Juan Cui


Assistant Research Scientist @ Computational Systems Biology Laboratory

Department of Biochemistry and Molecular Biology
A110, Davison Life Sciences Building, University of Georgia
120 Green Street
Athens, GA 30602
Phone: 706-542-3930
Fax: 706-542-9751
Email: juancui@csbl.bmb.uga.edu


Research Interests:

•  Cancer genome evolution study

•  Cancer biomarker discovery

•  Characterization of alternative splicing in cancer

•  Omics and NG sequencing analysis

•  Data mining, machine learning and feature selection

•  Computational immunology and vaccine design

•  Protein function prediction

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Education and Training:

•  Assistant Research Scientist/group leader in cancer bioinformatics (2011~present), Department of Biochemistry and Molecular Biology, University of Georgia

•  Postdoctoral Associate/group leader in cancer bioinformatics (2008~2011), Department of Biochemistry and Molecular Biology, University of Georgia

•  PhD in Bioinformatics (2008), Department of Pharmacy, National University of Singapore, Singapore

•  BE in Information Engineering (2002), School of Electronic Engineering, Northwestern Polytechnic University, China

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Publications:

[1] J. Cui, XZ. Mao, P.J. Hastings, Y. Xu.Hypoxia and miscoupling between reduced energy efficiency and signaling to cell proliferation drive cancer to grow increasingly faster (2012) Journal of Molecular Cell Biology (online)

[2] J. Cui, YC. Liang, Y. Xu. Systems Biology in Frontier of Cancer Research, Chinese Journal of Cancer, September issue, 2012 ( in press)

[3] YY Su, ZH Ni, GQ Wang, J. Cui, CG Wei, JH Wang, Q. Yang, Y. Xu, F. Li. Aberrant Expression of MicroRNAs in Gastric Cancer and Biological Significance of miR-574-3p. Int Immunopharmacol. 2012 Aug;13(4):468-75

[4] Q. Liu, H. Zhou, J. Gao, RX Zhu, J. Cui, ZW Cao and Y. Xu. Improved siRNA design through cross-platform feature selection (2012) PLoS ONE (2012) 7(5): e37879. doi:10.1371/journal.pone.0037879

[5] K. Xu, XZ Mao, M. Mehta, J. Cui, C. Zhang, Y. Xu.A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers." PLoS ONE (2011) 7(1): e30750. doi:10.1371/journal.pone.0030750

[6] J. Cui, J.B. Eldredge, Y. Xu, D. Puett. MicroRNA Expression and Regulation in Human Ovarian Carcinoma Cells by Luteinizing Hormone.(2011) PLoS ONE 2011;6(7):e21730

[7] J. Cui, Ying Xu, David Puett. "Transcriptome Profiling of Ovarian Cancer Cells" in Ovarian cancer - Methods in molecular Biology by Humana Press (Springer publishing group), 2011

[8] J. Cui, Ying Xu, David Puett."Transcriptomic Analysis of Human Ovarian Cancer Cells: Changes Mediated by Luteinizing Hormone Receptor Activation", Chapter in Ovarian Cancer / Book 1 ISBN 978-953-307-812-0, Samir A. Farghaly (eds.), InTech, 2011, ISBN 978-953-307-812-0 (online)

[9] J. Cui, B. M. Miner, J. B. Eldredge, S. W. Warrenfeltz, P. Dam, Y. Xu, D. Puett. Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation. BMC Cancer 2011, 11:280

[10] J. Cui, F. Li, G.Q. Wang, X.D. Fang, D. Puett, Y. Xu. Gene-Expression Signatures Can Distinguish Gastric Cancer Grades and Stages. (2011) PLoS ONE 6(3): e17819. doi:10.1371/journal.pone.0017819

[11] J. Gao*, J. Cui*, Y. Wang, Z.N. Dong, Y.M. Lu, Y.P. T, Y. Xu. Identification of potential predictors for subtype IgA nephropathy through analyses of blood biochemistry measures. Clinica Chimica Acta412(5-6):441-445, 2011

