Publications
2024
Abbas A, Chandratre K, Gao Y, Yuan J, Zhang MQ, Mani RS. ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features. Genome Biol. 2024 Jan 12;25(1):15. doi: 10.1186/s13059-023-03158-7. PMID: 38217027; PMCID: PMC10785520.
Tang B, Wang X, He H, Chen R, Qiao G, Yang Y, Xu Z, Wang L, Dong Q, Yu J, Zhang M*, Shi M*, Wang J*. (2024) Aging-disturbed FUS Phase Transition Impairs Hematopoietic Stem Cell by Altering Chromatin Structure. Blood, PMID: 37748139
Hongbin Ji; Xinyuan Tong; Ayushi S. Patel; Eejung Kim; Hongjun Li; …; Juntao Gao; …; Dong Gao; Michael Q. Zhang; Andrew J. Aguirre; Kwok-Kin Wong. (2024) Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer. Cancer Cell, in press.
Yongge Li, Kaili Wang, Minglei Shi *, Michael Q Zhang *, Juntao Gao* (2024) Sequential GAM constructs the single cell geometric 3D genome structure. Nature Communications, 2023 second revision.
2023
Zhang, M.Q. (2023), Dialog between artificial intelligence & natural intelligence. Quantitative Biology, 11: 359-362. https://doi.org/10.1002/qub2.5
Can artificial intelligence improve life science? As much as life science can improve AI, researchers say: https://phys.org/news/2023-12-artificial-intelligence-life-science-ai.html#google_vignette
Guo T, Yuan Z, Pan Y, Wang J, Chen F, Zhang MQ*, LX* (2023) SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies. Genome Biol. 24:241. PMID: 37864231.
Zhang W, Suo J, Yan Y, Yang R, Lu Y, Jin Y, Gao S, Li S, Gao J*, Zhang M*, Dai Q*. (2023), iSMOD: Integrative browser for image-based single-cell multi-omic data. Nucl Acid Res, 51:8348-8366
Huo W, Price VJ, Sharifi A, Zhang MQ, Palmer KL (2023). Enterococcus faecalis Strains with Compromised CRISPR-Cas Defense Emerge under Antibiotic Selection for a CRISPR-Targeted Plasmid. Appl Environ Microbiol. 89(6):e0012423. PMID: 37278656
Liu C, Huo Y, Zhang Y, Yin F, Chen T, Wang Z, Gao J, Jin P, Li X, Shi M, Zhang MQ. (2023) Development and experimental validation of a novel prognostic signature for gastric cancer. Cancers (Basel), 15:1610. PMID: 36900401.
SODB facilitates comprehensive exploration of spatial omics data. Nat Methods. 2023 Mar;20(3):387-399. doi: 10.1038/s41592-023-01773-7. Epub 2023 Feb 16. PubMed PMID: 36797409.
2022
Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture. Cancer Discov. 2022 Dec 2;12(12):2838-2855. doi: 10.1158/2159-8290.CD-22-0027. PubMed PMID: 36108240; PubMed Central PMCID: PMC9722594.
SOTIP is a versatile method for microenvironment modeling with spatial omics data. Nat Commun. 2022 Nov 28;13(1):7330. doi: 10.1038/s41467-022-34867-5. PubMed PMID: 36443314; PubMed Central PMCID: PMC9705407.
Profiling and characterization of constitutive chromatin-enriched RNAs. iScience. 2022 Nov 18;25(11):105349. doi: 10.1016/j.isci.2022.105349. eCollection 2022 Nov 18. PubMed PMID: 36325053; PubMed Central PMCID: PMC9618790.
Computational modeling and analysis of the morphogenetic domain signaling networks regulating C. elegans embryogenesis. Comput Struct Biotechnol J. 2022;20:3653-3666. doi: 10.1016/j.csbj.2022.05.058. eCollection 2022. PubMed PMID: 35891777; PubMed Central PMCID: PMC9289785.
Avian influenza viruses suppress innate immunity by inducing trans-transcriptional readthrough via SSU72. Cell Mol Immunol. 2022 Jun;19(6):702-714. doi: 10.1038/s41423-022-00843-8. Epub 2022 Mar 24. PubMed PMID: 35332300; PubMed Central PMCID: PMC9151799.
CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming. Cell Rep. 2022 Apr 5;39(1):110626. doi: 10.1016/j.celrep.2022.110626. PubMed PMID: 35385732.
Integration of single cell data by disentangled representation learning. Nucleic Acids Res. 2022 Jan 25;50(2):e8. doi: 10.1093/nar/gkab978. PubMed PMID: 34850092; PubMed Central PMCID: PMC8788944.
MyoD is a 3D genome structure organizer for muscle cell identity. Nat Commun. 2022 Jan 11;13(1):205. doi: 10.1038/s41467-021-27865-6. PubMed PMID: 35017543; PubMed Central PMCID: PMC8752600.
MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection. Nucleic Acids Res. 2022 Jan 11;50(1):46-56. doi: 10.1093/nar/gkab1132. PubMed PMID: 34850940; PubMed Central PMCID: PMC8754642.
A data-driven method to learn a jump diffusion process from aggregate biological gene expression data.J Theor Biol. 2022 Jan 7;532:110923. doi: 10.1016/j.jtbi.2021.110923. Epub 2021 Oct 1. PubMed PMID: 34606876.
Polarization modulation with optical lock-in detection reveals universal fluorescence anisotropy of subcellular structures in live cells. Light Sci Appl. 2022 Jan 1;11(1):4. doi: 10.1038/s41377-021-00689-1. PubMed PMID: 34974519; PubMed Central PMCID: PMC8720311.
2021
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment. Nat Methods. 2021 Oct;18(10):1223-1232. doi: 10.1038/s41592-021-01276-3. Epub 2021 Oct 4. PubMed PMID: 34608315.
Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index. Genome Biol. 2021 Aug 17;22(1):229. doi: 10.1186/s13059-021-02456-2. PubMed PMID: 34404448; PubMed Central PMCID: PMC8369651.
LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency. J Mol Cell Biol. 2021 Aug 4;13(4):295-313. doi: 10.1093/jmcb/mjaa056. PubMed PMID: 33049031; PubMed Central PMCID: PMC8339366.
The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence. Genome Res. 2021 Jul;31(7):1121-1135. doi: 10.1101/gr.275235.121. Epub 2021 Jun 17. PubMed PMID: 34140314; PubMed Central PMCID: PMC8256869.
3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia. Nat Commun. 2021 Jun 17;12(1):3708. doi: 10.1038/s41467-021-24044-5. PubMed PMID: 34140506; PubMed Central PMCID: PMC8211852.
Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models. Clin Cancer Res. 2021 Jun 15;27(12):3383-3396. doi: 10.1158/1078-0432.CCR-19-3975. Epub 2021 Mar 5. PubMed PMID: 33674273.
Deciphering hierarchical organization of topologically associated domains through change-point testing. BMC Bioinformatics. 2021 Apr 10;22(1):183. doi: 10.1186/s12859-021-04113-8. PubMed PMID: 33838653; PubMed Central PMCID: PMC8037919.
2020
A novel cytogenetic method to image chromatin interactions at subkilobase resolution: Tn5 transposase-based fluorescence in situ hybridization. J Genet Genomics. 2020 Dec 20;47(12):727-735. doi: 10.1016/j.jgg.2020.04.008. Epub 2020 Nov 7. PubMed PMID: 33750643.
Molecular basis for histone H3 “K4me3-K9me3/2” methylation pattern readout by Spindlin1. J Biol Chem. 2020 Dec 4;295(49):16877-16887. doi: 10.1074/jbc.RA120.013649. Epub 2020 Sep 29. PubMed PMID: 32994220; PubMed Central PMCID: PMC7864079.
Beta-amyloid deposition around hepatic bile ducts is a novel pathobiological and diagnostic feature of biliary atresia. J Hepatol. 2020 Dec;73(6):1391-1403. doi: 10.1016/j.jhep.2020.06.012. Epub 2020 Jun 16. PubMed PMID: 32553668.
Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition. BMC Genomics. 2020 Nov 30;21(1):842. doi: 10.1186/s12864-020-07222-5. PubMed PMID: 33256598; PubMed Central PMCID: PMC7706239.
The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer. J Clin Invest. 2020 Aug 3;130(8):3987-4005. doi: 10.1172/JCI134260. PubMed PMID: 32343676; PubMed Central PMCID: PMC7410051.
Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq. PLoS One. 2020;15(7):e0236666. doi: 10.1371/journal.pone.0236666. eCollection 2020. PubMed PMID: 32735574; PubMed Central PMCID: PMC7394367.
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome. BMC Bioinformatics. 2020 Apr 29;21(1):159. doi: 10.1186/s12859-020-3501-2. PubMed PMID: 32349677; PubMed Central PMCID: PMC7191778.
Single‑cell RNA sequencing of t(8;21) acute myeloid leukemia for risk prediction. Oncol Rep. 2020 Apr;43(4):1278-1288. doi: 10.3892/or.2020.7507. Epub 2020 Feb 18. PubMed PMID: 32323795; PubMed Central PMCID: PMC7057921.
Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol. 2020 Mar 5;21(1):59. doi: 10.1186/s13059-020-01973-w. PubMed PMID: 32138752; PubMed Central PMCID: PMC7059722.
Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development. Front Bioeng Biotechnol. 2020;8:35. doi: 10.3389/fbioe.2020.00035. eCollection 2020. PubMed PMID: 32117919; PubMed Central PMCID: PMC7019016.
2019
Single-cell stochastic gene expression kinetics with coupled positive-plus-negative feedback. Phys Rev E. 2019 Nov;100(5-1):052406. doi: 10.1103/PhysRevE.100.052406. PubMed PMID: 31869986.
Group-Sparsity-Based Super-Resolution Dipole Orientation Mapping. IEEE Trans Med Imaging. 2019 Nov;38(11):2687-2694. doi: 10.1109/TMI.2019.2910221. Epub 2019 Apr 11. PubMed PMID: 30990177.
SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nat Commun. 2019 Oct 8;10(1):4576. doi: 10.1038/s41467-019-12630-7. PubMed PMID: 31594952; PubMed Central PMCID: PMC6783552.
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell. 2019 Jun 27;178(1):107-121.e18. doi: 10.1016/j.cell.2019.06.001. PubMed PMID: 31251911; PubMed Central PMCID: PMC6760001.
A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass. Aging (Albany NY). 2019 Jun 20;11(12):4011-4031. doi: 10.18632/aging.102034. PubMed PMID: 31219803; PubMed Central PMCID: PMC6628988.
SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles. Nucleic Acids Res. 2019 May 7;47(8):e48. doi: 10.1093/nar/gkz116. PubMed PMID: 30799483; PubMed Central PMCID: PMC6486558.
Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. Nat Commun. 2019 May 3;10(1):2049. doi: 10.1038/s41467-019-10005-6. PubMed PMID: 31053705; PubMed Central PMCID: PMC6499832.
2018
Global transcriptional activity dynamics reveal functional enhancer RNAs. Genome Res. 2018 Dec;28(12):1799-1811. doi: 10.1101/gr.233486.117. Epub 2018 Oct 23. PubMed PMID: 30352805; PubMed Central PMCID: PMC6280751.
HiCDB: a sensitive and robust method for detecting contact domain boundaries. Nucleic Acids Res. 2018 Nov 30;46(21):11239-11250. doi: 10.1093/nar/gky789. PubMed PMID: 30184171; PubMed Central PMCID: PMC6265446.
Polarization-based super-resolution imaging of surface-enhanced Raman scattering nanoparticles with orientational information. Nanoscale. 2018 Nov 1;10(42):19757-19765. doi: 10.1039/c8nr04808h. PubMed PMID: 30211422.
Developing novel methods to image and visualize 3D genomes. Cell Biol Toxicol. 2018 Oct;34(5):367-380. doi: 10.1007/s10565-018-9427-z. Epub 2018 Mar 26. Review. PubMed PMID: 29577183; PubMed Central PMCID: PMC6133007.
Wang C*, Tan Z*, Niu B, Tsang KY, Tai A, Chan WC, Lo RL, Leung KK, Dung NW, Itoh N, Zhang MQ, Chan D, Cheah KS (2018) Inhibiting the integrated stress response pathway prevents aberrant chondrocyte differentiation thereby alleviating chondrodysplasia. eLife. 7:37673. PMID: 30024379
Ray P, Torck A, Quigley L, Wangzhou A, Neiman M, Rao C, Lam T, Kim JY, Kim TH, Zhang MQ, Dussor G, Price TJ (2018) Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research. bioRxiv 165431; doi: https://doi.org/10.1101/165431. PAIN. 159:1325-1345. PMID: 29561359
Liu X, Zhang Y, Chen Y, Li M, Shao Z, Zhang MQ, Xu J (2018) CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9. Curr Protoc Mol Biol 123:e64. PMID: 29927077 PMCID: PMC6028316
Dong Q, Wei L, Zhang MQ*, Wang X* (2018) Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence. Aging. 10:1489-1505. PMID: 29936497
MTGIpick allows robust identification of genomic islands from a single genome. Brief Bioinform. 2018 May 1;19(3):361-373. doi: 10.1093/bib/bbw118. PubMed PMID: 28025178; PubMed Central PMCID: PMC6454522.
Co-inhibitory Molecule B7 Superfamily Member 1 Expressed by Tumor-Infiltrating Myeloid Cells Induces Dysfunction of Anti-tumor CD8(+) T Cells. Immunity. 2018 Apr 17;48(4):773-786.e5. doi: 10.1016/j.immuni.2018.03.018. Epub 2018 Apr 3. PubMed PMID: 29625896.
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 (2018) Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. PLoS Genet, 14:e1007346. PMID: 29659575 PMCID: PMC5919691.
Djekidel MN, Chen Y* and Zhang MQ* (2018) FIND: difFerential chromatin INteractions Detection using a spatial Poisson process. Genome Research. In press. [Epub ahead of print] PMID: 29440282.
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* (2018) Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation. Cell Death and Disease, 9:200. PMID: 29422670 PMCID: PMC5833835.
Guo W, Zhu P, Pellegrini M, Zhang MQ, Wang X, Ni Z (2018) CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. Bioinformatics, 34:381-387. PMID: 28968643.
2017
Small-molecule TFEB pathway agonists that ameliorate metabolic syndrome in mice and extend C. elegans lifespan. Nat Commun. 2017 Dec 22;8(1):2270. doi: 10.1038/s41467-017-02332-3. PubMed PMID: 29273768; PubMed Central PMCID: PMC5741634.
Hydralazine induces stress resistance and extends C. elegans lifespan by activating the NRF2/SKN-1 signalling pathway. Nat Commun. 2017 Dec 20;8(1):2223. doi: 10.1038/s41467-017-02394-3. PubMed PMID: 29263362; PubMed Central PMCID: PMC5738364.
Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level. Sci Rep. 2017 Nov 22;7(1):16037. doi: 10.1038/s41598-017-15464-9. PubMed PMID: 29167445; PubMed Central PMCID: PMC5700158.
BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions. Nat Commun. 2017 Nov 20;8(1):1622. doi: 10.1038/s41467-017-01754-3. PubMed PMID: 29158486; PubMed Central PMCID: PMC5696378.
Infection of Caenorhabditis elegans with Vesicular Stomatitis Virus via Microinjection. Bio Protoc. 2017 Nov 20;7(22). doi: 10.21769/BioProtoc.2617. PubMed PMID: 29276724; PubMed Central PMCID: PMC5739071.
Li X, Chen W, Chen Y, Zhang X, Gu J, Zhang MQ (2017) Network embedding based representation learning for single cell RNA-seq data. NAR, 45:e166. PMID: 28977434
Jia C, Zhang MQ, Qian H (2017) Emergent Lévy behavior in single-cell stochastic gene expression. Phys. Rev. E, 96:040402. PMID: 29347590. arXiv:1708.05938
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. (2017) PAF1 Regulation of Promoter-Proximal Pause-Release via Enhancer Activation. Science, 357:1294-1298. PMID: 28860207.
