Michael Q. Zhang - Publications

Computational Biology and Bioinformatics Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 
 Director of the Center for Systems Biology University of Texas at Dallas, Richardson, TX, United States 

282 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Wei L, Li S, Zhang P, Hu T, Zhang MQ, Xie Z, Wang X. Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits. Cell Reports. 36: 109573. PMID 34433047 DOI: 10.1016/j.celrep.2021.109573  1
2021 Shi M, You K, Chen T, Hou C, Liang Z, Liu M, Wang J, Wei T, Qin J, Chen Y, Zhang MQ, Li T. Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index. Genome Biology. 22: 229. PMID 34404448 DOI: 10.1186/s13059-021-02456-2  1
2021 Yang Y, Paul A, Bach TN, Huang ZJ, Zhang MQ. Single-cell alternative polyadenylation analysis delineates GABAergic neuron types. Bmc Biology. 19: 144. PMID 34301239 DOI: 10.1186/s12915-021-01076-3  1
2021 Yang M, Fan Y, Wu ZY, Gu J, Feng Z, Zhang Q, Han S, Zhang Z, Li X, Hsueh YC, Ni Y, Li X, Li J, Hu M, Li W, ... ... Zhang MQ, et al. DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations. Ebiomedicine. 69: 103446. PMID 34157485 DOI: 10.1016/j.ebiom.2021.103446  1
2021 Yang L, Chen F, Zhu H, Chen Y, Dong B, Shi M, Wang W, Jiang Q, Zhang L, Huang X, Zhang MQ, Wu H. 3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia. Nature Communications. 12: 3708. PMID 34140506 DOI: 10.1038/s41467-021-24044-5  1
2021 Zhang X, Liu X, Du Z, Wei L, Fang H, Dong Q, Niu J, Li Y, Gao J, Zhang MQ, Xie W, Wang X. The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence. Genome Research. PMID 34140314 DOI: 10.1101/gr.275235.121  1
2021 Xing H, Wu Y, Zhang MQ, Chen Y. Deciphering hierarchical organization of topologically associated domains through change-point testing. Bmc Bioinformatics. 22: 183. PMID 33838653 DOI: 10.1186/s12859-021-04113-8  1
2021 Yang G, Guan W, Cao Z, Guo W, Xiong G, Zhao F, Feng M, Qiu J, Liu Y, Zhang MQ, You L, Zhang T, Zhao Y, Gu J. Integrative genomic analysis of gemcitabine resistance in pancreatic cancer by patient-derived xenograft models. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 33674273 DOI: 10.1158/1078-0432.CCR-19-3975  1
2020 Zhao F, Liu Y, Su X, Lee JE, Song Y, Wang D, Ge K, Gao J, Zhang MQ, Li H. Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1. The Journal of Biological Chemistry. 295: 16877-16887. PMID 33453918 DOI: 10.1074/jbc.RA120.013649  1
2020 Gupta H, Chandratre K, Sinha S, Huang T, Wu X, Cui J, Zhang MQ, Wang SM. Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition. Bmc Genomics. 21: 842. PMID 33256598 DOI: 10.1186/s12864-020-07222-5  1
2020 Yan P, Lu JY, Niu J, Gao J, Zhang MQ, Yin Y, Shen X. LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency. Journal of Molecular Cell Biology. PMID 33049031 DOI: 10.1093/jmcb/mjaa056  1
2020 Zhao F, Liu Y, Su X, Lee JE, Song Y, Wang D, Ge K, Gao J, Zhang MQ, Li H. Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1. The Journal of Biological Chemistry. PMID 32994220 DOI: 10.1074/jbc.RA120.013649  1
2020 Chen Y, Wang Y, Liu X, Xu J, Zhang MQ. Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq. Plos One. 15: e0236666. PMID 32735574 DOI: 10.1371/Journal.Pone.0236666  1
2020 Kong R, Xu X, Liu X, He P, Zhang MQ, Dai Q. 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome. Bmc Bioinformatics. 21: 159. PMID 32349677 DOI: 10.1186/S12859-020-3501-2  1
2020 Ramanand SG, Chen Y, Yuan J, Daescu K, Lambros M, Houlahan KE, Carreira S, Yuan W, Baek G, Sharp A, Paschalis A, Kanchwala M, Gao Y, Aslam A, Safdar N, ... ... Zhang MQ, et al. The landscape of RNA polymerase II associated chromatin interactions in prostate cancer. The Journal of Clinical Investigation. PMID 32343676 DOI: 10.1172/Jci134260  1
2020 Xiong Q, Huang S, Li YH, Lv N, Lv C, Ding Y, Liu WW, Wang LL, Chen Y, Sun L, Zhao Y, Liao SY, Zhang MQ, Zhu BL, Yu L. Single‑cell RNA sequencing of t(8;21) acute myeloid leukemia for risk prediction. Oncology Reports. PMID 32323795 DOI: 10.3892/Or.2020.7507  1
2020 Liu X, Chen Y, Zhang Y, Liu Y, Liu N, Botten GA, Cao H, Orkin SH, Zhang MQ, Xu J. Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biology. 21: 59. PMID 32138752 DOI: 10.1186/S13059-020-01973-W  1
2020 Xing Y, Yang W, Liu G, Cui X, Meng H, Zhao H, Zhao X, Li J, Liu Z, Zhang MQ, Cai L. Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development. Frontiers in Bioengineering and Biotechnology. 8: 35. PMID 32117919 DOI: 10.3389/fbioe.2020.00035  1
2019 Jia C, Wang LY, Yin GG, Zhang MQ. Single-cell stochastic gene expression kinetics with coupled positive-plus-negative feedback. Physical Review. E. 100: 052406. PMID 31869986 DOI: 10.1103/Physreve.100.052406  1
2019 Wang D, Zhu Y, Tang J, Lian Q, Luo G, Wen W, Zhang MQ, Wang H, Chen L, Gu J. Integrative molecular analysis of metastatic hepatocellular carcinoma. Bmc Medical Genomics. 12: 164. PMID 31722693 DOI: 10.1186/S12920-019-0586-4  1
2019 An Z, Liu P, Zheng J, Si C, Li T, Chen Y, Ma T, Zhang MQ, Zhou Q, Ding S. Sox2 and Klf4 as the Functional Core in Pluripotency Induction without Exogenous Oct4. Cell Reports. 29: 1986-2000.e8. PMID 31722212 DOI: 10.1016/J.Celrep.2019.10.026  1
2019 Xiong L, Xu K, Tian K, Shao Y, Tang L, Gao G, Zhang M, Jiang T, Zhang QC. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications. 10: 4576. PMID 31594952 DOI: 10.1038/S41467-019-12630-7  0.56
2019 Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lécuyer E, ... ... Zhang MQ, et al. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell. 178: 107-121.e18. PMID 31251911 DOI: 10.1016/J.Cell.2019.06.001  1
2019 Liu X, Wei L, Dong Q, Liu L, Zhang MQ, Xie Z, Wang X. A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass. Aging. PMID 31219803 DOI: 10.18632/aging.102034  1
2019 Abbas A, He X, Niu J, Zhou B, Zhu G, Ma T, Song J, Gao J, Zhang MQ, Zeng J. Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. Nature Communications. 10: 2049. PMID 31053705 DOI: 10.1038/S41467-019-10005-6  1
2019 Chen L, Wang M, Zhang X, Zhang M, Hu Y, Shi Z, Xi P, Gao J. Group-sparsity-based super-resolution dipole orientation mapping (GS-SDOM). Ieee Transactions On Medical Imaging. PMID 30990177 DOI: 10.1109/Tmi.2019.2910221  1
2019 Xie P, Gao M, Wang C, Zhang J, Noel P, Yang C, Von Hoff D, Han H, Zhang MQ, Lin W. SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles. Nucleic Acids Research. PMID 30799483 DOI: 10.1093/Nar/Gkz116  1
2018 Kim YJ, Xie P, Cao L, Zhang MQ, Kim TH. Global transcriptional activity dynamics reveal functional enhancer RNAs. Genome Research. PMID 30352805 DOI: 10.1101/Gr.233486.117  1
2018 Wang M, Chen M, Zhanghao K, Zhang X, Jing Z, Gao J, Zhang MQ, Jin D, Dai Z, Xi P, Dai Q. Polarization-based super-resolution imaging of surface-enhanced Raman scattering nanoparticles with orientational information. Nanoscale. PMID 30211422 DOI: 10.1039/C8Nr04808H  1
2018 Chen F, Li G, Zhang MQ, Chen Y. HiCDB: a sensitive and robust method for detecting contact domain boundaries. Nucleic Acids Research. PMID 30184171 DOI: 10.1093/Nar/Gky789  1
2018 Wang C, Tan Z, Niu B, Tsang KY, Tai A, Chan WCW, Lo RLK, Leung KKH, Dung NWF, Itoh N, Zhang MQ, Chan D, Cheah KSE. Inhibiting the integrated stress response pathway prevents aberrant chondrocyte differentiation thereby alleviating chondrodysplasia. Elife. 7. PMID 30024379 DOI: 10.7554/Elife.37673  1
