Publications (* co-first author, # corresponding author)

2016

  • Hemnes. AR, Zhao M *, West. J, Newman. JH, Rich. S, Archer. SL, Robbins. IM, Blackwell. TS, Cogan. J, Loyd. JE, Zhao. Z, Gaskill. C, Jetter. C, Kropski. JA, Majka. SM and Austin. ED. Critical Genomic Networks and Vasoreactive Variants in Idiopathic Pulmonary Arterial Hypertension. American Journal of Respiratory and Critical Care Medicine. 2016.
  • Zhao M, Liu. Y and Qu. H. Expression of epithelial-mesenchymal transition-related genes increases with copy number in multiple cancer types. Oncotarget. 2016:008742.
  • Zhao M #,Lumin Chen, Liu. Y and Qu. H. GCGene: a gene resource for gastric cancer with literature evidence. Oncotarget. 2016:011117.
  • Zhao M, Liu. D and Qu. H. Systematic review of next-generation sequencing simulators: computational tools, features and perspectives. Briefings in Functional Genomics. 2016.
  • Zhao M and Zhao. Z. Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study. BMC Genomics. 2016; 17.
  • Zhao M #, Jingchun Sun, Yining Liu. (2015) Literature-based knowledgebase of pancreatic cancer gene to prioritize the key genes and pathways. Journal of Genetics and Genomics. doi:10.1016/j.jgg.2016.04.006
  • Liu Y and Zhao M #. lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes. Bioinformatics. 2016:btw017.
  • Zhao M, Rotgans. B, Wang. T and Cummins. SF. REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer. Sci Rep. 2016; 6:srep25400.
  • Zhao M #, Yining Liu, Fuda Huang & Hong Qu. A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes. Sci Rep. 2016; 6:srep30624.
  • Zhao M, Wang. T, Adamson. KJ, Storey. KB and Cummins. SF. Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana. Sci Rep. 2016; 6:srep20685.
  • Zhao M, Kim P, Mitra R, Zhao J and Zhao Z. TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Res. 2016; 44(D1):D1023-1031.
  • Zhao M, Chen L and Qu H. CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. Cell Death Dis. 2016; 7:e2053.
  • Wang T, Zhao M, Rotgans BA, Strong A, Liang D, Ni G, Limpanont Y, Ramasoota P, McManus DP and Cummins SF. Proteomic Analysis of the Schistosoma mansoni Miracidium. PLoS One. 2016; 11(1):e0147247.
  • Suwansa-Ard S, Zhao M, Thongbuakaew T, Chansela P, Ventura T, Cummins SF, Sobhon P. Gonadotropin-releasing hormone and adipokinetic hormone/corazonin-related peptide in the female prawn. Gen Comp Endocrinol. 2016 Jul 9;236:70-82. doi: 10.1016/j.ygcen.2016.07.008.
  • Wang T, Zhao M, Rotgans BA, Ni G, Dean JF, Nahrung HF, Cummins SF. Proteomic analysis of the venom and venom sac of the woodwasp, Sirex noctilio - Towards understanding its biological impact. J Proteomics. 2016 Jul 5;146:195-206. doi: 10.1016/j.jprot.2016.07.002.
  • Wei R, Yao Y, Yang W, Zheng CH, Zhao M, Xia J. dbCPG: A web resource for cancer predisposition genes. oncotarget, 10.18632/oncotarget.9334

2015

  • Zhao M, Ma L, Liu Y and Qu H. Pedican: an online gene resource for pediatric cancers with literature evidence. Sci Rep. 2015; 5:11435.
  • Zhao M #, Liu Y and O'Mara TA. ECGene: A Literature-Based Knowledgebase of Endometrial Cancer Genes. Hum Mutat. 2015:humu.22950.
  • Zhao M, Li Z and Qu H. An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. Sci Rep. 2015; 5:15478.
  • Zhao M, Kong L, Liu Y and Qu H. dbEMT: an epithelial-mesenchymal transition associated gene resource. Sci Rep. 2015; 5:11459.
  • Zhao M, Chen Y, Qu D and Qu H. METSP: A Maximum-Entropy Classifier Based Text Mining Tool for Transporter-Substrate Identification with Semistructured Text. Biomed Res Int. 2015; 2015:254838.
  • Suwansa-Ard S, Thongbuakaew T, Wang T, Zhao M, Elizur A, Hanna PJ, Sretarugsa P, Cummins SF and Sobhon P. In silico Neuropeptidome of Female Macrobrachium rosenbergii Based on Transcriptome and Peptide Mining of Eyestalk, Central Nervous System and Ovary. PLoS One. 2015; 10(5):e0123848.
  • Sun J, Zhao M, Jia P, Wang L, Wu Y, Iverson C, Zhou Y, Bowton E, Roden DM, Denny JC, Aldrich MC, Xu H and Zhao Z. Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput Biol. 2015; 11(6):e1004202.
  • Sun B, Wang YF, Li CS, Yang J, Li JF, Li YL, Deng T, Wang SQ, Zhao M, Spicer RA, Ferguson DK and Mehrotra RC. Early Miocene elevation in northern Tibet estimated by palaeobotanical evidence. Sci Rep. 2015; 5:10379.
  • Liu Y, Xia J, Sun J and Zhao M#. OCGene: a database of experimentally verified ovarian cancer-related genes with precomputed regulation information. Cell Death Dis. 2015; 6:e2036.
  • Cogan JD, Kropski JA, Zhao M, Mitchell DB, Rives L, Markin C, Garnett ET, Montgomery KH, Mason WR, McKean DF, Powers J, Murphy E, Olson LM, Choi L, Cheng DS, Blue EM, et al. Rare variants in RTEL1 are associated with familial interstitial pneumonia. Am J Respir Crit Care Med. 2015; 191(6):646-655.
  • Chen X, Zhao M# and Qu H. Cellular Metabolic Network Analysis: Discovering Important Reactions in Treponema pallidum. Biomed Res Int. 2015; 2015:328568.
  • Adamson KJ, Wang T, Zhao M, Bell F, Kuballa AV, Storey KB and Cummins SF. Molecular insights into land snail neuropeptides through transcriptome and comparative gene analysis. BMC Genomics. 2015; 16:308.

