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2022
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[496] Liu A, Manuel AM, Dai Y, Fernandes BS, Enduru N, Jia P, Zhao Z. (2022) Identifying candidate genes and drug targets for Alzheimer's disease by an integrative network approach using genetic and brain region-specific proteomic data. doi:10.1093/hmg/ddac124
[495] Ghose P, Alavi M, Tabassum M, Ashraf Uddin M, Biswas M, Mahbub K, Gaur L, Mallik S, Zhao Z. (2022) Detecting COVID-19 infection status from chest X-ray and CT scan via single transfer learning-driven approach. doi:10.3389/fgene.2022.980338
[494] Liu W, Jia J, Dai Y, Chen W, Pei G, Yan Q, Zhao Z. (2022) Delineating COVID-19 immunological features using single-cell RNA sequencing. doi:10.1016/j.xinn.2022.100289
[493] Ghosh A, Jana ND, Mallik S, Zhao Z. (2022) Designing optimal convolutional neural network architecture using differential evolution algorithm. doi:10.1016/j.patter.2022.100567
[492] Gu Z, Yao Y, Yang G, Zhu G, Tian Z, Wang R, Wu Q, Wang Y, Wu Y, Chen L, Wang C, Gao J, Kang X, Zhang J, Wang L, Duan S, Zhao Z, Zhang Z, Sun S. (2022) Pharmacogenomic landscape of head and neck squamous cell carcinoma informs precision oncology therapy. doi:10.1126/scitranslmed.abo5987
[491] Nie L, Wang C, Liu X, Teng H, Li S, Huang M, Feng X, Pei G, Hang Q, Zhao Z, Gan B, Ma L, Chen J. (2022) USP7 substrates identified by proteomics analysis reveal the specificity of USP7. doi:10.1101/gad.349848.122
[490] Fekry B, Ribas-Latre A, Drunen RV, Santos RB, Shivshankar S, Dai Y, Zhao Z, Yoo SH, Chen Z, Sun K, Sladek FM, Younes M, Eckel-Mahan K. (2022) Hepatic circadian and differentiation factors control liver susceptibility for fatty liver disease and tumorigenesis. doi:10.1096/fj.202101398R
[489] Fernandes BS, Salagre E, Enduru N, Grande I, Vieta E, Zhao Z. (2022) Insulin resistance in depression: A large meta-analysis of metabolic parameters and variation. doi:10.1016/j.neubiorev.2022.104758
[488] Fernandes BS, Dai Y, Jia P, Zhao Z. (2022) Charting the proteome landscape in major psychiatric disorders: From biomarkers to biological pathways towards drug discovery. doi:10.1016/j.euroneuro.2022.06.001
[487] Li G, Li X, Yang L, Wang S, Dai Y, Fekry B, Veillon L, Tan L, Berdeaux R, Eckel-Mahan K, Lorenzi PL, Zhao Z, Lehner R, Sun K. (2022) Adipose tissue-specific ablation of Ces1d causes metabolic dysregulation in mice. doi:10.26508/lsa.202101209
[486] Dai Y, Jia P, Zhao Z, Gottlieb A. (2022) A Method for Bridging Population-Specific Genotypes to Detect Gene Modules Associated with Alzheimer's Disease. doi:10.3390/cells11142219
[485] Dai Y, Yu H, Yan Q, Li B, Liu A, Liu W, Jiang X, Kim Y, Guo Y, Zhao Z. (2022) Drug-Target Network Study Reveals the Core Target-Protein Interactions of Various COVID-19 Treatments. doi:10.3390/genes13071210
[484] Dai Y, Hu R, Liu A, Cho KS, Manuel AM, Li X, Dong X, Jia P, Zhao Z. (2022) WebCSEA: web-based cell-type-specific enrichment analysis of genes. doi:10.1093/nar/gkac392
[483] Pan S, Liu X, Liu T, Zhao Z, Dai Y, Wang YY, Jia P, Liu F. (2022) Causal Inference of Genetic Variants and Genes in Amyotrophic Lateral Sclerosis. doi:10.3389/fgene.2022.917142
[482] Pothiawala A, Sahbazoglu BE, Ang BK, Matthias N, Pei G, Yan Q, Davis BR, Huard J, Zhao Z, Nakayama N. (2022) GDF5+ chondroprogenitors derived from human pluripotent stem cells preferentially form permanent chondrocytes. doi:10.1242/dev.196220
[481] Ravirala D, Pei G, Zhao Z, Zhang X. (2022) Comprehensive characterization of tumor immune landscape following oncolytic virotherapy by single-cell RNA sequencing. doi:10.1007/s00262-021-03084-2
[480] Feng X, Tang M, Dede M, Su D, Pei G, Jiang D, Wang C, Chen Z, Li M, Nie L, Xiong Y, Li S, Park JM, Zhang H, Huang M, Szymonowicz K, Zhao Z, Hart T, Chen J. (2022) Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors. doi:10.1126/sciadv.abm6638
[479] Liu A, Manuel AM, Dai Y, Zhao Z. (2022) Prioritization of risk genes in multiple sclerosis by a refined Bayesian framework followed by tissue-specificity and cell type feature assessment. doi:10.1186/s12864-022-08580-y
[478] Bhadra T, Mallik S, Sohel A, Zhao Z. (2022) Unsupervised Feature Selection Using an Integrated Strategy of Hierarchical Clustering With Singular Value Decomposition: An Integrative Biomarker Discovery Method With Application to Acute Myeloid Leukemia. doi:10.1109/TCBB.2021.3110989
[477] Bhadra T, Mallik S, Hasan N, Zhao Z. (2022) Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer. doi:10.1186/s12859-022-04678-y
[476] Sharma P, Balabantaray BK, Bora K, Mallik S, Kasugai K, Zhao Z. (2022) An Ensemble-Based Deep Convolutional Neural Network for Computer-Aided Polyps Identification From Colonoscopy. doi:10.3389/fgene.2022.844391
[475] Tu J, Huo Z, Yu Y, Zhu D, Xu A, Huang MF, Hu R, Wang R, Gingold JA, Chen YH, Tsai KL, Forcioli-Conti NR, Huang SXL, Webb TR, Su J, Bazer DA, Jia P, Yustein JT, Wang LL, Hung MC, Zhao Z, Huff CD, Shen J, Zhao R, Lee DF. (2022) Hereditary retinoblastoma iPSC model reveals aberrant spliceosome function driving bone malignancies. doi:10.1073/pnas.2117857119
