Publications
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# Co-first authors; * Co-corresponding authors
2024
- Zhang Z#, Bao S#, Yan D, Zhai M, Qu J*,
Zhou M*. Causal Relationships Between Retinal Diseases and Psychiatric Disorders Have Implications for Precision Psychiatry. Molecular Neurobiology, 2024, doi: 10.1007/s12035-024-04456-2. [Abstract] - Wang Y#, Yang Z#, Guo X#, Jin W, Lin D, Chen A and
Zhou M*. Automated early detection of acute retinal necrosis from ultra-widefield color fundus photography using deep learning. Eye and Vision, 2024, 11(1):27. [Abstract] - Shi X, Lu M, Li X, Li J, Bao S, Jia C, Chen H*,
Zhou M*. The transcriptional landscape and clinico-biological characterization of human endogenous retroviruses in esophageal squamous cell carcinoma. International Journal of Cancer, 2024, doi: 10.1002/ijc.35147. [Abstract] - Zhuo L#, Meng F#, Sun K,
Zhou M*,Sun J*. Integrated immuno-transcriptomic analysis of ovarian cancer identifies a four-chemokine-dominated subtype with antitumor immune-active phenotype and favorable prognosis. British Journal of Cancer, 2024, 131(6):1068-1079. [Abstract] - Zhang Z#, Sun X#, Liu Y*, Zhang Y, Yang Z, Dong J, Wang N, Ying J,
Zhou M*, Yang L*. Spatial Transcriptome-Wide Profiling of Small Cell Lung Cancer Reveals Intra-Tumoral Molecular and Subtype Heterogeneity. Advanced Science, 2024, 11(31):e2402716. [Abstract] - Sun L#, Cen Y#, Liu X#, Wei J, Ke X, Wang Y, Liao Q, Chang M,
Zhou M*, Wu W*. Systemic whole transcriptome analysis identified underlying molecular characteristics and regulatory networks implicated in the retina following optic nerve injury. Experimental Eye Research, 2024, 244:109929. [Abstract] - Chi R, Yang X, Yang Z, Xia H, Li H, Pan L, Hao J, Yan D, Si X, Shi C*,
Sun J*, Li W*. Tumor microenvironment-responsive hyaluronic acid-oxaliplatin nanoparticles enhanced tumor cell elimination. Polymers for Advanced Technologies, 2024, 35(4):e6405. doi:10.1002/pat.6405. - Zhai M#, Zhang Y#, Yan D, Wang Y, Li W*,
Sun J*. Genetic Insights into the Association and Causality Between Blood Metabolites and Alzheimer’s Disease. Journal of Alzheimer’s Disease, 2024, 98(3):885-896. [Abstract] - Chen H, Yan D,
Sun J*,Zhou M*. Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning. Journal of Chemical Information and Modeling, 2024, 64(8):3579-3591. [Abstract] - Wu Y#, Shi R#, Chen H, Zhang Z, Bao S, Qu J*,
Zhou M*. Effect of the gut microbiome in glaucoma risk from the causal perspective. BMJ Open Ophthalmology, 2024, 9(1):e001547. [Abstract] - Zhang Y#, Yang Z#, Chen R#, Zhu Y#, Liu L, Dong J, Zhang Z, Sun X, Ying J, Lin D*, Yang L* &
Zhou M*. Histopathology images-based deep learning prediction of prognosis and therapeutic response in small cell lung cancer. npj Digital Medicine, 2024, 7(1):15. [Abstract] - Shi R#, Wu Y#, Chen H#, Zhang Z, Bao S, Qu J*,
Zhou M*. The causal effect of oxidative stress on the risk of glaucoma. Heliyon, 2024, 10(3):E24852. [Abstract] - Yang Z#, Zhang Y#, Zhuo L, Sun K, Meng F*,
Zhou M*,Sun J*. Prediction of prognosis and treatment response in ovarian cancer patients from histopathology images using graph deep learning: a multicenter retrospective study. European Journal of Cancer, 2024, 199:113532. [Abstract] - Li CX#, Chen H#, Kermani NZ, Adcock IM, Sköld CM,
