Profile

The research interest of the Bioinformatics and Systems Biology Laboratory (BSBL, http://bioinfo.mc.vanderbilt.edu/) focus on the application of bioinformatics and systems biology approaches to studying complex diseases such as cancer and schizophrenia, aiming to uncover their molecular mechanisms that are otherwise undetected by classical approaches. The ongoing projects use data generated from high throughput technologies such as next generation sequencing and microarrays. Integrative genomics approaches are often applied.

Publications

The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

1. Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. 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) BioData Min : 7
   › Primary publication · 25670967 (PubMed) · PMC4323225 (PubMed Central)
2. Integrated approach in systems biology. Zheng H, Jiang R, Zhao Z (2014) Comput Math Methods Med : 656473
   › Primary publication · 25628754 (PubMed) · PMC4297625 (PubMed Central)
3. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z (2015) Sci Rep : 8004
   › Primary publication · 25614300 (PubMed) · PMC4648438 (PubMed Central)
4. Rare variants in RTEL1 are associated with familial interstitial pneumonia. 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 JA, Blackwell TS (2015) Am J Respir Crit Care Med 191(6): 646-55
   › Primary publication · 25607374 (PubMed) · PMC4384777 (PubMed Central)
5. The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer. Mitra R, Zhao Z (2014) Int J Comput Biol Drug Des 7(4): 384-93
   › Primary publication · 25539849 (PubMed) · PMC4779644 (PubMed Central)
6. Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach. Jiang W, Jia P, Hutchinson KE, Johnson DB, Sosman JA, Zhao Z (2015) Oncotarget 6(4): 2496-508
   › Primary publication · 25537510 (PubMed) · PMC4385866 (PubMed Central)
7. Optimizing the sequence of anti-EGFR-targeted therapy in EGFR-mutant lung cancer. Meador CB, Jin H, de Stanchina E, Nebhan CA, Pirazzoli V, Wang L, Lu P, Vuong H, Hutchinson KE, Jia P, Chen X, Eisenberg R, Ladanyi M, Politi K, Zhao Z, Lovly CM, Cross DA, Pao W (2015) Mol Cancer Ther 14(2): 542-52
   › Primary publication · 25477325 (PubMed) · PMC4338015 (PubMed Central)
8. Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer. Wang Q, Jia P, Cheng F, Zhao Z (2015) Genes Chromosomes Cancer 54(2): 110-21
   › Primary publication · 25407423 (PubMed) · PMC4785867 (PubMed Central)
9. Identification and diagnostic performance of a small RNA within the PCA3 and BMCC1 gene locus that potentially targets mRNA. 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 JW (2015) Cancer Epidemiol Biomarkers Prev 24(1): 268-75
   › Primary publication · 25392181 (PubMed)
10. Common variants in the MKL1 gene confer risk of schizophrenia. Luo XJ, Huang L, Oord EJ, Aberg KA, Gan L, Zhao Z, Yao YG (2015) Schizophr Bull 41(3): 715-27
    › Primary publication · 25380769 (PubMed) · PMC4393692 (PubMed Central)
11. Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach. Vuong H, Cheng F, Lin CC, Zhao Z (2014) Genome Med 6(10): 81
    › Primary publication · 25360158 (PubMed) · PMC4213513 (PubMed Central)
12. Algorithms for network-based identification of differential regulators from transcriptome data: a systematic evaluation. Yu H, Mitra R, Yang J, Li Y, Zhao Z (2014) Sci China Life Sci 57(11): 1090-102
    › Primary publication · 25326829 (PubMed) · PMC4779643 (PubMed Central)
13. Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation. Xu Y, Guo X, Sun J, Zhao Z (2015) Bioinformatics 31(1): 84-93
    › Primary publication · 25192743 (PubMed) · PMC4271146 (PubMed Central)
14. Rationale for co-targeting IGF-1R and ALK in ALK fusion-positive lung cancer. Lovly CM, McDonald NT, Chen H, Ortiz-Cuaran S, Heukamp LC, Yan Y, Florin A, Ozretić L, Lim D, Wang L, Chen Z, Chen X, Lu P, Paik PK, Shen R, Jin H, Buettner R, Ansén 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) Nat Med 20(9): 1027-34
    › Primary publication · 25173427 (PubMed) · PMC4159407 (PubMed Central)
15. Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy. Kallianpur AR, Jia P, Ellis RJ, Zhao Z, Bloss C, Wen W, Marra CM, Hulgan T, Simpson DM, Morgello S, McArthur JC, Clifford DB, Collier AC, Gelman BB, McCutchan JA, Franklin D, Samuels DC, Rosario D, Holzinger E, Murdock DG, Letendre S, Grant I, CHARTER Study Group (2014) PLoS One 9(8): e103123
    › Primary publication · 25144566 (PubMed) · PMC4140681 (PubMed Central)
16. A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. Lin CC, Mitra R, Zhao Z (2014) PLoS One 9(7): e103142
    › Primary publication · 25054916 (PubMed) · PMC4108425 (PubMed Central)
17. Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites. Jiang J, Jia P, Shen B, Zhao Z (2014) Oncotarget 5(15): 6168-77