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 , Shao Z, Xu J (2017) In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell. 170:1028-1043.e19. PMID: 28841410.
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* , Gao J, Dixon JR, Wang X, Zeng J, Xie W (2017) Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature. 547:232-235. PMID: 28703188.
Liu Z, Lou H, Xie K, Wang H, Chen N, Aparicio OM, Zhang MQ , Jiang R, Chen T (2017) Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. Nat Commun. 8:22. PMID: 28630425
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 , Yu L (2017) A novel epigenetic AML1-ETO/THAP10/miR-383 mini-circuitry contributes to t(8;21) leukaemogenesis. EMBO Mol Med. 9:933-949. PMID: 28539478.
Dong Q, Han H, Liu X, Wei L, Zhang W, Zhao Z, Zhang MQ , Wang X(2017) HCSGD: An integrated database of human cellular senescence genes. J Genet Genomics. 44:227-234. PMID: 28529078.
Pavlovic M, Ray P, Pavlovic K, Kotamarti A, Chen M, Zhang MQ* (2017) DIRECTION: A machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. Bioinformatics. 2017 May 12. doi: 10.1093/bioinformatics/btx316. [Epub ahead of print] PMID: 28505334.
Ni Y, Cao B, Ma T, Niu G, Huo Y, Huang J, Chen D, Liu Y, Yu B, Zhang MQ* , Niu H* (2017) Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes. Elife. 6. pii: e21660. doi: 10.7554/eLife.21660. PMID: 28485713.
Shi M, Gao J, Zhang MQ* (2017) Web3DMol: interactive protein structure visualization based on WebGL. NAR, 45:W523-W527, PMID: 28482028.
Li G, Chen Y, Snyder MP, Zhang MQ* (2017) ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. NAR, 45:e4, PMID: 27625391.
Yang Y, Chen L, Gu J, Zhang H, Yuan J, Lian Q, Lv G, Wang S, Wu Y, Yang YT, Wang D, Liu Y, Tang J, Luo G, Li Y, Hu L, Sun X, Wang D, Guo M, Xi Q, Xi J, Wang H, Zhang MQ* , Lu ZJ* (2017). Recurrently deregulated lncRNAs in hepatocellular carcinoma. Nat Commun. 8:14421. PMID: 28194035.
Reciprocal signaling by Wnt and Notch specifies a muscle precursor in the C. elegans embryo. Development. 2017 Feb 1;144(3):419-429. doi: 10.1242/dev.145391. Epub 2017 Jan 3. PubMed PMID: 28049659; PubMed Central PMCID: PMC5339420.
Wang Y, Xuan Z, Zhu X, Sun M, Chen Y, Zhang MQ, Chen M,Chen Y, Tu S (2017) RSQ: a statistical method for quantification of isoform-specific structurome using transcriptome-wide structural profiling data. bioRxiv 043232; doi: https://doi.org/10.1101/043232
2016
Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT). Nucleic Acids Res. 2016 Dec 1;44(21):e156. doi: 10.1093/nar/gkw734. Epub 2016 Aug 23. PubMed PMID: 27557708; PubMed Central PMCID: PMC5137427.
Super-resolution dipole orientation mapping via polarization demodulation. Light Sci Appl. 2016 Oct;5(10):e16166. doi: 10.1038/lsa.2016.166. eCollection 2016 Oct. PubMed PMID: 30167126; PubMed Central PMCID: PMC6059828.
Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Sci Rep. 2016 Aug 30;6:32207. doi: 10.1038/srep32207. PubMed PMID: 27573482; PubMed Central PMCID: PMC5004121.
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, Sun Y, Lu H, Zhang MQ* , Jin N, Jiang C(2016) FAT10 Is Critical in Influenza A Virus Replication by Inhibiting Type I IFN. J Immunol. 197:824-33. PMID: 27354218
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* (2016) MTGIpick allows robust identification of genomic islands from a single genome. Brief Bioinform. PMID: 28025178. DOI: 10.1093/bib/bbw118.
Jingyu Wang, Fengling Chen, Longwei Liu, Chunxiao Qi, Bingjie Wang, Xiaojun Yan, Chenyu Huang, Wei Hou, Michael Q. Zhang* , Yang Chen, Yanan Du (2016) Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation. Biomaterials 91:11-22. PMID: 26994875
Ma X*, Zhan G*, Sleumer MC, Chen S, Liu W, Zhang MQ , Liu X (2016) Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT). NAR, 44:e156. PMID: 27557708.
Chen Y, Wang Y, Xuan Z, Chen M, Zhang MQ* (2016) De novo deciphering three dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. NAR, 44:e106. PMID: 27060148.
Zhao Y, Li H, Fang SS, Kang Y, Wu W, Hao YJ, Li ZY, Bu DC, Sun NH, Zhang MQ*, Chen RS* (2016) NONCODE 2016: an informative and valuable data source of long noncoding RNAs. NAR, 44:D203-8. PMID: 26586799, PMCID: PMC4702886.
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, Kalhor N, Xie Y, Zhang MQ, Minna JD, Gazdar AF (2015) Validation of SCT Methylation As a Hallmark Biomarker for Lung Cancers. J. Thorac Oncol. Pii: S1556-0864(15)00052-0. PMID: 26725182. PDF
Zhang H*, Zhu C*, Zhao Y*, Li M, Wu L, Yang X, Wan X, Wang A, Zhang MQ+, Sang X+, Zhao H+ (2015) Long non-coding RNA expression profiles of Hepatitis Cvirus-related dysplasia and hepatocellular carcinoma. Oncotarget, 6:43770-8. PMID: 26540467. PDF
Sathe, A.*; Zhang, Yu-An*; Ma, X.*; Ray, P.; Cadinu, D.; Wang, Yi-Wei; Yao, X.; Liu, Xiao-Yun; Tang, H.; Wang, Y.; Huang, Y.; Liu, C.; Gu, J.; Akerman, M.; Mo, Y.; Cheng, C.; Xuan, Z.; Chen, L.; Xiao, G.; Xie, Y.; Girard, L.; Wang, H.; Lam, S.; Wistuba, I.I.; Zhang, L.; Gazdar, A.F.; Zhang M.Q. (2015) SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers, in Life Sciences Letters, IEEE , vol.PP, no.99, pp.1-1,doi: 10.1109/LLS.2015.2488438. PMID: 7293614. PDF
Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park I, Kim TH (2015) Histone deacetylases positively regulate transcription through the elongation machinery. Cell Rep. 13:1444-55. PMID: 26549458. PDF
Mehta+ H, Liu Y+, Zhang MQ*, Spiro S* (2015) Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073. Microbial Genomics, . MGen, 2015 1, doi: 10.1099/mgen.0.000031. PMID: 28348816. PDF
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, Ren B, Krainer AR, Maniatis T, Wu Q (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell 162:900-10. PMID:26276636. PDF
Ehrhardt K, Guinn MT, Quarton T, Zhang MQ, Bleris L (2015) Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting. Biosens Bioelectron. 74:744-750, PMCID:PMC4549190, PMID: 26210472. PDF
Hu L, Di C, Kai M, Yang Y-C, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ (2015) A common set of distinct features that characterize noncoding RNAs across multiple species. NAR. 43:104-14. PMID:25505163. PDF
Orozco LD, Marco Morselli M, Rubbi L, Guo W, Go J, Shi H, Lopez D, Furlotte NA, Bennett BJ, Charles R. Farber CR, Ghazalpour A, Zhang MQ, Bahous R, Rozen R, Lusis AJ, Pellegrini M (2015) Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice. Cell Metabolism, 21:905-17. PMID: 26039453 PMCID: PMC4454894. . PDF
Sun G, Hu Z, Min Z, Yan X, Guan Z, Su H, Fu Y, Ma X, Chen Y-G, Zhang MQ*, Tao Q*, Wu W* (2015) Small C-terminal Domain Phosphatase 3 Dephosphorylates the Linker Sites of Receptor-regulated Smads (R-Smads) to Ensure Transforming Growth Factor β (TGFβ)-mediated Germ Layer Induction in Xenopus Embryos. JBC, 290:17239-49. PMID:26013826. PDF
Akerman M, Fregoso O, Das S, Ruse C, Jensen MA, Pappin DL, Zhang MQ, Krainer A. (2015) Differential connectivity of splicing activators and repressors to the human spliceosome.Genome Biol. 16:119. PMID:26047612. PDF
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, Pellegrini M (2015) Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice. Cell Metabolism, Vol.21, Iss. 6, p905-917. DOI: 10.1016/j.cmet.2015.04.025, PMCID:PMC445489
Wang T, Xiao G; Chu Y, Zhang MQ, Corey D, Xie Y (2015) Design and bioinformatics analysis of genome-wide CLIP experiments. NAR, PMCID:PMC4477666, PMID:25958398. PDF
Huo W, Adams HM, Zhang MQ, Palmer KL (2015) Genome modification in Enterococcus faecalis OG1RF assessed by bisulfite sequencing and single molecule real time sequencing. J. Bacteriology 197:1939-51. PMID:25825433. PMCID:PMC4420909.