Zhou M*, Wheelock ÅM*, U-BIOPRED study group. Consensus clustering with missing labels (ccml): a consensus clustering tool for multi-omics integrative prediction in cohorts with unequal sample coverage. Briefings in Bioinformatics, 2024, 25(1):bbad501. [Abstract] - Li K#, Zhang R#, Wen F#, Zhao Y, Meng F, Li Q, Hao A, Yang B, Lu Z*, Cui Y*,
Zhou M*. Single-cell dissection of the multicellular ecosystem and molecular features underlying microvascular invasion in hepatocellular carcinoma. Hepatology, 2024, 79(6):1293-1309. [Abstract]
2023
- Liu Z#, Xie H#, Li L#, Jiang D, Qian Y, Zhu X, Dai M, Li Y, Wei R, Luo Z, Xu W, Zheng Q, Shen J,
Zhou M, Zeng W*, Chen W*. Single-Cell Landscape Reveals the Epithelial Cell-Centric Proinflammatory Immune Microenvironment in Dry Eye Development. Mucosal Immunology, 2023, S1933-0219(23)00091-0. [Abstract] - Xu K#, Huang S#, Yang Z#, Zhang Y, Fang Y, Zheng G, Lin B*,
Zhou M*,Sun J*. Automatic detection and differential diagnosis of age-related macular degeneration from color fundus photographs using deep learning with hierarchical vision transformer. Computers in Biology and Medicine, 2023, 167:107616. [Abstract] - Li K#, Sun L#, Wang Y#, Cen Y, Zhao J, Liao Q, Wu W*,
Sun J*andZhou M*. Single-cell characterization of macrophages in uveal melanoma uncovers transcriptionally heterogeneous subsets conferring poor prognosis and aggressive behavior. Experimental & Molecular Medicine, 2023, 55(11):2433-2444. [Abstract] - Zhao N#, Zhang Z#, Wang Q#, Li L#, Wei Z, Chen H*,
Zhou M*, Liu Z*, Su J*. DNA damage repair profiling of esophageal squamous cell carcinoma uncovers clinically relevant molecular subtypes with distinct prognoses and therapeutic vulnerabilities. eBioMedicine, 2023, 96:104801. [Abstract] - Zhang Y#, Yan C#, Yang Z,
Zhou M*,Sun J*. Multi-omics Deep-learning Prediction of Homologous Recombination Deficiency-like Phenotype Improved Risk Stratification and Guided Therapeutic Decisions in Gynecological Cancers. IEEE Journal of Biomedical and Health Informatics, 2023, doi: 10.1109/JBHI.2023.3308440. [Abstract] - Chen L#, Ma R#, Luo C#, Xie Q#, Ning X, Sun K, Meng F*,
Zhou M*,Sun J*. Noninvasive early differential diagnosis and progression monitoring of ovarian cancer using the copy number alterations of plasma cell-free DNA. Translational Research, 2023, 262:12-24. [Abstract] - Zhang Z#, Chen H#, Yan D, Chen L,
Sun J*&Zhou M*. Deep learning identifies a T-cell exhaustion-dependent transcriptional signature for predicting clinical outcomes and response to immune checkpoint blockade. Oncogenesis, 2023, 12(1):37. [Abstract] - Yang L#, Zhang Z#, Dong J, Zhang Y, Yang Z, Guo Y, Sun X, Li J, Xing P*, Ying J*,
Zhou M*. Multi-dimensional characterization of immunological profiles in small cell lung cancer uncovers clinically relevant immune subtypes with distinct prognoses and therapeutic vulnerabilities. Pharmacological Research, 2023, 194:106844. [Abstract] Zhou M#, Bao S#, Gong T#, Wang Q#,Sun J, Li J, Lu M, Sun W, Su J*, Chen H* & Liu Z*. The transcriptional landscape and diagnostic potential of long non-coding RNAs in esophageal squamous cell carcinoma. Nature Communications, 2023, 14(1):3799. [Abstract]- Yang Z, Zhang Y, Xu K,