2018 Dong Q, Wei L, Zhang MQ, Wang X. Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence. Aging. PMID 29936497 DOI: 10.18632/aging.101485  1
2018 Liu X, Zhang Y, Chen Y, Li M, Shao Z, Zhang MQ, Xu J. CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9. Current Protocols in Molecular Biology. e64. PMID 29927077 DOI: 10.1002/cpmb.64  1
2018 Tan Z, Niu B, Tsang KY, Melhado IG, Ohba S, He X, Huang Y, Wang C, McMahon AP, Jauch R, Chan D, Zhang MQ, Cheah KSE. Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. Plos Genetics. 14: e1007346. PMID 29659575 DOI: 10.1371/Journal.Pgen.1007346  1
2018 Li J, Lee Y, Li Y, Jiang Y, Lu H, Zang W, Zhao X, Liu L, Chen Y, Tan H, Yang Z, Zhang MQ, Mak TW, Ni L, Dong C. Co-inhibitory Molecule B7 Superfamily Member 1 Expressed by Tumor-Infiltrating Myeloid Cells Induces Dysfunction of Anti-tumor CD8T Cells. Immunity. PMID 29625896 DOI: 10.1016/J.Immuni.2018.03.018  1
2018 Ma T, Chen L, Shi M, Niu J, Zhang X, Yang X, Zhanghao K, Wang M, Xi P, Jin D, Zhang M, Gao J. Developing novel methods to image and visualize 3D genomes. Cell Biology and Toxicology. PMID 29577183 DOI: 10.1007/S10565-018-9427-Z  1
2018 Ray P, Torck A, Quigley L, Wangzhou A, Neiman M, Rao C, Lam T, Kim JY, Kim TH, Zhang MQ, Dussor G, Price TJ. Title: Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. Pain. PMID 29561359 DOI: 10.1097/J.Pain.0000000000001217  1
2018 Djekidel MN, Chen Y, Zhang MQ. FIND: difFerential chromatin INteractions Detection using a spatial Poisson process. Genome Research. PMID 29440282 DOI: 10.1101/Gr.212241.116  1
2018 Li Y, He Y, Liang Z, Wang Y, Chen F, Djekidel MN, Li G, Zhang X, Xiang S, Wang Z, Gao J, Zhang MQ, Chen Y. Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation. Cell Death & Disease. 9: 200. PMID 29422670 DOI: 10.1038/S41419-017-0173-6  1
2018 Sarver J, Zhang M, Liu L, Nyenhuis D, Cafiso DS. A Dynamic Protein-Protein Coupling Between the TonB-dependent Transporter FhuA and TonB. Biochemistry. PMID 29338257 DOI: 10.1021/Acs.Biochem.7B01223  1
2018 Wang C, Tan Z, Niu B, Tsang KY, Tai A, Chan WCW, Lo RLK, Leung KKH, Dung NWF, Itoh N, Zhang MQ, Chan D, Cheah KSE. Author response: Inhibiting the integrated stress response pathway prevents aberrant chondrocyte differentiation thereby alleviating chondrodysplasia Elife. DOI: 10.7554/Elife.37673.039  1
2018 Li B, Ge P, Murray KA, Sheth P, Zhang M, Nair G, Sawaya MR, Shin WS, Boyer DR, Ye S, Eisenberg DS, Zhou ZH, Jiang L. Cryo-EM of full-length alpha-synuclein reveals fibril polymorphs with a common structural kernel. Nature Communications. 9: 3609-3609. DOI: 10.2210/Pdb6Cu7/Pdb  0.24
2017 Jia C, Zhang MQ, Qian H. Emergent Lévy behavior in single-cell stochastic gene expression. Physical Review. E. 96: 040402. PMID 29347590 DOI: 10.1103/Physreve.96.040402  1
2017 Meyers K, Cogan DA, Burke J, Arenas R, Balestra M, Brown NF, Cerny MA, Clifford HE, Colombo F, Fader L, Frederick KS, Guo X, Hornberger KR, Kugler S, Lord J, ... Zhang M, et al. Dihydrobenzisoxazole-4-one compounds are novel selective inhibitors of aldosterone synthase (CYP11B2) with in vivo activity. Bioorganic & Medicinal Chemistry Letters. PMID 29254646 DOI: 10.1016/J.Bmcl.2017.12.015  0.12
2017 Jia C, Xie P, Chen M, Zhang MQ. Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level. Scientific Reports. 7: 16037. PMID 29167445 DOI: 10.1038/S41598-017-15464-9  1
2017 Liang Z, Li G, Wang Z, Djekidel MN, Li Y, Qian MP, Zhang MQ, Chen Y. BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions. Nature Communications. 8: 1622. PMID 29158486 DOI: 10.1038/S41467-017-01754-3  1
2017 Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X, Sun L, Zhang MQ, Chen R, Zhao Y. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Research. PMID 29140524 DOI: 10.1093/Nar/Gkx1107  1
2017 Li X, Chen W, Chen Y, Zhang X, Gu J, Zhang MQ. Network embedding-based representation learning for single cell RNA-seq data. Nucleic Acids Research. PMID 28977434 DOI: 10.1093/Nar/Gkx750  1
2017 Chen FX, Xie P, Collings CK, Cao K, Aoi Y, Marshall SA, Rendleman EJ, Ugarenko M, Ozark PA, Zhang A, Shiekhattar R, Smith ER, Zhang MQ, Shilatifard A. PAF1 regulation of promoter-proximal pause release via enhancer activation. Science (New York, N.Y.). PMID 28860207 DOI: 10.1126/Science.Aan3269  1
2017 Liu X, Zhang Y, Chen Y, Li M, Zhou F, Li K, Cao H, Ni M, Liu Y, Gu Z, Dickerson KE, Xie S, Hon GC, Xuan Z, Zhang MQ, et al. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell. 170: 1028-1043.e19. PMID 28841410 DOI: 10.1016/J.Cell.2017.08.003  1
2017 Du Z, Zheng H, Huang B, Ma R, Wu J, Zhang X, He J, Xiang Y, Wang Q, Li Y, Ma J, Zhang X, Zhang K, Wang Y, Zhang MQ, et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature. 547: 232-235. PMID 28703188 DOI: 10.1038/Nature23263  1
2017 Liu Z, Lou H, Xie K, Wang H, Chen N, Aparicio OM, Zhang MQ, Jiang R, Chen T. Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. Nature Communications. 8: 22. PMID 28630425 DOI: 10.1038/S41467-017-00039-Z  1
2017 Li Y, Ning Q, Shi J, Chen Y, Jiang M, Gao L, Huang W, Jing Y, Huang S, Liu A, Hu Z, Liu D, Wang L, Nervi C, Dai Y, ... Zhang MQ, et al. A novel epigenetic AML1-ETO/THAP10/miR-383 mini-circuitry contributes to t(8;21) leukaemogenesis. Embo Molecular Medicine. PMID 28539478 DOI: 10.15252/Emmm.201607180  1
2017 Dong Q, Han H, Liu X, Wei L, Zhang W, Zhao Z, Zhang MQ, Wang X. HCSGD: An integrated database of human cellular senescence genes. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 28529078 DOI: 10.1016/J.Jgg.2017.04.001  1
2017 Pavlovic M, Ray P, Pavlovic K, Kotamarti A, Chen M, Zhang MQ. DIRECTION: A machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. Bioinformatics (Oxford, England). PMID 28505334 DOI: 10.1093/Bioinformatics/Btx316  1
2017 Ni Y, Cao B, Ma T, Niu G, Huo Y, Huang J, Chen D, Liu Y, Yu B, Zhang MQ, Niu H. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes. Elife. 6. PMID 28485713 DOI: 10.7554/Elife.21660  1
2017 Shi M, Gao J, Zhang MQ. Web3DMol: interactive protein structure visualization based on WebGL. Nucleic Acids Research. PMID 28482028 DOI: 10.1093/Nar/Gkx383  1
2017 Guo W, Zhang MQ, Wu H. Erratum: Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Scientific Reports. 7: 39440. PMID 28294112 DOI: 10.1038/srep39440  1
2017 Du J, Zhang M, Guo Z, Chen J, Zhu X, Hu G, Peng P, Zheng Z, Zhang H. Phosphorene quantum dot saturable absorbers for ultrafast fiber lasers. Scientific Reports. 7: 42357. PMID 28211471 DOI: 10.1038/Srep42357  1
2017 Liu H, Zhang M, Han J, Song J, Qiao W. P1.01-072 Epithelial-To-Mesenchymal Transition (EMT) in Lung Cancer: Classic Reproduction Journal of Thoracic Oncology. 12. DOI: 10.1016/J.Jtho.2017.09.726  1
2016 Zhanghao K, Chen L, Yang XS, Wang MY, Jing ZL, Han HB, Zhang MQ, Jin D, Gao JT, Xi P. Super-resolution dipole orientation mapping via polarization demodulation. Light, Science & Applications. 5: e16166. PMID 30167126 DOI: 10.1038/Lsa.2016.166  1
2016 Srivastava S, Potla S, Torck A, Zhang M, Dussor G, Ray P, Price T. (278) A potential role for eIF4A in regulation of nociceptor plasticity: a motif-based genome-wide search for eIF4A targets. The Journal of Pain : Official Journal of the American Pain Society. 17: S45. PMID 28162511 DOI: 10.1016/J.Jpain.2016.01.184  1