Yuan Y, Liu B, Xie P, Zhang MQ, Li Y, Zhen X, Wang X (2015) Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit. PNAS, 112:3158-63. PMID:25713348. PMCID:PMC4364186.
Roadmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518:317-30.PMCID:PMC4530010. PMID:25693563. PDF
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, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B (2015) Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature, 518:350-4. PMID:25693566. PMCID:PMC4449149.
2014
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. PMID:24572141. PDF
Gu J, Chen Y, Huang H, Yin L, Xie Z, Zhang MQ. (2014) Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Mol Biosyst, 10:3249-54. PMID:25286864. PDF
Heidari N, Phanstiel DH, He C, Grubert F, Jahanbanian F, Kasowski M, Zhang MQ, Snyder MP (2014). Genome-wide map of regulatory interactions in the human genome. Genome Res. 24:1905-17, PMID:25228660. PMCID:PMC4248309
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 (2014) Activity-Dependent FUS Dysregulation Disrupts Synaptic Homeostasis. PNAS, 111:E4769-78. PMID:25324524. PMCID:PMC4226112
Cheng J, Zhou X, Lu Y, Chen J, Han B, Zhu Y, Liu L, Choy K-W, Han D, Sham PC, Zhang MQ, Zhang X, Yuan H (2014) Exome sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nosyndromic hearing loss in a Chinese family. AHG. 78:410-423. PMID:25227905. PDF
Sheng MM, 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*(2014) Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Sci China Life Sci 57:959-972. PMID:25218824. PDF
Liao W, Ouyang W, Zhang MQ, Li MO (2014) Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes. Genomics Data, 2:280-281. PMID:25302145. PMCID:PMC4185926
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. PMID:25122670. PMCID:PMC4232531
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.PMCID:PMC4521291, PMID:25231367. PDF
Li Y, Ehrhardt K, Zhang MQ, Bleris L (2014) Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries. Sci. Rep. 4:4857. PMID:24798576. PMCID:PMC4010924
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. PMID:24782518. PMCID:PMC4066761
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. PMID:24818823. PMCID:PMC4151132
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. PMID:24668253. PDF
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. PMID:24788790. PMCID:PMC4006751
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. PMCID:PMC3992522
2013
Steijger T, .., Akerman M,..Wu J., Zhang MQ, Hubbard TJ, Guigo R, Harrow J, Bertone P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat. Meth. 10:1177-84. PMID:24185837. PMCID:PMC3851240
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. 42:3009-16. PMID:24343027. PMCID:PMC3950701
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. PMID:24206606. PMCID:PMC3840619
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, Steinbuchel A, Fujimoto T, Cichello S, Yu J, Liu P. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR,42:1052-64, PMID:24150943. PMCID:PMC3902926
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. PMCID:PMC3951422
Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 8(9):e74275. PMID:24040221. PMCID:PMC3764200
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:23932570. PMCID:PMC3809840
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, 12:3379-87. PMID:23924514. PMCID:PMC3820948
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. PMID:26085954. PMCID:PMC4467561. PDF
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. PMCID:PMC3786220
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, 4:335-346. PDF
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. PDF
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. PDF
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. PMCID:PMC3664805
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. PMCID:PMC4357786.
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. PMCID:PMC3689739
2012
Tang MH, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J. (2012) Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Front Oncol. 2:197. PMID:23293768. PMCID:PMC3530719
We H*, Li Y*, Malek SN, Kim YC, Xu J, Chen P, Xiao F, Huang X, Zhou X, Xuan Z, Mankala S, Rowley JD, Zhang MQ, Wang SM (2012) New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS ONE. 7:e51203. PMID:23251452. PMCID:PMC3520980
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 rb Function. Nature. 491:554-9. PMID:23135404. PMCID:PMC3771531
Xing H, Liao W, Mo Y, Zhang MQ. (2012) A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types. J Vis Exp, Dec 10;(70). doi:pii: 4273. PMID:23271069. PMCID:PMC3565849
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:e1002613. PMID:22844240. PMCID:PMC3406014
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. PDF
Li R, Guo W, Gu J, Zhang MQ, Wang XW (2012) Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics. 100:297-302. PMID:22824656. PMCID:PMC3771509.
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. PMCID:PMC3387189.
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. PMCID:PMC3384172.
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. PDF
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. PDF
He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ (2012) Cell-type based analysis of microRNA profiles in the mouse brain. Neuron. 73:35-48. PMID:22243745. PMCID:PMC3270494.
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. 40:e50. PMID:22228832. PMCID:PMC3326300.
2011
Rajan P, Dalgliesh C, Carling P, Buist T, Zhang C, Grellscheid SN, Armstrong K, Stockley J, Simillion C, Gaughan L, Kalna G, Zhang MQ, Robson CN, Leung HY, Elliott DJ. (2011) Identification of novel androgen-related pathways and mRNAs isoforms through genome-wide exon-specific profiling of LNCaP transcriptome. Endocrine-Related Cancer, PLoS ONE, 6(12):e29088. PMID:22194994. PMCID:PMC3237596.
Dai Q, Lihua Li L, Liu X, Yao Y, Zhao F, Zhang MQ(2011) Integrating overlapping structures and background information of words significantly improves biological sequence comparison. PLoS ONE, 6:e26779. PMID:22102867. PMCID:PMC3213098.
Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N*, Zhang MQ*, Lucito R* (2011) Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer. PLoS ONE, 6(12):e28503. PMID:22174824. PMCID:PMC3234280
Hu Z, Qian M, Zhang MQ (2011) Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. BMC Systems Biology. 5(Suppl 2):S8. PMID:22784579. PMCID:PMC3287488.
Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J (2011) EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 6:1505-12. PMID:22139581. PDF
Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27:3010-6. PMID:21896509. PMCID:PMC3198574.
Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S (2011) 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. NAR, 39:9720-30. PMID:21880592. PMCID:PMC3239178.
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, Li H, Chen ZY, Yuan H (2011) Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64. Am J Hum Genet. 89:56-66. PMID:21722859. PMCID:PMC3135809.
Watts JA, Zhang C, Klein-SzantoAJ, Kormish JD, Zhang MQ, Zaret K, (2011) Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development. PLoS Genet. 7:e1002277. PMID:21935353. PMCID:PMC3174211.
Zhang Z, Zhang MQ (2011) Histone modification profiles are predictive for both protein-coding and microRNA gene’s tissue.cell-type specific expression. BMC Bioinformatics. 12:155. PMID:21569556. PMCID:PMC3120700
Yang S, Yalamanchili HK, Li X, Yao K-M, Sham PC, Zhang MQ, Wang J. (2011) Correlated evolution of transcription factors and their binding sites. Bioinformatics, 21:2972-2978. PMID:21896508. PDF
Qin J, Li MJ, Wang P, Zhang MQ, Wang J (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. NAR, 39:W430-6. PMID:21586587. PMCID:PMC3125757.
Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ (2011) Inferring Haplotype of Copy Number variations from High-throughput data with Uncertainty. G3 genes genomes genetics, 1:35-42. PMID:22384316. PMCID:PMC3276117.
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 (2011) The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene, 30:3207-21. PMID:21423206. PMCID:PMC3136551.