Sun J*, Wu Y*,Zhou M*. DeepDrRVO: A GAN-auxiliary two-step masked transformer framework benefits early recognition and differential diagnosis of retinal vascular occlusion from color fundus photographs. Computers in Biology and Medicine, 2023, 163:107148. [Abstract] - Su J#*, Yuan J#, Xu L#, Xing S#, Sun M#, Yao Y, Ma Y, Chen F, Jiang L, Li K, Yu X, Xue Z, Zhang Y, Fan D, Zhang J, Liu H, Liu X, Zhang G, Wang H,
Zhou M, Lyu F, An G, Yu X, MAGIC, Xue Y*, Yang J* and Qu J*. Sequencing of 19,219 exomes identifies a low-frequency variant in FKBP5 promoter predisposing to high myopia in a Han Chinese population. Cell Reports, 2023, 42(5):112510. [Abstract] - Jiang D#, Yan C#, Ge L, Yang C, Huang Y, Chan YK, Chen C, Chen W,
Zhou M*and Lin B*. Metabolomic analysis of aqueous humor reveals potential metabolite biomarkers for differential detection of macular edema. Eye and Vision, 2023,10(1):14. [Abstract] - Yan C#, Li K#, Meng F#, Chen L, Zhao J, Zhang Z, Xu D*,
Sun J*,Zhou M*. Integrated immunogenomic analysis of single-cell and bulk tissue transcriptome profiling unravels a macrophage activation paradigm associated with immunologically and clinically distinct behaviors in ovarian cancer. Journal of Advanced Research, 2023, 44:149-160 [Abstract] - Yan C#, Hu X#, Liu X#, Zhao J, Le Z, Feng J,
Zhou M, Ma X*, Zheng Q*,Sun J*. Upregulation of SLC12A3 and SLC12A9 Mediated by the HCP5/miR-140-5p Axis Confers Aggressiveness and Unfavorable Prognosis in Uveal Melanoma. Laboratory Investigation, 2023, 103(3):100022. [Abstract]
2022
- Bao S#, Zhou T#, Yan C, Bao J, Yang F, Chao S,
Zhou M*and Xu Z*. A blood-based miRNA signature for early non-invasive diagnosis of preeclampsia. BMC Medicine, 2022, 20(1):303 [Abstract] - Zhang Z#, Chen L#, Chen H, Zhao J, Li K,
Sun J*,Zhou M*. Pan-cancer landscape of T-cell exhaustion heterogeneity within the tumor microenvironment revealed a progressive roadmap of hierarchical dysfunction associated with prognosis and therapeutic efficacy. eBioMedicine, 2022, 83:104207. [Abstract] - Li C#, Shi X#, Yang J, Li K, Dai L, Zhang Y,
Zhou M*, Su J*. Genome-wide characterization of RNA editing highlights roles of high editing events of glutamatergic synapse during mouse retinal development. Computational and Structural Biotechnology Journal, 2022, 20:2648-2656. [Abstract] - Zhao J#, Yi Q#, Li K, Chen L, Dai L, Feng J, Li Y*,
Zhou M*,Sun J*. A multi-omics deep learning model for hypoxia phenotype to predict tumor aggressiveness and prognosis in uveal melanoma for rationalized hypoxia-targeted therapy. Computational and Structural Biotechnology Journal, 2022, 20:3182-3194. [Abstract] - Ren Y#, Yan C#, Wu L#, Zhao J, Chen M,
Zhou M, Wang X, Liu T*, Yi Q* andSun J*. iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma. npj Systems Biology and Applications, 2022, 8(1):18. [Abstract] - Yu Y#, Zhang Z#, Meng Q#, Wang K, Li Q, Ma Y, Yao Y,
Sun J*and Wang G*. Efficacy of Different Number of XELOX or SOX Chemotherapy Cycles After D2 Resection for Stage III Gastric Cancer. Journal of Gastric Cancer, 2022,22(2):107-119. [Abstract] - Xi Y#, Lin Y#, Guo W#, Wang X, Zhao H, Miao C, Liu W, Liu Y, Liu T, Luo Y, Fan W, Lin A, Chen Y, Sun Y, Ma Y, Niu X, Zhong C, Tan W,
Zhou M, Su J*, Wu C* and Lin D*. Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma. Signal Transduction and Targeted Therapy, 2022, 7(1):53. [Abstract] - Ji W#, Chen L#, Yang W#, Li K, Zhao J, Yan C, You C, Jiang M,
