Bioinformatics and Systems Medicine Laboratory

Selected publications      Keyword Cloud from Google     Google Scholar

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


[316] Tang D, Li B, Xu T, Hu R, Tan D, Song X, Jia P, Zhao Z. (2019). VISDB: a manually curated database of viral integration sites in the human genome. Nucleic Acids Research, gkz867,

[315] Jia P, Pei G, Zhao Z. (2019). CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures. Bioinformatics, btz441,

[314] Dai, Y., Pei, G., Zhao, Z., & Jia, P. (2019). A convergent study of genetic variants associated with Crohn’s Disease: evidence from GWAS, gene expression, methylation, eQTL and TWAS. Frontiers in Genetics, 10, 318.

[313] Pei, G., Dai, Y., Zhao, Z., & Jia, P. (2019). deTS: tissue-specific enrichment analysis to decode tissue specificity. Bioinformatics, Volume 35, Issue 19, Pages 3842–3845,

[312] Pei G, Sun H, Dai Y, Zhao Z*, Jia P* (2019) Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics. BMC Genomics, 20(Suppl 1):79

[311] Du J, Jia P, Dai Y, Tao C, Zhao Z*, Zhi D* (2019) Gene2Vec: distributed representation of genes based on co-expression captures functional relationships among genes. BMC Genomics, 20(Suppl 1): 82.


[310] Hu R, Dai Y, Jia P, Zhao Z; ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence, Database, Volume 2018, Issue 1, 1 January 2018, bay121,

[309] Jia P, Chen X, Xie W, Kendler KS, and Zhao Z* (2018) Mega-analysis of Odds Ratio (MegaOR): A convergent method for a deep understanding of the genetic evidence in schizophrenia. Schizophrenia Bulletin, sby085. PumMed

[308] Lu P, Zhao Z* (2018) Advances on PPARγ research in the emerging era of precision medicine. Current Drug Targets. 19:663-673.PumMed   PDF

[307] Ruan J*, Zheng W, Liu Z, Zhao Z* (2018) Recent advances in computational systems biology and bioinformatics. International Journal of Computational Biology and Drug Design (IJCBDD) 11(1/2):1-4

[306] O’Brien T, Jia P, Aldrich M, Zhao Z* (2018) Lung cancer: one disease or many? Human Heredity, 83(2):65-70. PumMed

[305] Jia P, Chen X, Fanous AH, Zhao Z (2018) Convergent Roles of De Novo Mutations and Common Variants in Schizophrenia in Tissue-specific and Spatiotemporal Co-expression Network. Translational Psychiatry. 8(1):105. doi: 10.1038/s41398-018-0154-2. PubMed

[304] Yang Q, Wu J, Zhao J, Zhao Z*, Song X*, Han P* (2018) Circular RNA Expression Profiles during the Differentiation of Mouse Neural Stem Cells. BMC Systems Biology.(Accepted)

[303] Saxon JA, Yu H, Polosukhin VV, Gleaves LA, McLoed AG, Massion PP, Yull FE, Zhao Z, Blackwell TS (2018) p52 expression enhances lung cancer progression. Scientific Reports. 8(1):6078. doi: 10.1038/s41598-018-24488-8. PubMed

[302] Dai Y, Li C, Pei G, Dong X, Ding G, Zhao Z, Li Y, Jia P (2018) Multiple transcription factors contribute to inter-chromosomal interaction in yeast. BMC Systems Biology.(Accepted)

[301] Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi P, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas G, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, The Cancer Genome Atlas Research Network, Bathe OF, Liang H (2018) Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Reports 23:255-269 PubMed

[300] Knijnenburg T, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Shen H, Fan H, Greene C, Way G, Liu Y, Akbani R, Feng B, Miller C, Shen Y, Karimi M, Chen G, Kim P, Jia P, Shinbrot E, Zhang S, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, The Cancer Genome Atlas Research Network, PanCanAtlas DDR AWG, Monnat, Jr. RJ, Xiao Y, Wang C (2018) Genomic and Molecular Landscape of DNA Damage Repair Deficiency Across The Cancer Genome Atlas. Cell Reports 23:239-254 PubMed

[299] Du J, Jia P, Dai Y, Tao C, Zhao Z*, Zhi D* (2018) Gene2Vec: distributed representation of genes based on co-expression captures functional relationships among genes. BMC Genomics preprint: bioRxiv 286096,

[298] Mallik S, Zhao Z* (2018) Cervical Cancer Signature Detection through Pareto-Optimal Cluster Identification for RNASeq Data. BMC Systems Biology (Accepted)

[297] Sun H, Kim P, Jia P, Park AK, Liang H, Zhao Z* (2018) Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor. Briefings in Bioinformatics Mar 20. doi: 10.1093/bib/bby020. [Epub ahead of print] PubMed

[296] Suzuki A, Abdallah N, Gajera M, Jia P, Jun G, Zhao Z, Iwata J (2018) Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis. Mechanisms of Development 150 (2018): 21-27 PubMed

[295] Li A, Jia P, Qin G, Suzuki A, Gejera M, Iwata J, Zhao Z* (2018) Network-based identification of critical regulators as putative drivers of human cleft lip development. BMC Genomics (Accepted)

[294] O’Brien T, Jia P, Caporaso NE, Landi MT, Zhao Z* (2018) Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels. Genome Medicine10(1):16. PubMed

[293] Ma L, Jia P, Zhao Z* (2018) Splicing QTL of human adipose-related traits. Scientific Reports 8:318 PubMed

[292] Kim P, Park A, Han G, Sun H, Jia P, Zhao Z (2018) TissGDB: Tissue specific Gene DataBase in cancer. Nucleic Acids Research 2017 Sept 25. pii:gkx850, doi: 10.1093/nar/gkx850 PubMed

[291] Mallik S, Zhao Z* (2018) ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis. Genes 9:7 (25 pages) PubMed

[290] Zhao J, Cheng F, Jia P, Denny JC, Zhao Z* (2018) Comprehensive investigation of regulatory variants in phenome-wide association studies and genome-wide association studies. Genome Medicine 10:7 (15 pages)  PubMed


[289] Mallik S, Zhao Z Towards integrated oncogenic marker recognition through mutual information-based statistically significant feature extraction: an association rule mining based study on cancer expression and methylation profiles. Quantitative Biology, 5(4):302-327, DOI: 10.1007/s40484-017-0119-0 PaperLink

[288] Wang H, Luo J, Liu C, Niu H, Wang J, Liu Q, Zhao Z, Xu H, Ding Y, Sun J, Zhang Q (2017) Investigating microRNA and transcription factor co-regulatory networks in colorectal cancer. BMC Bioinformatics. 2017 Sep 2;18(1):388. doi: 10.1186/s12859-017-1796-4. PubMed

[287] Zheng WJ, Ruan J, Xu H, Zhao Z, Liu Z. (2017) The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC Syst Biol. 2017 Oct 3;11(Suppl 5):88. doi: 10.1186/s12918-017-0461-x. PubMed

[286] Fries GR, Colpo GD, Monroy-Jaramillo N, Zhao J, Zhao Z, Arnold J, Bowden CL, Walss-Bass C (2017) Distinct lithium-induced gene expression effects in lymphoblastoid cell lines from patients with bipolar disorder. European Neuropsychopharmacology, 27(11):1110-1119. doi: 10.1016/j.euroneuro.2017.09.003. Epub 2017 Sep 20. PubMed

[285] Duerrschmid C, He Y, Wang C, Li C, Bournat J, Romere C, Saha PK, Lee M, Phillips KJ, Jain M, Jia P, Zhao Z, Farias M, Wu Q, Milewicz DM, Sutton VR, Moore DD, Butte NF, Krashes MJ, Xu Y, Chopra AR (2017) Asprosin Activates the Hypothalamic Hunger-Circuitry. Nature Medicine 23(12):1444-1453. doi: 10.1038/nm.4432. Epub 2017 Nov 6. PubMed

[284] Mitra R, Chen X, Greenawalt E, Maulik U, Jiang W, Zhao Z, Eischen CM (2017) Decoding critical long-noncoding RNA in ovarian cancer epithelial-to-mesenchymal transition. Nature Communications 8 (1):1604 PaperLink