2016 Ray P, Torck A, Zhang M, Dussor G, Price T. (277) Searching for the transcriptomic footprint of chronic pain. The Journal of Pain : Official Journal of the American Pain Society. 17: S45. PMID 28162510 DOI: 10.1016/J.Jpain.2016.01.183  1
2016 Torck A, Kim J, Zhang M, Dussor G, Price T, Ray P. (274) RNA-seq based transcriptome profiling of human and mouse dorsal root ganglia provides insight into potential new pain targets. The Journal of Pain : Official Journal of the American Pain Society. 17: S44. PMID 28162506 DOI: 10.1016/J.Jpain.2016.01.180  1
2016 Dai Q, Bao C, Hai Y, Ma S, Zhou T, Wang C, Wang Y, Huo W, Liu X, Yao Y, Xuan Z, Chen M, Zhang MQ. MTGIpick allows robust identification of genomic islands from a single genome. Briefings in Bioinformatics. PMID 28025178 DOI: 10.1093/Bib/Bbw118  1
2016 Li G, Chen Y, Snyder MP, Zhang MQ. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. Nucleic Acids Research. PMID 27625391 DOI: 10.1093/Nar/Gkw809  1
2016 Guo W, Zhang MQ, Wu H. Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Scientific Reports. 6: 32207. PMID 27573482 DOI: 10.1038/Srep32207  1
2016 Ma X, Zhan G, Sleumer MC, Chen S, Liu W, Zhang MQ, Liu X. Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT). Nucleic Acids Research. PMID 27557708 DOI: 10.1093/Nar/Gkw734  1
2016 Zhang Y, Tang J, Yang N, Liu Q, Zhang Q, Zhang Y, Li N, Zhao Y, Li S, Liu S, Zhou H, Li X, Tian M, Deng J, Xie P, ... ... Zhang MQ, et al. FAT10 Is Critical in Influenza A Virus Replication by Inhibiting Type I IFN. Journal of Immunology (Baltimore, Md. : 1950). PMID 27354218 DOI: 10.4049/Jimmunol.1501563  1
2016 Meng Y, Wang L, Chen D, Chang Y, Zhang M, Xu JJ, Zhou R, Zhang QY. LAPTM4B: an oncogene in various solid tumors and its functions. Oncogene. PMID 27212036 DOI: 10.1038/onc.2016.189  1
2016 Chen Y, Wang Y, Xuan Z, Chen M, Zhang MQ. De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. Nucleic Acids Research. PMID 27060148 DOI: 10.1093/Nar/Gkw225  1
2016 Wang J, Chen F, Liu L, Qi C, Wang B, Yan X, Huang C, Hou W, Zhang MQ, Chen Y, Du Y. Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation. Biomaterials. 91: 11-22. PMID 26994875 DOI: 10.1016/J.Biomaterials.2016.03.001  1
2016 Shen X, Kan S, Hu J, Li M, Lu G, Zhang M, Zhang S, Hou Y, Chen Y, Bai Y. EMC6/TMEM93 suppresses glioblastoma proliferation by modulating autophagy. Cell Death & Disease. 7: e2043. PMID 26775697 DOI: 10.1038/cddis.2015.408  1
2016 Ni Y, Cao B, Ma T, Niu G, Huo Y, Huang J, Chen D, Liu Y, Yu B, Zhang MQ, Niu H. Author response: Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes Elife. DOI: 10.7554/Elife.21660.022  1
2016 Sathe A, Chen Y, Yoo H, Zhang MQ. Abstract 773: Analysis of oncogene affected networks in tumorigenesis of lung cancer Cancer Research. 76: 773-773. DOI: 10.1158/1538-7445.Am2016-773  1
2015 Sathe A, Zhang YA, Ma X, Ray P, Cadinu D, Wang YW, Yao X, Liu X, Tang H, Wang Y, Huang Y, Liu C, Gu J, Akerman M, Mo Y, ... ... Zhang MQ, et al. SCT Promoter Methylation is a Highly Discriminative Biomarker for Lung and Many Other Cancers. Ieee Life Sciences Letters. 1: 30-33. PMID 33758771 DOI: 10.1109/lls.2015.2488438  1
2015 Mehta HH, Liu Y, Zhang MQ, Spiro S. Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073. Microbial Genomics. 1: e000031. PMID 28348816 DOI: 10.1099/mgen.0.000031  1
2015 Zhang YA, Ma X, Sathe A, Fujimoto J, Wistuba II, Lam S, Yatabe Y, Wang YW, Stastny V, Gao B, Larsen JE, Girard L, Liu X, Song K, Behrens C, ... ... Zhang MQ, et al. Validation of SCT Methylation As a Hallmark Biomarker for Lung Cancers. Journal of Thoracic Oncology : Official Publication of the International Association For the Study of Lung Cancer. PMID 26725182 DOI: 10.1016/J.Jtho.2015.11.004  1
2015 Djekidel MN, Liang Z, Wang Q, Hu Z, Li G, Chen Y, Zhang MQ. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome Biology. 16: 288. PMID 26694485 DOI: 10.1186/S13059-015-0851-6  1
2015 Wu D, Wang D, Zhang MQ, Gu J. Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification. Bmc Genomics. 16: 1022. PMID 26626453 DOI: 10.1186/S12864-015-2223-8  1
2015 Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, Li Z, Bu D, Sun N, Zhang MQ, Chen R. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Research. PMID 26586799 DOI: 10.1093/Nar/Gkv1252  1
2015 Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park IH, Kim TH. Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Reports. PMID 26549458 DOI: 10.1016/J.Celrep.2015.10.013  1
2015 Zhang H, Zhu C, Zhao Y, Li M, Wu L, Yang X, Wan X, Wang A, Zhang MQ, Sang X, Zhao H. Long non-coding RNA expression profiles of hepatitis Cvirus-related dysplasia and hepatocellular carcinoma. Oncotarget. PMID 26540467 DOI: 10.18632/Oncotarget.6087  1
2015 Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell. 162: 900-10. PMID 26276636 DOI: 10.1016/J.Cell.2015.07.038  1
2015 Gao M, Zhao Z, Lv P, Li Y, Gao J, Zhang M, Zhao B. Quantitative combination of natural anti-oxidants prevents metabolic syndrome by reducing oxidative stress. Redox Biology. 6: 206-217. PMID 26262997 DOI: 10.1016/J.Redox.2015.06.013  1
2015 He C, Zhang MQ, Wang X. MICC: an R package for identifying chromatin interactions from ChIA-PET data. Bioinformatics (Oxford, England). PMID 26231426 DOI: 10.1093/Bioinformatics/Btv445  1
2015 Ehrhardt K, Guinn MT, Quarton T, Zhang MQ, Bleris L. Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting. Biosensors & Bioelectronics. 74: 744-750. PMID 26210472 DOI: 10.1016/J.Bios.2015.07.035  1
2015 Akerman M, Fregoso OI, Das S, Ruse C, Jensen MA, Pappin DJ, Zhang MQ, Krainer AR. Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biology. 16: 119. PMID 26047612 DOI: 10.1186/S13059-015-0682-5  1
2015 Orozco LD, Morselli M, Rubbi L, Guo W, Go J, Shi H, Lopez D, Furlotte NA, Bennett BJ, Farber CR, Ghazalpour A, Zhang MQ, Bahous R, Rozen R, Lusis AJ, et al. Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice. Cell Metabolism. 21: 905-17. PMID 26039453 DOI: 10.1016/J.Cmet.2015.04.025  1
2015 Sun G, Hu Z, Min Z, Yan X, Guan Z, Su H, Fu Y, Ma X, Chen YG, Zhang MQ, Tao Q, Wu W. Small C-terminal Domain Phosphatase 3 Dephosphorylates the Linker Sites of R-Smads to Ensure TGFβ-mediated Germ Layer Induction in Xenopus Embryos. The Journal of Biological Chemistry. PMID 26013826 DOI: 10.1074/Jbc.M115.655605  1
2015 Wang T, Xiao G, Chu Y, Zhang MQ, Corey DR, Xie Y. Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Research. 43: 5263-74. PMID 25958398 DOI: 10.1093/Nar/Gkv439  1
2015 Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang J. ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. Nucleic Acids Research. 43: W264-9. PMID 25916854 DOI: 10.7490/F1000Research.1110240.1  1
2015 Huo W, Adams HM, Zhang MQ, Palmer KL. Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing. Journal of Bacteriology. 197: 1939-51. PMID 25825433 DOI: 10.1128/Jb.00130-15  1
2015 Yuan Y, Liu B, Xie P, Zhang MQ, Li Y, Xie Z, Wang X. Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit. Proceedings of the National Academy of Sciences of the United States of America. 112: 3158-63. PMID 25713348 DOI: 10.1073/Pnas.1413896112  1
