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Kashyap, N., Pham, B., Xie, Z., & Bleris, L. (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular bioSystems. doi:10.1039/c3mb70043g

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang, MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. In press.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774.

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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 (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.
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Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

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

Dingming Wu, Jin Gu, Michael Zhang. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

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

Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, accepted, 2013.

Li R, Ma T, Gu J, Liang X, Li S. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013;3:1543.

Zhang B, Wang X, Li S. An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based.

Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 2013:278405.

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Rajagopal N, Ernst J, Ray R, Wu J, Zhang MQ, Kellis M, Ren B (2014) Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers and Gene Bodies. G3, 4:2051-55.

Lu Y, Zhou X, Jin Z, Cheng J, Shen W, Ji F, Liu L, Zhang X, Zhang M, Cao Y, Han D, Choy K, Yuan H. (2014) Resolving the Genetic Heterogeneity of Prelingual Hearing Loss within One Family: Performance Comparison and Application of Two Targeted Next Generation Sequencing Approaches. JHG, 59:599-607.

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Li L, Tang J, Zhang B, Yang W, Liugao M, Wang R, Tan Y, Fan J, Chang Y, Fu J, Jiang F, Chen C, Yang Y, Gu J, Wu D, Guo L, Cao D, Li H, Cao G, Wu M, Zhang MQ, Chen L, Wang H (2014) Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut 64:156-67.

He C, Wang X*, Zhang MQ* (2014) Nucleosome eviction and multiple co-factor binding predict estrogen receoptor alpha associated long-range interactions. NAR, 42:6935-44.

Li W, Wu J, Kim S-Y, Zhao M, Zhang MQ, Meistrich ML, Mills AA (2014) Chd5 orchestrates chromatin remodeling during sperm development. Nat. Comm. 5:3812.

Xie P, Liu Y, Li Y, Zhang MQ*, Wang X* (2014) MIROR: a method for cell-type specific microRNA occupancy rate prediction. Mol. BioSyst. 10:1377-84.

Li GP, Li M, Zhang YW, Wang D, Li R, Guimera R, Gao J*, Zhang MQ* (2014) ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks. PLoS ONE, 9:e94608.

16. Weyn-Vanhentenryck S, Sun S, Yan Q, Mele A, Farny N, Silver Z, Zhang MQ, Krainer AR, Darnell RB, Zhang C (2014) HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Reports, S2211-1247(14)00084-9. PMID:24613350.

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

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

YingXue Li, XueNing Liu, XiaoWo Wang, XueGong Zhang*. (2014) Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 57(1): 52-58.

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

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. (2014) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic Acids Research, 42(2): 1042-1064.

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

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. (2014) 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.

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. (2014) 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.

Chao Ye, Xuegong Zhang. (2014) A simulation study on gene expression regulation via stochastic model, Proceedings of the 33rd Chinese Control Conference, pp. 6885-6888, July 28-30, Nanjing, China.

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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. doi:10.1021/sb300093y

Kashyap, N., Pham, B., Xie, Z., & Bleris, L. (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular bioSystems. doi:10.1039/c3mb70043g

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang, MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. In press.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774.

Jiang R, Zhang X, Zhang MQ (2013) Basics of Bioinformatics: Lecture Notes of Graduate Summer School on Bioinformatics of China. Book, ISBN-10:3642389503, ISBN-13: 978-3642389504. Springer 2013 edition.

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. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR, [Epub ahead of print], PMID:24150943.

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 (2013) CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non-Small-Cell Lung Cancer. J Thorac Oncol. 8:1378-88. PMID:24077454.

Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 2013 Sep 5;8(9):e74275. PMID:24040221.

Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. (2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39:286-97. PMID:23924514.

Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. Mol. Cell. Proteomics, [PubMed – in process] PMID:23924514.

Zhou D, Wu D, Li Z, Qian M, Zhang MQ (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol. 2:2095-4689. DOI: 10.1007/s40484-013-0014-2.

Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tiam S, Hawkins DR, Leung D, Yang H, Wang T, Swanson SA, Zhang J, Zhu Y, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Eckert JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 153:1134-48. PMID:23664764.