[283] Tenenbaum JD, Bhuvaneshwar K, Hollis KF, Jia P, Ma L, Nagarajan R, Rakesh G, Subbian V, Visweswaran S, Zhao Z, Leon R (2017) Translational Bioinformatics in Mental Health: Open Access Data Sources and Computational Biomarker Discovery. Briefings in Bioinformatics 2017 Nov 27. doi: 10.1093/bib/bbx157. [Epub ahead of print] PubMed

[282] Mallik S, Zhao Z* (2017) TrapRM: Transcriptomic and Proteomic Rule Mining Using Weighted Shortest Distance Based Multiple Minimum Supports for Multi-Omics Dataset. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine Workshops, ISBN: 978-1-5090-3050-7/17/, November 13-16, 2017, Kansas City, MO, USA, pages 2168-2175. PaperLink

[281] Kim P, Ballester-fuentes L, Zhao Z* (2017) Domain retention in transcription factor fusion genes and its biological and clinical implications: a pan-cancer study. Oncotarget, 8(66):110103-110117 PubMed

[280] Tao C, Gong Y, Xu H, Zhao Z (2017) The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: Special Focus on Medical Informatics and Big Data. BMC Medical Informatics and Decision Making, 17(Suppl 2): 77 PubMed

[279] Liu Z, Zheng WJ, Allen GI, Liu Y, Ruan J, Zhao Z. (2017) The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):405. doi: 10.1186/s12859-017-1797-3. PubMed

[278] Giancardo L, Roberts K, Zhao Z (2017) Representation learning for retinal vasculature embeddings. 4thMICCAI Workshop on Ophthalmic Medical Image Analysis, September 10-14, 2017, Quebec City, Canada. PaperLink

[277] Xu T, Wu J, Han P, Zhao Z (co-corresponding author), Song X. (2017) Circular RNA expression profiles and features in human tissues: a study using RNA-seq data. BMC Genomics. 2017 Oct 3;18(Suppl 6):680. doi: 10.1186/s12864-017-4029-3. PubMed

[276] Ruan J, Huang K, Zhao Z, Liu Y (2017) Machine learning in systems biology. International Journal of Computational Biology and Drug Design (IJCBDD) 10(2):87-90

[275] Hanker AB, Estrada MV, Bianchini G, Moore PD, Zhao J, Cheng F, Gianni L, Koch JP, Tyson DR, Sanchez V, Rexer BN, Sanders M, Zhao Z, Stricker T, Arteaga CL.(2017) Extracellular matrix/integrin signaling promotes resistance to combined inhibition of HER2 and PI3K in HER2+ breast cancer. Cancer Research 77(12):3280-3292  PubMed

[274] Jia P, Zhao Z, Hulgan T, Bush W, Samuels DC, Bloss C, Heaton R, Ellis R, Schork N, Marra C, Collier AC, Clifford D, Gelman B, Sacktor N, Morgello S, Simpson D, McCutchan JA, Letendre S, Barnholtz-Sloan J, Franklin DR, and Grant I for the CHARTER Study Group, Kallianpur, AR (2017) Genome-wide association study of HIV-Associated Neurocognitive Disorder (HAND): a CHARTER Group Study. American Journal of Medical Genetics 174(4):413-426 PubMed

[273] Fang J, Cai C, Wang Q, Lin P, Zhao Z*, Cheng F* (2017) Systems pharmacology-based discovery of natural products for precision oncology through targeting cancer mutated genes. CPT: Pharmacometrics & Systems Pharmacology 6:177-187 PubMed

[272] Cao Y, Zhu J, Jia P, Zhao Z* (2017) scRNASeqDB: a database for gene expression profiling in human single cell by RNA-seq 8(12). pii: E368. doi: 10.3390/genes8120368 PubMed

[271] Zhao Z, Liu Z, Chen K, Guo Y, Allen GI, Zhang J, Jim Zheng W, Ruan J. (2017) The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics. BMC Genomics. 2017 Oct 3;18(Suppl 6):703. doi:10.1186/s12864-017-4018-6. PubMed

[270] Patton SM, Wang Q, Hulgan T, Connor JR, Jia P, Zhao Z, Letendre S, Ellis R, Bush WS, Samuels DC, Franklin DR, Kaur H, Iudicello J, Grant I, Kallianpur A (2017) Cerebrospinal Fluid (CSF) Iron and Biomarkers of Iron Transport are Associated with Age, Sex, Ancestry, and CSF Viral Load in HIV-Infected Adults. Fluids and Barriers of the CNS 14(1):11  PubMed

[269] Zhao J, Cheng F, Zhao Z* (2017) Tissue-specific signaling networks rewired by major somatic mutations in human cancer revealed by proteome-wide discovery. Cancer Research. 77(11):2810-2821 PubMed

[268] Jia P, Han G, Zhao J, Lu P, Zhao Z* (2017) SZGR2.0: a one-stop shop of schizophrenia-associated genes. Nucleic Acids Research Advanced online access October 13, 2016, 45(D1):D915-D924, doi: 10.1093/nar/gkw902 PubMed

[267] Kim P, Zhao J, Lu P, Zhao Z (2017) mutLBSgeneDB: mutated Ligand Binding Site gene DataBase. Nucleic Acids Research Online advanced access October 7, 2016, 45(D1):D256-D263, doi: 10.1093/nar/gkw905 PubMed


[266] Kim P, Jia P, Zhao Z* (2016) Kinase impact assessment in the landscape of fusion genes that retain kinase domains: A pan-cancer study. Briefings in Bioinformatics. December 24, 2016, pii: bbw127 PubMed

[265] Moore JH1, Jennings SF, Greene CS, Hunter LE, Perkins AD, Williams-Devane C, Wunsch DC, Zhao Z, Huang X. (2016) NO-BOUNDARY THINKING IN BIOINFORMATICS. Pacific Symposium on Biocomputing2016;22:646-648. PubMed

[264]  Cheng F, Zhao J, Hanker AB, Monica BR, Arteaga CL, Zhao Z (2016) Transcriptome and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CA H1047R in HER2/ER-positive breast cancer. Breast Cancer Research and Treatment 160(3):457-474 PubMed

[263] Shen Q, Cheng F, Song H, Lu W, Zhao Z (co-corresponding author), Zhang J (2016) Proteome-scale investigation of protein allosteric regulation perturbed by somatic mutations in 7,000 cancer genomes. American Journal of Human Genetics. 2016 Nov 24. pii: S0002-9297(16)30401-3. doi: 10.1016/j.ajhg.2016.09.020. PubMed

[262] Liu S, Mitra R, Zhao MM, Fan W, Eischen CM, Yin F, Zhao Z (2016) The potential roles of long non-coding RNAs (lncRNAs) in glioblastoma development. Molecular Cancer Therapeutics 15(12):2977-2986 PubMed

[261] Han G, Zhao W, Song X, Kwok-Shing Ng P, Karam JA, Jonasch E, Mills GB, Zhao Z, Ding Z, Jia P. (2017) Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening. BMC Genomics. 2017 Oct 3;18(Suppl 6):678. doi: 10.1186/s12864-017-4026-6. PubMed

[260] Cheng F, Murray JL, Sheng J, Zhao Z, Rubin DH (2016) Systems biology-based analysis of cellular antiviral drug targets identified by gene-trap insertional mutagenesis. PLoS Computational Biology 12(9):e1005074 (selected for PLoS journal’s press release) PubMed

[259] Huang K, Liu Y, Huang Y, Li L, Ruan J, Zhao Z* (2016) Intelligent Biology and Medicine in 2015: advancing interdisciplinary education, collaboration, and data science. BMC Genomics 17 (Suppl 2):S1  PubMed

[258] Zhao Z, Liu Y, Huang Y, Huang K, Ruan J (2016) Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. BMC Systems Biology 10(Suppl 2):S1 PubMed

