2014 Selected Publications

NGS (Next-Generation Sequencing) Data Analysis

1. Zhixing Feng, Jing Li, Jing-Ren Zhang, Xuegong Zhang*, qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data, Nucleic Acids Research, 42(22): 13488-13499, 2014

2. Xavier Roge, Xuegong Zhang*, RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892, 2014

Metagenomics

3. Mengmeng Wu, Rui Jiang*, Detecting epistatic interactions in metagenome-wide association studies by metaBOOST, BioMed Research International, 398147, 2014

4. Xujun Liang, Huiying Li, Geng Tian, Shao Li*, Dynamic microbe and molecular networks in a mouse model of colitis-associated colorectal cancer, Scientific Reports, 4: 4985, 2014

5. O. Tanaseichuk, J. Borneman, Tao Jiang*, Phylogeny-based classification of microbial communities, Bioinformatics, 30(4): 449-456, 2014

Epigenomics and Gene Regulation

6. Weilong Guo, Wen-Yu Chung, Minping Qian, Matteo Pellegrini, Michael Q. Zhang*, Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells, Nucleic Acids Research, 42(5): 3009-3016, 2014

7. Chao He, Xiaowo Wang*, Michael Q. Zhang*, Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions, Nucleic Acids Research, 42(11): 6935-4944, 2014

8. Leying Guan, Qian Yang, Mengting Gu, Liang Chen, Xuegong Zhang*, Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation, Quantitative Biology, 2(2): 71-79, 2014

9. Yingxue Li, Xuening Liu, Xiaowo Wang, Xuegong Zhang*, Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 57(1): 52-58, 2014

10. S.M. Weyn-Vanhentenryck, A. Mele, Q. Yan, S. Sun, N. Famy, Z. Zhang, C. Xue, M. Herre, P.A. Silver, M.Q. Zhang, A.R. Krainer, R.B. Darnell, Chaolin Zhang, HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism, Cell Reports, 6: 1139-1152, 2014

11. N. Heidari, D.H. Phanstiel,, Chao He, F. Grubert, F. Jahanbani, M. Kasowski, M.Q. Zhang, M.Q. Snyder, Genome-wide map of regulatory interactions in the human genome, Genome Research, 24: 1905-1917, 2014

12. N. Rajagopal, J. Ernst, P. Ray, J. Wu, M.Q. Zhang, M. Kellis, Bing Ren, Distinct and predictive histone lysine acetylation patterns at promoters, enhancers and gene bodies, G3: Genes, Genomes, Genetics, 4: 2051-2063, 2014

13. Wangzhi Li, Jie Wu, Sang-Yong Kim, Ming Zhao, Stephen A. Hearn, Michael Q. Zhang, Marvin L. Meistrich, Alea A. Mills, Chd5 orchestrates chromatin remodeling during sperm development, Nature Communications, 5: 3812, 2014

Network Pharmacology

14. L Wang, Y Wang, Q Hu, S Li*, Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks, CPT: Pharcometrics and Systems Pharmacology, 3: e146, 2014

15. Huiying Li, Linhua Zhao, Bo Zhang, Yuyu Jiang, Xu Wang, Yun Guo, Hongxingn Liu, Shao Li*, Xiaolin Tong*, A network pharmacology approach to determine active compounds and action mechanisms of Ge-Gen-Qin-Lian decoction for treatment of type 2 diabetes, Evidence-based Complementary and Alternative Medicine, 495840, 2014

16. Shao Li*, Tai-Ping Fan, Wei Jia, Aiping Lu, Weidong Zhang, Network pharmacology in traditional Chinese medicine, Evidence-based Complementary and Alternative Medicine, 138460, 2014

17. Xujun Liang, Huiying Li, Shao Li*, A Dynamic microbe pharmacology approach to analyse traditional herbal formular: the Liu-Wei-Di-Huang pill as a case study, Molecular BioSystems, 10(3): 1014-1022, 2014

18. Shi-Bing Su, Wei Jia, Aiping Lu, Shao Li, Evidence-based Zheng: a traditional Chinese medicine syndrome 2013, Evidence-based Complementary and Alternative Medicine, 484201, 2014

Medical Genetics

19. Shufang Zhang, Xueya Zhou*, Shengnan Liu, Tingting Bai, Yingai Zhang, Jing Wang, Shunlan Wang, Xuegong Zhang, Binbin, Wang*, MYH9-related disease: description of a large Chinese pedigree and a survey of reported mutations, Acta Haematologica, 132: 193-198, 2014

20. Jing Cheng, Xueya Zhou, Yu Lu, Jing Chen, Bing Han, Yuhua Zhu, Liyang Liu, Kwong-Wai Choy, Dongyi Han, Pak C. Sham, Michael Q. Zhang*, Xuegong Zhang*, Huijun Yuan*, Exom sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nonsyndromic hearing loss in a Chinese Family, Annals of Human Genetics, 78: 410-423, 2014

21. Yu Lu, Xueya Zhou, Zhanguo Jin, Jing Cheng, Weidong Shen, Fei Ji, Liyang Liu, Xuegong Zhang, Michael Zhang, Ye Cao, Dongyi Han, KwongWai Choy, Huijun Yuan, Resolving the genetic heterogeneity of prelingual hearing loss within one family: performance comparison and application of two targeted next generation sequencing approaches, Journal of Human Genetics, 59: 599-607, 2014

22. Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang*, Prioritizing protein complexes implicated in human diseases by network optimization, BMC Systems Biology, 8(Suppl 1): S2, 2014

23. Jiaxin Wu, Yanda Li, Rui Jiang*, Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing status, PLoS Genetics, 10(3): e1004237, 2014

24. Jiaxin Wu, Silu Yang, Rui Jiang*, Inferring non-synonymous single-nucleotide polymorphisms-disease associations via integration of multiple similarity networks, IET Systems Biology, 8(2): 33-40, 2014

25. Jian-Feng Yang, Xiao-Fan Ding, Lei Chen, Wai-Kin Mat, Michelle Zhi Xu, Jin-Fei Chen, Jian-Min Wang, Lin Xu, Wai-Sang Poon, Ava Kwong, Gilberto Ka-Kit Leung, Tze-Ching Tan, Chi-Hung Yu, Yue-Bin Ke, Xin-Yun Xu, Xiao-Yan Ke, Ronald CW Ma, Juliana CN Chan, Wei-Qing Wan, Li-Wei Zhang, Yogesh Kumar, Shui-Ying Tsang, Shao Li, Hong-Yang Wang, Hong Xue, Copy number variation analysis based on AluScan sequences, Clinical Bioinformatics, 4: 15, 2014