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 (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.
Ma X, Wang YW, Zhang MQ, Gazdar AF (2013) DNA methylation data analysis and its application to cancer research. Epigenomics. 5:301-16. PMID:23750645.

Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

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

Dingming Wu, Jin Gu, Michael Zhang. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

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

Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, accepted, 2013.

Li R, Ma T, Gu J, Liang X, Li S. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013;3:1543.

Zhang B, Wang X, Li S. An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based.

Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 2013:278405.

Freeberg MA, Han T,Moresco JJ, Kong A, Yang YC2, Lu ZJ2, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology.

Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology.

Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180–2196.

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. doi:10.1021/sb300093y

Kashyap, N., Pham, B., Xie, Z., & Bleris, L. (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular bioSystems. doi:10.1039/c3mb70043g

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang, MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. In press.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774.

Jiang R, Zhang X, Zhang MQ (2013) Basics of Bioinformatics: Lecture Notes of Graduate Summer School on Bioinformatics of China. Book, ISBN-10:3642389503, ISBN-13: 978-3642389504. Springer 2013 edition.

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. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR, [Epub ahead of print], PMID:24150943.

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 (2013) CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non-Small-Cell Lung Cancer. J Thorac Oncol. 8:1378-88. PMID:24077454.

Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 2013 Sep 5;8(9):e74275. PMID:24040221.

Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. (2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39:286-97. PMID:23924514.

Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. Mol. Cell. Proteomics, [PubMed – in process] PMID:23924514.

Zhou D, Wu D, Li Z, Qian M, Zhang MQ (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol. 2:2095-4689. DOI: 10.1007/s40484-013-0014-2.

Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tiam S, Hawkins DR, Leung D, Yang H, Wang T, Swanson SA, Zhang J, Zhu Y, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Eckert JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 153:1134-48. PMID:23664764.

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 (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.
Ma X, Wang YW, Zhang MQ, Gazdar AF (2013) DNA methylation data analysis and its application to cancer research. Epigenomics. 5:301-16. PMID:23750645.

Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

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

Dingming Wu, Jin Gu, Michael Zhang. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

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

Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, accepted, 2013.

Li R, Ma T, Gu J, Liang X, Li S. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013;3:1543.

Zhang B, Wang X, Li S. An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based.

Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 2013:278405.

Freeberg MA, Han T,Moresco JJ, Kong A, Yang YC2, Lu ZJ2, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology.

Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology.

Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180–2196.

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. doi:10.1021/sb300093y

Kashyap, N., Pham, B., Xie, Z., & Bleris, L. (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular bioSystems. doi:10.1039/c3mb70043g

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang, MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. In press.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774.

Jiang R, Zhang X, Zhang MQ (2013) Basics of Bioinformatics: Lecture Notes of Graduate Summer School on Bioinformatics of China. Book, ISBN-10:3642389503, ISBN-13: 978-3642389504. Springer 2013 edition.

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. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR, [Epub ahead of print], PMID:24150943.

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 (2013) CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non-Small-Cell Lung Cancer. J Thorac Oncol. 8:1378-88. PMID:24077454.

Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 2013 Sep 5;8(9):e74275. PMID:24040221.

Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. (2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39:286-97. PMID:23924514.

Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. Mol. Cell. Proteomics, [PubMed – in process] PMID:23924514.

Zhou D, Wu D, Li Z, Qian M, Zhang MQ (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol. 2:2095-4689. DOI: 10.1007/s40484-013-0014-2.

Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tiam S, Hawkins DR, Leung D, Yang H, Wang T, Swanson SA, Zhang J, Zhu Y, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Eckert JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 153:1134-48. PMID:23664764.

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 (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.
Ma X, Wang YW, Zhang MQ, Gazdar AF (2013) DNA methylation data analysis and its application to cancer research. Epigenomics. 5:301-16. PMID:23750645.

Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

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

Dingming Wu, Jin Gu, Michael Zhang. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

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

Feng Zeng, Rui Jiang, Ting Chen, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, accepted, 2013.

Li R, Ma T, Gu J, Liang X, Li S. Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013;3:1543.

Zhang B, Wang X, Li S. An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based.

Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 2013:278405.

Freeberg MA, Han T,Moresco JJ, Kong A, Yang YC2, Lu ZJ2, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology.

Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology.

Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180–2196.