[257] Chen J, Bacanu SA, Yu H, Zhao Z, Jia P, Kendler KS, Kranzler HR, Gelernter J, Farrer L, Minica C, Pool R, Milaneschi Y, Boomsma DI, Penninx BWJH, Tyndale RF, Ware JJ, Cotinine meta-analysis group, FTND meta-analysis group, Vink J, Kaprio J, Munafo M, Chen X (2016) Genetic relationship between schizophrenia and nicotine dependence. Scientific Reports 6:25671 PubMed

[256] Jia P, Zhao Z* (2016) Impacts of somatic mutations on gene expression: an association perspective. Briefings in Bioinformatics Advanced online access April 28, 2016 PubMed

[255]  Heist RS, Shim HS, Gingipally S, Mino-Kenudson M, Le L, Gainor JF, Zheng Z, Aryee M, Xia J, Jia P, Jin H, Zhao Z, Pao W, Engelman JA, Iafrate AJ (2016) MET exon 14 skipping in non-small cell lung cancer. Oncologist. 21(4):481-486 PubMed

[254]  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, Austin ED (2016) Critical genomic networks and vasoreactive variants in idiopathic pulmonary arterial hypertension. The American Journal of Respiratory and Critical Care Medicine (AJRCCM) 194(4):464-75 PubMed

[253] Tenenbaum JD, Avillach P, Benham-Hutchins M, Breitenstein MK, Crowgey EL, Hoffman MA, Jiang X, Madhavan S, Nagarajan R, Ray B, Shin D, Visweswaran S, Zhao Z, Freimuth R (2016) An informatics research agenda to support precision medicine: 7 key areas. JAMIA, 23(4):791-5 PubMed

[252] Jin VX, Huang Y, Ruan J, Zhao Z (2016) Advanced computational approaches for complex biological data. International Journal of Computational Biology and Drug Design (IJCBDD) 9(1/2):1-5

[251] Liu S, Yin F, Wang S, Zhao M, Zhou C, Ding X, Zhao Z, Fan W, Fan M (2016) TThe homing and inhibiting effects of hNSCs-BMP4 on human glioma stem cells. Oncotarget, 7(14):17920-17931 PubMed

[250] Cheng F, Zhao J, Fooksa M, Zhao Z* (2016) A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. JAMIA 23(4):681-91 PubMed

[249] Hart T, Dider S, Xu H, Zhao Z, Xie L (2016) Toward repurposing metformin as a precision anti-cancer therapy using structural systems pharmacology. Scientific Reports 6:20441 PubMed

[248] Pardo L, Schluter A, Valor LM, Barco A, Giralt M, Hidalgo JM, Jia P, Zhao Z, Portero-Otin M, Gimenez-Llort L, Masgrau R, Pujol A, Galea E (2016) Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury. GLIA. 64(5):853-74 PubMed

[247] Zhao J, Cheng F, Wang L, Arteaga CL, Zhao Z (2016): Systematic prioritization of druggable mutations in ~5,000 genomes across 16 cancer types using a structural genomics-based approach. The Molecular and Cellular Proteomics, 15(2):642-56 PubMed

[246] Edmonds MD, Boyd KL, Moyo T, Mitra R, Duszynski R, Arrate MP, Chen X, Zhao Z, Blackwell TS, Andl T, Eischen CM (2016) MicroRNA-31 initiates lung tumorigenesis and promotes mutant KRAS-driven lung cancer. J Clin Invest. 126(1):349-64 PubMed

[245] Kallianpur AR, Wang Q, Jia P, Hulgan T, Zhao Z, Letendre S, Ellis R, Heaton R, Franklin D, Barnhlotz-Sloan J, Collier AC, Marra C, Clifford D, Gelman B, McArthur JC, Morgello S, Simpson D, McCutchan JA, Grant I for the CHARTER Study Group (2016) Anemia and red cell indices predict HIV-associated neurocognitive impairment in the HAART Era. The Journal of Infectious Diseases. 213(7):1065-73 PubMed

[244] Zhao M, Zhao Z (2016) Concordance of copy number loss and down-regulation of gene expression: a pan-cancer study of tumor suppressor genes. BMC Genomics 17(Suppl 2) S12 PubMed

[243] Wang Y, Bray M, Guo X, Ding Z, Zhao Z (2016) Integrated genomics analyses revealed novel functional consequences of PBRM1 truncated mutations in clear-cell renal cell carcinoma. BMC Genomics 17(Suppl 2) S14

[242] Cheng F, Liu C, Shen B, Zhao Z (2016) Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Systems Biology 10(Suppl 2) S5 PubMed


[241] Jiang W, Mitra R, Lin CC, Wang Q, Cheng F, Zhao Z (2015) Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. Briefings in Bioinformatics, 2015 Dec 9. pii: bbv107. [Epub ahead of print] PubMed

[240] Zhao M, Kim P, Mitra R, Zhao J, Zhao Z (2015) TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Research, 2015 Nov 20. pii: gkv1268. [Epub ahead of print] PubMed

[239] Kim P, Cheng F, Zhao J, Zhao (2015) ccmGDB: a database for cancer cell metabolism genes. Nucleic Acids Research, 2015 Oct 30. pii: gkv1128. [Epub ahead of print] PubMed

[238] Lin CC, Mitra R, Cheng F, Zhao Z (2015) Cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules. Molecular BioSystems 11(12):3244-52 PubMed

[237] Jin VX, Huang Y, Ruan J, Zhao Z (2015) Advanced computational approaches for complex biological data.International Journal of Computational Biology and Drug Design (IJCBDD) (in press)

[236] Cheng F, Liu C, Lin CC, Jia P, Li WH, Zhao Z (2015) A gene gravity model for the evolution of cancer genomes: A study of 3,000 cancer genomes across 9 cancer types. PLoS Computational Biology 11(9), e1004497 PubMed

[235] Cheng F, Zhao J, Zhao Z* (2015) Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Briefings in Bioinformatics 17(4):642-56  PubMed

[234] Zhao Z, Jin V, Huang Y, Guda C, Ruan J (2015) Frontiers in integrative genomics and translational bioinformatics. BioMed Research International. Vol. 2015, Article ID: 725491, 4 pages PubMed

[233] Lin CC, Jiang W, Mitra R, Cheng F, Yu H, Zhao Z (2015) Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers. Scientific Reports 5:12063 PubMed

[232] McGirt LY, Jia P, Baerenwald DA, Dahlman K, Zic JA, Zwerner JP, Hucks D, Dave U, Zhao Z, Eischen CM (2015) Whole genome analysis reveals oncogenic alterations in mycosis fungoides. Blood 126(4): 508-519 PubMed

[231] Hutchinson KE, Johnson DB, Johnson AS, Sanchez V, Kuba M, Lu P, Chen X, deStanchina E, Kelley M, Wang Q, Zhao Z, Kris M, Berger MF, Sosman JA, Pao W (2015) ERBB activation modulates sensitivity to MEK1/2 inhibition in a subset of driver-negative melanoma. Oncotarget Advanced online access June 13, 2015 PubMed

[230] Sun J, Zhao M, Jia P, Wang L, Wu Y, Iverson C, Zhou Y, Denny J, Barton E, Roden D, Aldrich MC, Xu H, Zhao Z (2015) Deciphering signaling pathway networks to understand molecular mechanism of action of metformin. PLoS Computational Biology 2015 Jun 17;11(6):e1004202 PubMed

[229] Zhu K, Liu Q, Zhou Y, Tao C, Zhao Z, Sun J, Xu H (2015) Oncogenes and tumor suppressor genes: comparative genomics and network perspectives. BMC Genomics 16(Suppl 7):8 PubMed

[228] Guo X, Xu Y, Zhao Z (2015) In-depth genomic data analyses revealed complex transcriptional and epigenetic dysregulations of BRAFV600E in melanoma. Molecular Cancer 14:60 PubMed

[227] O'Brien TD, Jia P, Xia J, Saxena U, Jin H, Vuong H, Kim P, Wang Q, Aryee MJ, Mino-Kenudson M, Engelman JA, Le L, Iafrate AJ, Heist RS, Pao W, Zhao Z* (2015) Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer. Methods, 83:118-127 PubMed