[474] Mishra I, Xie WR, Bournat JC, He Y, Wang C, Silva ES, Liu H, Ku Z, Chen Y, Erokwu BO, Jia P, Zhao Z, An Z, Flask CA, He Y, Xu Y, Chopra AR. (2022) Protein tyrosine phosphatase receptor ? serves as the orexigenic asprosin receptor. doi:10.1016/j.cmet.2022.02.012
[473] Otani Y, Yoo JY, Lewis CT, Chao S, Swanner J, Shimizu T, Kang JM, Murphy SA, Rivera-Caraballo K, Hong B, Glorioso JC, Nakashima H, Lawler SE, Banasavadi-Siddegowda Y, Heiss JD, Yan Y, Pei G, Caligiuri MA, Zhao Z, Chiocca EA, Yu J, Kaur B. (2022) NOTCH-Induced MDSC Recruitment after oHSV Virotherapy in CNS Cancer Models Modulates Antitumor Immunotherapy. doi:10.1158/1078-0432.CCR-21-2347
[472] Munquad S, Si T, Mallik S, Das AB, Zhao Z. (2022) A Deep Learning-Based Framework for Supporting Clinical Diagnosis of Glioblastoma Subtypes. doi:10.3389/fgene.2022.855420
[471] Suzuki A, Yoshioka H, Liu T, Gull A, Singh N, Le T, Zhao Z, Iwata J. (2022) Crucial Roles of microRNA-16-5p and microRNA-27b-3p in Ameloblast Differentiation Through Regulation of Genes Associated With Amelogenesis Imperfecta. doi:10.3389/fgene.2022.788259
[470] Gaur L, Bhandari M, Razdan T, Mallik S, Zhao Z. (2022) Explanation-Driven Deep Learning Model for Prediction of Brain Tumour Status Using MRI Image Data. doi:10.3389/fgene.2022.822666
[469] Fernandes BS, Quevedo J, Zhao Z. (2022) Fostering precision psychiatry through bioinformatics. doi:10.1590/1516-4446-2021-2083
[468] Seth S, Mallik S, Bhadra T, Zhao Z. (2022) Dimensionality Reduction and Louvain Agglomerative Hierarchical Clustering for Cluster-Specified Frequent Biomarker Discovery in Single-Cell Sequencing Data. doi:10.3389/fgene.2022.828479
[467] Hsieh K, Wang Y, Chen L, Zhao Z, Savitz S, Jiang X, Tang J, Kim Y. (2022) Drug repurposing for COVID-19 using graph neural network and harmonizing multiple evidence. doi:
[466] Tang D, Li Y, Tan D, Fu J, Tang Y, Lin J, Zhao R, Du H, Zhao Z. (2022) KCOSS: an ultra-fast k-mer counter for assembled genome analysis. doi:10.1093/bioinformatics/btab797
[465] Li H, Xiao Y, Li Q, Yao J, Yuan X, Zhang Y, Yin X, Saito Y, Fan H, Li P, Kuo WL, Halpin A, Gibbons DL, Yagita H, Zhao Z, Pang D, Ren G, Yee C, Lee JJ, Yu D. (2022) The allergy mediator histamine confers resistance to immunotherapy in cancer patients via activation of the macrophage histamine receptor H1. doi:10.1016/j.ccell.2021.11.002
[464] Olcum M, Cheedipudi SM, Rouhi L, Fan S, Jeong HH, Zhao Z, Gurha P, Marian AJ. (2022) The WNT/?-catenin pathway regulates expression of the genes involved in cell cycle progression and mitochondrial oxidative phosphorylation in the postmitotic cardiac myocytes. doi:10.20517/jca.2021.35
[463] Rouhi L, Fan S, Cheedipudi SM, Olcum M, Jeong HH, Zhao Z, Gurha P, Marian AJ. (2022) Effects of tamoxifen inducible MerCreMer on gene expression in cardiac myocytes in mice. doi:10.20517/jca.2021.30
2021
[462] Jewell BE, Xu A, Zhu D, Huang MF, Lu L, Liu M, Underwood EL, Park JH, Fan H, Gingold JA, Zhou R, Tu J, Huo Z, Liu Y, Jin W, Chen YH, Xu Y, Chen SH, Rainusso N, Berg NK, Bazer DA, Vellano C, Jones P, Eltzschig HK, Zhao Z, Kaipparettu BA, Zhao R, Wang LL, Lee DF. (2021) Patient-derived iPSCs link elevated mitochondrial respiratory complex I function to osteosarcoma in Rothmund-Thomson syndrome. doi:10.1371/journal.pgen.1009971
[461] Ravirala D, Pei G, Zhao Z, Zhang X. (2021) Single-cell RNA sequencing reveals a strong connection between Gadd45g upregulation and oncolytic HSV infection in tumor tissue. doi:10.1016/j.omto.2021.10.006
[460] Xu H, Yan F, Hu R, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z. (2021) CleftGeneDB: a resource for annotating genes associated with cleft lip and cleft palate. doi:10.1016/j.scib.2021.07.008
[459] Mendez EF, Wei H, Hu R, Stertz L, Fries GR, Wu X, Najera KE, Monterey MD, Lincoln CM, Kim JW, Moriel K, Meyer TD, Selvaraj S, Teixeira AL, Zhao Z, Xu J, Wu J, Walss-Bass C. (2021) Angiogenic gene networks are dysregulated in opioid use disorder: evidence from multi-omics and imaging of postmortem human brain. doi:10.1038/s41380-021-01259-y
[458] Fan H, Jia P, Zhao Z. (2021) Cell-Type-Specific Profibrotic Scores across Multi-Organ Systems Predict Cancer Prognosis. doi:10.3390/cancers13236024
[457] Hsieh K, Wang Y, Chen L, Zhao Z, Savitz S, Jiang X, Tang J, Kim Y. (2021) Drug repurposing for COVID-19 using graph neural network and harmonizing multiple evidence. doi:10.1038/s41598-021-02353-5
[456] Liu A, Dai Y, Mendez EF, Hu R, Fries GR, Najera KE, Jiang S, Meyer TD, Stertz L, Jia P, Walss-Bass C, Zhao Z. (2021) Genome-Wide Correlation of DNA Methylation and Gene Expression in Postmortem Brain Tissues of Opioid Use Disorder Patients. doi:10.1093/ijnp/pyab043
[455] Jia P, Manuel AM, Fernandes BS, Dai Y, Zhao Z. (2021) Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity. doi:10.1093/bib/bbab214
[454] Rodriguez E, Pei G, Zhao Z, Kim ST, German A, Robinson P. (2021) Erratum: Rodriguez et al. Substance P Antagonism as a Novel Therapeutic Option to Enhance Efficacy of Cisplatin in Triple Negative Breast Cancer and Protect PC12 Cells against Cisplatin-Induced Oxidative Stress and Apoptosis. Cancers 2021, 13, 3871. doi:10.3390/cancers13205178
