*** A list of recent NGS publications or manuscripts can be accessed here.

Xia J, Wang Q, Jia P, Wang B, Pao W, Zhao Z (2012) NGS Catalog: A database of next generation sequencing studies in humans. Human Mutation 33:E2341-2355 PubMed      Access the database here.

Sun J, Wu Y, Xu H, Zhao Z (accepted) DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics

Flynn R, Zheng S, Fessel J, Cogan J, Austin E, Loyd J, West J, Zhao Z, Hamid R (2012) Connectivity Map analysis of NMD+ BMPR2 related HPAH provides insights into disease penetrance. American Journal of Respiratory Cell and Molecular Biology (AJRCCM) (in press)

Coburn LA, Gong X, Singh K, Asim M, Scull BP, Allaman MM, Williams CS, Rosen MJ, Washington MK, Barry DP, Piazuelo MB, Casero, RA, Chaturvedi R, Zhao Z, Wilson KT (accepted) L-arginine supplementation improves responses to injury and inflammation in dextran sulfate sodium colitis. PLoS ONE

Fanous AH, Middleton F, Gentile K, Amdur RL, Maher BS, Zhao Z, Medeiros H, Carvalho C, Ferreira SR, Macedo A, Knowles JA, Azevedo MH, Pato MT, Pato CN (accepted) Genetic Overlap of Schizophrenia and Bipolar Disorder in a High-Density Linkage Survey in the Portuguese Island Population. American Journal of Medical Genetics: NeuroPsychiatric Genetics

Webb BT, Guo AY, Zhao Z, Maher BS, van den Oord E, Kendler KS, Riley BP, Gillespie NA, Prescott, CA, Chen X, Prescott CA, Middeldorp CM, Willemsen G, de Geus EJC, Hottenga JJ, Boomsma DI, Slagboom E, Wray NR, Montgomery GW, Martin NG, Wright MJ, Heath AC, Madden PA, Gelernter J, Knowles, JA, Hamilton SP, Weissman MM, Fyer AJ, Huezo-Diaz P, McGuffin P, Farmer A, Craig IW, Lewis C, Sham P, Crowe RR, Flint J, Hettema JM (accepted) Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes. Eur. J. Hum. Genet.

Jia P, Wang L, Fanous AH, Chen X, Kendler KS, the International Schizophrenia Consortium, Zhao Z (2012) A bias-reducing pathway enrichment analysis of GWAS datasets confirmed association of the MHC region with schizophrenia. Journal of Medical Genetics 49:96-103 PubMed

Kao CF, Jia P, Zhao Z [co-corresponding author], Kuo PH (2012) Enriched pathways for major depressive disorder identified from a genome-wide association study. International Journal of Neuropsychopharmacology (in press)

Zheng S, Zhao Z (2012) GenRev: exploring gene relevance in molecular networks. Genomics 99:183-188 PubMed

Sun J, Jayathilake K, Zhao Z [co-corresponding author], Meltzer HY (2012) Investigating association of four genes GABRB3, MAOB, PAH, and SLC6A4 with five symptoms in schizophrenia. Psychiatry Res (in press)

Putman D, Sun J, Zhao Z (2011) Exploring schizophrenia drug-gene Interactions through molecular network and pathway modeling. AMIA Annu Symp Proc 2011:1127-1133 PubMed

Su Z, Xia J, Zhao Z (2011) Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome. BMC Genomics 12(Suppl 5):S15 download paper here

Zhao Z, Guo AY, van den Oord EJ, Aliev F, Jia P, Edenberg HJ, Riley BP, Dick DM, Bettinger JC, Davies A, Grotewiel MS, Schuckit MA, Agrawal A, Kramer J, Nurnberger JI, Kendler KS, Webb BT, Miles MF (accepted) Multi-species data integration and gene ranking enriches significant results in a genome-wide association study of human alcohol dependence symptoms. Chemistry and Biodiversity

Jia P, Kao CF, Kuo PH, Zhao Z (2011) A comprehensive network and pathway analysis of candidate genes in major depressive disorder. BMC Systems Biology 5(Suppl 3):S12 download paper here