[226] Mitra R, Lin CC, Eischen C, Bandyopadhyay S, Zhao Z (2015) Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: A lung cancer study. RNA 21:1055-65. PubMed

[225] Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z (2015) MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. Scientific Reports 5:8004. PubMed

[224] Mitra R, Sun J, Zhao Z. (2015) microRNA regulation in cancer: One arm or two arms? International Journal of Cancer. 137(6):1516-8.PubMed

[223] Wang Q, Yu H, Zhao Z*, Jia P* (2015) EW_dmGWAS: Edge-Weighted dense module search for genome-wide association studies and gene expression profiles. Bioinformatics, 31, 2591-2594 PubMed

[222] Huang LC, Soysal E, Zheng WJ, Zhao Z, Xu H, Sun J (2015) A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. BMC Systems Biology 9(Suppl S4):S2 PubMed

[221] Masuzaki R, Yu H, Kingsley P, Marnett L, Zhao Z, Karp S (2015) Functional implications of biochemical and molecular characteristics of donation after circulatory death livers. Transplantation Direct 1:e18 Online access

[220] Thomas LR, Wang Q, Dey S, Howard GC, Ess K, Grieb B, Eischen C, Lorey S, Foshage A, Fesik S, Zhao Z, Clark T, Tansey TP (2015) Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC. Molecular Cell, 58(3): 440-452. PubMed

[219] The Network and Pathway Analysis Subgroup of the Psychiatric Genomics Consortium (O'Dushlaine C, Rossin E, Lee P, ........ co-authors, Zhao Z, Geschwind DH, Sullivan PF, Smoller JW, Holmans PA, Breen G) (2015) Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. Nature Neuroscience 18(2):199-209 Online access

[218] Tang H, Zhao Z (2015) Bioinformatics drives the applications of next-generation sequencing in translational biomedical research. Methods 2015 Jun;79-80:1-2 PubMed

[217] Chen Y, Sun J, Huang LC, Xu H, Zhao Z (2015) Classification of cancer primary sites using machine learning and somatic mutations. BioMed Research International Article 491502 Online Access

[216] Cui W, Qian Y, Zhou X, Lin Y, Jiang J, Chen J, Zhao Z, Shen B (2015) Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data. BMC Genomics16(Suppl 7):S3 PubMed

[215] Ruan J, Jin V, Huang Y, Chen Y, Xu H, Wang Y, Zhao Z (2015) Education, collaboration, and innovation: Intelligent biology and medicine in the era of big data. BMC Genomics 16(Suppl S7):S1 PubMed

[214] Wang Q, Jia P, Zhao Z (2015) VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome Medicine 7:2 PubMed

[213] 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, Young LR, Lancaster LH, Steele MP, Brown KK, Schwarz MI, Fingerlin TE, Schwartz DA, Lawson WE, Loyd JE, Zhao Z, Phillips Iii JA, Blackwell TS (2015) Rare Variants in RTEL1 are Associated with Familial Interstitial Pneumonia. American Journal of Respiratory Cell and Molecular Biology (AJRCCM) 191(6):646-55 PubMed

[212] Huang X, Jennings SF, Bruce B, Buchan A, Cai L, Chen P, Cramer CL, Guan W, Hilgert UK, Jiang H, Li Z, McClure G, McMullen DF, Nanduri B, Perkins A, Rekepalli B, Salem S, Specker J, Walker K, Wunsch D, Xiong D, Zhang S, Zhang Y, Zhao Z, Moore JH (2015) Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. BioData Mining 2015 Feb 6;8:7 PubMed

[211] Luo XJ, Mattherisen M, Li M, Huang L, Rietschel M, Borglum A, van den Oord E, Aberg KA, Mors O, Mortensen PB, Luo Z, Cichon S, Schulze T, Nothen MM, Degenhardt F, iPSYCH-GEMS SCZ working group, MooDS SCZ Consortium, Su B, Zhao Z, Gan L, Yao YG, (2015) Systematic integration of brain eQTL and GWAS identifies ZNF323 as a novel schizophrenia risk gene and suggests recent positive selection based on compensatory advantage on pulmonary function. Schizophrenia Bulletin, 2015 Mar 10. pii: sbv017. [Epub ahead of print] PubMed

[210] Xu Y, Guo X, Sun J, Zhao Z (2015) Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation. Bioinformatics, 31(1):84-93 PubMed

[209] Meador CB, Jin H, de Stanchina E, Nebhan CA, Pirazzoli V, Wang L, Lu P, Vuong H, Hutchinson K, Jia P, Chen X, Eisenberg R, Viale A, Ladanyi M, Politi K, Zhao Z, Lovly CM, Cross D, Pao W (2015) Optimizing the sequence of anti-EGFR targeted therapy in EGFR-mutant lung cancer. Molecular Cancer Therapeutics 14(2):542-52 PubMed

[208] Wang Q, Jia P, Cheng F, Zhao Z (2015) Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of co-expression connectivity in colorectal cancer. Genes, Chromosomes and Cancer54(2):110-21 PubMed

[207] Drayton RM, Rehman I, Clarke R, Zhao Z, Pang K, Miah S, Stoehr R, Hartmann A, Blizard S, Lavin M, Bryant HE, Martens-Uzunova ES, Jenster G, Hamdy FC, Gardiner RA, Catto JWF (2015) Identification and diagnostic performance of a small RNA within the PCA3 and BMCC1 gene locus that potentially targets mRNA. Cancer Epidemiology, Biomarkers & Prevention 24(1):268-75 PubMed

[206] Luo X, Huang L, van den Oord EJ, Aberg KA, Gan L, Zhao Z, Yao YG (2015) Common variants in gene MLK1 confer risk to schizophrenia. Schizophrenia Bulletin, 41(3):715-27 PubMed

[205] Zhao Z, Xu J, Chen J, Kim S, Reimers M, Bacanu SA, Yu H, Liu C, Sun J, Wang Q, Jia P, Xu F, Zhang Y, Kendler KS, Peng Z, Chen X (2015) Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder. Molecular Psychiatry, 20(5):563-72 PubMed (IF 15.15)


[204] Jia P, Wang Q, Chen Q, Hutchinson K, Pao W, Zhao Z (2014) MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis. Genome Biology 15(10):489 PubMed Editor's pick.

[203] Jiang W, Johnson D, Jia P, Hutchinson K, Sosman J, Zhao Z (2014) Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach. Oncotarget, Advanced Online access December 10, 2014 PubMed

[202] Vuong H, Cheng F, Lin CC, Zhao Z (2014) Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach. Genome Medicine 6:81 Editors' pick

[201] Mitra R, Zhao Z (2014) The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer. Int J Comput Biol Drug Des. 2014;7(4):384-93. PubMed

[200] Lovly CM, McDonald NT, Chen H, Ortiz-Cuaran S, Heukamp LC, Yan Y, Florin A, Ozreti? L, Lim D, Wang L, Chen Z, Chen X, Lu P, Paik PK, Shen R, Jin H, Buettner R, Ans?n S, Perner S, Brockmann M, Bos M, Wolf J, Gardizi M, Wright GM, Solomon B, Russell PA, Rogers TM, Suehara Y, Red-Brewer M, Tieu R, de Stanchina E, Wang Q, Zhao Z, Johnson DH, Horn L, Wong KK, Thomas RK, Ladanyi M, Pao W (2014) Rationale for co-targeting IGF-1R and ALK in ALK fusion positive lung cancer. Nature Medicine, 20(9):1027-34 PubMed

[199] Jiang J, Jia P, Zhao Z*, Shen B* (2014) Key regulators in prostate cancer identified by co-expression module analysis. BMC Genomics 15(1):1015 PubMed

[198] Yu H, Mitra R, Yang J, Li YY, Zhao Z (2014) Algorithms for network-based identification of differential regulators from transcriptome data: a systematic evaluation. Science China 57(11):1090-1102 PubMed

[197] Cheng F, Jia P, Wang Q, Lin CC, Li WH, Zhao Z (2014) Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. Molecular Biology and Evolution, 31(8):2156-2169 PubMed (IF 14.31)