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, 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. Nat Biotechnol. 28:1097-105. PMID:20852635. PMCID:PMC2955169.
Zhang MQ, Smith AD (2010) Challenges in Understanding Genome-Wide DNA Methylation. J. Comp. & Tech. 25:26-34. DOI:10.1007/s11390-010-9302-8. PDF
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. PMID:20729808. PMCID:PMC2944070
Bandyopadhyay S, Mitra R, Maulik U, Zhang MQ (2010) Development of the human cancer microRNA network. Silence, 1:6. PMID:20226080. PMCID:PMC2835996.
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. PMID:20122194. PMCID:PMC3009493.
Chicas A., Wang, X., Zhang, C., McCurrach, M., Zhao Z., Ozlem, M., Dickins, R., Narita, M., Zhang, M.Q., Lowe, S.W. (2010). Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence. Cancer Cell, 17:376-87. PMID:20385362. PMCID:PMC2889489.
Wang SM, Zhang MQ (2010) Transcriptome study for early hematopoiesis—achievement, challenge and new opportunity. J. Cell. Physiol. Review. 223:549-552. PMID:20143329. PMCID:PMC2875260.
2009
Zhang MQ, Waterman MS, Zhang X (2009): The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinformatics; 2009;10 Suppl 1:S1. PMID:19208108. PMCID:PMC2648764.
Smith AD, Chung W, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ (2009) Updates to the RMAP short-read mapping software. Bioinformatics. 25:2841-2842. PMID: 19736251. PMCID:PMC2895571.
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 J (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 19:1593-605. PMID:19581485. PMCID:PMC2752124.
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. PNAS. 106:8278-83. PMID:19416867. PMCID:PMC2688877
Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung, DC, Xavier RJ. (2009) An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1) target genes that form the core response to hypoxia. Nucleic Acids Res. 37:4587-602. PMID:19491311. PMCID:PMC2724271
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, 10:71. PMID:19243633. PMCID:PMC2674431.
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. PMID:19335899. PMCID:PMC2667539.
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. PMID:19015022. PMCID:PMC2995988.
Wang X, Xuan Z, Zhao X, Li Y and Zhang MQ (2009) High-resolution Human Core-promoter prediction with CoreBoost_HM. Genome Res. 22:2902. PMID:18997002. PMCID:PMC2652208.
2008
Castle, J.C., Zhang, C., Shah, J.K., Kulkarni, A.V., Cooper, T.A., Johnson, J.M. (2008). Differential expression of 24,426 human alternative splicing events and predicted cis-regulation in 48 tissues. Nature Genet. 40:1416-1425. PMID:18978788. PMCID:PMC3197713
Hsieh MC, Das D, Sambandam N, Zhang MQ, Nahle Z. (2008) Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem. 2008 Oct 10;283(41):27410-7. PMID:18667418. PDF
Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu C-I, Wang SM (2008) Poly A- Transcripts Expressed in HeLa Cells, PLoS ONE, 3:e2803. PMID:18665230. PMCID:PMC2481391.
Fan S, Zhang MQ, Zhang X (2008) Histone Methylation Marks Play Important Roles in Predicting the Methylation Status of CpG Islands. BBRC, 374:559-64. PMID:18656446. PMCID:PMC2974564.
Lin H, Zhang Z, Zhang MQ, Ma B, Li M (2008) ZOOM! Zillions of oligos mapped. Bioinformatics 24(21):2431-7. PMID:18684737. PMCID:PMC2732274.
Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer AR, Zhang MQ (2008) Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev. 22:2550-63. Erratum in: Genes Dev. 22:2902. PMID:18794351. PMCID:PMC2546699.
Zhang C, Li W-H, Krainer AR, Zhang MQ (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc. Acad. Natl Sci. USA, 105:5797-802. PMID:18391195. PMCID:PMC2311341.
Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T (2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. Bioinformatics, 9:404. PMID:18823535. PMCID:PMC2572072
Zhao X, Yoon S, Zhang MQ, Ye K, Geschwind DH, Sebat J, Iakoucheva LM (2008) High Connectivity among Autism Gene Candidates in Biological Networks: Evidence for Common Pathways. Submitted.
Smith AD, Xuan Z, Zhang MQ (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9:128. PMID:18307793. PMCID:PMC2335322
Chen G, Li W, Zhang Q-S, Regulski M, Sinha N, Barditch J, Tully T, Krainer AR, Zhang MQ, Dubnau J (2008) Identification of synaptic targets of Drosophila Pumilio. PLoS Comp Biol. (joint corresponding authors). 4(2)e1000026. PMID:18463699. PMCID:PMC2265480
Chen J, Kim YC, Jung Y-C, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM (2008) Scanning the human genome at kilobase resolution. Genome Res. 18:751-62. PMID:18292219. PMCID:PMC2336809
Nahle Z, Hsieh M, Pietka T, Coburn CC, Grimaldi PA, Zhang MQ, Das D, Abumrad NA. (2008) CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPARgamma/beta-mediated Adaptation to Metabolic Stress. J. Biol. Chem. 283:14317-26. PMID:18308721. PMCID:PMC2386936.
Cuddapah S, Chen X, Xuan Z, Roh T-Y, Cui K, Smith AD, Byun JS, Zhang MQ, Fuller MT, Zhao K (2008) Identification of potential human polycomb response elements in T cells. (unpublished).
Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B (2008) Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res. 18:46-59. PMID:18042645. PMCID:PMC2134779
Wang Z*, Zang C*, Rosenfeld J*, Schones DE, Barski A, Cuddapah S, Cui K, Roh T-Y, Peng W, Zhang MQ, Zhao K (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. (*equal contributing first author), 40:897-903. PMID:18552846, PMCID:PMC2769248.
Wu X, Jiang R., Zhang MQ, Li S (2008) Network-based global inference of human disease genes. Mol. Sys. Biol. 4:189. PMID:18463613. PMCID:PMC2424293.
Wang X, Gu J, Zhang MQ, Li Y (2008) Identification of phylogenetically conserved microRNA cisregulatory elements across 12 Drosophila species. Bioinformatics, 24:165-71. PMID:18037683. PDF
Eguchi J, Yan Q-W, Schones DE, Kamal M, Hsu C-H, Zhang MQ, Crawford GE, Rosen ED (2008) Identification of interferon-regulatory factors (IRFs) as regulators of adipocyte gene expression by mapping DNase hypersensitive sites during adipogenesis. Cell Metabolism. 7:86-94. PMID:18177728. PMCID:PMC2278019.
2007
Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ. (2007) A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A. 104:19291-6.
Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet. 39:1522-7.
Fan S, Fang F, Zhang X, Zhang MQ (2007) Putative Zinc Finger Protein Binding Sites Are Over-represented in the Boundaries of Methylation-resistant CpG Islands in the Human Genome. PLoS ONE, 2(11):e1184.
Zhang MQ (2007) Computational analyses of eukaryotic promoters. Review proceeding of Otto Warburg International Summer School and Workshop on Networks and Regulation, Peter F Arndt & Martine Vingron eds. BMC Bioinformatics, 8(Suppl 6):S2.
Wang X, Bandyopadhya S, Xuan Z, Zhao X, Zhang MQ, Zhang X (2007) PREDICTION OF TRANSCRIPTION START SITES BASED ON FEATURE SELECTION USING AMOSA. Proc. Comp. Sys. Bioinf. Conference. San Diego, Aug. 2007. World Scientific. eProceedings.
Zhang C, Krainer AR, Zhang MQ. (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends in Genetics. 23:484-8.
Zhang C, Hastings ML Krainer AR, Zhang MQ. (2007) Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites. Proc. Natl. Acad. Sci. USA 104, 15028-15033.
Zhao X, Leotta A, Kustanovich V, Lajonchere C, Geschwind DH, Law K, Law P, Qiu S, Lord C, Sebat J, Ye K, Wigler M. (2007) A unified genetic theory for sporadic and inherited autism. Proc Natl Acad Sci U S A. 104:12831-6.
Jiang B, Zhang MQ and Zhang X. (2007) OSCAR: One-class SVM for Accurate Recognition of Cis-elements. Bioinformatics, 23:2823-8.