[12] C. Hong, J. Cui, Z.H. Ni, Y.Y. Sun,D. Puett, F. Li, Y. Xu. A Computational Method for Prediction of Excretory Proteins and Application to Identification of Gastric Cancer Markers in Urine. PLoS ONE 2011 Feb 18;6(2):e16875

[13] K. Xu*, J. Cui*, V. Olman, Q. Yang, D. Puett, Y. Xu. A Comparative Analysis of Gene-Expression Data of Multiple Cancer Types.(2010) PLoS ONE 5(10):e13696. doi:10.1371/journal.pone.0013696

[14] J. Cui, Y.B. Chen, J. Chou, L.K. Sun, L. Chen, J. Suo, Z.H. Ni, M. Zhang, X.X Kong, E. Hauffman, J.S. Kang, X.Y. Lv, Y.Y. Su, Y. Gao, H.Y. Zhang, V. Olman, G.J. Li, J. Amster, D. Tench, J. D. Puett, F. Li, Y. Xu. An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. Nucleic Acids Res. 2011 Mar;39(4):1197-207

[15] X.B. Zhang, J. Cui, D. Nilsson, K. Gunasekera, I. Roditi, A. Chanfon, X.F. Song, H.N Wang, Y. Xu* and T. Ochsenreiter. The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development. Nucleic Acids Res. 2010 Nov;38(21):7378-87

[16] Q. Liu, J. Cui, Q. Yang, Y. Xu. In silico prediction of blood-secreted human proteins based on manifold ranking. BMC Bioinformatics 11:250(2010)

[17] Y.M. Lu, Y.H. Gao, Z.B. Cao, J. Cui, Z.N. Dong, Y.P. Tian, Y. X. A Study of Health Effects of Long-Distance Ocean Voyages on Seamen Using a Data Classification Approch. BMC Medical Informatics and Decision Making 10:13(2010)

[18] H. Diao, S. Xiao, J. Cui, J. Chun, Y. Xu and X.Q. Ye. Progesterone receptor-mediated upregulation of transthyretin (TTR) in pre-implantation mouse uterus. Fertility and Sterility 93(8):2750-3(2010)

[19] J. Jia, J. Cui, X.H Liu, Z.W. Cao, Y.X. Li, S.Y. Yang, Y.Q. W and Y.Z. Chen. Genome-Scale Search of Tumor-Specific Antigens by Collective Analysis of Mutations, Expressions and T-Cell Recognition. Mol. Immunol. 46:1824-1829(2009)

[20] J. Cui, Q. Liu, D. Puett and Y. Xu. Computational Prediction of Human Proteins That Can Be Secreted into the Bloodstream. Bioinformatics 24(20):2370-2375 (2008)

[21] J. Cui, L.Y. Han, H.H. Lin, Z.Q. Tang, Z.L. Ji, Z.W. Cao, Y.X. Li, and Y.Z. Chen. Advances in exploration of machine learning methods for predicting functional class and interaction of profiles of proteins and peptides irrespective of sequence homology. Curr. Bioinformatics 2(2): 95-112 (2007)

[22] Z.Q. Tang, L. Y. Han, H. H. Lin, J. Cui, B. C. Low, B. W. Li, Y. Z. Chen. Derivation of stable microarray cancer-differentiating signatures by feature-selection with consensus scoring of multiple random sampling and evaluation of gene-ranking consistency. Cancer Res. 67(20):9996-10003 (2007)

[23] J. Cui, L.Y. Han, H.H. Lin, H.L. Zhang, Z.Q. Tang, C.J. Zheng, Z.W. Cao, and Y.Z. Chen. Prediction of MHC-Binding Peptides of Flexible Lengths from Sequence-Derived Structural and Physicochemical Properties. Mol. Immunol . 44: 866-877 (2007).

[24] J. Cui, L.Y. Han, H.H. Lin, Z.Q. Tang, C.J. Zheng, Z.W. Cao, and Y.Z. Chen. Computer Prediction of Allergen Proteins from Sequence-Derived Protein Structural and Physicochemical Properties. Mol. Immunol. 44(4): 514-520 (2007).

