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Publications
 
Selected publications in the past five years by members of the CSBC prior to the establishment of the Center, to showcase the diverse background of this group of people who now join force to tackle complex issues in cancer systems biology.


2018


Multi-label Deep Learning for Gene Function Annotation in Cancer Pathways. Renchu Guan, Xu Wang, Mary Qu Yang, Yu Zhang, Fengfeng Zhou, Chen Yang, and Yanchun Liang, Scientific Reports, 8:267, DOI:10.1038/s41598-017-17842-9, 2018.


2017


Transcription Regulation by DNA Methylation under Stressful Conditions in Human Cancer, Sha Cao, Yi Zhou, Yue Wu, Tianci Song, Burair Alsaihati, Ying Xu, Quantitative Biology, 5, 4,328–337, 2017.

Competition Regulation among DNA Methylation, Nucleotide Synthesis and Anti-Oxidation, Sha Cao, Xiwen Zhu, Hong Qian, Bernd Schuttler, Ying Xu, Cancer Research, DOI: 10.1158/0008-5472, 2017.

Systematic analyses of glutamine and glutamate metabolisms across different cancer types. Tian Y, Du W, Cao S, Wu Y, Dong N, Wang Y, Xu Y. Chinese Journal of Cancer,2017, 36, 88.

Solid-State 15N and 17O NMR of S-Nitrosothiols, Y. Gao, Y. Dai, and G. Wu, Journal of Physical Chemistry B, 121: 7311-7317, 2017.

A Novel Unsupervised Algorithm for Biological Process-based Analysis on Cancer. Song T, Cao S, Sheng T, Liang S, Du W, Liang Y. Scientific Reports, 2017, 7 (1), 4671.

Computational Analysis of Specific microRNA Biomarkers for Noninvasive Early Cancer Detection. Song T,Liang Y,Cao Z,Du W,Li Y,Biomed Research International,2017,4680650 .

p62/SQSTM1 as an oncotarget mediates cisplatin resistance through activatingRIP1‐NF‐κB pathway in human ovarian cancer cells. Xiao-Yu Yan, Yu Zhang, Juan-Juan Zhang, Li-Chao Zhang, Ya-Nan Liu, Yao Wu, Ya-Nan Xue, Sheng-Yao Lu, Jing Su and Lian-Kun Sun, Cancer Science, 2017, 108(7):1405-1413.

Cytoprotective Effect of the UCP2-SIRT3 Signaling Pathway by Decreasing Mitochondrial Oxidative Stress on Cerebral Ischemia-Reperfusion Injury. Jing Su, Jie Liu, Xiao-Yu Yan, Yong Zhang, Juan-Juan Zhang, Li-Chao Zhang and Lian-Kun Sun, International Journal of Molecular Sciences, 2017, 18(7).

Association between single nucleotide variants of vascular endothelial growth factor A and the risk of thyroid carcinoma and nodular goiter in a Han Chinese population, Rui Liu, Lingfeng Ning, Xiaoli Liu, Huiping Zhang, Yaqin Yu, Shangchao Zhang, Wenwang Rao, Jieping Shi, Hui Sun, Qiong Yu, Oncotarget, 8(9):15838-15845, 2017.

Effect of Amino Acid Mutations on Intra-Dimer Tubulin–Tubulin Binding Strength of Microtubules, N. Liu, R. Pidaparti and X. Wang, Integrative Biology, 9: 925-933, 2017.

Nanoparticle-Mediated Mechanical Destruction of Cell Membranes: A Coarse-Grained Molecular Dynamics Study, L. Zhang, Y. Zhao and X. Wang, ACS Applied Materials & Interfaces, 9: 26665-26673, 2017.

Mechanical Role of a Growing Solid Tumor on Cortical Folding, M. J. Razavi, M. Reeves and X. Wang, Computer Methods in Biomechanics and Biomedical Engineering, 20: 1212-1221, 2017.

Diabatic-At-Construction Method for Diabatic and Adiabatic Ground and Excited States Based on Multistate Density Functional Theory, Adam Grofe, Zexing Qu, Donald G. Truhlar, Hui Li, and Jiali Gao, J. Chem. Theory Comput. 13, 1176-1187, 2017; doi: 10.1021/acs.jctc.6b01176.

An OMIC biomarker detection algorithm TriVote and its application in methylomic biomarker detection. Cheng Xu, Jiamei Liu, Weifeng Yang, Yayun Shu, Zhipeng Wei, Weiwei Zheng, Xin Feng, and Fengfeng Zhou. Accepted by Epigenomics, 2017.

Cortical and Subcortical Brain Morphometry Differences Between Patients with Autism Spectrum Disorder and Healthy Individuals Across the Lifespan: Results From the ENIGMA ASD Working Group. van Rooij D, Anagnostou E, …, Fengfeng Zhou, Buitelaar JK1. Accepted by American Journal of Psychiatry, 2017.


2016


Caspase-mediated cleavage of Beclin1 inhibits autophagy and promotes apoptosis induced by S1 in human ovarian cancer SKOV3 cells, Xiaoning Li, Jing Su, Meihui Xia, Hongyan Li, Ye Xu, Chunhui Ma, Liwei Ma, Jingsong Kang, Huimei Yu, Zhichao Zhang, Liankun Sun, Apoptosis, 2016, 21(2):225-238.

Association between the KRAS Gene Polymorphisms and Papillary Thyroid Carcinoma in a Chinese Han Population, Ning Lifeng, Rao Wenwang, Yaqin Yu, Xiaoli Liu, Yuchen Pan, Yuan Ma, Rui Liu, Shangchao Zhang, Hui Sun, Qiong Yu, Journal of Cancer, 7(15): 2420-2426, doi: 10.7150/jca.16507, 2016.