He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA, Hannon GJ (2007) A microRNA component of the p53 tumour suppressor network. Nature. 447, 1130-4.
Yang Z, Jiang H, Zhao F, Shankar DB, Sakamoto KM, Zhang MQ, Lin S (2007) A highly conserved distal regulatory element controls hematopoietic expression of GATA-2. BMC Developmental Biology, 7:97.
Kim TH, Abdullaev Z, Smith AD, Ching KA, Loukinow D, Green RD, Zhang MQ, Lobanenkov V, Ren B (2007) Analysis of the vertebrate insulator protein CTCF binding sites in the human genome. Cell 128(6):1231-45.
Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, Hannon GJ (2007) Critical roles for Dicer in the female germine. Gene & Dev. 21:682-93.
Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA, Gleiberman A, Zhang MQ, Enikolopov G. (2007) Neural Potential of a Stem Cell Population in the Hair Follicle. Cell Cycle 6:2161-70. (cover image!)
D. Das and M.Q. Zhang. (2007) Predictive Models of Gene Regulation: Application of Regression Methods to Microarray Data. Methods in Molecular Biology, ed. M. Korenberg. 377:95.
Zhang J, Jiang B, Li M, Tromp J, Zhang X and Zhang MQ (2007) Computing exact p-values for DNA motifs (Part I). Bioinformatics. 23:531-7.
Schones DE, Smith AD and Zhang MQ (2007) Statistical significance of cis-regulatory modules. BMC Bioinformatics 8:19.
Jiang C, Xuan Z, Zhao F, Zhang MQ (2007) TRED: A Transcriptional Regulatory Element Database, new entries and other development. Nucleic Acid Res 35: D137-D140
Zhang C, Zhao X, Zhang MQ (2007) Functional in silico analysis of gene regulatory polymorphism – Chapter 12 in: Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data, 2nd edition
(M.R. Barnes, ed.) Pp281-310 Wiley-VCH
Zhao X, Xuan Z, Zhang MQ (2007) Boosting with stumps for predicting transcription start sites. Genome Biology 8:R17
Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. (2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics. 23:21-29.
Smith AD, Sumazin P and Zhang MQ (2007) Tissue-specific regulatory elements in mammalian promoters. Mol Sys Biol. 3:73.
Zhang C, Zhang X, Zhang MQ, Li Y (2007) Neighbor number, valley seeking and clustering. Pattern Recognition Letters. 28:173-180.
Zhang MQ (2007) Inferring Gene Regulatory Networks – Chapter 21 in: Bioinformatics – From Genomes to Therapies (T. Lengauer, ed.) Wiley-VCH. p807-828.
2006
Kim YC, Jung Y-C, Xuan Z, Tong H, Zhang MQ, Wang SM (2006) Pan-genome isolation of low abundant transcripts through SAGE. FEBS Lett 580:6721-6729.
Schaffer JD, Dimitrova N, Zhang MQ (2006) Bioinformatics. Chap. 26 in Advances in Healthcare Technology: Shaping the Future of Medical Care. Spekowius G & Wendler T eds. Pp421-438. Springer.
Li J, Zhang MQ and Zhang X (2006) A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. Am. J. Hum. Genet. 79:628-639.
Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, Edwards JR, Ju J, Bestor TH, Zhang MQ (2006) Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A. 103:10713-6.
Smith PJ, Zhang C, Wang J, Chew SL, Zhang MQ, Krainer AR (2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonix splicing enhancers. Hum Mol Genet 15(16):2490-2508.
Fang F, Fan SC, Zhang X and Zhang MQ (2006) Predicting Methylation Status of CpG Islands in the Human Brain. Bioinformatics, 22:2204-2209.
Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A (2006) Characterization of RNase R-digested DNA source that consists of lariat and circular RNAs derived from pre-mRNA splicing. Nucl. Acid. Res. 34(8):e63.
Zhang C, Xuan Z, Mandel G, Zhang MQ (2006) A Clustering Property of Highly-degenerate Transcription Factor Binding Sites in the Mammalian Genome. Nucleic Acid Res 34(8):2238-2246.
Benita Y, Oosting RS, Xuan Z, Wise MJ, Zhang QM, Humphery-Smith I (2006). Challenges in the prediction of small genes in the human genome. In preparation*. Review.
Smith AD, Sumazin P, Xuan Z, Zhang MQ (2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc. Natl. Acad. Sci. USA, 103:6275-6280.
Das D, Nahle Z, Zhang MQ (2006) Adaptively Inferring Human Transcriptional Subnetworks. Mol Sys Biol. 2:2006.0029. Commentary1 Commentary2
Zhang C, Li HR, Fan JB, Fu XD and Zhang MQ (2006) Profiling alternative spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics 2006 Apr;7:202.
Rollins RA, Haghighi FG, Edwards JR, Das R, Zhang MQ, Ju J, Bester TH (2006) The Large-Scale Structure of Genomic Methylation Patterns. Genome Research, 16:157-163.
2005
Zhang MQ (2005) Computational Molecular Biology of Genome Expression and Regulation. PReMI05 Lecture Notes in Computer Science, pp31-38, Springer-Verlag GMbH.
Prasanth KV, Prasanth SG, Xuan ZY, Sachidandam R, Hearn S, Frier SM, Bennett CF, Zhang MQ and Spector DL (2005) Regulating Gene Expression Through RNA Nuclear Retention. Cell, 123:249-263.
Wang J, Smith PH, Krainer AR, Zhang MQ (2005) Distribution of SR Protein Exonic Splicing Enhancer Motifs in Human Protein-Coding Genes. Nucl Acid Res, 33:5053-5062.
Xuan ZY, Zhao F, Wang JH, Chen GX and Zhang MQ (2005) Genome-Wide Promoter Extraction and Analysis in Human, Mouse and Rat. Genome Biology, 6:R74.
Zhang MQ (2005) Finding Human Core Promoter Regions. in: Current Protocols in Bioinformatics. (A. D. Baxevanis & D. B. Davison, Eds.), John Wiley & Sons.
Smith AD, Sumazin P, Das D and Zhang MQ (2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Accepted talk, ISMB2005. Bioinformatics. 21 Suppl 1:i403-i412
Zhao F, Xuan ZY, Liu Lihua and Zhang MQ (2005) TRED: a Transcription Regulatory Element Database and a platform for in silico gene regulation studies. Nucl Acid Res, 33:D103-107.
Xuan ZY and Zhang MQ (2005) From worm to human:Bioinformatics approaches to identify FOXO target genes. Special issue on Functional Genomics of Ageing 2004. Mech. Ageing Dev. 126:209-215.
Smith AD, Sumazin P and Zhang MQ (2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci USA, 102:1560-1565.
Schones DE, Sumazin P and Zhang MQ (2005) Similarity of Position Frequency Matrices for Transcription Factor Binding Sites. Bioinformatics, 21:307-313.
Sumazin P, Chen GX, Hata N, Smith AD and Zhang MQ (2005) DWE: Discriminant Word Enumerator. Bioinformatics, 21:31-38.
Banerjee N and Zhang MQ (2005) Transcription Regulatory Networks in Yeast Cell Cycle. A chapter in ‘Microarrays and gene regulation networks in yeast’, in Shannon MF; Rao S (ed.), Microarrays and Transcription Networks, Landes Bioscience, USA.
2004
Zhang J, Li F, Li J, Zhang MQ and Zhang XG (2004) Evidence and Characteristics of Putative Human α Recombination Hotspots. Hum. Mol. Genet. 13:2823-2828.
Long F, Liu H, Hahn C, Sumazin P, Zhang MQ and Zilberstein A (2004) Genome-wide Prediction and Analysis of Function-Specific Transcription Factor Binding Sites. In Silico Biology, 4:0033.
Guigo R and Zhang MQ (2005) Gene predictions and annotations, Chap17 in Mammalian Genomics, eds. A. Ruvinsky and J.A. Marshall Graves. Pp 429 Wallingford:CAB International.
Das D, Banerjee N and Zhang MQ (2004) Interacting Models of Cooperative Gene Regulation. Proc. Natl Acad Sci. USA, 101:16234-16239.