[453] Chen X, Chen DG, Zhao Z, Balko JM, Chen J. (2021) Artificial image objects for classification of breast cancer biomarkers with transcriptome sequencing data and convolutional neural network algorithms. doi:10.1186/s13058-021-01474-z
[452] Yoshioka H, Li A, Suzuki A, Ramakrishnan SS, Zhao Z, Iwata J. (2021) Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice. doi:10.1093/hmg/ddab151
[451] Manuel AM, Dai Y, Freeman LA, Jia P, Zhao Z. (2021) An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. doi:10.1016/j.mcn.2021.103656
[450] Dai Y, Wang J, Jeong HH, Chen W, Jia P, Zhao Z. (2021) Association of CXCR6 with COVID-19 severity: delineating the host genetic factors in transcriptomic regulation. doi:10.1007/s00439-021-02305-z
[449] Fang Z, Zhao Z, Eapen V, Clarke RA. (2021) siRNA Mediate RNA Interference Concordant with Early On-Target Transient Transcriptional Interference. doi:10.3390/genes12081290
[448] Yan F, Zhao Z, Simon LM. (2021) EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data. doi:10.1016/j.patter.2021.100311
[447] Chen X, Chen DG, Zhao Z, Zhan J, Ji C, Chen J. (2021) Artificial image objects for classification of schizophrenia with GWAS-selected SNVs and convolutional neural network. doi:10.1016/j.patter.2021.100303
[446] Dai J, Leung M, Guan W, Guo HT, Krasnow RE, Wang TJ, El-Rifai W, Zhao Z, Reed T. (2021) Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death. doi:10.3390/genes12081183
[445] Tang M, Pei G, Su D, Wang C, Feng X, Srivastava M, Chen Z, Zhao Z, Chen J. (2021) Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2. doi:10.1093/nar/gkab540
[444] Yoo JY, Yeh M, Wang YY, Oh C, Zhao ZM, Kaur B, Lee TJ. (2021) MicroRNA-138 Increases Chemo-Sensitivity of Glioblastoma through Downregulation of Survivin. doi:10.3390/biomedicines9070780
[443] Pei G, Hu R, Jia P, Zhao Z. (2021) DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner. doi:10.1093/nar/gkab429
[442] Ravirala D, Mistretta B, Gunaratne PH, Pei G, Zhao Z, Zhang X. (2021) Co-delivery of novel bispecific and trispecific engagers by an amplicon vector augments the therapeutic effect of an HSV-based oncolytic virotherapy. doi:10.1136/jitc-2021-002454
[441] Li B, Pei G, Yao J, Ding Q, Jia P, Zhao Z. (2021) Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types. doi:10.1038/s41388-021-01870-x
[440] Xu T, Wang L, Jia P, Song X, Zhao Z. (2021) An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change. doi:10.3390/biomedicines9060657
[439] Yuan P, Cheedipudi SM, Rouhi L, Fan S, Simon L, Zhao Z, Hong K, Gurha P, Marian AJ. (2021) Single-Cell RNA Sequencing Uncovers Paracrine Functions of the Epicardial-Derived Cells in Arrhythmogenic Cardiomyopathy. doi:10.1161/CIRCULATIONAHA.120.052928
[438] Xu H, Jia P, Zhao Z. (2021) Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. doi:10.1093/bib/bbaa099
[437] Kim P, Li H, Wang J, Zhao Z. (2021) Landscape of drug-resistance mutations in kinase regulatory hotspots. doi:10.1093/bib/bbaa108
[436] Zhang Y, Yang B, Davis JM, Drake MM, Younes M, Shen Q, Zhao Z, Cao Y, Ko TC. (2021) Distinct Murine Pancreatic Transcriptomic Signatures during Chronic Pancreatitis Recovery. doi:10.1155/2021/5595464
[435] Xu H, Jia P, Zhao Z. (2021) DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery. doi:10.1002/advs.202004958
[434] Sopariwala DH, Likhite N, Pei G, Haroon F, Lin L, Yadav V, Zhao Z, Narkar VA. (2021) Estrogen-related receptor ? is involved in angiogenesis and skeletal muscle revascularization in hindlimb ischemia. doi:10.1096/fj.202001794RR
[433] Hu R, Pei G, Jia P, Zhao Z. (2021) Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model. doi:10.1016/j.ymeth.2019.10.012
[432] Yu H, Guo Y, Chen J, Chen X, Jia P, Zhao Z. (2021) Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods. doi:10.3390/genes12050665
[431] Tondo LP, Viola TW, Fries GR, Kluwe-Schiavon B, Rothmann LM, Cupertino R, Ferreira P, Franco AR, Lane SD, Stertz L, Zhao Z, Hu R, Meyer T, Schmitz JM, Walss-Bass C, Grassi-Oliveira R. (2021) White matter deficits in cocaine use disorder: convergent evidence from in vivo diffusion tensor imaging and ex vivo proteomic analysis. doi:10.1038/s41398-021-01367-x
[430] Yeh M, Wang YY, Yoo JY, Oh C, Otani Y, Kang JM, Park ES, Kim E, Chung S, Jeon YJ, Calin GA, Kaur B, Zhao Z, Lee TJ. (2021) MicroRNA-138 suppresses glioblastoma proliferation through downregulation of CD44. doi:10.1038/s41598-021-88615-8
[429] Jeong HH, Jia J, Dai Y, Simon LM, Zhao Z. (2021) Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches. doi:10.3390/genes12050635
[428] Berg NK, Li J, Kim B, Mills T, Pei G, Zhao Z, Li X, Zhang X, Ruan W, Eltzschig HK, Yuan X. (2021) Hypoxia-inducible factor-dependent induction of myeloid-derived netrin-1 attenuates natural killer cell infiltration during endotoxin-induced lung injury. doi:10.1096/fj.202002407R
[427] Su F, Daquinag AC, Ahn S, Saha A, Dai Y, Zhao Z, DiGiovanni J, Kolonin MG. (2021) Progression of prostate carcinoma is promoted by adipose stromal cell-secreted CXCL12 signaling in prostate epithelium. doi:10.1038/s41698-021-00160-9
[426] Simon LM, Wang Y, Zhao Z* (2021) INSCT: Integrating millions of single cells using batch-aware triplet neural networks. Nature Machine Intelligence. 3:705-715