Zheng S, Tansey WP, Hiebert SW, Zhao Z (2011) Integrative network analysis identifies key genes and pathways in the progression of Hepatitis C virus induced hepatocellular carcinoma. BMC Medical Genomics 4: 62 PubMed

Yang J, Chen T, Sun L, Zhao Z, Qi X, Zhou K, Cao Y, Wang X, Qiu Y, Su M, Zhao A, Wang P, Yang P, Wu J, Feng G, He L, Jia W, Wan C (2011) Potential metabolite markers of schizophrenia. Molecular Psychiatry, Advanced online access October 26, 2011

Garcia CB, Shaffer CM, Alfaro MP, Smith AL, Sun J, Zhao Z, Young PP, VanSaun MN, Eid JE (2011) Reprogramming of mesenchymal stem cells by the synovial sarcoma-associated oncogene SYT-SSX2. Oncogene. Advanced access online September 26, 2011 PubMed

Hettema JM, Webb BT, Guo AY, Zhao Z, Maher BS, Chen X, An SS, Sun C, Kendler KS, Kuo PH, Flint J, van den Oord E (2011) Prioritization and association analysis of murine-derived candidate genes in anxiety-spectrum disorders. Biological Psychiatry PubMed

Chen J, Lee G, Fanous AH, Zhao Z, Jia P, O'Neil A, Walsh D, The International Schizophrenia Consortium, Kendler KS, Chen X (2011) Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia. Schizophrenia Research Advance online access July 12, 2011 PubMed

Sun Y, Zheng S, Speirs C, Zhao Z [co-corresponding author], Lu B (accepted) The role of IGF-1 signaling pathway in cisplatin-resistant lung cancer cells. International Journal of Radiation Oncology, Biology and Physics.

Leung A, Cajigas I, Jia P, Ezhkova E, Brickner J, Zhao Z, Geng F, Tansey WP (2011) Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Molecular Biology of the Cell 22(15): 2741-2753 PubMed

Simpson DR, Yu M, Zheng S, Zhao Z, Muthuswamy SK, Tansey WP (2011) Epithelial cell organization suppresses Myc function by attenuating Myc expression. Cancer Research 71(11):3822-3830 PubMed

Bigdeli TB, Maher BS, Zhao Z, van den Oord EJCG, Thiselton DL, Sun J, Webb BT, Amdur RL, Wormley B, O'Neill FA, Walsh D, Riley BP, Kendler KS, Fanous AH (accepted) Comprehensive gene-based association study of a chromosome 20 linked region implicates novel risk loci for depressive symptoms in psychotic illness. PLoS ONE

Wang L, Jia P, Wolfinger RD, Chen X, Zhao Z (2011) Pathway analysis of genome-wide association studies: methodological issues and perspectives. Genomics. 98(1) 1-8 PubMed

Smalley-Freed WG, Efimov A, Short SP, Jia P, Zhao Z, Washington MK, Robine S, Coffey RJ, Reynolds AB (2011) Adenoma formation following limited ablation of p120-catenin in the mouse intestine. PLoS ONE 6(5) e19880 PubMed

Xia J, Sun J, Jia P, Zhao Z (2011) Do cancer proteins really interact strongly in the human protein-protein interaction network? Computational Biology and Chemistry. 35:121-125 PubMed

Jia P, Jayathilake K, Zhao Z*, Meltzer HY* (2011) Association of the TNF-alpha receptor Fas gene with treatment resistant schizophrenia. Schizophrenia Research. 129(2-3) 211-212 PubMed

Kao C-F, Fang Y-S, Zhao Z, Kuo P-H (2011) Prioritization and evaluation of depression candidate genes by combining multidimensional data resources. PLoS ONE 6(4): e18696 PubMed

Jia P, Zheng S, Long J, Zheng W, and Zhao Z (2011) dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics 27(1):95-102 PubMed    This paper was evaluated by Faculty1000 and was ranked top 2% of published articles in biology and medicine.

