Ivan Garcia-Bassets* and Dong Wang. Cistrome plasticity and mechanisms of cistrome reprogramming. Cell Cycle, 2012, 11:3199-3210.

Hairi Li, Hongyan Zhou, Dong Wang,JinsongQiu,Yu Zhou,Xiangqiang Li,Michael G. Rosenfeld,Sheng Ding, and Xiang-Dong Fu. Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery. PNAS, 2012, 109: 4609-4614.

Li R, Guo W, Gu J, Zhang MQ, Wang X. Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics. 2012 Nov;100(5):297-302. doi: 10.1016/j.ygeno.2012.07.009. Epub 2012 Jul 21.

Aksoy O, Chicas A, Zeng T, Zhao Z, McCurrach M, Wang X, Lowe SW. The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence. Genes Dev. 2012 Jul 15;26(14):1546-57. doi: 10.1101/gad.196238.112.

Chicas A, Kapoor A, Wang X, Aksoy O, Evertts AG, Zhang MQ, Garcia BA, Bernstein E, Lowe SW. H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):8971-6. doi: 10.1073/pnas.1119836109. Epub 2012 May 21.

Ratnakumar K, Duarte LF, LeRoy G, Hasson D, Smeets D, Vardabasso C, Bönisch C, Zeng T, Xiang B, Zhang DY, Li H, Wang X, Hake SB, Schermelleh L, Garcia BA, Bernstein E. ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression. Genes Dev. 2012 Mar 1;26(5):433-8. doi: 10.1101/gad.179416.111.

He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ. Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron. 2012 Jan 12;73(1):35-48. doi: 10.1016/j.neuron.2011.11.010. Erratum in: Neuron. 2012 Sep 6;75(5):930. Neuron. 2012 Feb 9;73(3):620.

Miao He, Yu Liu, Xiaowo Wang, Michael Q. Zhang, Gregory Hannon, Z. Josh Huang, Cell-type based analysis of microRNA profiles in the mouse brain, Neuron, 2012, doi:10.1016/j.neuron.2011.11.010

Schmid-Burgk JL, Xie Z, Frank S, Virreira Winter S, Mitschka S, Kolanus W, Murray A, Benenson Y.Rapid hierarchical assembly of medium-size DNA cassettes.(2012)Nucleic Acids Res.Epub ahead of print

Leisner M, Bleris L, Lohmueller J, Xie Z and Benenson Y. MicroRNA circuits for transcriptional logic. (2012) Methods Molecular Biology. 813:169-86.

Ouyang W, Will L, Luo CT, Yin N, Huse M, Kim MV, Peng M, Chan P, Ma Q, Mo Y, Meijer D, Zhao K, Rudensky AY, Atwal G, Zhang MQ*, Li MO* (2012) Novel Foxo1-dependent Transcriptional Programs Control Treg Cell Function. Nature. In press.

Xing H*, Mo Y, Liao W, Zhang MQ* (2012) Genomewide localization of protein-DNA binding and histone modification by BCP with ChIP-seq data. PLoS CB, 8(7): e1002613.

Sleumer MC, Wei G, Wang Y, Chang H, Xu T, Chen R, Zhang MQ (2012) Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BMC Genomics. 13:433. PMID:22401550.

Zhang Z, Ma X, Zhang MQ (2012) Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS ONE, 7:e38112. PMID:22768038.

Chicas A*, Kapoor A*, Wang X*, Evertts AG, Benjam G, Zhang MQ, Bernstein E, Lowe SW, (2012) H3K4 demethylation by Jarid1a and Jarid1b contributes to RB-mediated gene silencing during cellular senescence. PNAS, 109:8971-6. PMID:22615382.

Zhang J, Wu Z, Gao C, Zhang MQ (2012) High-order interactions in Rheumatoid Arthritis detected by Bayesian method using GWAS data. American Medical Journal, 3:56-66.

Zhang C, Zhang MQ (2012) Identification of Splicing Factor Target Genes by High-throughput Sequencing. Chap. 51 in Alternative pre-mRNA Splicing: Theory and Protocols. Eds. Stamm S, Smith C, Luhrmann R. Wiley-Blackwell, Weinheim, Germany.

Zhang MQ (2012), Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data. Chap 12 in Bioinformatics for High Throughput Sequencing, eds. Rodriguez-Ezpeleta N, Hackenberg M, Aransay AM. p209. ISBN978-1-4614-0781-2, Springer.

Zhang J, Zhang Q, Lewis D, Zhang MQ (2012) A Bayesian Method for Disentangling Dependent Structure of Epistatic Interaction. Am. J. Biostat., 2:1-10.

Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ (2012) POSMO: A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucl. Acid. Res. PMID:22228832.

Zhu TF, Adamala K, Zhang, N, Szostak JW. Photochemically driven redox chemistry induces protocell membrane pearling and division. Proc Natl Acad Sci USA,109(25): 9828-9832, (2012).

Xu Tan, Zhi John Lu, Geng Gao, et al., Stephen J. Elledge. Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy. (2012) Proc. Natl. Acad. Sci. U. S. A., doi: 10.1073/pnas.1119873109

Jiang B, Liang X, Chen Y, Ma T, Liu L, Li J, Jiang R, Chen T, Zhang X*, Li S*. Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Scientific Reports 2012;2:936, pages:1-12

Zhao S, Li S*. A co-module approach for elucidating drug-disease associations and revealing their molecular basis. Bioinformatics (published online January 28, 2012, doi:10.1093/bioinformatics/bts057)

Chen Y, Gu J, Li D, Li S*. Time-course network analysis reveals TNF-alpha can promote G1/S transition of cell cycle in vascular endothelial cells. Bioinformatics 2012;28(1):1-4

Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data. Jiang R, Gan M, Wu J. Int J Comput Biol Drug Des. 2012;5(3-4):206-21. doi: 10.1504/IJCBDD.2012.049204. Epub 2012 Sep 24.

Comparison of metagenomic samples using sequence signatures. Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X. BMC Genomics. 2012 Dec 27;13:730. doi: 10.1186/1471-2164-13-730.

Opportunities and methods for studying alternative splicing in cancer with RNA-Seq. Feng H, Qin Z, Zhang X. Cancer Lett. 2012 Nov 27.

Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. Wu C, Zhu J, Zhang X. BMC Bioinformatics. 2012 Jul 28;13:182.