tian, Y. & Xu, Y., 2010, In : BMC Medical Informatics and Decision Making. 10, 1, 13.

Research output: Contribution to journalArticle

9 Scopus citations

In-silico prediction of blood-secretory human proteins using a ranking algorithm

Liu, Q., Cui, J., Yang, Q. & Xu, Y., May 14 2010, In : BMC bioinformatics. 11, 250.

Research output: Contribution to journalArticle

11 Scopus citations