Wang L, Jia P, Wolfinger RD, Chen X, Grayson BL, Aune TM, Zhao Z (2011) An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. Bioinformatics 27(5):686-92. PubMed

Sun J, Wan C, Jia P, Kendler KS, Riley BP, Zhao Z (2011) Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophrenia Res PubMed

Su Z, Han L, Zhao Z (2011) Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes. Epigenetics 6(2):134-140PubMed   

Jia P, Ewers JM, Zhao Z (2011) Prioritization of Epilepsy Associated Candidate Genes by Convergent Analysis. PLoS ONE 6(2): e17162 PubMed

Bhaskara S, Knutson SK, Jiang G, Chandrasekharan MB, Wilson AJ, Zheng S, Yenamandra A, Locke K, Yuan J, Summers A, Washington K, Zhao Z, Sun ZW, Xia F, Khabele D, Hiebert SW (2010) Hdac3 is essential for maintenance of chromatin structure and genome stability. Cancer Cell 18(5):436-447. PubMed

Chen X, Lee G, Maher BS, Fanous AH, Chen J, Jackson K, Zhao Z, Guo AY, van den Oord E, Sullivan PF, Shi J, Levinson DF, Gejman PV, Owen MJ, Craddock NJ, O'Donovan MC, Qin W, Schwab S, Wildenauer D, Chowdari K, Nimgaonkar V, Straub R, Weinberger D, O'Neil AF, Walsh D, Darvasi A, Malhotra AK, Rujescu D, Werge T, Cichon S, Andressen OA, The International Schizophrenia Consortium, Kendler KS (2010) GWA study data-mining and independent replication identify cardiomyopathy associated 5 (CMYA5) as a risk gene for schizophrenia. Molecular Psychiatry Epub ahead of print Sept 14, 2010 PubMed

Chmielecki J, Peifer M, Jia P, Socci N, Hutchinson K, Viale A, Zhao Z, Thomas R, Pao W (2010) Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. Nucleic Acids Research, Access published June 29, 2010    PubMed

Jia P, Wang L, Meltzer HY, Zhao Z (2010) Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data. Schizophrenia Research, 122:38-42 PubMed

Aberg K, Adkins DE, Liu Y, McClay JL, Buksz�r J, Jia P, Zhao Z, Perkins, D, Stroup S, Lieberman JA, Sullivan PF, van den Oord E (2010) Genome-wide association study of antipsychotic induced QTc interval prolongation. The Pharmacogenomics Journal PubMed

Archer KJ, Zhao Z, Guennel T, Maluf DG, Fisher RA, Mas VR (2010) Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. International Journal of Computational Biology and Drug Design (IJCBDD) 3(1): 52-67 PubMed

Sun J, Jia P, Fanous AH, van den Oord EJCG, Chen X, Riley BP, Amdur RL, Kendler KS, Zhao Z (2010) Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PLoS ONE 5(6): e11351 PubMed

Huang, HC, Zheng S, VanBuren V, Zhao Z (2010) Discovering Disease-specific Biomarker Genes for Cancer Diagnosis and Prognosis. Technologies in Cancer Research and Treatment, 9(3): 219-230 PubMed   

Jia P, Sun J, Guo AY, Zhao Z (2010) SZGR: a comprehensive schizophrenia gene resource . Molecular Psychiatry 15:453-462 PubMed

Sun J, Zhao Z (2010) A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics 11(Suppl 3):S5 PubMed

Kalsi G, Kuo PH, Aliev F, Alexander J, McMichael O, Patterson DG, Walsh D, Zhao Z, Schuckit M, Nurnberger J, Edenberg H, Kramer J, Vladimirov V, Prescott CA, Dick DM, Kendler KS, Riley BR (2010) A systematic gene-based screen of Chr4q22-q32 identifies associate of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. Hum Mol Genet, 19(12):2497-2506 PubMed

Adkins DE, Aberg K, McClay JL, Bukszar J, Zhao Z, Jia P, Stroup ST, Perkins D, McEvoy JP, Lieberman JA, Sullivan PF, van den Oord E (2010) Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. Molecular Psychiatry, Epub ahead of print March 2, 2010 PubMed