[196] Kallianpur AR, Jia P, Ellis RJ, Zhao Z, Bloss C, Wanqing W, Marra CM, Hulgan T, Simpson DM, Morgello S, McArthur JC, Clifford DB, Collier AC, Gelman BB, McCutchan JA, Franklin D, Samuels D, Rosario D, Holzinger E, Murdock D, Letendre S, Grant I, the CHARTER Group (2014) Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy. PLoS ONE 9(8):e103123 PubMed

[195] Jiang J, Jia P, Shen B, Zhao Z (2014) Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites. Oncotarget, 5(15):6168-6177 PubMed

[194] Mitra R, Edmonds MD, Sun J, Zhao M, Yu H, Eischen CM, Zhao Z (2014) Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. RNA, 20(9):1356-68 PubMed

[193] Zheng H, Jiang R, Zhao Z (2014) "Integrated Approaches in Systems Biology" Computational and Mathematical Methods in Medicine Article ID 656473 PubMed

[192] Lin CC, Mitra R, Zhao Z (2014) A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. PLoS ONE 9(7):e103142 PubMed

[191] Cheng F, Jia P, Wang Q, Zhao Z (2014) Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy. Oncotarget, 5(11):3697-3710 online access PubMed

[190] Xia J, Jia P, Hutchinson KE, Dahlman KB, Johnson D, Sosman J, Pao W, Zhao Z (2014) A meta-analysis of somatic mutations from next generation sequencing of 241 melanomas: a road map for the study of genes with potential clinical relevance. Molecular Cancer Therapeutics 13(7):1918-28 Advanced online access April 22, 2014PubMed

[189] Pirazzoli V, Nebhan C, Song X, Wurtz A, Walther Z, Cai G, Zhao Z, Jia P, de Stanchina E, Shapiro EM, Gale M, Yin R, Horn L, Carbone D, Stephens PJ, Miller V, Gettinger S, Pao W, Politi K (2014) Acquired resistance of EGFR mutant lung adenocarcinomas to afatinib plus cetuximab is associated with activation of mTORC1. Cell Reports, 7(4):999-1008 PubMed

[188] Cheng F, Zhao Z (2014) Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. JAMIA 21(e2):e278-86 PubMed

[187] McDermott JE, Huang Y, Zhang B, Xu H, Zhao Z (2014) Integrative genomics and computational systems medicine. BioMed Research International Vol. 2014, Article ID: 945253 Online Access PubMed

[186] Meador CB, Micheel CM, Levy MA, Lovly CM, Horn L, Warner JL, Johnson DB, Zhao Z, Anderson IA, Sosman JA, Vnencak-Jones CL, Dahlman KB, Pao W (2014) Beyond Histology: Translating Tumor Genotypes into Clinically Effective Targeted Therapies. Clinical Cancer Research, 20(9):2264-75 PubMed

[185] Jia P, Zhao Z (2014) VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-generation Sequencing Data. PLoS Computational Biology 10(2): e1003460 Article online    PubMed

[184] Zhao Z, Zhang B, Huang Y, Xu H, McDermott JE (2014) Computational methods for biomedical big data. International Journal of Computational Biology and Drug Design (IJCBDD) 7(2-3):97-101 PubMed

[183] Zheng H, Wang H, Xu H, Wu Y, Zhao Z, Azuaje F (2014) Linking biochemical pathways and networks to adverse drug reactions. IEEE Transactions on NanoBioscience 13(2):131-137 PubMed

[182] Jia P, Pao W, Zhao Z (2014) Patterns and processes of somatic mutations in nine major cancers. BMC Medical Genomics 7:11 online access   PubMed

[181] Sun J, Huang LC, Xu H, Zhao Z (2014) Network-assisted prediction of potential drugs for addiction. Biomed Research International 2014:258784 PubMed [This paper was selected in AMIA TBI Translational Bioinformatics Year-in-Review]

[180] Zhao M, Austin ED, Hemnes AR, Loyd JE, Zhao Z (2014) An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. Molecular BioSystems 10(4):732-40.    PubMed   Access the PAHKB database here,  Recommendation by Faculty 1000    [selected for the cover artwork of the issue].

[179] Jia P, Zhao Z (2014) Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives. Human Genetics 133(2): 125-138    online access    PubMed

[178] Luo XJ, Huang L, Jia P, Li M, Su B, Zhao Z, Gan L (2014) Protein-protein interaction and pathway analyses of top schizophrenia genes reveal schizophrenia susceptibility genes converge on common molecular networks and enrichment of nucleosome (chromatin) assembly genes in schizophrenia susceptibility loci. Schizophrenia Bulletin 40(1):39-49.PubMed


[177] Hill MF, Patel AV, Murphy A, Smith HM, Galindo CL, Pentassuglia L, Peng X, Lenneman CG, Odiete O, Friedman DB, Kronenberg MW, Zheng S, Zhao Z, Song Y, Harrell FE, Srinivas M, Ganguly A, Iaci F, Parry TJ, Caggiano AO, Sawyer DB (2013) Intravenous glial growth factor 2 (GGF2) isoform of neuregulin-1β improves left ventricular function, gene and protein expression in rats after myocardial infarction. PLoS ONE, 8(2): e55741 PubMed

[176] Wang Q, Jia P, Li F, Hucks D, Dahlman K, Ji H, Chen H, Pao W, Zhao Z (2013) Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome Medicine 5:91 Access the paper    Editor's Pick    highly accessed paper    PubMed

[175] Zhao M, Zhao Z (2013) CNVannotator: a Comprehensive Annotation Server for Copy Number Variation in the Human Genome. PLoS ONE 8(11):e80170 Article online    PubMed

[174] Yang J, Yu H, Liu BH, Zhao Z, Liu L, Li YX, Li YY (2013) DCGL v2.0: an R package for unveiling differential regulation from differential co-expression. PLoS ONE 8(11): e79729 Article online    PubMed

[173] Zheng H, Wang H, Xu H, Zhao Z, Azuaje F (2013) Correlating adverse drug reactions with biochemical pathways in humans. Proceedings of 2013 IEEE International Conference on Bioinformatics and Biomedicine, Shanghai, China, ISBN: 978-1-4799-1310-7, page 197-200

[172] Zhang B, Huang Y, McDermott JE, Posey RH, Xu H, Zhao Z (2013) Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent biology and medicine in and beyond 2013. BMC Genomics 14 (Suppl S6):S1 Article online

[171] Huang X, Bruce B, Buchan A, Congdon CB, another 16 co-authors, Xiong D, Zhang S, Zhao Z (2013) No-boundary thinking in bioinformatics research. BMC BioData Mining 6:19 Article online    PubMed

[170] Wang Q, Jia P, Wang L, Feingold E, Cuenco KT, Marazita ML, Zhao Z (2013) Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules. PLoS ONE 8(10):e76666 Online access    PubMed

[169] Zhao M, Sun J, Zhao Z (2013) Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Molecular BioSystems 9 (12): 3187-3198    PubMed

[168] Jia P, Jin H, Meador CB, Xia J, Ohashi K, Dahlman KB, Politi K, Zhao Z* (co-corresponding author), Pao W* (2013) Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome Research, 23: 1434-1445 PubMed    Cover image of the September issue    VUMC Reporter.