[25] B. Xie, C.J. Zheng, L. Y. Han, S. Ong, J. Cui, H.L. Zhang, L. Jiang, X. Chen and Y. Z. Chen. PharmGED: Pharmacogenetic Effect Database. Clin. Pharmacol. Ther. 81(1): 29 (2007).

[26] J. Cui, L.Y. Han, H.H. Lin, Z.Q. Tang, C.J. Zheng, Z.W. Cao, and Y.Z. Chen. MHC-BPS: MHC-Binder Prediction Server for Identifying Peptides of Flexible Lengths from Sequence-Derived Physicochemical Properties. Immunogenetics 58(8): 607-13 (2006)

[27] L.Y. Han, J. Cui, H.H. Lin, Z.L. Ji, Z.W. Cao, Y.S. Li, and Y.Z. Chen. Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity. Proteomics . Vol.6: 4023-4037 (2006).

[28] C.J. Zheng, L.Y. Han, X. Chen, Z.W. Cao, J. Cui, H.H. Lin, H.L. Zhang, H. Li and Y. Z. Chen. Information of ADME-associated proteins and potential application for pharmacogenetic prediction of drug responses. Curr. Pharmacogenomics . 4(2): 87-103 (2006).

[29] C.J.Zheng, L.Y.Han, B.Xie, S.Ong, J.Cui, H.L.Zhang, Z.Q.Tang, S.H.Gan, L.Jiang and Y.Z. Chen. PharmGED: Pharmacogenetic Effect Database. Nucleic Acids Res. (Database issue): D1-D6 (2006).

[30] J. Cui, L. Y. Han, C. Z. Cai, C.J. Zheng, Z. L. Ji, and Y. Z. Chen. Prediction of Functional Class of Novel Bacterial Proteins without the Use of Sequence Similarity by a Statistical Learning Method. J. Mol. Microbiol. Biotech. 9 (2): 86-100 (2005)

[31] L. Y. Han, C. J. Zheng, H. H. Lin, J. Cui, H. Li, H. L. Zhang, Z. Q. Tang, and Y. Z. Chen. Prediction of Functional Class of Novel Plant Proteins by a Statistical Learning Method. New Phytologist. 168:109-121(2005)

[32] L.Y. Han, C.Z. Cai, Z.L. Ji, Z.W. Cao, J. Cui, Y.Z. Chen. Predicting Functional Family of Novel Enzymes Irrespective of Sequence Similarity: A Statistical Learning Approach. Nucleic Acids Res. 32(21): 6437-6444 (2004)

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Manuscripts Submitted or in Preparation:

[1] XY Dong, GQ Wang, GQ Zhang, ZH Ni, J. Suo, J. Cui, A. Cui, Y. Xu, F. Li. The endothelial lipase protein is Promising Urinary Biomarker for Diagnosis of Gastric Cancer. Ready to submit

[2] J. Cui, Y. Wang, Y. Xu. Cell Growth and Metabolism in Cancer: New Insights Gained through Comparative Transcriptome Analysis across Different Cancers. In preparation

[3] J. Cui, et. al. The genomic characterization of primary human gastric cancer. In preparation

[4] Y. Wang*, J. Cui*, W. Du, C. Zhang, FL Mao, JX Wang, L. Chen, Y. Xu. Identification of Highly-specific Gene Markers in Gastric Cancer through Meta- transciptome Anlaysis on Multiple Human Diseaseas Gastric Gene Markers with High Specificity Based on Gene Expression Data of Multiple Human Diseases.To be submitted.