Sun J, Zhao Z (2010) Functional features, biological pathways and protein interaction networks of addiction-related genes. Chem Biodiv, 7:1153-1161 PubMed

Guo AY, Sun J, Jia P, Zhao Z (2010) A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Systems Biology 4:10 PubMed

Guo AY, Sun J, Jia P, Zhao Z (2010) Network analysis of ethanol-related candidate genes. Chem Biodiv, 7:1142-1152 PubMed

Zhao Z (2010) Network-based approaches to biomarker discovery and disease classification. In Francisco Azuaje Ed. Bioinformatics and biomarker discovery: "Omic" data analysis for personalised medicine. John Wiley and Sons. Pg 130-135 (ISBN 9780470744604)

Fanous AH, Zhao Z, van den Oord EJCG, Thiselton DL, Bergen SE, Wormley B, Bigdeli T, Amdur RL, O'Neill FA, Walsh D, Kendler KS, Riley BP (2010) Association study of SNAP25 and schizophrenia in Irish family and case-control samples. American Journal of Medical Genetics B: Neuropsychiatric Genetics 153B(2):663-674 PubMed

Riley B, Kuo PH, Maher BS, Fanous AH, Sun J, Wormley B, O'Neill FA, Walsh D, Zhao Z, and Kendler KS (2009) The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophrenia Research, 115(2):245-253  PubMed

Han L, Zhao Z (2009) Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics 94:117-124 PubMed

Sun J, Jia P, Fanous AH, Webb BT, van den Oord EJCG, Chen X, Bukszar J, Kendler KS, Zhao Z (2009)A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases – Schizophrenia as a case. Bioinformatics  PubMed

Chen X, Sun C, Chen Q, O'Neill FA, Walsh D, Fanous AH, Nimgaonkar VL, Schwab SG, Wildenauer DB, Che R, Shi Y, He L, Su B, Luo XJ, Edwards TL, Zhao Z, Kendler KS (2009) Apoptotic engulfment pathway and schizophrenia PLoS ONE 4(9):e6875 PubMed

Clarke R#, Zhao Z#, [#co-first author] Guo A-Y, Roper K, Cheng L, Fang Z-M, Samaratunga H, Lavin MF and Gardiner RA (2009) New Genomic Structure of the Prostate Cancer Specific Gene PCA3 within the BMCC1 gene: Implications for prostate cancer detection and progression. PLoS ONE 4(3):e4995 PubMed

Zhao Z, Han L (2009) CpG islands: Algorithms and applications in methylation studies. Biochem. Biophys. Res. Commun. 382(4):643-645 PubMed

Han L, Zhao Z (2009) CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? BMC Bioinformatics 10:65 PubMed

Guo AY, Webb BT, Miles MF, Zimmerman MP, Kendler KS, Zhao Z (2009) ERGR: An ethanol-related gene resource. Nucleic Acids Research 37:D840-845 PubMed

Guo AY, Sun J, Riley BP, Thiselton DL, Kendler KS, Zhao Z (2009) The dystrobrevin binding protein 1 (DTNBP1) gene: features and networks. Molecular Psychiatry 14(1):18-29 PubMed

Zhao Z Khan F, Borker M, Herrera R, Agrawal S (2009) Presence of three different paternal lineages among North Indians: A study of 560 Y chromosomes. Annals Human Biology 36 (1): 46-59 PubMed

Luo XJ, Diao HB, Wang JK, Zhang H, Zhao Z, Su B (2008) Association of haplotypes spanning PDZ-GEF2, LOC728637 and ACSL6 with schizophrenia in Han Chinese. Journal of Medical Genetics 45(12):816-826 PubMed

Han L, Su B, Li W-H, Zhao Z (2008) CpG island density and its correlations with genomic features in mammalian genomes. Genome Biology 9:R79 PubMed

Sun J, Kuo PH, Riley BP, Kendler KS, Zhao Z (2008) Candidate genes for schizophrenia: a survey of association studies and gene ranking. American Journal of Medical Genetics Neuropsychiatric Genetics 147B:1173-1181 PubMed