2015 Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, ... ... Zhang MQ, et al. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 518: 350-4. PMID 25693566 DOI: 10.1038/Nature14217  1
2015 Hu L, Di C, Kai M, Yang YC, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ. A common set of distinct features that characterize noncoding RNAs across multiple species. Nucleic Acids Research. 43: 104-14. PMID 25505163 DOI: 10.1093/Nar/Gku1316  1
2015 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, ... ... Zhang MQ, et al. Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut. 64: 156-67. PMID 24572141 DOI: 10.1136/Gutjnl-2013-305715  1
2015 Cheah KSE, Au T, Niu B, Chan D, Zhang MQ. The Changing RNAome of the Developing Nucleus Pulposus of the Intervertebral Disc: Implications for Intervertebral Disc Disease Global Spine Journal. 5. DOI: 10.1055/S-0035-1554146  1
2015 Gao M, Zhao Z, Lv P, Li Y, Gao J, Zhang M, Zhao B. Quantitative combination of natural anti-oxidants prevents metabolic syndrome by reducing oxidative stress Redox Biology. 6: 206-217. DOI: 10.1016/j.redox.2015.06.013  1
2014 Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. Murine CD8 T Cell Killing Assay. Bio-Protocol. 4. PMID 29170744 DOI: 10.21769/BioProtoc.1172  1
2014 Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. Murine In vitro Memory T Cell Differentiation. Bio-Protocol. 4. PMID 29104880 DOI: 10.21769/BioProtoc.1171  1
2014 Sephton CF, Tang AA, Kulkarni A, West J, Brooks M, Stubblefield JJ, Liu Y, Zhang MQ, Green CB, Huber KM, Huang EJ, Herz J, Yu G. Activity-dependent FUS dysregulation disrupts synaptic homeostasis. Proceedings of the National Academy of Sciences of the United States of America. 111: E4769-78. PMID 25324524 DOI: 10.1073/Pnas.1406162111  1
2014 Liao W, Ouyang W, Zhang MQ, Li MO. Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes. Genomics Data. 2: 280-281. PMID 25302145 DOI: 10.1016/J.Gdata.2014.08.006  1
2014 Gu J, Chen Y, Huang H, Yin L, Xie Z, Zhang MQ. Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular Biosystems. 10: 3249-54. PMID 25286864 DOI: 10.1039/C4Mb00329B  1
2014 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. 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. PMID 25231367 DOI: 10.1038/Jhg.2014.78  1
2014 Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. Genome-wide map of regulatory interactions in the human genome. Genome Research. 24: 1905-17. PMID 25228660 DOI: 10.1101/Gr.176586.114  1
2014 Cheng J, Zhou X, Lu Y, Chen J, Han B, Zhu Y, Liu L, Choy KW, Han D, Sham PC, Zhang MQ, Zhang X, Yuan H. Exome 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. PMID 25227905 DOI: 10.1111/Ahg.12084  1
2014 Sheng M, Zhong Y, Chen Y, Du J, Ju X, Zhao C, Zhang G, Zhang L, Liu K, Yang N, Xie P, Li D, Zhang MQ, Jiang C. Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Science China. Life Sciences. 57: 959-72. PMID 25218824 DOI: 10.1007/S11427-014-4742-Y  1
2014 Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3 (Bethesda, Md.). 4: 2051-63. PMID 25122670 DOI: 10.1534/G3.114.013565  1
2014 Li W, Wu J, Kim SY, Zhao M, Hearn SA, Zhang MQ, Meistrich ML, Mills AA. Chd5 orchestrates chromatin remodelling during sperm development. Nature Communications. 5: 3812. PMID 24818823 DOI: 10.1038/Ncomms4812  1
2014 Li Y, Ehrhardt K, Zhang MQ, Bleris L. Assembly and validation of versatile transcription activator-like effector libraries. Scientific Reports. 4: 4857. PMID 24798576 DOI: 10.1038/Srep04857  1
2014 Li G, Li M, Zhang Y, Wang D, Li R, Guimerà R, Gao JT, Zhang MQ. ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks. Plos One. 9: e94608. PMID 24788790 DOI: 10.1371/Journal.Pone.0094608  1
2014 He C, Wang X, Zhang MQ. Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions. Nucleic Acids Research. 42: 6935-44. PMID 24782518 DOI: 10.1093/Nar/Gku327  1
2014 Xie P, Liu Y, Li Y, Zhang MQ, Wang X. MIROR: a method for cell-type specific microRNA occupancy rate prediction. Molecular Biosystems. 10: 1377-84. PMID 24668253 DOI: 10.1039/C3Mb70610A  1
2014 Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Reports. 6: 1139-52. PMID 24613350 DOI: 10.1016/J.Celrep.2014.02.005  1
2014 Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ. Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Research. 42: 3009-16. PMID 24343027 DOI: 10.1093/Nar/Gkt1306  1
2014 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 MQ, et al. Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Research. 42: 1052-64. PMID 24150943 DOI: 10.1093/Nar/Gkt932  1
2014 Zhang Y, Ma X, Fujimoto J, Wistuba I, Lam S, Stastny V, Gao B, Larsen J, Liu X, Minna JD, Zhang MQ, Gazdar AF. Abstract 1855: SCT methylation is a potential cancer biomarker for lung cancer Cancer Research. 74: 1855-1855. DOI: 10.1158/1538-7445.Am2014-1855  1
2013 Zhou D, Wu D, Li Z, Qian M, Zhang MQ. Population dynamics of cancer cells with cell state conversions. Quantitative Biology (Beijing, China). 1: 201-208. PMID 26085954 DOI: 10.1007/s40484-013-0014-2  1
2013 Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. Bmc Genomics. 14: 774. PMID 24206606 DOI: 10.1186/1471-2164-14-774  1
2013 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, ... ... Zhang MQ, et al. CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer. Journal of Thoracic Oncology : Official Publication of the International Association For the Study of Lung Cancer. 8: 1378-88. PMID 24077454 DOI: 10.1097/Jto.0B013E3182A46C0C  1
2013 Wu D, Gu J, Zhang MQ. FastDMA: an infinium humanmethylation450 beadchip analyzer. Plos One. 8: e74275. PMID 24040221 DOI: 10.1371/Journal.Pone.0074275  1
2013 Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39: 286-97. PMID 23932570 DOI: 10.1016/J.Immuni.2013.07.013  1
2013 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 & Cellular Proteomics : McP. 12: 3379-87. PMID 23924514 DOI: 10.1074/Mcp.O112.019851  1
2013 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. PMID 23900278 DOI: 10.1038/Ncomms3145  1
2013 Rajaram M, Zhang J, Wang T, Li J, Kuscu C, Qi H, Kato M, Grubor V, Weil RJ, Helland A, Borrenson-Dale AL, Cho KR, Levine DA, Houghton AN, Wolchok JD, ... ... Zhang M, et al. Two Distinct Categories of Focal Deletions in Cancer Genomes. Plos One. 8: e66264. PMID 23805207 DOI: 10.1371/Journal.Pone.0066264  1
2013 Ma X, Wang YW, Zhang MQ, Gazdar AF. DNA methylation data analysis and its application to cancer research. Epigenomics. 5: 301-16. PMID 23750645 DOI: 10.2217/Epi.13.26  1
2013 Wang C, Zhang MQ, Zhang Z. Computational identification of active enhancers in model organisms. Genomics, Proteomics & Bioinformatics. 11: 142-50. PMID 23685394 DOI: 10.1016/J.Gpb.2013.04.002  1
2013 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, ... ... Zhang MQ, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/J.Cell.2013.04.022  1
2013 Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C. OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Research. 41: 5149-63. PMID 23571760 DOI: 10.1093/Nar/Gkt216  1
2013 Zhou D, Wu D, Li Z, Qian M, Zhang MQ. Population dynamics of cancer cells with cell-state conversions between cancer stem cells and non-stem cancer cells F1000research. 4. DOI: 10.7490/F1000Research.1093108.1  1