Multistate Density Functional Theory for Effective Diabatic Electronic Coupling, Haisheng Ren, Makenzie R. Provorse, Peng Bao, Zexing Qu, and Jiali Gao, J. Phys. Chem. Lett. 7, 2286−2293, 2016; doi: 10.1021/acs.jpclett.6b00915.

Text Classification Based on Deep Belief Network and Softmax Regression. Mingyang Jiang, Yanchun Liang, Xiaoyue Feng, Xiaojing Fan, Zhili Pei, Yu Xue, Renchu Guan. Neural Computing and Applications, 1-10, 2016.

Machine learning based detection of age-related macular degeneration (AMD) and diabetic macular edema (DME) from optical coherence tomography (OCT) images. Yu Wang, Yaonan Zhang, Zhaomin Yao, Ruixue Zhao, Fengfeng Zhou. BioMedical Optics Express, 7 (12): 4928-4940, 2016.


2015


Somatic Mutations Are Facilitators Rather Than Drivers of Cancer Formation, S. Cao, C. Zhang and Ying Xu, International Journal of Cancer, 06/2015; 137(11), DOI: 10.1002/ijc.29639, 2015

Elucidation of High-Level Production of Lactates throughout a Cancer Development, Chi Zhang, Chao Liu, Sha Cao and Ying Xu, Journal of Molecular Cell Biology, DOI: 10.1093/jmcb/mjv031, 2015.

Direct NMR detection of the unstable “red product” from reaction between nitroprusside and 2-mercaptosuccinic acid, Y. Gao, B. Mossing and G. Wu, Dalton Transactions, 44(47): 20338-20343, 2015.

Solving the 170-Year-Old mystery about red-violet and blue transient intermediates in the Gmelin reaction, Y. Gao, A. Toubaei, X. Kong and G. Wu, European Journal of Chemistry, 21: 17172-17177, 2015.

Identification of Gene-Expression Signatures and Protein Markers for Breast Cancer Grading and Staging. Yao F, Zhang C, Du W, Liu C and Xu Y. PLOS One, 2015, 10(9): e0138213.

p62 participates in the inhibition of NF-κB signaling and apoptosis induced by sulfasalazine in human glioma U251 cells[J]. Jing Su, Fei Liu, Meihui Xia, Ye Xu, Xiaoning Li, Jinsong Kang, Yulin Li and Liankun Sun, Oncology Reports, 2015, 34(1):235.

Association Analysis of MET Gene Polymorphism with Papillary Thyroid Carcinoma in a Chinese Population. Int J Endocrinol. Ning L, Yu Y, Liu X, Ai L, Zhang X, Rao W, Shi J, Sun H, Yu Q. 2015:405217. doi: 10.1155/2015/405217. 2015

Coarse-Grained Modeling of Vesicle Responses to Active Rotational Nanoparticles, L. Zhang and X. Wang, Nanoscale, 7: 13458-13467, 2015.

Nanotube-enabled Vesicle-Vesicle Communication: A Computational Model L. Zhang and X. Wang, Journal of Physical Chemistry Letters, 6: 2530-2537, 2015.

Photoisomerization of Silyl-Substituted Cyclobutadiene Induced by σ → π* Excitation: A Computational Study, Zexing Qu, Chen Yang, and Chungen Liu J. Phys. Chem. A, 119, 442−451, 2015; doi: 10.1021/jp503220q.

A Comparative Study for Biomedical Named Entity Recognition. Xu Wang, Chen Yang, Renchu Guan. International Journal of Machine Learning and Cybernetics, 1-10, 2015.


2014


Cancer Bioinformatics, Ying Xu, Juan Cui and J. Dave Puett, Springer, 2014.

Acidity and hydrogen exchange dynamics of iron(II)-bound nitroxyl in aqueous solution, Y. Gao, A. Toubaei, X. Kong and G. Wu, Angewandte Chemie International Edition, 53(43): 11547-11551, 2014.

Bcl-2 family proteins are involved in the signal crosstalk between endoplasmic reticulum stress and mitochondrial dysfunction in tumor chemotherapy resistance. Jing Su, Lei Zhou, Mei-hui Xia, Ye Xu, Xi-yan Xiang, and Lian-kun Sun, Biomed Research International, 2014, 2014(2014):234370.

Associations between rs965513/rs944289 and papillary thyroid carcinoma risk: a meta-analysis, Lizhe Ai, Xiaoli Liu, Yuhang Yao, Yaqin Yu, Hui Sun, Qiong Yu, Endocrine, 47: 428-434, DOI 10.1007/s12020-014-0256-4, 2014.

Are the SNPs of NKX2-1 associated with papillary thyroid carcinoma in the Han population of Northern China? Ai L, Yu Y, Liu X, Wang C, Shi J, Sun H, Yu Q, Front Med,8(1):113-117, doi: 10.1007/s11684-014-0310-x, 2014


2013


Acceptor specificities and selective inhibition of recombinant human Gal- and GlcNAc-transferases that synthesize core structures 1, 2, 3 and 4 of O-glycans, Y. Gao, R.P. Aryal, T. Ju, R.D. Cummings, G. Gahlay, D. L. Jarvis, K. Matta, J. Z. Vlahakis, W.A. Szarek, I. Brockhausen, Biochimica et Biophysica Acta, 1830(8): 4274-4281, 2013.

A non-adiabatic dynamics study of octatetraene: The radiationless conversion from S2 to S1, Zexing Qu and Chungen Liu, J. Chem. Phys. 139, 244304, 2013; doi: 10.1063/1.4853715

Full Text Clustering and Relationship Network Analysis of Biomedical Publications. Renchu Guan, Chen Yang, Maurizio Marchese, Yanchun Liang, Xiaohu Shi. PLoS One, 9(9), e108847, 2014.