[425] Jia P, Hu R, Pei G, Dai Y, Wang Y, Zhao Z* (2021) Deep generative neural network for accurate drug response imputation. Nature Communications 12:1740
[424] Pei G, Hu R, Jia P, Zhao Z* (2021) DeepFun: A deep learning sequence-based model to decipher noncoding variant effect in a tissue and cell type specific manner. Nucleic Acids Research 49:W131-139. doi: 10.1093/nar/gkab429
[423] Dai Y, Wang J, Jeong HH, Chen W, Manuel AM, Jie P, Zhao Z* (2021) Association of CXCR6 with severe COVID-19: Delineating the host genetic factors in transcriptomic regulation. Human Genetics. In press DOI: 10.1007/s00439-021-02305-z
[422] Hu R, Xu H, Jia P, Zhao Z* (2021) KinaseMD: kinase mutation and drug response database. Nucleic Acids Research. 49:D552-D561
[421] Dai Y, Hu R, Manuel AM, Liu A, Jia P, Zhao Z* (2021) CSEA-DB: An omnibus for human complex trait and cell type associations. Nucleic Acids Research. 49:D862-D870
[420] Yan F, Zhao Z*, Simon L* (accepted) EmptyNN: A neural network based on positive-unlabeled learning to remove cell-free droplets and recover lost cells in single-cell RNA sequencing data. Patterns (a Cell series journal)
[419] Ravirala D, Mistretta B, Gunaratne P, Pei P, Zhao Z, Zhang X (accepted) Co-delivery of novel bi-specific and tri-specific engagers by an amplicon vector augments the therapeutic effect of a HSV-based oncolytic virotherapy. Journal for ImmunoTherapy of Cancer (IF: 13.75)
[418] Bhadra T, Mallik S, Hasan N, Zhao Z (conditionally accepted) Comparison of four supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer. BMC Genomics
[417] Liu A, Manuel AM, Dai Y, Zhao Z* (conditionally accepted) Prioritization of risk genes in multiple sclerosis by a refined Bayesian framework followed by tissue-specificity and cell type feature assessment. BMC Medical Genomics
[416] Yan F, Zhao Z*, Simon L* (accepted) EmptyNN: A neural network based on positive-unlabeled learning to remove cell-free droplets and recover lost cells in single-cell RNA sequencing data. Patterns (a Cell series journal)
[415] Xu H, Yan F, Hu R, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z* (accepted) CleftGeneDB: A resource for annotating genes associated with cleft lip and cleft palate. Science Bulletin
[414] Fernandes BS, Quevedo J, Zhao Z (accepted) Fostering Precision Psychiatry through Bioinformatics. Brazilian Journal of Psychiatry
[413] Tang M, Pei G, Su D, Wang C, Feng X, Srivastava M, Chen Z, Zhao Z*, Chen, J* (2021) Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2. Nucleic Acids Research. gkab540, https://doi.org/10.1093/nar/gkab540
[412] Liu A, Dai Y, Mendez E, Hu R, Fries G, Najera K, Jiang S, Meyer T, Stertz L, Jia P, Walss-Bass C, Zhao Z* (2021) Genome-wide correlation of DNA methylation and gene expression in postmortem brain tissues of opioid use disorder patients. International Journal of Neuropsychopharmacology. pyab043, advanced online access July 2, 2021, https://doi.org/10.1093/ijnp/pyab043
[411] Xu H, Jia P, Zhao Z* (2021) Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. Briefings in Bioinformatics. 22(3):bbaa099
[410] Yoo JY, Yeh M, Wang YY, Oh C, Zhao Z, Kaur B, Lee TJ (2021) MicroRNA-138 increases chemo-sensitivity of glioblastoma through downregulation of survivin. Biomedicines 9:780
[409] Chen X, Chen DG, Zhao Z, Zhan J, Ji C, Chen J (2021) Artificial image objects for classification of schizophrenia with GWAS selected SNVs and convolutional neural network. Patterns (a Cell series journal) 2, 100303. https://doi.org/10.1016/j.patter.2021.100303
[408] Yoshioka H, Li A, Suzuki A, Ramakrishnan SS, Zhao Z*, Iwata J* (2021) Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice. Human Molecular Genetics. ddab151. Advanced online June 8, 2021
[407] Xu T, Wang L, Jia P, Song X, Zhao Z* (2021) An integrative transcriptomic and methylation approach for identifying differentially expressed circular RNAs associated with DNA methylation change. Biomedicines 9(6):657
[406] Jia P, Manuel AM, Fernandes BS, Dai Y, Zhao Z* (2021) Distinct effect of prenatal and postnatal brain expression on neuropsychiatric versus neurodegenerative disorders: a study of temporal modularity of 20 brain disorders. Briefings in Bioinformatics. Advanced access online June 4, 2021. bbab214, https://doi.org/10.1093/bib/bbab214
[405] Li B, Pei G, Yao J, Ding Q, Jia P, Zhao Z* (2021) Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types. Oncogene. Advanced online access June 17, 2021
[404] Yu H, Guo Y, Chen J, Chen X, Jia P, Zhao Z* (2021) Rewired pathways and disrupted pathway crosstalk in schizophrenia transcriptomes by multiple differential coexpression methods. Genes 12:665
[403] Zhang Y, Yang B, Davis JM, Drake MM, Younes M, Shen Q, Zhao Z, Cao Y, Ko TC (2021) Distinct murine pancreatic transcriptomic signatures during chronic pancreatitis recovery. Mediators of Inflammation Article ID 5595464
[402] Jeong HH, Jia J, Dai Y, Simons LM, Zhao Z* (2021) Investigating cellular trajectories in the severity of COVID-19 and their transcriptional programs using machine learning approaches. Genes 12:635