2013 Hao B, Zhang C, Li Y, Li H, Wei L, Kanehisa M, Lai L, Chen R, Rajewsky N, Zhang MQ, Han J, Jiang R, Zhang X. Advanced topics in bioinformatics and computational biology Basics of Bioinformatics: Lecture Notes of the Graduate Summer School On Bioinformatics of China. 369-395. DOI: 10.1007/978-3-642-38951-1_12  1
2012 Tang MH, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J. Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Frontiers in Oncology. 2: 197. PMID 23293768 DOI: 10.3389/Fonc.2012.00197  1
2012 Xing H, Liao W, Mo Y, Zhang MQ. A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. Journal of Visualized Experiments : Jove. e4273. PMID 23271069 DOI: 10.3791/4273  1
2012 Wen H, Li Y, Malek SN, Kim YC, Xu J, Chen P, Xiao F, Huang X, Zhou X, Xuan Z, Mankala S, Hou G, Rowley JD, Zhang MQ, Wang SM. New fusion transcripts identified in normal karyotype acute myeloid leukemia. Plos One. 7: e51203. PMID 23251452 DOI: 10.1371/Journal.Pone.0051203  1
2012 Ouyang W, Liao W, 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, et al. Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature. 491: 554-9. PMID 23135404 DOI: 10.1038/Nature11581  1
2012 Sleumer MC, Wei G, Wang Y, Chang H, Xu T, Chen R, Zhang MQ. Regulatory elements of Caenorhabditis elegans ribosomal protein genes. Bmc Genomics. 13: 433. PMID 22928635 DOI: 10.1186/1471-2164-13-433  1
2012 Xing H, Mo Y, Liao W, Zhang MQ. Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data. Plos Computational Biology. 8: e1002613. PMID 22844240 DOI: 10.1371/Journal.Pcbi.1002613  1
2012 Li R, Guo W, Gu J, Zhang MQ, Wang X. Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics. 100: 297-302. PMID 22824656 DOI: 10.1016/J.Ygeno.2012.07.009  1
2012 Zhang Z, Ma X, Zhang MQ. Bivalent-like chromatin markers are predictive for transcription start site distribution in human. Plos One. 7: e38112. PMID 22768038 DOI: 10.1371/Journal.Pone.0038112  1
2012 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. Proceedings of the National Academy of Sciences of the United States of America. 109: 8971-6. PMID 22615382 DOI: 10.1073/Pnas.1119836109  1
2012 He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ. Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron. 73: 35-48. PMID 22243745 DOI: 10.1016/J.Neuron.2011.11.010  1
2012 Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ. A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Research. 40: e50. PMID 22228832 DOI: 10.1093/Nar/Gkr1135  1
2012 He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ. Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain Neuron. 75: 930-932. DOI: 10.1016/j.neuron.2012.08.018  1
2011 Hu Z, Qian M, Zhang MQ. Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. Bmc Systems Biology. 5: S8. PMID 22784579 DOI: 10.1186/1752-0509-5-S2-S8  1
2011 Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ. Inferring haplotypes of copy number variations from high-throughput data with uncertainty. G3 (Bethesda, Md.). 1: 35-42. PMID 22384316 DOI: 10.1534/G3.111.000174  1
2011 Rajan P, Dalgliesh C, Carling PJ, Buist T, Zhang C, Grellscheid SN, Armstrong K, Stockley J, Simillion C, Gaughan L, Kalna G, Zhang MQ, Robson CN, Leung HY, Elliott DJ. Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. Plos One. 6: e29088. PMID 22194994 DOI: 10.1371/Journal.Pone.0029088  1
2011 Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R. Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. Plos One. 6: e28503. PMID 22174824 DOI: 10.1371/Journal.Pone.0028503  1
2011 Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 6: 1505-12. PMID 22139581 DOI: 10.4161/Epi.6.12.18176  1
2011 Dai Q, Li L, Liu X, Yao Y, Zhao F, Zhang M. Integrating overlapping structures and background information of words significantly improves biological sequence comparison. Plos One. 6: e26779. PMID 22102867 DOI: 10.1371/Journal.Pone.0026779  1
2011 Watts JA, Zhang C, Klein-Szanto AJ, Kormish JD, Fu J, Zhang MQ, Zaret KS. Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. Plos Genetics. 7: e1002277. PMID 21935353 DOI: 10.1371/Journal.Pgen.1002277  1
2011 Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics (Oxford, England). 27: 3010-6. PMID 21896509 DOI: 10.1093/Bioinformatics/Btr508  1
2011 Yang S, Yalamanchili HK, Li X, Yao KM, Sham PC, Zhang MQ, Wang J. Correlated evolution of transcription factors and their binding sites. Bioinformatics (Oxford, England). 27: 2972-8. PMID 21896508 DOI: 10.1093/Bioinformatics/Btr503  1
2011 Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S. Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Research. 39: 9720-30. PMID 21880592 DOI: 10.1093/Nar/Gkr684  1
2011 Cheng J, Zhu Y, He S, Lu Y, Chen J, Han B, Petrillo M, Wrzeszczynski KO, Yang S, Dai P, Zhai S, Han D, Zhang MQ, Li W, Liu X, et al. Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64. American Journal of Human Genetics. 89: 56-66. PMID 21722859 DOI: 10.1016/J.Ajhg.2011.05.027  1
2011 Renault VM, Thekkat PU, Hoang KL, White JL, Brady CA, Kenzelmann Broz D, Venturelli OS, Johnson TM, Oskoui PR, Xuan Z, Santo EE, Zhang MQ, Vogel H, Attardi LD, Brunet A. The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene. 30: 3207-21. PMID 21423206 DOI: 10.1038/Onc.2011.35  1
2011 Wrzeszczynski KO, Varadan V, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R. Abstract 30: Identification of genomic and epigenetic features of tumor suppressors and oncogenes in ovarian cancer Cancer Research. 71: 30-30. DOI: 10.1158/1538-7445.Am2011-30  1
2011 Tang MHE, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J. A method for finding novel associations between genome-wide copy number and dna methylation patterns Proceedings - Ieee International Workshop On Genomic Signal Processing and Statistics. 78-82.  1
2010 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, ... ... Zhang MQ, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682  1
2010 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. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. The Embo Journal. 29: 3082-93. PMID 20729808 DOI: 10.1038/Emboj.2010.199  1
2010 Chicas A, Wang X, Zhang C, McCurrach M, Zhao Z, Mert O, Dickins RA, Narita M, Zhang M, Lowe SW. Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence. Cancer Cell. 17: 376-87. PMID 20385362 DOI: 10.1016/J.Ccr.2010.01.023  1
2010 Bandyopadhyay S, Mitra R, Maulik U, Zhang MQ. Development of the human cancer microRNA network. Silence. 1: 6. PMID 20226080 DOI: 10.1186/1758-907X-1-6  1
2010 Wang SM, Zhang MQ. Transcriptome study for early hematopoiesis—achievement, challenge and new opportunity Journal of Cellular Physiology. 223: 549-552. PMID 20143329 DOI: 10.1002/Jcp.22065  1
2010 Mitra R, Bandyopadhyay S, Maulik U, Zhang MQ. SFSSClass: an integrated approach for miRNA based tumor classification. Bmc Bioinformatics. 11: S22. PMID 20122194 DOI: 10.1186/1471-2105-11-S1-S22  1
2009 Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. Updates to the RMAP short-read mapping software. Bioinformatics (Oxford, England). 25: 2841-2. PMID 19736251 DOI: 10.1093/Bioinformatics/Btp533  1
2009 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. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research. 19: 1593-605. PMID 19581485 DOI: 10.1101/Gr.095190.109  1