2014

  • Zhao M, Kong L and Qu H. A systems biology approach to identify intelligence quotient score-related genomic regions, and pathways relevant to potential therapeutic treatments. Sci Rep. 2014; 4:4176.
  • Zhao M, Austin ED, Hemnes AR, Loyd JE and Zhao Z. An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. Mol Biosyst. 2014; 10(4):732-740.
  • Ye AY, Liu QR, Li CY, Zhao M # and Qu H. Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes. PLoS One. 2014; 9(2):e88883.
  • Stewart MJ, Favrel P, Rotgans BA, Wang T, Zhao M, Sohail M, O'Connor WA, Elizur A, Henry J and Cummins SF. Neuropeptides encoded by the genomes of the Akoya pearl oyster Pinctata fucata and Pacific oyster Crassostrea gigas: a bioinformatic and peptidomic survey. BMC Genomics. 2014; 15:840.
  • Mitra R, Edmonds MD, Sun J, Zhao M, Yu H, Eischen CM and Zhao Z. Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. RNA. 2014; 20(9):1356-1368.

2013

  • Zhao M and Zhao Z. CNVannotator: a comprehensive annotation server for copy number variation in the human genome. PLoS One. 2013; 8(11):e80170.
  • Zhao M, Wang Q, Wang Q, Jia P and Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics. 2013; 14 Suppl 11:S1.
  • Zhao M, Sun J and Zhao Z. TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res. 2013; 41(Database issue):D970-976.
  • Zhao M, Sun J and Zhao Z. Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Mol Biosyst. 2013; 9(12):3187-3198.
  • Zhao M, Li X and Qu H. EDdb: a web resource for eating disorder and its application to identify an extended adipocytokine signaling pathway related to eating disorder. Sci China Life Sci. 2013; 56(12):1086-1096.
  • Sun J, Zhao M, Fanous AH and Zhao Z. Characterization of schizophrenia adverse drug interactions through a network approach and drug classification. Biomed Res Int. 2013; 2013:458989.
  • Mitra R, Sun J, Zhao M and Zhao Z. Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer. BMC Bioinformatics. 2013; 14(Suppl 17):A14-A14.
  • Kong L, Cheng L, Fan LY, Zhao M # and Qu H. IQdb: an intelligence quotient score-associated gene resource for human intelligence. Database (Oxford). 2013; 2013:bat063.

Before 2013

  • Zhao M, Sun J and Zhao Z. Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One. 2012; 7(8):e44175.
  • Xu LM, Li JR, Huang Y, Zhao M, Tang X and Wei L. AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res. 2012; 40(Database issue):D1016-1022.
  • Zhao M, Jingchun S and Zhongming Z. (2012). Comprehensive analyses of tumor suppressor genes in protein-protein interaction networks: A topological perspective. Genomic Signal Processing and Statistics, (GENSIPS), 2012 IEEE International Workshop on, pp. 101-102.
  • Zhao M and Qu H. High similarity of phylogenetic profiles of rate-limiting enzymes with inhibitory relation in Human, Mouse, Rat, budding Yeast and E. coli. BMC Genomics. 2011; 12 Suppl 3:S10.
  • Zhao M, Chen Y, Qu D and Qu H. TSdb: a database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates. Sci China Life Sci. 2011; 54(1):60-64.
  • Zhao M and Qu H. PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis. BMC Genomics. 2010; 11 Suppl 4:S13.
  • Chinese Human Liver Proteome Profiling C. First insight into the human liver proteome from PROTEOME(SKY)-LIVER(Hu) 1.0, a publicly available database. J Proteome Res. 2010; 9(1):79-94.
  • Zhao M and Qu H. Human liver rate-limiting enzymes influence metabolic flux via branch points and inhibitors. BMC Genomics. 2009; 10 Suppl 3:S31.
  • Zhao M, Chen X, Gao G, Tao L and Wei L. RLEdb: a database of rate-limiting enzymes and their regulation in human, rat, mouse, yeast and E. coli. Cell Res. 2009; 19(6):793-795.
  • Zhang W, Zhang Y, Zheng H, Zhang C, Xiong W, Olyarchuk JG, Walker M, Xu W, Zhao M, Zhao S, Zhou Z and Wei L. SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res. 2007; 35(Database issue):D737-741.