[167] Zhao Z, Shen B, Lu X, Vongsangnak W (2013) Translational Biomedical Informatics and Computational Systems Medicine. BioMed Research International 2013:237465 PubMed

[166] Wang Q, Jia P, Wang L, Feingold E, Cuenco KT, Marazita ML, Zhao Z (2013) Association signals unveiled by a comprehensive gene set enrichment analysis of dental caries genome-wide association studies. PLoS ONE 8(8):e72653 PubMed

[165] Bigdeli TB, Maher BS, Zhao Z, Sun J, Mederios H, Akula N, McMahon FJ, Carvalho C, Ferreira SR, Azevedo MH, Knowles JA, Pato CN Fanous AH (2013) Association study of 83 candidate genes for bipolar disorder in chromosome 6q selected using an evidence-based prioritization algorithm. American Journal of Medical Genetics Neuropsychiatric Genetics Online access    PubMed

[164] Sun J, Zhao M, Fanous AH, Zhao Z (2013) Characterization of schizophrenia adverse drug interactions through a network approach and drug classification. BioMed Research International, Volume 2013 (2013), Article ID 458989, 10 pages Paper online    PubMed

[163] Yu H, Lin CC, Li YY, Zhao Z (2013) Dynamic protein interaction modules in human hepatocellular carcinoma progression. BMC Systems Biology, 7(Suppl 5):S2 Paper online

[162] Wang Q, Jia P, Zhao Z (2013) VirusFinder: software to detect viruses and their integration sites in host genome through next generation sequencing data. PLoS ONE 8(5): e64465 PubMed

[161] Zhao Z, Webb BT, Jia P, Bigdeli TB, Maher BS, van den Oord EJ, Bergen S, Amdur RL, O'Neil FA, Walsh D, Thiselton DL, Chen X, The International Schizophrenia Consortium, Riley BP, Kendler KS, Fanous AH (2013) Association study of 167 candidate genes for schizophrenia selected by a multi-domain evidence-based prioritization algorithm and neurodevelopmental hypothesis. PLoS ONE 8(7): e67776 PubMed

[160] Ali R, Chen Z, Zhu S, Jia P, Zhao Z, Washington MK, Belkhiri A, El-Rifai W (2013) Deciphering the unique microRNA signature in human esophageal adenocarcinoma. PLoS ONE 8(5):e64463 Paper online    PubMed

[159] Erdogan B, Bosompem A, Peng D, Han L, Smith E, Kennedy ME, Alford CE, Zhao Z, Mosse CA, El-Rifai W, Kim A (2013) Methylation of MicroRNA promoters in Myelodysplastic Syndromes. Leukemia and Lymphoma, Epub ahead of print April 2, 2013 PubMed

[158] Atrey R, Sun J, Zhao Z (2013) Exploring drug-target interaction networks of illicit drugs. BMC Genomics 14(Suppl 4):S1 Paper online   PubMed

[157] Zhao M, Wang Q, Wang Q, Jia P, Zhao Z (2013) Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 14(Suppl 11):S1 Paper online

[156] Chen W, Chen X, Archer KJ, Liu N, Zhao Z, Sun S, Gao G (2013) A rapid association test procedure robust under different genetic models accounting for population stratification. Human Heredity 75(1):23-33. PubMed

[155] Chen Z, Ali R, Jia P, Peng D, Zhu S, Washington MK, Zhao Z, Xu Z, El-Rifai W (2013) Gastric adenocarcinoma has a unique microRNA signature not present in esophageal adenocarcinoma. Cancer, 119(11):1985-1993 PubMed

[154] Bacanu SA, Chen J, Sun J, Richardson K, Lai CQ, Zhao Z, O'Donovan MC, Kendler KS, Chen X (2013) Functional SNPs are enriched for schizophrenia association signals. Molecular Psychiatry, Epub ahead of print April 2, 2013 PubMed

[153] Hill MF, Patel AV, Murphy A, Smith HM, Galindo CL, Pentassuglia L, Peng X, Lenneman CG, Odiete O, Friedman DB, Kronenberg MW, Zheng S, Zhao Z, Song Y, Harrell FE, Srinivas M, Ganguly A, Iaci F, Parry TJ, Caggiano AO, Sawyer DB (2013) Intravenous Glial Growth Factor 2 (GGF2) Isoform of Neuregulin-1? Improves Left Ventricular Function in Rats after Myocardial Infarction. PLoS ONE, 8(2):e55741 PubMed

[152] Zhao Z, Vuong H, Jia P (2013) Spectrum of point mutations in the human genome and major subpopulations. Encyclopedia of Life Sciences (ELS), article ID: A24819 Paper online

[151] Zhao Z, Xu H, Zhang B, Huang Y (2013) Advances in Intelligent Biology and Medicine (editorial). International Journal of Computational Biology and Drug Design (IJCBDD) 6(1-2): 1-4 PubMed

[150] Zhao M, Sun J, Zhao Z (2013) TSGene: Tumor Suppressor Gene Database. Nucleic Acids Research, 41: D970-D976    PubMed    Access the database here

[149] Wang Q, Xia J, Jia P, Pao W, Zhao Z (2013) Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Briefings in Bioinformatics, 14(4):506-519 PubMed


[148] Dahlman KB, Xia J, Hutchinson K, Ng C, Hucks D, Jia P, Atefi M, Su Z, Branch S, Lyle P, Hicks DJ, Bozon V, Glaspy JA, Rosen N, Solit D, Netterville JL, Vnencak-Jones CL, Sosman JA, Ribas A, Zhao Z [co-corresponding author], Pao W (2012) BRAF L597 mutations in melanoma are associated with sensitivity to MEK inhibitors. Cancer Discovery. 2(9):791-797, Journal cover page      Commentary      PubMed

[147] Jia P, Zhao Z (2012) Personalized pathway enrichment map of putative cancer genes from next generation sequencing data. PLoS ONE 7(5): e37595 PubMed

[146] Jia P, Liu Y, Zhao Z (2012) Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. BMC Systems Biology 6(Suppl S3):S13 PubMed

[145] 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.   

[144] Xia J, Han L, Zhao Z (2012) Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics 13 (Suppl S8):S7 PubMed

[143] Jia P, Wang L, Fanous, AH, Pato CN, Edwards TL, The International Schizophrenia Consortium, Zhao Z (2012) Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia. PLoS Computational Biology, 8(7): e1002587 PubMed

[142] Sun J, Purow B, Zhao Z (2012) Uncovering microRNA and transcription factor mediated regulatory networks in glioblastoma. PLoS Computational Biology 8(7): e1002488 PubMed

[141] Zhao Z, Zhang B, Shyr Y, Huang Y, Xu H (2012) Genomics in 2012: challenges and opportunities in the next generation sequencing era. BMC Genomics 13 (Suppl S8):S1 PubMed

[140] Zhao M, Sun J, Zhao Z (2012) Distinct and competitive regulatory patterns of tumor suppressors and oncogenes in ovarian cancer. PLoS ONE 7:e44175 PubMed

[139] Huang Y, Zhao Z, Xu H, Shyr Y, Zhang B (2012) Advances in Systems Biology: Computational Algorithms and Applications. BMC Systems Biology 6 (Suppl S3):S1 PubMed

[138] Jia P, Zhao Z (2012) Searching joint association signals in CATIE schizophrenia genome-wide association studies through a refined integrative network approach. BMC Genomics 13(S6:):S15 PubMed

[137] Xu J, Sun J, Helm M, Li A, Chen J, Zhao Z [co-corresponding author], Chen X (2012) RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia. BMC Genomics 13 (Suppl S8):S2 PubMed

[136] Zhao Z, Zheng H, Jiang R (2012) Systems biology approaches in biological and biomedical research: opportunities and challenges (editorial). International Journal of Computational Biology and Drug Design (IJCBDD) 5(3/4): 181-184 PubMed

[135] Jia P, Li F, Xia J, Chen H, Ji H, Pao W, Zhao Z (2012) Consensus rules in variant detection from next-generation sequencing data. PLoS ONE 7(5): e38470 PubMed

[134] Zhao Z, Guo AY, van den Oord EJ, Aliev F, Jia P, Edenberg HJ, Riley BP, Dick DM, Bettinger JC, Davies AG, Grotewiel MS, Schuckit MA, Agrawal A, Kramer J, Nurnberger JI, Kendler KS, Webb BT, Miles MF (2012) Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study. BMC Genomics 13 (Suppl S8):S16 PubMed

[133] Zhao M, Sun J, Zhao Z (2012) Comprehensive analyses of tumor suppressor genes and oncogenes in protein-protein interaction networks: a topological perspective. GENSiPS 2012:101-102

[132] Wang Q, Zhao Z (2012) A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing data. GENSiPS 2012:38-41

[131] Sun J, Xu H, Zhao Z (2012) Network-assisted investigation of antipsychotic drugs and their targets. Chem Biodiv 9(5):900-910 PubMed   

[130] Sun J, Wu Y, Xu H, Zhao Z (2012) DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics 13(Suppl 9):S7 PubMed