[401] Tondo LP, Viola TW, Fries GR, Kluwe-Schiavon B, Cupertino R, Vieira BS, Ferreira P, Franco AR, Lane S, Sterz L, Zhao Z, Hu R, Meyer T, Schimidt J, Walss-Bass C, Grassi-Oliveira R (2021) White matter deficits in cocaine use disorder: Convergent evidence from in vivo diffusion tensor imaging and ex vivo proteomics analysis. Translational Psychiatry 11:252
[400] Yeh M, Wang Y, Yoo JY, Oh C, Otani Y, Kang JM, Park E, Kim E, Chung S, Jeon YJ, Calin GA, Karu B, Zhao Z*, Lee TJ* (2021) MicroRNA-138 suppresses glioblastoma proliferation through downregulation of CD44. Scientific Reports 11:9219
[399] Yuan P, Cheedipudi SM, Louhi L, Fan S, Simon L, Zhao Z, Hong K, Gurha P, Marian A (2021) Single cell RNA-sequencing uncovers paracrine functions of the epicardial-derived cells in arrhythmogenic cardiomyopathy. Circulation 143(22):2169-2187
[398] Xu H, Jia P, Zhao Z* (2021) DeepVISP: Deep learning for virus site integration prediction and motif discovery. Advanced Science 2021:2004958
[397] Su F, Daquiang AC, Ahn S, Saha A, Dai Y, Zhao Z, DiGiovanni J, Kolonin MG (2021) Progression of prostate carcinoma is promoted by adipose stromal cell-secreted CXCL12 signaling in prostate epithelium. NPJ Precision Oncology 2021:26
[396] Yoshioka H, Wang Y, Suzuki A, Shayegh M, Gajera M, Zhao Z*, Iwata J* (2021) Overexpression of miR-1306-5p, miR-3195, and miR-3914 inhibits ameloblast differentiation through suppression of genes associated with human amelogenesis imperfecta. International Journal of Molecular Sciences 22:2202 (https://doi.org/10.3390/ijms22042202)
[395] Kim P, Li H, Wang S, Zhao Z* (2021) Landscape of drug-resistance mutations in kinase regulatory hotspots. Briefings in Bioinformatics 22(3):bbaa108, https://doi.org/10.1093/bib/bbaa108
[394] Pei G, Hu R, Dai Y, Manuel AM, Zhao Z*, Jia P* (2021) Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations. Nucleic Acids Research. 49(1):53-66
[393] Hong BH, Chapa V, Saini U, Modgil P, Cohn DE, Sood A, Yan Y, Saruppaiyah S, Pei G, Zhao Z, Yoo JY, Kaur B (2021) Oncolytic HSV therapy modulates vesicular trafficking inducing cisplatin sensitivity and antitumor immunity. Clinical Cancer Research 27(2):542-553. PMID: 33087329
[392] Pei G, Wang Y, Simon L, Dai Y, Zhao Z*, Jia P* (2021) Gene expression imputation and cell type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders. Genome Research 31:146-158
[391] Mallik S, Qin G, Jia P, Zhao Z* (2021) Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours. Epigenetics 16(2):162-176
[390] Sopariwala DH, Likhite N, Pei G, Haroon F, Lin L, Yadav V, Zhao Z, Narkar VA (2021) Estrogen-related receptor α is involved in angiogenesis and skeletal muscle revascularization in hindlimb ischemia. The FASEB Journal 35:e21480. DOI: 10.1096/fj.202001794RR
[389] Bora K, Bhuyan MK, Sarma P, Kasugai K, Mallik S, Zhao Z* (2021) Computational learning of features for automated colonic polyp classification. Scientific Reports 11(1):4347
[388] Berg NK, Li J, Kim B, Mills T, Pei G, Zhao Z, Li X, Zhang X, Ruan W, Eltzschig HK, Yuan X (2021). Hypoxia-inducible factor-dependent induction of myeloid-derived netrin-1 attenuates natural killer cell infiltration during endotoxin-induced lung injury. The FASEB Journal, 35:e21334
[387] Stertz L, Di Re J, Pei G, Fries G, Li S, Smith-Callahan L, Raventos H, Tipo J, Zhao Z, Liu Y, Jia P, Laezza F, Walss-Bass C (2021) Convergent genomic and pharmacological evidence of PI3K/GSK3 signaling alterations in neurons from schizophrenia patients. Neuropsychopharmacology 46(3):673-682
2020
[386] Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; (Zhao is a co-author in) PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium (2020) Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578(7793):102-111
[385] The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (Zhao Z is a co-author) (2020) Pan-cancer analysis of whole genomes. Nature 578(7793): 82-93.
[384] Carlevaro-Fita J, Lanzos A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen J; [Zhao Z is a co-author in] PCAWG Drivers and Functional Interpretation Working Group, Johnson R, PCAWG Consortium (2020) Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Nature Communications Biology 3(1):56
[383] Shuai S; [Zhao Z is a co-author in] PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein L; PCAWG Consortium (2020) Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications 11(1):734
[382] Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; [Zhao Z is a co-author in] PCAWG Drivers and Functional Interpretation Working Group, Reimand J; PCAWG Consortium. (2020) Integrative pathway enrichment analysis of multivariate omics data. Nature Communications 11(1):735
[381] Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A; Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; [Zhao Z a co-author in] PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium (2020) Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications 11(1):729
[380] Hsieh KL, Wang Y, Chen L, Zhao Z, Savitz S, Jiang X, Tang J, Kim Y (2020) Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation. Res Seq 2020 Dec 11;rs.3.rs-114758. doi: 10.21203/rs.3.rs-114758/v1.