Zhou M*& Shen X*. Transcriptional landscape of circulating platelets from patients with COVID-19 reveals key subnetworks and regulators underlying SARS-CoV-2 infection: implications for immunothrombosis. Cell & Bioscience, 2022, 12(1):15. [Abstract] Sun J#, Yan C#, Xu D#, Zhang Z, Li K, Li X,Zhou M*& Hao D*. Immuno-genomic characterisation of high-grade serous ovarian cancer reveals immune evasion mechanisms and identifies an immunological subtype with a favourable prognosis and improved therapeutic efficacy. British Journal of Cancer, 2022, 126(11):1570-1580. [Abstract]- Bao S#, Li K, Yan C, Zhang Z, Qu J*,
Zhou M*. Deep learning-based advances and applications for single-cell RNA-sequencing data analysis. Briefings in Bioinformatics, 2022, 23(1):bbab473. [Abstract] - Li K#, Yan C#, Li C#, Chen L, Zhao J, Zhang Z, Bao S,
Sun J*,Zhou M*. Computational elucidation of spatial gene expression variation from spatially resolved transcriptomics data. Molecular Therapy - Nucleic Acids, 2022, 27:404-411. [Abstract]
2021
- Li CX#, Gao J#, Zhang Z, Chen L, Li X*,
Zhou M*, Wheelock ÅM*. Multiomics integration-based molecular characterizations of COVID-19. Briefings in Bioinformatics, 2021, 23(1):bbab485. [Abstract] - Ji X#, Zhang Z#, Lin D, Dai M, Zhao X, Guo X, Du J,
Zhou M*, WangY*. A novel clinical five-risk factor panel for individualized recurrence risk assessment of patients with acute anterior uveitis. Transl Vis Sci Technol, 2021,10(13):29. [Abstract] Zhou M#, Hou P#, Yan C#, Chen L, Li K, Wang Y, Zhao J, Su J* &Sun J*. Cell-free DNA 5-hydroxymethylcytosine profiles of long non-coding RNA genes enable early detection and progression monitoring of human cancers. Clinical Epigenetics, 2021, 13(1):197. [Abstract]- Xu L#, Zhuang Y#, Zhang G#, Ma Y#, Yuan J#, Tu C, Li MM, Wang W, Zhang Y, Lu X, Li J, Liu X, Xue Z,
Zhou M,Sun J, Bao J, Li M, Lu F*, Wang H*, Su J*, Qu J*. Design, methodology, and baseline of whole city-million scale children and adolescents myopia survey (CAMS) in Wenzhou, China. Eye and Vision, 2021,8(1):31 [Abstract] - Wang G#, Xu D#, Zhang Z#, Li X, Shi J,
Sun J, Liu HZ, Li X*,Zhou M*& Zheng T*. The pan-cancer landscape of crosstalk between epithelial-mesenchymal transition and immune evasion relevant to prognosis and immunotherapy response. npj Precision Oncology, 2021, 5(1):56. [Abstract] - Zhang Z#, Yan C#, Li K, Bao S, Li L, Chen L, Zhao J,
Sun J*&Zhou M*. Pan-cancer characterization of lncRNA modifiers of immune microenvironment reveals clinically distinct de novo tumor subtypes. npj Genomic Medicine, 2021, 6(1):52. [Abstract] - Wang X#, Qian T#, Bao S#, Zhao H, Chen H, Xing Z, Li Y, Zhang M, Meng X, Wang C, Wang J, Gao H, Liu J*,
Zhou M*, Wang X*. Circulating exosomal miR-363-5p inhibits lymph node metastasis by downregulating PDGFB and serves as a potential noninvasive biomarker for breast cancer. Molecular Oncology, 2021, 15(9):2466-2479. [Abstract] - Xu L#, Ma Y#, Yuan J#, Zhang Y#, Wang H#, Zhang G, Tu C, Lu X, Li J, Xiong Y, Chen F, Liu X, Xue Z,