26. C. Xu, X. Ju, D. Song, F. Huang, D. Tang, Z. Zou, C. Zhang, T. Joshi, L. Jia, W. Xu, K-F. Xu, Q. Wang, Y. Xiong, Z. Guo, X. Chen, F. Huang, J. Xu, Y. Zhong, Y. Zhu, Y. Peng, L. Wang, X. Zhang, R. Jiang, D. Li, T. Jiang, D. Xu, C. Jiang, An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus, Molecular Psychiatry, doi:10.1038/mp.2014.72, 1-9, 2014

Systems Biology

27. Peng Xie, Yu Liu, Yanda Li, Michael Q. Zhang*, Xiaowo Wang*, MIROR: a method for cell-type specific microRNA occupancy rate prediction, Molecular BioSystems, 10: 1377, 2014

28. Dongfang Wang, Jin Gu*, Ting Wang, Zijian Ding, OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs, Bioinformatics, 30(15): 2237-2238, 2014

29. Ting Wang, Jin Gu*, Yanda Li, Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method, BMC Bioinformatics, 15: 255, 2014

30. Guipeng Li, Ming Li, Yiwei Zhang, Dong Wang, Rong Li, Roger Guimera, Juntao Tony Gao, Michael Q. Zhang*, ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks, PLoS ONE, 9(5): e94608, 2014

31. Honglei Liu,Yanda Li,Xiaowo Wang, OP-Synthetic: identification of optimal genetic manipulations for the overproduction of native and non-native metabolites, Quantitative Biology. 2014, 2 (3): 100-109.

32. Muxuan Liang, Zhizhong Li, Ting Chen, Jianyang Zeng, Integrative data analysis of multi-platform cancer data with a multimodal deep learning approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2014, Volume:PP , Issue: 99

Synthetic Biology

33. S. Kiani, J. Beal, M.R. Ebrahimkhani, J. Huh, R.N. Hall, Z. Xie, Y. Li, R. Weiss, CRISPR transcriptional repression devices and layered circuits in mammalian cells, Nature Methods, 11(7): 723-726, 2014

34. Yi Li, Kristina Ehrhardt, Michael Q. Zhang, Leobidas Bleris, Assembly and validation of versatile transcription activator-like effector libraries, Scientific Reports, 4: 4857, 2014

Cancer Biology and other diseases
35. Jin Gu*, Yang Chen, Huiya Huang, Lingyu Yin, Zhen Xie, Michael Q. Zhang*, Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer, Molecular BioSystems, 10: 3249-3254, 2014

36. Miaomiao Sheng, Ying Zhong, Yang Chen, Jianchao Du, Xiangwu Ju, Chen Zhao, Guigeng Zhang, Lifang Zhang, Kangtai Liu, Ning Yang, Peng Xie, Dangsheng Li, Michael Q. Zhang, Chengyu Jiang, Has-miR-1246, has-miR-320a and has-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro, Science China Life Sciences, 57(10): 959-972, 2014

37. C.F. Sephton, A.A. Tang, A. Kulkarni, J. West, M. Brooks, J.J. Stubblefield, Y. Liu, M.Q. Zhang, C.B. Green, K.M. Huber, E.J. Huang, J. Herz, G. Yu, Activity-dependent FUS dysregulation disrupts synaptic homeostasis, PNAS, E4769-4778, 2014

Genomic Applications

38. Guang-Zhong Wang, Simone Marini, Xinyun Ma, Qiang Yang, Xuegong Zhang*, Yan Zhu*, Improvement of Dscam hemophilic binding affinity throughout Drosophila evolution, BMC Evolutionary Biology, 4: 186, 2014

39. Yong Chen, Yunfeng Ding, Yi Yang, Jinhai Yu, Guiing Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Alexander Steinbuchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu*, Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic Acids Research, 42(2): 1042-1064, 2014


2013 Selected Publications

NGS (2nd- and 3rd-Generation Sequencing) Data Analysis

1. Xavier Roge, Xuegong Zhang, RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, advanced access publication on Nov. 8, 2013

2. Jie Wu, Olga Anczukow, Adrian R. Krainer, Michael Q. Zhang, Chaolin Zhang, OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds, Nucleic Acids Research, 41(10): 5149-5163, 2013

3. Huijuan Feng, Zhiyi Qin, Xuegong Zhang, Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer Letters, 340: 179-191, 2013

4. Xinyun Ma, Xuegong Zhang, NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data, BMC Bioinformatics, 14: 220, 2013

5. Weichen Wang, Zhiyi Qin, Zhixing Feng, Xi Wang, Xuegong Zhang, Identifying differentially spliced genes from two groups of RNA-seq samples, GENE, 518: 164-170, 2013

6. Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, 41(13): e136, 2013

7. Feng Zeng, Rui Jiang, Ting Chen, PhyoHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data, Bioinformatics, 29(22): 2859-2868, 2013

8. Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric Schadt, Detecting DNA modification from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic, PLoS Computational Biology, 9(3): e1002935, March 2013

9. Hongfei Cui, Xuegong Zhang, Alignment-free supervised classification of metagenomes by recursive SVM, BMC Genomics, 14: 641, 2013

10. Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun, Alignment-free sequence comparison based on next-generation sequencing reads, Journal of Computational Biology, 20(2): 64-79, 2013

Network Pharmacology, Traditional Chinese Medicine and Systems Biology

11. Shao Li, Bo Zhang, Traditional Chinese medicine network pharmacology: theory, methodology and application, Chinese Journal of Natural Medicine, 11(2): 110-120, 2013

12. Bo Zhang, Xu Wang, Shao Li, An integrative platform of TCM network pharmacology and its application on a herbal formula, Qing-Luo-Yin, Evidence-Based Complementary and Alternative Medicine, 2013: 456747

13. Bo Zhang, Lu Liu, Shiwen Zhao, Xu Wang, Liyang Liu, Shao Li, Vitexicarpin acts as a novel angiogenesis inhibitor and its target network, Evidence-Based Complementary and Alternative Medicine, 2013: 278405

14. Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li, Inferring pathway crosstalk networks using gene set co-expression signatures, Molecular BioSystems, 9: 1822, 2013

15. Rui Li, Tao Ma, Jin Gu, Xujun Liang, Shao Li, Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients, Scientific Reports, 3: 1543, 2013

16. 马鸿雁,周婉珊,褚夫江,王东,梁生旺,李梢,苦参中黄酮类成分的高效液相指纹图谱及5 种成分的含量测定,《中国中药杂志》,38(16): 2690-2695, 2013

17. Chao Wu, Jun Zhu, Xuegong Zhang, Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma, BMC Bioinformatics, 14: 365, 2013

18. Jin Gu, Zhenyu Xuan, Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures, PLoS ONE, 8(11): e81032, 2013

19. Yong Chen, Jingjing Hao, Wei Jiang, Tong He, Xuegong Zhang, Tao Jiang, Rui Jiang, Identifying potential cancer driver genes by genomic data integration, Scientific Reports, 3: 3538, 2013

20. Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang, Prioritizing protein complexes implicated in human diseases by netnwork optimization, BMC Systems Biology, 8(Suppl 1): S2, 2014

21. Thibault Jacquemin, Rui Jiang, Walking on a tissue-specific disease-protein-complex heterogeneous network for the discovery of disease-related protein coplexes, BioMed Research International, Article ID 732650, 2013

Transcription Regulation and Epigenomics

22. Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q. Zhang, Pao-Yang Chen, Metteo Pellegrini, BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data, BMC Genomics, 14: 774, 2013

23. Dingming Wu, Jin Gu, Michael Q. Zhang, FastDMA: an infinium HumanMethylation 450 Beedchip analyzer, PLoS ONE, 9: e74275, 2013

24. Weilong Guo, Wen-Yu Chung, Minping Qian, Matteo Pellegrini, Michael Q. Zhang, Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Research, 2013 advance online access published Dec. 16, 2013

Mathematical Modeling of Biological Processes

25. Zhou D, Wu D, Li Z, Qian M, Zhang MQ, Population dynamics of cancer cells with cell-state conversions. Quantitative Biology, 2:201-108, 2013

Medical Genetics

26. Jiaxin Wu, Rui Jiang, Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases, The Scientific World Journal, 2013: 675851

27. Yong Chen, Xuebing Wu, Rui Jiang, Integrating human omics data to prioritize candidate genes, BMC Medical Genomics, 6:57, 2013

28. Yan Wang, Yi Zhang, Yan Li, Xueya Zhou, Xiaofeng Wang, Pingjin Gao, Li Jin, Xuegong Zhang, Dingliang Zhu, Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population, Molecular Biology Reports, 40: 1867-1873, 2013

29. Xueya Zhou, Suying Bao, Binbin Wang, Xuegong Zhang, You-Qiang Song, Short read mapping for exome sequencing, Chapter 6 of Noam Shomron (ed.), Deep Sequencing Data Analysis, Methods in Molecular Biology, vol. 1038, NY: Springer, 2013

30. Suying Bao, Xueya Zhou, Liangcai Zhang, Jie Zhou, Kelvin Kai-Wang To, Binbin Wang, Liqiu Wang, Xuegong Zhang, You-Qiang Song, Prioritizing genes responsible for host resistance to influenza using network approaches, BMC Genomics, 14: 816, 2013

Synthetic Biology

31. Xie Z., Wroblewska L. and Weiss R. RNAi synthetic logic circuits for sensing, information processing and actuation. Encyclopedia of Molecular Cell Biology and Molecular Medicine. In press (Book chapter)

32. Kashyap, N., Pham, B., Xie, Z., & Bleris, L. Transcripts for combined synthetic microRNA and gene delivery. Molecular BioSystems. 9(7): 1919-1925, 2013

33. Kang, T., White, J. T., Xie, Z., Benenson, Y., Sontag, E., & Bleris, L. (2013). Reverse engineering validation using a benchmark synthetic gene circuit in human cells. ACS Synthetic Biology. 2(5): 255–262, 2013

34. Lee, Y.Y., Hsu, C.Y., Lin, L.J., Chang, C.C., Cheng, H.C., Yeh, T.H., Hu, R.H., Lin C., Xie Z., Chen, B.S. Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries. BMC Systems Biology. 7(1): 109, 2013

Other Collaborated Publications

35. Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X, Zhang S, Yu D, Song L, Zhang H, Zhang C, Huo L, Huo C, Wang Y, Du Y, Zhang H, Zhang P, Na H, Xu S, Zhu Y, Xie Z, He T, Zhang Y, Wang G, Fan Z, Yang F, Liu H, Wang X, Zhang X, Zhang MQ, Li Y, Steinbüchel A, Fujimoto T, Cichello S, Yu J, Liu P., Integrated omics study delineates the dynamics of lipid droplets in hodococcus opacus, Nucleic Acids Research, 2013 [Epub ahead of print]

36. Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J., ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data, Molecular Cell Proteomics, 12(11): 3379-3387, 2013

37. Wen-Yu Chung, Robert J. Schmitz, Tanya Biorac, Delia Ye, Miroslav Dudas, Gavin D. Meredith, Christopher C. Adams, Joseph R. Ecker and Michael Q. Zhang, Constructing hepitypes: phasing local genotype and DNA methylation. Journal of Neuroscience and Neuroengineering, 2(4): 335-346, 2013

38. Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B., Epigenomic analysis of multilineage differentiation of human embryonic stem cells, Cell, 153(5); 1134-1148, 2013

39. Myoungloo V. Kim, Weiming Ouyang, Will Liao, Michael Q. Zhang, Ming O. Li, The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity, 39(2): p. 286-97, 2013

40. Ma X, Wang YW, Zhang MQ, Gazdar AF., DNA methylation data analysis and its application to cancer research, Epigenomics, 5(3): 301-316, 2013

41. May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA., The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development, Nature Communications, 4: 2145, 2013

42. Tam KW, Zhang W, Soh J, Stastny V, Chen M, Sun H, Thu K, Rios JJ, Yang C, Marconett CN, Selamat SA, Laird-Offringa IA, Taguchi A, Hanash S, Shames D, Ma X, Zhang MQ, Lam WL, Gazdar A., CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer, Journal of Thoracic Oncology, 8(11); 1378-1388, 2013