Yu Q-B, Li G, Wang G, Sun J-C, Wang P-C, Wang C, Mi H-L, Ma W-M, Cui J, Cui Y-L, Chong K, Li Y-X, Li Y-H, Zhao Z, Shi T-L, Yang Z-N (2008) Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana. Cell Research 18:1007-1019 PubMed

Tassabehji M, Fang ZM, McGaughran J, Zhao Z, de Bock CE, Diwan A, Clarke RA (2008) Mutations in GDF6 are associated with vertebrate segmentation defects in Klippel-Feil syndrome. Human Mutation 29:1017-1027 PubMed

Han L, Zhao Z (2008) Comparative analysis of CpG islands in four fish genomes identified by three computational algorithms. Comparative and Functional Genomics. 2008:565631.

Sun J, Sun Y, Ding G, Liu Q, Wang C, He Y, Shi T, Li Y, Zhao Z (2007) InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics 8:414 PubMed

Jiang C, Han L, Su B, Li W-H, Zhao Z (2007) Features and Trend of Loss of Promoter-Associated CpG Islands in the Human and Mouse Genomes. Molecular Biology and Evolution 24:1991-2000

Zhao Z, Jiang C (2007) Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions. Molecular Biology and Evolution 24:23-25 PubMed

Sun J, Li Y, Zhao Z (2007) Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochem. Biophys. Res. Commun. 353:985-991 PubMed

Seo D, Jiang C, Zhao Z (2006) A novel statistical method to estimate the effective SNP size in vertebrate genomes and categorized genomic regions. BMC Genomics 7:329

Jiang C, Zhao Z (2006) Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome. BMC Genomics 7:316 PubMed

Zhao Z, Yu N, Fu Y-X, Li W-H (2006) Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations. Genetics 174:399-409

Zhao Z, Zhang F (2006) Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences. Genomics 87:68-74 PubMed

Jiang C, Zhao Z(2006) Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics 88:527-534 PubMed

Zhao Z, Zhang F (2006) Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome. Gene 366:316-324 PubMed

Zhang, F., & Zhao, Z. (2005) SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). Bioinformatics 21:2517-2519 PubMed

Yang, S., Liu, Y., Lin, A.A., Cavalli-Sforza, L.L., Zhao, Z., & Su, B. (2005) Adaptive evolution of MRGX2, a human sensory neuron specific gene involved in nociception. Gene 352:30-35 PubMed

Zhang, F., & Zhao, Z. (2004) The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs. Genomics 84:785-795 PubMed

Zhao, Z., Li, H., Wu, X., Zhong, Y., Zhang, K., Zhang, Y.-P., Boerwinkle, E., & Fu, Y.-X. (2004) Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol. Biol. 4:21 PubMed

Zhao, Z., Fu Y.-X., Hewett-Emmett, D., & Boerwinkle, E. (2003) Single nucleotide polymorphism (SNP) density in the human genome and its implications in molecular evolution. Gene 312:207-213 PubMed

Zhao, Z., & Boerwinkle, E. (2002) Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of 2.6 million polymorphisms across the human genome. Genome Research 12:1679-1686 PubMed

Yu, N., Zhao, Z., Fu, Y.-X., Sambuughin, N., Ramsay, M., Jenkins, T., Leskinen, E., Patthy, L., Jorde, L.B., Kuromori, T., & Li, W.-H. (2001) Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Molecular Biology and Evolution 18:214-222 PubMed

Zhao, Z., Jin, L., Fu, Y.-X., Ramsay, M., Jenkins, T., Leskinen, E., Pamilo, P., Trexler, M., Patthy, L., Jorde, L.B., Ramos-Onsins, S., Yu, N., & Li, W.-H. (2000) Worldwide DNA sequence variation in a 10 kb noncoding region on human chromosome 22. Proc. Natl. Acad. Sci. USA 97:11354-11358 Related commentary

Zhao, Z., Hewett-Emmett, D., & Li, W.-H. (1998) Frequent gene conversion between human red and green opsin genes. J. Mol. Evol. 46:494-496 PubMed