[379] Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; (Zhao is a co-author in) PCAWG Consortium (2020) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications 11(1):4748
[378] Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumor Subtypes and Clinical Translation, Boutros PC, (Zhao is a co-author in) PCAWG Consortium (2020) Sex differences in oncogenic mutational processes. Nature Communications 11(1):4330
[377] Strunz M, Simon LM, Ansari M, Mattner LF, Angelidis L, Mayr CH, Kathiriya J, Yee M, Ogar P, Sengupta A, Kukhtevich I, Schneider R, Zhao Z, Neumann J, Behr J, Voss C, Stöger T, Lehmann M, Königshoff M, Burgstaller G, O´Reilly M, Chapman HA, Theis FJ, Schiller HB (2020). Alveolar regeneration through a Krt8+ transitional stem cell state that aberrantly persists in human lung fibrosis. Nature Communications, 11:3559. bioRxiv 705244
[376] Yan F, Jia P, Yoshioka H, Suzuki A, Iwata J, Zhao Z* (2020) A developmental stage-specific network approach for studying dynamic co-regulation of transcription factors and microRNAs during craniofacial development. Development 147(24):dev192948 [selected as Research Highlight by the journal]
[375] Simon LM, Yan F, Zhao Z* (2020) DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data. (Preprint in bioRxiv 2019 doi: https://doi.org/10.1101/864165) GigaScience 9(12):giaa122 (doi: 10.1093/gigascience/giaa122)
[374] Gao Z, Daquinag AC, Fussell C, Zhao Z, Dai Y, Rivera A, Snyder BE, Eckel-Mahan KL, Kolonin MG (2020) Age-associated telomere attrition in adipocyte progenitors predisposes to metabolic disease. Nature Metabolism 2(12):1482-1497 [single cell RNA-seq]
[373] Pei G, Hu R, Dai Y, Zhao Z*, Jia P* (2020) Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network. Oncogene 39:5031-5041. PMCID: PMC7334101
[372] Xu H, Hu R, Jia P, Zhao Z* (2020) 6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes. Bioinformatics 36(10):3257-3259
[371] Dai Y, Hu R, Pei G, Zhao H, Zhao Z, Jia P (2020) Diverse types of genomic evidence converge on alcohol use disorder risk genes. Journal of Medical Genetics 57:733-743. jmedgenet-2019-106490
[370] Jia P, Dai Y, Hu R, Pei G, Manuel A, Zhao Z* (2020) TSEA-DB: A trait-tissue association map for human complex traits and diseases. Nucleic Acids Research 48(D1):D1022-D1030
[369] Tang D, Li B, Xu T, Hu R, Tan D, Song X, Jia P, Zhao Z* (2020) VISDB: a manually curated database of viral integration sites in the human genome. Nucleic Acids Research 48(D1):D633-D641
[368] Mallik S, Zhao Z* (2020) Graph- and rule-based learning algorithms: A comprehensive review of their applications for cancer type classification and prognosis using genomic data. Briefings in Bioinformatics. 21(2): 368-394
[367] Li A, Jia P, Mallik S, Fei R, Yoshioka H, Suzuki A, Iwata J, Zhao Z* (2020) Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. Briefing in Bioinformatics, 21(4):1465-1478
[366] Mandal M, Sahoo SK, Patra P, Mallik S, Zhao Z* (2020) In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells. BMC Bioinformatics 21(Suppl 21):499
[365] Dai Y, O’Brien T, Pei G, Zhao Z*, Jia P (2020) Characterization of genome-wide association study data reveals spatiotemporal heterogeneity of mental disorders. BMC Medical Genomics 13(Suppl 11):192
[364] Mallik S, Zhao Z* (2020) Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise. Scientific Reports. 10:22164 (Alzheimer’s Disease)
[363] Savarraj JP, Hergenroeder G, Zhu L, Chang T, Park S, Megjhani M, Vahidy FS, Zhao Z, Kitagawa R, Choi H (2020) Machine learning to predict delayed cerebral ischemia and outcomes in subarachnoid hemorrhage. Neurology 96(4), e553-e562
[362] Liu T, Jia P, Fang B, Zhao Z* (2020) Differential expression of viral transcripts from single-cell RNA sequencing of moderate and severe COVID-19 patients and its implications for case severity. Frontiers in Microbiology 11:603509. doi: 10.3389/fmicb.2020.603509
[361] Fritah S, Muller A, Jiang W, Mitra R, Sarmini M, Dieterie M, Golebiewska A, Ye T, Van Dyck E, Herold-Mende C, Zhao Z, Azuaje F, Niclou SP (2020) Temozolomide-induced RNA interactome uncovers novel lncRNA regulatory loops in glioblastoma. Cancers 12(9):E2583
[360] Jiang S, Zhou D, Wang Y, Jia P, Wan C, Li X, He G, Cao D, Jiang X, Kendler KS, Tsuang M, Mize T, Wu JS, Lu Y, He L, Chen J, Zhao Z*, Chen X* (2020) Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts. Translational Psychiatry 10(1):307
[359] Tang M, Feng X, Pei G, Srivastava M, Wang C, Chen Z, Li S, Zhang H, Zhao Z, Li X, Chen J (2020) FOXK1 participates in DNA damage response by controlling 53BP1 function. Cell Reports 32:108018
[358] Mallik S, Seth S, Bhardra T, Zhao Z* (2020) A linear regression and deep learning approach for detecting reliable genetic alterations in cancer using DNA methylation and gene expression data. Genes 11:931
[357] Li A, Mallik S, Luo H, Jia P, DF Lee, Zhao Z* (2020) H19, a long non-coding RNA, mediates transcription factors and target genes through interference of microRNAs in pan-cancer. Molecular Therapy – Nucleic Acids. 21:180-191
[356] Gebru MT, Atkinson JM, Young MM, Zhang L,Tang Z, Liu Z, Lu P, Dower CM, Chen L, Annageldiyev C, Sharma A, Kawasawa YI, Zhao Z, Miller BA, Claxton DF, Wang H-G (2020) Glucocorticoids enhance the anti-leukemic activity of FLT3 inhibitors in FLT3 mutant acute myeloid leukemia. Blood 136(9):1067-1079