    › Primary publication · 25026280 (PubMed) · PMC4171620 (PubMed Central)
18. Integrative genomics and computational systems medicine. McDermott JE, Huang Y, Zhang B, Xu H, Zhao Z (2014) Biomed Res Int : 945253
    › Primary publication · 25025078 (PubMed) · PMC4082850 (PubMed Central)
19. Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. Mitra R, Edmonds MD, Sun J, Zhao M, Yu H, Eischen CM, Zhao Z (2014) RNA 20(9): 1356-68
    › Primary publication · 25024357 (PubMed) · PMC4138319 (PubMed Central)
20. Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy. Cheng F, Jia P, Wang Q, Zhao Z (2014) Oncotarget 5(11): 3697-710
    › Primary publication · 25003367 (PubMed) · PMC4116514 (PubMed Central)
21. Acquired resistance of EGFR-mutant lung adenocarcinomas to afatinib plus cetuximab is associated with activation of mTORC1. 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 DP, Stephens PJ, Miller V, Gettinger S, Pao W, Politi K (2014) Cell Rep 7(4): 999-1008
    › Primary publication · 24813888 (PubMed) · PMC4074596 (PubMed Central)
22. 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. Xia J, Jia P, Hutchinson KE, Dahlman KB, Johnson D, Sosman J, Pao W, Zhao Z (2014) Mol Cancer Ther 13(7): 1918-28
    › Primary publication · 24755198 (PubMed) · PMC4090262 (PubMed Central)
23. Network-assisted prediction of potential drugs for addiction. Sun J, Huang LC, Xu H, Zhao Z (2014) Biomed Res Int : 258784
    › Primary publication · 24689033 (PubMed) · PMC3932722 (PubMed Central)
24. Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. Cheng F, Zhao Z (2014) J Am Med Inform Assoc 21(e2): e278-86
    › Primary publication · 24644270 (PubMed) · PMC4173180 (PubMed Central)
25. Beyond histology: translating tumor genotypes into clinically effective targeted therapies. 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) Clin Cancer Res 20(9): 2264-75
    › Primary publication · 24599935 (PubMed) · PMC4008689 (PubMed Central)
26. Dynamic protein interaction modules in human hepatocellular carcinoma progression. Yu H, Lin CC, Li YY, Zhao Z (2013) BMC Syst Biol : S2
    › Primary publication · 24564909 (PubMed) · PMC4029569 (PubMed Central)
27. Interdisciplinary dialogue for education, collaboration, and innovation: intelligent Biology and Medicine in and beyond 2013. Zhang B, Huang Y, McDermott JE, Posey RH, Xu H, Zhao Z (2013) BMC Genomics : S1
    › Primary publication · 24564388 (PubMed) · PMC4042234 (PubMed Central)
28. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. Zhao M, Wang Q, Wang Q, Jia P, Zhao Z (2013) BMC Bioinformatics : S1
    › Primary publication · 24564169 (PubMed) · PMC3846878 (PubMed Central)
29. Patterns and processes of somatic mutations in nine major cancers. Jia P, Pao W, Zhao Z (2014) BMC Med Genomics : 11
    › Primary publication · 24552141 (PubMed) · PMC3942057 (PubMed Central)
30. VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data. Jia P, Zhao Z (2014) PLoS Comput Biol 10(2): e1003460
    › Primary publication · 24516372 (PubMed) · PMC3916227 (PubMed Central)
31. An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. Zhao M, Austin ED, Hemnes AR, Loyd JE, Zhao Z (2014) Mol Biosyst 10(4): 732-40
    › Primary publication · 24448676 (PubMed) · PMC3950334 (PubMed Central)
32. Translational biomedical informatics and computational systems medicine. Zhao Z, Shen B, Lu X, Vongsangnak W (2013) Biomed Res Int : 237465
    › Primary publication · 24350252 (PubMed) · PMC3856116 (PubMed Central)
33. DCGL v2.0: an R package for unveiling differential regulation from differential co-expression. Yang J, Yu H, Liu BH, Zhao Z, Liu L, Ma LX, Li YX, Li YY (2013) PLoS One 8(11): e79729
    › Primary publication · 24278165 (PubMed) · PMC3835854 (PubMed Central)
34. Exploring drug-target interaction networks of illicit drugs. Atreya RV, Sun J, Zhao Z (2013) BMC Genomics : S1
    › Primary publication · 24268016 (PubMed) · PMC3849475 (PubMed Central)

Keywords & MeSH Terms

MeSH terms are retrieved from PubMed records. Learn more.

Key: MeSH Term Keyword

AC133 Antigen Adenocarcinoma Adult Antineoplastic Agents Antipsychotic Agents Biomarkers, Tumor Catalase Conserved Sequence Database Management Systems Data Interpretation, Statistical Emigration and Immigration Epithelial Cells Evolution, Molecular Genes, Viral Genotype Growth Differentiation Factor 6 Heterozygote Lung Diseases, Interstitial Mutation, Missense Mutation Rate Nuclear Receptor Co-Repressor 2 Population Density Protein Interaction Mapping Receptors, Cytokine Receptors, G-Protein-Coupled Smoking Species Specificity Thiobarbituric Acid Reactive Substances Virus Physiological Phenomena Xenopus laevis