[129] Du X, Han L, Guo AY, Zhao Z (2012) Features of methylation and gene expression in the promoter-associated CpG islands in the human genome using methylome data. Comparative and Functional Genomics vol. 2012, Article ID 598987 PubMed

[128] Schleker S, Sun J, Raghavan B, Srnec M, Muller N, Koepfinger M, Murthy L, Zhao Z, Klein-Seetharaman J (2012) The current Salmonella-host interactome. Proteomics Clinical Applications 6:117-133 PubMed

[127] Liu M, Wu Y, Chen Y, Sun J, Zhao Z, Chen XW, Matheny M, Xu H (2012) Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. Journal of the American Informatics Association (JAMIA) 19(e1):e28-e35 PubMed

[126] Zheng S, Zhao Z (2012) DNA methylation profiling distinguishes three clusters of breast cancer cell lines. Chemistry and Biodiversity 9(5):848-856 PubMed   

[125] Zhao Z, Kier LB, Buck GA (2012) Systems Biology: Molecular Networks and Disease (editorial). Chemistry & Biodiversity 9(5):841-847

[124] Atreya R, Sun J, Zhao Z (2012) A network and functional investigation of illicit drug targets and their pharmacological implications. Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, October 4-7, 2012, Philadelphia, PA, USA, ISBN: 978-1-4673-2558-5, pages 564-569

[123] Ahmed ST, Davulcu H, Nair R, Tikves S, Zhao Z (2012) BioEve search: A novel framework to facilitate interactive literature search. Advances in Bioinformatics vol. 2012, Article ID: 509126 PubMed

[122] 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), 47(1):20-27 PubMed

[121] 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 (2012) L-arginine supplementation improves responses to injury and inflammation in dextran sulfate sodium colitis. PLoS ONE, 7(3):e33546 PubMed

[120] 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 (2012) 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, 159B(4):383-391. PubMed

[119] 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 (2012) Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes. Eur. J. Hum. Genet. 20(10):1078-1084 PubMed

[118] Wu Y, Liu M, Zheng WJ, Zhao Z, Xu H (2012) Ranking gene-drug relationships in biomedical literature using latent dirichlet allocation. Pacific Symposium on Biocomputing 2012:422-433. PubMed

[117] Liu Y, Koyuturk M, Maxwell S, Zhao Z, Chance MR (2012) Integrative analysis of common neurodegenerative diseases using gene association, interaction networks and mRNA expression data. 2012 AMIA Summit on Translational Bioinformatics (TBI), March 19-21, 2012, San Francisco, CA, USA PubMed

[116] 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

[115] 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, 15(10):1401-1411 PubMed

[114] 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, 198(2012) 202:-206 PubMed

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


[112] Gordy LE, Bezbradica JS, Flyak AI, Spencer CT, Dunkle A, Sun J, Stanic AK, Florence WC, Boothby MR, He YW, Zhao Z, Kaer LV, Joyce S (2011) IL-15 regulates homeostasis and terminal maturation of NKT cells. Journal of Immunology 187(12):6335-45 PubMed

[111] Su Z, Xia J, Zhao Z (2011) Do microRNAs preferentially target the genes with low DNA methylation level at the promoter region? Lecture Notes in Bioinformatics (LNBI), 6840:253-258 Online access

[110] Zhao Z, Xia J-F, Tastan O, Singh I, Kshirsagar M, Carbonell J, Klein-Seetharaman J (2011) Virus interactions with human signal transduction pathways. International Journal of Computational Biology and Drug Design (IJCBDD) 4(1): 83-105 PubMed

[109] Jia P, Wang L, Meltzer HY, Zhao Z (2011) Pathway-based analysis of GWAS datasets: effective but caution required. International Journal of Neuropsychopharmacology 14(4):567-572 PubMed

[108] Sun J, Hart PR, Zhao Z (2011) Development and implementation of a novel computational tool for an efficient construction of drug-target interactome. Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, November 12-15, 2011, Atlanta, Georgia, USA, ISBN:978-1-4577-1911-9, pages 274-279 Online access

[107] Jia P, Zhao Z (2011) Network-assisted causal gene detection in genome-wide association studies: An improved module search algorithm. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11), December 4-6, 2011, San Antonio, Texas, USA Online access

[106] 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

[105] 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 PubMed

[104] Beeghly-Fediel A, Shu XO, Lu W, Long J, Cai Q, Xiang Y, Zheng Y, Zhao Z, Gu K, Gao YT, Zheng W (2011) Genetic variants in VEGF family genes and breast cancer risk: a report from the Shanghai Breast Cancer Genetics Study. Cancer Epidemiology, Biomarkers & Prevention 20(1):33-41 PubMed

[103] 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 PubMed

[102] 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

[101] Zheng H, Zhao Z, Jiang R (2011) Integrative data analysis in systems biology: Editorial. International Journal of Computational Biology and Drug Design (IJCBDD) 4(2): 107-110 PubMed

[100] 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, 18(1):67-78 PubMed

[99] 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. 31(18):2323-2334 PubMed

[98] 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 70(9):888-896 PubMed

[97] 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 131(1-3):43-51 PubMed

[96] Sun Y, Zheng S, Speirs C, Zhao Z [co-corresponding author], Lu B (2011) The role of IGF-1 signaling pathway in cisplatin-resistant lung cancer cells. International Journal of Radiation Oncology, Biology and Physics. 82(3) e563-572 PubMed

[95] Gong X, Sun J, Zhao Z (2011) Gene regulation in glioblastoma: A combinatorial analysis of microRNAs and transcription factors. International Journal of Computational Biology and Drug Design (IJCBDD) 4(2): 111-126 PubMed

[94] 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

[93] 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

[92] 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 (2011) Comprehensive gene-based association study of a chromosome 20 linked region implicates novel risk loci for depressive symptoms in psychotic illness. PLoS ONE 6(12):e21440 PubMed

[91] Xiong M, Zhao Z (co-corresponding author), Arnold J, Yu F (2011) Next-generation sequencing (editorial). Journal of Biomedicine and Biotechnology Vol. 2010, Article ID: 370710 PubMed

[90] 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

[89] 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

[88] 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

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

[86] 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

[85] 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.

[84] 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

[83] Zhao Z, Sanfilip A, Huang K (2011) Gene network and pathway generation and analysis (editorial). International Journal of Computational Biology and Drug Design (IJCBDD) 4(1): 1-4 PubMed

[82] 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

[81] 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 PMID: 22195173 PubMed

[80] 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):134-140 PubMed

[79] Zhang WR, Pandurangi AK, Peace KE, Zhang YQ, Zhao Z (2011) MentalSquares - a generic bipolar support vector machine for mental disorder classification, diagnostic analysis, and neurobiological data mining. International Journal of Data Mining and Bioinformatics (IJDMB) 5(5): 532-557 PubMed

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

[77] 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 (2011) Genome-wide association study of antipsychotic induced QTc interval prolongation. The Pharmacogenomics Journal 12(2) 165-172 PubMed

[76] 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 (2011) GWA study data-mining and independent replication identify cardiomyopathy associated 5 (CMYA5) as a risk gene for schizophrenia. Molecular Psychiatry 16(11):1117-1129 PubMed


[75] 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

[74] Zhao Z, Jiang C (2010) Features of recent codon evolution: A comparative polymorphism-fixation study. Journal of Biomedicine and Biotechnology. vol. 2010, Article ID 202918 PubMed

[73] Zhang M, Zhao Z, He L, Wan CL (2010) A meta-analysis of oxidative stress markers in schizophrenia. Science in China Series C-Life Sciences. 53(1)1-13 (doi: 10.1007/s11427-010-0000-0) PubMed

[72] Han L, Zheng S, Sun S, Huang T, Zhao Z (2010) Genome-wide DNA methylation profiling in 40 breast cancer cell lines. Lecture Notes in Computer Sciences (LNCS), 6215:277-284 Online access

[71] Jia P, Tian J, Zhao Z (2010) Assessing gene length biases in gene set analysis of genome-wide association studies. International Journal of Computational Biology and Drug Design (IJCBDD) 3(4): 297-310 PubMed

[70] 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, 38(20):6985-6996 PubMed

[69] 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

[68] Vaka D, Huang HC, Tansey WP, Zhao Z (2010) Evaluation of high-resolution scanners for the imaging of microarray experiments and subsequent feature extraction. In: Zhao Ed. Sequence and Genome Analysis: Methods and Applications. iConcept Press. Pages 305-313. [ISBN: 978-1-4537538-5-9]

[67] Gong X, Jia P, Zhao Z (2010) Investigating microRNA-transcription factor mediated regulatory networks in glioblastoma. Proceedings of 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, December 18-21, 2010 Hong Kong, page 258-263, ISBN:978-1-4244-8302-0.