2009 Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ. An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Research. 37: 4587-602. PMID 19491311 DOI: 10.1093/Nar/Gkp425  1
2009 Kim YC, Wu Q, Chen J, Xuan Z, Jung YC, Zhang MQ, Rowley JD, Wang SM. The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 106: 8278-83. PMID 19416867 DOI: 10.1073/Pnas.0903390106  1
2009 Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. Determination of enriched histone modifications in non-genic portions of the human genome. Bmc Genomics. 10: 143. PMID 19335899 DOI: 10.1186/1471-2164-10-143  1
2009 Zhang MQ, Waterman MS, Zhang X. The Seventh Asia Pacific Bioinformatics Conference (APBC2009). Bmc Bioinformatics. 10: S1. PMID 19208108 DOI: 10.1186/1471-2105-10-S1-S1  1
2009 Li T, Huang J, Jiang Y, Zeng Y, He F, Zhang MQ, Han Z, Zhang X. Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics. 93: 235-42. PMID 19015022 DOI: 10.1016/J.Ygeno.2008.10.006  1
2009 Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ. High-resolution human core-promoter prediction with CoreBoost_HM. Genome Research. 19: 266-75. PMID 18997002 DOI: 10.1101/Gr.081638.108  1
2008 Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer AR, Zhang MQ. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes & Development. 22: 2550-63. PMID 18794351 DOI: 10.1101/Gad.1703108  1
2008 Lin H, Zhang Z, Zhang MQ, Ma B, Li M. ZOOM! Zillions of oligos mapped. Bioinformatics (Oxford, England). 24: 2431-7. PMID 18684737 DOI: 10.1093/Bioinformatics/Btn416  0.36
2008 Hsieh MC, Das D, Sambandam N, Zhang MQ, Nahlé Z. Regulation of the PDK4 isozyme by the Rb-E2F1 complex. The Journal of Biological Chemistry. 283: 27410-7. PMID 18667418 DOI: 10.1074/Jbc.M802418200  1
2008 Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. Plos One. 3: e2803. PMID 18665230 DOI: 10.1371/Journal.Pone.0002803  1
2008 Fan S, Zhang MQ, Zhang X. Histone Methylation Marks Play Important Roles in Predicting the Methylation Status of CpG Islands Biochemical and Biophysical Research Communications. 374: 559-564. PMID 18656446 DOI: 10.1016/J.Bbrc.2008.07.077  1
2008 Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics. 40: 897-903. PMID 18552846 DOI: 10.1038/Ng.154  1
2008 Chen G, Li W, Zhang QS, Regulski M, Sinha N, Barditch J, Tully T, Krainer AR, Zhang MQ, Dubnau J. Identification of synaptic targets of Drosophila pumilio. Plos Computational Biology. 4: e1000026. PMID 18463699 DOI: 10.1371/Journal.Pcbi.1000026  1
2008 Wu X, Jiang R, Zhang MQ, Li S. Network-based global inference of human disease genes. Molecular Systems Biology. 4: 189. PMID 18463613 DOI: 10.1038/Msb.2008.27  1
2008 Zhang C, Li WH, Krainer AR, Zhang MQ. RNA landscape of evolution for optimal exon and intron discrimination. Proceedings of the National Academy of Sciences of the United States of America. 105: 5797-802. PMID 18391195 DOI: 10.1073/Pnas.0801692105  1
2008 Nahlé Z, Hsieh M, Pietka T, Coburn CT, Grimaldi PA, Zhang MQ, Das D, Abumrad NA. CD36-dependent regulation of muscle FoxO1 and PDK4 in the PPAR delta/beta-mediated adaptation to metabolic stress. The Journal of Biological Chemistry. 283: 14317-26. PMID 18308721 DOI: 10.1074/Jbc.M706478200  1
2008 Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. Bmc Bioinformatics. 9: 128. PMID 18307793 DOI: 10.1186/1471-2105-9-128  0.56
2008 Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. Scanning the human genome at kilobase resolution. Genome Research. 18: 751-62. PMID 18292219 DOI: 10.1101/Gr.068304.107  1
2008 Zhang H, Li ZH, Zhang MQ, Katz MS, Zhang BX. Heat shock protein 90beta1 is essential for polyunsaturated fatty acid-induced mitochondrial Ca2+ efflux. The Journal of Biological Chemistry. 283: 7580-9. PMID 18178560 DOI: 10.1074/jbc.M707192200  0.44
2008 Eguchi J, Yan QW, Schones DE, Kamal M, Hsu CH, Zhang MQ, Crawford GE, Rosen ED. Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metabolism. 7: 86-94. PMID 18177728 DOI: 10.1016/J.Cmet.2007.11.002  1
2008 Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Research. 18: 46-59. PMID 18042645 DOI: 10.1101/Gr.6654808  1
2008 Wang X, Gu J, Zhang MQ, Li Y. Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics (Oxford, England). 24: 165-71. PMID 18037683 DOI: 10.1093/Bioinformatics/Btm572  1
2008 Maulik U, Mukhopadhyay A, Bandyopadhyay S, Zhang MQ, Zhang X. Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure 2008 Ieee Congress On Evolutionary Computation, Cec 2008. 1536-1543. DOI: 10.1109/CEC.2008.4630996  1
2007 Fan S, Fang F, Zhang X, Zhang MQ. Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. Plos One. 2: e1184. PMID 18030324 DOI: 10.1371/Journal.Pone.0001184  1
2007 Wang X, Bandyopadhyay S, Xuan Z, Zhao X, Zhang MQ, Zhang X. Prediction of transcription start sites based on feature selection using AMOSA. Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference. 6: 183-93. PMID 17951823  1
2007 Zhang MQ. Computational analyses of eukaryotic promoters Bmc Bioinformatics. 8. PMID 17903284 DOI: 10.1186/1471-2105-8-S6-S3  1
2007 Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA, Gleiberman A, Zhang MQ, Enikolopov G. Neural potential of a stem cell population in the hair follicle. Cell Cycle (Georgetown, Tex.). 6: 2161-70. PMID 17873521 DOI: 10.4161/Cc.6.17.4593  1
2007 Zhang C, Hastings ML, Krainer AR, Zhang MQ. Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 15028-33. PMID 17848517 DOI: 10.1073/Pnas.0703773104  1
2007 Zhang C, Krainer AR, Zhang MQ. Evolutionary impact of limited splicing fidelity in mammalian genes. Trends in Genetics : Tig. 23: 484-8. PMID 17719121 DOI: 10.1016/J.Tig.2007.08.001  1
2007 Yang Z, Jiang H, Zhao F, Shankar DB, Sakamoto KM, Zhang MQ, Lin S. A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish. Bmc Developmental Biology. 7: 97. PMID 17708765 DOI: 10.1186/1471-213X-7-97  1
2007 Das D, Zhang MQ. Predictive models of gene regulation: application of regression methods to microarray data. Methods in Molecular Biology (Clifton, N.J.). 377: 95-110. PMID 17634611 DOI: 10.1007/978-1-59745-390-5_5  1
2007 Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 128: 1231-45. PMID 17382889 DOI: 10.1016/J.Cell.2006.12.048  1
2007 Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, Hannon GJ. Critical roles for Dicer in the female germline. Genes & Development. 21: 682-93. PMID 17369401 DOI: 10.1101/Gad.1521307  1
2007 Zhao X, Xuan Z, Zhang MQ. Boosting with stumps for predicting transcription start sites. Genome Biology. 8: R17. PMID 17274821 DOI: 10.1186/Gb-2007-8-2-R17  1
2007 Schones DE, Smith AD, Zhang MQ. Statistical significance of cis-regulatory modules. Bmc Bioinformatics. 8: 19. PMID 17241466 DOI: 10.1186/1471-2105-8-19  1
2007 Smith AD, Sumazin P, Zhang MQ. Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology. 3: 73. PMID 17224917 DOI: 10.1038/Msb4100114  1
2007 Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Research. 35: D137-40. PMID 17202159 DOI: 10.1093/Nar/Gkl1041  0.4
2007 Zhang M. Computational Dissection Of Mammalian Regulation Networks Genome Informatics. 19: 197-197. DOI: 10.11234/Gi1990.19.197  0.56
2006 Kim YC, Jung YC, Xuan Z, Dong H, Zhang MQ, Wang SM. Pan-genome isolation of low abundance transcripts using SAGE tag. Febs Letters. 580: 6721-9. PMID 17113583 DOI: 10.1016/J.Febslet.2006.11.013  1