Chen J, Lee S, Sun M, X ZY, Zhou G, Zhang RS, Rowley JD, Zhang MQ and Wang SM (2004) Exhaustive identification of novel transcription units in the human genome using novel SAGE tags. Unpublished.
Dike S, Vivekanand S. Balija, Lidia Gnoj, Zhenyu Xuan, Jacqueline Ou, Theresa Zutavern, Lance E. Palmer, Greg Hannon, Michael Q. Zhang, W. Richard McCombie (2004). The Mouse Genome: Experimental examination of gene predictions and transcriptional start sites. Genome Res 14:2424-2429..
Guigo R, Birney E, Brent M, Dermitzakis E, Pachter L, Roest Crollius H, Solovyev V and Zhang M (2004) Completion of the catalog of protein coding genes in the human genome. Quantitative Biology. Online, http://arxiv.org/abs/q-bio.GN/0410008
Wang JH, Hata N, Fu XD and Zhang MQ (2004). Searching for tissue specific splicing cis-elements in human alternatively spliced genes. Unpublished.
Kato M, Hata N, Banerjee B and Zhang MQ (2004). Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology 5:R56.
Chen GX, Hata N and Zhang MQ (2004). Transcription factor binding element detection using functional clustering of mutant expression data. Nucl. Acid Res. 32:2362-2371.
Banerjee N and Zhang MQ (2003) Identification of cooperativity among transcription factors controlling cell cycle in yeast. Nucl. Acid Res. 31:7024-7031.
Wang, JH, Xuan ZY, Fu XD and Zhang, MQ (2004). Cross-species comparison of alternative splicing between human and mouse. Unpublished.
2003
Zhang MQ (2003) Prediction, Annotation and Analysis of Human Promoters. Cold Spring Harbor Symposium Quantitative Biology 68:217-225, Cold Spring Harbor Press.
Davuluri R and Zhang MQ (2003) Computer software to find genes in plant genomic DNA.
Methods Mol Biol. 236:87-108.
Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ and Ren B (2003) A global transcriptional Regulatory role for c-myc in Burkitt’s lymphoma cells. Proc. Natl. Acad. Sci. USA 100:8164-8169.
Cartegni L, Wang JH, Zhu ZW, Zhang MQ and Krainer AR (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucl. Acid. Res. 31:3568-3571.
2002
Carmell M, Xuan ZY, Zhang MQ and Hannon GJ (2002) Argonaute proteins : tentacles that reach into RNAi, stem cell maintenance and tumorigenesis. G&D, 16:2733-2742.
Xuan ZY, Wang JH and Zhang MQ (2002) Computational comparison of two mouse draft genomes and the human goldenpath. Genome Biology, 4(1):R1.
Zhang MQ (2002) Extracting functional information from microarrays: A challenge for functional genomics.
Proc Natl Acad Sci U S A 99:12509-12511.
Nahle Z, Polyakoff J, Davuluri RV, Jacobson MD, McCurrach ME, Narita M, Zhang MQ, Lazebnik Y, Bar-Sagi D and Lowe SW (2002) Direct coupling of the cell cycle and cell death machinery by E2F. Nat. Cell Biol. 4:859-864.
Zhang MQ (2002) Computational prediction of eukaryotic protein-coding genes. Nat. Rev Genet. 3:698-709.
Grosse I, Zhang MQ and Herzel H (2002) On the dynamic origin of isochores. (presented at the CSHL Genome Meeting in May 2001) Unpublished.
Saied A. Jaradat, Tetsuya S. Tanaka, Lydia O’Neill, G. Chen, N. Banerjee, Kevin G. Becker, Michael Q. Zhang, Kenneth R. Boheler and Minoru S.H. Ko (2002) Dynamic genetic reprogramming of pluripotent embryonic stem cells during differentiation. Unpublished.
Zhang Y, Mei PC, Lou R, Zhang MQ, Wu G, Qiang B, Zhang ZG and Shen Y(2002). Gene expression profiling in developing human hippocampus. J. Neurosci. Res. 70:200-208.
Zhang MQ (2003) Using MZEF to Find Internal Coding Exons. In Current Protocols in Bioinformatics, Baxevanis A et al. eds. John Wiley & Sons.
Zhang MQ (2002) Predicting full-length transcripts. Trends Biotechnol. 20:275.
Xuan ZY, McCombie WR and Zhang MQ (2002) GFScan: a gene family search tool at genomic DNA sequence level. Genome Res. 12:1142-1149.
Banerjee N and Zhang MQ (2002) Functional genomics as applied to mapping transcription regulatory networks. Curr. Op. Microbiol. 5:313-317.
2001
Weinmann AS, Bartley SM, Zhang T, Zhang MQ and Farnham PJ (2001). Use of chromatin immunoprecipitation to clone novel e2f target promoters. Mol. Cell Biol. 21:6820-6832.
Davuluri R, Grosse I and Zhang MQ. (2001). Computational identification of promoters and first exons in the human genome. Nat. Genet. 29:412-417.
Zhang T and Zhang MQ (2001). Promoter extraction from GenBank (PEG): automatic extraction of promoter sequences in large sets of genes. Bioinformatics, 12:1232-1233.
Chen G, Jaradat SA, Banerjee N, Tanaka TS, Ko MSH and Zhang MQ (2002). Cluster analysis of microarray gene expression data: application to and evaluation with NIA mouse 15K array on ES cell differentiation. Statistica Sinica, 12:241-262.
Kel AE, Kel-Margoulis OV, Farnham PJ, Stephanie MB, Wingender E and Zhang MQ (2001). Computer-assisted identification of cell cycle-related genes – new targets for E2F transcription factors. J. Mol. Biol. 309:99-120.
Zhang MQ (2001). Computational methods for promoter recognition. Chapter 10 in Current Topics in Computational Biology (Jiang T, Smith T, Xu Y and Zhang MQ eds). pp249-268. MIT Press and TUP.
Wu Q, Zhang T, Cheng J-F, Kim Y, Grimwood J, Schmulz J, Dickson M, Noonan JP, Zhang MQ, Myers RM and Maniatis T. (2001) Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 11:389-404.
Tabaska JE, Davuluri R and Zhang MQ (2001). A novel 3′-Terminal exon recognition algorithm. (Result was presented at CSHL Computational Biology Workshop 9/99). Bioinformatics 17:602-607.
Liu H-X, Cartegni L, Zhang MQ and Krainer AR. (2001) Mechanism of exon skipping caused by a nonsense mutation in the BRCA1 gene. Nature Genetics, 27:55-58.
Zhang MQ (2001). Discriminant analysis and its application in DNA sequence motif recognition. Based on a lecture given at the EBI Symposium: Genome Based Gene Structure Determination.(Jun 1-2,2000, Cambridge, UK) Briefings in Bioinformatics, 1(4)331-342.
Ando S, Sarlis N, Krishnan J, Feng X, Refetoff S, Zhang MQ, Oldfield EH and Yen PM (2001). Brief report: A berrant alternative-splicing of thyroid hormone receptor is a mechanism for thyroid hormone resistance in a thyrotropin-producing pituitary tumor. Molecular Endocrinology, 15:1529-1538.
2000
Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O and Zhang MQ. (2000) A database and statistical analysis of aternative exons. DNA & Cell Biol., 19:739-756.
Davuluri R, Suzuki Y, Sugano S and Zhang MQ. (2000) CART classification of human 5’UTR sequences. Genome Res. 10:1807-1816.
Ioshikhes I and Zhang MQ (2000). Large-scale human promoter mapping using CpG islands. discrimination. Nature Genetics, 26:61-63.
Zhu J and Zhang MQ (2000). Cluster, function and promoter: analysis of yeast expression array. In Proceedings of Pacific Symposium on Biocomputing 2000. R.B. Altman et al. eds., 5:476-487.
Liu, H-X, Chew SL, Cartegni L, Zhang MQ and Krainer AR, (2000). Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. MCB, 20:1063-1071.
Getz G, Levine E, Domany E and Zhang MQ (2000). Super-paramagnetic clustering of yeast gene expression profiles. Physica A. 279:457-464.