Zhou M, Li W, Wu N, Bao J, Chen H, Lu F*, Su J*, Qu J*. COVID-19 quarantine reveals behavioral changes effect on myopia progression. Ophthalmology, 2021, S0161-6420(21)00257-8. [Abstract] - Liu J#, Zhao H#, Huang Y#, Xu S#, Zhou Y, Zhang W, Li J, Ming Y, Wang X, Zhao S, Li K, Dong X, Ma Y, Qian T, Chen X, Xing Z, Zhang Y, Chen H, Liu Z, Pang D,
Zhou M, Wu Z, Wang X, Wang X*, Wu N* and Su J*. Genome-wide cell-free DNA methylation analyses improve accuracy of non-invasive diagnostic imaging for early-stage breast cancer. Molecular Cancer, 2021, 20(1):36. [Abstract] - Bao S#, Hu T#, Liu J#, Su J,
Sun J, Ming Y, Li J, Wu N*, Chen H* andZhou M*. Genomic instability-derived plasma extracellular vesicle-microRNA signature as a minimally invasive predictor of risk and unfavorable prognosis in breast cancer. Journal of Nanobiotechnology, 2021, 19(1):22. [Abstract] - Hou P, Bao S, Fan D, Yan C, Su J, Qu J*,
Zhou M*. Machine learning-based integrative analysis of methylome and transcriptome identifies novel prognostic DNA methylation signature in uveal melanoma. Briefings in Bioinformatics, 2021, 22(4):bbaa371 [Abstract]
2020
- Chen XJ#, Zhang ZC#, Wang XY#, Zhao HQ, Li ML, Ma Y, Ji YY, Zhang CJ, Wu KC, Xiang L, Sun LF,
Zhou M*, Jin ZB*. The Circular RNome of Developmental Retina in Mice. Molecular Therapy - Nucleic Acids, 2020, 19:339-349. [Abstract] - Yang C, Zhang Z, Bao S, Hou P,
Zhou M, Xu C*,Sun J*. Computational Methods and Applications for Identifying Disease-Associated lncRNAs as Potential Biomarkers and Therapeutic Targets. Molecular Therapy - Nucleic Acids, 2020, 21:156-171. [Abstract] - Zhang Y#, Ma Y#, Huang Y, Zhang Y, Jiang Q,
Zhou M, Su J*. Benchmarking algorithms for pathway activity transformation of single-cell RNA-seq data. Computational and Structural Biotechnology Journal, 2020, 18:2953-2961 [Abstract] - Zhang Y#, Zhang Y#, Hu J#, Zhang J, Guo F,
Zhou M, Zhang G*, Yu F*, Su J*, scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures. Bioinformatics, 2020, 36(14):4217-4219. [Abstract] - Yu F#, Li K#, Li S#, Liu J, Zhang Y,
Zhou M, Zhao H, Chen H, Wu N, Liu Z*, Su J*. CFEA: a cell-free epigenome atlas in human diseases. Nucleic acids research, 2020, 48(D1): D40-D44. [Abstract] Sun J#, Zhang Z#, Bao S#, Yan C, Hou P, Wu N, Su J, Xu L*,Zhou M*. Identification of tumor immune infiltration-associated lncRNAs for improving prognosis and immunotherapy response of patients with non-small cell lung cancer. Journal for ImmunoTherapy of Cancer, 2020, 8(1):e000110. [Abstract]Zhou M#，Zhang Z#, Bao S#, Hou P, Yan C, Su J*,Sun J*. Computational recognition of lncRNA signature of tumor-infiltrating B lymphocytes with potential implications in prognosis and immunotherapy of bladder cancer. Briefings in Bioinformatics, 2020, 22(3):bbaa047. [Abstract]- Zhao H#, Gu S#, Bao S, Yan C, Zhang Z, Hou P,
Zhou M*，Sun J*. Mechanistically-derived patient-level framework for precision medicine identifies a personalized immune prognostic signature in high-grade serous ovarian cancer. Briefings in Bioinformatics, 2020, 22(3):bbaa069. [Abstract] - Zhang Z, Bao S, Hou P, Yan CC,
Zhou M*,Sun J*. Computational principles and practice for decoding immune contexture in the tumor microenvironment. Briefings in Bioinformatics, 2020, 22(3):bbaa075. [Abstract]
2019