43. Chengqi Wang, Michael Q. Zhang, Zhihua Zhang, Computational identification of active enhancers in model organisms, Genomics, Proteomics & Bioinformatics, 11(3): 142-150, 2013

44. Ali Nowrouze, Wing T. Cheung, Tingting Li, Xuegong Zhang, Anne Arens, Anna Paruzynski, Simon N. Waddington, Emma Osejindu, Safia Reja, Christof von Kalle, Yoahe Wang, Faisal Al-Allaf, Lisa Gregory, Matthew Themis, Maxine Holder, Niraja Dighe, Alaine Ruthe, Suzanne MK Buckley, Brian Bigger, Eugenio Montini, Adrian J. Thrasher, Robert Andrews, Terry P. Roberts, Robert F. Newbold, Charles Coutelle, Manfred Schmidt, Mike Themis, The fetal mouse is a sensitive genotoxicity model that exposes lentiviral-associated mutagenesis resulting in liver oncogenesis, Molecular Therapy, 21: 324-337, Feb. 2013

45. Hongshan Jiang, Ying Zhao, Wenguang Chen, Weimin Zheng, Xuegong Zhang, Improving cis-regulatory elements modeling by consensus scaffolded mixture models, Science in China – Information Sciences, 56: 012501:1-012501:11, 2013

46. Qiongshi Lu, Siin Ren, Ming Lu, Yong Zhang, Dahai Zhu, Xuegong Zhang, Tingting Li, Computational prediction of associations between long non-coding RNAs and proteins, BMC Genomics, 14: 651, 2013


2012 Selected Publications
NGS (2nd- and 3rd-Generation Sequencing) Data Analysis

1. Weichen Wang, Zhiyi Qin, Zhixing Feng, Xi Wang, Xuegong Zhang, Identifying differentially spliced genes from two groups of RNA-seq samples, Gene, doi: 10.1016/j.gene.2012.11.045, 2012

2. Huijuan Feng, Zhiyi Qin, Xuegong Zhang, Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer Letters, doi: 10.1016/j.canlet.2012.11.010

3. L. Wan, X. Yan, Ting Chen, Fengzhu Sun, Modeling RNA degradation for RNA-Seq with applications, Biostatistics, 13(4): 734-747, 2012

4. Wei Li, Tao Jiang, Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads, Bioinformatics, 28(22): 2914-2921, 2012

5. Z. Zhai, G. Reinert, K. Song, Michael S. Waterman, Y. Luan, Fengzhu Sun, Normal and compound Poisson approximations for pattern occurrences in NGS reads, Journal of Computational Biology, 19(6): 839-854, 2012

6. G. Fang, D. Munera, D.I. Friedman, A. Mandlik, M.C. Chao, O. Banerjee, Zhixing Feng, B. Losic, M.C. Mahajan, O.J. Jabado, G. Deikus, T.A. Clark, K. Luong, I.A. Murray, B.M. Davis, A. Keren-Paz, A. Chess, R.J. Roberts, J. Korlach, S.W. Turner, V. Kumar, M.K. Waldor, E.E. Schadt, Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing, Nature Biotechnology, 30(12): 1232-1239, 2012

Gene Expression, Regulation and Epigenomics

7. M. He, Yu Liu, Xiaowo Wang, Michael Q. Zhang, G.J. Hanon, Z.J. Huang, Cell-type-based analysis of microRNA profiles in the mouse brain, Neuron, 73: 35-48, 2012

8. Ruijuan Li, Weilong Guo, Jin Gu, Michael Q. Zhang, Xiaowo Wang, Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation, Genomics, 100: 297-302, 2012

9. W. Ouyang, W. Liao, C.T. Luo, N. Yin, M. Huse, M.V. Kim, M. Peng, P. Chan, Q. Ma, Y. Mo, D. Meijer, K. Zhao, A.Y. Rudensky, G. Atwal, Michael Q. Zhang, M.O. Li, Novel Foxo1-dependent transcriptional programs control Treg cell function, Nature, 491(22): 554-559, 2012

10. A. Chicas, A. Kapoor, Xiaowo Wang, O. Aksoy, A.G. Evertts, Michael Q. Zhang, B.A. Garcia, E. Bernstein, S.W. Lowe, H3k4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence, PNAS, 109 (23): 8971-8976, 2012

11. K. Ratnakumar, L.F. Duarte, G. LeRoy, D. Hasson, D. Smeets, C. Vardabasso, C. Bonisch, Tianying Zeng, B. Xiang, D.Y. Zhang, H. Li, Xiaowo Wang, S.B. Hake, L. Schermelleh, B.A. Garcia, E. Bernstein, ATRX-mediated chromatin association of histone variant macroH2A1 regulates alpha-globin expression, Genes & Development, 26: 433-438, 2012

12. H. Xing, Y. Mo, W. Liao, Michael Q. Zhang, Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data, PLoS Computational Biology, 8(7): e1002613, 2012

13. Monica C. Sleumer, G. Wei, Y. Wang, H. Chang, T. Xu, R. Chen, Michael Q. Zhang, Regulatory elements of Caenorhabditis elegans ribosomal protein genes, BMC Genomics, 13:433, 2012

14. Z. Zhang, X. Ma, Michael Q. Zhang, Bivalent-like chromatin markers are predictive for transcription start site distribution in human, PLoS ONE, 7(6): e38112, 2012

15. O. Aksoy, A. Chicas, Tianying Zeng, Z. Zhao, M. McCurrach, Xiaowo Wang, S.W. Lowe, The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence, Genes & Development, 26: 1546-1557, 2012

Bionetworks, Systems Biology and Systems Biomedicine

16. Yong Chen, Wangshu Zhang, Mingxin Gan, Rui Jiang, Constructing human phenome-interactome networks for the prioritization of candidate genes, Statistics and Its Interface, 5: 137-148, 2012

17. Chao Wu, Jun Zhu, Xuegong Zhang, Inegrating gene expression and protein-protein interaction network to prioritize cancer-associated genes, BMC Bioinformatics, 13: 182, 2012

18. Shiwen Zhao and Shao Li, A co-module approach for elucidating drug-disease associations and revealing their molecular basis, Bioinformatics, 28(7): 955-961, 2012