[355] He Y, Xu P, Wang C, Xia Y, Yu M, Yang Y, Yu K, Cai X, Qu N, Saito K, Wang J, Hyseni I, Robertson M, Piyarathna B, Gao M, Khan S, Liu F, Chen R, Coarfa C, Zhao Z, Tong Q, Sun Z, Xu Y (2020) Estrogen receptor-α expressing neurons in the ventrolateral VMH regulate glucose balance. Nature Communications 11(1):2165
[354] Ning X, Zhang C, Wang K, Zhao Z, Mathé E (2020) The International Conference on Intelligent Biology and Medicine 2019: Computational methods for drug interactions. BMC Medical Informatics and Decision Making 20(Suppl 2):51 (Correction: BMC Medical Informatics and Decision Making 20(1):77, doi: 10.1186/s12911-020-1096-1)
[353] Qin G, Mallik S, Mitra R, Li A, Jia P, Zhao Z* (2020) MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Scientific Reports 10(1):852
[352] Hua X, Wang YY, Jia P, Xiong Q, Hu Y, Chang Y, Lai S, Xu Y, Zhao Z*, Song J (2020) Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression. BMC Medicine 18:2
[351] Manuel AM, Dai Y, Freeman LA, Jia P, Zhao Z* (2020) Dense module searching for gene networks associated with multiple sclerosis. BMC Medical Genomics 13(suppl 5):48
[350] Chen J, Loukola A, Gillepie N, Peterson R, Jia P, Riley B, Maes H, Dick DM, Kendler KS, Damaj MI, Miles MF, Zhao Z, Li MD, Vink JM, Minica CC, Willemsen G, Boomsma DI, Qaiser B, Madden PAF, Korhonen T, Gelernter J, Kranzler HR, Sherva R, Farrer L, Maher B, Vanyukov M, Taylor M, Ware JJ, Munafò MR, Lutz SM, Hokanson JE, Gu F, Landi MT, Caporaso NE, Hancock DB, Gaddis NC, Baker TB, Bierut LJ, Johnson EO, Chenoweth M, Lerman C, Tyndale R, Kaprio J, Chen X (2020) Genome-wide meta-analysis of FTND and TTFC phenotypes. Nicotine & Tobacco Research 22(6):900-909
[349] Yan F, Dai Y, Iwata J, Zhao Z*, Jia P* (2020) An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate. BMC Medical Genomics. 13(suppl 5):39
[348] Zhang W, Zhao Z, Wang K, Shen L, Shi X (2020) The International Conference on Intelligent Biology and Medicine (ICIBM) 2020: Scalable techniques and algorithms for computational genomics. BMC Genomics 21(Suppl 11):831 [Introduction article]
[347] Shi X, Zhao Z, Wang K, Shen L (2020) The International Conference on Intelligent Biology and Medicine (ICIBM) 2020: Data-driven analytics in biomedical genomics. BMC Medical Genomics 13(Suppl 11):189 [Introduction article]
[346] Guo Y, Shen L, Shi X, Wang K, Dai Y, Zhao Z* (2020) Accelerating Bioinformatics Research with International Conference on Intelligent Biology and Medicine 2020. BMC Bioinformatics 21(Suppl 21):563 [Introduction article]
[345] Shen L, Shi X, Zhao Z, Wang K (2020) Informatics and machine learning methods for health applications. BMC Medical Informatics and Decision Making 20(Suppl 11):342 [Introduction article]
[344] Guo Y, Ning X, Mathé E, Wang K, Li L, Zhang C, Zhao Z* (2020) Innovating Computational Biology and Intelligent Medicine: ICIBM 2019. Genes 11:437
[343] Zhang C, Mathé E, Ning X, Zhao Z, Wang K, Li L, Guo Y (2020) The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics. BMC Medical Genomics 13(Suppl 5):47 [Introduction article]
[342] Zhou Y, Cai R, Wang K, Zhao Z (2020) Recent Advances in Computational Systems Biology and Bioinformatics. International Journal of Computational Biology and Drug Design (IJCBDD), 13(1): 1-4
2019
[341] Park AK, Kim P, Ballester LY, Esquenazi Y, Zhao Z* (2019) Subtype-specific signaling pathways and genomic aberrations associated with prognosis of glioblastoma. Neuro-Oncology 21(1): 59-70
[340] Jia P, Zhao Z* (2019) Characterization of tumor-suppressor gene inactivation events in 33 cancer types. Cell Reports 26:496-506
[339] Jia P, Pei G, Zhao Z. (2019). CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures. Bioinformatics, btz441, https://doi.org/10.1093/bioinformatics/btz441.
[338] 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.
[337] Li A, Jia P, Mallik S, Fei R, Yoshioka H, Suzuki A, Iwata J, Zhao Z* (2019) Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. Briefing in Bioinformatics, bbz082, https://doi.org/10.1093/bib/bbz082
[336] Hu R, Pei G, Jia P, Zhao Z* (2019) Decoding regulatory structures and features from epigenomics profiles: a Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model. Methods 2019 Oct 28. pii: S1046-2023(19)30269-5. doi: 10.1016/j.ymeth.2019.10.012. [Epub ahead of print]
[335] Suzuki A, Yoshioka H, Summakia D, Desai N, Jun G, Jia P, Loose D, Ogata K, Gajera M, Zhao Z, Iwata J (2019) MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse. BMC Genomics 20(1):852
[334] Chen J, Wu JS, Mize T, Moreno M, Hamid M, Servin F, Bashy B, Zhao Z, Jia P, Tsung MT, Kendler KS, Xiong M, Chen X (2019) Whole genome sequencing identified CHST9 as a schizophrenia candidate gene. Scientific Reports 9(1):12717
[333] Mallik S, Zhao Z* (2019) Graph- and rule-based learning algorithms: A comprehensive review of their applications for cancer type classification and prognosis using genomic data. Briefings in Bioinformatics. Advanced online access January 11, 2019
[332] Gallant JN, Sewell A, Almodovar K, Wang Q, Dahlman KB, Abramson RG, Kapp ME, Brown BT, Boyd KL, Gilbert J, Cohen DN, Yarbrough WG*, Zhao Z*, Lovly CM* (2019) Genomic landscape of a metastatic malignant proliferating tricholemmal tumor and its response to PI3K inhibition. Nature Precision Oncology 3:5
[331] Huang Y, Wang J, Jia P, Li X, Pei G, Wang C, Fang X, Zhao Z, Cai Z, Yi X, Wu S, Zhang B (2019) Clonal architectures predict clinical outcome in clear cell renal cell carcinoma. Nature Communications 10(1):1245
[330] 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, https://doi.org/10.1093/bioinformatics/btz138.