[5] Ying Xu, J. Cui and J. Dave Puett, Introduction to Cancer Bioinformatics, Springer, in preparation, 2012

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Invited Talks and Conference Posters:

•  Talk: "Biomarker identification for cancer diagnosis" in Winship Cancer Institute at Emory University, 08/2012

•  Talk: "Whole-genome sequence analysis reveals new insights about gastric cancer" in International Cancer System Biology conference, Changchun, China, 07/2012

•  Talk: "Bioinformatics in Cancer Research", Tongji University, China, 07/2012

•  Serial talks in Cancer informatics, Tallinn University and Tartu University, Estonia, 06/2012

•  Poster, "Biomarker identification for gastric cancer diagnosis" Cancer Detection and Diagnostics Technologies for Global Health Conference, NIH Campus, 08/2011

•  Talk: "Biomarker identification for cancer diagnosis" in International Cancer System Biology conference, Changchun, China, 07/2011

•  Talk: "Cancer biomarker identification" in Biostatistics department at Emory University, 03/2011

•  Talk: "Gene Expression Profiling of Ovarian Cancer Cells Post-Activation of the LH Receptor",Co-author, 14th World Congress of Gynecological Endocrinology, Florence, Italy, 03/2010

•  Poster: "An integrated approach to cancer marker identification" in GRA Vaccine Dinner Club at Emory University, GA, 02/2010

•  Talk: "A study of gastric cancer maker identification" in Department of Biomedicine Engineering, the Fourth Military Medical University, Xi'an, China 12/2009

•  Talk: "An integrated approach to cancer marker identification" in Department of Computer Science, Jilin University, Changchun, China 12/2009

•  Talk: "Identification of gene/protein signatures for gastric cancer diagnosis" in No. 2 Affiliated Hospital, Jilin University, Changchun, China 12/2009

•  Talk: "Gastric cancer biomarkers" in Department of Life Science, Northeastern Normal University, Changchun, China 11/2009

•  Talk: "Biomarker Identification for Cancer" in CHI's meeting: Accelerating Development & Advancing Personalized Therapy (ADAPT), Washington, 09/2009

•  Poster: "Towards Early Detection of Human Cancer: a systems biology approach to identify serum biomarker for gastric cancer" in Computational System Biology (CSB), Stanford, 08/2009

•  Poster: "A computational program for blood secreted protein prediction: toward serum marker identification" in Computational System Biology (CSB), Stanford, 08/2008

•  Poster: "Computational Prediction of Human Proteins That Can Be Secreted into the Bloodstream" in Third Annual CSBS 2008 Symposium, UGA, 03/2008

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Patents:

•  J. Cui , C. Hong, D. Puett, Y. Xu. PROTEIN MARKER IDENTIFICATION FOR GASTRIC CANCER DIAGNOSIS. (WO-2010-104662) 2010

•  J. Cui. , D. Puett, Y. Xu. A PREDICTION PROGRAM FOR HUMAN PROTEINS THAT CAN BE SECRETED INTO THE BLOODSTREAM. (WO-2010-017559) 2009

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Academic Services :

•  Associate Editor: BMC Research Notes

•  Editorial Board Member: Genomics, Proteomics & Bioinformatics

•  Chair of "Cancer Informatics" workshop at IEEE BIBM, Atlanta, 11/2011

•  Co-chair of the International Cancer System Biology conference, Changchun, China, 07/2011-2012

•  Organizing Member of "Forest Tree Microarray Workshop" UGA, 08/2009

•  Program Committee Member: BIBM 2008-2012, ICMLA 2008, FCST 2010-2011, IBW-2010, ICDM 2010-2012, ICCABS-2011, BMEI-2011,CIBCB 2012, ICIBM 2012, ICCABS 2012

•  Journal Reviewer: Bioinformatics, Nucleic Acids Research, Mathematical Biological Science, Frontier and Bioscience, Amino Acids, Journal of Biomedicine and Biotechnology, Journal of Bioinformatics and Computational Biology, PLoS ONE, International Journal of Data Mining and Bioinformatics,BMC Bioinformatics, Tumor Biology, Cancers, Journal of Bioinformatics and System Biology

•  Conference Reviewer: CSB 2008-2009, APBC 2009, ACM-BCB 2010, ICIC 2010-2011, CIBCB 2012

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Membership/Societies:

•  International Society for Computational Biology

•  American Association of Cancer Research

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Links:

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