19. Jin Gu, Shao Li, Towards integrative annotation of the cell-type specific gene functional and signaling map in vascular endothelial cells, Molecular BioSystems, 8: 2041-2049, 2012

20. Yang Chen, Jin Gu, Dan Li, Shao Li, Time-course network analysis reveals TNF-alpha promote G1/S transition of cell cycle in vascular endothelial cells, Bioinformatics, 28(1): 1-4, 2012

21. T. Li, Y. Du, Likun Wang, L. Huang, Wenlin Li, M. Lu, Xuegong Zhang, W.-G. Zhu,Characterization and prediction of lysine(k)-acetyl-transferase specific acetylation sites, Molecular & Cellular Proteomics, 11(1): M111.011080, 2012

22. S.-B. Su, A. Lu, Shao Li, W. Jia, Evidence-based ZHENG: a traditional Chinese medicine syndrome, Evidence-Based Complementary and Alternative Medicine, vol. 2012, Article ID 246538, 2012

23. R. Kanawong, T. Obafemi-Ajayi, Tao Ma, D. Xu, Shao Li, Y. Duan, Automated tongue feature extraction for ZHENG classification in traditional Chinese medicine, Evidence-Based Complementary and Alternative Medicine, Vol. 2012, Article ID 912852, 2012

Metagenomics

24. Bai Jiang, Xujun Liang, Yang Chen, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang, Shao Li, Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome, Scientific Reports, 2: 936, 2012

25. Q. Chang, Y. Luan, Ting Chen, J.A. Fuhrman, Fengzhu Sun, Computational methods for the analysis of tag sequences in metagenomics studies, Frontiers in Bioscience, S4: 1333-1343, 2012

26. K. Song, J. Ren, Z. Zhai, X. Liu, M. Deng, Fengzhu Sun, Alignment-free sequence comparison based on next generation sequencing reads: extended abstract, in B. Chor (Ed.): RECOMB 2012, LNBI, 7262: 272-285, 2012

27. Bai Jiang, K. Song, J. Ren, M. Deng, Fengzhu Sun, Xuegong Zhang, Comparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012

Statistical Genetics

28. L.C. Xia, D. Ai, J. Cram, J.A. Fuhrman, Fengzhu Sun, Efficient statistical significance approximation for local association analyis of high-throughput time series data, Bioinformatics, online publication Nov. 23, 2012

29. J. Zhang, Z. Wu, C. Gao, Michael Q. Zhang, High-order interactions in rheumatoid arthritis detected by Bayesian method using genome-wide association studies data, American Medical Journal, 3(1): 56-66, 2012


2011 Selected Publications

Next-Generation Sequencing

1. Zhengpeng Wu, Xi Wang, Xuegong Zhang, Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq, Bioinformatics, 27(4): 502-508, 2011

2. Likun Wang, Xiaowo Wang, Xi Wang, Yanchun Liang, Xuegong Zhang, Observations on novel splice junctions from RNA sequencing data, Biochemical and Biophysical Research Communications, 409: 299-303, 2011

3. Xi Wang, Xuegong Zhang, Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite, BMC Systems Biology, 5(Suppl 2): S3, 2011

4. Chao Ye, Linxi Liu, Xi Wang, Xuegong Zhang, Observations on potential novel transcripts from RNA-Seq data, Front. Electr. Electron. Eng. China, 6(2): 275-282, 2011

5. Suying Bao, Rui Jiang, WingKeung Kwan, BinBin Wang, Xu Ma, You-Qiang Song, Evaluation of next-generation sequencing software in mapping and assembly, Journal of Human Genetics, 56:406-414, 2011

6. Jianxing Feng, Wei Li, Tao Jiang, Inference of isoforms from short sequence reads, Journal of Computational Biology, 18(3): 305-321, 2011

Gene Expression and Regulation Analysis

7. Yang Chen, Jin Gu, Dan Li, Shao Li, Time-course network analysis reveals TNF-alpha can promote G1/S transition of cell cycle in vascular endothelial cells, Bioinformatics, 28(1):1-4, 2012

8. Chao Ye, Ying Liu, Xuegong Zhang, Observations on shifted cumulative regulation, Genome Biology, 12: 404, 2011

Bionetworks, Systems Biology and Systems Biomedicine

9. Shao Li, Bo Zhang, Ningbo Zhang. Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Systems Biology, 5(S1): S10, 2011

10. Yao X, Hao H, Li Y, Li S. Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network. BMC Systems Biology 5:79:1-11, 2011

11. 李梢,网络靶标:中药方剂网络药理学研究的一个切入点,《中国中药杂志》,36:2017-2020, 2011

12. Le Lu, Yanda Li, Shao Li. Computational identification of potential microRNA network biomarkers for the progression stages of gastric cancer. International Journal of Data Mining and Bioinformatics, 5:519-531, 2011

13. Rui Jiang, Mingxin Gan, Peng He, Constructing a gene semantic similarity network for the prioritization of candidate genes, BMC Systems Biology, 5(Suppl 2): S2, 2011

14. Yong Chen, Tao Jiang, Rui Jiang, Uncover disease genes by maximizing information flow in the phenome-interactome network, Bioinformatics, 27: i167-i176, 2011

15. Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang, DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases, BMC Systems Biology, 5:55, 2011

16. Wangshu Zhang, Fengzhu Sun, Rui Jiang, Integrating multiple protein-protein interaction networks to prioritize disease genes: A Bayesian regression approach, BMC Bioinformatics, 12(Supp 1):S11, 2011

17. Jianxing Feng, Rui Jiang, Tao Jiang, A max-flow based approach to the identification of protein complexes using protein interaction and microarray data, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 8(3): 621-634, 2011

18. Jiaxin Wu, Mingxin Gan, Wangshu Zhang, Rui Jiang, Prediction of disease-associated single amino acid polymorphisms based on physiochemical features, International Journal of Bioscience, Biochemistry and Bioinformatics, 1(2):102-108, 2011

19. Jiaxin Wu, Mingxin Gan, Wangshu Zhang, Rui Jiang, Extraction of sequence conservation features for the prioritization of candidate single amino acid polymorphisms, International Journal of Information Engineering and Electronic Business, 3(2):1-10, 2011