Zhou M#, Zhao H#, Wang X,Sun J*, Su J*. Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer’s disease. Briefings in Bioinformatics, 2019, 20(2): 598-608. [Abstract]Sun J#, Bao S, Xu D, Zhang Y, Su J, Liu J, Hao D*,Zhou M*. Large-scale integrated analysis of ovarian cancer tumors and cell lines identifies an individualized gene expression signature for predicting response to platinum-based chemotherapy. Cell death & disease, 2019, 10(9):661. [Abstract]- Bao S#, Zhao H, Yuan J, Fan D, Zhang Z, Su J*,
Zhou M*. Computational identification of mutator-derived lncRNA signatures of genome instability for improving the clinical outcome of cancers: a case study in breast cancer. Briefings in Bioinformatics, 2020, 21(5):1742-1755. [Abstract]
2018
Zhou M#, Zhang Z#, Zhao H, Bao S,Sun J*. A novel lncRNA-focus expression signature for survival prediction in endometrial carcinoma. BMC Cancer, 2018, 18(1):39. [Abstract]Zhou M#, Zhang Z#, Zhao H, Bao S, Cheng L,Sun J*. An Immune-Related Six-lncRNA Signature to Improve Prognosis Prediction of Glioblastoma Multiforme. Molecular Neurobiology, 2018, 55(5):3684-3697. [Abstract]- Cheng L#, Jiang Y#, Ju H,
Sun J, Peng J,Zhou M*, Hu Y*. InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. BMC Genomics, 2018, 19(Suppl 1):919. [Abstract] - Cheng L#, Hu Y#,
Sun J,Zhou M*, Jiang Q*. DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function. Bioinformatics, 2018, 34(11): 1953-1956. [Abstract]
Before 2017
Zhou M#, Zhao H#, Xu W, Bao S, Cheng L*,Sun J*. Discovery and validation of immune-associated long non-coding RNA biomarkers associated with clinically molecular subtype and prognosis in diffuse large B cell lymphoma. Molecular Cancer, 2017, 16(1):16. [Abstract]- Hu Y#,
Zhou M#, Shi H, Ju H, Jiang Q*, Cheng L*. Measuring disease similarity and predicting disease-related ncRNAs by a novel method. BMC Medical Genomics, 2017, 10(Suppl 5):71. [Abstract] Zhou M#, Zhao H#, Wang Z#, Cheng L, Yang L, Shi H, Yang H,Sun J*. Identification and validation of potential prognostic lncRNA biomarkers for predicting survival in patients with multiple myeloma. Journal of Experimental Clinical Cancer Research, 2015, 34(1):102. [Abstract]Zhou M#, Guo M#, He D#, Wang X, Cui Y, Yang H, Hao D*,Sun J*. A potential signature of eight long non-coding RNAs predicts survival in patients with non-small cell lung cancer. Journal of Translational Medicine, 2015, 13:231. [Abstract]Sun J#, Shi H#, Wang Z, Zhang C, Liu L, Wang L, He W, Hao D*, Liu S*,Zhou M*. Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network. Molecular Biosystems, 2014, 10:2074-2081. [Abstract]- Lu J, Wu D, Li C#,
Zhou M*, Hao D*. Correlation between gene expression and mutator phenotype predicts homologous recombination deficiency and outcome in ovarian cancer. Journal of Molecular Medicine (Berlin, Germany), 2014, 92:1159-1168. [Abstract] - Hao D#*, Wang G, Yin Z, Li C, Cui Y,
Zhou M*. Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. European Journal of Human Genetics, 2014, 22:1260-1267. [Abstract] - Hao D#*, Li C, Zhang S, Lu J, Jiang Y, Wang S,
Zhou M*. Network-based analysis of genotype-phenotype correlations between different inheritance modes. Bioinformatics, 2014, 30:3223-3231. [Abstract] Sun J#, Gao B#,Zhou M#*, Wang ZZ, Zhang F, Deng JE, Li X*. Comparative genomic analysis reveals evolutionary characteristics and patterns of microRNA clusters in vertebrates. Gene, 2013, 512:383-391. [Abstract]