[329] Tenenbaum JD, Bhuvaneshwar K, Gagliardi JP, Fultz Hollis K, Jia P, Ma L, Nagarajan R, Rakesh G, Subbian V, Visweswaran S, Zhao Z, Rozenblit L (2019) Translational bioinformatics in mental health: Open access data sources and computational biomarker discovery. Briefings in Bioinformatics 20(3):842-856
[328] Mallik S, Zhao Z* (2019) Multi-objective optimized fuzzy clustering for detecting cell clusters from single cell expression profiles. Genes 10(8), 611
[327] Liu J, Wu J, Lin J, Zhao J, Xu T, Yang Q, Zhao J*, Zhao Z*, Song X* (2019) Changes in the microbial community diversity of oil exploitation. Genes 10(8):556
[326] Suzuki A, Li A, Gajera M, Abdallah N, Pelikan RC, Zhao Z, Iwata J (2019) MicroRNA-374a, -4680, and -133b suppress cell proliferation through the regulation of genes associated with human cleft palate in cultured human palate cells. BMC Medical Genomics 12:93
[325] Endres BT, Begum K, Sun H, Walk ST, Memariani A, Lancaster C, Gonzales-Luna AJ, Dotson KM, Bassères E, Offiong C, Tupy S, Kuper K, Septimus E, Arafat R, Alam MJ, Zhao Z, Hurdle JG, Savidge TC, Garey KW (2019) Early emergence of epidemic Clostridioides difficile ribotype 027 lineages in the US: implications for fluoroquinolone use. Open Forum Infectious Diseases 6(2):ofz013
[324] Gajera, M, Desai N, Suzuki A, Li A, Zhang M, Jun G, Jia P, Zhao Z, Iwata J (2019) MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip. BMC Medical Genomics 12(1):70
[323] Chen H, Yu D, Fang R, Rabidou K, Wu D, Hu D, Jia P, Zhao Z, Wu Z, Peng J, Shi Y, Shi YG (2019) TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer. Cell Research 29(3), 248, Nature Publishing Group, 2019/3
[322] Zhou Y, Wang J, Song X, Zhao Z* (2019) Integrative Approaches and Machine Learning in Systems Biology. International Journal of Computational Biology and Drug Design (IJCBDD), 12(2): 101-104
[321] Mallik S, Zhao Z* (2019) Distance based knowledge retrieval through rule mining for complex biomarker recognition from tri-omics profiles. International Journal of Computational Biology and Drug Design 12(2):105-127
[320] Chen J, Loukola A, Gillepie N, Peterson R, Jia P, Riley B, Maes H, Dick DM, Kendler KS, Damaj MI, Miles MF, Zhao Z, Li MD, Vink JM, Minica CC, Willemsen G, Boomsma DI, Qaiser B, Madden PAF, Korhonen T, Gelernter J, Kranzler HR, Sherva R, Farrer L, Maher B, Vanyukov M, Taylor M, Ware JJ, Munafò MR, Lutz SM, Hokanson JE, Gu F, Landi MT, Caporaso NE, Hancock DB, Gaddis NC, Baker TB, Bierut LJ, Johnson EO, Chenoweth M, Lerman C, Tyndale R, Kaprio J, Chen X (2019) Genome-wide meta-analysis of FTND and TTFC phenotypes. Nicotine & Tobacco Research 2019 Jul 11. pii: ntz099. doi: 10.1093/ntr/ntz099. [Epub ahead of print]
[319] Wu Z, Yan J, Wang K, Liu X, Guo Y, Zhi D, Ruan J, Zhao Z* (2019) The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications. BMC Genomics 20(Suppl 1):80 [Introduction article]
[318] Wang J, Wang K, Liu X, Sham P, Zhao Z* (2019) Next-Generation Sequencing in Human Genetic Studies: Genome Technologies and Applications to Human Genetic Studies. Human Heredity, 83(3):105-106
[317] 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
[316] 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. https://doi.org/10.1101/286096
2018
[315] 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)
[314] Jia P, Zhao Z (2018) Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types, Cell Reports, 26: 496–506, https://doi.org/10.1016/j.celrep.2018.12.066
[313] 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. O'Brien PubMed 294
[312] Zhao J., Cheng F., Jia P., Cox N., Denny JC., & Zhao Z. (2018). An integrative functional genomics framework for effective identification of novel regulatory variants in genome–phenome studies. Genome medicine, 10(1), 7.
[311] 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
[310] Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L; [Zhao Z a co-author in] Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R (2018) A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell systems 7(4), 422-437. e7
[309] Smieszek S, Jia P, Samuels DC, Zhao Z, Barnholtz-Sloan J, Kaur H, Letendre S, Ellis R, Franklin DR, Hulgan T, Kallianpur A, Bush WS, for the CHARTER Study Group (2018) Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated neurocognitive impairment. Mitochondrion 2018 Jul 17. pii: S1567-7249(17)30356-2. doi: 10.1016/j.mito.2018.07.004. [Epub ahead of print]
[308] Jiang X, Lu W, Sheng X, Wang Q, Lv J, Liu M, Cheng F*, Zhao Z*, Peng X* (2018) Repurposing sertraline sensitizes non-small cell lung cancer cells to erlotinib by inducing autophagy. JCI Insight 3(11):e98921
[307] Mallik S, Zhao Z* (2018) Identification of gene signatures from RNA-seq data using Pareto-optimal cluster algorithm. BMC Systems Biology 12(Suppl 8):126
[306] 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, 12 (Suppl 8):140
[305] Hu R, Dai Y, Jia P, Zhao Z (2018) 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, https://doi.org/10.1093/database/bay121
[304] 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, https://doi.org/10.1093/schbul/sby085. Jia PubMed
[303] Lu P, Zhao Z* (2018) Advances on PPARγ research in the emerging era of precision medicine. Current Drug Targets. 19:663-673. Lu PubMed PDF
[302] 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
[301] O’Brien T, Jia P, Aldrich M, Zhao Z* (2018) Lung cancer: one disease or many? Human Heredity. 83:65–70. O'Brien PubMed
[300] 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. Jia P PubMed
[299] 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. 12 (Suppl 8) :128
[298] 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. Saxon PubMed
[297] 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 Peng PubMed
[296] 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 Knijnenburg PubMed
[295] Mallik S, Zhao Z* (2018) Cervical Cancer Signature Detection through Pareto-Optimal Cluster Identification for RNASeq Data. BMC Systems Biology. 12(Suppl 8): 126.
[294] 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] Sun PubMed
[293] 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 Suzuki PubMed
[292] 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)
[291] Ma L, Jia P, Zhao Z* (2018) Splicing QTL of human adipose-related traits. Scientific Reports 8:318 Ma PubMed
[290] 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) Mallik 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 Mallik 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. Wang 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. Zheng 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. Fries 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 is a centrally acting orexigenic hormone. Nature Medicine 23(12):1444-1453. doi: 10.1038/nm.4432. Epub 2017 Nov 6. Duerrschmid 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 Mitra 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] Tenenbaum 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. Mallik PaperLink 282
[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 Kim PubMed 281
[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 Tao 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. Liu 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. Giancardo 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. Xu 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 Hanker 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 Jia PubMed 274
[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 Fang 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, Genes (Basel). 8(12). pii: E368. doi: 10.3390/genes8120368 Cao 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. Zhao PubMed 271
[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 Patton 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 Zhao PubMed 269
[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 Jia PubMed 268
[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 Kim PubMed 267
[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) The 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, 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.162B(8):898-906. 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
[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, 7:1142-1152PubMed
[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
[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:R79PubMed
[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
[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 Drosophilaimmigrans geographic strains. (in Chinese) Acta Sci. Nat. 33:215-221
"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
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. https://doi.org/10.1016/B978-0-12-811414-8.20293-9 (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 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, Pages 1-24. Nova Science Publishers, Inc.,>new York (ISBN 1-60021-721-4)