20. Rui Jiang, Jiaxin Wu, Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs, in Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine workshops, 262-267, 2011

Metagenomics

21. Xiaolin Hao, Rui Jiang, Ting Chen, Clustering 16S rRNA for OTU prediction: A method of unsupervised Bayesian clustering, Bioinformatics, 27: 611-618, 2011

22. Qin Chang, Yihui Luan, Fengzhu Sun, Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny, BMC Bioinformatics, 12: 118, 2011

Sequence Analysis

23. Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman, Sequence alignment as hypothesis testing, Journal of Computational Biology, 18(5): 677-691, 2011

24. Xuemei Liu, Lin Wan, Jing Li, Gesine Reinertc, Michael S. Waterman, Fengzhu Sun, New powerful statistics for alignment-free sequence comparison under a pattern transfer model, Journal of Theoretical Biology, 284(1): 106-116, 2011

Statistical Genetics

25. N. Kato et al, Meta-analysis of genome-wide association studies identifies five novel variants associated with blood pressure in east Asians, Nature Genetics, 43(6): 531-538, 2011

26. Weichen Wang & Xuegong Zhang, Network-based group variable selection for detecting expression quantitative trait loci (eQTL), BMC Bioinformatics, 12: 269, 2011

27. 周雪崖,张学工,基于拷贝数变异的遗传关联研究,《科学通报》, 56(6): 370-382, 2011

Epigenetics, Regulation and Beyond

28. Lily Yan Wang, Panwen Wang, Mulin Jun Li, Jing Qin, Xiaowo Wang, Michael Q. Zhang and Junwen Wang, EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans, Epigenetics, 6:12: 1505-1512, 2011

29. Zhirui Hu, Minping Qian, Michael Q. Zhang, Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming, BMC Systems Biology, 5(Suppl 2): S8, 2011

30. Yuchen Chien, Claudio Scuoppo, Xiaowo Wang, Xueping Fang, Brian Balgley, Jessica E. Bolden, Prem Premsriut, Weijun Luo, Agustin Chicas, Cheng S. Lee, Scott C. Kogan & Scott W. Lowe, Control of the senescence-associated secretory phenotype by NF-kB promotes senescence and enhances chemosensitivity, Genes & Development, 25:2125-2136, 2011

 


2010 Selected Publications

Next-Generation Sequencing

1. Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26(1):136-138, 2010

2. 王曦、汪小我、王立坤、冯智星、张学工, 新一代高通量RNA测序数据的处理与分析,《生物化学与生物物理进展》,37(8): 834-846, 2010

3. Xi Wang, Zhengpeng Wu, Xuegong Zhang, Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq, Journal of Bioinformatics and Computational Biology, 8(Suppl.1): 177-192, 2010

4. Jianxing Feng, Wei Li and Tao Jiang, Inference of isoforms from short sequence reads, RECOME’2010, 138-157, 2010

5. Zhengpeng Wu, Xi Wang, Xuegong Zhang, Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq, Bioinformatics, Advance Access on Dec. 17, 2010

6. David C. Schwartz & Michael S. Waterman, New generations: sequencing machines and their computational challenges, Journal of Computer Science and Technology, 25(1): 3-9, 2010

Gene Expression and Regulation Analysis

7. Yunfei Pei, Zhimin Wang, Fei Fei, Zhimin Shao, Wei Huang, Xuegong Zhang, Bioinformatics study indicates possible microRNA-regulated pathways in the differentiation of breast cancer, Chinese Science Bulletin, 50(10): 927-933, 2010
8. Tingting Li, Xueya Zhou, Xiaowo Wang, Dahai Zhu, Yong Zhang, Identification and characterization of human snoRNA core promoters, Genomics, 96(1): 50-56, 2010

9. Tingting Li, Bingbing Wan, Jian Huang, Xuegong Zhang, Comparison of gene expression in hepatocellular carcinoma, liver development and liver regeneration, Molecular Genetics and Genomics, 283: 485-492, 2010

10. The MAQC Consortium, The MAQC-II project: a comprehensive study of common practices for the development and validation of microarray-based predictive models, Nature Biotechnology , 28(8): 827-841, 2010

11. Bangpeng Yao, Shao Li, ANMM4CBR: a case-based reasoning method for gene expression data classification, Algorithms for Molecular Biology, 5(14): 1-11, 2010

Bionetworks and Systems Biology

12. Jin Gu, Yang Chen, Shao Li, Yanda Li, Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis, BMC Systems Biology, 4(47):1-18, 2010

13. Shiwen Zhao, Shao Li, Network-based relating pharmacological and genomic spaces for drug target identification, PLoS ONE, 5(7):e11764, 2010

14. Yezhou Huang, Shao Li, Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network, BMC Bioinformatics, 11(S1): S32, 2010

15. Lisha Li, Ningbo Zhang, Shao Li, Ranking effects of candidate drugs on biological process by integrating network analysis and Gene Ontology, Chinese Science Bulletin, 55(26): 2974-2980, 2010

16. Han Yan, Bo Zhang, Shao Li, Qianchuan Zhao, A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway, BMC Systems Biology, 4(50): 1-12, 2010

17. Ting Zhang, Xuegong Zhang, Zhirong Sun, Identifying changed protein-protein interactions in biological processes by gene coexpression analysis, Chinese Science Bulletin, 55(14): 1396-1402, 2010

18. Wenhui Wang, Wangshu Zhang, Rui Jiang*, Yihui Luan, Prioritisation of associations between protein domains and complex diseases using domain–domain interaction networks, IET Systems Biology, 4(3):212-222, 2010

19. Wangshu Zhang, Yong Chen, Rui Jiang, Comparative study of network-based prioritizations of human protein domains associated with complex diseases, Frontiers in Electronic Engineering in China, 5(2): 107-118, 2010

20. Tingting Li, Pufeng Du, Nanfang Xu, Identifying kinase-specific protein phosphorylation sites by integrating heterogeneous information from various sources, PLoS ONE, 5(11): e15411, 2010

Systems Biomedicine and Traditional Chinese Medicine

21. Shao Li, Bo Zhang, Duo Jiang, Yingying Wei, Ningbo Zhang, Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae, BMC Bioinformatics, 11(S11): S6, 2010

22. Tao Ma, Conge Tan, Hui Zhang, Miqu Wang, Weijun Ding, Shao Li, Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network, Molecular BioSystems, 6: 613-619, 2010