[66] 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

[65] 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

[64] Zhao Z (2010) Preface. In: Zhao Ed. Sequence and Genome Analysis: Methods and Applications. iConcept Press. Page vii-viii. [ISBN: 978-1-4537538-5-9]

[63] 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

[62] Sun J, Han L, Zhao Z (2010) Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. Artificial Intelligence in Medicine, 48:99-106 PubMed

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

[60] 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

[59] 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

[58] Zhao Z, Kier LB, Buck GA (2010) Systems biology in the microbial world and beyond. Chemistry & Biodiversity 7:1019-1025 PubMed

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

[56] 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, 16(3):321-332 PubMed

[55] Jia P, Zhao Z (2010) Convergent evidence for Wnt signaling pathway in psychotic disorders. 2010 Annual ORNL Biomedical Science & Engineering Conference. May 25-26, 2010 Oak Ridge, TN. IEEE Catalog Number: CFP1047G-ART. Online access

[54] Sun J, Zhao Z (2010) Pathway-assisted investigation of atypical antipsychotic drugs and serotonin receptors in schizophrenia. 2010 Annual ORNL Biomedical Science & Engineering Conference. May 25-26, 2010 Oak Ridge, TN. IEEE Catalog Number: CFP1047G-ART Online access

[53] 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

[52] 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)

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

[50] 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


[49] Yuan LY, Zhao Z (co-corresponding author), Ding GH (2009) Evolution of KRAB domains in mammalian zinc finger gene family. China Journal of Bioinformatics. 7(3):202-211

[48] 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

[47] 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

[46] 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 25(19):2595-2602 PubMed

[45] 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

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

[43] 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

[42] Jia P, Sun J, Han L, Zhao Z (2009) Pathway and network analysis of schizophrenia candidate genes under meta-analysis linkage peaks. IEEE Proceeding of 2009 International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS'09). page 442-447

[41] Sun J, Jia P, Zhao Z (2009) Global network features of cancer genes in the human interactome. IEEE Proceeding of 2009 International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS'09). page 412-416

[40] 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

[39] 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

[38] 1. Zhao Z, Kansal S, Bukaveckas BL (2009) SmartWarf: An automated warfarin dosing tool. IEEE Proceeding of the 2009 International Symposium on Collaborative Technologies and Systems (CTS09). Baltimore, Maryland, USA, Page 348-355

[37] Zhao Z, Han L (2009) CpG Islands in the Human Genome: Identification, Features, Mutations and Diseases. In: Matsumoto A and Nakano M Eds. Human Genome: Features, Variation and Genetic Disorders. Pages 1-27. Nova Science Publishers, Inc., New York (ISBN 978-1-60741-695-1)

[36] 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

[35] 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


[34] 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

[33] 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

[32] Zhao Z (2008) Spectrum of mutations in the human genome inferred by single nucleotide polymorphisms. In: Cooper, D. N. and Kehrer-Sawatzki, H. Eds. The Handbook of Human Molecular Evolution, John Wiley & Sons, Ltd: Chichester). ISBN: 978-0-470-51746-8 (selected from Encyclopedia of Life Sciences paper by the handbook editors)

[31] 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

[30] Friedline CJ, Zhang X, Zehner ZE, Zhao Z (2008) FindSUMO: A PSSM-based method for sumoylation site prediction. Lecture Notes in Artificial Intelligence (LNAI) 5227: 1004-1011

[29] Han L, Yang L, Su B, Zhao Z (2008) An SVM-based algorithm for classifying promoter-associated CpG islands in the human and mouse genomes. Lecture Notes in Artificial Intelligence (LNAI) 5227: 975-981

[28] 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

[27] Sun J, Han L, Zhao Z (2008) Schizophrenia genes: characteristics of function and protein interaction networks. Proceedings of IEEE 2008 International Conference on BioMedical Engineering and Informatics (BMEI). 1: 437-441

[26] 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

[25] Zhao Z (2008) Spectrum of mutations in the human genome inferred by single nucleotide polymorphisms. Encyclopedia of Life Sciences (ELS), article ID: A20852. DOI: 10.1002/9780470015902.a0020852

[24] 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. PubMed


[23] Sun J, Zhao Z (2007) Construction of phylogenetic profiles based on genetic distance of hundreds of genomes. Biochem. Biophys. Res. Commun. 355:849-853 PubMed

[22] Zhao Z, Jiang C (2007) Investigation of the CpG Effect in Mammalian Genomes. In: Kobayashi TB Ed. DNA Methylation Research Trends, Page 1-24. Nova Science Publishers, Inc., New York (ISBN 1-60021-721-4)

[21] 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

[20] 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 PubMed

[19] 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

[18] 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


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

[16] 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

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

[14] 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 PubMed

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

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

Before 2006

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

[10] 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

[9] 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 84:785-795PubMed

[8] 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

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

[6] 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

[5] Zhao Z, Lu J, Dai Z (2001) Genetic differentiation within Drosophila auraria species complex revealed by Random Amplified Polymorphic DNA (RAPD). Acta Zool. Sinica 47: 625-631 Access paper online

[4] 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

[3] 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 PubMed Related commentary

[2] 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 Pub Med

[1] Chen Y, Xu X, Zhao Z Zhang W, Dai Z (1997) Random amplified polymorphic DNA analysis of Drosophila immigrans geographic strains. (in Chinese) Acta Sci. Nat. 33:215-221 Access online

  • Book

"Sequence and Genome Analysis: Methods and Application", Chief Editor: Zhao Z. iConcept Press. 2010. (372 pages) ISBN: 978-0-9807330-4-4 (Hard Cover), 978-1-4537538-5-9 (Paperback) Amazon link

Sequence and Genome Analytics: Method and Applications book cover image

Book Chapters

[7] Zhao Z*, Xia J (2018) Computational approaches for the modeling signal transduction networks. In. The Encyclopedia of Bioinformatics and Computational Biology. Article ID: 20293. (8 pages)

[6] Vaka D, Huang HC, Tansey WP, Zhao Z (2010) Evaluation of high-resolution scanners for the imaging of microarray experiments and subsequent feature extraction. In: Zhao Ed. Sequence and Genome Analysis: Methods and Applications. iConcept Press. Pages 305-313. [ISBN: 978-1-4537538-5-9]

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

[4] Zhao Z, Han L (2009) CpG Islands in the Human genome: Identification, Features, Mutations and Diseases. In: Matsumoto A and Nakano M Eds. Human Genome: Features, Variation and genetic Disorders. Pages 1-27. Nova Science Publishers, Inc., new York (ISBN 978-1-60741-695-1)

[3] Zhao Z (2008) Spectrum of mutations in the human genome inferred by single nucleotide polymorphisms. In: Cooper, D. N. and Kehrer-Sawatzki, H. Eds. The Handbook of Human Molecular Evolution, John Wiley & Sons, Ltd: Chichester. ISBN: 978-0-470-51746-8 (1744 pages) (This paper was selected from Encyclopedia of Life Sciences by the handbook editors)

[2] Zhao Z (2008) Spectrum of mutations in the human genome inferred by single nucleotide polymorphisms. In Encyclopedia of Life Sciences (ELS), article ID: A20852. DOI: 10. 1002/9780470015902.a0020852

[1] Zhao Z, Jiang C (2007) Investigation of the CpG Effect in Mammalian Genomes. In: Kobayashi TB Ed. DNA Methylation Research Trends , Pages 1-24. Nova Science Publishers, Inc., new York (ISBN 1-60021-721-4)

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