2006 Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. Computational prediction of novel components of lung transcriptional networks. Bioinformatics (Oxford, England). 23: 21-9. PMID 17050569 DOI: 10.1093/Bioinformatics/Btl531  0.32
2006 Li J, Zhang MQ, Zhang X. A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. American Journal of Human Genetics. 79: 628-639. PMID 16960799 DOI: 10.1086/508066  1
2006 Fang F, Fan S, Zhang X, Zhang MQ. Predicting methylation status of CpG islands in the human brain. Bioinformatics (Oxford, England). 22: 2204-9. PMID 16837523 DOI: 10.1093/Bioinformatics/Btl377  1
2006 Smith PJ, Zhang C, Wang J, Chew SL, Zhang MQ, Krainer AR. An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Human Molecular Genetics. 15: 2490-508. PMID 16825284 DOI: 10.1093/Hmg/Ddl171  1
2006 Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, Edwards JR, Ju J, Bestor TH, Zhang MQ. Computational prediction of methylation status in human genomic sequences. Proceedings of the National Academy of Sciences of the United States of America. 103: 10713-6. PMID 16818882 DOI: 10.1073/Pnas.0602949103  1
2006 Das D, Nahlé Z, Zhang MQ. Adaptively inferring human transcriptional subnetworks. Molecular Systems Biology. 2: 2006.0029. PMID 16760900 DOI: 10.1038/Msb4100067  1
2006 Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Research. 34: e63. PMID 16682442 DOI: 10.1093/Nar/Gkl151  1
2006 Zhang C, Xuan Z, Otto S, Hover JR, McCorkle SR, Mandel G, Zhang MQ. A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Research. 34: 2238-46. PMID 16670430 DOI: 10.1093/Nar/Gkl248  1
2006 Zhang C, Li HR, Fan JB, Wang-Rodriguez J, Downs T, Fu XD, Zhang MQ. Profiling alternatively spliced mRNA isoforms for prostate cancer classification. Bmc Bioinformatics. 7: 202. PMID 16608523 DOI: 10.1186/1471-2105-7-202  1
2006 Smith AD, Sumazin P, Xuan Z, Zhang MQ. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proceedings of the National Academy of Sciences of the United States of America. 103: 6275-80. PMID 16606849 DOI: 10.1073/Pnas.0508169103  1
2006 Rollins RA, Haghighi F, Edwards JR, Das R, Zhang MQ, Ju J, Bestor TH. Large-scale structure of genomic methylation patterns. Genome Research. 16: 157-63. PMID 16365381 DOI: 10.1101/Gr.4362006  1
2006 Dimitrova N, Cheung YH, Zhang M. Analysis and visualization of DNA spectrograms: Open possibilities for the genome research Proceedings of the 14th Annual Acm International Conference On Multimedia, Mm 2006. 1017-1024. DOI: 10.1145/1180639.1180861  1
2006 Zhang M, Tateishi G, Bergmann G. Discrepancies between experiment and theory in the superconducting proximity effect Physical Review B - Condensed Matter and Materials Physics. 74. DOI: 10.1103/Physrevb.74.014506  1
2005 Zhang MQ. Using CorePromoter to find human core promoters Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. PMID 18428749 DOI: 10.1002/0471250953.Bi0209S10  1
2005 Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, Zhang MQ, Spector DL. Regulating gene expression through RNA nuclear retention. Cell. 123: 249-63. PMID 16239143 DOI: 10.1016/J.Cell.2005.08.033  1
2005 Wang J, Smith PJ, Krainer AR, Zhang MQ. Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Research. 33: 5053-62. PMID 16147989 DOI: 10.1093/Nar/Gki810  1
2005 Xuan Z, Zhao F, Wang J, Chen G, Zhang MQ. Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biology. 6: R72. PMID 16086854 DOI: 10.1186/Gb-2005-6-8-R72  1
2005 Smith AD, Sumazin P, Das D, Zhang MQ. Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (Oxford, England). 21: i403-12. PMID 15961485 DOI: 10.1093/Bioinformatics/Bti1043  1
2005 Smith AD, Sumazin P, Zhang MQ. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proceedings of the National Academy of Sciences of the United States of America. 102: 1560-5. PMID 15668401 DOI: 10.1073/Pnas.0406123102  1
2005 Xuan Z, Zhang MQ. From worm to human: bioinformatics approaches to identify FOXO target genes. Mechanisms of Ageing and Development. 126: 209-15. PMID 15610780 DOI: 10.1016/J.Mad.2004.09.021  0.44
2005 Zhao F, Xuan Z, Liu L, Zhang MQ. TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Research. 33: D103-7. PMID 15608156 DOI: 10.1093/Nar/Gki004  0.4
2005 Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ. DWE: discriminating word enumerator. Bioinformatics (Oxford, England). 21: 31-8. PMID 15333453 DOI: 10.1093/Bioinformatics/Bth471  1
2005 Schones DE, Sumazin P, Zhang MQ. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (Oxford, England). 21: 307-13. PMID 15319260 DOI: 10.1093/Bioinformatics/Bth480  1
2004 Dike S, Balija VS, Nascimento LU, Xuan Z, Ou J, Zutavern T, Palmer LE, Hannon G, Zhang MQ, McCombie WR. The mouse genome: experimental examination of gene predictions and transcriptional start sites. Genome Research. 14: 2424-9. PMID 15574821 DOI: 10.1101/Gr.3158304  1
2004 Das D, Banerjee N, Zhang MQ. Interacting models of cooperative gene regulation. Proceedings of the National Academy of Sciences of the United States of America. 101: 16234-9. PMID 15534222 DOI: 10.1073/Pnas.0407365101  1
2004 Zhang J, Li F, Li J, Zhang MQ, Zhang X. Evidence and characteristics of putative human alpha recombination hotspots. Human Molecular Genetics. 13: 2823-8. PMID 15385449 DOI: 10.1093/Hmg/Ddh310  0.44
2004 Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology. 5: R56. PMID 15287978 DOI: 10.1186/Gb-2004-5-8-R56  1
2004 Chen G, Hata N, Zhang MQ. Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Research. 32: 2362-71. PMID 15115798 DOI: 10.1093/Nar/Gkh557  1
2003 Zhang MQ. Prediction, annotation, and analysis of human promoters Cold Spring Harbor Symposia On Quantitative Biology. 68: 217-225. PMID 15338621 DOI: 10.1101/Sqb.2003.68.217  1
2003 Banerjee N, Zhang MQ. Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Research. 31: 7024-7031. PMID 14627835 DOI: 10.1093/Nar/Gkg894  1
2003 Davuluri RV, Zhang MQ. Computer software to find genes in plant genomic DNA. Methods in Molecular Biology (Clifton, N.J.). 236: 87-108. PMID 14501060 DOI: 10.1385/1-59259-413-1:87  1
2003 Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Research. 31: 3568-71. PMID 12824367 DOI: 10.1093/Nar/Gkg616  1
2003 Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proceedings of the National Academy of Sciences of the United States of America. 100: 8164-9. PMID 12808131 DOI: 10.1073/Pnas.1332764100  1
2003 Xuan Z, Wang J, Zhang MQ. Computational comparison of two mouse draft genomes and the human golden path. Genome Biology. 4: R1. PMID 12537546 DOI: 10.1186/Gb-2002-4-1-R1  1
2003 Kato M, Hata N, Banerjee N, Zhang MQ. Integrative Method for Identifying Combinatorial Regulation of Transcription Factors Genome Informatics. 14: 358-359. DOI: 10.11234/Gi1990.14.358  1
2002 Carmell MA, Xuan Z, Zhang MQ, Hannon GJ. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes & Development. 16: 2733-42. PMID 12414724 DOI: 10.1101/Gad.1026102  0.32
2002 Nahle Z, Polakoff J, Davuluri RV, McCurrach ME, Jacobson MD, Narita M, Zhang MQ, Lazebnik Y, Bar-Sagi D, Lowe SW. Direct coupling of the cell cycle and cell death machinery by E2F. Nature Cell Biology. 4: 859-64. PMID 12389032 DOI: 10.1038/Ncb868  1