23. Shao Li, Aiping Lu, YongyanWang, Symptomatic comparison in efficacy on patients with benign prostatic hyperplasia treated with two therapeutic approaches, Complementary Therapies in Medicine, 18(1): 21-27, 2010

Sequence Analysis

24. Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman, Alignment-free sequence comparison (II): theoretical power of comparison statistics, Journal of Computational Biology, 17(11); 1467-1490, 2010

25. Zhiyuan Zhai, Shih-Yen Ku, Yihui Luan, Michael S. Waterman, Fengzhu Sun, The power of detecting enriched patterns: an HMM approach, Journal of Computational Biology, 17(4): 581-582, 2010

26. Xiaolin Hao,, Rui Jiang and Ting Chen, Clustering 16S rRNA for OUT prediction: a method of unsupervised Bayesian clustering, Bioinformatics, Advance Access on Jan 13, 2011

27. Tao Jiang, Some algorithmic challenges in genome-wide ortholog assignment, Journal of Computer Science and Technology, 25(1): 42-52, 2010

Bioinformatics Applications in Disease Studies

28. Agustin Chicas, Xiaowo Wang, Chaolin Zhang, Mila McCurrach, Zhen Zhao, Ozlem Mert, Ross Dickins, Masashi Narita, Michael Zhang, Scott Lowe, Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence, Cancer Cell, 17(4): 376-387, 2010

29. San Ming Wang & Michael Q. Zhang, Transcriptome study for early hematopoiesis – achievement, challenge and new opportunity, Journal of Cellular Physiology, 223: 549-552, 2010


2009 Selected Publications

Gene Expression, Splicing and Transcription Regulation

1. Ying Liu, Bo Jiang, Xuegong Zhang. Gene set analysis identifies master transcription factors in developmental courses, Genomics 2009;94:1-10 (cover story)
2. Tingting Li, Jian Huang, Ying Jiang, Yan Zeng, Fuchu He, Michael Q. Zhang, Zeguang Han, Xuegong Zhang. Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development, Genomics 2009;93:235-242

3. Xiaowo Wang, Zhenyu Xuan, Xiaoyue Zhao, Yanda Li, Michael Q. Zhang, High-resolution human core-promoter prediction with CoreBoost_HM. Genome Research 2009;19(2):266-75

MicroRNA and RNA-editing

4. R. Mitra, S. Bandyopadhyay, U. Maulik, M. Q. Zhang, SFSSClass: an integrated approach for miRNA based tumor classification, BMC Bioinformatics 2009, 10 (Suppl 1)

5. Pufeng Du, Shengjiao Cao, Yanda Li. SubChlo: Predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm. Journal of Theoretical Biology 2009;261(2):330-335

6. Pufeng Du, Liyan Jia, Yanda Li. CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics 2009;10:135

7. Yunfei Pei, Xi Wang, Xuegong Zhang, Predicting the fate of microRNA target genes based on sequence features, Journal of Theoretical Biology, 261: 17-22, 2009

8. Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 2009; In press

9. Yunfei Pei, Xuegong Zhang. MicroRNA-regulated pathways in the differentiation of histological grades of breast cancer. Chinese Science Bulletin (In Press)

10. Pufeng Du, Yanda Li. Computational analysis of RNA editing: seeking tiny discrepancies between transcriptome and genome. Frontiers of Electrical and Electronic Engineering in China 2009;4(3): 251-258

11. Pufeng Du, Yang Chen, Yanda Li. Computational evidence of A-to-I RNA editing in nucleus transcriptome of Arabidopsis thaliana. Frontiers of Electrical and Electronic Engineering in China 2009;4(4):349-361

Genome-Wide Association Studies

12. Li Zhu, Wanwan Tang, Guisen Li, Jicheng Lv, Jiaxiang Ding, Lei Yu, Minghui Zhao, Yanda Li, Xuegong Zhang, Yan Shen, Hong Zhang, Haiyan Wang. Interaction between variants of two glycosyltransferase genes in IgA nephropathy. Kidney International 2009;76:190-198

13. Wanwan Tang, Xuebing Wu, Rui Jiang, Yanda Li. Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy. PLoS Genet 2009, 5(5):e1000464

14. Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu. A random forest approach to the detection of epistatic interactions in case-control studies, BMC Bioinformatics 2009;10 (Suppl 1):S65

15. Yulong Zhang and Liang Ji. Main-effects model is a special kind of additive model in the presence of linkage disequilibrium. Human Heredity 2009; 67: 13-25

16. Tao Peng, Pufeng Du, Yanda Li. PBEAM: A parallel implementation of BEAM for genome-wide inference of epistatic interactions. Bioinformation 2009; 3(8): 349-351

Systems Biology Study of Complex Diseases and Traditional Chinese Medicine

17. Li Wang, Zhidong Tu, Fengzhu Sun. A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. BMC Genomics 2009;10:220

18. Shao Li. Network systems underlying traditional Chinese medicine syndrome and herb formula. Current Bioinformatics 2009;4(3):188-196

19. Yezhou Huang, Shao Li. Detection of characteristic sub-pathway network for angiogenesis based on the comprehensive pathway network. BMC Bioinformatics 2010;11:S32

20. Xuebing Wu, Qifang Liu, Rui Jiang. Align human interactome with phenome to identify causative genes and networks underlying disease families, Bioinformatics 2009;25:98-104

21. Bangpeng Yao, Shao Li. ANMM4CBR: a case-based reasoning method for gene expression data classification. Algorithms for Molecular Biology 2010,5:14

22. Lisha Li, Ningbo Zhang, Shao Li. Ranking effects of candidate drugs on biological process by integrating network analysis and Gene Ontology. Chinese Science Bulletin (In Press)

23. Shao Li, Aiping Lu, Yongyan Wang. Symptomatic comparison in efficacy on patients with benign prostatic hyperplasia treated with two therapeutic approaches. Complementary Therapies in Medicine (In Press)

24. Tao Ma, Conge Tan, Hui Zhang, Miqu Wang, Weijun Ding, Shao Li. Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network. Molecular BioSystems (In Press)

25. Le Lu, Yanda Li, Shao Li. Computational identification of potential microRNA network biomarkers for the progression stages of gastric cancer. International Journal of Data Mining and Bioinformatics (In Press)

