Bioinformatics and Systems Medicine Laboratory

Selected NGS publications in BSML

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 PumMed [TCGA analysis]

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 PumMed [TCGA analysis]

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 PumMed [WGS]

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 PumMed [MiSeq]

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 PumMed [TCGA analysis]

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 PumMed [RNA-seq and WES variant comparison]

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. PumMed [TCGA analysis]

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 [RNA-seq]

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 tumorigensis by MYC. Molecular Cell, 58(3): 440-452. PumMed [ChIP-seq]

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 PumMed [method: virus detection from NGS data]

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 PumMed (>350 WES)

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 PumMed [method]

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 PumMed [MiSeq]

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 PumMed Editor's pick. [method]

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 [TCGA somatic mutations]

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, AnsÚn 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 PumMed (WGS)

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 PumMed (IF 15.15) [RNA-seq]

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 PumMed [NGS somatic mutations, TCGA]

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

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, 2014 PumMed [NGS data analysis]

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 PumMed (TCGA NGS analysis)

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 PumMed [xenograph NGS]

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

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 [NGS tool]

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    PumMed [NGS tool comparison]

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    PumMed

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. [NGS: WES, WGS, RNA-Seq]

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 [NGS tool: virus integration]

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 [NGS: CNV detection]

Wang Q, Zhao Z (2012) A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing data. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'12), December 2-4, 2012, Washington DC, USA [NGS: somatic variant detection]

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 [NGS commentary]

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 [WGS]

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. [NGS database]

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 [NGS validation technique]

Wang Q, Xia J, Jia P, Pao W, Zhao Z (2012) Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Briefings in Bioinformatics PubMed [NGS, gene fusion]

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 [RNA-Seq]

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

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 [RNA-Seq, yeast]

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 [ChIP-Seq]

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    [NGS methylation analysis]

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 [454 for gene fusion detection]

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