2002 Zhang MQ. Extracting functional information from microarrays: A challenge for functional genomics Proceedings of the National Academy of Sciences of the United States of America. 99: 12509-12511. PMID 12271149 DOI: 10.1073/Pnas.212532499  1
2002 Zhang MQ. Computational prediction of eukaryotic protein-coding genes Nature Reviews Genetics. 3: 698-709. PMID 12209144 DOI: 10.1038/Nrg890  1
2002 Xuan Z, McCombie WR, Zhang MQ. GFScan: a gene family search tool at genomic DNA level. Genome Research. 12: 1142-9. PMID 12097353 DOI: 10.1101/Gr.220102  1
2002 Banerjee N, Zhang MQ. Functional genomics as applied to mapping transcription regulatory networks Current Opinion in Microbiology. 5: 313-317. PMID 12057687 DOI: 10.1016/S1369-5274(02)00322-3  1
2002 Zhang T, Zhang M. Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinformatics (Oxford, England). 17: 1232-3. PMID 11751235 DOI: 10.1093/Bioinformatics/17.12.1232  0.36
2002 Kato M, Hata N, Banerjee N, Zhang MQ. Inferring Combinatorial Regulation of Binding Sites and Transcription Factors on Gene Expression Genome Informatics. 13: 303-304. DOI: 10.11234/Gi1990.13.303  1
2001 Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nature Genetics. 29: 412-7. PMID 11726928 DOI: 10.1038/Ng780  1
2001 Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Molecular and Cellular Biology. 21: 6820-32. PMID 11564866 DOI: 10.1128/Mcb.21.20.6820-6832.2001  1
2001 Ando S, Sarlis NJ, Krishnan J, Feng X, Refetoff S, Zhang MQ, Oldfield EH, Yen PM. Aberrant alternative splicing of thyroid hormone receptor in a TSH-secreting pituitary tumor is a mechanism for hormone resistance. Molecular Endocrinology (Baltimore, Md.). 15: 1529-38. PMID 11518802 DOI: 10.1210/Mend.15.9.0687  0.28
2001 Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ. Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology. 309: 99-120. PMID 11491305 DOI: 10.1006/Jmbi.2001.4650  1
2001 Tabaska JE, Davuluri RV, Zhang MQ. Identifying the 3'-terminal exon in human DNA. Bioinformatics (Oxford, England). 17: 602-7. PMID 11448878 DOI: 10.1093/Bioinformatics/17.7.602  0.6
2001 Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J, Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Research. 11: 389-404. PMID 11230163 DOI: 10.1101/Gr.167301  1
2001 Liu HX, Cartegni L, Zhang MQ, Krainer AR. A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nature Genetics. 27: 55-8. PMID 11137998 DOI: 10.1038/83762  1
2000 Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O, Zhang MQ. An alternative-exon database and its statistical analysis. Dna and Cell Biology. 19: 739-756. PMID 11177572 DOI: 10.1089/104454900750058107  1
2000 Davuluri RV, Suzuki Y, Sugano S, Zhang MQ. CART Classification of Human 5′ UTR Sequences Genome Research. 10: 1807-1816. PMID 11076865 DOI: 10.1101/Gr.Gr-1460R  1
2000 Ioshikhes IP, Zhang MQ. Large-scale human promoter mapping using CpG islands. Nature Genetics. 26: 61-63. PMID 10973249 DOI: 10.1038/79189  1
2000 Liu HX, Chew SL, Cartegni L, Zhang MQ, Krainer AR. Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Molecular and Cellular Biology. 20: 1063-71. PMID 10629063 DOI: 10.1128/Mcb.20.3.1063-1071.2000  1
1999 Mayeda A, Badolato J, Kobayashi R, Zhang MQ, Gardiner EM, Krainer AR. Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. The Embo Journal. 18: 4560-70. PMID 10449421 DOI: 10.1093/Emboj/18.16.4560  1
1999 Tabaska JE, Zhang MQ. Detection of polyadenylation signals in human DNA sequences Gene. 231: 77-86. PMID 10231571 DOI: 10.1016/S0378-1119(99)00104-3  0.12
1999 Ioshikhes I, Trifonov EN, Zhang MQ. Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure Proceedings of the National Academy of Sciences of the United States of America. 96: 2891-2895. PMID 10077607 DOI: 10.1073/Pnas.96.6.2891  0.68
1999 Zhang MQ. Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Research. 9: 681-688. DOI: 10.1101/Gr.9.8.681  0.01
1998 Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell. 9: 3273-97. PMID 9843569 DOI: 10.1091/Mbc.9.12.3273  1
1998 Zhang MQ. Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis Plant Molecular Biology. 37: 803-806. PMID 9678575 DOI: 10.1023/A:1006023912378  0.01
1998 Chen T, Zhang MQ. Pombe: A gene-finding and exon-intron structure prediction system for fission yeast Yeast. 14: 701-710. PMID 9675815 DOI: 10.1002/(Sici)1097-0061(19980615)14:8<701::Aid-Yea247>3.0.Co;2-#  1
1998 Liu HX, Zhang M, Krainer AR. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Development. 12: 1998-2012. PMID 9649504 DOI: 10.1101/Gad.12.13.1998  1
1998 Zhang MQ. Statistical Features of Human Exons and Their Flanking Regions Human Molecular Genetics. 7: 919-932. PMID 9536098 DOI: 10.1093/Hmg/7.5.919  0.01
1998 Zhang MQ. Identification of human gene core promoters in silico Genome Research. 8: 319-326. PMID 9521935 DOI: 10.1101/Gr.8.3.319  1
1997 Zhang MQ. Identification of protein coding regions in the human genome by quadratic discriminant analysis Proceedings of the National Academy of Sciences of the United States of America. 94: 565-568. PMID 9012824 DOI: 10.1073/Pnas.94.2.565  0.01
1995 Zhang MQ, Marr TG. Alignment of molecular sequences seen as random path analysis Journal of Theoretical Biology. 174: 119-129. PMID 7643608 DOI: 10.1006/Jtbi.1995.0085  1
1994 Zhang MQ, Marr TG. Fission yeast gene structure and recognition. Nucleic Acids Research. 22: 1750-9. PMID 8202381 DOI: 10.1093/Nar/22.9.1750  1
1994 Stamm S, Zhang MQ, Marr TG, Helfman DM. A sequence compilation and comparison of exons that are alternatively spliced in neurons Nucleic Acids Research. 22: 1515-1526. PMID 8202349 DOI: 10.1093/Nar/22.9.1515  1
1993 Zhang MQ, Marr TG. Genome mapping by nonrandom anchoring: a discrete theoretical analysis. Proceedings of the National Academy of Sciences of the United States of America. 90: 600-4. PMID 8421694 DOI: 10.1073/Pnas.90.2.600  1
1993 Zhang MQ, Marr TG. A weight array method for splicing signal analysis. Computer Applications in the Biosciences : Cabios. 9: 499-509. PMID 8293321 DOI: 10.1093/Bioinformatics/9.5.499  1
1993 Zhang MQ, Marr TG. Genome mapping by random anchoring: A discrete theoretical analysis Journal of Statistical Physics. 73: 611-623. DOI: 10.1007/Bf01054342  1
1991 Zhang MQ. The nonuniform hard-rod fluid revisited Journal of Statistical Physics. 63: 1191-1202. DOI: 10.1007/Bf01030006  1
1990 Zhang MQ. Zero-thickness membrane interface and Schrödinger equation Physical Review A. 42: 4588-4590. DOI: 10.1103/Physreva.42.4588  1
1990 Zhang MQ. Entropy functional of a nonuniform Ising model on a two-row lattice Journal of Physics a: General Physics. 23: 2173-2181. DOI: 10.1088/0305-4470/23/11/038  1
1989 Zhang MQ. A fast vectorized multispin coding algorithm for 3D Monte Carlo simulations using Kawasaki spin-exchange dynamics Journal of Statistical Physics. 56: 939-950. DOI: 10.1007/Bf01016787  1
1988 Zhang MQ. Nonequilibrium steady states of some stochastic lattice gas models Nuclear Physics B (Proceedings Supplements). 5: 278-283. DOI: 10.1016/0920-5632(88)90055-2  1
1988 Zhang MQ. Pair correlation function for Ising spins with competing dynamics Journal of Statistical Physics. 53: 1217-1225. DOI: 10.1007/Bf01023865  1
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