26. Rui Jiang, Ting Chen, Fengzhu Sun. Bayesian models and Gibbs sampling strategies for local graph alignment and motif finding in stochastic networks, Communications in Systems and Information (special issue for Michael Waterman’s 67th birthday) (In Press)

27. Jianxing Feng, Rui Jiang, Tao Jiang. A max-flow based approach to the identification of protein complexes using protein interaction and microarray data, IEEE Transactions on Computational Biology and Bioinformatics (In Press)

28. 李梢.中医证候生物分子网络标志的构想与研究.中医杂志2009;50(9):773-776

29. 李梢,张宁波,李志红,丁皓,叶永安.慢性乙型肝炎患者肝胆湿热证和肝郁脾虚证的决策树诊断模型初探.中国中西医结合杂志 2009

30. 段天璇,马长华,王文全,阎永红,魏胜利,李梢. HPLC-MS法鉴定甘草的指纹图谱.中国药师.2009;12(4): 414-417

Computational Epigenetics and Post-translational Modification

31. Shicai Fan, Xuegong Zhang. CpG island methylation pattern in different human tissues and its correlation with gene expression. Biochem Biophys Res Commun 2009;383:421-425
32. 凡时财,张学工.DNA甲基化的生物信息学研究进展.生物化学与生物物理进展.2009; 36(2):143-150

General

33. Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang, Introduction: the seventh Asia Pacific Bioinformatics Conference (APBC2009), BMC Bioinformatics 2009, 10(Suppl 1): S1
34. Yunfei Pei, Ting Zhang, Victor Renault, Xuegong Zhang. An overview of hepatocellular carcinoma study by omics-based methods. Acta Biochimica et Biophysica Sinica 2009; 41(1): 1-15


2008 Selected Publications
Gene Expression, Splicing and Transcription Regulation

1. Tao Peng, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang, Yanda Li. Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse. BMC Genomics, 9(1):191, 2008

2. Bi J, Peng T, Li Y. Evidence for the association of multi-exon skipping events with tumors. Frontiers of Electrical and Electronic Engineering in China, 3(3): 260-266, 2008

3. 李婷婷,蒋博,汪小我,张学工. 转录因子结合位点的计算分析方法. 《生物物理学报》, 24(5): 334-346, 2008

4. Tingting Li, Jian Huang, Ying Jiang, Yan Zeng, Fuchu He, Michael Q. Zhang, Zeguang Han, Xuegong Zhang. Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics, 93: 235-242, 2009

5. Xiaowo Wang, Zhengyu Xuan, Xiaoyue Zhao, Yanda Li and Michael Q.Zhang. High-resolution human core-promoter prediction with CoreBoost_HM,. Genome Research, 19: 266-275, 2009

MicroRNA and RNA-editing

6. Xiaowo Wang, Xuegong Zhang, Yanda Li. Complicated evolutionary patterns of miRNAs in vertebrates. Science China Ser C-Life Sci., 51 (6): 552-559, 2008

7. Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li. Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics, 24(2):165-171, 2008

8. Pufeng Du and Yanda Li. Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information. J Theor Biol, 253, 579-586, 2008

9. Pufeng Du, Yanda Li. Computational analysis of RNA editing: seeking for tiny discrepancies between the transcriptome and genome. Front Electr Electron Eng China 2008

10. 凡时财,张学工. DNA甲基化的生物信息学研究进展. 《生物物理与生物化学进展》, 36(2): 143-150, 2009

Genomics and Systems Biology Study of Diseases

11. Xuebing Wu, Rui Jiang, Michael Q. Zhang, Shao Li. Network-based global inference of human disease genes. Molecular Systems Biology, 4:189, 2008

12. Xuesong Lu, Xin Lu, Zhigang C. Wang, J. Dirk Iglehart, Xuegong Zhang and Andrea L. Richardson. Predicting features of breast cancer with gene expression patterns. Breast Cancer Research and Treatment, 108(2): 191-201, 2008

13. Jing Zhang, Tao Ma, Yanda Li, Shao Li. Building multilayer network for drug-NEI-disease. Bioinformatics, 24: 2409-2411, 2008

14. Yunfei Pei, Ting Zhang, Victor Renault, Xuegong Zhang. An overview of hepatocellular carcinoma study by omics-based methods. Acta Biochimica et Biophysica Sinica, 41(1): 1-15, 2009

15. Xuebing Wu, Qifang Liu, Rui Jiang. Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinformatics, 25(1):98-104, 2009

16. Li S. Network systems underlying traditional Chinese medicine syndrome and herb formula. Current Bioinformatics, A(2), 2009

17. Min Wu, Changhua Ma, Ying Wu, Shao Li. Simultaneous LC analysis of five bioactive alkaloids in an anti-angiogenesis herbal formula. Chromatographic, 68:579-585, 2008

18. Guo-lian Kang, Shao Li, Ji-feng Zhang. Entropy-based model for interpreting life systems in traditional Chinese medicine. Evidence-based Complementary and Alternative Medicine, 5(3):273-279, 2008

19. 李梢. 基于生物网络的中医药系统生物信息学研究. 《中药药理与临床研究进展第七册》, 人民卫生出版社,2009

20. Yulong Zhang and Liang Ji. Main-effects model is a special kind of additive model in the presence of linkage disequilibrium. Human Heredity, 67: 13-25, 2009

21. Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu. A random forest approach to the detection of epistatic interactions in case-control studies. BMC Bioinformatics, 10(Suppl 1):S65, 2009

Computational Epigenetics and Post-translational Modification

22. Shicai Fan, Michael Q. Zhang, Xuegong Zhang. Histone methylation marks play important roles in predicting the methylation status of CpG islands. BBRC, 374: 559-564, 2008

23. Tingting Li, Fei Li, Xuegong Zhang. Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach. Proteins: Structure, Function, and Bioinformatics, 70: 404-414, 2008

Machine Learning and Statistics

24. Bo Jiang, Xuegong Zhang, Tianxi Cai. Estimating the confidence interval for prediction errors of support vector machine classifiers. Journal of Machine Learning Research, 9(March): 521-540, 2008

General

25. Michael Q. ZHang, Michael S. Waterman, Xuegong Zhang. The seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinformatics, 10(Suppl 1): S1, 2009