Center for
Systems Biology

Pitch Image 1 Pitch Image 2 Pitch Image 3

University of Texas at Dallas

Available Online

Correlated evolution of transcription factors and their binding sites

Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok-Ming Yao, Pak Chung Sham, Michael Q. Zhang and Junwen Wang

Bioinformatics (2011) doi:10.1093/bioinformatics/btr503

University of Texas at Dallas



Jason A. Watts, Chaolin Zhang, Andres J. Klein-Szanto, Jay D Kormish, Jian Fu, Michael Q. Zhang, and Kenneth S. Zaret (2011) Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development. PLoS Genetics. doi:10.1371/journal.pgen.1002277

Jing Qin, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, Junwen Wang. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Research. 10.1093/nar/gkr332

Zhang MQ, (2011) Computational Promoter Prediction in a Vertebrate genome. Chap. In Handbook of Statistical Bioinformatics. Springer Handbooks of Computational Statistics. Lu H, Scholkopf B and Zhao H (Eds). In press. ISBN: 978-3-642-16344-9

Valérie M. Renault, Pramod U. Thekkat, Kimmi L. Hoang, Jamie L. White, Colleen A. Brady, Daniela Kenzelmann, Ophelia S. Venturelli, Thomas M. Johnson, Zhenyu Xuan, Evan E. Santo, Michael Q. Zhang, Hannes Vogel, Laura D. Attardi, Anne Brunet (2011) The pro-longevity gene FoxO3 is a direct target of the tumor suppressor p53. Oncogene, In press.

Zhihua Zhang and Michael Q Zhang (2011) Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics. (Accepted).


Mitra R, Bandyopadhyay S, Maulik U, Zhang MQ. (2010) SFSSClass: an integrated approach for miRNA based tumor classification.BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S22.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ , Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications Nature Biotechnology 2010 Sep 19 [ePub ahead of print] PMID: 20852635[PubMed - as supplied by publisher]

Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ , Sedel F, Jourdren L, Coulpier F, Triller A, Spector DL, Bessis A. (2010) A long nuclear -retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J, 29:3082-93

Wang SM, Zhang MQ. (2010) The progress and challenge for transcriptome study on human CD34+ hematopoietic stem-progenitor cells. J Cell Physiology Review. 223:549-552.

Wang SM, Zhang MQ. (2010) Transcriptome study for early hematopoiesis - achievement, challenge and new opportunity. J Cell Physiology ePub ahead of print.

Shin Y. J. and L. G. Bleris. (2010) Linear control theory for gene network modeling. PLoS One, 5(9).

Leisner, M., L. G. Bleris, J. Lohmueller, Z. Xie, Y. Benenson. (2010) Rationally designed logic integration of regulatory signals in mammalian cells. Nature Nanotechnology 5, 666-670.

Xie, Z., S. J. Liu, L. G. Bleris and Y. Benenson. (2010) Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Research 38(8):2692-701.


Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. (2009) Updates to the RMAP short-read mapping softwarei. Bioinformatics 25(21):2841-2.

*Hodges E, *Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB. (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.(*joint corresponding authors) Genome Res 19(9):1593-605.

Zhang MQ, Waterman MS, Zhang X. (2009) The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinformatics 10 Suppl 1:S1.

Li T, Huang J, Jiang Y, Zeng Y, He F, Zhang MQ, Han Z, Zhang X. (2009) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics 93(3):235-42.

Kim Y-C, Wu Q, Chen J, Xuan X, Jung Y-C, Zhang MQ, Rowley J, Wang SM. (2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A 106(20):8278-83.

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung, DC, Xavier RJ. (2009) An integrative genomics approach identifies Hyposix Inducible Factor-1 (HIF-1) target genes that form the core response to hypoxia. Nucleic Acids Res (14):4587-602.

Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T. (2009) Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics 10(1):71.

Wang X, Xuan Z, Zhao X, Li Y and Zhang MQ. (2009) High-resolution Human Core-promoter prediction with CoreBoost_HM. Genome Res 19(2):266-75.

Rosenfeld, JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. (2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 10:143.