1999
Mayeda A, Badolato J, Kobayashi R, Zhang MQ, Gardiner EM and Krainer AR.(1999) Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing, EMBL 18:4560-4570.
Machida M, Yamazaki S, Kunihiro S, Tanaka T, Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S, Sekine M, Ogudhi A, Nagai Y, Sakai M, Aoki K, Ogura K, Kudoh Y, Kikuchi H, Zhang MQ and Yanagida M.(2000) A. 38 kb segment containing cdc2 gene from the left arm of fission yeast chromosome II: sequence analys is and characterization of the genomic DNA and cDNAs encoded on the segment, Yeast, 16:71-80.
Zhang, M.Q.(1999) Large scale gene expression data analysis: a new challenge to computational biologists, Genome Res. 9:681-688.
Tabaska, J.E. and Zhang, M.Q.(1999), Detection of polyadenylation signals in human DNA sequences. Gene, 231:77-86.
Ioshikhes, I., Trifonov, E.N. and Zhang, M.Q. (1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc. Natl. Acad. Sci. USA, 96:2891-2895.
Zhang, M.Q., (1999) Promoter Analysis of Co-regulated Genes in the Yeast Genome. Computers and Chemistry, 23:233-250.
Zhu, J. and Zhang, M.Q., (1999) SCPD: A Promoter Database of Yeast Saccharomyces cerevisiae, Bioinformatics, 15:607-611.
1998
Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998). Comprehensive Identification of Cell Cycle Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol. Biol. Cell. 9:3273-3297.
Liu, H.-X., Zhang, M.Q. and Krainer, A.R., (1998). Identification of Functional Exonic Splicing Enhancer Motifs Recognized by Individual SR Proteins. Gene & Dev. 12:1998-2012.
Zhang, M.Q., (1998). Identification of Protein Coding Regions in Arabidopsis thaliana Genome Based on Quadratic Discriminant Analysis. Mol. Plant. Biol., 37:803-806.
Zhang, M.Q., (1998). Identification of Human Gene Core-promoters In Silico. Genome Res., 8:319-326.
Zhang, M.Q., (1998). Statistical Features of Human Exons and Their Flanking Regions. Hum. Mol. Genet., 7:919-932.
Zhang, M.Q.,(1998). A Discrimination Study of Human Core-promoters, in Proceedings of Pacific Symposium on Biocomputing 1998. R.B. Altman et al. eds. pp240-251, World Scientific, Singapore.
Chen, T., and Zhang, M.Q. (1998). POMBE: A Fission Yeast Gene-finding and Exon-intron Structure Prediction System. Yeast, 14:701-710.
1997
Zhang, M.Q. (1997). Identification of Protein Coding Regions in the Human Genome Based on Quadratic Discriminant Analysis. Proc. Natl. Acad. Sci. USA, 94:565-568.
1995
N.Kaplan, M.Lodhi, A.Johnson, M.Q.Zhang, T.G.Marr and W.R.McCombie (1995), The Schizosaccharomyces Pombe Genome Project, Cold Spring Harb. Symp., Genome Mapping and Sequencing.
M.Q.Zhang and T.G.Marr (1995), Molecular Sequence Alignment Seen as Random Path Analysis, J. Theor. Biol., 174:119-130.
M.Q.Zhang and T.G.Marr (1995), Exploratory Analysis of Long Genomic DNA Sequences using the Wavelet Transform: Examples using Polyomavirus Genomes, Genome Sequencing and Analysis Conference VI, Hilton Head, NC, pp.72, Mary Ann Liebert, Inc..
1994
S.Stamm, M.Q.Zhang, T.G.Marr and D.M.Helfman (1994), A Sequence Compilation and Comparison of Exons That Are Alternatively Spliced in Neurons, Nucl. Acid. Res., 22:1515-1526.
M.Q.Zhang and T.G.Marr (1994), Statistical Analysis of the fission yeast genomic DNA sequences and gene recognition, Nucl. Acid. Res., 22:1750-1759.
M.Q.Zhang and T.G.Marr (1994), Genome Mapping with Random Anchored Clones: A Discrete Theoretical Analysis, J. Stat. Phys., 73:611-623.
M.Q.Zhang and T.G.Marr (1993), Large-scale Structure of Yeast Chromosome III: Implications in Genome Evolution, Cold Spring Harb. Symp., Genome Mapping and Sequencing.
M.Q.Zhang and T.G.Marr (1993), A Weight Array Method for Splicing Signal Analysis, CABIOS 9:499-509.
M.Q.Zhang and T.G.Marr (1993),Genome Mapping by Nonrandom Anchored Clones: A Discrete Theoretical Analysis, Proc. Natl. Acad. Sci. USA, 90:600-604.
1991
M.Q.Zhang (1991), How to Find the Lax Pairs from the Yang-Baxter Equations, Comm. Math. Phys.141:523.
M.Q.Zhang (1991), The Nonuniform Hard Rod Fluids Revisited, J. Stat. Phys.342:1191.
M.Q.Zhang (1991), Exact Response Functions of a 2D Fermion Fluid, J. Math. Phys. 32:1344.
M.Q.Zhang (1991), Crystallization of One-dimensional Hard Rods with a Periodic Interaction, J. Phys. A24:3949.
1990
M.Q.Zhang (1990), Zero-thickness Membrane Interface and Schrodinger Equation, {em Phys. Rev.,A42:4588.
M.Q.Zhang and J.K.Percus (1990), A Recursive Density Functional Formalism of Nonuniform Fluids, J. Chem. Phys. 92:6779.
M.Q.Zhang (1990), Entropy Functional of a Nonuniform Ising Model on a Two Row Lattice, J. Phys., A23:1.
1989
J.K.Percus and M.Q.Zhang (1989), The Quasi-One Dimensional Hard Square Gas, Mol. Phys.,69:347.
M.Q.Zhang (1989). Inhomogeneous Ising Model on a Multiconnected Networks, J.Stat.Phys., 56:695.
M.Q.Zhang and J.K.Percus (1989), Direct Correlations of the Capillary Wave Model and Construction of Free Energy Density Functional for the Liquid-Vapor Interface System, J. Chem. Physics, 90:3795.
M.Q.Zhang (1989), A Fast Vectorized Multispin Coding Algorithm for 3D Monte Carlo Simulations Using Kawasaki Spin-exchange Dynamics, J.Stat.Phys., 56:939.
1988
M.Q.Zhang and J.K.Percus (1988), 1-D Inhomogeneous Ising Model with Periodic Boundary Condition, Phys.Rev., B38:11737.
G.Ord, J.K.Percus and M.Q.Zhang (1988), Energetics of a Discrete Interface, Nucl.Phys., B305[FS23]:271.
M.Q.Zhang (1988), Exact Pair Correlation Function for Ising Spins with Competing Dynamics,J.Stat.Phys., 53:1217.
M.Q.Zhang, J.S.Wang, J.L.Lebowitz and J.L.Valles (1988), Power Law Decay of Correlations in Stationary Nonequilibrium Lattice Gases with Conservative Dynamics, J.Stat.Phys., 52:1461.
M.Q.Zhang (1988), Nonequilibrium Steady States of Some Stochastic Lattice Gas Models, Nucl.Phys.,B(Proc.Suppl.)5A:278.
1987
M.Q.Zhang (1987), Supersymmetrical Approach to Critical Dynamics of Relaxational Models, Phys.Rev., B36:3824.
M.Q.Zhang (1987), Exact Results on the Steady State of a Hopping Model,Phys.Rev., A35:2266.
1986
J.Krug,J.L.Lebowitz, H.Spohn and M.Q.Zhang (1986), The Fast Rate Limit of Diffusive System, J.Stat.Phys., 44:535
Book Chapters
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.
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 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). pp73-85. ISBN: 978-3-642-16344-9. http://www.springer.com/statistics/book/9783642163449
Zhang, C., Zhang, M.Q. 2008. Biomedical literature mining. Chapter 10 in Bioinformatics: A Concept-Based Introduction. (Mathura, V. & Kangueane, P., ed) Springer. 115-127.